Tuesday, March 13, 2007

Scientists Say Darwin's 'Tree of Life' Not The Theory Of Everything



ARTICLE: physorg.com

AUTHOR: Lisa Zyga

COMMENTARY: Allen MacNeill

First the news item, followed by some commentary:

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There is only one figure in On the Origin of Species, and that is a tree diagram. As Darwin’s model for the theory of evolution, he used the Tree of Life (TOL) to clearly and visually explain the interrelatedness of all living things, implying that from one common ancestor (the root) sprung branches, which produced smaller offshoots as genetic progeny, etc.

In this model, similarities between species reveal a common ancestor, and differences result from (and explain) Darwin’s main catalysts: competition and natural selection, which generate improvement in future generations. As a simile, the TOL served a vital purpose for introducing the theory of evolution to the community in an understandable way. Although there is no external evidence to support the idea that evolution is inclusively hierarchical, many evolutionists believe the TOL provides an accurate general representation of the history of life, which could potentially be completely reconstructed by knowing the relevant data.

In recent times, however, a minority of biologists and evolutionists have questioned the accuracy of the TOL hypothesis, including W. Ford Doolittle and Eric Bapteste. In a recent paper in the Proceedings of the National Academy of Sciences, “Pattern Pluralism and the Tree of Life Hypothesis,” the scientists investigate the shortcomings of the TOL, as well as propose alternative models that would better explain how to classify the history of evolving life forms.

Much of the initial concern over TOL was provoked by biologists studying the complex relationships among prokaryotes, the most primitive life forms that include bacteria and archaea. Prokaryotes have a much simpler DNA structure than eukaryotes (all other life forms). Because of this, prokaryotes often transfer their DNA via processes such as lateral gene transfer as opposed to vertical gene transfer (direct transmission form parent to progeny) which is the basis for the “phylogenetic” (evolutionary relatedness) TOL scheme.

“Surely a tree is the right model for most multi-cellular animals and plants,” Doolittle explained to PhysOrg.com. “Thus the TOL is great for fossils and museums and dinosaurs and most of visible life, over the last billion years. But unicellular eukaryotes and prokaryotes represent the bulk of the biomass and diversity of life on earth, as well as the first two-thirds of its history.”

In their paper, Doolittle and Bapteste highlight research that shows other causes of genetic modification, suggesting that evolutionary history is more complex than described by the TOL. For example, recombination, gene loss, duplication, and gene creation are a few of the processes whereby genes can be transferred within and between species, causing variation that’s not due to vertical transfer. These transfer methods give results that don’t fit on the TOL, including species that cannot be traced to a common ancestor.

While such diverse methods might appear to obviously point to a more complex nonhierarchical evolutionary scheme, Doolittle and Bapteste explain that the TOL thinking persists due to confusion between the roles of “process” and “pattern.” The above methods are processes and are widely accepted by modern evolutionists, whereas the TOL is a pattern that, as Doolittle and Bapteste explain, has been ingrained in biologists’ minds from early education as a single, unifying model. As the researchers explain of the current biology scene, “We may be process pluralists, but we remain pattern monists.”

If this combination of thinking seems to clash, Doolittle and Bapteste suggest that the Western philosophical tradition of thinking in universal patterns has caused biologists to cling to classification without realizing it. The authors point out that many algorithms used to study evolutionary hierarchies impose or extract the TOL structure due to their intrinsic design. TOL is a paradigm that has stuck. But Doolittle sees ways to alter this mentality.

“Sure we can [re-train Western thinking]. That's what ‘postmodernism’ is about,” he said. “I would agree that the need to classify might be built in, but the coupling of this practice to a specific theory about what classifications are ‘natural’ is surely not.

As an alternative to the TOL, the scientists suggest that relationships among life forms may be represented by whatever model fits for a certain purpose, a certain taxonomic group, or a certain scale. In contrast to pattern monism, they call this belief “pattern pluralism.” While parts of evolution certainly are tree-like, other parts may be nets or webs or other complex models. Most importantly, however, there seems to be no “theory of everything” in evolution, no metanarrative to unify all life forms.

“In 2006, our understanding of evolution at the molecular, population genetic, and ecological levels is rich and pluralistic in character,” the scientists conclude, “and does not require (or justify) a monistic view of the phylogenetic pattern.”

As for any blow to Darwin’s ego, the scientists point out that he never wrote about reconstructing the tree in an attempt to relate every living thing, but rather used the model as a general guide.

“I'd like to think he would adjust,” Doolittle said about Darwin. “After all, his theory was developed before there was any understanding of genetics and when bacteria were still believed to be spontaneously generated.”

REFERENCES CITED:
Doolittle, W. Ford, and Bapteste, Eric. “Pattern pluralism and the Tree of Life hypothesis.” PNAS, February 13, 2007, vol. 104, no. 7, 2043-2049.

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COMMENTARY:

Ford Doolittle has been saying this for many years, and has been joined by Lynn Margulis, who has argued that the concept of "species" does not apply to prokaryotes.

But, that's not what I want to talk about. What I want to talk about is how "intelligent design theorists" quote-mine and otherwise distort reality to the point of outright lying. Why do I say this? Because former lawyer and professional propagandist, Casey Luskin, has a postat Evolution News, propaganda outlet for the Discovery Institute in which he says

"By invoking insufficient data, horizontal gene swapping, rapid evolution, and other ad hoc explanations, Darwinists reveal that neo-Darwinism is trying explaining away the data; it is not explaining the data. Perhaps the inability to construct robust phylogenetic trees using molecular data stems from the fact that common descent is simply wrong."

And the alternative? Why, magic of course. All of the living forms on Earth today were created, all at once, on Tuesday 25 October 4004 BC at 9 AM...or some other time in the past, exact date unspecified. Because, of course, that is the only alternative to common descent. Either you and your siblings are the offspring of your parents (i.e. common descent) or you aren't, and if the latter is true, then you must all have been created separately, not by your parents, but rather by God...excuse me, the Grand Omnipotent Designer. And with your memories of your childhood already inserted into your minds, so that the jarring discontinuity of your separate creations would not disturb you too much...would lead you, in fact, into the damning conclusion that you were, in fact, the offspring of your parents, and thus consign yourself to everlasting torment in the lake of fire.

Or not. You see, this is what the kind of egregious propagandizing of the folks of the Disco Institute leads to. Not discussion of the science of biology on its merits, on the basis of reason and evidence, but pure assertions without any alternatives at all (not that they want you to read in public, anyway).

I'm tired (our new baby is keeping Leah and me awake at night), and so I'll sign off now. But damn, people like Luskin just make me want to scream sometimes...

"Against stupidity, the gods themselves contend in vain."
- Friedrisch Schiller

--Allen

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4 Comments:

At 3/14/2007 04:15:00 AM, Blogger BC8 said...

In their paper, Doolittle and Bapteste highlight research that shows other causes of genetic modification, suggesting that evolutionary history is more complex than described by the TOL. For example, recombination, gene loss, duplication, and gene creation are a few of the processes whereby genes can be transferred within and between species, causing variation that’s not due to vertical transfer. These transfer methods give results that don’t fit on the TOL, including species that cannot be traced to a common ancestor.

I'm a little confused by this paragraph. What does "recombination, gene loss, duplication, and gene creation" have to do with gene transfer "between species, causing variation that’s not due to vertical transfer"?

Second, Regarding Luskin's comment:
"By invoking insufficient data, horizontal gene swapping, rapid evolution, and other ad hoc explanations, Darwinists reveal that neo-Darwinism is trying explaining away the data; it is not explaining the data. Perhaps the inability to construct robust phylogenetic trees using molecular data stems from the fact that common descent is simply wrong."

I have to wonder just what this lawyer thinks the genome looks like? Does he think that close species like humans and chimps have vastly different genomes, but those differences are "explained away" by invoking horizontal gene transfer? As far as I know, invoking horizontal gene transfer is unnecessary the large majority of the time, but if you want to explain the genomes of "higher" organisms, and fit all the "higher" organisms into the TOL, you need to consider horizontal gene transfer.

 
At 3/14/2007 04:49:00 AM, Blogger Lee Bowman said...

Lisa Zyga's comments mention lateral gene transfer for prokaryotes, and the modifying of the TOL concept to conform, and cites Doolittle and Bapteste's research.

But according to commenter Allen, there's only two possibilities: Common Descent by RM/NS, or instantaneous creation event(s) (Genesis account).

I propose another possibility, call it Common Designer, or CGE (Cosmic Genetic Engineering). Not provable, but arguably possible. The method would entail code alterations. Regarding your rebut, are you quoting from a religious tenet Allen, or do you really believe in 'omnipotence'. There's no such thing, anymore than there's an infinite quantity of anything else.

This planet is obviously a genetic workshop, and the 'designers' may be many, varied and not omnipotent in the least. With the current ID hypotheses, the Biblical view of creation is not the contender, so drop the straw man arguments, unless your debate is with AnswersInGenesis.com

The evidence is gradual changes for adaptation and diversity (micro), and 'punctuated' alterations that point to gene alterations by intelligent means (speciation). Due to the times involved, instantaneous ('magic') means are simply not a viable presumption. Also, the fact that population isolation may lead to species alterations, and even extirpation, radical species changes by purely naturalistic means have not been demonstrated.

Design, purpose, aesthetics, and complex synergistic systems are everywhere in nature. A fly is an engineering marvel, a mosquito (flying syringe) even more so. The retractable stylet and surrounding labial sheath with anticoagulant glands on either side point to design. The vertebrate eye, with no 'look ahead' ability, would never evolve stepwise, since the intermediate 'selected' random mutations would 1) never occur, and 2) if they did would not be selected (no immediate advantage). Co-option (exaption) might happen rarely, but never to the degree that would solve the 'gradualistic' dilemma.

Simply stated, millions of years (and only post Cambrian for vertebrates) does not lead to complexity (in reality, there is no one word to describe it). Belief in a personal (and perfect) male deity is not a prerequisite to buy into the design paradigm. The evidence, and one's willingness to at least consider it, is a first step to opening a new door. Science is not harmed by the concept. The tyranny of enforced belief in Darwinian evolution is what hurts not only science, but open inquiry.

 
At 3/14/2007 08:43:00 PM, Blogger BC8 said...

The vertebrate eye, with no 'look ahead' ability, would never evolve stepwise, since the intermediate 'selected' random mutations would 1) never occur, and 2) if they did would not be selected (no immediate advantage).

I don't believe that for a second. Looking at the varieties of eyes in the animal world, it's clear that simple eyes exist and are functional, and that complex eyes exist and are functional. In nature, there are so many variations on the eye, that it's not hard to see that transition from simple eyes to complex eyes could happen in a stepwise fashion. And the simplest eyes are simple enough that it isn't so hard to imagine them coming into existence. By in large, I consider the eye argument to be just another drum to for ID proponents to beat. It doesn't convince anyone in the know, but it makes an impression on laypeople. The only way you could consider this to be irreducible is if you think purely about the modern, complex eyes of vertebrates and ignore the fact that simpler eyes exist and could still function quite well.

 
At 6/21/2007 02:49:00 AM, Anonymous Anonymous said...

in concerns to the eye. how it is postulated that the eye was first conceived is by saying that mostly all cells have a sensitivity to light. (fair enough so far). then, by a *random* mutation a small pit was created that allowed an angling mechanism to be enforced for the organism to derive (in minute amounts) where the light is coming from. then since this is a favorable trait. it is kept and advanced up to the current complex eye by adding mucus and a lens.

nonsense! so *random* mutations are occuring for all forms of life to create an eye? random... im sure. of course this is over X amount of years too. nevermind that those same X amounts of years could've been used against such a *random* mutation by maybe the pit become a prime area to become infected. and if this is happening over X amount of years, then it can be assumed that the same creature is not living that long, but rather passing this mutation along to its offspring. which, if my notes are correct, is impossible. i believe a mutation in the skin (which is what this is as far as i know) is called a somatic mutation which the mutation is not passed on to offpring because the cells involved have no gametes.

 

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