The Crumbling "Tree Of Life"

I've been debating another atheist online the past few days about the topic of the "evolutionary tree of life" (or "phylgenic trees"). Evolutionism assumes that all life evolved from common ancestors and that most similarity between organisms is because of this common ancestry. However the classic "tree of life" is falling apart as science has descended into analyzing genes and DNA. The stories they thought they had figured out, with a tidy tree of branching organisms from the beginning of life until now, is looking vastly different when you study the genes rather than the physical (morphological) structures and features. This really isn't that surprising to people who believe that everything did NOT evolve from common ancestors. However it's seriously shaking up the Neo-Darwin community as it sets fire to one of the core tenets/beliefs. The following is one of my responses to the atheist I've been debating. The topic is about how the "tree of life" is having some very serious problems recently. The other point I've been making is that the reason for these problems is that the "tree of life" is based on an assumption first with the data and information then placed upon that tree by scientists in order to make it all fit their presumptions. It's a case of, "This is how we believe it is, so this is how we'll make it look."


EvolutionNews.org (May 12 2009):  A Primer on the Tree of Life (by Casey Luskin)

http://www.discovery.org/a/10651

"“Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth,” but because “different genes told contradictory evolutionary stories,” the notion of a tree of life is now quickly becoming a vision of the past — as the article stated “today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded,” and as scientists quoted in the article said, “We have no evidence at all that the tree of life is a reality” or the tree is being “annihilated.”"

ScienceDaily (Sep. 23, 2011): Evolutionary Tree of Life for Mammals Greatly Improved
http://www.sciencedaily.com/releases/2011/09/110922141907.htm

This article does not discuss the major contradictions between molecular genetic analysis and morphological versions of the "tree of life" (which is one area where a great amount of conflict is arising), however it does give a good example of one of my other points, the fact that all these "trees" are generated with a substantial amount of human direction. The algorithms and systems are purposefully programmed and organized in such a way as to include, exclude, connect and disconnect things based on a set of pre-input criteria and adjustments. Essentially it's a case of telling the program, "This is how you must handle all this data and these are the bounds within which you will work and connect the dots." When you get down to it, the program is told what the scientists already believe, and must simply figure out the little in-betweens and unknowns based on the greater whole that's already assumed.

To quote from the article...

"To date divergence times on their phylogeny of mammalian families, Springer and colleagues used a "relaxed molecular clock." This kind of molecular clock allows for the use of multiple rates of evolution instead of using one rate of evolution that governs all branches of the Tree of Life. They also used age estimates for numerous fossil mammals to calibrate their time tree.

"We need to have calibrations to input into the analysis so that we know, for example, that elephants and their nearest relatives have been separate from each other since at least the end of the Paleocene -- more than 55 million years ago," Springer said. "We were able to put together a diverse assemblage of fossil calibrations from different parts of the mammalian tree, and we used it in conjunction with molecular information to assemble the most robust time tree based on sequenced data that has been developed to date.""

 There's a massive amount of calibration done on these "trees" in order to make them "turn out right". Otherwise they'd turn out VERY wrong. Garbage in, garbage out. In this instance, the scientists included a lot of known fossils and dates, "relaxed" the molecular clocks (mutation rates, etc.) to allow a vast amount of variability in mutation rates so that the mutation analysis and predictions would NOT end up outside the KNOWN bounds. This is basically building the tree themselves and telling the program to fill in the gaps based on the pre-constructed tree, and allow the program to use whatever mutation rate it needs to in order to achieve the results the scientists/programmers want. Wow.


Nature (27 June 2012): Phylogeny: Rewriting evolution
http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885

"Yet, says Peterson, the tree is all wrong."

""I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree," he says. The technique "just changes everything about our understanding of mammal evolution"."

This is a very recent example of how analyzing different parts of genomes and DNA return drastically different results in evolutionary relationships, something that should NOT be so all over the map for progressive step-wise evolution if it were true. Trying to extrapolate a gene backwards or forwards along the same kinds of understanding and lines as a "tree of life" results in dramatically different outcomes depending on the gene or genes included or analyzed, as if each gene has a completely different evolutionary history from the other, yet all these genes are supposed to be interconnected along ancestral reproductive lines and mutation.


Trends In Ecology And Evolution (June 2009): Gene tree discordance, phylogenetic inference and the multispecies coalescent
http://www.sciencedirect.com/science/article/pii/S0169534709000846

"Many of the first studies to examine the conflicting signal of different genes have found considerable discordance across gene trees: studies of hominids, pines, cichlids, finches, grasshoppers and fruit flies have all detected genealogical discordance so widespread that no single tree topology predominates."

 Telegraph.co.uk (January 2009): Charles Darwin's tree of life is 'wrong and misleading', claim scientists
http://www.telegraph.co.uk/science/4312355/Charles-Darwins-tree-of-life-is-wrong-and-misleading-claim-scientists.html 

"Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: "For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality."

"" More fundamentally recent research suggests the evolution of animals and plants isn't exactly tree-like either.Dr Dupré said: "There are problems even in that little corner." Having uprooted the tree of unicellular life biologists are now taking their axes to the remaining branches.Dr Bapteste said: "If you don't have a tree of life what does it mean for evolutionary biology. At first it's very scary -- but in the past couple of years people have begun to free their minds."

 Both he and co-researcher Dr Ford Doolittle stressed that downgrading the tree of life doesn't mean the theory of evolution is wrong just that evolution is not as tidy as we would like to believe."

 EvolutionNews.org (January 2011): Common Design in Bat and Whale Echolocation Genes?
http://www.evolutionnews.org/2011/01/common_design_in_bat_and_whale042291.html


On top of all this is the very serious issue of convergence, especially genetic convergence where identical or near identical genes appear in very disconnected lineages and have arisen entirely independent, yet are so shockingly similar even at the molecular level. As more and more genomes are being sequenced, species very distantly separated on the typical "tree of life" are showing some shocking genetic similarities in the convergent features they have independently evolved. These things cannot be explained adequately by common ancestry because of the rarity and sudden appearance of them, however there they are, as if entire chunks of functional DNA from one distant species were copied and pasted into a completely different organism separated by many millions of years of evolution. This is NOT what Neo-Darwinism expects to find or can explain. Neo-Darwinism requires slow gradual mutation (changes) of existing genes over large quantities of time in a generally stepwise fashion. But whole systems and structures of function are appearing out of nowhere and they just don't line up along a neat evolutionary path. This is not at all a problem for the Intelligent Design community as we don't assume first that all life is traceable back to common ancestors from beginning to end. However this is catastrophic for Neo-Darwinism because it relies so heavily on this belief that all things evolved from common ancestors way way back.