The Nature of Consciousness

Piero Scaruffi

(Copyright © 2013 Piero Scaruffi | Legal restrictions )
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These are excerpts and elaborations from my book "The Nature of Consciousness"

Genes

An organism is a set of cells.  Every cell of an individual (or, better, the nucleus of each cell) contains the DNA molecule for that individual, or its "genome".

"Polymerizing" is the process by which molecules form chains, therefore called "polymers". The polymer of life is formed by molecules of four kinds (four "nucleotides").

A DNA molecule is made of two strings, or "strands", each one the mirror image of the other (in the shape of a "double helix"). Each string is a sequence of "nucleotides" or "bases", which come in four kinds (adenine, guanine, cytosine, thymine). These four bases are paired together (adenine is paired with thymine and cytosine is paired with guanine). Each nucleotide in a string is "mirrored" in a nucleotide of the other string.  Each strand of the helix acts therefore as a template to create the other template. Nucleotides are the elementary unit of the "genetic code". In other words, the genetic code is written in an alphabet of these four chemical units.

Cells split all the time, and each new cell gets one of the two strings of DNA of the original cell, but each string will quickly rebuild its mirror image out of protoplasm. This process is known as "mitosis". Each cell in an individual has almost exactly the same DNA, which means that it carries the same genome.

The genome is made of genes. A gene is a section of the DNA molecule which instructs the cell to manufacture proteins (indirectly, a gene determines a specific trait of the individual). Genes vary in size, from 500 bases long to more than two million bases (long genes tend to have just a very long waste).

The most abused metaphor in biology is that genes represent a program that results in some behavior (the "digital gene" metaphor). In reality, the behavior of genes is not so linear as the digital metaphor imply. Genes tend to work in communities of genes: it is not always clear what a gene does. Some genes are used for more than one chore (the "housekeeping genes"). And some genes do not encode discrete values, but continuous values. Many genes, in other words, are not digital at all. And the genome is not a sequential program, that is executed mechanically one gene after the other. It is more like a network of genes that "regulate" each other. The genetic "program" behaves more like a network of switches.

The DNA is organized into chromosomes (23 pairs in the case of the human race) which are in turn organized into genes. The human genome has 3 billion base pairs of DNA.

This means that each cell contains three billion bases of DNA, which is a string of genes about 2 meters long.  If we multiply for all the cells in the human body, we get a total length of genetic material which is about 16,000 times the distance between the Earth and the Moon.

The way offspring is designed is simple: male sperm and female eggs carry only 23 chromosomes (instead of the 46 that each body cell contains) and when they join they generate a 46-chromosome embryo. The embryo therefore contains some of the chromosomes of the father and some of the chromosomes of the mother.  (As Mendel discovered, the embryo does not contain a "blend" of the mother and the father, but rather some of the mother's attributes and some of the father's attributes).

(Notable among the human chromosomes are the X and Y chromosomes, that are responsible for determining the sex of the offspring. Reptiles do not have genes that decode sex: sex is determined by environmental conditions, mostly the incubation temperature, not by genetic information. The X and Y chromosomes were acquired by mammals much later in evolution. The Y chromosome is only one third  the size of the X chromosome, and the  Y chromosome has disappeared in several mammals. Human males have one X and one Y chromosome, while females have two X chromosomes).

All living organisms use DNA to store hereditary information and they use the exact same code (the "genetic" code) to write such information in DNA: the genome of an individual is written in the genetic code. It is inappropriate (although commonplace) to refer to the "genetic code" of an individual, as all living things on this planet share the same genetic code. The genetic code is a code, just like the Morse code. It specifies how nucleotides (through a "transcription" of the four nucleotides into ribonucleic acid, or RNA, and a translation of RNA into the twenty aminoacids) are mapped into aminoacids, which in turn make up proteins, which in turn make up bodies. Different genomes yield different bodies. But they always employ the same genetic code to carry out this transformation.

 The genetic code is the code used by Nature to express a set of instructions for the growth and behavior of the organism. Each individual is the product of a genome, a specific repertory of genes written in the genetic code. The genome defines the “genotype” of an organism. Genotype is the "genetic makeup" of the organism. The organism itself is the “phenotype”. Phenotype refers to how the genetic makeup is expressed in the body (the physical expression of a gene). The genotype is the repertory of genes of an organism; the phenotype is the physical manifestation of the genotype (the "body").

"Sequencing" the genome refers to the process of identifying the genes.

Humans have about 30,000 genes (out of 3.2 billion DNA units). That is a relatively low number for the complexity of the human body (only six times more than the Escherichia Coli bacterium).

A single gene can often be responsible for important traits. For example, chimpanzees share 98.6% of the human genome, but there is hardly a single trait in common between the two species. 98% of the human genome contains the same DNA found in most other vertebrates. The roundworm has 19,000 genes, just a third less than humans. But a single gene can make a huge difference and very similar genetic programs can differ wildly in phenotypic (bodily) effects. In other words, the relationship between genome and phenotype is nonlinear: the genotypes of humans and chimps differ by only 1.4%, but the difference in the corresponding phenotypes is much more striking than a mere 1.4% (at least from the admittedly biased viewpoint of us humans).  To be fair, the 30,000 genes represent only 1.5% of the genome, the rest being “junk”, i.e. chemicals that don’t seem to encode any instruction.

Some of those genes that humans share with chimps, incidentally, have been around for millions of years, and humans share them with bacteria.  As the British biologist Steven Jones wrote, "everyone is a living fossil".

The smallest genome that is known is the genome of the Mycoplasma Genitalium: 470 genes. One could wonder what is the smallest amount of genes that is required to have life.

 


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