Intelligent Design Theory: Science or Religion?

so youre just gonna spritz me with your Vedantic science crap and not look up any ID evidence eh Lamont?

PNAS: Proceedings of the National Academy of Sciences of the United States of America

The frailty of adaptive hypotheses for the origins of organismal complexity

Author: Michael Lynch, Indiana University

The goal here is to dispel a number of myths regarding the evolution of organismal complexity...What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms.

It is impossible to understand evolution purely in terms of natural selection, and many aspects of genomic, cellular, and developmental evolution can only be understood by invoking a negligible level of adaptive involvement...

The literature is permeated with dogmatic statements that natural selection is the only guiding force of evolution, with mutation creating variation but never controlling the ultimate direction of evolutionary change... it is now known that genome composition is governed by biases in mutation and gene conversion, some of which (e.g., mobile-element proliferation) operate via internal drive-like mechanisms...The notion that mutation pressure can be a driving force in evolution is not new...The hypothesis that expansions in the complexity of genomic architecture are largely driven by nonadaptive evolutionary forces is capable of explaining a wide range of previously disconnected observations.

Simply making the counterclaim that natural selection is all powerful (without any direct evidence) is not much different from invoking an intelligent designer (without any direct evidence).

Although compelling adaptive arguments are always accompanied by a formal rejection of simpler nonadaptive hypotheses, credible null hypotheses have rarely been pursued in evolutionary developmental biology.

Because it deals with observations on historical outcomes, frequently in the face of incomplete information, the field of evolution attracts significantly more speculation than the average area of science...the burden of evidence for invoking an all-powerful guiding hand of natural selection should be no less stringent than one would demand of a creationist. If evolutionary science is to move forward, the standards of the field should be set no lower than in any other area of inquiry....many aspects of biology that superficially appear to have adaptive roots almost certainly owe their existence in part to nonadaptive processes.

Such conclusions would be difficult to reach without a formal population-genetic framework, but they equally rely on observations from molecular, genomic, and cell biology. Such conclusions also raise significant challenges. If complexity, modularity, evolvability, and/or robustness are entirely products of adaptive processes, then where is the evidence?

Because the forces of mutation, recombination, and genetic drift are now readily quantifiable in multiple species, there is no longer any justification for blindly launching suppositions about adaptive scenarios...the origins of biological complexity should no longer be viewed as extraordinarily low-probability outcomes of unobservable adaptive challenges, but expected derivatives of the special population-genetic features of DNA-based genomes.

IDers like to portray evolution as being built entirely on an edifice of darwinian natural selection. This caricature of evolutionary biology is not too surprising. Most molecular, cell and developmental biologists subscribe to the same creed, as do many popular science writers. However, it has long been known that purely selective arguments are inadequate to explain many aspects of biological diversity.

Michael Lynch, May 2005

The blind worship of natural selection is not evolutionary biology. It is arguably not even science.

It is quite remarkable that most biologists continue to interpret nearly aspect of biodiversity as an outcome of adaptive processes. This blind acceptance of natural selection as the only force relevant to evolution has led to a lot of sloppy thinking, and is probably the primary reason why evolution is viewed as a soft science by much of society.

A central point to be explained in this book is that most aspects of evolution at the genome level cannot be fully explained in adaptive terms, and moreover, that many features could not have emerged without a near-complete disengagement of the power of natural selection. This contention is supported by a wide array of comparative data, as well as by well-established principles of population genetics.

However, it has long been known that purely selective arguments are inadequate to explain many aspects of biological diversity.

Michael Lynch, May 2005

It's looking like the evidence is already here waiting for farmer et al to acknowledge.

Evolutionary(you mean ID)" theorists" are proposing all kinds of ways to interpret and understand the "complexity." None of them are saying "God" did it, but it has to be explained, if possible. They're doing "science," like it or not.

Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.It should be emphasized here that the sins of panselectionism are by no means restricted to developmental biology, but simply follow the tradition embraced by many areas of evolutionary biology itself, including paleontology and evolutionary ecology (as cogently articulated by Gould and Lewontin in 1979). The vast majority of evolutionary biologists studying morphological, physiological, and or behavioral traits almost always interpret the results in terms of adaptive mechanisms, and they are so convinced of the validity of this approach that virtually no attention is given to the null hypothesis of neutral evolution, { THIS is total bullshit by one who thinks his writing signals a "paradigm shift"}
despite the availability of methods to do so (Lande 1976; Lynch and Hill 1986; Lynch 1994). For example, in a substantial series of books addressed to the general public, Dawkins (e,g., 1976, 1986, 1996, 2004) has deftly explained a bewildering array of observations in terms of hypothetical selection scenarios. Dawkins's effort to spread the gospel of the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, and because more people have probably read Dawkins than Darwin, his words have in some ways been profoundly misleading. To his credit, Gould, who is also widely read by the general public, frequently railed against adaptive storytelling, but it can be difficult to understand what alternative mechanisms of evolution Gould had in mind and Gould's own writing style was his own worse enemy

Maybe I was too pessimistic in my thinking that science would eventually find enough evidence to kill the assumptions of abiogenesis and macro evolution. It's looking like the evidence is already here waiting for farmer et al to acknowledge.

I seem to have picked your direction of preaching.

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"Kimuras "so called neutral theory" is that it provides a baseline assumption of how DNA should change as a function of time,if no other force intervenes . When measurements of change deviate from the path that neutrality would predict, thats a very important signal-a signal that natural selection has intervened.

It's a signal that "something" has intervened, Farmer. That something could be natural selection, or it could be some other factor. But what is your point? As written, your sentence isn't coherent. What "is that it" in your sentence? The significance of neutral theory, you mean?

Quote:

Could it be that Kimura was dead wrong. That his hypothesis does NOT conflict with Darwin?

If there's a way to detect the possibility of natural selection at work, AND IF, test after test shows that it does NOT appear, then there's no evidence for it, get it? It's not per se "inconsistent" with natural selection, as you suggest, but what is your point? If the "null hypothesis" regularly prevails, there goes the evidence for natural selection.

It is inconsistent with the proposition that "natural selection drives evolution," if it is routinely absent, that's all. It not inconsistent with the proposition that natural selection can be a factor.

Quote:

Since you stealthily ignore very one of my questions while claiming I dont answer you.

What question are you talking about? You make statements. I seldom see any "questions." When I do, I try to respond to them.

What would it take for that one trait to become "fixed" in the population? What would it take, in other words, for all the others with "lesser" traits, who have been surviving just fine, to "die out" so that ONLY that one recently created trait prevails in the entire population? How is that one innovation ever going to completely "take over" and change the entire population? Hmmmm?

Motoo Kimura’s Neutral Theory of Molecular Evolution provides the central organizing concepts for modern evolutionary biology...My purpose here is to review the concept of “near-neutrality” in relation to the Neutral Theory and to review some recent evidence relating to the importance of slightly deleterious mutations in evolution.

In its inception, population genetics was a field characterized by a wealth of theory and a paucity of data....Now population genetics is a field awash with data, whereas the theoretical framework used to interpret this data is often inadequate (Hughes et al. 2006; Hughes 2007a). In such a situation, it is important that studies be designed so as to constitute critical tests among competing hypotheses.

I will show how the nearly-neutral theory, by providing a more plausible explanation of the observed results than does the hypothesis of widespread positive selection, has the potential to resolve this crisis in favor of Kimura’s theory.

the nearly-neutral theory makes testable predictions regarding the dynamics of a certain class of mutation – those that are slightly deleterious in their fitness effect – under realistic conditions. Critics of Kimura have sometimes dismissed the Neutral Theory as a mere null hypothesis – a theory of “no effect.”

But near-neutrality describes conditions under which the Neutral Theory is not a mere null hypothesis; indeed, conditions under which the Neutral Theory makes bold predictions which are based on rigorous reasoning and yet seem counter-intuitive to biologists schooled on decades of selectionist story-telling. Near-neutrality thus represents the leading edge of the Neutral Theory, where that theory as a whole stands or falls.

Perhaps the most important aspect of Neo-Darwinism was its emphasis on evolutionary change as a population process, leading to an appreciation of the population as a level of biological reality beyond the molecular, the cellular, and the organismal. However, there were other aspects of the Neo-Darwinian synthesis that were not constructive. One was a tendency to elevate assumptions into dogmas.

Kimura never denied the importance of positive Darwinian selection in adaptive evolution. Rather, he predicted that, although genetic drift and purifying selection predominate at the molecular level, positive selection does occur, although relatively rarely....However, because several widely used methods of testing for positive selection are both biologically and statistically problematic, there have been a vast number of poorly justified claims of positive selection in recent years.

Note that I am not simply arguing that these methods have a high rate of “false positives.” Rather, I am arguing that these methods are inherently invalid because they are based on a false premise. As a consequence, the vast majority of cases of “positive selection” inferred by these methods are likely to be erroneous....Statistical methods may often identify as “positively selected” changes that in fact represent the fixation of slightly deleterious mutations.

Molecular biology has made us aware of categories of mutation unknown to the Neo-Darwinists, including mutations in regulatory regions; complete or partial gene duplication and deletion; recombination that brings together portions of different genes (“exon shuffling”); and the restructuring of the genome by transposable elements and retroviruses. According to the hypothesis of Nei (2007), mutations fixed by genetic drift rather than natural selection play a major role in phenotypic evolution as well as in molecular evolution. Several recent studies have demonstrated that mutations in transcription factor binding sites (almost certainly not positively selected) can cause phenotypic differences among species....the contemporary biotic world is profoundly marked by slightly deleterious mutations.

What makes you think what you call "lesser" traits will die out?

Well, you COULD study population genetics. Happens faster than you think.

When the neutral theory of molecular evolution was first proposed by, among others, the great Japanese geneticist Motoo Kimura, it was controversial. Some version of it is now widely accepted and, without going into the detailed evidence here, I am going to accept it in this book.

Since I have a reputation as an arch-“adaptationist” (allegedly obsessed with natural selection as the major or even the only driving force of evolution) you can have some confidence that if even I support the neutral theory it is unlikely that many other biologists will oppose it!

Dawkins doubts that any mutation giving rise to a visible phenotype can be neutral. Such mutations are only important in molecular evolution....Does Neutral Theory only apply to invisible mutations that can only be detected by molecular geneticists?

At this point, some evolutionists will protest that we are caricaturing their view of adaptation. After all, do they not admit genetic drift, allometry, and a variety of reasons for non-adaptive evolution?... Then, you often congratulate yourself for being such an undogmatic and ecumenical chap.

You acknowledge the rival but circumscribe its domain of action so narrowly that it cannot have any importance in the affairs of nature. Have we not all heard the catechism about genetic drift: it can only be important in populations so small that they are likely to become extinct before playing any sustained evolutionary role?

To which I would add the following argument: "We've all heard about Neutral Theory but it only applies to inconsequential mutations detectable only by molecular geneticists."