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Daddy4UdderSlut -> RE: God, Darwin, and Kansas (8/7/2006 8:35:13 PM)
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Mastermind,
I have to say I appreciate the sincereity of your response, as you seem to be treating this as a discussion, and not an arguement to be won. So, first, hat's off for that.
I am a scientist, a chemist by degrees, but with a fair amount of university biology training as well (biochemistry, microbiology, genetics). I will try to be careful to qualify any statement for which that's appropriate though.
I am not aware of a separation between fact and theory of evolution. Hopefully I won't insult you with the following, but here is an overview of what is required for an evolutionary process:
1. A means of encoding all of the "traits", i.e. form and functions of an individual. For most organisms, this is done by the DNA. The DNA is, if you will, an instruction set for constructing the individual, as well as for its operation. The construction portion is still fairly hazy, but the interdisciplinary field of Developmental Biology is making strong inroads into these mysteries - that is, how do we get from a single fertilized egg to a complex and fully functioning animal? Understanding the operation is further along - likewise there are likely decades yet before this understanding is completed, but a lot is already known, thanks to the fields of Genomics, Proteomics, and the new Systems Biology.
2. A means for passing the instruction set from parent to "child", and I use the latter term loosely, as asexual reproduction by bacteria and even the reproduction of viruses by the host cells still follows the general process.
3. A means for introducing variation into the instruction set received by the "child". That is, a mechanism for introducing arbitrary variation of those traits passed on by the "parent". Considering the population as a system, this is a mechanism for "experimentation" (no I am not implying though controlled experimentation or a guiding hand). This variation takes two principle forms - random "mutations" of bases in the DNA, and random shuffling or "recombination" of the parent genetic codes. In sexual reproduction, there is also the random mixing of traits from mother and father to generate the diploid genes of the child. There are of course other specific forms of variation, but what's already been discussed is sufficient.
4. An "environmental selection mechanism". While often a survival threat to individuals within the population, that's not necessary. All that's necessary is a mechanism for differentiating who is likely to reproduce, and how much, since it's the act of reproduction that actually determines the form of the generation that follows.
That's all you need. With such a system, you will necessarily get a greater preponderous of the traits of individuals who are better suited to reproduce in the succeeding generations. Depending on the strength of the environmental pressure to discriminate between "fit" and "unfit" individuals, evolution will proceed more or less rapidly. A strong environmental pressure, like a drug that kills 99% of the microbes in a patient's body before they can reproduce, rapidly selects for the fittest individuals.
I have carried out computer simulations of evolution. Not for the reason of abstract curiousity, but to optimize otherwise "intractable" mathematical functions (applied math work). In these simulations, you have an environmental pressure or "fitness function", you have random mutations, random shuffling of the traits, and generations producing offspring. Individuals in the population constitute solutions in progress to the optimization problem. It works, and it works extremely well to optimize functions. You can find this sort of work under "Genetic Algorithms" or "Evolutionary Optimization". Certainly once you've done that kind of work, you know that evolution can solve very difficult problems, and can move very far within a relatively small number of generations (usually 100-500) to achieve optimization.
As far as historical evidence for organisms essentially tuning to prevailing environmental conditions of their period, we know for example that during the ice age, animals developed that had thick fat insulation and heavy fur coats to withstand the cold, e.g. wooly mammoths. They weren't there before the ice age, and they weren't there afterwards. They developed as variants on existing animals over a relatively small number of generations and dissappeared the same way.
I don't think that nature tends to either move towards or against differentiation - nature doesn't care. Because of the mechanisms of genetic variation though, individuals are constantly being created that are different than their "parents". If that difference creates a reproductive advantage - for instance, greater height to reach food above the ground that other individuals cannot, then it tends to be perpetuated by straightforward the straightforward probabilistic reinforcement of the traits that are desirable under the prevailing environmental condition. If not, then the trait will tend to be eliminated or "averaged out".
When you "upset the balance of nature", creating a different environment, you will tend to get development of modifications that work better under the new environment, as in the case of the Wooly Mammoth. There is really no limit to the extent of such modifications, except in the case where a survival pressure is very strong and virtually no individuals in the population are able to survive to produce offspring. Then the species may simply be wiped out within a few generations.
What constitutes a species is actually somewhat arbitrary. The concept is extremely useful, because it allows organisms to be grouped and the groups thought about collectively, a simplifying principle if you will. But there is no fundamental line dividing species, rather there are just widely agreed upon conventions for what is "different enough" to constitute a species. Furthermore, distinctions may be compared in "phenotype" or observable traits, or, increasingly, by genotype. Indeed, taxonimists argue about that sort of thing all the time!
Certainly one of my weakest areas in biology is what is now called "Evolutionary Biology", which studies not the process of evolution or whether it exists, but rather the historical process that evolution has actually taken for life on our planet - basically trying to look back in time and understand the timeline from "Genesis" if you will until today. This field is a mixture of physical evidence, theory, and imagination, as it must necessarily be, when looking back millions and even billions of years ago.
When you look at an evolutionary tree, a taxonomic tree, you are looking back into time, even if you look only at extant (as opposed to extinct) species. The more distantly organisms are related, the further back in time they diverged from one another in the evolutionary process over the millenia.
It may seem odd for example that you might share some kinship with a plant. But, even looking at plants today and humans today, considerable homology (correspondence) is found in their DNA, even though they diverged by most scientists' reckoning over 1 billion years ago. In fact, in the drug industry, where we study human biology extensively, if a new protein is discovered, and it's folding structure and its function are unknown, we use as the starting point for our analysis the closest known related protein, which often comes from another animal. The reason that this works is that the common ancestor gave an ancestral protein both to us and to the model organism. While its structure has been modified over evolutionary time in both organisms, there is also a pressure for it to remain the same, if it is important. Hence there is normally very useful structural and functional correspondence at the protein level - that is, between homologous proteins from different species.
I don't want to go down too much into the weeds of how whole genomes are compared, but that is the subject of the new discipline of Comparative Genomics, only made possible by new technologies allowing very rapid sequencing, as the DNA code for an entire organism is huge. There are in fact multiple ways to calculate such a metric as "DNA in common". Broadly speaking though, it means that they found an overlap between the two genomes of 98%, meaning, they found corresponding genes for 98% of those genes evaluated, where correspond means "similar enough" at some threshold chosen by the analyst. It doesn't mean 98% of genes were *identical* at the sequence level, it means 98% of the genes were very similar. For more on this read about "genomic sequence comparison", "sequence alignment" and the like.
Whether it's due to the use of new methods of analysis (such as comparative DNA analysis to look into the existing physical evidence, or the discovery of new physical evidence (some new fossil remains found that reveal a previously unknown species), the historical tree of biology, including those branches close to humans, continues to be revised. This though doesn't call into question the existence of evolution as the historical and present process that transforms and adapts the form of living things. It merely revises the historical relationships of exactly what came when, and from where.
As far as historical evidence for evolution causing branching and divergence, this can be seen just by looking at the fossil record. Not only have species become "obsolete" and extinct which didn't compete with the "new models" under new environmental conditions, but life has become increasingly diverse over geologic time. The conceptual basis for this is simple - any time an "experiment" produces something that has a new advantage (fills a previously unsatisfied or poorly satsified ecological niche), it will be preserved and extended through reproduction and further variation. It's only in the past few centuries, due to the proliferation of man and the ascendency of his technology, that the earth is decreasing in biological diversity - man is wiping everything else out, whether by killing as nuisance, as food source, or by toxic effluent, elimination of habitat or food supply.
Evolution does indicate that all species had a common ancestor. The theoretical evidence for this is just to mentally run the divergent evolutionary process backwards, and you'll see it becomes convergent when one runs it backwards in time. While we don't know precisely what the ancestral organism(s) are, a lot is known about this, because the structures and DNA that we have today, are simply modified versions of what has come before, and so, at the molecular level, one can also look back into time. There is for example, considerable evidence to indicate that Eukaryotes (which have a nucleus) have arisen from symbiotic absorption of one prokaryote into another. See endosymbiotic theory, for example here:
http://en.wikipedia.org/wiki/Serial_endosymbiosis_theory. It may seem fanciful at first, but there is a lot to back this up.
People tend to be very interested in themselves (their own species), so if you want to look a bit into the taxonomy and history of human like creatures, here is a pointer into Wikipedia:
http://en.wikipedia.org/wiki/Hominidae
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