Horizontal Gene Transfer and Intelligent Design Theory

AUTHOR: Graham Lawton

SOURCE: "Why Darwin was Wrong About the Tree of Life"

COMMENTARY: Allen MacNeill

A recent article in the New Scientist trumpeted the news that "Darwin was wrong", at least insofar as his "tree of life" was concerned. To be specific, the author stated that new discoveries in the field of horizontal gene transfer had invalidated Darwin's "tree of life", as illustrated by his diagram in the Origin of Species.

Horizontal gene transfer (especially as the result of viral transduction) has been known to occur for almost half a century. In my undergraduate genetics course at Cornell (which I took in the spring of 1972) we did a lab in which we used lambda bacteriophage to transfer genetic material from one bacterial colony to another. Ergo, none of the mechanisms of HGT described in the article in New Scientist are all that new.

Indeed, I have listed at least six mechanisms of HGT in my blogpost on the “engines of variation” located here. In that list, they are numbers 28, 29, 33, 36, 40, and 41. Most of these HGT mechanisms have been known for decades and are among the best understood mechanisms of increasing both genetic and phenotypic variation.

What is relatively new is the application of the information gained about HGT to phylogenetic reconstruction. HGT is the rule among bacteria, and apparently occurs fairly frequently among eukaryotes as well. Evolutionary biologists, and especially phylogeneticists and systematists have been using HGT data for phylogenetic reconstruction for over a decade, even among eukaryotes. So, once again this is not new.

However, there is currently a tread at Uncommon Descent to the effect that

(1) the New Scientist article is pointing out that "Darwinism" is a bankrupt theory, and

(2) that HGT is more easily explained as part of "intelligent design theory" (ID).

Does the increasing recognition of HGT and its use in phylogenetic reconstruction mean that the current theory of evolution is invalid, or that ID can explain these phenomena better? On the contrary, the more we learn about HGT the more it seems to be even more random and undirected than vertical gene transfer (i.e. genetic recombination and heredity via reproduction). To be specific, the overwhelming majority of identified HGTs are of non-coding DNA sequences that have no detectable effect on the phenotypes of the organisms in which it has occurred.

That is, almost all of the DNA sequences that have been unambiguously shown to be the result of HGT are sequences that do not code for proteins nor participate in the regulation of coding sequences. Rather, they are sequences that have “gone along for the ride”, especially as the result of RNA retroviral HGT. Such sequences are so common that they are routinely used to construct and modify genetic phylogenies, as well as to determine genetic homologies.

The vast majority of HGTs are essentially neutral genetic mutations, as first described by Motoo Kimura in his neutral theory of molecular evolution. As such, they produce an immense amount of genetic variation without producing a corresponding amount of phenotypic variation. Furthermore, when such phenotypic variation does occur, it is more often deleterious than beneficial (usually mildly deleterious, as pointed out by Tomoko Ohta in her nearly neutral theory of molecular evolution). Only very rarely are such HGTs beneficial, and then only in relatively restricted ecological and evolutionary settings.

But neutral or slightly deleterious genetic changes (such as those produced by the vast majority of HGTs) are exactly the opposite of what one would expect to see as the work of an “intelligent designer”. Such an entity would (as several of the commentators in this thread have suggested) tailor HGTs to produce adaptive (i.e. beneficial) changes in the phenotypes of the recipients of its HGTs. Either that, or the “intelligent designer” doesn’t “tailor” its HGTs at all, but rather produces them randomly, rather like a dealer in a card game. But in that case, the actions of a soi dissant “intelligent designer” would be indistinguishable from Darwinian evolution, and including any reference to its actions (and/or inferring its existence) would be unnecessary (and would therefore violate Occam’s razor).

One last point: although the vast majority of HGTs produce either no phenotypic effect or slightly deleterious phenotypic effects, a relatively small number produce phenotypic effects that are correlated with increased survival and/or reproductive success. Unlike the vast majority of HGTs, these beneficial HGTs rapidly proliferate in the populations in which they arise, in exactly the way Darwin proposed in 1859. That is, they are preserved and passed on (while deleterious HGTs are eliminated), and thereby become more common over time among the populations in which they occur.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Serial Endosymbiosis and Intelligent Design

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

It's very gratifying to see Lynn Margulis finally getting the recognition that she deserves. As the most effective exponent of the serial endosymbiosis theory (SET) for the origin of eukaryotes, Lynn's work provides an excellent example of how ID should (but currently doesn't) proceed. During the late 1960s, Lynn published a series of revolutionary papers on the evolution of eukaryotic cells, culminating in her landmark book Symbiosis and Cell Evolution, in which she carefully laid out the empirical evidence supporting the theory that mitochondria, choloroplasts, and undulapodia (eukaryotic cilia and flagella) were once free living bacteria (purple sulfur bacteria, cyanobacteria, and spirochaetes, respectively).

Her theory was greeted with contempt and scorn by almost all evolutionary biologists (sound familiar?), who believed at the time that all eukaryotic cellular organelles evolved by gradual elaboration of invaginations of the plasma membrane. But Lynn didn't give up, or continue to simply restate her original theory (sound familiar?). Instead, she continued to do extensive field and laboratory research, publishing hundreds of papers and dozens of books in which she presented the accumulating empirical evidence supporting her theory. With time, other researchers (encouraged by the success of her field and lab research) began to test her hypotheses themselves, and discovered yet more empirical evidence supporting her theory.

And so today, Lynn Margulis's SET has become the dominant theory explaining not only the origin of eukaryotes, but also the origin of evolutionary novelty at dozens of different levels in biology (see her book, Acquiring Genomes for a comprehensive review). So well accepted has her work become by evolutionary biologists that finally, after almost four decades, creationists and ID supporters have begun to attack her theories. As she said at our Darwin Day celebration at Cornell this past February, no greater affirmation of one's "having arrived" as a major theorist in evolutionary biology could be imagined.

The point here is that, if ID wants to become accepted as part of evolutionary biology in the same way that Lynn Margulis's SET has become accepted, then ID supporters have to do the same thing she did: get out in the field and get your hands dirty, and get into the lab and do the same thing. Her ideas were just as unorthodox and unacceptable in 1969 as ID is now. However, she didn't put all of her effort into public relations and political propaganda. No "Symbiosis Institute" dumped millions into the production of deliberately distorted press kits and one-sided propaganda films. Legions of self-appointed experts whose only exposure to biology was in high school classes or what they read on Answers in Genesis or Uncommon Descent bloviated on SET and declared themselves experts after a week of superficial study of articles on Wikipedia.

No, Lynn and her colleagues did the hard work of finding the empirical evidence that eventually carried the day and established her SET as one of the bedrock foundations now worthy enough of respect as to earn the ire of the creationists and IDers. Her ideas are still radical, and still raise the blood pressure of many evolutionary biologists. Her dismissal of the "modern evolutionary synthesis" in particular is not popular among many evolutionary biologists, who are largely still mired in paradigms that are at least four decades of out of date. She has said some things about the "modern synthesis" that have brought smiles to the faces of the creationist quote-miners. The difference between her and them is that they can't even begin to claim any credibility in science; their "work" is entirely parasitic on hers, and deserves nothing but contempt.

When the history of evolutionary biology in the 20th century is written (I hope to contribute to it myself, if I live long enough), the work of Lynn Margulis will rank right up there with the work of Fisher, Haldane, Wright, Dobzhansky, Mayr, Simpson, Stebbins, Gould, Lewontin, Kimura, Williams, Hamilton, Trivers, and the two Wilsons. And unless and until IDers decide that it's finally time to stop doing agitprop and start doing science, they and the creationists will at best be a trivial footnote.

Comments, criticisms, and suggestions are warmly welcomed!

--Allen

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