Friday, July 31, 2009

Genetics 333

Genetic influences on Learning.
By Rao S Lakkaraju

An attempt is made here to examine the genetic aspects of Learning; basically to estimate the influence of genes in the art of Intelligence and Learning of human beings. Towards that end, the basic elements in genetic transcription and the basic elements in learning process are introduced first and later critically examined their role in the learning process.

The inspiration to this essay is “The Origins of Life” by John Maynard Smith and Eors Szathmary, Oxford Press 1999.

The Cell

Living organisms are of two types, Uni Cellular and Multi Cellular. The Power House driving the living systems is the Cell.

Cells are two types, those which do not have a nucleus (prokaryotic) and those which have a nucleus (eukaryotic). Human cells are advanced Cells and have a nucleus. The nucleus looks like a liquid droplet within the cell with defined contours. The liquid in the nucleus is called nucleoplasm. The outer membranes of the Cell and the nucleus are semi permeable and selectively allow nutrients needed for cell processes. All Human Cells, although they are very similar in structure, will have specific characteristics and needs depending upon their unique location. For example red blood cells are different from brain cells in their functionality. The difference in functionality and the generation of necessary framework for that unique functionality are dictated by the genetic material in the nucleus.

Cells have the replication capacity and can duplicate themselves. The Cell replication process is known as Mitosis. In practicality exact replication may not happen sometimes. In that case if the replication has errors beyond the repair capabilities of the cells (ex: nuclear DNA degradation), they also have the capacity to kill themselves. This programmed cell death (PCD) is known as Apoptosis. There are other types of cell deaths like Necrosis which occurs after tissue damage or Anoikis which occurs exclusively for cells in the eye.

The cell looks like a liquid drop with defined contours. The liquid is Cytoplasm and the contour is the cell membrane. In order for the Power House to function by giving life to the living organisms, it has to create energy from what it can get from outside. Extracting energy from raw input (food) is a complex chemical process. In order to do this in a systematic way Nature incorporated Organelle (small organs) in the cell to do specific functions.

The Organelle

These are some of the Organelle found in cells. Mitochondria which is the energy factory, produces energy (ATP) from nutrients. Endoplasmic reticulum helps in interpreting genetic code and producing enzymes. Golgi apparatus used for sorting and modification of enzymes. Nucleus is for storing and transmitting genetic information.

The Nucleus

The nucleus is one of the organelle in the cell and has chromosomes. Chromosomes have DNA and proteins. DNA is the genetic material and proteins are long chains of amino acids. All proteins (enzymes) are multiple combinations of 20 amino acids. They are assembled in the cell as dictated by the genetic coding from DNA. The DNA is same in all human cells but the specific coding required to generate specific proteins (enzymes) is activated by the specific cell. For example the kidney protein coding in DNA is activated by the kidney cells. Parental genetic identity is determined by using Chromosome markings. It should be noted that the DNA of parent and the child are different.

The Chromosome

Chromosomes are considered as packages of DNA (Genes) in the nucleus of a cell. There are two types of Chromosomes, Autosomes and Sex chromosomes. Both types of chromosomes contain DNA and proteins. The DNA in the nucleus is actively involved in the energy conversion and transportation process providing the know how to build the required setup. Using the information coming from DNA, enzymes are assembled and are driven to act upon the nutrients and trigger the chemical processes for providing energy (ATP) for the living organisms. Enzymes are proteins which are formed with a combination of 20 amino acids.

Human cells contain 23 pairs of chromosomes, out of which 22 pairs are auto chromosomes and the remaining pair is sex chromosomes(X, Y). Chromosomes are composed of DNA and proteins. The process of cell division where germ cells are produced (sperm, egg) is called Meiosis. In Meiosis, gametes are produced with half of the number of chromosomes in parental cells (haploid).

In human reproduction, the sperm floating around after its injection fertilizes the egg. The resulting combination, fertilized egg (zygote), has all the instructions for making structures of an adult form. The resulting adult form is a male (XY) or female (XX) depends upon the chromosome combination of Y chromosome in sperm combining with X of the egg or X of sperm combining with X of egg in fertilization.

The haploid (sperm or egg) which has single copies of sex chromosomes X and Y, results in a diploid (two copies of sex chromosomes) embryo after fertilization.

The genetic (DNA) characters of embryo are unique and have genetic contributions from male and female partners in fertilization. These genetic instructions which are in the chromosomes (Genes) are used not only to create structure of the adult form but also to transmit hereditary information to next generation.

The fertilized egg using genetic instructions start building the adult form first by creating Stem cells in the first few days of fertilization. These Stem Cells have all the genetic information of the adult and also have the unique capacity of transforming themselves into different specialized cell types (Kidney cells, pancreatic cells, Brain cells etc.) as dictated by the structural necessities of the genetic information.

Stem cells – Evolution

The embryonic stem cells transform themselves to specialized adult stem cells and then to specialized cells for the particular body organ being built. Although the stem cell DNA is same as any other cell DNA, the specificity of forming specialized cells comes because of the activation of that particular code in the stem cell’s DNA. Undifferentiated stem cells are also called somatic cells.

All cells have the capacity of replication and have the capacity of regeneration in the case of a loss. If there are drastic errors in replication, the cells have a mechanism to kill themselves and get eliminated by the body. The less drastic errors result in mutations of the original and may result in having slight changes of properties. As these mutations continue and accumulate, they result in different formations and different characteristics which may eventually lead to the evolution of new species.

The DNA

Deoxyribo nucleic acid (DNA) has a double stranded structure consisting of four nucleotides, Adenine (A), Cytosine(C), guanine (G) and Thymine (T). These are called bases. The nucleotides in each strand of DNA are paired with the nucleotides on the other strand with a hydrogen bond giving rise to a stable structure. This is what is known as base pairing. The pairings are A-T and G-C. DNA has the genetic code to make enzymes (proteins, RNA). The genetic code is called Gene. Since there are 20 amino acids which form proteins (enzymes), the code coming from 4 nucleotides of a DNA gene should be a triplet code (4 to the power of 3). This triplet code is known as a Codon (ex; GAA specifies amino acid Glutamic Acid). As there are 64 codes to identify 20 amino acids, there is a possibility of having multiple Codons for a single amino acid.

DNA is unique to each individual and occurs in each cell in the body although the function of DNA is different in different cells. Although DNA has all the genetic material, only the specific DNA parts are activated to generate specific enzymes needed for that location. Ex: Genetic code activated in Brain cells is different from that activated in Kidney cells. In other words function of DNA is site specific.

After the activation, the genetic code of DNA is transferred to RNA through an enzyme called RNA polymerase.

The RNA

Ribo nucleic acid (RNA) has a Single stranded structure and is derived from DNA. It is a combination of four nucleotides, Adenine (A), Cytosine(C), guanine (G) and Uracil (U). RNA has a structure very similar to single stranded DNA except Thymine is replaced by Uracil. There are many types of RNAs differentiated by their function and place. Ex: Ribosomal RNA, RNA polymerase etc.

The Genome

The entire DNA in an organism (including Mitochondrial DNA) is known as Genome.

The Gene

It was identified that the building blocks of human biological system, the polypeptides (Enzymes) are a combination of 20 amino acids. They are assembled in the Cell using the directions from genetic material DNA gene. Gene is the portion of genome in DNA which codes for a protein.

Although genes are the building blocks of an organism, the number of genes may not specify the complexity of an organism. For example humans (about 25,000 genes) have more genes than a fruit fly (about 13,000genes); mouse has about the same number of genes as humans.

Enzymes (Proteins)

Enzymes are catalysts which facilitate the chemical reactions taking place inside the cell. They make chemical reactions go faster. There are lots of chemical reactions occurring inside the cells for production of necessary chemical energy for survival. Enzymes are long chain amino acids (proteins).

The Genetic Transmission – Enzyme synthesis

In the nucleus, the genetic code in the DNA Gene is transferred to a single stranded RNA. This RNA is known as messenger RNA. Messenger RNA is nothing but a mini DNA strand which has the codes specifying the enzyme protein. The messenger RNA was moved out of the nucleus into the Cytoplasm, the liquid material with all the nutrients in the cell.

The messenger RNA transfers the message to transfer RNA, Codon by Codon, specifying the amino acids constituting the protein. Transfer RNA will have only one codon at a time. Some codons start the Enzyme (protein) building process. Likewise some codons stop the building process.

At what is called a ribosomal site, the transfer RNA codons get interpreted and protein synthesis begins. The transfer RNA interprets the codon and picks up the particular amino acid from the nutrient pool. The amino acid will be attached to the protein chain being built at the ribosomal site. This amino acid and building the protein continued until all the codons were interpreted. The last codon is the stop codon signaling the genetic code for the particular enzyme (protein) is complete. The protein is released to do its function.

The human biological system depends upon the exact duplication and regeneration processes in cells as dictated by genetic instructions. If we ingest chemicals which are not native to the cell structures, we may end up with unnecessary mutations and or duplication errors which may have an impact on our survival.

Information Processing --- Human Systems

There are two types of information processing in human systems. First one is genetic information processing. The genetic information which has all the structural information which includes the basic back bones of storing and retrieval of internal information of the human being is controlled by DNA and Stem Cells. We have seen how the information gets out of DNA ends up in enzymes which facilitate all chemical reactions in the cells for structural and energy creation in human beings. The brain is created; the basic neural network and memory structures for the survival of human being were built from DNA information. Automatic systems like heart beat, breathing etc are built into the human system. Identifying and responding to external basic stimuli is one of them. For example baby crying after a pinch on the skin is built into the memory systems.

The second type of information processing is accumulating external signal data, storing, evaluating and responding to them. This is all done in the Brain. We will examine what is brain and how it coordinates information, thought and action in the human body.

Brain

The controlling system which produces responses to output stimuli is known as brain. The size of the brain actually determines the number of stimuli the brain responds to. For example a touch of a snail (input signal ) will generate a response to retract into shell (Output signal); not much information processing is done while in humans the input signals come from touch, sound, taste, smell and light and the processing of those signals is complex. The size of the human brain is 1350 cc, which is huge compared to the snail. The generation of input and output signals in the biological systems is done by the Neuron.

Brain Formation

The book Creating Mind by Dowling describes it beautifully.

A neural plate is formed about three weeks after conception on the back side of the embryo with about a group of 125,000 cells.

Between third and fourth week of development, the neural plate folds itself and forms a long tube called neural tube. All of the central nervous system is formed from this neural tube. The front part becomes brain and the later part the spinal cord.

By about 40 days of development three swellings in the anterior part are visible and eventually form forebrain, mid brain and hind brain.

As the neural tube forms, some cells on the either side are left behind. These cells are known as neural crest cells from which the peripheral nervous system is formed.

Neural Cell (Neuron)

Neural cell looks like an octopus. There are many types of neural cells depending upon their site of activation and their intended purpose. The principle ability of a neuron is to receive electrical inputs and respond with electrical outputs. To accommodate this, brain cell has multiple input channels called Dendrites and one output channel called Axon. The ending of Axon has connecting branches setup to connect to various sites if needed. Axons from many neurons are bundled together like a fiber optic cable in passing through various regions of the brain. The signal transmission junction between two neurons is called synapse. There are multiple billions of Synapses as there are billions of neurons.

The main purpose of the brain is to receive information, digest it and respond to the received information. The information may come from various sources but the response may be to a specific site. The signals are produced and transmitted by the creation of chemical ions (Na, K, Cl, and Ca) in the neuron.

Central Nervous System

In humans the central Nervous system divided into two parts 1) Spinal cord and brain 2) Peripheral nervous system (Nerves and Axons outside the spinal cord and brain).

The peripheral nervous system largely used to send signals to and fro from the Spinal cord and brain to the sensing and muscular system. As such it mainly consists of motor axons and sensory neurons. These axons are segregated and formed as bundles depending on their function (whether they are motor or sensory axons). These bundles look like white matter because of the myelin sheaths of the glial cells.

Although the neural mechanisms in both the systems are same, the axons in the peripheral nervous system could regenerate easily compared to axons in the brain and spinal cord. This is the reason why we recoup all our senses after a cut in the body as compared to brain or spinal cord injuries. This specialized regeneration activity of neural cells in the peripheral system is due to the activity of glial cells surrounding nerve cell axons and form the myelin sheath which forms the insulation around the axons.

The sensory information coming from peripheral nervous system to spinal cord is called somotosensory consisting of touch, pain, temperature , pressure etc. some of this information also goes directly to brain. The spinal cord may react to the sensory information by activating motor neurons and informs the brain the actions it has taken. The brain compares information what it received directly with what it received from the spinal cord and takes action if necessary. This is a sort of a failsafe mechanism.

The brain sits on the top of spinal cord. It is divided into three regions. The hindbrain starts from the spinal cord; the mid brain is in-between hindbrain and the third region forebrain.

The hind brain has three structures, the medulla, pons and cerebellum.

The mid brain is relatively small and sits between the other two brain regions.

The forebrain is the prominent part of the brain and has two regions, thalamus and hypothalamus in one region and cerebrum (basal ganglia and cerebral cortex) in the other region.

Functional Brain

The hypothalamus and medulla are the brain’s principal regulatory centers. They regulate internal organs, including the heart, digestive system, lungs, bladder, blood vessels, glands and the pupil of the eye.

Medulla regulates vital body functions respiration, heart rate etc.

Hypothalamus regulates basic drives eating, drinking, body temperature and sexual activity. The pituitary gland sits under hypothalamus and hypothalamus regulates pituitary gland. Pituitary gland in turn regulates the glands elsewhere in the body such as thyroid and adrenal glands.

Bibliography

The Origins of Life by John Maynard Smith and Eors Szathmary, Oxford Press 1999.

Big Brain the Origins and Future of Human Intelligence by Gary Lynch and Richard Granger, Palgrave Macmillan 2008

How Brains think: evolving intelligence, then and now by William H. Calvin, Basic Books 1996

Your Brain how you got it and how it works by Tabitha M. Powledge, Macmillan 1994

Creating Mind; How the brain works by John E. Dowling, W. W. Norton & Co 1998