[i](I'm helping deludedgod to try to get some theists to respond to this.)[/i]
A few days ago I started a thread where a requested people to give me stupid myths of evolution. It was great and we assembled 30 things. Now, I realize that there are many theists who do not attack evolution, but the ones who do always beat the same dead horses. therefore, I have collated some of my evolution posts on this site as well as some old articles on evolutionary genetics I wrote, and assembled them into The fundamental axioms of evolution.
Theists, your challenge is to debunk this:
The axioms of Evolution
The statements of the average theist regarding evolution make it immediately clear to me that their understanding of evolution is roughly equivalent to a fish’s understanding of the game of chess. Therefore, to understand why they are completely wrong, you must first understand the axioms of evolution.
The first one is that organisms adapt to their environment through natural selection, meaning that the environmental factors both cull the herd and remove organisms with unfavorable traits, and propagate those with favorable traits. The mechanism for this is the second axiom: Evolution is brought about by genetic mutation. An organism cannot adapt to its environment per se. It is the genes that must adapt, and that process takes millions of years. The next axiom is that the determinate of what constitutes an advantage is the environment. The rest of it is really simple, Evolutionary models study this axiom because it is complex. An environment includes lots of factors like other animals, temperature, gas concentration, climate etc. etc. This axiom is the driver of evolution, the guide, Adam Smith’s invisible hand. Genetic mutation is random. It is up to the environment to nurture useful genes and ensure they get passed on, and to eliminate poor genes. This is the fundamental axiom of natural selection mechanisms. It is something that no theist I have yet encountered understands.
Therefore, we must understand the mechanisms of mutation and the functions of DNA.
DNA is made up of polymerated strings of bases, which are nucleotides bound to sugar-phosphate backbones. DNA has two functions:
Holds the code to create various proteins from amino acids
Regulating the rate of producing proteins: By definition, one gene is a string of nucleotides that codes for one protein
The language of DNA is base-pairs. DNA is entirely comprised of four molecules. Cytosine, Guanine, Adenine and Thymine. These are the nucleotides. The nucleotides are complementary. Like magnets, they will only fit to a certain opposite. G fits with C and A fits with T (A also fits with U, Uracil, but that is an RNA base). So there are only four possible base-pairs: CG, GC, TA and AT. But these four pairs will dictate every single protein imaginable.
There are four ways that DNA can innovate.
Intragenic mutation: Errors during mitosis can swap base-pairs around, creating new strings of bases, and a new gene
Segment Shuffling: Two different genes can recombine and form two new hybrids
Duplication error: Sometimes during mitosis, a parent cell will by accident only pass part of it’s genome to the daughter cell, thus it retains a redundant copy of a gene string. This copy is completely free to mutate based on random frequency probability.
Horizontal Transfer: During sexual reproduction, organisms exchange genes. If the organism is a diploid meaning that it’s offspring has the code of two parents, then it’s offspring will have a completely new genome, combing both parents. This is the most successful method of innovation.
There are two types of genes. Introns and exons, which have these separate functions. Exons code for proteins. Introns are mostly junk or redundant, but they flank all the exons. Sometimes they are just punctuation, dictating where a gene starts and stops, but their most important function by far is to regulate the speed of protein transcription, a mechanism we will look at it more detail later. Exons dictate how a protein will be assembled. They do this because a protein is essentially a string of amino acids or a polypeptide. Therefore, exons dictate the order of amino acids in a protein. They do this by representing each amino acid with a codon. A codon is three nucleotides. Three nucleotides make up an amino acid. There are 20 possible amino acids, but 64 possible codons, therefore, exons are highly sensitive. They are also sensitive because they are ordered very precisely. For instance, let’s look at a simple string of three codons in a gene: AGG CTT GCC. Now let’s assume that an extra base is accidentally inserted (Like a G for example). The new string would be totally different, it would look like this. GAG GCT TTG CC, so every base would be shifted down one, and the entire gene would change. This would be completely devastating. This is why DNA repair mechanisms quickly target such errors. On the other hand, Introns, which are not so sensitive or precisely executed, or are sometimes just junk or redundant, mutate based solely on random frequency. As there are 44 codons that don't correspond to an amino acid, these are used in introns. Therefore, the next axiom of evolution is that evolution is driven by the Introns. Obviously it is more complicated, Introns can become exons during shuffling/shifting, and exons can become Introns, and sometimes exons can be mutated harmlessly, so long as the mutation changes only a tiny chunk of the gene, but this axiom still applies.
Genetic drift drives evolution. Some mutations are good, some are bad, most do nothing, but through the endless cycles, organisms evolve. The analogy I like to use is the telemarketer. About 90% of people hang up on them, but the 10% who say yes make the enterprise quite profitable.
Genes which only have a regulatory role (like a mass of old paper, our genomes retain a lot of junk code) will mutate based on the random frequency probability. But a gene that codes for an essential amino acid will not mutate. When errors occur they are quickly repaired. Thus, throughout evolution, about 400 genes critical to all life have remained unchanged in three billion years. Such genes are called highly conserved genes. This is the common descent.
We now must look at the mechanisms of DNA innovation, and how they affect evolution. At the heart of evolution is mitosis. Every time a cell divides, its genetic material lines up and splits. As the DNA base pairs replicate, 6 billion bases have to go into the right place (at least for humans), this is really hard, the only way a nucleotide can recognize it’s counterpart is that the activation energy needed for them to bond is less than if incorrect nucleotides bonded, so if it takes place with an abundance of adenosine triphosphate, it is guaranteed some will end up in the wrong slots on the ribose-phosphate ring, thus forming new strings of genes. DNA controls protein synthesis. The proteins carry out every cellular function. When a protein is needed, the transcriptase enzyme for that protein is secreted, as this enters the cell’s nucleolus, it causes the chromosome containing the DNA to unwind, where a piece of single helix containing a particular string of base pairs is “cut” from the double helix by the enzyme. This piece is identical to the code of the protein. Using templated polymerization, free bases (a nucleotide bound to a sugar-phosphate) make the mirror image of this code, where the correct nucleotides are slotted in, A to T and C to G. Then the strand is peeled apart and the template is returned to the genetic code, where the new strand is ejected from the nucleus where RNA (differs only in one nucleotide and ribose instead of D-Ribose for the backing) called messenger ribonucleic acid (mRNA) is assembled from a second round of polymerization, the mRNA binds to a ribosome (a ribosome is a giant macromolecular protein assembling machine that just trundles along) in the endoplasmic reticulum, where it is run through it like a conveyer belt, as different tRNAs (transfer RNA) line up with the codons in order, bound to a specific amino acid, stitching them together before leaving the ribosome, creating the protein necessary for whatever function the cell needs to perform.
The next axiom we must understand is that phenotype depends on genotype and the genotype does not change very much. When I hear creationists talk of the incredible diversity of life, I laugh. What makes life remarkable is how similar it is. The greatest diversity in life is seen among the prokaryotes, the humble single celled bacteria. We have more in common with a mouse than an Escheria coli has in common with Mycoplasmodium genetalium. The phenotype refers to the trait. This is determined by external features and internal anatomy. Of course, today we understand that phenotype depends on genotype. The speciation variable is not that huge. A human shares 99% of his DNA with a chimpanzee. That means that 1% (5,000 genes) produces 5,000 proteins that the chimps do not have, or transcribes them at a different rate. We only differ in 2 amino acids (out of 22 known to life) but these two can create vast combinations of proteins. These proteins control advanced neurogenesis, hair follicle growth, skin collagen makeup, eye colour variables, hormone-stimulated growth, all the ways in which we differ from chimps. Evolution works with scaffolding. The vast majority of genes in all mammals are the same, the genes that control enzymatic response, angio and vasculogenesis, the genes that control immunological responses and stem cell arrangements, they control basic development of brain functions that all mammals have, they control metabolism, mitosis, apoptosis, sensory development, the development of spermatogenesis in male mammals and mammary glands in females. By far and large, the genome across the mammalian class is identical. Massive changes in phenotype are caused by a few changes in genes. Even with the simple banana, 50% of our genotype is identical. This groundbreaking work was done by Richard Dawkins, who wrote about the crucial part of the genotype in his book The Selfish Gene.
This axiom has a logical follow up: Small genetic changes can make massive phenotype changes. This is why the constant claims that “sometimes fossils are found in the wrong striations” is an idiot idea. In phenotype it may appear to be very different and cannot fit in the taxonomy, but now with recent advances in genetics, we can track tiny mutations with huge consequences, comparing genotypes with a keystroke. If the mutated gene in question sits atop a master chain, then a single mutation can make a huge change. For instance, in a petal flower, if a single protein is changed on the master chain, then a stem will grow in place of a flower.
Now that we understand the genetic mutation mechanisms, we must look at the next axiom. The mechanism of natural selection will nurture good genes and get rid of bad ones depending on how they affect reproductive capacity. Simply put, a useful trait will increase an organism’s survival chance, therefore it will reproduce more, therefore, the gene will become more prominent in the pool through generations. A bad gene on the other hand, will make it more likely for an organism to die out quickly without the chance to reproduce, and the gene will wane from the pool. This brings us to a mathematical axiom. The time taken for a gene to establish itself or die out depends on the Trait Advantage Gradient. Simply put, the more advantageous the trait, the more reproductive capacity and survival odds it bestows on it’s carrier, the fewer generations it takes to establish itself.
There is a good example of this for contemporary society. The survival advantage of trait is inversely proportional to the amount of time it takes. It is relatively easy to observe genotype transition today. For instance, in parts of Africa where malaria is most prevalent, the allele containing the single copy of sickle-cell anemia can be found in almost 100% of the population. Another good instance of this is common lawn grass. Consider dandelions, a totally nuisance type of weed. As people of suburbia ruthlessly take their lawnmowers to the grass, the dandelions that happens to have genetic combinations that inhibit it’s Auxin growth factors find it useful because they are far more likely to survive, too short to be cut by the blades. These pass their genotype to their children who in turn will be unusually short and survive the lawnmower blades while their tall counterparts perish and in time, a new species, the lawnlion, may arise.
This brings us to the next axiom: Natural selection has two necessary mechanisms
Mechanism 1: Darwinism: This means that individuals who have unsuccessful traits will not survive to reproduce and therefore be eliminated from the pool. This leaves only the advantageous genes.
Mechanism 2: Genetic Innovation: At the same time, organisms obviously must improve because if there was nothing to improve, there would be nothing to cull. Therefore, organisms can experience advantage mutations, and this is how we evolve.
Mechanism one is definitely favored by evolution. It is easier to destroy than create. Mechanism two takes vastly more free energy from the environment, but it is absolutely necessary, otherwise, we would all be little single celled organisms.
This brings us to the final set of axioms: Evolution works on individuals not species. This is one so many people don’t understand. For instance, I often hear theists say synchronized random mutations do not exist in nature, then they uphold this as proof of intelligent design/creationsim. They do not understand the fundamental axiom of genetic mutation every mutation has a prototype. We’ve been through this already. An organism has an advantageous mutation. It reproduces more than the other organisms because of this. The mutation gets passed to his children, they reproduce more because of it, they pass it to their children…mutations are not synchronized. With each generation, it will become more and more prominent in the pool, until it is universal. This gives the illusion of genetic synchronicity.
This brings us to another stupid theistic argument: I often hear the argument, “if humans evolved from chimps, why are they still here”. A foolish argument. We can apply the previous axioms to this. Evolution by gene drift works on individuals, not species. If the new combination is successful, the individual will have a greater survival chance and reproduce more, passing the new gene to his children. As long as a gene exists in the pool, the individual and his offspring have the chance for further advantageous mutations to occur (and occur they will, for mutation happens during every single undergoing of mitosis, which happens millions of time per day). The survival of an organism matters little so long as s/he had reproduced, is the gene that matters. An old species does not “disappear” if a new one arises. It might disappear only if the new species is superior and destroys its predecessors (early humans most certainly undertook genocide against the Neanderthals).
This brings us to final axiom speciative divergence occurs when a mutation prototype’s offspring differ so much that the gametes will no longer fuse with those of the prototype’s species. This can happen quickly or very slowly, it depends on karyotype.
And, finally, the difference between micro and macroevolution. Theists often say: I believe in microevolution, I can see small changes in an organism, but I refuse to believe in macroevolution, the idea that organisms can completely change. This is an idiotic argument which uses subjective wordplay. At what point do we decide whether the cumulative mutation has been so much that it is macroevolution? If the organism changes color? During a speciation split? If it grows another eye?
In fact, macroevolution as so many successful mutations occurring within a pool that the phenotype of the organism is totally altered. This is essentially the same as microevolution, just over a longer time frame. DNA changes are not a microevolution topic. This is an extremely common misconception. Genes are very powerful, and they can easily massively alter the phenotype of an organism. You seemed to define macroevolution as speciation. That is, that the cumulative genetic change in an individual and their descendants has been large enough that the gametes no longer match with the original species of the prototype, that is the very first organism of a species that carried a mutation with a slight advantage, which over many hundreds of thousands of years and generations, eventually became so much that the gametes will no longer fuse with those of the original species, if it still exists.
The trick to macroevolution is a probability function called cumulative mutation. A prototype organism is bestowed with an advantageous mutation. He has increased survival probability and passes it on to his children. He reproduces more than the other organisms of the same species because of this advantage. So do his children, and the gene becomes more and more prominent in the pool. Since there are more of this mutated version of the organism of the sample, the probability function states that there is a higher likelihood that one of the mutated children will chance upon an advantage mutation, and then...the cycle continues. Go through this 200 times, and the organism will be unrecognizable. This is macroevolution.
The next axiom of evolution is that all functions must be autoregulatory. Interestingly enough, this is more than enough proof to debunk the idea that God created life. Any engineer would snicker at the sloppiness and inefficiency of the biosystem. Adenosine triphosphate synthesis during respiration takes about 200 steps, when it could reasonably be done in about one third that. There are major nerves which for some reason take huge wasteful loops before reaching their destination. The reason for all this is that biomechanisms are autoregulatory. That means they produce molecules that will automatically perform the necessary functions. A good example is the amphipathic bilayer of the cell membrane. This is not a very well designed structure, it has poor integrity. A designer would laugh at it. But evolution utilizes it because amphipathic molecules will automatically form a membrane. Try it yourself. Get a hydrocarbon chain like oil, mix it with a water soluble phosphorylate, add water and...it should form an impermeable ring. That is a eukaryotic cell membrane (if you are interested, the substance that makes it is cholesterol). The molecules automatically arrange themselves correctly. Every biological functions does the same thing.
A designer would choose far better materials. Evolution has no foresight, no objective. It is a driving force that reeks of impatience. A benefit now may be worthless in a million years. Intelligent Design (The idea that life was too complex to arise by evolution) likes to use the Watchmaker analogy, that if you found a watch, you wouldn’t assume it assembled itself. But evolution is a blind watchmaker. It cannot see what it is assembling, it tries different parts, but if it hears the tick, it knows it works.
Another example of the autoregulatory process is the fundamental autocatalytic cycle of life:
What makes life remarkable is that it needs no designer, it is an autocatalytic cycle, bound to happen by the laws of chemistry, fixed in the nature of molecular interaction. It’s processes are self assembling, it’s mechanisms self-regulating. The autocatalytic cycle looks like this
DNA replicates through templated polymerization, assembling polynucleotides out of free nucleotides
The polynucleotides are used to assemble polypeptides out of amino acids
The polypeptides catalytic function are used to replicate DNA through templated polymerization
And the cycle continues
This concludes my piece on evolution.
[b]Note:[/b] You can also check out [url=http://www.rationalresponders.com/forum/yellow_number_five/evolution_of_life/4756]Myths about evolution.[/url][/i]