Monday, 13 September 2010

Why Evolution is True pt1

Firstly, I’d just like to correct a common mistake regarding the notion of missing links in the fossil record. Fossils do not occur regularly; they are extremely rare events that require specific conditions to become successful artifacts. The mere fact that we possess as many as we do is testament to the amount of life this earth has put forth in its long history. Hard structures, such as bones and enamel, in organisms do fossilize much better that soft tissue or cartilage for soft tissue requires conditions even rarer than normal for fossilization. Bones and enamel do offer substantial evidence to work with for paleontologists but soft tissue fossils offer much more. 

Stephen Jay Gould wrote about some amazing soft tissue fossils in the Burgess Shale deposits in fantastically rich detail in the book ‘Wonderful Life’. This is a fascinating treatise on the details seen in fossils even dating back hundreds of millions of years. My point is that although there are many stages in the evolutionary tree that perhaps are missing, due to incremental changes and slow gradual steps through generations, we are certainly not experiencing a profound lack of evidence or examples of these organisms. I am not making an excuse when I talk about the rarity of fossil. Tectonic plate subduction and erosion may have destroyed a good deal of possible fossils before we evolved to get to them and the natural laying of sediments is not the correct process for fossil creation.

Take the human evolutionary lineage. In order to fully understand how our evolution took place I believe it is crucial not to view our history, and indeed evolutionary history as a whole, as a progressive ladder from single cell creatures advancing to humans at the top. Rather, earth’s natural history is better observed as a continued expansion of adaptation to changing environments and all species alive of earth today are equal on the outermost twigs of a great bush. Humans departed from our last common ancestor with chimps sometime about ~3 million years ago. There is much fossil evidence for presuming that our two species are closely related and for establishing such a lineage. A cursory look at the modern literature on human ancestry should reveal a whole list of names ranging from Australopithecines to Homo and more. There is always debate about whether or not a newly discovered human ancestor fits the current theories, but there has not been serious debate about the fossils being human ancestors for many, many years now. 

As you can see from these fossils there is adequate evidence suggesting our evolutionary descent. Some of these fossils do indeed lack a complete skeleton, but then again very few fossils of other lineages show complete structures due to the harsh conditions of erosion post-burial and decomposition of exposed body-parts prior to fossilization. Like I said before, teeth are more likely do fossilize than any other part of a body due to their high enamel content. And a lot can be discovered from studying a tooth, such as dietary habits, size of the host, conditions of life and death, age, etc. Neanderthalensis is still debated as to where in the human lineage its proper place should be but it is clear from the specimens we do have that while it was very similar to Homo sapiens, it was indeed a separate species. Homo erectus also attains the position of separate species and both these two lineages became extinct through unknown causes. Neanderthalensis did not perish because it possessed lower cranial space; in fact this species of Homo retained a larger brain than every present Homo Sapiens. Indeed, according to mDNA tests, our own species only just overcame extinction resulting from an environmental bottle-neck back in Africa some time ago and it was only when our adventurous ancestors migrated to fairer pastures that our species excelled and proliferated. Extinction, a terrible outcome that has happened to 99% of every species that has ever evolved on earth, could have very easily included us on its morbid list of scalps.

I will take time to point out here that while fossil evidence of human evolutionary ancestry and cousinship with the other great apes is quite profound and does seem to suggest the theories proposed there has been no greater leap in the understanding of evolutionary lineages than the sequencing of the human genome. Perhaps the crowning achievement of this endeavor was the discovery of Endogenous Retroviruses (ERV’s) and their unique placement on chromosomal pairing. These viral infections from the distant past reverse-transcribe themselves onto the RNA and DNA of an organism unfortunate enough to encounter them. They can play a role in autoimmune diseases and cancers and are difficult to remove once they latch themselves onto germ-line cells (sperm and egg). However, the key fact that I want to point out here is that in the human genome project found thousands of such ERV’s in their work that comprise nearly 8% of our entire genome. They only affect viviparous mammals (all mammals except for Monotremes, of which the Platypus resides) and seem to do a whole host of things such as protecting the infant from the mother’s immune system.

Now, closely related species have closely related DNA sequences and comparison of human DNA with other primates shows the most similarity with Chimps and Bonobos, followed by the gorilla, and then the orangutan. Only 1.2% of the bases differ in the 95% that is aligned with chimps. Biologically speaking, we are African apes. Our DNA sequences are a record of our genetic history, having suffered many deletions and alterations in the past. These changes include minute alterations, such as single base changes. They also involve very large rearrangements involving DNA segments thousands or millions of bases long.

Here’s where ERV’s come in. Since abnormalities in genetic sequences function as specific markers that can indicate whether one sequence is a copy of another. Our chromosomal structure has diverged from that of the chimps by an end-to-end joining of two chromosomes called a ‘fusion’. New genes have been formed by copying and modifying old ones (called ‘duplications’). Old genes fade away (into ‘pseudogenes’) and the DNA of genetic parasites (ERV) is added to chromosomal DNA as ‘insertions’. The generation of each duplication or pseudogene and the insertion of each parasite is a random and unique event, given the literally billions of possibilities on a chromosome. And yet we share particular duplications, pseudogenes, and insertions with other primate species. This shows that we and other species possessing a uniquely arising genetic construction (because many other species share some, but not all, of the same anomalies tucked away in their genes) are related by descent from an ancestor in which the singular genetic change occurred.

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