Fundamentals of Evolution, Genetics and Inheritance (v1.0)
Most of this material is derived from classes by Professor Mohamed Noor of Duke University.
The solar system came together around five billion years ago. DNA based life first occurred on earth about 3.5 billion years ago. Vertibrates evolved about 520 million years ago. Homo Sapiens emerged about 200,000 years ago. Science and evolution do not say how or why life first appeared on earth with any degree of confidence. There is still some room for a theological explanation. But Charles Darwin’s evolution pinpoints how life changed gradually over time and how it forked at various points driven by natural selection and other forces. The key factor in evolution is mostly founded in genetics and simple laws. Inheritance to an offspring is also controlled largely by genetics and simple laws. Science however does not really explain in a convincing way how or why consciousness and higher cognitive capabilities evolved in life, although we could argue that it gave a natural selection advantage to flourish and is a survival skill. So, there is still some room for a theological interpretation in this area also.
Some of the scientific thinking on how life emerged on earth that does not invoke a theological answer is captured here. It is not really satisfactory.
There are lots of theories on consciousness from religion, cognitive science and philosophy. There are just a few submissions on how consciousness evolved from evolution scientists. Here is one and it is not really satisfactory.
Some models of consciousness from Indian philosophy from Swami Sarvapriyananda is below.
Evolution is change through time over generations. One cause is natural selection but this is not the only one. Natural selection is the process whereby organisms better adapted to their environment tend to survive and produce more offspring. Evolution by natural selection is a mathematical inevitability. Evolution consists of two fundamental processes – change within a lineage, and formation of new lineages. There are two fundamental principles. Firstly, much of evolutionary change is caused by natural selection which produces the appearance of design. Secondly, all species share common ancestry – result of splitting lineages from one ancestral life form. Charles Darwin first described these. Fossil records clearly show life on earth started with quite simple forms and only later evolved to more complex forms. Also, species gradually changed in the fossil record into new species/forms. Lastly, we find transitional fossils that connect modern groups to their common ancestors. Besides the copious fossil records, other evidence for evolution is vestigial organs and vestigial genes, biogeography (examples are life forms on islands and different geographies), and inefficient design like the loop of the laryngeal nerve all the way down to the aorta and all the way back (Evolution works with the material available – not produce more efficient designs). Laryngeal nerve design works fine for fish but not mammals – especially giraffe. Evolution is not just a theory but a fact. Not a single scientist disputes it although there might be discussions about the relative importance of the different forces driving it.
The definitive characteristic of life is reproduction. Life on Earth is based on DNA, although some quite simple forms like viruses are based on RNA. The DNA is a double helical structure of two strands. Watson and Crick first described it. The strands contain nucleotides (also called bases) called A (Adenine), C (Cytosine), G (Guanine), T (Thymine). Each nucleotide contains a five-carbon sugar, a phosphate molecule, and a nitrogen containing base. Strands of nucleotides that form a unit is called a gene and large segments of the strand are called chromosomes. Genes act like genetic instructions and control traits and/or protein coding. Intergenic regions are the regions between genes. Humans have about 23,000 protein coding genes and 23 chromosomes. The human genome has about 3.1 * 10 **9 bases. The most famous chromosomes are the X and Y. Males have X and Y while females have two X’s. The complete DNA structure is called a genome. Recently the complete genome of humans was published. Earlier (about 20 years ago) the human genome project pieced together 92% of the human DNA. Some of the benefits of knowing the human genome are ancestry and relative tracking by sites like 23andme, risk factor analysis for susceptibility to various diseases or disorders, guide drug development, and forensics and criminal investigations. Many genetics-based diseases and disorders have been genetically mapped already but there are many more and this is an active area of research. Genetics on a bigger scale allows us to understand evolution much better by looking at it at the DNA level.
Most species are diploids – have one gene copy from each of two parents. RNA is an intermediate, that is a complement of a segment of one strand of a DNA (ex A->U, C->G, G->C. T->A). Formation of messenger RNA from DNA is called transcription. String of amino acids is translated from messenger RNA. A sequence of three nucleotides in RNA is a codon and creates a specific amino acid. There are three stop codons that end the amino acid chain translation. So, this is how we go from a DNA via the RNA to amino acids in our body. Genes often have amino acid (or protein) coding segments but not always.
The most obvious difference between Haploid and Diploid is the number of chromosomes sets that are found in the nucleus. Haploid cells are those that have only a single set of chromosomes while diploid cells have two sets of chromosomes. Mitosis is the process of creating two diploid daughter cells genetically identical to one diploid parent cell. It is essential for growth and development. Mutation is a change in the genetic code. If there is a mutation during mitosis, there is a genetic mosaic. Meiosis produces haploid daughter cells with one copy(1N) of genes from each parent diploid cell. It is a precursor to fertilization. Fertilization brings two 1N meiotic gametes (gametes are reproductive cells - eggs and sperms) to come together to form a 2N diploid cell. Half the genetic material is from mother, the other half from father. Details of Mitosis and Meiosis are beyond the scope of this blog.
Genetics controls inheritance. Gregor Mendel first identified the laws of inheritance. Meiosis + fertilization is needed for Mendelian inheritance. Genes control a trait. Alleles are a specific part of genes that control the variations in that trait. Genes do not occur in pairs while alleles occur in pairs (one from each parent). For traits controlled by a single gene (like color of a pea pod), the variation can be recessive or dominant. If green is dominant and yellow is recessive, then crossing a green and yellow would result in green because it is dominant. The resultant pod is called heterozygous since have both the green and yellow alleles. If we cross two of these heterozygous together, a Punnett square can be used to calculate the probabilities for the offspring. It works out to three greens for one yellow. Similarly other breeding scenarios can be analyzed, and probabilities calculated using Punnett squares. Some genes are not present on both copies – classic example is male is XY chromosomes and female is XX chromosomes. There are not the same set of genes on X and Y despite their pairing. There is a different pattern of inheritance here and it depends on who is mom and dad and the sex of the offspring. Green color blindness is X linked recessive. Muscular dystrophy is another. It can also be studied with Punnett squares but with a small twist. The chromosomes are randomly and independently inherited from each parent by any offspring. So, for two traits on two different chromosomes, multiply the probability of each trait for the combination to occur since they are independent. This is called independent assortment.
Homologous chromosomes refer to a pair of chromosomes having the same gene sequences, each derived from one parent. Sometimes the two cross over and a part of one links with a part of another to give a new chromosome sequence. This is called recombination. This is a recombinant gamete. If two genes are close together in a chromosome, they tend to stay together in the chromosome. However, if they are further apart, recombination may put them on different chromosomes in the pair which results in a recombinant gamete. This complicates probability computation of offspring’s traits (does not follow independent assortment) and is beyond the scope of this blog. Also beyond this blog is how genetic maps are created in practice and how complex traits controlled by multiple genes are managed in genetics. A lot of traits are controlled by multiple genes.
Mutations are the ultimate source of all genetic variations. The most common cause is an error in the replication during Meiosis that results in a change in the base. Mutations do not happen when we need them. They are random when they happen (relative to need). Some mutations do not matter. Many mutations are bad. Rarely, a mutation is good. After mutation, the new variant may spread in the population. Over time, mutation generates a lot of variation in natural populations. Traits controlled by multiple genes also show a lot of variations in natural population over time. In Humans, there are 63 mutations per person per generation. This is quite high!! Mutations increase with father’s age. Most mutations come from the father. Even though the probability of a good mutation is low, and timing is random, it along with natural selection is a key driver of evolution.
The way evolution occurs is that mutations are constantly and randomly occuring all the time. They happen mainly when there is an error during replication of the DNA during the biological process called meosis. These mutations spreads through reproduction and causes variations in a population over time. Some of these mutations have no effect. Others are actually harmful and causes that strain to fail to survive over time. Others are good mutations, that gives a new trait to the species. Then natural selection takes over. The variants that are better adapted to the environment survive and produce more offspring. Over time they become dominant in the population. Some members of the population without the mutation are still there in the population. This is how species evolve and genetic mutation coupled with natural selection is what caused evolution from simple living things to humans. There is still no clear explanation using science on how life first formed or how consciousness and higher-level cognitive skills in humans evolved. Looking at it from a distance evolution has the appearance of design. But nature has had billions of years for the process to cause all the evolutionary changes that we see.
Are human traits controlled more by genetics or environment? The answer is both. But degree of contribution of each varies.
Isn't it interesting that random mutations are a key to understand evolution of life and quantum mechanics which is about uncertainty is the key to understand the universe and its evolution?
As I indicated there is not clarity from science on how the reflective introspective consciousness humans have, and higher-level cognitive skills emerged. Is atman in Hindu philosophy similar to consciousness or some superset? Is there a divine hand in the injection of the reflective introspective consciousness humans have into the biochemical body? That has to necessarily be true for atman = brahman. I don't know.
Comments
2. Osho has an interesting take on scientific analysis. When water was unknown, there was one unknown entity. Then we analysed water & now we "know" as H2O. In the process, we have increased knowledge but also we now have two unknowns H & O !! All research (including origins of life, DNA, RNA, ...) increases knowledge and paradoxically, also ignorance! So, it may be impossible to reach a stage of complete knowledge of reality + zero ignorance by "scientific " analysis!
3. What might be "reality" and how might we "know" it without encountering the dilemma posed by scientific analysis, as above. That might take a whole new blog, so I will just pose the question here.