A simple understanding of humans

Contents —

From  ref1087 — An overview of the Human Body

Our bodies consist of a number of biological systems that carry out specific functions necessary for everyday living.

The job of the circulatory system is to move blood, nutrients, oxygen, carbon dioxide, and hormones, around the body.  It consists of the heart, blood, blood vessels, arteries and veins.

The digestive system consists of a series of connected organs that together, allow the body to break down and absorb food, and remove waste.  It includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, and anus.  The liver and pancreas also play a role in the digestive system because they produce digestive juices.

The endocrine system consists of eight major glands that secrete hormones into the blood.  These hormones, in turn, travel to different tissues and regulate various bodily functions, such as metabolism, growth and sexual function.

The immune system is the body’s defence against bacteria, viruses and other pathogens that may be harmful.  It includes lymph nodes, the spleen, bone marrow, lymphocytes (including B-cells and T-cells), the thymus and leukocytes, which are white blood cells.

The lymphatic system includes lymph nodes, lymph ducts and lymph vessels, and also plays a role in the body’s defences.  Its main job is to make is to make and move lymph, a clear fluid that contains white blood cells, which help the body fight infection.  The lymphatic system also removes excess lymph fluid from bodily tissues, and returns it to the blood.

The brain’s most dedicated job is to control your body — i.e. to manage “allostasis” — by predicting energy needs before they arise so you can efficiently make worthwhile movements and survive

Reproduction & Growth

Each human has a limited life-span, so reproduction is required to enable the  continuity of humanity.

The basic human cell is —

Fig 209

Contents —

From  ref1087 — An overview of the Human Body

Our bodies consist of a number of biological systems that carry out specific functions necessary for everyday living.

The job of the circulatory system is to move blood, nutrients, oxygen, carbon dioxide, and hormones, around the body.  It consists of the heart, blood, blood vessels, arteries and veins.

The digestive system consists of a series of connected organs that together, allow the body to break down and absorb food, and remove waste.  It includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, and anus.  The liver and pancreas also play a role in the digestive system because they produce digestive juices.

The endocrine system consists of eight major glands that secrete hormones into the blood.  These hormones, in turn, travel to different tissues and regulate various bodily functions, such as metabolism, growth and sexual function.

The immune system is the body’s defence against bacteria, viruses and other pathogens that may be harmful.  It includes lymph nodes, the spleen, bone marrow, lymphocytes (including B-cells and T-cells), the thymus and leukocytes, which are white blood cells.

The lymphatic system includes lymph nodes, lymph ducts and lymph vessels, and also plays a role in the body’s defences.  Its main job is to make is to make and move lymph, a clear fluid that contains white blood cells, which help the body fight infection.  The lymphatic system also removes excess lymph fluid from bodily tissues, and returns it to the blood.

The brain’s most dedicated job is to control your body — i.e. to manage “allostasis” — by predicting energy needs before they arise so you can efficiently make worthwhile movements and survive.

Reproduction & Growth

Each human has a limited life-span, so reproduction is required to enable the  continuity of humanity.

Fig122  ref1166 — Human Anatomy

Fig 209

Gamete  — A sex cell containing only a single — haploid — set of chromosomes.  A diploid has 2 sets.

Organelles — a specialized subunit, usually within a cell, that has a specific function — such as Ribosomess

Organisms grow and reproduce through cell division. In humans the production of new cells occurs as a result of meiosis and mitosis — see below. Cells can also merge, for example, Sex Cells in order to combine parental Genes.

From  ref1234Differences between meiosis and mitosis.

These two nuclear division processes are similar but distinct.  Both processes involve the division of a diploid cell, or a cell containing two sets of chromosomes (one chromosome donated from each parent).

Meiosis is the process by which gametes — sex cells are generated in organisms that reproduce sexually.

Gametes are produced in male and female gonads and contain one-half the number of chromosomes as the original cell.

New gene combinations are introduced in a population through the genetic recombination that occurs during meiosis. The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

In mitosis, the genetic material (DNA) in a cell is duplicated and divided equally between two cells.  Tis process replicates Somatic (body)  cells

Fig 352   ref1228  Part 2  — In the cells going through mitosis you can clearly see the individual chromosomes

From  ref1228 — Part 3 Sexual reproduction, meiosis and gamete formation –inc. https://www.bbc.co.uk/bitesize/guides/zghqfcw/revision/3

Sexual reproduction uses a type of cell division called meiosis, which creates gametes — sperm and egg cells.

(Sperm are small and for example do not contain Ribosomes — these and other items are provided by the egg — Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains)

The process of meiosis happens in the male and female reproductive organs.

Before a dividing cell enters meiosis, it undergoes a period of growth called interphase.

From   ref1235 — stages of meiosis

Fig 350   ref1228  part 3 — Meiosis and gamete formation

The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

Fig 349 ref1228 — Towards forming the Zygote Cell

The Human Egg, ready for fertilisation is at the end of the Fallopian Tube, so the Sperm has to get there from the Cervix — thus the mobility through its tail.

Growth

A Cell can divide in order to provide the means of growing and/or repairing the body.  A cell can also release from its DNA the proteins necessary for growth or repair.

The dividing cell goes through an ordered series of events called the cell cycle.

Fig 350a  ref1228 2 — Mitosis — cell division

The mitotic cell cycle is initiated by the presence of certain growth factors or other signals that indicate that the production of new cells is needed.

Typical ways in which the need for a process to be initiated are given in Appendix “Comms”.

Examples of somatic cells include fat cellsblood cells, skin cells, or  any body-cell that is not a sex-cell . Mitosis is necessary to replace dead cells, damaged cells, or cells that have short life spans.

In mitosis a single cell divides into two cells that are replicas of each other and have the same number of chromosomes. This type of cell division is good for basic growth, repair, and maintenance.  Mitosis is how somatic—or non-reproductive cells — divide. Somatic cells make up most of your body’s tissues and organs, including skin, muscles, lungs, gut, and hair cells.

Since the daughter cells have exact copies of their parent cell’s DNA, no genetic diversity is created through mitosis in normal healthy cells.

From  ref1198 — Developmental genetics

https://www2.le.ac.uk/projects/vgec/schoolsandcolleges/topics/developmental-genetics

The process that changes a single cell into a new person is called development.

During the course of development, complex structures develop from simple ones. A single cell transforms itself into an adult organism. How does something complicated come from something simple? Appendix Comms has examples of how this is done  xxx

Creating an organism from a single cell involves three important processes:

  1. Cell division: cells divide to produce more cells.
  2. Cell differentiation: cells change into different types of cell to do specific jobs in the body, from nerve cells to muscle cells.
  3. Morphogenesis:groups of cells move and change their shape to produce the structure of the organism.

From  ref1202 — Proteins

Proteins are the key working molecules and building blocks in all cells. They are produced in a similar two-step process in all organisms – DNA is first transcribed into RNA, then RNA is translated into protein.

Proteins are the major ‘working molecules’ within every organism. Among their many jobs, proteins catalyse reactions, transport oxygen and defend organisms from infection. They’re also crucial building blocks of organisms. They are the major components of wool, cartilage and milk, they package up the DNA in chromosomes and they insulate the  nervous system!

Proteins are made of large numbers of amino acids joined end to end. The chains fold up to form three-dimensional molecules with complex shapes – you could think of it as origami with a very long and thin piece of paper. The precise shape of each protein, along with the amino acids it contains, determines what it does.

From   ref1183Central Dogma of Biology —  DNA to RNA to a Protein

DNA gives the instructions for various functional proteins to be produced inside the cell — this process is also known as the Central dogma of molecular biology —

Fig 353   ref1236 — DNA to RNA to a Protein

Explanation —    ref1230Gene expression

The process of turning on a gene to produce RNA and protein is called Gene Expression

Fig 354  ref1230 — Gene expression

From  ref1234 — Central Dogma of Biology  DNA to RNA to a Protein

  • The central dogma suggests that DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes.
  • The ribosomes serve as factories in the cell where the information is ‘translated’ from a code into the functional product.
  • In transcription, the information in the DNA of every cell is converted into small, portable RNA messages — small enough to pass from the nucleus of the cell
  • During translation, these messages travel from where the DNA is in the cell nucleus to the ribosomes where they are ‘read’ to make specific proteins.
  • The central dogma states that the pattern of information that occurs most frequently in our cells is:
    1. From existing DNA to make new DNA (DNA replication?)
    2. From DNA to make new RNA (transcription)
    3. From RNA to make new proteins (translation).

From  ref1136   —  When life begins

The zygote is the start of a biological continuum that automatically grows and develops, passing gradually and sequentially through the stages we call foetus, baby, child, adult, old person and ending eventually in death.

Fig 337   ref1136 — 3 day old embryo

Fig 355   ref1136 — 40 day old embryo

The full genetic instructions to guide the development of the continuum, in interaction with its environment, are present in the zygote.  Every stage along the continuum is biologically human and each point along the continuum has the full human properties appropriate to that point.

From  ref1232 — Definitions

xxx insert

Genetic — DNA, Chromosomes, Genome and Epigenome

Your genome is the instructions for making and maintaining you. It is written in a chemical code called DNA.

It contains 3 billion bases, 20,000 genes, and 23 pairs of chromosomes!

DNA is a vitally important molecule for not only humans, but for most other organisms as well.

DNA contains our hereditary material and our genes.— it’s what makes us a major part of our uniqueness.

Genes — unit of hereditary information that occupies a fixed position on a chromosome. Genes direct the synthesis of proteins  — From ref1205

Chromosomes   — There are 23 chromosomes in each structure and these are each intertwined with an identical set of 23.

Each chromosome has a role in the growth and renewal of the human body.

Each  chromosome is formed into functional blocks which can be activated to perform the specific task — These blocks  are called genes —   These tasks can be further defined by epigenetic changes.

However, DNA modifications which do not change the DNA sequence but can affect gene activity and alter human traits and health — From  ref1205 — the Epigenome

Chemical compounds that are added to individual genes can regulate their activity; these modifications are known as epigenetic changes.

The epigenome comprises all of the chemical compounds that have been added to the entirety of one’s genome in a way to regulates the activity (expression) of all the genes,  The chemical compounds of the epigenome are not part of the DNA sequence, but are on or attached to DNA.

The following diagram incorporates all of these aspects

Fig345   ref1221 — DNA, Histones, Chromosomes and  Epigenetics

Definitions —

Chromatin — The primary function of chromatin is to compress the DNA into a compact unit that will be less voluminous and can fit within the nucleus.

Histones are basic proteins found in the nuclei of cells. These proteins help organize very long strands of DNA, the genetic “blueprint” of every living thing, into condensed structures that can fit into comparatively small spaces within the nucleus.

Histones do not serve merely as scaffolding for DNA strands. They also take part in gene regulation by affecting when certain genes — that is, lengths of DNA associated with a single protein product — are “expressed,” or activated to transcribe RNA and ultimately the protein product a given gene carries instructions for making.

From  ref1227What is epigenetics

The Epigenetic effects include Factors such as stress, environment, medications, diet, the contents of water, etc.

In addition to DNA methylation being vital to healthy growth and development, it also enables the expression of retroviral genes to be suppressed. However,  along with other potentially dangerous sequences of DNA that have entered and may damage the host. is associated with many diseases including asthma, aging, and cancer,

From   ref1233The factors that influence genes turn on and off

 

  1. Transcription factors (TFs) are molecules involved in regulating gene expression. They are usually proteins, although they can also consist of short, non-coding RNA. TFs are also usually found working in groups or complexes, forming multiple interactions that allow for varying degrees of control over rates of transcription. In people (and other eukaryotes), genes are usually in a default “off” state, so TFs serve mainly to turn gene expression “on”.
  2. Epigenetics involves genetic control by factors other than an individual’s DNA sequence. Epigenetic changes can switch genes on or off and determine which proteins are transcribed. Gene silencing is a general term describing epigenetic processes of gene regulation. Within cells, there are three systems that can interact with each other to silence genes: DNA methylation, histonemodifications, and RNA-associated silencing
  3. Environmental Influences on Gene Expression. The expression of genes in an organism can be influenced by the environment, including the external world in which the organism is located or develops, as well as the organism’s internal world, which includes such factors as its hormones and metabolism. One major internal environmental influence that affects gene expression is gender, as is the case with sex-influenced and sex-limited traits. Similarly, drugs, chemicals, temperature, and light are among the external environmental factors that can determine which genes are turned on and off, thereby influencing the way an organism develops and functions.

A phenotype is how these genes are actually expressed (applied).  This is due to a combination of genes and the effects of Epigenomics — these effects occur at different times during a lifetime, and can be reversed.  The phenotype can include physical traits, such as height and color or the eyes, as well as non-physical traits such as shyness and extroversion.

Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed).

Each cell type in your body has a different set of active genes —despite the fact that almost all the cells of your body contain the exact same DNA.

Transcription DNA to RNA

Fig356  ref1237 — A Guide to Understanding Gene Expression

The Messenger mRNA small enough to proceed through the Nucleus

Again  ref1205 — Understanding how genes work & epigenome

Environmental influences, such as a person’s diet and exposure to pollutants, can also impact the epigenome.

Epigenetic changes can help determine whether genes are turned on or off and can influence the production of proteins in certain cells, ensuring that only necessary proteins are produced.

For example, proteins that promote bone growth are not produced in muscle cells. Patterns of epigenetic modification vary among individuals, different tissues within an individual, and even different cells.

A common type of epigenetic modification is called DNA methylation. This involves attaching small molecules to segments of DNA. When these methyl groups are added to a particular gene, that gene is turned off or silenced, and no protein is produced from that gene.

Because errors in the epigenetic process, such as modifying the wrong gene or failing to add a compound to a gene, can lead to abnormal gene activity or inactivity, they can cause genetic disorders. Conditions including cancers, metabolic disorders, and degenerative disorders have all been found to be related to epigenetic errors.

Scientists continue to explore the relationship between the genome and the chemical compounds that modify it. In particular, they are studying what effect the modifications have on gene function, protein production, and human health.

From  ref1121 — How Children’s Experiences Affect Their Genes

Epigenetics shows how environmental influences—children’s experiences—actually affect the expression of their genes.

This means the old idea that genes are “set in stone” has been disproven. Nature vs. Nurture is no longer a debate. It’s nearly always both!

During development, the DNA that makes up our genes accumulates chemical marks that determine how much or little of the genes is expressed. This collection of chemical marks is known as the “epigenome.” The different experiences children have rearrange those chemical marks. This explains why genetically identical twins can exhibit different behaviors, skills, health, and achievement.

The marks do not change the sequence of the DNA, but they do change the way cells use the DNA’s instructions.  They may, or may not, be permanent.

The marks can be passed on from cell to cell as they divide, and they can even be passed from one generation to the next.

The genes children inherit from their biological parents provide information that guides their development. For example, how tall they could eventually become or the kind of temperament they could have.

When experiences during development rearrange the epigenetic marks that govern gene expression, they can change whether and how genes release the information they carry.

Thus, the epigenome can be affected by positive experiences, such as supportive relationships and opportunities for learning, or negative influences, such as environmental toxins or stressful life circumstances, which leave a unique epigenetic “signature” on the genes. These signatures can be temporary or permanent and both types affect how easily the genes are switched on or off. Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning. But the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning.

Experiences very early in life, when the brain is developing most rapidly, cause epigenetic adaptations that influence whether, when, and how genes release their instructions for building future capacity for health, skills, and resilience. That’s why it’s crucial to provide supportive and nurturing experiences for young children in the earliest years.

Services such as high-quality health care for all pregnant women, infants, and toddlers, as well as support for new parents and caregivers can—quite literally— affect the chemistry around children’s genes. Supportive relationships and rich learning experiences generate positive epigenetic signatures that activate genetic potential.

Injurious experiences, such as malnutrition, exposure to chemical toxins or drugs, and toxic stress before birth or in early childhood are not “forgotten,” but rather are built into the architecture of the developing brain through the epigenome. The “biological memories” associated with these epigenetic changes can affect multiple organ systems and increase the risk not only for poor physical and mental health outcomes but also for impairments in future learning capacity and behavior.

Research has shown that specific epigenetic modifications do occur in brain cells as cognitive skills like learning and memory develop, and that repeated activation of brain circuits dedicated to learning and memory through interaction with the environment, such as reciprocal “serve and return” interaction with adults, facilitates these positive epigenetic modifications.

We also know that sound maternal and fetal nutrition, combined with positive social-emotional support of children through their family and community environments, will reduce the likelihood of negative epigenetic modifications that increase the risk of later physical and mental health impairments.

Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning, but that takes a lot more effort, may not be successful at changing all aspects of the signatures, and is costly. Thus, the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning, helping children grow up to be healthy, productive members of society.

From  ref1207 — Primary functions of protein in the body

https://study.com/academy/lesson/primary-functions-of-protein-in-the-body.html

Protein is a vital molecule that carries out many functions in your body. Learn how proteins provide structure, regulate body processes, transport materials throughout your body, help your immune system and act as a source of energy.

Proteins are all similar in that they are made up of chains of amino acids; these basic building blocks of proteins are linked together by unique chemical bonds called peptide bonds.

Amino acids being the building blocks of proteins, but we could also say that proteins themselves are building blocks of the body.

And this brings us to the first important function of protein, which is to provide structure.

Provide Structure

Structural proteins make up integral parts of your body. For example, keratin is a type of protein found in your hair, nails and skin that helps give these structures strength. Inside your body, protein provides structure to every cell. Collagen, which is a structural protein found in various connective tissues, provides the framework for the ligaments that hold your bones together and the tendons that attach muscles to those bones.

Regulate Body Processes

Proteins also regulate body processes. For example, enzymes are proteins that speed up chemical reactions in the body. Without them, basic activities like breaking down the foods you eat would happen too slowly to support your life. You can think of enzymes as proteins that shift your body processes into high gear.

Body processes are also influenced by hormones, which are proteins that regulate the activity of cells or organs. Hormones are like chemical messengers that carry an order from one part of your body to another. For example, insulin is a hormone that regulates blood sugar by carrying a message to your body cells about how much sugar is present in your blood.

Transport Materials

Another function of protein is to transport materials throughout your body. A great example of this is haemoglobin, which is the oxygen-transporting protein found in your red blood cells. When you breathe air into your lungs, the oxygen molecules from that air wait in your lung cells for a ride on a red blood cell. Once the oxygen attaches to the haemoglobin of that red cell, it can travel anywhere in your body.

Protein Production

https://vocal.media/futurism/protein-production-in-a-cell

ref1206 — protein production in a cell

Fig340  Protein production  ref1206

The nucleus first receives a chemical signal to make a specific protein. This message is contained in the DNA (deoxyribonucleic acid), which is copied into RNA (ribonucleic acid). (This is done because RNA is smaller than DNA, which would allow it to leave through the nuclear pores.)

The RNA then leaves through a nuclear pore, and arrives at the ribosome. The ribosome creates the protein; this protein goes through the endoplasmic reticulum. A vesicle forms off the endoplasmic reticulum, carrying the protein to the Golgi body.

The Golgi body repackages the protein, and a vesicle carrying the protein forms off. This vesicle then carries the protein to the cell membrane; the vesicle attaches to the cell membrane, and its proteins are released out of the cell.

Learning & Living

 

From  ref 597  Whole Brain  Neural Plasticity

 

xxx

 

ref1209 — Secret language of Cells

A child is born with the ability to learn — but starts with a blank memory/learning  record.  Learning is essential for coping with the complexities and changing nature of our environment.

Humans have adapted to living in different climates, regimes, etc – and also to travel — and become adept at making and using tools and weapons, developing a system of communication through symbols and sounds, and developing social, political and economic systems of interaction.

We each compete and commune as we experience life.  Our Human Body/Mind is the result of how humans evolved to deal with these demands.

Evolution has provided us with the means by which a human grows, learns and develops.  Our acquired “Apps” include a wide range of the good habits/skills needed to relieve us of having to consciously work through routine daily activities.

But our ability to learn these and further life enhancing Apps also means that we can acquire bad Apps – damage-prone habits and antagonizing attitudes.  These may emerge in response to unfortunate experiences such as Toxic Stresses.

During development, from infancy on, the new person is motivated to  seek to fulfil Core Needs.   Clearly the seeds of these Needs are present in the DNA.   The Needs change as the individual develops — notably at adolescence.

From ref650 — “Hardwiring Happiness” by Rick Hanson

Humans have 3 Core Needs or Operating Systems —
• Safety ————Avoiding Harm
• Connection —– Attaching/relating to others
• Satisfaction —– Using our Rewards system.

Each Need has two modes of responding —

  • The Responsive Mode — Controlled, Mindful
  • The Reactive Mode —Stressed. Emotional — Insecure people, and those affected by trauma are more prone to this mode.

As a child grows they learn from their experiences — largely from the Need for Satisfaction.  This learning is enhanced if their experiences can be made to keep  “interesting”.

At the early stages infant is totally dependent on the mother, and/or appropriate carer.  This Nurture is critical in the progression to realising socially acceptable traits.   (Though, much of human history has been based on individuals whose upbringing departed from sound

 

Contents —

From  ref1087 — An overview of the Human Body

Our bodies consist of a number of biological systems that carry out specific functions necessary for everyday living.

The job of the circulatory system is to move blood, nutrients, oxygen, carbon dioxide, and hormones, around the body.  It consists of the heart, blood, blood vessels, arteries and veins.

The digestive system consists of a series of connected organs that together, allow the body to break down and absorb food, and remove waste.  It includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, and anus.  The liver and pancreas also play a role in the digestive system because they produce digestive juices.

The endocrine system consists of eight major glands that secrete hormones into the blood.  These hormones, in turn, travel to different tissues and regulate various bodily functions, such as metabolism, growth and sexual function.

The immune system is the body’s defence against bacteria, viruses and other pathogens that may be harmful.  It includes lymph nodes, the spleen, bone marrow, lymphocytes (including B-cells and T-cells), the thymus and leukocytes, which are white blood cells.

The lymphatic system includes lymph nodes, lymph ducts and lymph vessels, and also plays a role in the body’s defences.  Its main job is to make is to make and move lymph, a clear fluid that contains white blood cells, which help the body fight infection.  The lymphatic system also removes excess lymph fluid from bodily tissues, and returns it to the blood.

The brain’s most dedicated job is to control your body — i.e. to manage “allostasis” — by predicting energy needs before they arise so you can efficiently make worthwhile movements and survive.

Reproduction & Growth

Each human has a limited life-span, so reproduction is required to enable the  continuity of humanity.

The basic human cell is —

Fig122  ref1166 — Human Anatomy

More xxx

Fig 209

Gamete  — A sex cell containing only a single — haploid — set of chromosomes.  A diploid has 2 sets.

Organelles — a specialized subunit, usually within a cell, that has a specific function — such as Ribosomess

Organisms grow and reproduce through cell division. In humans the production of new cells occurs as a result of meiosis and mitosis — see below. Cells can also merge, for example, Sex Cells in order to combine parental Genes.

From  ref1234Differences between meiosis and mitosis.

These two nuclear division processes are similar but distinct.  Both processes involve the division of a diploid cell, or a cell containing two sets of chromosomes (one chromosome donated from each parent).

Meiosis is the process by which gametes — sex cells are generated in organisms that reproduce sexually.

Gametes are produced in male and female gonads and contain one-half the number of chromosomes as the original cell.

New gene combinations are introduced in a population through the genetic recombination that occurs during meiosis. The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

In mitosis, the genetic material (DNA) in a cell is duplicated and divided equally between two cells.  Tis process replicates Somatic (body)  cells

Fig 352   ref1228  Part 2  — In the cells going through mitosis you can clearly see the individual chromosomes

ccc

From   ref1228 — Part 3 Sexual reproduction, meiosis and gamete formation –inc. https://www.bbc.co.uk/bitesize/guides/zghqfcw/revision/3

Sexual reproduction uses a type of cell division called meiosis, which creates gametes — sperm and egg cells.

(Sperm are small and for example do not contain Ribosomes — these and other items are provided by the egg — Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains)

The process of meiosis happens in the male and female reproductive organs.

Before a dividing cell enters meiosis, it undergoes a period of growth called interphase.

From   ref1235 — stages of meiosis

Fig 350   ref1228  part 3 — Meiosis and gamete formation

The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

Fig 349 ref1228 — Towards forming the Zygote Cell

The Human Egg, ready for fertilisation is at the end of the Fallopian Tube, so the Sperm has to get there from the Cervix — thus the mobility through its tail.

ccc

Growth

A Cell can divide in order to provide the means of growing and/or repairing the body.  A cell can also release from its DNA the proteins necessary for growth or repair.

The dividing cell goes through an ordered series of events called the cell cycle.

Fig 350a  ref1228 2 — Mitosis — cell division

The mitotic cell cycle is initiated by the presence of certain growth factors or other signals that indicate that the production of new cells is needed.

Typical ways in which the need for a process to be initiated are given in Appendix “Comms”.

Examples of somatic cells include fat cellsblood cells, skin cells, or  any body-cell that is not a sex-cell . Mitosis is necessary to replace dead cells, damaged cells, or cells that have short life spans.

In mitosis a single cell divides into two cells that are replicas of each other and have the same number of chromosomes. This type of cell division is good for basic growth, repair, and maintenance.  Mitosis is how somatic—or non-reproductive cells — divide. Somatic cells make up most of your body’s tissues and organs, including skin, muscles, lungs, gut, and hair cells.

Since the daughter cells have exact copies of their parent cell’s DNA, no genetic diversity is created through mitosis in normal healthy cells.

From  ref1198 — Developmental genetics

https://www2.le.ac.uk/projects/vgec/schoolsandcolleges/topics/developmental-genetics

The process that changes a single cell into a new person is called development.

During the course of development, complex structures develop from simple ones. A single cell transforms itself into an adult organism. How does something complicated come from something simple? Appendix Comms has examples of how this is done  xxx

Creating an organism from a single cell involves three important processes:

  1. Cell division: cells divide to produce more cells.
  2. Cell differentiation: cells change into different types of cell to do specific jobs in the body, from nerve cells to muscle cells.
  3. Morphogenesis:groups of cells move and change their shape to produce the structure of the organism.

From  ref1202 — Proteins

Proteins are the key working molecules and building blocks in all cells. They are produced in a similar two-step process in all organisms – DNA is first transcribed into RNA, then RNA is translated into protein.

Proteins are the major ‘working molecules’ within every organism. Among their many jobs, proteins catalyse reactions, transport oxygen and defend organisms from infection. They’re also crucial building blocks of organisms. They are the major components of wool, cartilage and milk, they package up the DNA in chromosomes and they insulate the  nervous system!

Proteins are made of large numbers of amino acids joined end to end. The chains fold up to form three-dimensional molecules with complex shapes – you could think of it as origami with a very long and thin piece of paper. The precise shape of each protein, along with the amino acids it contains, determines what it does.

From   ref1183Central Dogma of Biology —  DNA to RNA to a Protein

DNA gives the instructions for various functional proteins to be produced inside the cell — this process is also known as the Central dogma of molecular biology

Fig 353   ref1236 — DNA to RNA to a Protein

Explanation —    ref1230Gene expression

Gene Expression

The process of turning on a gene to produce RNA and protein is called gene Expression

Fig 354  ref1230 — Gene expression

From  ref1234 — Central Dogma of Biology  DNA to RNA to a Protein

  • The central dogma suggests that DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes.
  • The ribosomes serve as factories in the cell where the information is ‘translated’ from a code into the functional product.
  • In transcription, the information in the DNA of every cell is converted into small, portable RNA messages — small enough to pass from the nucleus of the cell
  • During translation, these messages travel from where the DNA is in the cell nucleus to the ribosomes where they are ‘read’ to make specific proteins.
  • The central dogma states that the pattern of information that occurs most frequently in our cells is:
    1. From existing DNA to make new DNA (DNA replication?)
    2. From DNA to make new RNA (transcription)
    3. From RNA to make new proteins (translation).

From  ref1136   —  When life begins

The zygote is the start of a biological continuum that automatically grows and develops, passing gradually and sequentially through the stages we call foetus, baby, child, adult, old person and ending eventually in death.

Fig 337   ref1136 — 3 day old embryo

Fig 355   ref1136 — 40 day old embryo

The full genetic instructions to guide the development of the continuum, in interaction with its environment, are present in the zygote.  Every stage along the continuum is biologically human and each point along the continuum has the full human properties appropriate to that point.

From  ref1232 — Definitions

xxx insert

Genetic — DNA, Chromosomes, Genome and Epigenome

Your genome is the instructions for making and maintaining you. It is written in a chemical code called DNA.

It contains 3 billion bases, 20,000 genes, and 23 pairs of chromosomes!

DNA is a vitally important molecule for not only humans, but for most other organisms as well.

DNA contains our hereditary material and our genes.— it’s what makes us a major part of our uniqueness.

Genes — unit of hereditary information that occupies a fixed position on a chromosome. Genes direct the synthesis of proteins  — From ref1205

Chromosomes   — There are 23 chromosomes in each structure and these are each intertwined with an identical set of 23.

Each chromosome has a role in the growth and renewal of the human body.

Each  chromosome is formed into functional blocks which can be activated to perform the specific task — These blocks  are called genes —   These tasks can be further defined by epigenetic changes.

However, DNA modifications which do not change the DNA sequence but can affect gene activity and alter human traits and health — From  ref1205 — the Epigenome

Chemical compounds that are added to individual genes can regulate their activity; these modifications are known as epigenetic changes.

The epigenome comprises all of the chemical compounds that have been added to the entirety of one’s genome in a way to regulates the activity (expression) of all the genes,  The chemical compounds of the epigenome are not part of the DNA sequence, but are on or attached to DNA.

The following diagram incorporates all of these aspects

Fig345   ref1221 — DNA, Histones, Chromosomes and  Epigenetics

Definitions —

Chromatin — The primary function of chromatin is to compress the DNA into a compact unit that will be less voluminous and can fit within the nucleus.

Histones are basic proteins found in the nuclei of cells. These proteins help organize very long strands of DNA, the genetic “blueprint” of every living thing, into condensed structures that can fit into comparatively small spaces within the nucleus.

Histones do not serve merely as scaffolding for DNA strands. They also take part in gene regulation by affecting when certain genes — that is, lengths of DNA associated with a single protein product — are “expressed,” or activated to transcribe RNA and ultimately the protein product a given gene carries instructions for making.

From  ref1227What is epigenetics

The Epigenetic effects include Factors such as stress, environment, medications, diet, the contents of water, etc.

In addition to DNA methylation being vital to healthy growth and development, it also enables the expression of retroviral genes to be suppressed. However,  along with other potentially dangerous sequences of DNA that have entered and may damage the host. is associated with many diseases including asthma, aging, and cancer,

From   ref1233The factors that influence genes turn on and off

 

  1. Transcription factors (TFs) are molecules involved in regulating gene expression. They are usually proteins, although they can also consist of short, non-coding RNA. TFs are also usually found working in groups or complexes, forming multiple interactions that allow for varying degrees of control over rates of transcription. In people (and other eukaryotes), genes are usually in a default “off” state, so TFs serve mainly to turn gene expression “on”.
  2. Epigenetics involves genetic control by factors other than an individual’s DNA sequence. Epigenetic changes can switch genes on or off and determine which proteins are transcribed. Gene silencing is a general term describing epigenetic processes of gene regulation. Within cells, there are three systems that can interact with each other to silence genes: DNA methylation, histonemodifications, and RNA-associated silencing
  3. Environmental Influences on Gene Expression. The expression of genes in an organism can be influenced by the environment, including the external world in which the organism is located or develops, as well as the organism’s internal world, which includes such factors as its hormones and metabolism. One major internal environmental influence that affects gene expression is gender, as is the case with sex-influenced and sex-limited traits. Similarly, drugs, chemicals, temperature, and light are among the external environmental factors that can determine which genes are turned on and off, thereby influencing the way an organism develops and functions.

A phenotype is how these genes are actually expressed (applied).  This is due to a combination of genes and the effects of Epigenomics — these effects occur at different times during a lifetime, and can be reversed.  The phenotype can include physical traits, such as height and color or the eyes, as well as non-physical traits such as shyness and extroversion.

xxx.

Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed).

Each cell type in your body has a different set of active genes —despite the fact that almost all the cells of your body contain the exact same DNA.

Transcription DNA to RNA

Fig356  ref1237 — A Guide to Understanding Gene Expression

The Messenger mRNA small enough to proceed through the Nucleus

3n

Again  ref1205 — Understanding how genes work & epigenome

Environmental influences, such as a person’s diet and exposure to pollutants, can also impact the epigenome.

Epigenetic changes can help determine whether genes are turned on or off and can influence the production of proteins in certain cells, ensuring that only necessary proteins are produced.

For example, proteins that promote bone growth are not produced in muscle cells. Patterns of epigenetic modification vary among individuals, different tissues within an individual, and even different cells.

A common type of epigenetic modification is called DNA methylation. This involves attaching small molecules to segments of DNA. When these methyl groups are added to a particular gene, that gene is turned off or silenced, and no protein is produced from that gene.

Because errors in the epigenetic process, such as modifying the wrong gene or failing to add a compound to a gene, can lead to abnormal gene activity or inactivity, they can cause genetic disorders. Conditions including cancers, metabolic disorders, and degenerative disorders have all been found to be related to epigenetic errors.

Scientists continue to explore the relationship between the genome and the chemical compounds that modify it. In particular, they are studying what effect the modifications have on gene function, protein production, and human health.

From  ref1121 — How Children’s Experiences Affect Their Genes

Epigenetics shows how environmental influences—children’s experiences—actually affect the expression of their genes.

This means the old idea that genes are “set in stone” has been disproven. Nature vs. Nurture is no longer a debate. It’s nearly always both!

During development, the DNA that makes up our genes accumulates chemical marks that determine how much or little of the genes is expressed. This collection of chemical marks is known as the “epigenome.” The different experiences children have rearrange those chemical marks. This explains why genetically identical twins can exhibit different behaviors, skills, health, and achievement.

The marks do not change the sequence of the DNA, but they do change the way cells use the DNA’s instructions.  They may, or may not, be permanent.

The marks can be passed on from cell to cell as they divide, and they can even be passed from one generation to the next.

The genes children inherit from their biological parents provide information that guides their development. For example, how tall they could eventually become or the kind of temperament they could have.

When experiences during development rearrange the epigenetic marks that govern gene expression, they can change whether and how genes release the information they carry.

Thus, the epigenome can be affected by positive experiences, such as supportive relationships and opportunities for learning, or negative influences, such as environmental toxins or stressful life circumstances, which leave a unique epigenetic “signature” on the genes. These signatures can be temporary or permanent and both types affect how easily the genes are switched on or off. Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning. But the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning.

Experiences very early in life, when the brain is developing most rapidly, cause epigenetic adaptations that influence whether, when, and how genes release their instructions for building future capacity for health, skills, and resilience. That’s why it’s crucial to provide supportive and nurturing experiences for young children in the earliest years.

Services such as high-quality health care for all pregnant women, infants, and toddlers, as well as support for new parents and caregivers can—quite literally— affect the chemistry around children’s genes. Supportive relationships and rich learning experiences generate positive epigenetic signatures that activate genetic potential.

Injurious experiences, such as malnutrition, exposure to chemical toxins or drugs, and toxic stress before birth or in early childhood are not “forgotten,” but rather are built into the architecture of the developing brain through the epigenome. The “biological memories” associated with these epigenetic changes can affect multiple organ systems and increase the risk not only for poor physical and mental health outcomes but also for impairments in future learning capacity and behavior.

Research has shown that specific epigenetic modifications do occur in brain cells as cognitive skills like learning and memory develop, and that repeated activation of brain circuits dedicated to learning and memory through interaction with the environment, such as reciprocal “serve and return” interaction with adults, facilitates these positive epigenetic modifications.

We also know that sound maternal and fetal nutrition, combined with positive social-emotional support of children through their family and community environments, will reduce the likelihood of negative epigenetic modifications that increase the risk of later physical and mental health impairments.

Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning, but that takes a lot more effort, may not be successful at changing all aspects of the signatures, and is costly. Thus, the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning, helping children grow up to be healthy, productive members of society.

From  ref1207 — Primary functions of protein in the body

https://study.com/academy/lesson/primary-functions-of-protein-in-the-body.html

Protein is a vital molecule that carries out many functions in your body. Learn how proteins provide structure, regulate body processes, transport materials throughout your body, help your immune system and act as a source of energy.

Proteins are all similar in that they are made up of chains of amino acids; these basic building blocks of proteins are linked together by unique chemical bonds called peptide bonds.

Amino acids being the building blocks of proteins, but we could also say that proteins themselves are building blocks of the body.

And this brings us to the first important function of protein, which is to provide structure.

Provide Structure

Structural proteins make up integral parts of your body. For example, keratin is a type of protein found in your hair, nails and skin that helps give these structures strength. Inside your body, protein provides structure to every cell. Collagen, which is a structural protein found in various connective tissues, provides the framework for the ligaments that hold your bones together and the tendons that attach muscles to those bones.

Regulate Body Processes

Proteins also regulate body processes. For example, enzymes are proteins that speed up chemical reactions in the body. Without them, basic activities like breaking down the foods you eat would happen too slowly to support your life. You can think of enzymes as proteins that shift your body processes into high gear.

Body processes are also influenced by hormones, which are proteins that regulate the activity of cells or organs. Hormones are like chemical messengers that carry an order from one part of your body to another. For example, insulin is a hormone that regulates blood sugar by carrying a message to your body cells about how much sugar is present in your blood.

Transport Materials

Another function of protein is to transport materials throughout your body. A great example of this is haemoglobin, which is the oxygen-transporting protein found in your red blood cells. When you breathe air into your lungs, the oxygen molecules from that air wait in your lung cells for a ride on a red blood cell. Once the oxygen attaches to the haemoglobin of that red cell, it can travel anywhere in your body.

Protein Production

https://vocal.media/futurism/protein-production-in-a-cell

ref1206 — protein production in a cell

Fig340  Protein production  ref1206

The nucleus first receives a chemical signal to make a specific protein. This message is contained in the DNA (deoxyribonucleic acid), which is copied into RNA (ribonucleic acid). (This is done because RNA is smaller than DNA, which would allow it to leave through the nuclear pores.)

The RNA then leaves through a nuclear pore, and arrives at the ribosome. The ribosome creates the protein; this protein goes through the endoplasmic reticulum. A vesicle forms off the endoplasmic reticulum, carrying the protein to the Golgi body.

The Golgi body repackages the protein, and a vesicle carrying the protein forms off. This vesicle then carries the protein to the cell membrane; the vesicle attaches to the cell membrane, and its proteins are released out of the cell.

Learning & Living

 

From  ref 597  Whole Brain  Neural Plasticity

 

xxx

 

ref1209 — Secret language of Cells

A child is born with the ability to learn — but starts with a blank memory/learning  record.  Learning is essential for coping with the complexities and changing nature of our environment.

Humans have adapted to living in different climates, regimes, etc – and also to travel — and become adept at making and using tools and weapons, developing a system of communication through symbols and sounds, and developing social, political and economic systems of interaction.

We each compete and commune as we experience life.  Our Human Body/Mind is the result of how humans evolved to deal with these demands.

Evolution has provided us with the means by which a human grows, learns and develops.  Our acquired “Apps” include a wide range of the good habits/skills needed to relieve us of having to consciously work through routine daily activities.

But our ability to learn these and further life enhancing Apps also means that we can acquire bad Apps – damage-prone habits and antagonizing attitudes.  These may emerge in response to unfortunate experiences such as Toxic Stresses.

During development, from infancy on, the new person is motivated to  seek to fulfil Core Needs.   Clearly the seeds of these Needs are present in the DNA.   The Needs change as the individual develops — notably at adolescence.

From ref650 — “Hardwiring Happiness” by Rick Hanson

Humans have 3 Core Needs or Operating Systems —
• Safety ————Avoiding Harm
• Connection —– Attaching/relating to others
• Satisfaction —– Using our Rewards system.

Each Need has two modes of responding —

  • The Responsive Mode — Controlled, Mindful
  • The Reactive Mode —Stressed. Emotional — Insecure people, and those affected by trauma are more prone to this mode.

As a child grows they learn from their experiences — largely from the Need for Satisfaction.  This learning is enhanced if their experiences can be made to keep  “interesting”.

At the early stages infant is totally dependent on the mother, and/or appropriate carer.  This Nurture is critical in the progression to realising socially acceptable traits.   (Though, much of human history has been based on individuals whose upbringing departed from sound

 

Contents —

From  ref1087 — An overview of the Human Body

Our bodies consist of a number of biological systems that carry out specific functions necessary for everyday living.

The job of the circulatory system is to move blood, nutrients, oxygen, carbon dioxide, and hormones, around the body.  It consists of the heart, blood, blood vessels, arteries and veins.

The digestive system consists of a series of connected organs that together, allow the body to break down and absorb food, and remove waste.  It includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, and anus.  The liver and pancreas also play a role in the digestive system because they produce digestive juices.

The endocrine system consists of eight major glands that secrete hormones into the blood.  These hormones, in turn, travel to different tissues and regulate various bodily functions, such as metabolism, growth and sexual function.

The immune system is the body’s defence against bacteria, viruses and other pathogens that may be harmful.  It includes lymph nodes, the spleen, bone marrow, lymphocytes (including B-cells and T-cells), the thymus and leukocytes, which are white blood cells.

The lymphatic system includes lymph nodes, lymph ducts and lymph vessels, and also plays a role in the body’s defences.  Its main job is to make is to make and move lymph, a clear fluid that contains white blood cells, which help the body fight infection.  The lymphatic system also removes excess lymph fluid from bodily tissues, and returns it to the blood.

The brain’s most dedicated job is to control your body — i.e. to manage “allostasis” — by predicting energy needs before they arise so you can efficiently make worthwhile movements and survive.

Reproduction & Growth

Each human has a limited life-span, so reproduction is required to enable the  continuity of humanity.

The basic human cell is —

Fig122  ref1166 — Human Anatomy

More xxx

Fig 209

Gamete  — A sex cell containing only a single — haploid — set of chromosomes.  A diploid has 2 sets.

Organelles — a specialized subunit, usually within a cell, that has a specific function — such as Ribosomess

Organisms grow and reproduce through cell division. In humans the production of new cells occurs as a result of meiosis and mitosis — see below. Cells can also merge, for example, Sex Cells in order to combine parental Genes.

From  ref1234Differences between meiosis and mitosis.

These two nuclear division processes are similar but distinct.  Both processes involve the division of a diploid cell, or a cell containing two sets of chromosomes (one chromosome donated from each parent).

Meiosis is the process by which gametes — sex cells are generated in organisms that reproduce sexually.

Gametes are produced in male and female gonads and contain one-half the number of chromosomes as the original cell.

New gene combinations are introduced in a population through the genetic recombination that occurs during meiosis. The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

In mitosis, the genetic material (DNA) in a cell is duplicated and divided equally between two cells.  Tis process replicates Somatic (body)  cells

Fig 352   ref1228  Part 2  — In the cells going through mitosis you can clearly see the individual chromosomes

ccc

From   ref1228 — Part 3 Sexual reproduction, meiosis and gamete formation –inc. https://www.bbc.co.uk/bitesize/guides/zghqfcw/revision/3

Sexual reproduction uses a type of cell division called meiosis, which creates gametes — sperm and egg cells.

(Sperm are small and for example do not contain Ribosomes — these and other items are provided by the egg — Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains)

The process of meiosis happens in the male and female reproductive organs.

Before a dividing cell enters meiosis, it undergoes a period of growth called interphase.

From   ref1235 — stages of meiosis

Fig 350   ref1228  part 3 — Meiosis and gamete formation

The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

Fig 349 ref1228 — Towards forming the Zygote Cell

The Human Egg, ready for fertilisation is at the end of the Fallopian Tube, so the Sperm has to get there from the Cervix — thus the mobility through its tail.

ccc

Growth

A Cell can divide in order to provide the means of growing and/or repairing the body.  A cell can also release from its DNA the proteins necessary for growth or repair.

The dividing cell goes through an ordered series of events called the cell cycle.

Fig 350a  ref1228 2 — Mitosis — cell division

The mitotic cell cycle is initiated by the presence of certain growth factors or other signals that indicate that the production of new cells is needed.

Typical ways in which the need for a process to be initiated are given in Appendix “Comms”.

Examples of somatic cells include fat cellsblood cells, skin cells, or  any body-cell that is not a sex-cell . Mitosis is necessary to replace dead cells, damaged cells, or cells that have short life spans.

In mitosis a single cell divides into two cells that are replicas of each other and have the same number of chromosomes. This type of cell division is good for basic growth, repair, and maintenance.  Mitosis is how somatic—or non-reproductive cells — divide. Somatic cells make up most of your body’s tissues and organs, including skin, muscles, lungs, gut, and hair cells.

Since the daughter cells have exact copies of their parent cell’s DNA, no genetic diversity is created through mitosis in normal healthy cells.

From  ref1198 — Developmental genetics

https://www2.le.ac.uk/projects/vgec/schoolsandcolleges/topics/developmental-genetics

The process that changes a single cell into a new person is called development.

During the course of development, complex structures develop from simple ones. A single cell transforms itself into an adult organism. How does something complicated come from something simple? Appendix Comms has examples of how this is done  xxx

Creating an organism from a single cell involves three important processes:

  1. Cell division: cells divide to produce more cells.
  2. Cell differentiation: cells change into different types of cell to do specific jobs in the body, from nerve cells to muscle cells.
  3. Morphogenesis:groups of cells move and change their shape to produce the structure of the organism.

From  ref1202 — Proteins

Proteins are the key working molecules and building blocks in all cells. They are produced in a similar two-step process in all organisms – DNA is first transcribed into RNA, then RNA is translated into protein.

Proteins are the major ‘working molecules’ within every organism. Among their many jobs, proteins catalyse reactions, transport oxygen and defend organisms from infection. They’re also crucial building blocks of organisms. They are the major components of wool, cartilage and milk, they package up the DNA in chromosomes and they insulate the  nervous system!

Proteins are made of large numbers of amino acids joined end to end. The chains fold up to form three-dimensional molecules with complex shapes – you could think of it as origami with a very long and thin piece of paper. The precise shape of each protein, along with the amino acids it contains, determines what it does.

From   ref1183Central Dogma of Biology —  DNA to RNA to a Protein

DNA gives the instructions for various functional proteins to be produced inside the cell — this process is also known as the Central dogma of molecular biology

Fig 353   ref1236 — DNA to RNA to a Protein

Explanation —    ref1230Gene expression

Gene Expression

The process of turning on a gene to produce RNA and protein is called gene Expression

Fig 354  ref1230 — Gene expression

From  ref1234 — Central Dogma of Biology  DNA to RNA to a Protein

  • The central dogma suggests that DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes.
  • The ribosomes serve as factories in the cell where the information is ‘translated’ from a code into the functional product.
  • In transcription, the information in the DNA of every cell is converted into small, portable RNA messages — small enough to pass from the nucleus of the cell
  • During translation, these messages travel from where the DNA is in the cell nucleus to the ribosomes where they are ‘read’ to make specific proteins.
  • The central dogma states that the pattern of information that occurs most frequently in our cells is:
    1. From existing DNA to make new DNA (DNA replication?)
    2. From DNA to make new RNA (transcription)
    3. From RNA to make new proteins (translation).

From  ref1136   —  When life begins

The zygote is the start of a biological continuum that automatically grows and develops, passing gradually and sequentially through the stages we call foetus, baby, child, adult, old person and ending eventually in death.

Fig 337   ref1136 — 3 day old embryo

Fig 355   ref1136 — 40 day old embryo

The full genetic instructions to guide the development of the continuum, in interaction with its environment, are present in the zygote.  Every stage along the continuum is biologically human and each point along the continuum has the full human properties appropriate to that point.

From  ref1232 — Definitions

xxx insert

Genetic — DNA, Chromosomes, Genome and Epigenome

Your genome is the instructions for making and maintaining you. It is written in a chemical code called DNA.

It contains 3 billion bases, 20,000 genes, and 23 pairs of chromosomes!

DNA is a vitally important molecule for not only humans, but for most other organisms as well.

DNA contains our hereditary material and our genes.— it’s what makes us a major part of our uniqueness.

Genes — unit of hereditary information that occupies a fixed position on a chromosome. Genes direct the synthesis of proteins  — From ref1205

Chromosomes   — There are 23 chromosomes in each structure and these are each intertwined with an identical set of 23.

Each chromosome has a role in the growth and renewal of the human body.

Each  chromosome is formed into functional blocks which can be activated to perform the specific task — These blocks  are called genes —   These tasks can be further defined by epigenetic changes.

However, DNA modifications which do not change the DNA sequence but can affect gene activity and alter human traits and health — From  ref1205 — the Epigenome

Chemical compounds that are added to individual genes can regulate their activity; these modifications are known as epigenetic changes.

The epigenome comprises all of the chemical compounds that have been added to the entirety of one’s genome in a way to regulates the activity (expression) of all the genes,  The chemical compounds of the epigenome are not part of the DNA sequence, but are on or attached to DNA.

The following diagram incorporates all of these aspects

Fig345   ref1221 — DNA, Histones, Chromosomes and  Epigenetics

Definitions —

Chromatin — The primary function of chromatin is to compress the DNA into a compact unit that will be less voluminous and can fit within the nucleus.

Histones are basic proteins found in the nuclei of cells. These proteins help organize very long strands of DNA, the genetic “blueprint” of every living thing, into condensed structures that can fit into comparatively small spaces within the nucleus.

Histones do not serve merely as scaffolding for DNA strands. They also take part in gene regulation by affecting when certain genes — that is, lengths of DNA associated with a single protein product — are “expressed,” or activated to transcribe RNA and ultimately the protein product a given gene carries instructions for making.

From  ref1227What is epigenetics

The Epigenetic effects include Factors such as stress, environment, medications, diet, the contents of water, etc.

In addition to DNA methylation being vital to healthy growth and development, it also enables the expression of retroviral genes to be suppressed. However,  along with other potentially dangerous sequences of DNA that have entered and may damage the host. is associated with many diseases including asthma, aging, and cancer,

From   ref1233The factors that influence genes turn on and off

 

  1. Transcription factors (TFs) are molecules involved in regulating gene expression. They are usually proteins, although they can also consist of short, non-coding RNA. TFs are also usually found working in groups or complexes, forming multiple interactions that allow for varying degrees of control over rates of transcription. In people (and other eukaryotes), genes are usually in a default “off” state, so TFs serve mainly to turn gene expression “on”.
  2. Epigenetics involves genetic control by factors other than an individual’s DNA sequence. Epigenetic changes can switch genes on or off and determine which proteins are transcribed. Gene silencing is a general term describing epigenetic processes of gene regulation. Within cells, there are three systems that can interact with each other to silence genes: DNA methylation, histonemodifications, and RNA-associated silencing
  3. Environmental Influences on Gene Expression. The expression of genes in an organism can be influenced by the environment, including the external world in which the organism is located or develops, as well as the organism’s internal world, which includes such factors as its hormones and metabolism. One major internal environmental influence that affects gene expression is gender, as is the case with sex-influenced and sex-limited traits. Similarly, drugs, chemicals, temperature, and light are among the external environmental factors that can determine which genes are turned on and off, thereby influencing the way an organism develops and functions.

A phenotype is how these genes are actually expressed (applied).  This is due to a combination of genes and the effects of Epigenomics — these effects occur at different times during a lifetime, and can be reversed.  The phenotype can include physical traits, such as height and color or the eyes, as well as non-physical traits such as shyness and extroversion.

xxx.

Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed).

Each cell type in your body has a different set of active genes —despite the fact that almost all the cells of your body contain the exact same DNA.

Transcription DNA to RNA

Fig356  ref1237 — A Guide to Understanding Gene Expression

The Messenger mRNA small enough to proceed through the Nucleus

3n

Again  ref1205 — Understanding how genes work & epigenome

Environmental influences, such as a person’s diet and exposure to pollutants, can also impact the epigenome.

Epigenetic changes can help determine whether genes are turned on or off and can influence the production of proteins in certain cells, ensuring that only necessary proteins are produced.

For example, proteins that promote bone growth are not produced in muscle cells. Patterns of epigenetic modification vary among individuals, different tissues within an individual, and even different cells.

A common type of epigenetic modification is called DNA methylation. This involves attaching small molecules to segments of DNA. When these methyl groups are added to a particular gene, that gene is turned off or silenced, and no protein is produced from that gene.

Because errors in the epigenetic process, such as modifying the wrong gene or failing to add a compound to a gene, can lead to abnormal gene activity or inactivity, they can cause genetic disorders. Conditions including cancers, metabolic disorders, and degenerative disorders have all been found to be related to epigenetic errors.

Scientists continue to explore the relationship between the genome and the chemical compounds that modify it. In particular, they are studying what effect the modifications have on gene function, protein production, and human health.

From  ref1121 — How Children’s Experiences Affect Their Genes

Epigenetics shows how environmental influences—children’s experiences—actually affect the expression of their genes.

This means the old idea that genes are “set in stone” has been disproven. Nature vs. Nurture is no longer a debate. It’s nearly always both!

During development, the DNA that makes up our genes accumulates chemical marks that determine how much or little of the genes is expressed. This collection of chemical marks is known as the “epigenome.” The different experiences children have rearrange those chemical marks. This explains why genetically identical twins can exhibit different behaviors, skills, health, and achievement.

The marks do not change the sequence of the DNA, but they do change the way cells use the DNA’s instructions.  They may, or may not, be permanent.

The marks can be passed on from cell to cell as they divide, and they can even be passed from one generation to the next.

The genes children inherit from their biological parents provide information that guides their development. For example, how tall they could eventually become or the kind of temperament they could have.

When experiences during development rearrange the epigenetic marks that govern gene expression, they can change whether and how genes release the information they carry.

Thus, the epigenome can be affected by positive experiences, such as supportive relationships and opportunities for learning, or negative influences, such as environmental toxins or stressful life circumstances, which leave a unique epigenetic “signature” on the genes. These signatures can be temporary or permanent and both types affect how easily the genes are switched on or off. Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning. But the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning.

Experiences very early in life, when the brain is developing most rapidly, cause epigenetic adaptations that influence whether, when, and how genes release their instructions for building future capacity for health, skills, and resilience. That’s why it’s crucial to provide supportive and nurturing experiences for young children in the earliest years.

Services such as high-quality health care for all pregnant women, infants, and toddlers, as well as support for new parents and caregivers can—quite literally— affect the chemistry around children’s genes. Supportive relationships and rich learning experiences generate positive epigenetic signatures that activate genetic potential.

Injurious experiences, such as malnutrition, exposure to chemical toxins or drugs, and toxic stress before birth or in early childhood are not “forgotten,” but rather are built into the architecture of the developing brain through the epigenome. The “biological memories” associated with these epigenetic changes can affect multiple organ systems and increase the risk not only for poor physical and mental health outcomes but also for impairments in future learning capacity and behavior.

Research has shown that specific epigenetic modifications do occur in brain cells as cognitive skills like learning and memory develop, and that repeated activation of brain circuits dedicated to learning and memory through interaction with the environment, such as reciprocal “serve and return” interaction with adults, facilitates these positive epigenetic modifications.

We also know that sound maternal and fetal nutrition, combined with positive social-emotional support of children through their family and community environments, will reduce the likelihood of negative epigenetic modifications that increase the risk of later physical and mental health impairments.

Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning, but that takes a lot more effort, may not be successful at changing all aspects of the signatures, and is costly. Thus, the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning, helping children grow up to be healthy, productive members of society.

From  ref1207 — Primary functions of protein in the body

https://study.com/academy/lesson/primary-functions-of-protein-in-the-body.html

Protein is a vital molecule that carries out many functions in your body. Learn how proteins provide structure, regulate body processes, transport materials throughout your body, help your immune system and act as a source of energy.

Proteins are all similar in that they are made up of chains of amino acids; these basic building blocks of proteins are linked together by unique chemical bonds called peptide bonds.

Amino acids being the building blocks of proteins, but we could also say that proteins themselves are building blocks of the body.

And this brings us to the first important function of protein, which is to provide structure.

Provide Structure

Structural proteins make up integral parts of your body. For example, keratin is a type of protein found in your hair, nails and skin that helps give these structures strength. Inside your body, protein provides structure to every cell. Collagen, which is a structural protein found in various connective tissues, provides the framework for the ligaments that hold your bones together and the tendons that attach muscles to those bones.

Regulate Body Processes

Proteins also regulate body processes. For example, enzymes are proteins that speed up chemical reactions in the body. Without them, basic activities like breaking down the foods you eat would happen too slowly to support your life. You can think of enzymes as proteins that shift your body processes into high gear.

Body processes are also influenced by hormones, which are proteins that regulate the activity of cells or organs. Hormones are like chemical messengers that carry an order from one part of your body to another. For example, insulin is a hormone that regulates blood sugar by carrying a message to your body cells about how much sugar is present in your blood.

Transport Materials

Another function of protein is to transport materials throughout your body. A great example of this is haemoglobin, which is the oxygen-transporting protein found in your red blood cells. When you breathe air into your lungs, the oxygen molecules from that air wait in your lung cells for a ride on a red blood cell. Once the oxygen attaches to the haemoglobin of that red cell, it can travel anywhere in your body.

Protein Production

https://vocal.media/futurism/protein-production-in-a-cell

ref1206 — protein production in a cell

Fig340  Protein production  ref1206

The nucleus first receives a chemical signal to make a specific protein. This message is contained in the DNA (deoxyribonucleic acid), which is copied into RNA (ribonucleic acid). (This is done because RNA is smaller than DNA, which would allow it to leave through the nuclear pores.)

The RNA then leaves through a nuclear pore, and arrives at the ribosome. The ribosome creates the protein; this protein goes through the endoplasmic reticulum. A vesicle forms off the endoplasmic reticulum, carrying the protein to the Golgi body.

The Golgi body repackages the protein, and a vesicle carrying the protein forms off. This vesicle then carries the protein to the cell membrane; the vesicle attaches to the cell membrane, and its proteins are released out of the cell.

Learning & Living

 

From  ref 597  Whole Brain  Neural Plasticity

 

xxx

 

ref1209 — Secret language of Cells

A child is born with the ability to learn — but starts with a blank memory/learning  record.  Learning is essential for coping with the complexities and changing nature of our environment.

Humans have adapted to living in different climates, regimes, etc – and also to travel — and become adept at making and using tools and weapons, developing a system of communication through symbols and sounds, and developing social, political and economic systems of interaction.

We each compete and commune as we experience life.  Our Human Body/Mind is the result of how humans evolved to deal with these demands.

Evolution has provided us with the means by which a human grows, learns and develops.  Our acquired “Apps” include a wide range of the good habits/skills needed to relieve us of having to consciously work through routine daily activities.

But our ability to learn these and further life enhancing Apps also means that we can acquire bad Apps – damage-prone habits and antagonizing attitudes.  These may emerge in response to unfortunate experiences such as Toxic Stresses.

During development, from infancy on, the new person is motivated to  seek to fulfil Core Needs.   Clearly the seeds of these Needs are present in the DNA.   The Needs change as the individual develops — notably at adolescence.

From ref650 — “Hardwiring Happiness” by Rick Hanson

Humans have 3 Core Needs or Operating Systems —
• Safety ————Avoiding Harm
• Connection —– Attaching/relating to others
• Satisfaction —– Using our Rewards system.

Each Need has two modes of responding —

  • The Responsive Mode — Controlled, Mindful
  • The Reactive Mode —Stressed. Emotional — Insecure people, and those affected by trauma are more prone to this mode.

As a child grows they learn from their experiences — largely from the Need for Satisfaction.  This learning is enhanced if their experiences can be made to keep  “interesting”.

At the early stages infant is totally dependent on the mother, and/or appropriate carer.  This Nurture is critical in the progression to realising socially acceptable traits.   (Though, much of human history has been based on individuals whose upbringing departed from sound

 

Contents —

From  ref1087 — An overview of the Human Body

Our bodies consist of a number of biological systems that carry out specific functions necessary for everyday living.

The job of the circulatory system is to move blood, nutrients, oxygen, carbon dioxide, and hormones, around the body.  It consists of the heart, blood, blood vessels, arteries and veins.

The digestive system consists of a series of connected organs that together, allow the body to break down and absorb food, and remove waste.  It includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, and anus.  The liver and pancreas also play a role in the digestive system because they produce digestive juices.

The endocrine system consists of eight major glands that secrete hormones into the blood.  These hormones, in turn, travel to different tissues and regulate various bodily functions, such as metabolism, growth and sexual function.

The immune system is the body’s defence against bacteria, viruses and other pathogens that may be harmful.  It includes lymph nodes, the spleen, bone marrow, lymphocytes (including B-cells and T-cells), the thymus and leukocytes, which are white blood cells.

The lymphatic system includes lymph nodes, lymph ducts and lymph vessels, and also plays a role in the body’s defences.  Its main job is to make is to make and move lymph, a clear fluid that contains white blood cells, which help the body fight infection.  The lymphatic system also removes excess lymph fluid from bodily tissues, and returns it to the blood.

The brain’s most dedicated job is to control your body — i.e. to manage “allostasis” — by predicting energy needs before they arise so you can efficiently make worthwhile movements and survive.

3n

ccc

 

Reproduction & Growth

Each human has a limited life-span, so reproduction is required to enable the  continuity of humanity.

The basic human cell is —

Fig122  ref1166 — Human Anatomy

More xxx

Fig 209

Gamete  — A sex cell containing only a single — haploid — set of chromosomes.  A diploid has 2 sets.

Organelles — a specialized subunit, usually within a cell, that has a specific function — such as Ribosomess

Organisms grow and reproduce through cell division. In humans the production of new cells occurs as a result of meiosis and mitosis — see below. Cells can also merge, for example, Sex Cells in order to combine parental Genes.

From  ref1234Differences between meiosis and mitosis.

These two nuclear division processes are similar but distinct.  Both processes involve the division of a diploid cell, or a cell containing two sets of chromosomes (one chromosome donated from each parent).

Meiosis is the process by which gametes — sex cells are generated in organisms that reproduce sexually.

Gametes are produced in male and female gonads and contain one-half the number of chromosomes as the original cell.

New gene combinations are introduced in a population through the genetic recombination that occurs during meiosis. The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

In mitosis, the genetic material (DNA) in a cell is duplicated and divided equally between two cells.  Tis process replicates Somatic (body)  cells

Fig 352   ref1228  Part 2  — In the cells going through mitosis you can clearly see the individual chromosomes

ccc

From   ref1228 — Part 3 Sexual reproduction, meiosis and gamete formation –inc. https://www.bbc.co.uk/bitesize/guides/zghqfcw/revision/3

Sexual reproduction uses a type of cell division called meiosis, which creates gametes — sperm and egg cells.

(Sperm are small and for example do not contain Ribosomes — these and other items are provided by the egg — Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains)

The process of meiosis happens in the male and female reproductive organs.

Before a dividing cell enters meiosis, it undergoes a period of growth called interphase.

From   ref1235 — stages of meiosis

Fig 350   ref1228  part 3 — Meiosis and gamete formation

The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

Fig 349 ref1228 — Towards forming the Zygote Cell

The Human Egg, ready for fertilisation is at the end of the Fallopian Tube, so the Sperm has to get there from the Cervix — thus the mobility through its tail.

ccc

Growth

A Cell can divide in order to provide the means of growing and/or repairing the body.  A cell can also release from its DNA the proteins necessary for growth or repair.

The dividing cell goes through an ordered series of events called the cell cycle.

Fig 350a  ref1228 2 — Mitosis — cell division

The mitotic cell cycle is initiated by the presence of certain growth factors or other signals that indicate that the production of new cells is needed.

Typical ways in which the need for a process to be initiated are given in Appendix “Comms”.

Examples of somatic cells include fat cellsblood cells, skin cells, or  any body-cell that is not a sex-cell . Mitosis is necessary to replace dead cells, damaged cells, or cells that have short life spans.

In mitosis a single cell divides into two cells that are replicas of each other and have the same number of chromosomes. This type of cell division is good for basic growth, repair, and maintenance.  Mitosis is how somatic—or non-reproductive cells — divide. Somatic cells make up most of your body’s tissues and organs, including skin, muscles, lungs, gut, and hair cells.

Since the daughter cells have exact copies of their parent cell’s DNA, no genetic diversity is created through mitosis in normal healthy cells.

From  ref1198 — Developmental genetics

https://www2.le.ac.uk/projects/vgec/schoolsandcolleges/topics/developmental-genetics

The process that changes a single cell into a new person is called development.

During the course of development, complex structures develop from simple ones. A single cell transforms itself into an adult organism. How does something complicated come from something simple? Appendix Comms has examples of how this is done  xxx

Creating an organism from a single cell involves three important processes:

  1. Cell division: cells divide to produce more cells.
  2. Cell differentiation: cells change into different types of cell to do specific jobs in the body, from nerve cells to muscle cells.
  3. Morphogenesis:groups of cells move and change their shape to produce the structure of the organism.

From  ref1202 — Proteins

Proteins are the key working molecules and building blocks in all cells. They are produced in a similar two-step process in all organisms – DNA is first transcribed into RNA, then RNA is translated into protein.

Proteins are the major ‘working molecules’ within every organism. Among their many jobs, proteins catalyse reactions, transport oxygen and defend organisms from infection. They’re also crucial building blocks of organisms. They are the major components of wool, cartilage and milk, they package up the DNA in chromosomes and they insulate the  nervous system!

Proteins are made of large numbers of amino acids joined end to end. The chains fold up to form three-dimensional molecules with complex shapes – you could think of it as origami with a very long and thin piece of paper. The precise shape of each protein, along with the amino acids it contains, determines what it does.

From   ref1183Central Dogma of Biology —  DNA to RNA to a Protein

DNA gives the instructions for various functional proteins to be produced inside the cell — this process is also known as the Central dogma of molecular biology

Fig 353   ref1236 — DNA to RNA to a Protein

Explanation —    ref1230Gene expression

Gene Expression

The process of turning on a gene to produce RNA and protein is called gene Expression

Fig 354  ref1230 — Gene expression

From  ref1234 — Central Dogma of Biology  DNA to RNA to a Protein

  • The central dogma suggests that DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes.
  • The ribosomes serve as factories in the cell where the information is ‘translated’ from a code into the functional product.
  • In transcription, the information in the DNA of every cell is converted into small, portable RNA messages — small enough to pass from the nucleus of the cell
  • During translation, these messages travel from where the DNA is in the cell nucleus to the ribosomes where they are ‘read’ to make specific proteins.
  • The central dogma states that the pattern of information that occurs most frequently in our cells is:
    1. From existing DNA to make new DNA (DNA replication?)
    2. From DNA to make new RNA (transcription)
    3. From RNA to make new proteins (translation).

From  ref1136   —  When life begins

The zygote is the start of a biological continuum that automatically grows and develops, passing gradually and sequentially through the stages we call foetus, baby, child, adult, old person and ending eventually in death.

Fig 337   ref1136 — 3 day old embryo

Fig 355   ref1136 — 40 day old embryo

The full genetic instructions to guide the development of the continuum, in interaction with its environment, are present in the zygote.  Every stage along the continuum is biologically human and each point along the continuum has the full human properties appropriate to that point.

From  ref1232 — Definitions

xxx insert

Genetic — DNA, Chromosomes, Genome and Epigenome

Your genome is the instructions for making and maintaining you. It is written in a chemical code called DNA.

It contains 3 billion bases, 20,000 genes, and 23 pairs of chromosomes!

DNA is a vitally important molecule for not only humans, but for most other organisms as well.

DNA contains our hereditary material and our genes.— it’s what makes us a major part of our uniqueness.

Genes — unit of hereditary information that occupies a fixed position on a chromosome. Genes direct the synthesis of proteins  — From ref1205

Chromosomes   — There are 23 chromosomes in each structure and these are each intertwined with an identical set of 23.

Each chromosome has a role in the growth and renewal of the human body.

Each  chromosome is formed into functional blocks which can be activated to perform the specific task — These blocks  are called genes —   These tasks can be further defined by epigenetic changes.

However, DNA modifications which do not change the DNA sequence but can affect gene activity and alter human traits and health — From  ref1205 — the Epigenome

Chemical compounds that are added to individual genes can regulate their activity; these modifications are known as epigenetic changes.

The epigenome comprises all of the chemical compounds that have been added to the entirety of one’s genome in a way to regulates the activity (expression) of all the genes,  The chemical compounds of the epigenome are not part of the DNA sequence, but are on or attached to DNA.

The following diagram incorporates all of these aspects

Fig345   ref1221 — DNA, Histones, Chromosomes and  Epigenetics

Definitions —

Chromatin — The primary function of chromatin is to compress the DNA into a compact unit that will be less voluminous and can fit within the nucleus.

Histones are basic proteins found in the nuclei of cells. These proteins help organize very long strands of DNA, the genetic “blueprint” of every living thing, into condensed structures that can fit into comparatively small spaces within the nucleus.

Histones do not serve merely as scaffolding for DNA strands. They also take part in gene regulation by affecting when certain genes — that is, lengths of DNA associated with a single protein product — are “expressed,” or activated to transcribe RNA and ultimately the protein product a given gene carries instructions for making.

From  ref1227What is epigenetics

The Epigenetic effects include Factors such as stress, environment, medications, diet, the contents of water, etc.

In addition to DNA methylation being vital to healthy growth and development, it also enables the expression of retroviral genes to be suppressed. However,  along with other potentially dangerous sequences of DNA that have entered and may damage the host. is associated with many diseases including asthma, aging, and cancer,

From   ref1233The factors that influence genes turn on and off

 

  1. Transcription factors (TFs) are molecules involved in regulating gene expression. They are usually proteins, although they can also consist of short, non-coding RNA. TFs are also usually found working in groups or complexes, forming multiple interactions that allow for varying degrees of control over rates of transcription. In people (and other eukaryotes), genes are usually in a default “off” state, so TFs serve mainly to turn gene expression “on”.
  2. Epigenetics involves genetic control by factors other than an individual’s DNA sequence. Epigenetic changes can switch genes on or off and determine which proteins are transcribed. Gene silencing is a general term describing epigenetic processes of gene regulation. Within cells, there are three systems that can interact with each other to silence genes: DNA methylation, histonemodifications, and RNA-associated silencing
  3. Environmental Influences on Gene Expression. The expression of genes in an organism can be influenced by the environment, including the external world in which the organism is located or develops, as well as the organism’s internal world, which includes such factors as its hormones and metabolism. One major internal environmental influence that affects gene expression is gender, as is the case with sex-influenced and sex-limited traits. Similarly, drugs, chemicals, temperature, and light are among the external environmental factors that can determine which genes are turned on and off, thereby influencing the way an organism develops and functions.

A phenotype is how these genes are actually expressed (applied).  This is due to a combination of genes and the effects of Epigenomics — these effects occur at different times during a lifetime, and can be reversed.  The phenotype can include physical traits, such as height and color or the eyes, as well as non-physical traits such as shyness and extroversion.

xxx.

Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed).

Each cell type in your body has a different set of active genes —despite the fact that almost all the cells of your body contain the exact same DNA.

Transcription DNA to RNA

Fig356  ref1237 — A Guide to Understanding Gene Expression

The Messenger mRNA small enough to proceed through the Nucleus

3n

Again  ref1205 — Understanding how genes work & epigenome

Environmental influences, such as a person’s diet and exposure to pollutants, can also impact the epigenome.

Epigenetic changes can help determine whether genes are turned on or off and can influence the production of proteins in certain cells, ensuring that only necessary proteins are produced.

For example, proteins that promote bone growth are not produced in muscle cells. Patterns of epigenetic modification vary among individuals, different tissues within an individual, and even different cells.

A common type of epigenetic modification is called DNA methylation. This involves attaching small molecules to segments of DNA. When these methyl groups are added to a particular gene, that gene is turned off or silenced, and no protein is produced from that gene.

Because errors in the epigenetic process, such as modifying the wrong gene or failing to add a compound to a gene, can lead to abnormal gene activity or inactivity, they can cause genetic disorders. Conditions including cancers, metabolic disorders, and degenerative disorders have all been found to be related to epigenetic errors.

Scientists continue to explore the relationship between the genome and the chemical compounds that modify it. In particular, they are studying what effect the modifications have on gene function, protein production, and human health.

From  ref1121 — How Children’s Experiences Affect Their Genes

Epigenetics shows how environmental influences—children’s experiences—actually affect the expression of their genes.

This means the old idea that genes are “set in stone” has been disproven. Nature vs. Nurture is no longer a debate. It’s nearly always both!

During development, the DNA that makes up our genes accumulates chemical marks that determine how much or little of the genes is expressed. This collection of chemical marks is known as the “epigenome.” The different experiences children have rearrange those chemical marks. This explains why genetically identical twins can exhibit different behaviors, skills, health, and achievement.

The marks do not change the sequence of the DNA, but they do change the way cells use the DNA’s instructions.  They may, or may not, be permanent.

The marks can be passed on from cell to cell as they divide, and they can even be passed from one generation to the next.

The genes children inherit from their biological parents provide information that guides their development. For example, how tall they could eventually become or the kind of temperament they could have.

When experiences during development rearrange the epigenetic marks that govern gene expression, they can change whether and how genes release the information they carry.

Thus, the epigenome can be affected by positive experiences, such as supportive relationships and opportunities for learning, or negative influences, such as environmental toxins or stressful life circumstances, which leave a unique epigenetic “signature” on the genes. These signatures can be temporary or permanent and both types affect how easily the genes are switched on or off. Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning. But the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning.

Experiences very early in life, when the brain is developing most rapidly, cause epigenetic adaptations that influence whether, when, and how genes release their instructions for building future capacity for health, skills, and resilience. That’s why it’s crucial to provide supportive and nurturing experiences for young children in the earliest years.

Services such as high-quality health care for all pregnant women, infants, and toddlers, as well as support for new parents and caregivers can—quite literally— affect the chemistry around children’s genes. Supportive relationships and rich learning experiences generate positive epigenetic signatures that activate genetic potential.

Injurious experiences, such as malnutrition, exposure to chemical toxins or drugs, and toxic stress before birth or in early childhood are not “forgotten,” but rather are built into the architecture of the developing brain through the epigenome. The “biological memories” associated with these epigenetic changes can affect multiple organ systems and increase the risk not only for poor physical and mental health outcomes but also for impairments in future learning capacity and behavior.

Research has shown that specific epigenetic modifications do occur in brain cells as cognitive skills like learning and memory develop, and that repeated activation of brain circuits dedicated to learning and memory through interaction with the environment, such as reciprocal “serve and return” interaction with adults, facilitates these positive epigenetic modifications.

We also know that sound maternal and fetal nutrition, combined with positive social-emotional support of children through their family and community environments, will reduce the likelihood of negative epigenetic modifications that increase the risk of later physical and mental health impairments.

Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning, but that takes a lot more effort, may not be successful at changing all aspects of the signatures, and is costly. Thus, the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning, helping children grow up to be healthy, productive members of society.

From  ref1207 — Primary functions of protein in the body

https://study.com/academy/lesson/primary-functions-of-protein-in-the-body.html

Protein is a vital molecule that carries out many functions in your body. Learn how proteins provide structure, regulate body processes, transport materials throughout your body, help your immune system and act as a source of energy.

Proteins are all similar in that they are made up of chains of amino acids; these basic building blocks of proteins are linked together by unique chemical bonds called peptide bonds.

Amino acids being the building blocks of proteins, but we could also say that proteins themselves are building blocks of the body.

And this brings us to the first important function of protein, which is to provide structure.

Provide Structure

Structural proteins make up integral parts of your body. For example, keratin is a type of protein found in your hair, nails and skin that helps give these structures strength. Inside your body, protein provides structure to every cell. Collagen, which is a structural protein found in various connective tissues, provides the framework for the ligaments that hold your bones together and the tendons that attach muscles to those bones.

Regulate Body Processes

Proteins also regulate body processes. For example, enzymes are proteins that speed up chemical reactions in the body. Without them, basic activities like breaking down the foods you eat would happen too slowly to support your life. You can think of enzymes as proteins that shift your body processes into high gear.

Body processes are also influenced by hormones, which are proteins that regulate the activity of cells or organs. Hormones are like chemical messengers that carry an order from one part of your body to another. For example, insulin is a hormone that regulates blood sugar by carrying a message to your body cells about how much sugar is present in your blood.

Transport Materials

Another function of protein is to transport materials throughout your body. A great example of this is haemoglobin, which is the oxygen-transporting protein found in your red blood cells. When you breathe air into your lungs, the oxygen molecules from that air wait in your lung cells for a ride on a red blood cell. Once the oxygen attaches to the haemoglobin of that red cell, it can travel anywhere in your body.

Protein Production

https://vocal.media/futurism/protein-production-in-a-cell

ref1206 — protein production in a cell

Fig340  Protein production  ref1206

The nucleus first receives a chemical signal to make a specific protein. This message is contained in the DNA (deoxyribonucleic acid), which is copied into RNA (ribonucleic acid). (This is done because RNA is smaller than DNA, which would allow it to leave through the nuclear pores.)

The RNA then leaves through a nuclear pore, and arrives at the ribosome. The ribosome creates the protein; this protein goes through the endoplasmic reticulum. A vesicle forms off the endoplasmic reticulum, carrying the protein to the Golgi body.

The Golgi body repackages the protein, and a vesicle carrying the protein forms off. This vesicle then carries the protein to the cell membrane; the vesicle attaches to the cell membrane, and its proteins are released out of the cell.

Learning & Living

 

From  ref 597  Whole Brain  Neural Plasticity

 

xxx

 

ref1209 — Secret language of Cells

A child is born with the ability to learn — but starts with a blank memory/learning  record.  Learning is essential for coping with the complexities and changing nature of our environment.

Humans have adapted to living in different climates, regimes, etc – and also to travel — and become adept at making and using tools and weapons, developing a system of communication through symbols and sounds, and developing social, political and economic systems of interaction.

We each compete and commune as we experience life.  Our Human Body/Mind is the result of how humans evolved to deal with these demands.

Evolution has provided us with the means by which a human grows, learns and develops.  Our acquired “Apps” include a wide range of the good habits/skills needed to relieve us of having to consciously work through routine daily activities.

But our ability to learn these and further life enhancing Apps also means that we can acquire bad Apps – damage-prone habits and antagonizing attitudes.  These may emerge in response to unfortunate experiences such as Toxic Stresses.

During development, from infancy on, the new person is motivated to  seek to fulfil Core Needs.   Clearly the seeds of these Needs are present in the DNA.   The Needs change as the individual develops — notably at adolescence.

From ref650 — “Hardwiring Happiness” by Rick Hanson

Humans have 3 Core Needs or Operating Systems —
• Safety ————Avoiding Harm
• Connection —– Attaching/relating to others
• Satisfaction —– Using our Rewards system.

Each Need has two modes of responding —

  • The Responsive Mode — Controlled, Mindful
  • The Reactive Mode —Stressed. Emotional — Insecure people, and those affected by trauma are more prone to this mode.

As a child grows they learn from their experiences — largely from the Need for Satisfaction.  This learning is enhanced if their experiences can be made to keep  “interesting”.

At the early stages infant is totally dependent on the mother, and/or appropriate carer.  This Nurture is critical in the progression to realising socially acceptable traits.   (Though, much of human history has been based on individuals whose upbringing departed from sound

 

Contents —

From  ref1087 — An overview of the Human Body

Our bodies consist of a number of biological systems that carry out specific functions necessary for everyday living.

The job of the circulatory system is to move blood, nutrients, oxygen, carbon dioxide, and hormones, around the body.  It consists of the heart, blood, blood vessels, arteries and veins.

The digestive system consists of a series of connected organs that together, allow the body to break down and absorb food, and remove waste.  It includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, and anus.  The liver and pancreas also play a role in the digestive system because they produce digestive juices.

The endocrine system consists of eight major glands that secrete hormones into the blood.  These hormones, in turn, travel to different tissues and regulate various bodily functions, such as metabolism, growth and sexual function.

The immune system is the body’s defence against bacteria, viruses and other pathogens that may be harmful.  It includes lymph nodes, the spleen, bone marrow, lymphocytes (including B-cells and T-cells), the thymus and leukocytes, which are white blood cells.

The lymphatic system includes lymph nodes, lymph ducts and lymph vessels, and also plays a role in the body’s defences.  Its main job is to make is to make and move lymph, a clear fluid that contains white blood cells, which help the body fight infection.  The lymphatic system also removes excess lymph fluid from bodily tissues, and returns it to the blood.

The brain’s most dedicated job is to control your body — i.e. to manage “allostasis” — by predicting energy needs before they arise so you can efficiently make worthwhile movements and survive.

3n

ccc

 

Reproduction & Growth

Each human has a limited life-span, so reproduction is required to enable the  continuity of humanity.

The basic human cell is —

Fig122  ref1166 — Human Anatomy

More xxx

Fig 209

Gamete  — A sex cell containing only a single — haploid — set of chromosomes.  A diploid has 2 sets.

Organelles — a specialized subunit, usually within a cell, that has a specific function — such as Ribosomess

Organisms grow and reproduce through cell division. In humans the production of new cells occurs as a result of meiosis and mitosis — see below. Cells can also merge, for example, Sex Cells in order to combine parental Genes.

From  ref1234Differences between meiosis and mitosis.

These two nuclear division processes are similar but distinct.  Both processes involve the division of a diploid cell, or a cell containing two sets of chromosomes (one chromosome donated from each parent).

Meiosis is the process by which gametes — sex cells are generated in organisms that reproduce sexually.

Gametes are produced in male and female gonads and contain one-half the number of chromosomes as the original cell.

New gene combinations are introduced in a population through the genetic recombination that occurs during meiosis. The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

In mitosis, the genetic material (DNA) in a cell is duplicated and divided equally between two cells.  Tis process replicates Somatic (body)  cells

Fig 352   ref1228  Part 2  — In the cells going through mitosis you can clearly see the individual chromosomes

ccc

From   ref1228 — Part 3 Sexual reproduction, meiosis and gamete formation –inc. https://www.bbc.co.uk/bitesize/guides/zghqfcw/revision/3

Sexual reproduction uses a type of cell division called meiosis, which creates gametes — sperm and egg cells.

(Sperm are small and for example do not contain Ribosomes — these and other items are provided by the egg — Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains)

The process of meiosis happens in the male and female reproductive organs.

Before a dividing cell enters meiosis, it undergoes a period of growth called interphase.

From   ref1235 — stages of meiosis

Fig 350   ref1228  part 3 — Meiosis and gamete formation

The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

Fig 349 ref1228 — Towards forming the Zygote Cell

The Human Egg, ready for fertilisation is at the end of the Fallopian Tube, so the Sperm has to get there from the Cervix — thus the mobility through its tail.

ccc

Growth

A Cell can divide in order to provide the means of growing and/or repairing the body.  A cell can also release from its DNA the proteins necessary for growth or repair.

The dividing cell goes through an ordered series of events called the cell cycle.

Fig 350a  ref1228 2 — Mitosis — cell division

The mitotic cell cycle is initiated by the presence of certain growth factors or other signals that indicate that the production of new cells is needed.

Typical ways in which the need for a process to be initiated are given in Appendix “Comms”.

Examples of somatic cells include fat cellsblood cells, skin cells, or  any body-cell that is not a sex-cell . Mitosis is necessary to replace dead cells, damaged cells, or cells that have short life spans.

In mitosis a single cell divides into two cells that are replicas of each other and have the same number of chromosomes. This type of cell division is good for basic growth, repair, and maintenance.  Mitosis is how somatic—or non-reproductive cells — divide. Somatic cells make up most of your body’s tissues and organs, including skin, muscles, lungs, gut, and hair cells.

Since the daughter cells have exact copies of their parent cell’s DNA, no genetic diversity is created through mitosis in normal healthy cells.

From  ref1198 — Developmental genetics

https://www2.le.ac.uk/projects/vgec/schoolsandcolleges/topics/developmental-genetics

The process that changes a single cell into a new person is called development.

During the course of development, complex structures develop from simple ones. A single cell transforms itself into an adult organism. How does something complicated come from something simple? Appendix Comms has examples of how this is done  xxx

Creating an organism from a single cell involves three important processes:

  1. Cell division: cells divide to produce more cells.
  2. Cell differentiation: cells change into different types of cell to do specific jobs in the body, from nerve cells to muscle cells.
  3. Morphogenesis:groups of cells move and change their shape to produce the structure of the organism.

From  ref1202 — Proteins

Proteins are the key working molecules and building blocks in all cells. They are produced in a similar two-step process in all organisms – DNA is first transcribed into RNA, then RNA is translated into protein.

Proteins are the major ‘working molecules’ within every organism. Among their many jobs, proteins catalyse reactions, transport oxygen and defend organisms from infection. They’re also crucial building blocks of organisms. They are the major components of wool, cartilage and milk, they package up the DNA in chromosomes and they insulate the  nervous system!

Proteins are made of large numbers of amino acids joined end to end. The chains fold up to form three-dimensional molecules with complex shapes – you could think of it as origami with a very long and thin piece of paper. The precise shape of each protein, along with the amino acids it contains, determines what it does.

From   ref1183Central Dogma of Biology —  DNA to RNA to a Protein

DNA gives the instructions for various functional proteins to be produced inside the cell — this process is also known as the Central dogma of molecular biology

Fig 353   ref1236 — DNA to RNA to a Protein

Explanation —    ref1230Gene expression

Gene Expression

The process of turning on a gene to produce RNA and protein is called gene Expression

Fig 354  ref1230 — Gene expression

From  ref1234 — Central Dogma of Biology  DNA to RNA to a Protein

  • The central dogma suggests that DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes.
  • The ribosomes serve as factories in the cell where the information is ‘translated’ from a code into the functional product.
  • In transcription, the information in the DNA of every cell is converted into small, portable RNA messages — small enough to pass from the nucleus of the cell
  • During translation, these messages travel from where the DNA is in the cell nucleus to the ribosomes where they are ‘read’ to make specific proteins.
  • The central dogma states that the pattern of information that occurs most frequently in our cells is:
    1. From existing DNA to make new DNA (DNA replication?)
    2. From DNA to make new RNA (transcription)
    3. From RNA to make new proteins (translation).

From  ref1136   —  When life begins

The zygote is the start of a biological continuum that automatically grows and develops, passing gradually and sequentially through the stages we call foetus, baby, child, adult, old person and ending eventually in death.

Fig 337   ref1136 — 3 day old embryo

Fig 355   ref1136 — 40 day old embryo

The full genetic instructions to guide the development of the continuum, in interaction with its environment, are present in the zygote.  Every stage along the continuum is biologically human and each point along the continuum has the full human properties appropriate to that point.

From  ref1232 — Definitions

xxx insert

Genetic — DNA, Chromosomes, Genome and Epigenome

Your genome is the instructions for making and maintaining you. It is written in a chemical code called DNA.

It contains 3 billion bases, 20,000 genes, and 23 pairs of chromosomes!

DNA is a vitally important molecule for not only humans, but for most other organisms as well.

DNA contains our hereditary material and our genes.— it’s what makes us a major part of our uniqueness.

Genes — unit of hereditary information that occupies a fixed position on a chromosome. Genes direct the synthesis of proteins  — From ref1205

Chromosomes   — There are 23 chromosomes in each structure and these are each intertwined with an identical set of 23.

Each chromosome has a role in the growth and renewal of the human body.

Each  chromosome is formed into functional blocks which can be activated to perform the specific task — These blocks  are called genes —   These tasks can be further defined by epigenetic changes.

However, DNA modifications which do not change the DNA sequence but can affect gene activity and alter human traits and health — From  ref1205 — the Epigenome

Chemical compounds that are added to individual genes can regulate their activity; these modifications are known as epigenetic changes.

The epigenome comprises all of the chemical compounds that have been added to the entirety of one’s genome in a way to regulates the activity (expression) of all the genes,  The chemical compounds of the epigenome are not part of the DNA sequence, but are on or attached to DNA.

The following diagram incorporates all of these aspects

Fig345   ref1221 — DNA, Histones, Chromosomes and  Epigenetics

Definitions —

Chromatin — The primary function of chromatin is to compress the DNA into a compact unit that will be less voluminous and can fit within the nucleus.

Histones are basic proteins found in the nuclei of cells. These proteins help organize very long strands of DNA, the genetic “blueprint” of every living thing, into condensed structures that can fit into comparatively small spaces within the nucleus.

Histones do not serve merely as scaffolding for DNA strands. They also take part in gene regulation by affecting when certain genes — that is, lengths of DNA associated with a single protein product — are “expressed,” or activated to transcribe RNA and ultimately the protein product a given gene carries instructions for making.

From  ref1227What is epigenetics

The Epigenetic effects include Factors such as stress, environment, medications, diet, the contents of water, etc.

In addition to DNA methylation being vital to healthy growth and development, it also enables the expression of retroviral genes to be suppressed. However,  along with other potentially dangerous sequences of DNA that have entered and may damage the host. is associated with many diseases including asthma, aging, and cancer,

From   ref1233The factors that influence genes turn on and off

 

  1. Transcription factors (TFs) are molecules involved in regulating gene expression. They are usually proteins, although they can also consist of short, non-coding RNA. TFs are also usually found working in groups or complexes, forming multiple interactions that allow for varying degrees of control over rates of transcription. In people (and other eukaryotes), genes are usually in a default “off” state, so TFs serve mainly to turn gene expression “on”.
  2. Epigenetics involves genetic control by factors other than an individual’s DNA sequence. Epigenetic changes can switch genes on or off and determine which proteins are transcribed. Gene silencing is a general term describing epigenetic processes of gene regulation. Within cells, there are three systems that can interact with each other to silence genes: DNA methylation, histonemodifications, and RNA-associated silencing
  3. Environmental Influences on Gene Expression. The expression of genes in an organism can be influenced by the environment, including the external world in which the organism is located or develops, as well as the organism’s internal world, which includes such factors as its hormones and metabolism. One major internal environmental influence that affects gene expression is gender, as is the case with sex-influenced and sex-limited traits. Similarly, drugs, chemicals, temperature, and light are among the external environmental factors that can determine which genes are turned on and off, thereby influencing the way an organism develops and functions.

A phenotype is how these genes are actually expressed (applied).  This is due to a combination of genes and the effects of Epigenomics — these effects occur at different times during a lifetime, and can be reversed.  The phenotype can include physical traits, such as height and color or the eyes, as well as non-physical traits such as shyness and extroversion.

xxx.

Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed).

Each cell type in your body has a different set of active genes —despite the fact that almost all the cells of your body contain the exact same DNA.

Transcription DNA to RNA

Fig356  ref1237 — A Guide to Understanding Gene Expression

The Messenger mRNA small enough to proceed through the Nucleus

3n

Again  ref1205 — Understanding how genes work & epigenome

Environmental influences, such as a person’s diet and exposure to pollutants, can also impact the epigenome.

Epigenetic changes can help determine whether genes are turned on or off and can influence the production of proteins in certain cells, ensuring that only necessary proteins are produced.

For example, proteins that promote bone growth are not produced in muscle cells. Patterns of epigenetic modification vary among individuals, different tissues within an individual, and even different cells.

A common type of epigenetic modification is called DNA methylation. This involves attaching small molecules to segments of DNA. When these methyl groups are added to a particular gene, that gene is turned off or silenced, and no protein is produced from that gene.

Because errors in the epigenetic process, such as modifying the wrong gene or failing to add a compound to a gene, can lead to abnormal gene activity or inactivity, they can cause genetic disorders. Conditions including cancers, metabolic disorders, and degenerative disorders have all been found to be related to epigenetic errors.

Scientists continue to explore the relationship between the genome and the chemical compounds that modify it. In particular, they are studying what effect the modifications have on gene function, protein production, and human health.

From  ref1121 — How Children’s Experiences Affect Their Genes

Epigenetics shows how environmental influences—children’s experiences—actually affect the expression of their genes.

This means the old idea that genes are “set in stone” has been disproven. Nature vs. Nurture is no longer a debate. It’s nearly always both!

During development, the DNA that makes up our genes accumulates chemical marks that determine how much or little of the genes is expressed. This collection of chemical marks is known as the “epigenome.” The different experiences children have rearrange those chemical marks. This explains why genetically identical twins can exhibit different behaviors, skills, health, and achievement.

The marks do not change the sequence of the DNA, but they do change the way cells use the DNA’s instructions.  They may, or may not, be permanent.

The marks can be passed on from cell to cell as they divide, and they can even be passed from one generation to the next.

The genes children inherit from their biological parents provide information that guides their development. For example, how tall they could eventually become or the kind of temperament they could have.

When experiences during development rearrange the epigenetic marks that govern gene expression, they can change whether and how genes release the information they carry.

Thus, the epigenome can be affected by positive experiences, such as supportive relationships and opportunities for learning, or negative influences, such as environmental toxins or stressful life circumstances, which leave a unique epigenetic “signature” on the genes. These signatures can be temporary or permanent and both types affect how easily the genes are switched on or off. Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning. But the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning.

Experiences very early in life, when the brain is developing most rapidly, cause epigenetic adaptations that influence whether, when, and how genes release their instructions for building future capacity for health, skills, and resilience. That’s why it’s crucial to provide supportive and nurturing experiences for young children in the earliest years.

Services such as high-quality health care for all pregnant women, infants, and toddlers, as well as support for new parents and caregivers can—quite literally— affect the chemistry around children’s genes. Supportive relationships and rich learning experiences generate positive epigenetic signatures that activate genetic potential.

Injurious experiences, such as malnutrition, exposure to chemical toxins or drugs, and toxic stress before birth or in early childhood are not “forgotten,” but rather are built into the architecture of the developing brain through the epigenome. The “biological memories” associated with these epigenetic changes can affect multiple organ systems and increase the risk not only for poor physical and mental health outcomes but also for impairments in future learning capacity and behavior.

Research has shown that specific epigenetic modifications do occur in brain cells as cognitive skills like learning and memory develop, and that repeated activation of brain circuits dedicated to learning and memory through interaction with the environment, such as reciprocal “serve and return” interaction with adults, facilitates these positive epigenetic modifications.

We also know that sound maternal and fetal nutrition, combined with positive social-emotional support of children through their family and community environments, will reduce the likelihood of negative epigenetic modifications that increase the risk of later physical and mental health impairments.

Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning, but that takes a lot more effort, may not be successful at changing all aspects of the signatures, and is costly. Thus, the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning, helping children grow up to be healthy, productive members of society.

From  ref1207 — Primary functions of protein in the body

https://study.com/academy/lesson/primary-functions-of-protein-in-the-body.html

Protein is a vital molecule that carries out many functions in your body. Learn how proteins provide structure, regulate body processes, transport materials throughout your body, help your immune system and act as a source of energy.

Proteins are all similar in that they are made up of chains of amino acids; these basic building blocks of proteins are linked together by unique chemical bonds called peptide bonds.

Amino acids being the building blocks of proteins, but we could also say that proteins themselves are building blocks of the body.

And this brings us to the first important function of protein, which is to provide structure.

Provide Structure

Structural proteins make up integral parts of your body. For example, keratin is a type of protein found in your hair, nails and skin that helps give these structures strength. Inside your body, protein provides structure to every cell. Collagen, which is a structural protein found in various connective tissues, provides the framework for the ligaments that hold your bones together and the tendons that attach muscles to those bones.

Regulate Body Processes

Proteins also regulate body processes. For example, enzymes are proteins that speed up chemical reactions in the body. Without them, basic activities like breaking down the foods you eat would happen too slowly to support your life. You can think of enzymes as proteins that shift your body processes into high gear.

Body processes are also influenced by hormones, which are proteins that regulate the activity of cells or organs. Hormones are like chemical messengers that carry an order from one part of your body to another. For example, insulin is a hormone that regulates blood sugar by carrying a message to your body cells about how much sugar is present in your blood.

Transport Materials

Another function of protein is to transport materials throughout your body. A great example of this is haemoglobin, which is the oxygen-transporting protein found in your red blood cells. When you breathe air into your lungs, the oxygen molecules from that air wait in your lung cells for a ride on a red blood cell. Once the oxygen attaches to the haemoglobin of that red cell, it can travel anywhere in your body.

Protein Production

https://vocal.media/futurism/protein-production-in-a-cell

ref1206 — protein production in a cell

Fig340  Protein production  ref1206

The nucleus first receives a chemical signal to make a specific protein. This message is contained in the DNA (deoxyribonucleic acid), which is copied into RNA (ribonucleic acid). (This is done because RNA is smaller than DNA, which would allow it to leave through the nuclear pores.)

The RNA then leaves through a nuclear pore, and arrives at the ribosome. The ribosome creates the protein; this protein goes through the endoplasmic reticulum. A vesicle forms off the endoplasmic reticulum, carrying the protein to the Golgi body.

The Golgi body repackages the protein, and a vesicle carrying the protein forms off. This vesicle then carries the protein to the cell membrane; the vesicle attaches to the cell membrane, and its proteins are released out of the cell.

Learning & Living

 

From  ref 597  Whole Brain  Neural Plasticity

 

xxx

 

ref1209 — Secret language of Cells

A child is born with the ability to learn — but starts with a blank memory/learning  record.  Learning is essential for coping with the complexities and changing nature of our environment.

Humans have adapted to living in different climates, regimes, etc – and also to travel — and become adept at making and using tools and weapons, developing a system of communication through symbols and sounds, and developing social, political and economic systems of interaction.

We each compete and commune as we experience life.  Our Human Body/Mind is the result of how humans evolved to deal with these demands.

Evolution has provided us with the means by which a human grows, learns and develops.  Our acquired “Apps” include a wide range of the good habits/skills needed to relieve us of having to consciously work through routine daily activities.

But our ability to learn these and further life enhancing Apps also means that we can acquire bad Apps – damage-prone habits and antagonizing attitudes.  These may emerge in response to unfortunate experiences such as Toxic Stresses.

During development, from infancy on, the new person is motivated to  seek to fulfil Core Needs.   Clearly the seeds of these Needs are present in the DNA.   The Needs change as the individual develops — notably at adolescence.

From ref650 — “Hardwiring Happiness” by Rick Hanson

Humans have 3 Core Needs or Operating Systems —
• Safety ————Avoiding Harm
• Connection —– Attaching/relating to others
• Satisfaction —– Using our Rewards system.

Each Need has two modes of responding —

  • The Responsive Mode — Controlled, Mindful
  • The Reactive Mode —Stressed. Emotional — Insecure people, and those affected by trauma are more prone to this mode.

As a child grows they learn from their experiences — largely from the Need for Satisfaction.  This learning is enhanced if their experiences can be made to keep  “interesting”.

At the early stages infant is totally dependent on the mother, and/or appropriate carer.  This Nurture is critical in the progression to realising socially acceptable traits.   (Though, much of human history has been based on individuals whose upbringing departed from sound

Fig122  ref1166 — Human Anatomy

More xxx

Fig 209

Gamete  — A sex cell containing only a single — haploid — set of chromosomes.  A diploid has 2 sets.

Organelles — a specialized subunit, usually within a cell, that has a specific function — such as Ribosomess

Organisms grow and reproduce through cell division. In humans the production of new cells occurs as a result of meiosis and mitosis — see below. Cells can also merge, for example, Sex Cells in order to combine parental Genes.

From  ref1234Differences between meiosis and mitosis.

These two nuclear division processes are similar but distinct.  Both processes involve the division of a diploid cell, or a cell containing two sets of chromosomes (one chromosome donated from each parent).

Meiosis is the process by which gametes — sex cells are generated in organisms that reproduce sexually.

Gametes are produced in male and female gonads and contain one-half the number of chromosomes as the original cell.

New gene combinations are introduced in a population through the genetic recombination that occurs during meiosis. The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

In mitosis, the genetic material (DNA) in a cell is duplicated and divided equally between two cells.  Tis process replicates Somatic (body)  cells

Fig 352   ref1228  Part 2  — In the cells going through mitosis you can clearly see the individual chromosomes

ccc

From   ref1228 — Part 3 Sexual reproduction, meiosis and gamete formation –inc. https://www.bbc.co.uk/bitesize/guides/zghqfcw/revision/3

Sexual reproduction uses a type of cell division called meiosis, which creates gametes — sperm and egg cells.

(Sperm are small and for example do not contain Ribosomes — these and other items are provided by the egg — Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains)

The process of meiosis happens in the male and female reproductive organs.

Before a dividing cell enters meiosis, it undergoes a period of growth called interphase.

From   ref1235 — stages of meiosis

Fig 350   ref1228  part 3 — Meiosis and gamete formation

The meiotic cell cycle produces four cells that are genetically different and these then merge (combining the genes from the parents) to produce identical sex cells for the chromosomes.

Fig 349 ref1228 — Towards forming the Zygote Cell

The Human Egg, ready for fertilisation is at the end of the Fallopian Tube, so the Sperm has to get there from the Cervix — thus the mobility through its tail.

ccc

Growth

A Cell can divide in order to provide the means of growing and/or repairing the body.  A cell can also release from its DNA the proteins necessary for growth or repair.

The dividing cell goes through an ordered series of events called the cell cycle.

Fig 350a  ref1228 2 — Mitosis — cell division

The mitotic cell cycle is initiated by the presence of certain growth factors or other signals that indicate that the production of new cells is needed.

Typical ways in which the need for a process to be initiated are given in Appendix “Comms”.

Examples of somatic cells include fat cellsblood cells, skin cells, or  any body-cell that is not a sex-cell . Mitosis is necessary to replace dead cells, damaged cells, or cells that have short life spans.

In mitosis a single cell divides into two cells that are replicas of each other and have the same number of chromosomes. This type of cell division is good for basic growth, repair, and maintenance.  Mitosis is how somatic—or non-reproductive cells — divide. Somatic cells make up most of your body’s tissues and organs, including skin, muscles, lungs, gut, and hair cells.

Since the daughter cells have exact copies of their parent cell’s DNA, no genetic diversity is created through mitosis in normal healthy cells.

From  ref1198 — Developmental genetics

https://www2.le.ac.uk/projects/vgec/schoolsandcolleges/topics/developmental-genetics

The process that changes a single cell into a new person is called development.

During the course of development, complex structures develop from simple ones. A single cell transforms itself into an adult organism. How does something complicated come from something simple? Appendix Comms has examples of how this is done  xxx

Creating an organism from a single cell involves three important processes:

  1. Cell division: cells divide to produce more cells.
  2. Cell differentiation: cells change into different types of cell to do specific jobs in the body, from nerve cells to muscle cells.
  3. Morphogenesis:groups of cells move and change their shape to produce the structure of the organism.

From  ref1202 — Proteins

Proteins are the key working molecules and building blocks in all cells. They are produced in a similar two-step process in all organisms – DNA is first transcribed into RNA, then RNA is translated into protein.

Proteins are the major ‘working molecules’ within every organism. Among their many jobs, proteins catalyse reactions, transport oxygen and defend organisms from infection. They’re also crucial building blocks of organisms. They are the major components of wool, cartilage and milk, they package up the DNA in chromosomes and they insulate the  nervous system!

Proteins are made of large numbers of amino acids joined end to end. The chains fold up to form three-dimensional molecules with complex shapes – you could think of it as origami with a very long and thin piece of paper. The precise shape of each protein, along with the amino acids it contains, determines what it does.

From   ref1183Central Dogma of Biology —  DNA to RNA to a Protein

DNA gives the instructions for various functional proteins to be produced inside the cell — this process is also known as the Central dogma of molecular biology

Fig 353   ref1236 — DNA to RNA to a Protein

Explanation —    ref1230Gene expression

Gene Expression

The process of turning on a gene to produce RNA and protein is called gene Expression

Fig 354  ref1230 — Gene expression

From  ref1234 — Central Dogma of Biology  DNA to RNA to a Protein

  • The central dogma suggests that DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes.
  • The ribosomes serve as factories in the cell where the information is ‘translated’ from a code into the functional product.
  • In transcription, the information in the DNA of every cell is converted into small, portable RNA messages — small enough to pass from the nucleus of the cell
  • During translation, these messages travel from where the DNA is in the cell nucleus to the ribosomes where they are ‘read’ to make specific proteins.
  • The central dogma states that the pattern of information that occurs most frequently in our cells is:
    1. From existing DNA to make new DNA (DNA replication?)
    2. From DNA to make new RNA (transcription)
    3. From RNA to make new proteins (translation).

From  ref1136   —  When life begins

The zygote is the start of a biological continuum that automatically grows and develops, passing gradually and sequentially through the stages we call foetus, baby, child, adult, old person and ending eventually in death.

Fig 337   ref1136 — 3 day old embryo

Fig 355   ref1136 — 40 day old embryo

The full genetic instructions to guide the development of the continuum, in interaction with its environment, are present in the zygote.  Every stage along the continuum is biologically human and each point along the continuum has the full human properties appropriate to that point.

From  ref1232 — Definitions

xxx insert

Genetic — DNA, Chromosomes, Genome and Epigenome

Your genome is the instructions for making and maintaining you. It is written in a chemical code called DNA.

It contains 3 billion bases, 20,000 genes, and 23 pairs of chromosomes!

DNA is a vitally important molecule for not only humans, but for most other organisms as well.

DNA contains our hereditary material and our genes.— it’s what makes us a major part of our uniqueness.

Genes — unit of hereditary information that occupies a fixed position on a chromosome. Genes direct the synthesis of proteins  — From ref1205

Chromosomes   — There are 23 chromosomes in each structure and these are each intertwined with an identical set of 23.

Each chromosome has a role in the growth and renewal of the human body.

Each  chromosome is formed into functional blocks which can be activated to perform the specific task — These blocks  are called genes —   These tasks can be further defined by epigenetic changes.

However, DNA modifications which do not change the DNA sequence but can affect gene activity and alter human traits and health — From  ref1205 — the Epigenome

Chemical compounds that are added to individual genes can regulate their activity; these modifications are known as epigenetic changes.

The epigenome comprises all of the chemical compounds that have been added to the entirety of one’s genome in a way to regulates the activity (expression) of all the genes,  The chemical compounds of the epigenome are not part of the DNA sequence, but are on or attached to DNA.

The following diagram incorporates all of these aspects

Fig345   ref1221 — DNA, Histones, Chromosomes and  Epigenetics

Definitions —

Chromatin — The primary function of chromatin is to compress the DNA into a compact unit that will be less voluminous and can fit within the nucleus.

Histones are basic proteins found in the nuclei of cells. These proteins help organize very long strands of DNA, the genetic “blueprint” of every living thing, into condensed structures that can fit into comparatively small spaces within the nucleus.

Histones do not serve merely as scaffolding for DNA strands. They also take part in gene regulation by affecting when certain genes — that is, lengths of DNA associated with a single protein product — are “expressed,” or activated to transcribe RNA and ultimately the protein product a given gene carries instructions for making.

From  ref1227What is epigenetics

The Epigenetic effects include Factors such as stress, environment, medications, diet, the contents of water, etc.

In addition to DNA methylation being vital to healthy growth and development, it also enables the expression of retroviral genes to be suppressed. However,  along with other potentially dangerous sequences of DNA that have entered and may damage the host. is associated with many diseases including asthma, aging, and cancer,

From   ref1233The factors that influence genes turn on and off

 

  1. Transcription factors (TFs) are molecules involved in regulating gene expression. They are usually proteins, although they can also consist of short, non-coding RNA. TFs are also usually found working in groups or complexes, forming multiple interactions that allow for varying degrees of control over rates of transcription. In people (and other eukaryotes), genes are usually in a default “off” state, so TFs serve mainly to turn gene expression “on”.
  2. Epigenetics involves genetic control by factors other than an individual’s DNA sequence. Epigenetic changes can switch genes on or off and determine which proteins are transcribed. Gene silencing is a general term describing epigenetic processes of gene regulation. Within cells, there are three systems that can interact with each other to silence genes: DNA methylation, histonemodifications, and RNA-associated silencing
  3. Environmental Influences on Gene Expression. The expression of genes in an organism can be influenced by the environment, including the external world in which the organism is located or develops, as well as the organism’s internal world, which includes such factors as its hormones and metabolism. One major internal environmental influence that affects gene expression is gender, as is the case with sex-influenced and sex-limited traits. Similarly, drugs, chemicals, temperature, and light are among the external environmental factors that can determine which genes are turned on and off, thereby influencing the way an organism develops and functions.

A phenotype is how these genes are actually expressed (applied).  This is due to a combination of genes and the effects of Epigenomics — these effects occur at different times during a lifetime, and can be reversed.  The phenotype can include physical traits, such as height and color or the eyes, as well as non-physical traits such as shyness and extroversion.

xxx.

Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed).

Each cell type in your body has a different set of active genes —despite the fact that almost all the cells of your body contain the exact same DNA.

Transcription DNA to RNA

Fig356  ref1237 — A Guide to Understanding Gene Expression

The Messenger mRNA small enough to proceed through the Nucleus

3n

Again  ref1205 — Understanding how genes work & epigenome

Environmental influences, such as a person’s diet and exposure to pollutants, can also impact the epigenome.

Epigenetic changes can help determine whether genes are turned on or off and can influence the production of proteins in certain cells, ensuring that only necessary proteins are produced.

For example, proteins that promote bone growth are not produced in muscle cells. Patterns of epigenetic modification vary among individuals, different tissues within an individual, and even different cells.

A common type of epigenetic modification is called DNA methylation. This involves attaching small molecules to segments of DNA. When these methyl groups are added to a particular gene, that gene is turned off or silenced, and no protein is produced from that gene.

Because errors in the epigenetic process, such as modifying the wrong gene or failing to add a compound to a gene, can lead to abnormal gene activity or inactivity, they can cause genetic disorders. Conditions including cancers, metabolic disorders, and degenerative disorders have all been found to be related to epigenetic errors.

Scientists continue to explore the relationship between the genome and the chemical compounds that modify it. In particular, they are studying what effect the modifications have on gene function, protein production, and human health.

From  ref1121 — How Children’s Experiences Affect Their Genes

Epigenetics shows how environmental influences—children’s experiences—actually affect the expression of their genes.

This means the old idea that genes are “set in stone” has been disproven. Nature vs. Nurture is no longer a debate. It’s nearly always both!

During development, the DNA that makes up our genes accumulates chemical marks that determine how much or little of the genes is expressed. This collection of chemical marks is known as the “epigenome.” The different experiences children have rearrange those chemical marks. This explains why genetically identical twins can exhibit different behaviors, skills, health, and achievement.

The marks do not change the sequence of the DNA, but they do change the way cells use the DNA’s instructions.  They may, or may not, be permanent.

The marks can be passed on from cell to cell as they divide, and they can even be passed from one generation to the next.

The genes children inherit from their biological parents provide information that guides their development. For example, how tall they could eventually become or the kind of temperament they could have.

When experiences during development rearrange the epigenetic marks that govern gene expression, they can change whether and how genes release the information they carry.

Thus, the epigenome can be affected by positive experiences, such as supportive relationships and opportunities for learning, or negative influences, such as environmental toxins or stressful life circumstances, which leave a unique epigenetic “signature” on the genes. These signatures can be temporary or permanent and both types affect how easily the genes are switched on or off. Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning. But the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning.

Experiences very early in life, when the brain is developing most rapidly, cause epigenetic adaptations that influence whether, when, and how genes release their instructions for building future capacity for health, skills, and resilience. That’s why it’s crucial to provide supportive and nurturing experiences for young children in the earliest years.

Services such as high-quality health care for all pregnant women, infants, and toddlers, as well as support for new parents and caregivers can—quite literally— affect the chemistry around children’s genes. Supportive relationships and rich learning experiences generate positive epigenetic signatures that activate genetic potential.

Injurious experiences, such as malnutrition, exposure to chemical toxins or drugs, and toxic stress before birth or in early childhood are not “forgotten,” but rather are built into the architecture of the developing brain through the epigenome. The “biological memories” associated with these epigenetic changes can affect multiple organ systems and increase the risk not only for poor physical and mental health outcomes but also for impairments in future learning capacity and behavior.

Research has shown that specific epigenetic modifications do occur in brain cells as cognitive skills like learning and memory develop, and that repeated activation of brain circuits dedicated to learning and memory through interaction with the environment, such as reciprocal “serve and return” interaction with adults, facilitates these positive epigenetic modifications.

We also know that sound maternal and fetal nutrition, combined with positive social-emotional support of children through their family and community environments, will reduce the likelihood of negative epigenetic modifications that increase the risk of later physical and mental health impairments.

Recent research demonstrates that there may be ways to reverse certain negative changes and restore healthy functioning, but that takes a lot more effort, may not be successful at changing all aspects of the signatures, and is costly. Thus, the very best strategy is to support responsive relationships and reduce stress to build strong brains from the beginning, helping children grow up to be healthy, productive members of society.

From  ref1207 — Primary functions of protein in the body

https://study.com/academy/lesson/primary-functions-of-protein-in-the-body.html

Protein is a vital molecule that carries out many functions in your body. Learn how proteins provide structure, regulate body processes, transport materials throughout your body, help your immune system and act as a source of energy.

Proteins are all similar in that they are made up of chains of amino acids; these basic building blocks of proteins are linked together by unique chemical bonds called peptide bonds.

Amino acids being the building blocks of proteins, but we could also say that proteins themselves are building blocks of the body.

And this brings us to the first important function of protein, which is to provide structure.

Provide Structure

Structural proteins make up integral parts of your body. For example, keratin is a type of protein found in your hair, nails and skin that helps give these structures strength. Inside your body, protein provides structure to every cell. Collagen, which is a structural protein found in various connective tissues, provides the framework for the ligaments that hold your bones together and the tendons that attach muscles to those bones.

Regulate Body Processes

Proteins also regulate body processes. For example, enzymes are proteins that speed up chemical reactions in the body. Without them, basic activities like breaking down the foods you eat would happen too slowly to support your life. You can think of enzymes as proteins that shift your body processes into high gear.

Body processes are also influenced by hormones, which are proteins that regulate the activity of cells or organs. Hormones are like chemical messengers that carry an order from one part of your body to another. For example, insulin is a hormone that regulates blood sugar by carrying a message to your body cells about how much sugar is present in your blood.

Transport Materials

Another function of protein is to transport materials throughout your body. A great example of this is haemoglobin, which is the oxygen-transporting protein found in your red blood cells. When you breathe air into your lungs, the oxygen molecules from that air wait in your lung cells for a ride on a red blood cell. Once the oxygen attaches to the haemoglobin of that red cell, it can travel anywhere in your body.

Protein Production

https://vocal.media/futurism/protein-production-in-a-cell

ref1206 — protein production in a cell

Fig340  Protein production  ref1206

The nucleus first receives a chemical signal to make a specific protein. This message is contained in the DNA (deoxyribonucleic acid), which is copied into RNA (ribonucleic acid). (This is done because RNA is smaller than DNA, which would allow it to leave through the nuclear pores.)

The RNA then leaves through a nuclear pore, and arrives at the ribosome. The ribosome creates the protein; this protein goes through the endoplasmic reticulum. A vesicle forms off the endoplasmic reticulum, carrying the protein to the Golgi body.

The Golgi body repackages the protein, and a vesicle carrying the protein forms off. This vesicle then carries the protein to the cell membrane; the vesicle attaches to the cell membrane, and its proteins are released out of the cell.

Learning & Living

 

From  ref 597  Whole Brain  Neural Plasticity

 

xxx

 

ref1209 — Secret language of Cells

A child is born with the ability to learn — but starts with a blank memory/learning  record.  Learning is essential for coping with the complexities and changing nature of our environment.

Humans have adapted to living in different climates, regimes, etc – and also to travel — and become adept at making and using tools and weapons, developing a system of communication through symbols and sounds, and developing social, political and economic systems of interaction.

We each compete and commune as we experience life.  Our Human Body/Mind is the result of how humans evolved to deal with these demands.

Evolution has provided us with the means by which a human grows, learns and develops.  Our acquired “Apps” include a wide range of the good habits/skills needed to relieve us of having to consciously work through routine daily activities.

But our ability to learn these and further life enhancing Apps also means that we can acquire bad Apps – damage-prone habits and antagonizing attitudes.  These may emerge in response to unfortunate experiences such as Toxic Stresses.

During development, from infancy on, the new person is motivated to  seek to fulfil Core Needs.   Clearly the seeds of these Needs are present in the DNA.   The Needs change as the individual develops — notably at adolescence.

From ref650 — “Hardwiring Happiness” by Rick Hanson

Humans have 3 Core Needs or Operating Systems —
• Safety ————Avoiding Harm
• Connection —– Attaching/relating to others
• Satisfaction —– Using our Rewards system.

Each Need has two modes of responding —

  • The Responsive Mode — Controlled, Mindful
  • The Reactive Mode —Stressed. Emotional — Insecure people, and those affected by trauma are more prone to this mode.

As a child grows they learn from their experiences — largely from the Need for Satisfaction.  This learning is enhanced if their experiences can be made to keep  “interesting”.

At the early stages infant is totally dependent on the mother, and/or appropriate carer.  This Nurture is critical in the progression to realising socially acceptable traits.   (Though, much of human history has been based on individuals whose upbringing departed from sound

Contents
Introduction
Addiction
Age stages
Anatomy
Art
Autonomic Nervous System
Brains — Artificial Intelligence
Carbon Dioxide
Cognition & Emotion
Communities
Competences
Control System
Conventions — Social Norms
Criminality
Dis-ease
Emotions
Enteric System
Gender
Genetics
Gestalt
Habits
Honesty & Lying
Humour

Immunity
Intuition — Insights
Language
Learning
Medications
Memory

To Contents
Introduction

In a profound way each of us is on our own.

In a profound way we are each part of humanity.

We each compete and commune as we experience life.  Our Human Body /Mind is the result of how humans evolved to deal with these opposing demands.

Fig. 26

Each generation has to grow from a zygote — the single cell resulting from the fertilization of the female egg cell by the male sperm cell.

The basic program for our development is in our individual DNA.

See Genetic human traits  — ref 619

A controversial recent development in genetics focuses on Gender Issues — Ref643   —  ref955

GENETICS and —

Evolution has provided us with the means by which a human grows, learns and develops. Our “Apps” include a wide range of the good habits/skills — crucially those needed to relieve us of having to consciously work through routine daily activities — walking, etc.

Initially, we are dependant — helpless — for the first few years.  But generally blessed with the abilities to learn the complex basics in preparation for later sophistication

Fig.112

The early learning rate is curtailed to allow appropriate re-enforcement, by practice.

Fig.6

We are a combination of Body and Mind.  These are interlinked so that the Body is maintained and responsive to our Needs.  The Mind has to deal with what we perceive whether from the Body and/or our Environs.  The context is a changing, developing one, possibly subject to toxic stresses, demands, failures and successes.

Personality is a major part of this development — ref 485  — What is Personality?

Fig.199 ref 617 — showing a summary of the traits, attitudes from different personalities.

Fig. 183 Emotions, progressively experienced and noted — arousal — motivations — feelings

An Emotion is our initial response to a significant perception, and this enables us to respond quickly and, hopefully, appropriately.  In order to do so we should develop “Emotional Intelligence”.

THE MIND

So we have inherent and learned abilities. These are “on standby ” in our Mind —

The Mind is generally perceived as the Conscious and the Nonconscious (variants — Near, Sub and Un-Conscious)

Freud’s Personality Theory (1923) visualised the Psyche (Mind) structured into three parts — the Id, Ego and Superego, all developing at different stages in our lives — ref907

Fig.252

According to Freud’s model of the Mind/Psyche, the ID is the primitive and instinctual part of the mind that contains sexual and aggressive drives and hidden memories, the SUPER-EGO operates as a moral conscience, and the EGO is the realistic part that mediates between the desires of the ID and the SUPER-EGO.

This illuminating model does not clearly address the general motivations/needs — but first —

From — ref738f
The two most powerful functions of the developing Conscious Mind —
1. The ability to imagine — Jokes, acting, etc.
2. The ability to direct your focus — Thinking hard, enjoying a pleasant event, etc.

We “imagine” our awareness through our senses can be supplemented by inputs from our Nonconscious Mind.

Both of these involve dealing with our complex of —
• Emotional reactions
• Realising our Core Human Needs

There exists various theories and observations about the Mind. These are the products of various minds who have felt the compulsion to understand what humans are all about. They are all of interest, and hopefully contain some partial validity, even if not fully illuminating.

Our Conscious thinking, perceiving, and learning account for only a small fraction of our total mental activity — with the rest being entirely Nonconscious

Our Conscious Minds work much more slowly than our Nonconscious Mind, and are overall less adept at processing information, less efficient at the task.

The Nonconscious Mind therefore can be said to be more intelligent than the Conscious Mind.– ref897

Our Conscious thinking, perceiving, and learning account for only a small fraction of our total mental activity — with the rest being entirely Nonconscious

Because the Nonconscious Mind is responsible for the bulk of our mental processing, it can also be said to be responsible for the development of a large part of our personality, tastes, talents, and so on — It determines, in essence, how we function — and here we have to beware !

There are indications  that the Nonconscious will adapt to “your” way of thinking — for example — ref867 –The brain adapts to dishonesty.

However, there may be instances for second thoughts — ref868 — trade-off between honesty, self-interest !

The Nonconscious Mind is thought to be composed only of what it has absorbed from the external environment, and to be responsible for the following processes —
1. Nonconscious learning and the development of personality traits
2. The Nonconscious influence that our Nonconscious learning has on our judgments, decisions, and emotions (both feelings and reactions); and
3. The various organizations and reorganizations that occur spontaneously in Nonconscious knowledge systems.

As point three suggests, our Nonconscious knowledge systems are far from rigid; they constantly change, and we change with them, leading to what we interpret as the growth and alteration of the personality.

Generally, these changes can be seen as a computer re-ordering itself to become more and more efficient in its processing of the external environment, but in some circumstances, the same processes may lead to the state of maladaptation that we refer to as mental illness.

NEEDS — Motivations

Abraham Harold Maslow (1908 –  1970) was an American psychologist who studied Human Motivations/Needs — ref926

Maslow first developed his famous theory of individual development and motivation in the 1940’s. He suggested that human beings have a hierarchy of needs. That is, that all humans act in a way which will address basic needs, before moving on to satisfy other, so-called higher level needs.

Maslow represented this theory as a hierarchical triangle. This shows how basic needs must be met before one can “climb” the hierarchy, to address more complex needs.

  • Physiological needs – such as hunger, thirst and sleep
  • Safety needs – such as security, protection from danger and freedom from pain.
  • Social needs – sometimes also referred to as love needs such as friendship, giving and receiving love, engaging in social activities and group membership.
  • Esteem needs – these include both self-respect and the esteem of others. For example, the desire for self-confidence and achievement, and recognition and appreciation.
  • Self-actualization – This is about the desire to develop and realize your full potential. To become everything you can be.

Fig 4

A different aspect of these Needs/Motivations is offered by Rick Hanson in his book “Hardwiring Happiness”

He observed that humans have 3 Core Needs or Operating Systems (Freud?):
• Safety ————Avoiding Harm
• Connection —– Attaching/relating to others
• Satisfaction —– Using our Rewards system.

These Operating Systems are defined by their function and not the evolved anatomy — Each operating system has its own set of capabilities, and they can be running at the same time.

They are complex, each individual has a different version of a range of Needs.

Each has two modes of responding to circumstances:
• The Responsive Mode — Controlled, Mindful
• The Reactive Mode — Alert, Stressed. Emotional — Insecure people, and those affected by trauma are more prone to this mode.

Avoiding harm seems to have evolved a Human Brain that has a negativity bias, tending to simulate —
• Velcro for negative experiences — an expectation or precaution
• Teflon for positive ones.

In past and some current societies there was the expectation of physical danger.

Currently toxic stress, bullying (such as from Social Media), loneliness due to loss of Family links — seem to be creating serious Psychological pressures.

Attaching/relating to others

According to the Attachment theory, approximately 50% of economically “comfortable” people in Western Society enjoy good relationships with others, 20% tend to avoid relationships with others, another 10% tend to cling to relationships, the remaining 10% swing between clinging and avoiding — however it should noted that we all probably experience Avoiding and Clinging in some relationships.

The “belongingness hypothesis” states that people have a basic psychological need to feel closely connected to others, and that caring, affectionate bonds from close relationships are a major part of human behaviour — ref778

We have a Need for:
• Forming social bonds
• Not breaking bonds
• Cognition –- feeling close to others
• Emotional highs and lows
• Avoiding the Consequences of deprivation
• Avoiding Partial deprivation
• Avoiding Satiation and substitution

There is such a thing as too many close relationships. People strongly prefer to have (and are only capable of having) a few very close friendships and a larger number of casual friendships. In this case, quality is more important than quantity.

ref779 — Why We Are Wired to Connect

Satisfaction (Reward).

Emotions are a reward or punishment for a specific motivated behaviour  — ref360

The School at Medicine at Mt Sinai explains that we have “reward pathways” — ref 291
The most important reward pathway in brain is a dopamine system.

Fig.247

Under normal conditions, the pathway controls an individual’s responses to natural rewards, such as food, sex, and social interactions, and is therefore an important determinant of motivation and incentive drive.

FIG.187 Reward Cycle Eating

From — ref806 The neurobiology of pleasure, reward processes, addiction and their health implications

Natural rewarding or pleasurable activities are necessary for survival and appetitive motivation, usually governing beneficial biological behaviors like eating, sex and reproduction.

Thus, pleasure is much needed.

However, artificial stimulants (e.g., addictive drugs) or ‘too much’ of a pleasurable activity may not be as beneficial, since flexibility and natural control of behaviours may be deteriorated.

Clearly, addiction includes a loss of control over normal behaviors and appetitive motivational goals. Addictive drugs, in addition, are capable of directly and strongly acting on reward pathways, thereby influencing motivation physiology.

Moderate pleasurable experiences, nonetheless, are able to enhance biological flexibility, complexity and health protection. Thus, pleasure can be a resistance resource, or it may serve

AGE STAGES and Hazards

Human Development has important stages — notably the early months and years — and adolescence.

In most Societies good parenting is largely left to chance.

Fig.8

Human Development has important stages — notably the early months and years — and adolescence.

At adolescence there is a re-alignment of the brain to cater for our emerging dispositions.

These seem likely to be carried forward to adulthood.

The Psychologist Oliver James in his book “They Fxxx You Up”, presents his version of Early Human Developments and relates these to Adult Personality Types:

He considers Genetics and Nurtures but maintains that we can and should focus on Nurture – because it can be changed!

Although no one can directly remember their earliest experiences, in infancy, it is back in this forgotten time that “personality disorder” may develop.

The psychoanalyst Donald Winnicott claimed that this could result from the sort of care given and responded to in the first few months of life.

See Personality Disorders —  ref486

A main focus is on emotional and social aspects, developed over 3 early stages:

Aspects of personality are developed in the following stages  ­­–

  • Becoming aware – to 6 months
  • Developing how to Relate to others – to 3 years
  • Realising a Conscience (morality) – 3 to 6 yrs

These are stages for sound development, but also when development can go wrong — ref749

The theory separates these working models of relationships into two main categories, secure attachment and insecure attachment, according to the degree of safety and security present within the relationships represented by the models. The category of insecure attachment is further subdivided based on how children react to others as a result of their working models: ambivalent,  avoidant, or disorganized

Fig.118

Sound development are as follows —

  • Becoming more aware of being separate from parents.
  • Recognising strangers and can react in a distressed way if stranger tries to interact too quickly.
  • Starting to be able to distract themselves when things go wrong.
  • More persistent in pursuing their own goals especially in play.

The Psychologist Oliver James visualised an ideal/Mature Human Adult as follows:

If you are this type it is relatively easy for you to become emotionally close to others. You are comfortable depending upon others and being depended upon by them, and don’t worry greatly about being alone or having others not accept us.

Adult romantic partners tend to be secure. When set a problem to solve with their partner, secure men are positive and supportive, trying to help rather than acting as a competitor or getting annoyed. Secure women are likely to seek emotional support from their man and to be happy to receive embraces or other physical expressions of affection and encouragement.

Secure couples have the least negative relationships of any combination of patterns – less critical, less conflict-ridden, more warm and friendly. The most common causes of rancour, like the man not spending enough time with the woman or disputes over the division of domestic labour, are less likely to be a problem. Followed over time, their relationships last longer and, if they include marriage, are less likely to end in divorce.

Such a person would be the beneficiary of sound genes, thoughtful nurture, a safe environment freedom from mental and physical ailments and addictions, etc. — This Utopia, even if wholly desirable, would take generations to achieve.

But our ability to learn these and further life enhancing Apps also means that we can acquire bad Apps – damage-prone habits and antagonizing attitudes. These may emerge in response to unfortunate experiences such as Toxic Stresses.

Although no one can directly remember their earliest experiences, in infancy, it is back in this forgotten time that “personality disorder” may develop. The psychoanalyst Donald Winnicott claimed that this could result from the sort of care given and responded to in the first few months of life – – Ref486 Personality – Personality Disorders

A baby starts of as a self-centred being in need of socialisation

80 per cent of criminals and about 13 per cent of the general population are significantly affected by personality disorder – but so do the majority of high achievers, be they in politics, business, the arts or show business.

However, far more than the 13 per cent of people have some personality disorder – all of us do, to some extent, in some situations.

Language is our basic means whereby we identify & recall what has to be dealt with.

Mindfulness seems to be providing ways of dealing with problem situations.  But even a basic concept such as “Acceptance”  — ref954

An Introduction — a narrative — but lots more to ponder !

To Contents
Addiction

Psychology Today looks at “Why alcoholics drink” — ref 183

And also considers the Alcohol use disorder” in — ref 184

Referring again to “Redefining Depression” ref 244, we note:

Researchers now believe that this may be due to the fact that people who are prone to depression have an active habit of suppressing positive feelings that come up naturally throughout the day.

This implies that only powerful feelings, such as the craving for alcohol, will get a ready response from depressed alcoholics – thus reinforcing the addiction.

From — ref847 — Alcohol & Neurotransmitter Interactions

Evidence suggests that alcohol affects brain function by interacting with multiple neurotransmitter systems, thereby disrupting the delicate balance between inhibitory and excitatory neurotransmitters.  Short-term alcohol exposure tilts this balance in favor of inhibitory influences.  After long-term alcohol exposure, however, the brain attempts to compensate by tilting the balance back toward equilibrium.

These neurological changes occur as the development of tolerance to alcohol’s effects.

Long-term alcohol intake also induces changes in many neurotransmitter systems that ultimately lead to the development of craving and alcohol-seeking behavior.

From (ref 112) — Psychology Today addresses “How Alcohol Affects You”

Alcohol, according to conventional wisdom, is a depressant.  Yet, that doesn’t fully explain alcohol’s effects.  People often drink to liven up a party, not mellow it out.  A few drinks can spark energy, elation and excitement; it gives you a buzz.

Classification of drugs can be explained by their chemical targets within the brain —
• Stimulants may influence Dopamine or Norepinephrine.
• Depressants target a chemical called GABA, the primary inhibitory Neurotransmitter and Receptors in the Brain

As alcohol begins to be consumed, drinkers gain increases in elation, excitement and extroversion, with simultaneous decreases in fatigue, restlessness, depression and tension.

Researchers found that drinking increases levels of Norepinephrine — the chemical target of many stimulants.

Elevated levels of Norepinephrine increase impulsivity, which helps explain why we lose our inhibitions whilst drinking.   PET brain scans show that regions, responsible for decision making and rational thought, have decreased activity and this explains why alcohol causes us to act impulsively, and aggressively — and drink excessively.  The reduced activity in parts of the brain indicates why walking is erratic and why drinkers can “black out”.

However, normally, as drinking proceeds there is a decrease in vigour and an increase in fatigue, relaxation, confusion, and depression.

The inhibatory GABA receptors respond to alcohol when the Blood alcohol content (BAC) reached 0.33 mL/L (The legal limit for driving is 0.08 mL/L).

BAC, for a given alcohol intake, depends on gender and weight — BAC calculator.

When drinking is stopped BAC reduces by 0.015/hr – to give the “morning after” hangover.

The delta receptor, one of the less common types of GABA, is concentrated in the same brain regions which had lowered activity through drinking.  It is still unclear what the delta receptor does, but because GABA is the primary inhibitory neuron in the brain, it can affect virtually every system.  Alcohol is more than simply a depressant.

When a drinking session ends BAC reduces by 0.015/hr – sometimes to give the “morning after” dilemna!

Summarising —

BAC (% by Volume) — Typical Behaviour — and possible Impairment
To 0.1———– Reduced inhibition ———–Reduced reasoning
0.1 – 0.2 ——- Boisterous/Angry————— Staggering
0.2 – 0.3 ——- Stupor——————————- Blackout
0.3 – 0.4 ——- Severe depression————–Incontinence
> 0.4 ————Coma ———————————Risk of death, damage

So, a simple model explains what happens as we continue to drink. Though an alcoholic has a greater tolerance to alcohol.

  • Alcohol first of all initiates pleasure by activating tan excitatory neurotransmitter, thus stimulating the body.,
    • However, above a BAC of around 0.33 mL/L they activate an inhibitory neurotransmitter as the body decides that enough is enough – the depressive phase.
    • However reduced inhibition and a much greater tolerance to alcohol cause the alcoholic to continue drinking – the inhibitory neuro-transmitter is ineffective

But there is evidence that alcoholics have less of a problem with hangovers — (ref 18)

Every Day Health asks “Why do we-get hangovers” in — ref 182

The Mayo Clinic also considers Hangovers in — ref 185

Addiction Treatment

Ref508 The Sinclair Method of Addiction Treatment

The Sinclair Method (TSM) uses the nervous system’s own mechanism, called “extinction”, for gradually removing the interest in alcohol and the behaviors involved in alcohol drinking. Therefore, the technical term for TSM is “pharmacological extinction.”

Re506 Naltrexone-for-alcoholism

The key scientific discovery underlying the treatment was that, contrary to earlier beliefs, detoxification and alcohol deprivation do not stop alcohol craving but in fact increase subsequent alcohol drinking. The old idea that alcoholism is caused by physiological dependence on alcohol, therefore, needed to be discarded, and a new understanding of alcoholism developed.

Subsequent research showed that alcohol drinking is a learned behavior.Some individuals, partly for genetic reasons, get so much reinforcement each time they drink, and have so many opportunities to drink and get reinforcement, that the behavior becomes too strong. They cannot always control their drinking; they cannot “just say ‘no’.” And society calls them alcoholics — see — Ref507 Addiction treatment – “A personal journey”

See also What you want to know about Selincro

While a number of Selincro’s predecessors focused on alcohol abstinence, Selincro’s mission is to decrease the amount of alcohol someone drinks. For example, over a one-month period, Selincro can reduce the number of “heavy-drinking days” experienced, along with decreasing the total number of drinks consumed on those drinking days, according to new research.

Selincro doesn’t reach peak effectiveness in the brain for at least two months.

Selincro (and Naltrexone) work to block the endorphins released so that reward isn’t passed on to the drinker’s brain and over a period of time (generally 3 to 6 months) pharmacological extinction is reached – which means that the drinker’s brain is able to function as a “normal” drinker as in “no buzz = no reward”.

To Contents

Human Developmental Stages

Not including the more obvious differences between Females and Males.

Fig 214

The American Institute for Learning and Human Development supports the creation of developmentally appropriate practices and rich learning environments for children, adolescents, and adult learner –it lists twelve Stages of a Human Life Cycle — Ref 412

  1. Prebirth:  Potential
  2. Birth:  Hope
  3. Infancy (Ages 0-3):   Vitality.
  4. Early Childhood (Ages 3-6):  Playfulness
  5. Middle Childhood (Ages 6-8): Imagination
  6. Late Childhood (Ages 9-11): Ingenuity
  7. Adolescence (Ages 12-20): Passion .
  8. Early Adulthood (Ages 20-35): Enterprise
  9. Midlife (Ages 35-50): Contemplation
  10. Mature Adulthood (Ages 50-80): Benevolence
  11. Late Adulthood (Age 80+):  Wisdom
  12. Death & Dying:  Life

See also Eriksons Stages of psychosocial development — Ref 509

  • Stage 1 – Trust vs. Mistrust
    • Stage 2 – Autonomy vs. Shame and Doubt
    • Stage 3 – Initiative vs. Guilt
    • Stage 4 – Industry vs. Inferiority
    • Stage 5 – Identity vs. Confusion
    • Stage 6 – Intimacy vs. Isolation
    • Stage 7 – Generativity vs. Stagnation
    • Stage 8 – Integrity vs. Despair

At each stage, Erikson, the Ego Psychologist, believed people experience a conflict that serves as a turning point in development. These conflicts are centered on either developing a psychological quality or failing to develop that quality. During these times, the potential for personal growth is high but so is the potential for failure.
If people successfully deal with the conflict, they emerge from the stage with psychological strengths that will serve them well for the rest of their lives. If they fail to deal effectively with these conflicts, they may not develop the essential skills needed for a strong sense of self.

Erikson also believed that a sense of competence motivates behaviors and actions. Each stage is concerned with becoming competent in an area of life. If the stage is handled well, the person will feel a sense of mastery, which is sometimes referred to as ego strength or ego quality. If the stage is managed poorly, the person will emerge with a sense of inadequacy in that aspect of development.

Moving on — Which stage of life is the most important? Some might claim that infancy is the key stage, when a baby’s brain is wide open to new experiences that will influence all the rest of its later life. Others might argue that it’s adolescence or young adulthood, when physical health is at its peak. Many cultures around the world value late adulthood more than any other, arguing that it is at this stage that the human being has finally acquired the wisdom necessary to guide others.

Early Development

The Psychologist Oliver James in his book “They Fxxx You Up”, presents his version of Early Human Developments and relates these to Adult Personality Types. He considers Genetics and Nurtures but maintains that we can and should focus on Nurture – because it can be changed!

His main focus is on emotional and social aspects, developed over 3 early stages.
o Stage 1 Becoming aware – to 6 months
o Stage 2 Developing how to Relate to others – to 3 years
o Stage 3 Realising a Conscience (morality) – 3 to 6 yrs

Early care that lacks empathy creates an immature adult with arrested development, prone to the reckless and amoral acts of a young child, to the ‘me, me, me’ selfishness and inflated grandiosity found in the fantasy life of the toddler. But the cause of such personality disorder is not wholly due to the sort of care in infancy. Subsequent experiences, especially sexual and physical abuse, can also play critical roles.

See Attachment Theory — ref432 — “The Attachment System Throughout the Life Course: Review and Criticisms of Attachment Theory”

and Personality Research — Ref 484

Another major development stage is Adolescence, with Puberty:

See Development of Values — Ref 391

Periods of development

Sociologist Morris Massey has described three major periods during which values are developed.

The Imprint Period
Up to the age of seven, we are like sponges, absorbing everything around us and accepting much of it as true, especially when it comes from our parents. The confusion and blind belief of this period can also lead to the early formation of trauma and other deep problems.The critical thing here is to learn a sense of right and wrong, good and bad. This is a human construction which we nevertheless often assume would exist even if we were not here (which is an indication of how deeply imprinted it has become).

The Modeling Period

Between the ages of eight and thirteen, we copy people, often our parents, but also others. Rather than blind acceptance of their values, we are trying them on like a suit of clothes, to see how they feel.At this age we may be much impressed with religion or our teachers. You may remember being particularly influenced by junior school teachers who seemed so knowledgeable–maybe even more so than your parents.

The Socialization Period
Between 13 and 21, we are very largely influenced by our peers. As we develop as individuals and look for ways to get away from the earlier programming, we naturally turn to people who seem more like us.Other influences at these ages include the media, especially those parts which seem to resonate with our the values of our peer groups.

Becoming principled
It’s tough to have high moral values, but some people get there.

Pre-moral
In the pre-moral state, we have no real values (we are thus ‘amoral’). Young children are premoral. So also are psychopaths. Our basic nature tells us to be Machiavellian, doing whatever it takes to achieve our goals, even if it means hurting other people.

Conventional
Most people have conventional values, as learned from their parents, teachers and peers. These basically say ‘here are the rules to live in reasonable harmony with other people.’The bottom line of this state is that we will follow them just so long as we think we need to. We will break our values occasionally, and especially if our needs are threatened or we are pretty sure we can get away with breaking values with nobody else knowing about it.

Principled
When we are truly principled, we believe in our values to the point where they are an integral and subconscious part of our person. Right and wrong are absolute things beyond the person, for example as defined by a religion.The test of a principled person is that they will stick to their values through thick and thin, and even will sacrifice themselves rather than break their principles. Many great leaders were principled (Martin Luther King, Gandhi, etc.)

To Contents 

• Stage 3 – Initiative vs. Guilt
• Stage 4 – Industry vs. Inferiority
• Stage 5 – Identity vs. Confusion
• Stage 6 – Intimacy vs. Isolation
• Stage 7 – Generativity vs. Stagnation
• Stage 8 – Integrity vs. Despair

At each stage, Erikson, the Ego Psychologist, believed people experience a conflict that serves as a turning point in development. These conflicts are centered on either developing a psychological quality or failing to develop that quality. During these times, the potential for personal growth is high but so is the potential for failure.
If people successfully deal with the conflict, they emerge from the stage with psychological strengths that will serve them well for the rest of their lives. If they fail to deal effectively with these conflicts, they may not develop the essential skills needed for a strong sense of self.

Erikson also believed that a sense of competence motivates behaviors and actions. Each stage is concerned with becoming competent in an area of life. If the stage is handled well, the person will feel a sense of mastery, which is sometimes referred to as ego strength or ego quality. If the stage is managed poorly, the person will emerge with a sense of inadequacy in that aspect of development.

Moving on — Which stage of life is the most important? Some might claim that infancy is the key stage, when a baby’s brain is wide open to new experiences that will influence all the rest of its later life. Others might argue that it’s adolescence or young adulthood, when physical health is at its peak. Many cultures around the world value late adulthood more than any other, arguing that it is at this stage that the human being has finally acquired the wisdom necessary to guide others.

Early Development

The Psychologist Oliver James in his book “They Fxxx You Up”, presents his version of Early Human Developments and relates these to Adult Personality Types. He considers Genetics and Nurtures but maintains that we can and should focus on Nurture – because it can be changed!

His main focus is on emotional and social aspects, developed over 3 early stages.
o Stage 1 Becoming aware – to 6 months
o Stage 2 Developing how to Relate to others – to 3 years
o Stage 3 Realising a Conscience (morality) – 3 to 6 yrs

Early care that lacks empathy creates an immature adult with arrested development, prone to the reckless and amoral acts of a young child, to the ‘me, me, me’ selfishness and inflated grandiosity found in the fantasy life of the toddler. But the cause of such personality disorder is not wholly due to the sort of care in infancy. Subsequent experiences, especially sexual and physical abuse, can also play critical roles.

See Attachment Theory — Ref 492 and Personality Research — Ref 484

Another major development stage is Adolescence, with Puberty:

See Development of Values — Ref 391

Periods of development

Sociologist Morris Massey has described three major periods during which values are developed.

The Imprint Period
Up to the age of seven, we are like sponges, absorbing everything around us and accepting much of it as true, especially when it comes from our parents. The confusion and blind belief of this period can also lead to the early formation of trauma and other deep problems.The critical thing here is to learn a sense of right and wrong, good and bad. This is a human construction which we nevertheless often assume would exist even if we were not here (which is an indication of how deeply imprinted it has become).

The Modeling Period

Between the ages of eight and thirteen, we copy people, often our parents, but also others. Rather than blind acceptance of their values, we are trying them on like a suit of clothes, to see how they feel.At this age we may be much impressed with religion or our teachers. You may remember being particularly influenced by junior school teachers who seemed so knowledgeable–maybe even more so than your parents.

The Socialization Period
Between 13 and 21, we are very largely influenced by our peers. As we develop as individuals and look for ways to get away from the earlier programming, we naturally turn to people who seem more like us.Other influences at these ages include the media, especially those parts which seem to resonate with our the values of our peer groups.

Becoming principled
It’s tough to have high moral values, but some people get there.

Pre-moral
In the pre-moral state, we have no real values (we are thus ‘amoral’). Young children are premoral. So also are psychopaths. Our basic nature tells us to be Machiavellian, doing whatever it takes to achieve our goals, even if it means hurting other people.

Conventional
Most people have conventional values, as learned from their parents, teachers and peers. These basically say ‘here are the rules to live in reasonable harmony with other people.’The bottom line of this state is that we will follow them just so long as we think we need to. We will break our values occasionally, and especially if our needs are threatened or we are pretty sure we can get away with breaking values with nobody else knowing about it.

Principled
When we are truly principled, we believe in our values to the point where they are an integral and subconscious part of our person. Right and wrong are absolute things beyond the person, for example as defined by a religion.The test of a principled person is that they will stick to their values through thick and thin, and even will sacrifice themselves rather than break their principles. Many great leaders were principled (Martin Luther King, Gandhi, etc.)

To Contents
Anatomy

Our bodies consist of 12 biological systems that carry out specific functions necessary for everyday living — Ref 528:

1. Skeletal
2. Articular – allows movement between bones
3. Muscular
4. Nervous
5. Circulatory
6. Integumentary – the skin and its appendages
7. Respiratory
8. Alimentary
9. Urinary
10. Reproductive
11. Lymphatic – part of the circulatorion and immune system,
12. Endocrine – regulate tissues by secretions directly into the circulation

Two of the 12 systems, the nervous system and the endocrine system, are responsible for control over all of the others so as to maintain the relatively simple stable environment required for normal cell functions:

To Contents
Art — neuroaesthetics

Scientists are using artists to learn about the mind. They’re looking for objective facts in the most subjective of places, using paintings and sculptures as sources of experimental data. Sometimes, it seems as if the scientists are simply trying to catch up with insights long ago “discovered” by artists.

10 PERCEPTUAL PRINCIPLES OF GREAT ART

PEAK SHIFT: We find deliberate distortions of a stimulus even more exciting than the stimulus itself—which is why cartoon caricatures grab our attention.

GROUPING: It feels nice when the distinct parts of a picture can be grouped into a pattern or form. The brain likes to find the signal amid the noise.

BALANCE: Successful art makes use of its entire representational space, and spreads its information across the entire canvas.

CONTRAST: Because of how the visual cortex works, it’s particularly pleasing for the brain to gaze at images rich in contrast, like thick black outlines or sharp angles—or, as in the geometric art of Mondrian, both at once.

ISOLATION: Sometimes less is more. By reducing reality to its most essential features—think a Matisse that’s all bright color and sharp silhouettes—artists amplify the sensory signals we normally have to search for.

PERCEPTUAL PROBLEM SOLVING: Just as we love solving crossword puzzles, we love to “solve” abstract paintings such as cubist still lifes or Cézanne landscapes.

SYMMETRY: Symmetrical things, from human faces to Roman arches, are more attractive than asymmetrical ones.

REPETITION, RHYTHM, ORDERLINESS: Beauty is inseparable from the appearance of order. Consider the garden paintings of Monet. Pictures filled with patterns, be it subtle color repetitions or formal rhythms, appear more elegant and composed.

GENERIC PERSPECTIVE: We prefer things that can be observed from multiple viewpoints, such as still lifes and pastoral landscapes, to the fragmentary perspective of a single person. They contain more information, making it easier for the brain to deduce what’s going on.

METAPHOR: Metaphor encourages us to see the world in a new way: Two unrelated objects are directly compared, giving birth to a new idea. Picasso did this all the time—he portrayed the bombing of Guernica, for example, with the imagery of a bull, a horse, and a lightbulb.

To Contents

Autonomic Nervous System (ANS)

From — ref825

The term “Autonomic” implies independent, self-controlling function.

This enables the maintenance of vital functions, such as heartbeat, breathing, blood pressure, and blood sugar without conscious effort — otherwise we would accomplish little else.

It is made up of two structurally and functionally distinct divisions: the Sympathetic division and the  Parasympathetic division. Nearly all organs are supplied with both Sympathetic and the Parasympathetic nerves.

Fig 191  Vagus Nerve plus Autonomic system — ref 446

The Sympathetic nervous system is responsible for the body’s reaction to stress; this is the “fight or flight” response.

The  Parasympathetic nervous system supports the vegetative bodily functions, such as digestion, and strives to conserve energy.

Both divisions of the ANS are active all of the time — Their effects on organs generally oppose one another.

Increased Sympathetic stimulation increases heart rate but increased Parasympathetic stimulation decreases heart rate. The heart rate at any given time of the day or night reflects the dominance of one division over the other at that time.

Each division of the ANS also directly inhibits activity in the other. A Sympathetic increase in heart rate occurs in part because Parasympathetic cardio-inhibitory nerves are themselves inhibited by Sympathetic nerve cells and vice-versa when Parasympathetic dominance occurs.

It was believed that Autonomic control of body functions could not intentionally or wilfully be altered.

However, a considerable amount of evidence now exists suggesting this is not true. Some of the effects of Autonomic control can be altered through bio-feedback training. The underlying principle of bio-feedback is that we have the innate ability and potential to influence Autonomic control of body functions through exertion of the will and mind.

With regard to “Flight or fight” —
In the response, NorEpinephrine unlocks receptors in the heart, and:–
• Increases heart beat
• Constricts so as to increase blood return to the heart so it can pump out more blood;
• Except in the skeletal muscles where the vessels dilate to accept more blood.

For the lungs
• Enlarges or dilates your bronchi and bronchioles so you can get more air in and out — so as to increasing oxygen and energy to the muscles

This can also be done by injecting a medication called Epinephrine.

Sympathetic receptors can also be called Adrenergic receptors. This is because the Adrenal gland is also involved with the body’s response to stress.

The Parasympathetic nerve endings where the chemical released is Acetylcholine, and it acts on the Parasympathetic or Cholinergic receptors on other nerves, cells or organs.

Consider ref827 — Sexual function, bladder control and Autonomic system

Much like control of the bladder, sexual responses are mediated by the coordinated activity of Sympathetic, Parasympathetic, and Somatic innervations.

Nervous System Works During Sexual Intercourse — From ref829 

The many physiological, behavioral and psychological reactions which accompany the sexual intercourse are mediated by a complex mechanism, involving:

Autonomic and somatic nervous systems;
Peripheral circulatory system at the level of the genitalia;
Spinal cord and peripheral nerves of the lower abdomen;
Central nervous system;
Endocrine system (sexual hormones).
All these systems interact among themselves in a complex fashion.

Fig 244 — Sexual Function

There is an Adrenal gland attached to the top of each kidney, and when these glands are stimulated they release NorEpinephrine and Epinephrine, which circulates in the blood stream to the Sympathetic or Adrenergic receptors on other nerves, cells or organs to produce an effect. In fact, another name for the medication Epinephrine is Adrenaline.

Autonomic System and Emotion — From ref828

The Sympathetic division acts in three major events, such as during
(a) Excitement, emotion of fear, anger and elation,
(b) Violent exercise and bodily activities and
(c) Extreme cold when the life is endangered.

Parasympathetic division is involved in the ordinary vital Ions of life. The Parasympathetic division maintains the ordinary processes of life. Protection of the eyes from the bright light is the work of this division. The constrictions of the pupils of the eyes are done by this division for protection purpose. It adjusts the lens of the eye for new vision.
The construction of food, its digestion and the excretion are done by Parasympathetic on. During sexual union more blood supply to the sex organs are made is division. It meets the physiological demands of the body to maintain. It stores up energy in abundance for future use by the Sympathetic division during emergency.

Physiological Changes Associated with Emotion — From ref887 (2001)

The most obvious signs of emotional arousal involve changes in the activity of the Autonomic (visceral motor) system  — The Somatic nervous system always acts on skeletal muscles but the Autonomic nervous system acts on smooth muscles, cardiac muscles, and also on glands.

Thus, increases or decreases in heart rate, Cutaneous blood flow (blushing or turning pale), Piloerection, sweating, and gastrointestinal motility can all accompany various emotions.

These responses are brought about by changes in activity in the Sympathetic, Parasympathetic, and Enteric components of the Autonomic System system, which govern smooth muscle, cardiac muscle, and glands throughout the body.

It is further suggested that the natural opposition of the expenditure and storage of resources is reflected in a parallel opposition of the emotions associated with these different physiological states — “The desire for food and drink, the relish of taking them, all the pleasures of the table are naught in the presence of anger or great anxiety.”

The responses of the Autonomic nervous system are quite specific, with different patterns of activation characterizing different situations and their associated emotional states — Indeed, emotion-specific expressions produced voluntarily can elicit distinct patterns of autonomic activity.

For example, if subjects are given muscle-by-muscle instructions that result in facial expressions recognizable as anger, disgust, fear, happiness, sadness, or surprise without being told which emotion they are simulating, each pattern of facial muscle activity is accompanied by specific and reproducible differences in visceral motor activity (as measured by indices such as heart rate, skin conductance, and skin temperature).

Moreover, Autonomic responses are strongest when the facial expressions are judged to most closely resemble actual emotional expression and are often accompanied by the subjective experience of that emotion!

One interpretation of these findings is that when voluntary facial expressions are produced, signals in the brain engage not only the Motor Cortex but also some of the circuits that produce emotional states. Perhaps this relationship helps explain how good actors can be so convincing.

Nevertheless, we are quite adept at recognizing the difference between a contrived facial expression and the spontaneous smile that accompanies a pleasant emotional state

This evidence, along with many other observations, indicates that one source of emotion is sensory drive from muscles and internal organs. This input forms the sensory limb of reflex circuitry that allows rapid physiological changes in response to altered conditions.

However, physiological responses can also be elicited by complex and idiosyncratic stimuli mediated by the Forebrain. For example, a suspenseful episode in a novel or film, stirring patriotic or religious music, or dishonest accusations can all lead to autonomic activation and strongly felt emotions.

The neural activity evoked by such complex stimuli is relayed from the Forebrain to autonomic and somatic motor nuclei via the hypothalamus and brainstem reticular formation, the major structures that coordinate the expression of emotional behavior (see next section).

In summary, emotion and motor behavior are inextricably linked. As William James put it more than a century ago — “What kind of an emotion of fear would be left if the feeling neither of quickened heart-beats nor of shallow breathing, neither of trembling lips nor of weakened limbs, neither of goose-flesh nor of visceral stirrings, were present, it is quite impossible for me to think … I say that for us emotion dissociated from all bodily feeling is inconceivable” — William James, 1893 (Psychology: p. 379.)

What can go Wrong — From ref828

But owing to prolonged emotion, if both the divisions of the Autonomic nervous system become overactive that may lead to organic pathology,

Parasympathetic over activity may lead to peptic ulcer, backache, and headache etc.

Sympathetic over activity may lead to psychosomatic diseases, such as asthma, tuberculosis, migraine etc. for which psychosomatic medicines are prescribed by the physicians.

To Contents

Autonomic Nervous System

To Contents
Brain — Artificial intelligence
nnn
723 ref723 Dog brain with NeoCortex on top
724 ref724 Prefrontal Cortex
725 ref275 functions-of-the-prefrontal-cortex.

Various descriptions of the physical, functional and connectional aspects of the brain(s) remain in use.


Fig 248

From — ref155 — new-brain-old-brain-mindfulness-compassion
OLD BRAIN – responsible for human drives — functions shared with many other animals
1. Motives (Safety, Food, Sex, Relationship Seeking, Caring, Status)
2. Emotions- guide us to our motivations/goals and respond if we are succeeding or threatened directs our Attention (what we notice and jumps out at us), Thoughts, Actions and Behaviours
3. Behaviours, which direct Whether we approach or avoid situations (Fight/ Flight) or even if we shut down

NEW BRAIN – responsible for
• Imagination, Creativity
• Planning
• Integration (fitting new and old pieces of information together in a way that makes sense to us to create a cohesive whole)
• Rumination (when we get stuck analyzing, and thinking about things, trying to “figure it out”)

The following versions are in use:

The Triune brain
• Forebrain or prosencephalon structures include the 1) cerebral hemisphere or neocortex, 2) corpus callosum, 3) ventricle, 4) fornix, 5) thalamus, and 6) pituitary.
• The midbrain or mesencephalon is labeled 11.
• The fully developed hindbrain or rhombencephalon is represented by structures 7) the pons, 8) the medulla oblongata, and 10) the cerebellum.
• The term brain stem refers to structures 7) the pons, 8) the medulla oblongata, and 11) the midbrain..

From — ref719 — Triune Brain Learning
Dr Paul MacLean of the National Institute of Mental Health, Washington DC suggests that the brain is made up of three distinct areas;

The Reptilian Brain. (5%)

This lies at the base of the brain and is likely to be the oldest, evolutionary part of the brain. The main responsibility of this brain is to ensure survival and to maintain routine body
functions (breathing, heart beat…etc)

In animals such as reptiles, the brain stem and cerebellum dominate. For this reason it is commonly referred to as the “reptilian brain”. It has the same type of archaic
behavioural programmes as snakes and lizards. It is rigid, obsessive, compulsive, ritualistic and paranoid, it is “filled with ancestral memories”. It keeps repeating the same behaviours
over and over again, never learning from past mistakes. This brain controls muscles, balance and autonomic functions, such as breathing and heartbeat. This part of the brain is active,
even in deep sleep.

The Limbic System/Mid-Brain (Emotional) (15% of the brain)

This is located at the seat of the emotions and regulates the sense of self-identity, belief, values and long term memory. A high level of self-esteem and motivation keeps the mid-brain
happy and open to successful learning. This is linked to the idea of Emotional Intelligence. It filters the data that flows through the senses- picking out the important pieces of
information and bringing them into consciousness.

The Neo-Cortex (80% of the brain)

The higher cognitive functions which distinguish Man from the animals are in the cortex. MacLean refers to the cortex as “the mother of invention and father of abstract thought
This is the academic brain where the higher order thinking skills occur. It is divided into twohemispheres; the right and the left. The brain is stimulated to learn by novelty, multi-sensory learning techniques, high stimulation and regular feedback. It works best in short bursts.

Each brain is unique and the individual must tailor learning approaches according to their own needs.

This hypothesis has become a very influential paradigm, which has forced a rethink of how the brain functions. It had previously been assumed that the highest level of the brain, the
neocortex, dominates the other, lower levels. MacLean has shown that this is not the case, and that the physically lower limbic system, which rules emotions, can hijack the higher
mental functions when it needs to.

Summary — Our brain relies on and utilises —
• Heredity – the ability to learn
• Our Conscious and our Unconscious (Subconscious) Minds
• Storing versions of experiences in the Unconscious
• Retrieving appropriate data from our Unconscious
• Learning – competences – habits such as expressing thoughts (conscious) or walking (subconscious)
• Our Senses
• Abilities to motivate, instruct, reason,
• The ability to respond promptly to aid safety

From– ref720 — Triune Brain Criticism

As the statistician George E.P. Box wrote, “essentially, all models are wrong, but some are useful”, then is there anything useful that we can retain from MacLean’s triune-brain model?

First, we can accept a few general ideas—for example, that some structures in our brains are older than others, from an evolutionary standpoint, and that our emotions involve some relatively primitive brain circuits that have been preserved over the course of mammalian evolution. The fear circuit and the pleasure circuit, for instance, are specific neuronal circuits that form what might best be called not our “emotional brain” but rather our “emotional neural networks”.

In short, if we want to continue associating the term “limbic system” with the emotions, then we need to redefine this term so that it includes these circuits specific to each emotion. The switches in these circuits consist of structures such as the amygdala, the nucleus accumbens, the hippocampus, the hypothalamus, the thalamus, and certain areas of the prefrontal cortex and the temporal cortex. And no doubt other structures are involved that remain to be discovered.

Right and left brain functions
From ref852

The left and right sides of the brain are connected by a great number of nerve fibers. In a healthy brain, the two sides communicate with one another.

The two sides do not necessarily have to communicate, though. If a person has an injury that separates the two brain hemispheres, they are still able to function relatively normally. A person uses both hemispheres of their brain and that there does not seem to be a dominant side. However, a person’s brain activity does differ, depending on what task they are doing. For example, a study in PLoS Biology says that the language centers in the brain are in the left hemisphere, while the right hemisphere is specialized for emotion and nonverbal communication.

Differences in the left and right brain hemisphere function exist in:
• Emotion — This is the domain of the right brain, in both humans and also in non-human primates. Emotions are expressed and recognized in others by the right brain.
• Language — The left brain is more active in speech production than the right. In most people, the two main language areas, known as Broca’s area and Wernicke’s area, are found in the left hemisphere.
• Sign language — Visually based languages are also the domain of the left brain. People who are deaf show speech-like brain activity when watching sign language.
• Handedness — Left- and right-handed people use the left and right brain differently. For example, a left-handed person uses their right brain for manual tasks and vice versa. Handedness is inbuilt, and it can even be detected while the baby is in the womb. Some babies prefer to suck their left or right thumb from as early as 15 weeks.
• Attention — The two brain hemispheres also differ in what they pay attention to. The left side of the brain is more involved with attention to the internal world. The right side is more interested in attending to the external world.

Recent brain imaging studies have shown no differences between males and females in terms of their brain lateralization.

In the first few years of a child’s life are a time of rapid brain growth. At birth, every neuron in the cerebral cortex has an estimated 2,500 synapses; by the age of three, this number has grown to 15,000 synapses per neuron.

The average adult, however, has about half that number of synapses — Because as we gain new experiences, some connections are strengthened while others are eliminated. This process is known as synaptic pruning. Neurons that are used frequently develop stronger connections and those that are rarely or never used eventually die. By developing new connections and pruning away weak ones, the brain is able to adapt to the changing environment.

Two changes associated with learning can occur, shown graphically as follows:

CCP197
How nerve impulses travel — ref 593

Myelin Production influenced by Neuron Electrical Activity produce fatty myelin sheaths and wrap them around the axons many times. This sheath greatly enhances the speed of the electrical signal along the axon.

However, learning, use of memory, etc require much more complex constructs. Previously, myelin was considered a simple process, but now research shows that it is a very complex and vital for this coordination and timing. Myelin, and with it the speed and timing of circuits, is altered during normal learning — 597a ref851 — Whole brain plasticity

Many different kinds of learning produce complex alterations in myelin amount, shape, size, pattern and distribution. These changes are part of neuroplasticity for many kinds of learning, not just the habit motor type. It is surprising how rapidly these changes can occur. It was previously thought that the only changes in myelin in the adult were damaging or responding to damage. Now, it has been shown that there is dynamic active modeling and remodeling of myelin in white matter in children and adults with learning. This includes re consolidation of memory. The alterations in myelin occur through oligodendrocyte stem cells that wander throughout the brain along blood vessels and then stop to differentiate into particular types of oligodendrotyes to make specific types of myelin.

In order to have coherent circuits functioning at large distances across multiple regions of the brain, the timing of individual neuronal electrical currents have to be very accurately in sync. The regulation of the timing and the strength and speed of currents in specific neuronal loops are vital factors in neuro-plasticity mechanisms.

Previously, myelin was considered a simple process, but now research shows that it is a very complex and vital for this coordination and timing. Myelin, and with it the speed and timing of circuits, is altered during normal learning and neuro-plasticity.

Like other aspects of neuroplasticity, such as regulating synapses, there is a vast array of mechanisms involved in myelin production. Studies of the ways white matter changes during neuroplasticity are just beginning.

Many different kinds of learning produce complex alterations in myelin amount, shape, size, pattern and distribution. These changes are part of neuroplasticity for many kinds of learning, not just the habit motor type. It is surprising how rapidly these changes can occur. It was previously thought that the only changes in myelin in the adult were damaging or responding to damage. Now, it has been shown that there is dynamic active modeling and re-modeling of myelin in white matter in children and adults with learning. This includes re consolidation of memory. The alterations in myelin occur through oligodendrocyte stem cells that wander throughout the brain along blood vessels and then stop to differentiate into particular types of oligodendrotyes to make specific types of myelin.

The junction of a neuron and oligodendrocyte that forms myelin is vastly complex—much more complex even than synapses and neuro muscular junctions. There are many stages that have to precisely timed and executed. It is necessary to coordinate huge amounts of material and then build precise shapes. It has to be spaced exactly with all the correct placement of ion channels. The enormous structure has to be maintained sometimes for a lifetime.

Once again, we must ask where the direction lies for stem cells wandering all over the brain constantly building and updating myelin of particular types to keep speeds in sync for neuroplasticity. No one can consider this a random process. This is another example of intelligent communication between a vast number of cells simultaneously all over the brain.

All of this is correlated with mental activity.

To start

Synapses and memory storage — See — ref 16

To Contents
Artificial Intelligence (AI)

Two aspects of AI have been researched and developed since around 1956 — From — ref853 — History of AI

Robotics has had remarkable success

But developments on “Artificial Thinking” have been restricted to Language Translation

Since around 2000 the question “Is the brain analogue or digital” has received attention.

From — ref854 — analog-or-digital and AI
Analog is a physical impression of the original. There is a direct link between the live performer and the recording.
Digital is an abstraction. The link between the live performer and the recording has been severed. The connection is lost.
There is also a growing body of experimental evidence suggesting that the way people actually think looks imagistic rather than abstract.

From — ref855 — Analog & Quantum Computers and AI
The number of quantum states becomes so large that classical mechanics becomes exact. When analog systems work classically, the quantized-energy argument fails.

From — ref856 — brains-as-analog-computers and AI
Here’s a good question: Is the brain a computer?
Analog computers have fallen out of favor, and as a consequence, we don’t think about them when we think about computation. And while the advantages of digital computation are clear for practical purposes, analog computation turns out to be an excellent way to think of computation more generally. When we look closely at how digital computation really works, it has almost nothing in common with how brains work. If digital computation is the only concept of computation you have, you might think we should abandon the idea that brains literally compute.
But that would be much too hasty: we just need a broader notion of computation, and it turns out that looking to analog computation helps us see how brains could be computers after all.

From — ref857 — Analog_vs_Digital and AI
The difference between analog and digital technologies is that in analog technology, information is translated into electric pulses of varying amplitude. In digital technology, translation of information is into binary format (zero or one) where each bit is representative of two distinct amplitudes.
Digital devices translate and reassemble data and in the process are more prone to loss of quality as compared to analog devices. Computer advancement has enabled use of error detection and error correction techniques to remove disturbances artificially from digital signals and improve quality.

ref858 — Freeman Dyson
Language is digital — and lots of insights & imaginings

To Contents
Carbon Dioxide

From —ref876

More carbon dioxide levels will help everyone, including future generations of our families. CO2 is the essential food for land-based plants.

The Earth’s biosphere has experienced a relative CO2 famine for millions of years, and the recent increase in CO2 levels has had a measurable, positive effect on plant life. Future CO2 increases will boost farm productivity, improve drought resistance, bolster food security and help create a greener, lusher planet.

To Contents
Cognition & Emotion

From — Ref 516 Cognition and Emotions

Cognition refers to processes such as memory, attention, language, problem solving, and planning.

Many cognitive processes are thought to involve sophisticated functions unique to primates.

They often involve so-called controlled processes, such as when the pursuit of a goal (e.g., maintaining information in Consciousness) needs to be protected from interference (e.g., a distracting stimulus).

A prototypical example of a neural correlate of a cognitive process is the sustained firing of cells in prefrontal cortex to maintain information in Consciousness for brief periods of time.

Whereas there is relative agreement about what constitutes cognition, the same cannot be said about emotions:–
• Some investigators use definitions that incorporate the concepts of drive and motivation: — emotions are states elicited by rewards and punishers.
• Others favour the view that emotions are involved in the conscious (or unconscious) evaluation of events (e.g., fear, anger),
• Others on an extended set of emotions, including moral ones (e.g., pride, envy).
• Strong evidence also links emotions to the body.

It is also important to consider the role of the ascending systems.

Of importance in the present context, the basal forebrain receives both Cortical and Amygdala inputs

In summary, the picture that emerges from anatomical connectivity data suggests a remarkable potential for integration of information.

Brain structures linked to emotion are often subcortical, such as the Amygdala (Limbic System), They are also believed to operate fast and in an automatic fashion, such that certain trigger expressions.

Anatomical basis for cognitive-emotional interactions

Advances in our understanding of brain connectivity suggest that a given brain region is only a few synapses away from every other brain region.

Prefrontal areas are among those most distant from the sensory periphery, suggesting that they receive highly-processed and integrated sensory information — is thought to be a key anatomical feature of this region and presumably confers the primate brain with a greater degree of flexibility.

Highly processed information would also be able to support more abstract processing that is required for cognition.

Interestingly, the Amygdala , a region often linked to emotional processing, appears to be equally removed from the sensory periphery — Overall, it appears that the Amygdala is very well situated to integrate and distribute information

CCP219

It is also instructive to consider the connectivity of the hypothalamus as it has been long recognized for its importance in emotional behaviours

In particular, via its descending connections that innervate brain-stem motor systems, this structure is thought to play a key role in the implementation of goal-directed behaviors.

Hypothalamic signals also can be conveyed to the cortex, mostly by way of the Thalamus.

Critically, prefrontal Cortical territories project directly to the Hypothalamus. Thus, the hypothalamus appears to be organized in such a way that it can generate both:
• Relatively reflexive behaviours, and
• Behaviours that are voluntarily triggered by inputs from the cerebral Cortex.

Overall, this structure appears to be connected with all levels of the nervous system, including the Neo-cortex, enabling important Hypothalamic regulatory signals to have widespread effects on the brain.

Emotion and cognition conjointly and equally contribute to the control of thought and behaviour.

While these statements were offered as a summary of specific findings concerning working memory performance following mood induction, they may aptly characterize a vast array of real-world situations.

In other words, whereas many behaviours may be reasonably well characterized in terms of cognitive/emotional interactions such that emotion and cognition are partly separable, in many situations, true integration of emotion and cognition may also take place .

Read More — Ref516 Cognition and Emotions

To Contents
Competences

Developing a complex of general competences is essential for day to day living, Other competences can be developed to support individual aspirations and social roles.

Learning: In this state you are exercising your cognitive skills, flexing your intellectual muscles. Whatever you’re up to, your thinking mind is engaged and in high gear

Realisation: Realisation means discovery, creativity, invention, and connection. It is related to a craving for attainment and occurs during the development of competence. Quite often what you are seeking can occur while you are having a break, or during sleep or sleepless episodes.

A Habit is generally beneficial — The person with the habit can choose to stop using it, and will subsequently stop successfully if they want to. The psychological/physical component is not an issue as it is with an addiction — ref808 habits-how-they-form-and-how-to-break-them

Neuroscientists have traced our habit-making behaviours to a part of the brain called the basal ganglia, which also plays a key role in the development of emotions, memories and pattern recognition. Decisions, meanwhile, are made in a different part of the brain called the prefrontal cortex. But as soon as a behaviour becomes automatic, the decision-making part of your brain goes into a sleep mode of sorts.

“In fact, the brain starts working less and less,” says Duhigg. “The brain can almost completely shut down. … And this is a real advantage, because it means you have all of this mental activity you can devote to something else.”

A habit may eventually develop into an addiction — with an addiction you are not in control of your choices.

To Contents
Control Systems Overview

Our control systems are based on our Central Nervous System, our Peripheral Nervous System Autonomic and Somatic Eelements and our Endocrine (Hormonal) System. There is also ref156 — the so-called brain in the Gut

The Autonomous Nervous System detects, generally through one or more specific Senses, when there is a Need. If, for example, it was to deal with the need to eat, and we do so, then we become aware of pleasurable feelings — the “reward” system!. When the need fulfilled the “inhibiting” system takes over, and we should feel satisfied.

Meeting the basic needs for sustenance, shelter, safety, has enabled the development of social groupings.

ref831 Nervous Systems

The SENSES

Our Nervous System is aware of our Environment, our current Mood. and our Body through a range of Senses — Ref79

Earlier we use to refer to our five Senses – Sight, Hearing, Taste, Smell & Touch. We now recognise a fuller list (21 items in a recent count): Thirst, Hunger, Ability to sense heat and cold, Pain, Balance, etc.

As we experience life, our Semses, Needs, and our complex of Memories (Conscious and U-nconscious) contend for Our Attention.

Our Senses evolved to provide data for our complex Nervous Systems — partly “Conscious” through our Central Nervous System and partly through our Autonomic Nervous System, in order:–
• To deal with some safety issues and to provide appropriate reflex responses — there is a fast response system.
• To deal with the multi-tasking of running a complex organism — an automatic, mainly sub-consvcious system
• To deal with extracting “meaning” of what is being sensed, and decide what to retain in memory –
• To balance this data with the complex of information and competences from previous experiences, and current attitudes —
Read More at Early learning is rapid though elementary.

The Nervous System
• Senses your external and internal surroundings
• Communicates information between your brain and spinal cord and other tissues
• Coordinates voluntary movements
• Coordinates and regulates involuntary functions like breathing, heart rate, blood pressure and body temperature.

The brain is the center of the nervous system, like the microprocessor in a computer. xx

The spinal cord and nerves are the connections, like the gates and wires in the computer. Nerves carry electrochemical signals to and from different areas of the nervous system as well as between the nervous system and other tissues and organs.

Nerves are divided into four classes:
1. Cranial nerves connect your sense organs (eyes, ears, nose, mouth) to your brain
2. Central nerves connect areas within the brain and spinal cord
3. Peripheral nerves connect the spinal cord with your limbs
4. Autonomic nerves connect the brain and spinal cord with your organs (heart, stomach, intestines, blood vessels, etc.)

The central nervous system consists of the brain and spinal cord, including cranial and central nerves.

The peripheral nervous system consists of the peripheral nerves, and the autonomic nervous system is made of autonomic nerves. Fast reflexes, like removing your hand quickly from a heat source, involve peripheral nerves and the spinal cord.

Thought processes and autonomic regulation of your organs involve various parts of the brain and are relayed to the muscles and organs through the spinal cord and peripheral/autonomic nerves.

Neural Communication

Neural Communication – Bio-Feedback

The endocrine system, are responsible for exerting control over all of the others so as to maintain the relatively stable internal environment required for normal cell functions. The endocrine system exerts control through the release of hormones and other chemical messengers that alter cell activities.

The nervous system exerts control by way of nerve impulses and the release of neurotransmitters that either inhibit or excite target cells.

Other cellular functions are altered by a combination of nervous and endocrine elements working together as a neuroendocrine control mechanism


CCP160
Some functions of the human body are voluntarily controlled; that is, you can willfully initiate, modify, or stop the function. Movements of the skeleton, as in walking or lifting a weight begin by voluntarily activating motor nerves that stimulate contraction of the appropriate skeletal muscles. Once the movement begins, control over the strength and speed of contraction, alternate contraction and relaxation of opposing muscles and coordination with other muscles acting at the same joints is shifted to involuntary neural control centers in the brain and spinal cord so that the intended movement proceeds normally while the brain’s attention is directed elsewhere. In other words, you need not concentrate on contracting and relaxing flexors and extensors at the appropriate time to continue walking. Instead, you can direct your attention to where you are going. However, the movement may be voluntarily speeded up, slowed, or stopped when it becomes desirable to do so. Thus, neural control of skeletal muscle is partially voluntary and partially involuntary. The division of the nervous system that exclusively controls skeletal muscle is called the somatic motor system.

The majority of body functions are involuntarily controlled. Most of the time we are unaware of the control because we do not have to voluntarily initiate it, although we may be able to sense the effects of control. For example, when core body temperature rises as we exercise, sweating becomes noticeable as the body attempts to cool itself, but we do not have to think about the need to sweat before we exercise, during the exercise, or after the exercise. Other examples of involuntarily controlled processes include gastrointestinal movements and secretion in response to ingested food, alteration of airway diameters in the lungs in response to the need for more or less air, increased formation of urine by the kidneys in response to increased drinking, and so forth. The part of the nervous system that controls involuntary functions of the body’s organs is called the autonomic nervous system (ANS).

The sympathetic nervous system is sometimes called the “fight or flight’ system. It heightens awareness, dilates pupils of the eyes, increases heart rate, dilates airways, increases breathing rate and depth, increases blood flow to skeletal muscles, and causes many other internal changes that prepare the body to preserve itself in the face of a short-term or acute stress.

The objective of parasympathetic nervous system control is to maintain the relatively stable internal environment of the body on a daily routine basis. When we rest from exercise, increased parasympathetic activity reduces heart rate and slows breathing. During and after a meal, parasympathetic stimulation of the organs of the digestive system increases secretion of digestive enzymes and increases contraction of smooth muscles that move the contents of the stomach to the small intestine, and from there to the large intestine. This allows for an orderly, routine processing of ingested food from which we can extract and absorb nutrients.

Both divisions of the ANS are active all of the time, displaying what is called autonomic tone. Their effects on organs generally oppose one another. As mentioned earlier, increased sympathetic stimulation increases heart rate but increased parasympathetic stimulation decreases heart rate. The heart rate at any given time of the day or night reflects the dominance of one division over the other at that time. Each division of the ANS also directly inhibits activity in the other. A sympathetic increase in heart rate occurs in part because parasympathetic cardio-inhibitory nerves are themselves inhibited by sympathetic nerve cells and vice-versa when parasympathetic dominance occurs.

For decades, many people believed that autonomic control of body functions could not intentionally or willfully be altered. A considerable amount of evidence now exists suggesting this is not true. Some of the effects of autonomic control can be altered through biofeedback training. The underlying principle of biofeedback is that we have the innate ability and potential to influence autonomic control of body functions through exertion of the will and mind. Biofeedback training is a learning process whereby people exert conscious control over physiological processes controlled by the autonomic nervous system. During the training periods, a biologic signal that changes with altered autonomic tone, such as the heart rate or skin temperature of the subject, is monitored and “fed back” to the subject in real time as a visual or auditory signal that the person can use to enhance a desired response. The use of a heart rate monitor during biofeedback training in stress management is a good example.

Mental or psychological stress increases sympathetic activity and decreases parasympathetic activity, resulting in an increase in heart rate, an increase in blood pressure, reduced gastrointestinal functions, and so forth. Over the short term, these changes may be beneficial, but when they are prolonged or become chronic, they become detrimental and can cause disease. Using heart rate biofeedback techniques, an affected person can be taught to relax and to increase parasympathetic tone and thus reduce sympathetic activity, evidenced by a decrease in heart rate. Initially, a machine monitors heart rate and provides the feedback signals that help the subject develop voluntary control. Eventually, the subject is able to recognize and control reactions to stress on his own by recalling and eliciting the same relaxed state of mind used in the biofeedback laboratory when he is at home or at work. Relaxation training using biofeedback has been successfully applied to the management of asthma, cerebral palsy, hypertension, migraine headache, irritable bowel syndrome, and numerous other maladies.

To Contents
Conventions — Social Norms

From — ref844 — Social Roles

Social norms, the informal rules that govern behavior in groups and societies, have been extensively studied in the social sciences

Since norms are mainly seen as constraining behavior, some of the key differences between moral, social, and legal norms—as well as differences between norms and conventions — have been blurred.

Conclusion
The study of social norms can help us understand a wide variety of seemingly puzzling behaviors. According to some accounts, a social norm results from conditional preferences for conforming to a relevant behavioral rule. Such preferences are conditional on two different kinds of beliefs: empirical and normative (describing a standard) expectations.

From — ref845

Social Norms are unwritten rules that are acceptable in a society. They provide us with an expected idea of how to behave in a particular social group or culture. Norms change according to the environment or situation and may change over time.

Social norms operate to build and maintain society.

Breaking social norms can make you a hero or an outcast. Many admire individuality, and breaking a small social norm can get you noticed. Breaking social norms has no legal recourse and social norms change with time. But there always exists consequences for breaking social norms. A person may face ostracization from society.

From ref846 — Social Gender and Sexual Norms

How can long-standing gender norms be redefined in order to allow for equality under the law? One could argue that as religion is the primary source of this conflict, religion itself should be regulated or possibly abolished from the political stage.

However, it is difficult to rationally argue for the banning of religion in any context apart from a separation of church and state.

In the majority of the countries and regions analyzed in this paper, we have found that attitudes toward social equality have grown more positive over time. This generational effect is the key to redefining social norms, and it will hopefully continue into the future, as citizens of the global community take these issues to heart.

To Contents
Criminality

From — ref848 How-organised-crime-in-the-uk-has-evolved-beyond-the-mafia (Date 2015)

The picture of organised crime in the UK leans away from the traditional Mafia model towards conglomerations of career criminals who temporarily join with others to commit crimes until they are completed and then reform with others to commit new crimes.

London emerges as the area where organised crime groups invest the most, but there is also a significant presence of business investments in Scotland (North-East, East and South-West) and in real estate abroad, especially in Spain.

Crime & Neurology
From — ref849 — Neurocriminology: Neuroethical and Neurolegal Implications

The very rapid developments taking place in brain imaging science are creating an uncomfortable tension between our concepts of responsibility and retribution on the one hand, and our concepts of understanding and mercy on the other.

Scientific evidence now documents structural and functional brain impairments not just in antisocial, violent, and psychopathic individuals, but also in white collar criminals and spouse abusers.

In addition, the brain circuits found to be impaired in offenders – including psychopaths – parallel the brain circuits found to underlie moral decision-making.

If the neural circuitry underling morality is compromised in offenders, is it morally right of us to punish prisoners as much as we do?

The author, Adrian Raine, is an internationally renowned expert in the emerging field of neurocriminology, integrates neuroscientific and social perspectives in the prediction and explanation of violent behavior, particularly in psychopaths.

We must take into account the early development of Conscience

From Oliver James’s book “They Fxxx you up” —

— Your Consciences — sensitive stage 3-6 years old

3 general variations have been identified:
• Punitive
• Weak
• Benign

The names don’t seem to be particularly appropriate — so let’s describe these traits and the possible causes/influences.

The associated behaviours seem to integrate with the Attachments Theory, presumably as the Carer/Familial influences generally follow through from earlier years.

Punitive Conscience

We crush our individuality and allow little space for instincts. We fear authority.

This Authoritarian Personality results from rigid and punitive parenting, in which sexual and aggressive childhood impulses were not tolerated. If we grew up in this background we had no alternative but to ban such wishes from our consciousness — to become unaware that we had them and anxious if they threatened to erupt, requiring heavy defence. – Fits in with Avoidant Relationships!

Weak Conscience

We are liable to random promiscuity and unstable relationships – with a symphony of antisocial behaviour, in which the instincts have all the best tunes, gets us into trouble from primary school onwards.

A Weak conscience can be the result of a lack of identification with either parent, or identification with loving parents who themselves possess weak or defective ones – fits in with Insecure Relationships, perhaps less so than for Avoidants.

Benign Conscience

We are not troubled by authority and its manifestations, and are not slaves to it either. Dirt or mess don’t bother us, but there are limits to what they can stand. The benign type can take or leave alcohol and cigarettes, and when young only dabbled in drugs: they know when to stop, when to say no

The kind of parenting that creates a benign conscience is called ‘authoritative’. It is both empathic to our needs and demanding of us – clearly “Secure”.

To Contents
Dis-ease

Human Beings have Basic Needs —
• Safety — Avoiding Harms, such as prolonged stress
• Connection — Attaching/relating to others
• Satisfaction — Using our Rewards system.

These cannot always be met and the resultant stresses can lead to Depression, Chronic Anxiety, and other dis-eases. Illness, Despair, Loss of Employment, Addiction, Shock (leading to PTSD), are all becoming more prevalent.

A Mental Health Epidemic is underway because of the duplicity of the wonderful human brain, as explained below.

Wayward Thoughts

Through the use of Technology, we know in some detail the means by which Brain Cells communicate – and what can go wrong!
• We know that what we ingest affects the Brain – Notably intoxicants, and nutrition has been shown to be crucial.
• We know that if meeting our Basic Personal Needs is frustrated then a mental disorder will probably follow.
• We know that the Brain stores and deploys Memories, Competences, Emotions, etc. but how this is accomplished has not (yet) been understood.

However by observations, and trial and error, humans have been able to learn competences, habits, etc. (Habit learning is very valuable, as it relieves us of having to consciously work through routine daily activities.

The MIND (whatever it is) is aware only of the current “stream of consciousness”. Note that we are able to learn to do things well, continue to sort of understand – then we make a big step forward and realise something new to us. This observation of the power of the sub-conscious to “think incisively” in parallel” with your conscious deliberations is crucial!

This ability to “Realise” indicates, albeit clandestine and uncertain, access to particular parts of what is hidden away in what Freud called the Sub-Conscious.

So, without understanding the complex processes of the Brain, We have learned to use one of its most important processes.

We have learned that apt or positive thinking is beneficial, though sometimes evasive.

Habitual negative thinking is intrusive and persists.

Bad habits may develop in many ways, such as:
• Negative responses to circumstances and events – this makes things worse
• Procrastination – rarely able to decide – this causes anxiety
• Worrying about what others may think – reduces this social contact
• Finding reasons for not doing something – this reduces commitment

Unfortunately, we have also realised that we can LEARN these “bad habits” – and they are often associated with depression, chronic anxiety; and are affected by chemicals, such as Intoxicants and unsuitable medications.

This is because the “Stream of Consciousness” has a Mind of its own – and the concept of “The Devil” should never have been discarded.

This malevolence lurks in the Sub-Conscious. It is inevitable that occasional stresses and negative emotional states occur – Rejection, disappointment, fear, jealousy, hatred, anger, unfairness and other painful emotions are natural and human so you can expect them sooner or later.

FREUD used the 3 level Consciousness model. When we are worried, interested, whatever, about something it seems that associated memories accumulate from the Sub-Conscious to the Near-Conscious.

Freud (1915) described CONSCIOUS mind, which consists of all the mental processes of which we are aware.

The PRECONSCIOUS contains thoughts and feelings that a person is not currently aware of, but which can easily be brought to consciousness (1924). It exists just below the level of consciousness, before the unconscious mind. The preconscious is like a mental waiting room, in which thoughts remain until they ‘succeed in attracting the eye of the conscious’ (Freud, 1924, p. 306).

Mild emotional experiences may be in the preconscious but sometimes traumatic and powerful negative emotions are repressed and hence not available in the preconscious.

Finally, the UNCONSCIOUS mind comprises mental processes that are inaccessible to consciousness but that influence judgements, feelings, or behavior (Wilson, 2002).

According to Freud (1915), the unconscious mind is the primary source of human behavior.

Our feelings, motives and decisions are actually powerfully influenced by our past experiences, and stored in the unconscious.

Freud applied these three systems to his structure of the personality, or psyche – the id, ego and superego. Here the id is regarded as entirely unconscious whilst the ego and superego have conscious, preconscious, and unconscious aspect.

To Contents
Emotions

Emotions and Moods
Emotions Moods Conditioning
Emotion & Cognition
Buddhist
Role of in Emotions in Autonomic System

From — ref 653
Emotions are more physiological than psychological — Any significant disruption of familiar sensory patterns triggers a biological response, commonly called emotion.

An Emotion is initially dealt with by the Emotional (Limbic) Brain — This enables us to respond immediately to indications of danger.

Whether triggered from outwith the body or within, emotions produce major changes all through the body. most notably in muscle-tone, energy level, tone of voice, and facial expressions. They signal organs and muscle groups, accelerate or decelerate cardiovascular rates, and mute or exaggerate messages of pain, deprivation, and pleasure.

People around you will be focused on the situation and their own emotional responses to it — they are unlikely to give the same meaning to the feelings you’re trying to explore or express.

The components of Emotion are:
• Arousal (energy)
• Motivation
• Feelings

Arousal is the energy that powers emotion. Even without emotional stimulation, arousal ebbs and flows in roughly 90-minute cycles throughout the day, including while we sleep. At peak arousal times we are more susceptible to intense emotional response.

Excitability and abundant energy mark periods of high arousal. Abnormally high levels produce over-stimulation, obsessions, compulsions, insomnia, or mania.

Periods of low arousal permit relaxation, letting go, or numbing out. Abnormally low levels of arousal create depression, muted emotions, or hypersomnia.

Specific emotions sometimes attach to arousal levels. For some people, high arousal produces increased anxiety or confidence. For others, low arousal stimulates shame, pride, anxiety, or withdrawal of interest.

Motivation. Emotions send action signals to the muscles and organs of the body to prepare us for to do something. Each emotion carries general motivation for behavior selected from the broad categories of approach, avoid, or attack.

If the change stimulating the emotion seems promising, the usual response is interest or enjoyment, which motivate various approach behaviors to “sense more, learn more, get more.”

If the change seems dangerous, anger, fear, or disgust emerges with motivation to attack (devalue) or avoid.

Motivation is the most important component of emotions. We cannot understand ourselves or other people without understanding motivation. We almost always fail to act in our best interests when we ignore motivation.

Types of Motivation. Below are examples of the primary motivations that foster growth and empowerment:
• Interest – find out more, get beneath the surface
• Passion – indulge, plunge
• Conviction – work to keep the status quo or change it
• Compassion – sympathize with the pain and hardship of self and other
• Enjoyment – appreciate, relax with
• Anxiety – learn more, increase ability to cope
• Shame – hide, cover-up.
• Distress – get back what was lost or compensate for its loss; consolidate gains
• Guilt – reconnect, compensate.

Motivations that have survival importance but are scarcely helpful in negotiating the complexities of most modern problems:
• Fear – freeze, run
• Disgust – recoil, get away from
• Anger – control, neutralize, devalue, punish, warn, threaten, intimidate, avenge
• Contempt/hatred – annihilate.

Feelings: The subjective experience of emotions—what they feel like—dominates our conceptions about them. However, this slowest component of emotion processing is only part of the emotional terrain. Trying to understand or change emotions through focus on how they feel is like trying to understand and change intestinal gas through focus on discomfort. Pop-psychologists make that error when they insist on “exploring and expressing” feelings.

The fact is, we cannot explore and express feelings without changing them. Mental focus amplifies and magnifies, creating the psychological equivalent to the observer effect in physics. Moreover, the brain loads into implicit memory other times you’ve experienced the feeling you’re trying to explore or express. This gives historical meaning to your feelings that go beyond the current situation. To complicate matters, the people around you will be focused on the situation and their own emotional responses to it. They are unlikely to give the same meaning to the feelings you’re trying to explore or express.

Read More — ref 653

Another Description of Emotions, From — Key elements of emotions (ref365)

Emotions rule our daily lives. We make decisions based on whether we are happy, angry, sad, bored, or frustrated. We choose activities and hobbies based on the emotions they incite.

There are three key elements:–
• Subjective experience
• Physiological response
• Behavioral response.

Subjective experience — While we have broad labels for emotions such as “angry,” “sad,” or “happy,” your own experience of these emotions may be much more multi-dimensional, hence (?) subjective.

Physiological Response — Many of the physiological responses you experience during an emotion, such as sweaty palms or a racing heartbeat, are regulated by the Sympathetic Nervous System

Behavioural response — Many expressions are universal, such as a smile to indicate happiness or a frown to indicate sadness. Socio-cultural norms also play a role in how we express and interpret emotions.

Emotions, Feelings, Moods vary in terms of Intensity and Duration.

Feelings are private to the person (but facial expressions show up!)

Emotion is distinguished from “mood” based on the period of time that they are present; a mood lasts longer than an emotion.

Interchangeably used with emotion, “affect” is the experience of emotion, and is associated with how the emotion is expressed (as seen on facial expressions or hand gestures).

Basic emotions possess motivational properties of their own. For example, happiness motivates a person to achieve better performance.

They result:
• From the Senses — from the Outside or the Body, or
• From the Sub-Conscious.
• A combination

If a “threat” is encountered then an immediate Instinctive Response may be required — But early on any Response/Emotion may be modified by our Emotional Intelligence capabilities — this may include perceiving an emotion in one or more other individuals


CCP220, ref788

Third view on emotions, From — ref788 Emotions and Energy

What we think of as emotion is the experience of energy moving through the body. This is generally felt as sensations of contraction such as tension or expansion such as calm. The Latin derivative for the word emotion, ‘emotere’, literally means energy in motion.

Understanding that emotions are energy implies that they are fluid, moving resources meant to be felt and released versus suppressed and ignored. The latter is the true culprit of low emotional intelligence and stress burnout.

The emotional brain is considered to have executive power in the brain. It influences all decision making, thought processes, memories, and present experiences. Your ability to understand, deal with, and effectively use your emotional energy is vital to your happiness levels.

The sensations you feel in your body hold the key to unlocking limiting patterns, transforming stress, and generating lasting happiness. Your body gives a constant stream of reliable information about your experience in the form of sensation. It’s a library of who you are at the deepest level, including all that has happened to you and all that you dream about. Understanding your body sensations will transform your life.

An Emotions often leads to thoughts — on what they mean, what to do about them, etc)

Sensory and emotional information is recorded into memory first; thoughts and perceptions, second. This distinction provides clues for increasing emotional intelligence while pointing out the limitations of purely thought-based approaches.

Read More — ref788 Emotions and Energy

To Contents
Role of in Emotions in Autonomic System<

The two states, emotions and memories, interconnect to form emotional memory, which produces the child’s responses to situations, experiences and learning. A number of factors can significantly impair Limbic System function Psychological and/or Emotional Trauma.

When not functioning properly due to injury or impairment, the limbic system becomes hypersensitive and begins to react to stimuli that it would usually disregard as not representing a danger to the body.


Figure 191

In addition the longer term emotions/Moods are habit-like and they can dominate our characters, in the extreme as Depression, GAD, etc.

From Hanson’s book Hard-wiring Happiness

Many psychological disorders involve extremes in one of the brain’s three operating systems — such as GAD, PTSD, OCD, dissociative disorder, social anxiety, and panic are related to the avoiding system — Also Substance abuse or dependence, and other addictive processes — and Insecure attachment, narcissism, borderline personality disorder, anti behaviour social behaviour — and the consequences of child abuse and neglect that arc related to the attaching system.

The Responsive and Reactive modes are the foundation of human nature. We have no choice about the vital needs the brain serves — avoiding harms, approaching rewards, and attaching to others — nor about its capacity to be in either mode.

Our only choice is which mode were in.

To Contents
Enteric System

From — Enteric Nervous System

The gut has a mind of its own, the “enteric nervous system”. Just like the larger brain in the head, researchers say, this system sends and receives impulses, records experiences and respond to emotions. Its nerve cells are bathed and influenced by the same neurotransmitters. The gut can upset the brain just as the brain can upset the gut.

The gut’s brain or the “enteric nervous system” is located in the sheaths of tissue lining the esophagus, stomach, small intestine and colon. Considered a single entity, it is a network of neurons, neurotransmitters and proteins that zap messages between neurons, support cells like those found in the brain proper and a complex circuitry that enables it to act independently, learn, remember and, as the saying goes, produce gut feelings.

The gut’s brain is reported to play a major role in human happiness and misery. Many gastrointestinal disorders like colitis and irritable bowel syndrome originate from problems within the gut’s brain. Also, it is now known that most ulcers are caused by a bacterium not by hidden anger at one’s mother.

Details of how the enteric nervous system mirrors the central nervous system have been emerging in recent years, according to Dr. Michael Gershon, professor of anatomy and cell biology at Columbia-Presbyterian Medical Center in New York. He is one of the founders of a new field of medicine called “neurogastroenterology.”

The gut contains 100 million neurons – more than the spinal cord. Major neurotransmitters like serotonin, dopamine, glutamate, norephinephrine and nitric oxide are in the gut. Also two dozen small brain proteins, called neuropeptides are there along with the major cells of the immune system. Enkephalins (a member of the endorphins family) are also in the gut. The gut also is a rich source of benzodiazepines – the family of psychoactive chemicals that includes such ever popular drugs as valium and xanax.

In evolutionary terms, it makes sense that the body has two brains, said Dr. David Wingate, a professor of gastrointestinal science at the University of London and a consultant at Royal London Hospital. “The first nervous systems were in tubular animals that stuck to rocks and waited for food to pass by,” according to Dr. Wingate. The limbic system is often referred to as the “reptile brain.” “As life evolved, animals needed a more complex brain for finding food and sex and so developed a central nervous system. But the gut’s nervous system was too important to put inside the newborn head with long connections going down to the body,” says Wingate. Offspring need to eat and digest food at birth. Therefore, nature seems to have preserved the enteric nervous system as an independent circuit inside higher animals. It is only loosely connected to the central nervous system and can mostly function alone, without instructions from topside.

This is indeed the picture seen by developmental biologists. A clump of tissue called the neural crest forms early in embryo genesis. One section turns into the central nervous system. Another piece migrates to become the enteric nervous system. According to Dr. Gershon, it is only later that the two systems are connected via a cable called the vagus nerve.

The brain sends signals to the gut by talking to a small number of “command neurons,” which in turn send signals to gut interneurons that carry messages up and down the pike. Both command neurons and interneurons are spread throughout two layers of gut tissue called the “myenteric plexus and the submuscosal plexus.” Command neurons control the pattern of activity in the gut. The vagus nerve only alters the volume by changing its rates of firing.

The plexuses also contain glial cells that nourish neurons, mast cells involved in immune responses, and a “blood brain barrier” that keeps harmful substances away from important neurons. They have sensors for sugar, protein, acidity and other chemical factors that might monitor the progress of digestions, determining how the gut mixes and propels its contents.

As light is shed on the circuitry between the two brains, researchers are beginning to understand why people act and feel the way they do. When the central brain encounters a frightening situation, it releases stress hormones that prepare the body to fight or flee. The stomach contains many sensory nerves that are stimulated by this chemical surge – hence the “butterflies.” On the battlefield, the higher brain tells the gut brain to shut down. A frightened running animal does not stop to defecate, according to Dr. Gershon.

Fear also causes the vagus nerve to “turn up the volume” on serotonin circuits in the gut. Thus over stimulated, the gut goes into higher gear and diarrhea results. Similarly, people sometimes “choke” with emotion. When nerves in the esophagus are highly stimulated, people have trouble swallowing.

Even the so-called “Maalox moment” of advertising can be explained by the interaction of the two brains, according to Dr. Jackie D. Wood, chairman of the department of physiology at Ohio State University in Columbus, Ohio. Stress signals from the head’s brain can alter nerve function between the stomach and esophagus, resulting in heartburn.

In cases of extreme stress, Dr. Wood say that the higher brain seems to protect the gut by sending signals to immunological mast cells in the plexus. The mast cells secrete histamine, prostaglandin and other agents that help produce inflammation. This is protective. By inflaming the gut, the brain is priming the gut for surveillance. If the barrier breaks then the gut is ready to do repairs. Unfortunately, the chemicals that get released also cause diarrhea and cramping.

There also is an interaction between the gut brain and drugs. According to Dr. Gershon, “when you make a drug to have psychic effects on the brain, it’s very likely to have an effect on the gut that you didn’t think about.” He also believes that some drugs developed for the brain could have uses in the gut. For example, the gut is loaded with the neurotransmitter serotonin. According to Gershon, when pressure receptors in the gut’s lining are stimulated, serotonin is released and starts the reflexive motion of peristalsis. A quarter of the people taking Prozac or similar antidepressants have gastrointestinal problems like nausea, diarrhea and constipation. These drugs act on serotonin, preventing its uptake by target cells so that it remains more abundant in the central nervous system.

Gershon also is conducting a study of the side effects of Prozac on the gut. Prozac in small doses can treat chronic constipation. Prozac in larger doses can cause constipation – where the colon actually freezes up. Moreover, because Prozac stimulates sensory nerves, it also can cause nausea.

Some antibiotics like erythromycin act on gut receptors to produce ascillations. People experience cramps and nausea. Drugs like morphine and heroin attach to the gut’s opiate receptors, producing constipation. Both brains can be addicted to opiates.

Victims of Alzheimer’s and Parkinson’s diseases suffer from constipation. The nerves in their gut are as sick as the nerve cells in their brains. Just as the central brain affects the gut, the gut’s brain can talk back to the head. Most of the gut sensations that enter conscious awareness are negative things like pain and bloatedness.

The question has been raised: Why does the human gut contain receptors for benzodiazepine, a drug that relieves anxiety? This suggests that the body produces its own internal source of the drug. According to Dr. Anthony Basile, a neurochemist in the Neuroscience Laboratory at the National Institutes of Health in Bethesda, MD, an Italian scientist made a startling discovery. Patients with liver failure fall into a deep coma. The coma can be reversed, in minutes, by giving the patient a drug that blocks benzodiazepine. When the liver fails, substances usually broken down by the liver get to the brain. Some are bad, like ammonia and mercaptan, which are “smelly compounds that skunks spray on you,” says Dr. Basile. But a series of compounds are also identical to benzodiazepine. “We don’t know if they come from the gut itself, from bacteria in the gut or from food, but when the liver fails, the gut’s benzodiazepine goes straight to the brain, knocking the patient unconscious, says Dr. Basile.

The payoff for exploring gut and head brain interactions is enormous, according to Dr. Wood. Many people are allergic to certain foods like shellfish. This is because mast cells in the gut mysteriously become sensitized to antigens in the food. The next time the antigen shows up in the gut, the mast cells call up a program, releasing chemical modulators that try to eliminate the threat. The allergic person gets diarrhea and cramps.

Many autoimmune diseases like Krohn’s disease and ulcerative colitis may involve the gut’s brain, according to Dr. Wood. The consequences can be horrible, as in “Chagas disease,” which is caused by a parasite found in South America. Those infected develop an autoimmune response to neurons in their gut. Their immune systems slowly destroy their own gut neurons. When enough neurons die, the intestines literally explode.

A big question remains. Can the gut’s brain learn? Does it “think” for itself? Dr. Gershon tells a story about an old Army sergeant, a male nurse in charge of a group of paraplegics. With their lower spinal cords destroyed, the patients would get impacted. “At 10am every morning, the patients got enemas. Then the sergeant was rotated off the ward. His replacement decided to give enemas only after compactions occurred. But at 10 the next morning everyone on the ward had a bowel movement at the same time, without enemas.” Had the sergeant trained those colons?

The human gut has long been seen as a repository of good and bad feelings. Perhaps emotional states from the head’s brain are mirrored in the gut’s brain, where they are felt by those who pay attention to them.

See also — ref156 Brain in the gut/, and ref 673

ref 673 enteric-nervous-system-second-brain

To Contents
Gender

From — ref752 — Disorders of sex development — Intersex

Disorders of sex development (DSDs) are a group of rare conditions where the reproductive organs and genitals don’t develop as expected.

If you have a DSD, you’ll have a mix of male and female sexual characteristics (Five forms of DSD are described, and there is a list of support groups).

See also — Ref643

From — ref814 — Homosexuality

This poses the question — Are people born gay or lesbian? — Scientists hesitate to provide a conclusive answer.

A slew of studies indicate that neurological factors greatly influence sexual orientation. The functionalities of regions in the brain like the amygdala and the hypothalamus have been proven to be determined genetically and are influenced by hormones. Developments in these regions kick in even before an individual learns cognitive skills or is exposed to environmental and educational settings. But scientists still do not negate the role of environmental factors.

However, a basic assumption about the normal nervous system is that its neurons possess identical genomes. Our bodies are made up of millions of cells, each with their own complete set of instructions for making us, like a recipe book for the body. This set of instructions is known as our genome and is made up of DNA?. Each cell in the body, for example, a skin cell or a liver cell, contains this same set of instructions — ref851

But, it is now known that Genomes are not identical– ref44 06Nov2001. The conclusions drawn in this reference indicate that the central nervous system, both during development and in adulthood, is a genetic mosaic: a euploid (Having a chromosome number that is an exact multiple of the haploid number for the species) population intermixed with a smaller but genetically diverse aneuploid population. Such mosaicism may have relevance to a variety of fields including stem cell biology, mammalian cloning, neuropsychiatric diseases, and genomics, neurogenetics — note the implications for gender!

In the past public attitudes were greatly influenced by “Societal Norms”, often religous, but directed at morality.

Take Gender and Sexual Orientation — are two distinct aspects of our identity.

Advice for parents of older children

Sometimes a DSD may be diagnosed if an older child doesn’t develop normally in puberty. For example, your child may not start the normal puberty changes, or may start puberty but not get periods.

Speak to your GP if you have any concerns about your child’s development at puberty. They can refer your child to a specialist, usually a consultant in paediatric endocrinology or an adolescent gynaecologist.

A team of different healthcare professionals will work with you to understand your child’s condition, and offer you and your child support and advice.
Read More — ref752

Gender is personal (how we see ourselves), while sexual orientation is interpersonal (who we are physically, emotionally and/or romantically attracted to)

There is currently a widespread belief that a unified ‘masculine’ or ‘feminine’ personality turns out not to describe many people — It describes stereotypes to which we constantly compare ourselves and each other, but more people are ‘gender non-conforming’ than we generally realize.”

The influences on Nurture and later life are generally complex and indistinct and the traits, although recognisable, are blurred.

How we respond to circumstances may arise from on-going awareness or from attitude, mood or temperament

Read more — ref955ref 60aref846

To Contents
Genetics — Epigenetics

From — ref861 — What is a Genome
A genome is an organism’s complete set of DNA, including all of its genes. Each genome contains all of the information needed to build and maintain that organism. In humans, a copy of the entire genome — more than 3 billion DNA base pairs — is contained in all cells that have a nucleus.


ccp209

It is now known that Genomes are not identical — ref44 06Nov2001.

The conclusions drawn in this reference indicate that the central nervous system, both during development and in adulthood, is a genetic mosaic: a euploid (Having a chromosome number that is an exact multiple of the haploid number for the species) population intermixed with a smaller but genetically diverse aneuploid population. Such mosaicism may have relevance to a variety of fields including stem cell biology, mammalian cloning, neuropsychiatric diseases, and genomics, neurogenetics — added comment “with implications re transgender, etc.”.

The study of Epigenetics now indicates that the genetic instructions are altered by our experiences

From — ref 505
Epigenetics is providing explanations of how our diets, our exposure to toxins, our stress levels at work – even one-off traumatic events – might be subtly altering the genetic legacy we pass on to our children.

To Contents
Gestalt

When you decide to deal with a problem you may find that Interrupts can hinder the completion of this intention!

Our desired “Stream of Consciousness” can be “deflected”.

Gestalt visualises the following causes:

Confluence:
o Healthy Confluence – that feeling of achievement! – The Esteem Need of prestige or managerial responsibility
o But with Unhealthy Confluence – the sort of feelings that lead to a panic attack – Loss of Safety Need – insecurity

Egotism is a state of observing oneself rather than fully experiencing oneself in a situation – Reduction in Social Need – Belongingness.

Introjects: These are due to experiences in ones development that lead to a fixed set of rules and values and language which may be full of shoulds, oughts and musts – Biological/Physiological need for sex frustrated.

Retroflections: Instead of directing energies outwards in an attempt to get his needs met, the person turns back on himself and suppresses this outward expression –
Depression due failure to achieve Self-Actualization Need of self-fulfillment.

Projections: The opposite of retroflection who self-blames, the projector will blame others. – not achieving the Esteem Need of managerial responsibility.

See also —
ref841 — What-is-gestalt-psychology
ref842 — Psychology-schools-of-thought
ref843 — Gestalt Cycle of change

To Contents
Habits

Each generation has to grow from a zygote — the single cell resulting from the fertilization of the female egg cell by the male sperm cell. The basic program for our development is in our individual DNA.

We have to learn to walk, talk, and so on, and in particular adapt to our social environment — these Habits enables us to cope readily with day to day activities.

A Habit is generally beneficial — The person with the habit can choose to stop using it, and will subsequently stop successfully if they want to. The psychological/physical component is not an issue as it is with an addiction — ref808 habits-how-they-form-and-how-to-break-them

Neuroscientists have traced our habit-making behaviours to a part of the brain called the basal ganglia, which also plays a key role in the development of emotions, memories and pattern recognition. Decisions, meanwhile, are made in a different part of the brain called the prefrontal cortex. But as soon as a behaviour becomes automatic, the decision-making part of your brain goes into a sleep mode of sorts.

“In fact, the brain starts working less and less,” says Duhigg. “The brain can almost completely shut down. … And this is a real advantage, because it means you have all of this mental activity you can devote to something else.”

Unfortunately, we are likely to learn Bad Habits, such as Addictions – our nature leaves us vulnerable! Bad habits can take a hefty toll on your health and happiness.

Longer term emotions/Moods are habit-like and they can dominate our characters, in the extreme as Depression, GAD, etc.

Learning is enabled by processes known as Neural Plasticity — ref23

A major part of learning is the generation of an extensive range of habits that we need to function – these are enhanced as we extend our capabilities.

William James, the American philosopher and Psychologist described the overwhelming importance of habits as follows:

“All our life, so far as it has definite form, mass of habits practical, emotional, and intellectual, — systematically organized for our weal or woe and bearing us irresistibly toward our destiny, whatever that may be”

Developing a complex of general competences is essential for day to day living, Other competences can be developed to support individual aspirations and social roles.

Each habit is re-enforced through use and may be lost if neglected. This has been described as “Use It or Lose It”.

Motivation

We need the motivational function to utilise the thinking capabilities . The bad habit of Depression has been explained as “Thinking without Motivation” — called Rumination — it also suppresses basic Needs!. So, if depressed, we need to free our cognition from rumination and get back our doggy sense of pleasure and our human sense of humour.

For most of the time our social obligations mean that we have to conceal or curtail our doggy impulses — we are obliged to act our way through life.

This acting imposes stresses, for some more than others, and often causes mental health issues. Alcohol, etc. have been used to release inhibitions in socially acceptable (almost) way.

We have to see concepts such as self-esteem in the context of our “acting life” and, as with many others, the concept of self-esteem needs to be better understood.

Abraham Maslow, attributed with first defining Needs, suggested that “people need both esteem from other people as well as inner self-respect. Both of these needs must be fulfilled in order for an individual to grow as a person and achieve self-actualisation.

Our everyday experience tells us that our emotions cause us to behave in certain ways. Feeling happy makes us smile, and feeling sad makes us frown. Case closed, mystery solved.

AS-if

However, James became convinced that this commonsense view was incomplete and proposed a radical new theory – that the relationship between emotion and behaviour was a two-way street, and that behaviour can cause emotion

Subsequent research has indicated that, in almost all aspects of our everyday lives, acting as if you are a certain type of person, you become that person – what James called the “As If” principle.

Thinking Habits

The following general purpose check-list of attitudes is a sound basis for on-going diligent application — Mindfulness!
• Self-Respect
• Self-reliance
• Composure
• Open mind
• Cautious judgment
• Acceptance (acknowledgement)
• Letting-Go
• Patience
• Non-striving

In adopting an attitude you must take account of your underlying moods and fatigue

Thus there are serious hindrances to the diligent practice of doing what is right for your well-being

In order to do the right things we need Achievement Habits, such as an Open Mind, Self-Respect, and Self-Reliance.

Self-Respect (Esteem) can be seriously undermined by bullies, bosses, bigots and other Bs — and all the worse if you are sensitive, responsive, isolated, etc. It is the way some people behave — any “victim” will bolster their ego.

Don’t let them get at you and dismiss (let-go) past malevolent impositions!

Self-reliance – also called Trust or confidence: It is far better to trust in your intuition and your own authority, even if you make some “mistakes” along the way, than always to look outside yourself for guidance – Next time you will be even better.

Open mind: Try sometimes to see things as new and fresh – as if for the first time – and with a sense of curiosity. A favourite Mindfulness example – The next time you see somebody you know – ask yourself if you are just seeing the reflection of your own thoughts about this person!

Then there are enabling habits: Patience, Acceptance, Letting-Go, and Composure

Acceptance is a willingness to accept matters as they are here and now. We often waste a lot of energy denying and resisting what is already so! Acceptance does not mean that you should stop trying to improve – to give up on your desire to change and grow – or tolerate injustice. You have to accept yourself as you are before you can really change – Do you want to change?)

(Letting-Go: We have to be aware of – and let go our negative thoughts, beliefs and feelings – apply yourself to this task (negative?) – You have to decide! Alternatively, we can allow ourselves to feel the negative feelings, identify them & then decide.)

Mindfulness also includes being Non-judgmental, and there are situations where this is applicable. However, in applying Attitudes/Habits of Acceptance, etc. we need to exercise sound Judgement. We should avoid being judgemental when Angry, in a Casual way, or as a Bad Habit, etc. as these give rise to “Red Reactions” .

We must practice the Mindfulness Attitude Habit of “Letting-Go” things that we can’t do anything about.

Finally, Self-Compassion. Mindfulness considers that you should cultivate love for yourself – as you are – without self-blame or criticism.

For more demanding learning, the stages in achieving a skill can follow this sort of pattern:
• Unconscious incompetence: I don’t really know what I want – Will this do what I want – Will I ever understand?
• Conscious incompetence: I’m getting a vague understanding! – This is what I want to do ….. If I’m diligent, I can afford to make little mistakes – I’ll backup as I go.
• Conscious competence: Why didn’t I see this before.
• Unconscious competence: I hardly notice how easy it is – I’m actually getting better at other things!

This proposed the self-perception view of emotion that behaviours cause feelings.

Subsequent research has shown that, in almost all aspects of our everyday lives, acting as if you are a certain type of person, you become that person – what I call the “As If” principle.

Our everyday experience tells us that our emotions cause us to behave in certain ways. Feeling happy makes us smile, and feeling sad makes us frown. Case closed, mystery solved. However, James became convinced that this commonsense view was incomplete and proposed a radical new theory.

James hypothesised that the relationship between emotion and behaviour was a two-way street, and that behaviour can cause emotion

For 10 quick and effective exercises that use the As If principle to transform how you think and behave. – see How to change
See ref824 — Self-help-positive-thinking

It helps if you are already interested or are motivated in some way.

To Contents
Honesty

From — ref871 — one-brain-region for-all-the-worlds-problem
Ever hear the expression “it’s all in your mind”? Well, according to Robert Sapolsky all the negativity in the world might all be coming from one part of the brain: the frontal cortex. The science of temptation runs parallel to the science of why people make “bad” decisions. Sapolsky talks about how active the frontal cortex can be in some people when they have the opportunity to do a bad thing… and how calm it can be in other people when presented with a similar situation. Performing full-frontal lobotomies on the world’s population to rid the world of negativity isn’t exactly in the cards—but understanding the basis of the world’s problems on a scientific (not to mention cranial level) might help make future generations much more adept at stopping humanity’s biggest mistakes. Robert Sapolsky’s most recent book is Behave: The Biology of Humans at Our Best and Worst.

From — ref868 — tradeoff between honesty, self-interest

From — ref869 — teaching-your-kids-be-honest
Some parents might believe it’s in a child’s nature to lie and it’s the parent’s job to punish dishonesty to prevent it from taking over. Actually parents often set their kids up to lie.

From — ref870 — What is honesty?
Many children think honesty means you “don’t tell a lie”– and that is definitely part of being honest. But honesty means more than not lying. A more complete definition of honesty shows that an honest person doesn’t do things that are morally wrong. If something you do is breaking the law or if you have to hide what you are doing because you’ll get in trouble, you are probably not being honest. So honesty is about speaking and acting truthfully.

From — ref866 — Small lies to big fibs

From — ref867 –The brain adapts to dishonesty

To Contents
Humour

From — ref859 — How Humour Evolved?
One theory holds that humour evolved because it encourages us to perform the arduous task of fact-checking our assumptions about other people’s intentions and perspectives. By this account, mirth is the reward we get when we debunk one of our presumptions and see things suddenly in a new light – jokes are ‘super-normal stimuli’ that exploit this system.

Once it evolved, humour became a social signal – we assume funny people are intelligent and friendly, and men and women alike prefer witty partners. On average, however, men tend to be more concerned that would-be partners will find their jokes funny, whereas women are more attracted to people who make them laugh.

From — ref860 — A Character Strength
Humour is now welcomed into mainstream experimental psychology as a desirable behavior or skill researchers want to understand. How do we comprehend, appreciate and produce humour?

Understanding and creating humor require a sequence of mental operations. Cognitive psychologists favor a three-stage theory of humor. To be in on the joke you need to be able to:
Mentally represent the set up of the joke.
Detect an incongruity in its multiple interpretations.

Studying humour allows us to investigate theoretical processes involved in memory, reasoning, time perspective, wisdom, intuition and subjective well-being. And it’s a behavior of interest in and of itself as we work to describe, explain, control and predict humor across age, genders and cultures.

Experimental psychologists are rewriting the book on humour as we learn its value in our daily lives and its relationship to other important mental processes and character strengths.

From — ref861 — Why did humans evolve a sense of humour
Experts explain how and why we find things funny and identify the reason humor is common to all human societies, its fundamental role in the evolution of homo sapiens and its continuing importance in the cognitive development of infants.

To Contents
Immunity — Immune System: Diseases, Disorders & Function

From — ref864, and ref865

The immune system is spread throughout the body and involves many types of cells, organs, proteins, and tissues. Crucially, it can distinguish our tissue from foreign tissue — self from non-self. Dead and faulty cells are also recognized and cleared away by the immune system.

If the immune system encounters a pathogen, for instance, a bacterium, virus, or parasite, it mounts a so-called immune response.

Everyone’s immune system is different but, as a general rule, it becomes stronger during adulthood as, by this time, we have been exposed to more pathogens and developed more immunity.

That is why teens and adults tend to get sick less often than children.

Once an antibody has been produced, a copy remains in the body so that if the same antigen appears again, it can be dealt with more quickly.

Because the immune system is so complex, there are many potential ways in which it can go wrong. Types of immune disorder fall into three categories:

Innate immunity is the immune system you’re born with, and mainly consists of barriers on and in the body that keep foreign threats out, according to the National Library of Medicine (NLM). Components of innate immunity include skin, stomach acid, enzymes found in tears and skin oils, mucus and the cough reflex. Innate immunity is non-specific, meaning it doesn’t protect against any specific threats.

Adaptive, or acquired, immunity targets specific threats to the body. After the threat is neutralized, the adaptive immune system “remembers” it, which makes future responses to the same germ more efficient.

IMMUNE SYSTEM DISORDERS
Because the immune system is so complex, there are many potential ways in which it can go wrong. Types of immune disorder fall into three categories:

Immuno-deficiencies
These arise when one or more parts of the immune system do not function. Immunodeficiencies can be caused in a number of ways, including age, obesity, and alcoholism. In developing countries, malnutrition is a common cause. AIDS is an example of an acquired immunodeficiency.

Auto-immunity
In autoimmune conditions, the immune system mistakenly targets healthy cells, rather than foreign pathogens or faulty cells. In this scenario, they cannot distinguish self from non-self.
Autoimmune diseases include celiac disease, type 1 diabetes, rheumatoid arthritis, and Graves’ disease.

Hyper-sensitivity
With hypersensitivity, the immune system overreacts in a way that damages healthy tissue. An example is anaphylactic shock where the body responds to an allergen so strongly that it can be life-threatening.

To Contents
Intuition

*Ref157 3 Brains xxx

We have three brains. They work independently of one another and yet they seek a creative balance together.

It was language that gave the two hemispheres of the human brain separate jobs. Language allows us to substitute words for elements of experience. We can deal with things that have happened through language. We can make sense of the past and learn from it. We can also make plans for the future. We can span space and time. We can integrate our history.

But this left brain ability to think and speak in words brought with it a right brain sense of wonder about how things work. We had to develop a right-brain intuition about how experience is ordered so we could provide for our needs. We also became acutely aware of death.

Our right brain intuition began to seek out the cosmic order. Language made us seek to understand how everything works. We must integrate our history, the whole of history. We need a framework of understanding to invest life with meaning. And creation myths won’t do in a global society. We need direct intuitive insight into how the cosmic order
works.

There are three dimensions to human experience. Our right-brain is intuitive and holistic. It seeks out integrated meaning and potential.

Our left brain is social. It uses language to formulate a commitment to behaviour. Our old brain is anchored to our evolutionary history. It emotionally assesses our performance.

To Contents
Language

Language is by nature imprecise and ambiguous

Ref157 3 Brains

It was language that gave the two hemispheres of the human brain separate jobs. Language allows us to substitute words for elements of experience. We can deal with things that have happened through language. We can make sense of the past and learn from it. We can also make plans for the future. We can span space and time. We can integrate our history.

But this left brain ability to think and speak in words brought with it a right brain sense of wonder about how things work. We had to develop a right-brain intuition about how experience is ordered so we could provide for our needs. We also became acutely aware of death.

Language made us seek to understand how everything works. We must integrate our history, the whole of history. We need a framework of understanding to invest life with meaning.

There are three dimensions to human experience. Our right-brain is intuitive and holistic. It seeks out integrated meaning and potential. Our left brain is social. It uses language to formulate a commitment to behaviour. Our old brain is anchored to our evolutionary history. It emotionally assesses our performance.

Since around 2000 the question “Is the brain analogue or digital” has received attention.

From — ref854 — analog-or-digital and AI
Analog is a physical impression of the original. There is a direct link between the live performer and the recording.
Digital is an abstraction. The link between the live performer and the recording has been severed. The connection is lost.
There is also a growing body of experimental evidence suggesting that the way people actually think looks imagistic rather than abstract.

Note that for recorded music Vynil is now the preferred choice for many people

From — ref857 — Analog_vs_Digital and AI
The difference between analog and digital technologies is that in analog technology, information is translated into electric pulses of varying amplitude. In digital technology, translation of information is into binary format (zero or one) where each bit is representative of two distinct amplitudes.
Digital devices translate and reassemble data and in the process are more prone to loss of quality as compared to analog devices. Computer advancement has enabled use of error detection and error correction techniques to remove disturbances artificially from digital signals and improve quality.

ref858 — Freeman Dyson
Language is digital — and lots of insights & imaginings

To Contents
Learning

Learning is what happens when information becomes understanding — Freeman Dyson — The free-thinker of our times — and he is only 94!

Individuals have generally found things they are interested in and give such topics their main attention — motivation is essential.

However, Society makes demands in terms of “jobs to be done”, etc and increasingly throughout the world “formal education” is expanding

Jobs to be done require transferable skills.

From — ref855 — Importance-of-education
• Ability to read and write
• Decent livelihood
• Better communication
• Use of technology
• Secure transactions
• Serve society
• Knowledge propagation
• Social harmony and more

Let’s repeat the entreaty by the Therapist, David A Yeats, noted “Without an awareness of how humans unfold developmentally, we are more inclined to live passively, not consciously, not deliberately, and to feel a greater sense of being a Victim of Life , rather than a creator of what we believe in, value, or desire for our lives. rather than a creator of what we believe in, value, or desire for our lives” — ref 396

Our Minds are a combination of the Conscious and the Unconscious (Some add an intermediate level — the Subconscious. However, experience indicates that ease of access to what is relevant varies with what we are thinking.

We must, as part of our education (the main part) is to learn to utilise our Unconscious.

Thus in memorising for say, a presentation, we should use what is shown here —

ccp166

Likewise we must provide for the rapid learning phases in the early years of children —

ccp111


ccp6a

To Contents
Medications

To Contents
Memory
Contents:
Memory and consciousness
Encoding
Types of Memory
Plasticity & Potentiation
Organisation of Memory
Recall

To Contents
Memory and consciousness

Memory is the selection, encoding and retention of, and the ability to recall, information, personal experiences, and procedures (skills and habits).

Our memories cannot record all that we sense — ref 97.

All of our experiences are filtered through our consciousness for interpretation, evaluation and response. Therefore, the only way we are capable of sensing reality is through the mediation of our consciousness – i.e. through our subjectivity — ref 598.

Subjectivity in remembering involves at least three important factors:
o Memories are constructions made in accordance with present needs, desires, influences, etc.
o Memories are often accompanied by feelings and emotions.
o Memory usually involves awareness of the memory.

There is no agreed model of how memory works — but a good model for how memory works must be consistent with the subjective nature of our consciousness — Too much information constantly flows in to be fully processed

The Attention Schema Theory (AST) seeks to explain how consciousness evolved — ref 280

To Contents
Memory encoding

The Memory System has the ability to encode, store and recall information. Memories give an organism the capability to learn and adapt from previous experiences as well as build relationships — ref 532

Encoding allows the perceived item of use or interest to be converted into a construct that can be stored within the brain and recalled later from short term or long term memory.

Working memory stores information for immediate use or manipulation which is aided through hooking onto previously archived items already present in the long-term memory of an individual

Visual, acoustic, and semantic encodings are the most intensively used. Tactile encoding is the processing and encoding of how something feels, normally through touch. Odours and tastes may also lead to encode.

Visual encoding is the process of encoding images and visual sensory information. Visual sensory information is temporarily stored within our iconic memory — the Short term Visual Memory and working memory, before being encoded into permanent long-term storage.

Acoustic encoding is the encoding of auditory impulses. When we hear any word, we do so by hearing to individual sounds, one at a time. Hence the memory of the beginning of a new word is stored in our echoic memory until the whole sound has been perceived and recognized as a word.

Semantic Encoding is the processing and encoding of sensory input that has particular meaning or can be applied to a context.

The Neural System & Memory

All perceived and striking sensations travel to the brain’s thalamus where all these sensations are combined into one single experience.

The amygdala is a complex structure that has an important role in visual encoding. It accepts visual input in addition to input from other systems and encodes the positive or negative values of conditioned stimuli.

The hippocampus is responsible for analyzing these inputs and ultimately deciding if they will be committed to long-term memory; these various threads of information are stored in various parts of the brain. However, the exact way in which these pieces are identified and recalled later remains unknown.

Acoustic encoding is the encoding of auditory impulses. When we hear any word, we do so by hearing to individual sounds, one at a time. Hence the memory of the beginning of a new word is stored in our echoic memory until the whole sound has been perceived and recognized as a word.

Encoding is achieved using a combination of chemicals and electricity. Neurotransmitters are released when an electrical pulse crosses the synapse which serves as a connection from nerve cells to other cells. The dendrites receive these impulses with their feathery extensions.

The brain organizes and reorganizes itself in response to one’s experiences, creating new memories prompted by experience, education, or training.

Therefore the use of a brain reflects how it is organised. This ability to re-organize is especially important if ever a part of the brain becomes damaged. Scientists are unsure of whether the stimuli of what we do not recall are filtered out at the sensory phase or if they are filtered out after the brain examines their significance.

Thus it may be concluded that as we grow old, failing memories may be the consequence of a failure to adequately encode stimuli as demonstrated in the lack of cortical and hippocampal activation during the encoding process.

Encoding and genetics

uman memory, including the process of encoding, is known to be a heritable trait that is controlled by more than one gene. In fact, twin studies suggest that genetic differences are responsible for as much as 50% of the variance seen in memory tasks.

ccc
Complementary processes

The idea that the brain is separated into two complementary processing networks (task positive and task negative) has recently become an area of increasing interest.

The task positive network deals with externally oriented processing whereas the task negative network deals with internally oriented processing.

Research indicates that these networks are not exclusive and some tasks overlap in their activation. A study done in 2009 shows encoding success and novelty detection activity within the task-positive network have significant overlap and have thus been concluded to reflect common association of externally-oriented processing. It also demonstrates how encoding failure and retrieval success share significant overlap within the task negative network indicating common association of internally oriented processing. Finally, a low level of overlap between encoding success and retrieval success activity and between encoding failure and novelty detection activity respectively indicate opposing modes or processing. In sum task positive and task negative networks can have common associations during the performance of different tasks.

To Contents
Types of Memory — ref 286 Short term memory — ref 247

Sensory memory is the earliest stage of memory. During this stage, sensory information from the environment is stored for a very brief period of time, generally for no longer than a half-second for visual information and 3 or 4 seconds for auditory information. We attend to only certain aspects of this sensory memory, allowing some of this information to pass into the next stage – short-term memory.

Paying attention to sensory memories generates the information in short-term memory.

Short-term memory ref 519

Also known as active memory, is the information we are currently aware of or thinking about.

In Freudian psychology, this memory would be referred to as the conscious mind. Most of the information stored in active memory will be kept for approximately 20 to 30 seconds. While many of our short-term memories are quickly forgotten, attending to this information allows it to continue to the next stage – long-term memory.

Short-term memory (or “primary” or “active memory”) — ref 519 is the capacity for holding, but not manipulating, a small amount of information in mind in an active, readily available state for a short period of time. The duration of short-term memory (when rehearsal or active maintenance is prevented) is believed to be in the order of seconds.
Short-term memory should be distinguished from working memory, which refers to structures and processes used for temporarily storing and manipulating information
Working memory, a core executive function, is a cognitive system with a limited capacity that is responsible for the transient holding, processing, and manipulation of information. Working memory is important for reasoning and the guidance of decision making and behaviour.

Working memory is often used synonymously with short-term memory, but neuropsychologists consider the two forms of memory distinct: working memory allows for the manipulation of stored information, while short-term memory only refers to the short-term storage of information. Working memory is a theoretical concept central to cognitive psychology, neuropsychology, and neuroscience.
Working memory stores information for immediate use or manipulation which is aided through hooking onto previously archived items already present in the long-term memory of an individual..

Long-Term Memory refers to the continuing storage of information. In Freudian psychology, long-term memory would be called the preconscious and unconscious. This information is largely outside of our awareness, but can be called into working memory to be used when needed. Some of this information is fairly easy to recall, while other memories are much more difficult to access.

ccc
Mapping activity

Positron emission tomography (PET) demonstrates a consistent functional anatomical blueprint of hippocampal activation during episodic encoding and retrival. Activation in the hippocampal region associated with episodic memory encoding has been shown to occur in the rostral portion of the region whereas activation associated with episodic memory retrieval occurs in the caudal portions.[10] This is referred to as the Hippocampal Encoding/Retrieval model or HIPER model.

One study used PET to measure cerebral blood flow during encoding and recognition of faces in both young and older participants. Young people displayed increased cerebral blood flow in the right hippocampus and the left prefrontal and temporal cortices during encoding and in the right prefrontal and parietal cortex during recognition.[11] Elderly people showed no significant activation in areas activated in young people during encoding, however they did show right prefrontal activation during recognition.[11] Thus it may be concluded that as we grow old, failing memories may be the consequence of a failure to adequately encode stimuli as demonstrated in the lack of cortical and hippocampal activation during the encoding process.

Recent findings in studies focusing on patients with post traumatic stress disorder demonstrate that amino acid transmitters, glutamate and GABA, are intimately implicated in the process of factual memory registration, and suggest that amine neurotransmitters, norepinephrine and serotonin, are involved in encoding emotional memory.

To Contents
Neuro-plasticity, Long Term Potentiation & Whole Brain Plasticity

Our Neural system is based on complex interconnections between Neurons.


CCP151 — from Theories of motivation ref 104

There is a outgoing “axon” from the transmitting neuron, a “synapse” and a ingoing link called a “dendrite”, each pair of neurons

CCP153 — ref 106

Two changes associated with learning can occur, shown graphically as follows:

CCP197 — How nerve impulses travel ref 593

Myelin Production influenced by Neuron Electrical Activity
Oligodendrocytes are multi polar cells that produce fatty myelin sheaths and wrap them around the axons many times. This sheath greatly enhances the speed of the electrical signal along the axon.

With myelin, the electrical signal rapidly jumps between nodes with long stretches of insulated


CCP196 — Long term potentition ref 590

This is due to increased Synapses activity.
However, learning, use of memory, etc require much more complex constructs, as explained in the following:
Whole Brain / — 597 ref 597

In order to have coherent circuits functioning at large distances across multiple regions of the brain, the timing of individual neuronal electrical currents have to be very accurately in sync. The regulation of the timing and the strength and speed of currents in specific neuronal loops are vital factors in neuro-plasticity mechanisms.

Previously, myelin was considered a simple process, but now research shows that it is a very complex and vital for this coordination and timing. Myelin, and with it the speed and timing of circuits, is altered during normal learning and neuro-plasticity.

Like other aspects of neuroplasticity, such as regulating synapses, there is a vast array of mechanisms involved in myelin production. Studies of the ways white matter changes during neuroplasticity are just beginning.

Many different kinds of learning produce complex alterations in myelin amount, shape, size, pattern and distribution. These changes are part of neuroplasticity for many kinds of learning, not just the habit motor type. It is surprising how rapidly these changes can occur. It was previously thought that the only changes in myelin in the adult were damaging or responding to damage. Now, it has been shown that there is dynamic active modeling and re-modeling of myelin in white matter in children and adults with learning. This includes re consolidation of memory. The alterations in myelin occur through oligodendrocyte stem cells that wander throughout the brain along blood vessels and then stop to differentiate into particular types of oligodendrotyes to make specific types of myelin.

The junction of a neuron and oligodendrocyte that forms myelin is vastly complex—much more complex even that synapses and neuro muscular junctions. There are many stages that have to precisely timed and executed. It is necessary to coordinate huge amounts of material and then build precise shapes. It has to be spaced exactly with all the correct placement of ion channels. The enormous structure has to be maintained sometimes for a lifetime.

Once again, we must ask where the direction lies for stem cells wandering all over the brain constantly building and updating myelin of particular types to keep speeds in sync for neuroplasticity. No one can consider this a random process. This is another example of intelligent communication between a vast number of cells simultaneously all over the brain.

All of this is correlated with mental activity.

Synapses and memory storage

See — ref 16

To Contents
The Organization of Memory

The ability to access and retrieve information from long-term memory allows us to use these memories to make decisions, interact with others, and solve problems.

But how is information organized in memory? The specific way information is organized in long-term memory is not well understood, but researchers do know that these memories are arranged in groups.

Clustering is used to organize related information into groups. Information that is categorized becomes easier to remember and recall. For example, consider the following group of words: Desk, apple, bookshelf, red, plum, table, green, pineapple, purple, chair, peach, yellow
Spend a few seconds reading them, then look away and try to recall and list these words. How did you group the words when you listed them? Most people will list using three different categories: colour, furniture, and fruit.

Another way of thinking about memory organization is known as the semantic network model. This model suggests that certain triggers activate associated memories. A memory of a specific place might activate memories about related things that have occurred in that location. For example, thinking about a particular campus building might trigger memories of attending classes, studying, and socializing with peers.

With regard to brain organisation — A phenomenon called Long-Term Potentiation allows a synapse to increase strength with increasing numbers of transmitted signals between the two neurons. These cells also organise themselves into groups specializing in different kinds of information processing. Thus, with new experiences the brain creates more connections and may ‘re-wire’.

The brain organizes and reorganizes itself in response to one’s experiences, creating new memories prompted by experience, education, or training. Therefore the use of a brain reflects how it is organised.

This ability to re-organize is especially important if ever a part of the brain becomes damaged. Scientists are unsure of whether the stimuli of what we do not recall are filtered out at the sensory phase or if they are filtered out after the brain examines their significance.

To Contents
Recall

Memory Encoding ref 532

The encoding process

A significant short-term biochemical change is the covalent modification of pre-existing proteins in order to modify synaptic connections that are already active. This allows data to be conveyed in the short term, without consolidating anything for permanent storage. From here a memory or an association may be chosen to become a long-term memory, or forgotten as the synaptic connections eventually weaken. The switch from short to long-term is the same concerning both implicit memory and explicit memory. This process is regulated by a number of inhibitory constraints, primarily the balance between protein phosphorylation and dephosphorylation. Finally, long term changes occur that allow consolidation of the target memory.

These changes include new protein synthesis, the formation of new synaptic connections and finally the activation of gene expression in accordance with the new neural configuration. The encoding process has been found to be partially mediated by serotonergic interneurons, specifically in regard to sensitization as blocking these inter-neurons prevented sensitization entirely. However, the ultimate consequences of these discoveries have yet to be identified. Furthermore, the learning process has been known to recruit a variety of modulatory transmitters in order to create and consolidate memories. These transmitters cause the nucleus to initiate processes required for neuronal growth and long term memory, mark specific synapses for the capture of long-term processes, regulate local protein synthesis and even appear to mediate attentional processes required for the formation and recall of memories.

Encoding and genetics

Human memory, including the process of encoding, is known to be a heritable trait that is controlled by more than one gene. In fact, twin studies suggest that genetic differences are responsible for as much as 50% of the variance seen in memory tasks.[13] Proteins identified in animal studies have been linked directly to a molecular cascade of reactions leading to memory formation, and a sizeable number of these proteins are encoded by genes that are expressed in humans as well. In fact, variations within these genes appear to be associated with memory capacity and have been identified in recent human genetic studies.[13] Peter D’Adamo, a naturopathic physician who advocates the Blood type diet, believes an individual’s blood type is related to their ability to encode information for prolonged periods of time. Those with Blood Type B are more susceptible to memory loss.

Complementary processes

The idea that the brain is separated into two complementary processing networks (task positive and task negative) has recently become an area of increasing interest.

The task positive network deals with externally oriented processing whereas the task negative network deals with internally oriented processing. Research indicates that these networks are not exclusive and some tasks overlap in their activation. A study done in 2009 shows encoding success and novelty detection activity within the task-positive network have significant overlap and have thus been concluded to reflect common association of externally-oriented processing.[17] It also demonstrates how encoding failure and retrieval success share significant overlap within the task negative network indicating common association of internally oriented processing.[17] Finally, a low level of overlap between encoding success and retrieval success activity and between encoding failure and novelty detection activity respectively indicate opposing modes or processing.[17] In sum task positive and task negative networks can have common associations during the performance of different tasks.

Depth of processing

Different levels of processing influence how well information is remembered. These levels of processing can be illustrated by maintenance and elaborate rehearsal.

Maintenance and elaborative rehearsal

Maintenance rehearsal is a shallow form of processing information which involves focusing on an object without thought to its meaning or its association with other objects.

For example the repetition of a series of numbers is a form of maintenance rehearsal. In contrast, elaborative or relational rehearsal is a deep form of processing information and involves thought of the object’s meaning as well as making connections between the object, past experiences and the other objects of focus. Using the example of numbers, one might associate them with dates that are personally significant such as your parents’ birthdays (past experiences) or perhaps you might see a pattern in the numbers that helps you to remember them.[18]
File:US penny 2003.jpg

Due to the deeper level of processing that occurs with elaborative rehearsal it is more effective than maintenance rehearsal in creating new memories.[18] This has been demonstrated in people’s lack of knowledge of the details in everyday objects. For example, in one study where Americans were asked about the orientation of the face on their country’s penny few recalled this with any degree of certainty. Despite the fact that it is a detail that is often seen, it is not remembered as there is no need to because the color discriminates the penny from other coins.[19] The ineffectiveness of maintenance rehearsal, simply being repeatedly exposed to an item, in creating memories has also been found in people’s lack of memory for the layout of the digits 0-9 on calculators and telephones.

Maintenance rehearsal has been demonstrated to be important in learning but its effects can only be demonstrated using indirect methods such as lexical decision tasks,[21] and word stem completion[22] which are used to assess implicit learning. In general, however previous learning by maintenance rehearsal is not apparent when memory is being tested directly or explicitly with questions like “ Is this the word you were shown earlier?”

Intention to learn

Studies have shown that the intention to learn has no direct effect on memory encoding. Instead, memory encoding is dependent on how deeply each item is encoded, which could be affected by intention to learn, but not exclusively. That is, intention to learn can lead to more effective learning strategies, and consequently, better memory encoding, but if you learn something incidentally (i.e. without intention to learn) but still process and learn the information effectively, it will get encoded just as well as something learnt with intention.[23]
The effects of elaborative rehearsal or deep processing can be attributed to the number of connections made while encoding that increase the number of pathways available for retrieval.

Optimal encoding

Organization can be seen as the key to better memory. As demonstrated in the above section on levels of processing the connections that are made between the to-be-remembered item, other to-be-remembered items, previous experiences and context generate retrieval paths for the to-be-remembered item. These connections impose organization on the to-be-remembered item, making it more memorable.[25]
Mnemonics

For simple material such as lists of words Mnemonics are the best strategy.[citation needed] Mnemonic Strategies are an example of how finding organization within a set of items helps these items to be remembered. In the absence of any apparent organization within a group organization can be imposed with the same memory enhancing results. An example of a mnemonic strategy that imposes organization is the peg-word system which associates the to- be-remembered items with a list of easily remembered items.

Another example of a mnemonic device commonly used is the first letter of every word system or acronyms. When learning the colours in a rainbow most students learn the first letter of every colour and impose their own meaning by associating it with a name such as Roy. G. Biv which stands for red, orange, yellow, green, blue, indigo, violet. In this way mnemonic devices not only help the encoding of specific items but also their sequence. For more complex concepts, understanding is the key to remembering. In a study done by Wiseman and Neisser in 1974 they presented participants with picture (the picture was of a Dalmatian in the style of pointillism making it difficult to see the image).[26] They found that memory for the picture was better if the participants understood what was depicted.

Chunking

Another way understanding may aid memory is by reducing the amount that has to be remembered via chunking. Chunking is the process of organizing objects into meaningful wholes.

These wholes are then remembered as a unit rather than separate objects. Words are an example of chunking, where instead of simply perceiving letters we perceive and remember their meaningful wholes: words. The use of chunking increases the number of items we are able to remember by creating meaningful “packets” in which many related items are stored as one.

State-dependent learning

For optimal encoding, connections are not only formed between the items themselves and past experiences, but also between the internal state or mood of the encoder and the situation they are in. The connections that are formed between the encoders internal state or the situation and the items to be remembered are State-dependent. In a 1975 study by Godden and Baddeley the effects of State-dependent learning were shown. They asked deep sea divers to learn various materials while either under water or on the side of the pool. They found that those who were tested in the same condition that they had learned the information in were better able to recall that information, i.e. those who learned the material under water did better when tested on that material under water than when tested on land. Context had become associated with the material they were trying to recall and therefore was serving as a retrieval cue.[27] Results similar to these have also been found when certain smells are present at encoding.

However, although the external environment is important at the time of encoding in creating multiple pathways for retrieval, other studies have shown that simply creating the same internal state that you had at the time of encoding is sufficient to serve as a retrieval cue.[29] Therefore putting yourself in the same mindset that you were in at the time of encoding will help recall in the same way that being in the same situation helps recall. This effect called context reinstatement was demonstrated by Fisher and Craik 1977 when they matched retrieval cues with the way information was memorized.[30]

Encoding specificity.

The context of learning shapes how information is encoded. For instance, Kanizsa in 1979 showed a picture that could be interpreted as either a white vase on a black background or 2 faces facing each other on a white background. The participants were primed to see the vase. Later they were shown the picture again but this time they were primed to see the black faces on the white background. Although this was the same picture as they had seen before, when asked if they had seen this picture before, they said no. T

he reason for this was that they had been primed to see the vase the first time the picture was presented, and it was therefore unrecognizable the second time as two faces. This demonstrates that the stimulus is understood within the context it is learned in as well the general rule that what really constitutes good learning are tests that test what has been learned in the same way that it was learned.[32] Therefore, to truly be efficient at remembering information, one must consider the demands that future recall will place on this information and study in a way that will match those demands.

Computational Models of Memory Encoding.

Computational models of memory encoding have been developed in order to better understand and simulate the mostly expected, yet sometimes wildly unpredictable, behaviours of human memory. Different models have been developed for different memory tasks, which include item recognition, cued recall, free recall, and sequence memory, in an attempt to accurately explain experimentally observed behaviours.

Item Recognition

In item recognition, one is asked whether or not a given probe item has been seen before. It is important to note that the recognition of an item can include context. That is, one can be asked whether an item has been seen in a study list. So even though one may have seen the word “apple” sometime during their life, if it was not on the study list, it should not be recalled.

Item recognition can be modeled using Multiple trace theory and the attribute-similarity model.[33] In brief, every item that one sees can be represented as a vector of the item’s attributes, which is extended by a vector representing the context at the time of encoding, and is stored in a memory matrix of all items ever seen. When a probe item is presented, the sum of the similarities to each item in the matrix (which is inversely proportional to the sum of the distances between the probe vector and each item in the memory matrix) is computed. If the similarity is above a threshold value, one would respond, “Yes, I recognize that item.” Given that context continually drifts by nature of a random walk, more recently seen items, which each share a similar context vector to the context vector at the time of the recognition task, are more likely to be recognized than items seen longer ago.

Cued Recall

In cued recall, one is asked to recall the item that was paired with a given probe item. For example, one can be given a list of name-face pairs, and later be asked to recall the associated name given a face.

Cued recall can be explained by extending the attribute-similarity model used for item recognition. Because in cued recall, a wrong response can be given for a probe item, the model has to be extended accordingly to account for that. This can be achieved by adding noise to the item vectors when they are stored in the memory matrix. Furthermore, cued recall can be modeled in a probabilistic manner such that for every item stored in the memory matrix, the more similar it is to the probe item, the more likely it is to be recalled. Because the items in the memory matrix contain noise in their values, this model can account for incorrect recalls, such as mistakenly calling a person by the wrong name.

Free Recall

In free recall, one is allowed to recall items that were learnt in any order. For example, you could be asked to name as many countries in Europe as you can. Free recall can be modeled using SAM (Search of Associative Memory) which is based on the dual-store model, first proposed by Atkinson and Shiffrin in 1968.[34] SAM consists of two main components: short-term store (STS) and long-term store (LTS). In brief, when an item is seen, it is pushed into STS where it resides with other items also in STS, until it displaced and put into LTS. The longer the an item has been in STS, the more likely it is to be displaced by a new item. When items co-reside in STS, the links between those items are strengthened. Furthermore, SAM assumes that items in STS are always available for immediate recall.

SAM explains both primacy and recency effects. Probabilistically, items at the beginning of the list are more likely to remain in STS, and thus have more opportunities to strengthen their links to other items. As a result, items at the beginning of the list are made more likely to be recalled in a free-recall task (primacy effect). Because of the assumption that items in STS are always available for immediate recall, given that there were no significant distractors between learning and recall, items at the end of the list can be recalled excellently (recency effect).

Incidentally, the idea of STS and LTS was motivated by the architecture of computers, which contain short-term and long-term storage.

Sequence Memory

Sequence memory is responsible for how we remember lists of things, in which ordering matters. For example, telephone numbers are a ordered list of one digit numbers. There are currently two main computational memory models that can be applied to sequence encoding: associative chaining and positional coding.

Associative chaining theory states that every item in a list is linked to its forward and backward neighbors, with forward links being stronger than backward links, and links to closer neighbors being stronger than links to farther neighbors.

For example, associative chaining predicts the tendencies of transposition errors, which occur most often with items in nearby positions. An example of a transposition error would be recalling the sequence “apple, orange, banana” instead of “apple, banana, orange.”

Positional coding theory suggests that every item in a list is associated to its position in the list. For example, if the list is “apple, banana, orange, mango” apple will be associated to list position 1, banana to 2, orange to 3, and mango to 4. Furthermore, each item is also, albeit more weakly, associated to its index +/- 1, even more weakly to +/- 2, and so forth. So banana is associated not only to its actual index 2, but also to 1, 3, and 4, with varying degrees of strength. For example, positional coding can be used to explain the effects of recency and primacy. Because items at the beginning and end of a list have fewer close neighbors compared to items in the middle of the list, they have less competition for correct recall.

Although the models of associative chaining and positional coding are able to explain a great amount of behaviour seen for sequence memory, they are far from perfect. For example, neither chaining nor positional coding is able to properly illustrate the details of the Ranschburg effect, which reports that sequences of items that contain repeated items are harder to reproduce than sequences of unrepeated items.

Associative chaining predicts that recall of lists containing repeated items is impaired because recall of any repeated item would cue not only its true successor but also the successors of all other instances of the item. However, experimental data have shown that spaced repetition of items resulted in impaired recall of the second occurrence of the repeated item.[35] Furthermore, it had no measurable effect on the recall of the items that followed the repeated items, contradicting the prediction of associative chaining. Positional coding predicts that repeated items will have no effect on recall, since the positions for each item in the list act as independent cues for the items, including the repeated items. That is, there is no difference between the similarity between any two items and repeated items. This, again, is not consistent with the data.

Because no comprehensive model has been defined for sequence memory to this day, it makes for an interesting area of research

Fig 123