The book Darwin Devolves

[Roy]

So they're based on what? I always thought they were based on the Modern Synthesis (formed in the 1950's).

Note that shunyadragon says that they "are not based on Neo-Darwinism, whatever that is."

If he doesn't know what Neo-Darwinism is, how can he know whether contemporary science is based on it?

[Roy]

I gather that they meant the dichotomy between mutations that degrade or disable genes and those that add to the genome.

You're wrong.

You're still wrong about sickle-cell being a degradation.

You should have stopped after identifying haemoglobin as a protein.

[Roy]

My emphasis:

No, we have come along way since the 1950's. The science of evolution has advanced in many areas particularly genetics. In the modern concept evolution 'natural selection still acts on genetic mutations and genetic diversity for evolution to take place in adaptation to changing environments, but this evolution takes place in populations, and not individuals.

The biggest change is the old beliefs in randomness in nature and evolution no longer apply except in outcome of individual events. It is the Laws of Nature and the changing environment that determine ultimate outcome of chains of cause and effect events are constrained by the Laws, like those involved in evolution and Nature in general. The morphological genesis self-determination was described in terms of fractal math was described in detail in a paper by Alan Turing.

Alan Turing died in the 1950s. Anything he wrote cannot possibly be part of what we've learnt since the 1950s.

[shunyadragon]

Note that shunyadragon says that they "are not based on Neo-Darwinism, whatever that is."

If he doesn't know what Neo-Darwinism is, how can he know whether contemporary science is based on it?

I consider Neo-Darwinism to vague highly misused term not used in scientific literature. It is supposed to mean modern Darwinism including advances in genetics, but like Darwinism it is not a meaningful useful term as far as contemporary science of evolution is concerned. I do like debating the vague use of layman terminology.

Contemporary science is based on the falsification and predictability of hypothesis, and objective verifiable evidence.

[lee_merrill]

And, as you'd expect based on past behavior, it's pretty bad, in that he undercuts his own argument. He's trying to suggest that lab based experiments reproduce the spectrum of mutations that we see in uncontrolled environments.

Well, that just stands to reason:

Source: Behe

… and it is called the “first” rule because that is what we should generally expect to happen first to help a species adapt, simply because there are many more ways to break a gene than to build a new constructive feature.

© Copyright Original Source

But then he goes on to point out that Lenski's seen a number of mutations that damage the DNA repair systems, which causes an elevated mutation rate - something that's helpful when they're desperately trying to adapt to the lab conditions.

As I recall, the cultures in Lenski's experiment are not being stressed.

What Behe doesn't mention is that DNA repair systems are nearly uniform throughout all life forms, indicating that these mutations are not typical of those that occur outside of lab conditions.

But it does illustrate that most often, degradative mutations are the primary mutations selected for survival.

Source: Behe

One big fly in their argument, however, is that they overlook the results from non-laboratory evolution that I give in the book. Every species that has been examined in sufficient detail so far shows the same pattern as seen in lab results.

© Copyright Original Source

And the lab results are clear:

Source: Behe

Whatever the resolution of that second-order question, one mutator led to a first order effect. The Lenski lab noticed that, after a while, the mutation rate of one of the mutator strains had decreased by half. Upon investigation they determined that the mutation rate had been reduced by breaking a second gene that is involved in DNA repair. Thus a problem caused by breaking one gene was partially offset by breaking a different gene. That’s what random mutation and natural selection do.

© Copyright Original Source

Blessings,
Lee

[lee_merrill]

I figured that was the case, which is why i pressed you on this issue. You only saw it that way because that's what you wanted to see. Read it again - it's referencing something else entirely, namely the topic of the previous sentence: the difference in duplications between stress and growth related genes.

Well, I was gearing off Lehigh's summary:

Source: Lehigh

For example, along the lineage leading to modern brewers’ yeast (Saccharomyces cerevisiae), historical rates of gene loss and gene gain are nearly matched such that the inferred ancestral genomes along the way are all predicted to have around 6000 genes (Wapinski et al. 2007), despite a large flux in gene content (including a whole‐genome duplication event;Wolfe and Shields 1997; Kellis et al. 2004).

© Copyright Original Source

Blessings,
Lee

[lee_merrill]

You're still wrong about sickle-cell being a degradation.

Well, it causes anemia.

You should have stopped after identifying haemoglobin as a protein.

Source: Brittanica

Hemoglobin, also spelled haemoglobin, iron-containing protein in the blood of many animals...

Source

© Copyright Original Source

Blessings,
Lee

[TheLurch]

Well, I was gearing off Lehigh's summary.

Which is an accurate summary of one aspect of the paper, but (as should be obvious) does not contain all the details. So you should try to read carefully.

[TheLurch]

As I recall, the cultures in Lenski's experiment are not being stressed.

Then either you recall incorrectly, or don't think starvation is stressful. But in this case, stress is completely orthogonal to the issues with Behe's "response."

But it does illustrate that most often, degradative mutations are the primary mutations selected for survival.

No, it doesn't. The yeast example shows that many of the changes that have been selected for survival involve gene duplications - which are selected for at least as often as the loss of a gene. Behe doesn't look at gene duplications at all - he essentially pretends they don't exist.

So yes, if you ignore one of the major sources of non-disabling mutations, disabling mutations look much more frequent. That doesn't make this a good argument, though.

The example Behe himself cites is also problematic. It is a loss of function mutation seen in Lenski's experiment - but it's one we do not see in populations in the wild. All of them have intact DNA repair systems. If it really is generally advantageous to disable these genes outside of lab experiments, we'd be seeing it happen.

We do not.

And that means this statement:

Source: Behe

One big fly in their argument, however, is that they overlook the results from non-laboratory evolution that I give in the book. Every species that has been examined in sufficient detail so far shows the same pattern as seen in lab results.

© Copyright Original Source

Is false.

Because it ignores the frequent gene duplications we see, and it ignores the fact that some of the specific types of mutations seen in the lab experiments are not seen in the wild.

[shunyadragon]

Well, it causes anemia.

Yes, this is side effect of sickle-cell, but the mutation does not represent degradation of the genes. The benefits of sickle-cell is the immunity against malaria.

[shunyadragon]

My emphasis:Alan Turing died in the 1950s. Anything he wrote cannot possibly be part of what we've learnt since the 1950s.

I did not say that Turing's paper suddenly learn nor changed things in the 50's. The paper was influential in the long term.

[DayOneish]

Most people here don't seem to understand the point Behe is making in his fantastic book, and his peer-reviewed scientific paper he built the idea in. Let me make it clear and simple, so even the densest Darwinist among us can understand it.

Beneficial adaptation can be found much easier by breaking than by constructing. Therefor, devolution (breaking of already-existing function) is expected to be far more prominent than evolution (building of previously non-existing function) in biology.

Simple stuff. It's backed up by mountains of evidence.

Now, there are two problems:

One, if evolution is driven by devolution (and it is), and is dependent on prior-function (again, it is), it begs the question of how any function originated to begin with.

Two, if we extrapolate devolution, we eventually end with mass extinction. It's very similar to John Sanford's genetic entropy.



Professor Behe has a fantastic series of rebuttals to Darwinist reviews up at the Evolution News & Views blog. Let's (kind of) quickly go over them.


Article #1: Woo-hoo! In Science Review of Darwin Devolves, Lenski Has No Response to My Main Argument

Lenski's initial attempted rebuttal was so weak that it gave Behe a good laugh. None of the reviewers even attempt to address Behe's primary point, and instead go off on unrelated tangents.


Article #2: Coyne and Polar Bears: Why You Should Never Rely on Incompetent Reviewers

Jerry Coyne offers one of the worst reviews in the history of science, showing off both his ignorance and his dishonesty. Behe, being the superior thinker and man, easily refutes it. By the way, for those not in the know, Coyne's commitment to Darwinism is motivated by his atheism, not by science.

Here's scummy Coyne's straw man argument which makes up the brunt of his review:

What Behe is saying is that harming genes is the only way that unguided mutations can ever help an organism.

And here's the gracious Behe's refutation:

Behold the bizarre absolute. Now all a devoted Darwinist has to do in order to knock down the strawman he set up is to, say, point to some duplicated gene or other that helps with something, and he no longer has to worry his little head about the argument.

I would advise readers who actually want to understand the argument to read it with attention; there are lots of distinctions made in the book. And I would advise Professor Coyne either to find a more reliable informant or to wait two weeks and read the book himself.

Below is the relevant information from Liu et al.’s Table S7. Those who can understand the table will see that it supports every actual, undistorted claim I made about the polar bear.

Next up, Behe (as promised) offers a more detailed rebuttal to Lenski and company's hit piece in Science.

Article #3: Train Wreck of a Review: A Response to Lenski et al. in Science

Behe offers a bullet point summary of the rebuttal:

For readers who don’t have time to plow all the way through, here are the take-home lessons:

• gene-level counter-examples cited by the reviewers are shamelessly question-begging; the reviewers simply gesture at genes and assume they were produced and/or integrated into living systems by random processes, but neither the reviewers nor anyone else has even tried to show that is possible;
• organ-level counter-examples cited by the reviewers as produced by exaptive processes are similarly question-begging;
• criticisms of my earlier books cited by the reviewers were similarly question-begging and/or relied on vague, imaginative stories;
• the reviewers are either unaware of or ignore my many detailed replies to earlier criticisms and to papers the reviewers themselves cite;
• as noted in my previous post, the reviewers don’t even attempt to grapple with the main argument of the book, that beneficial degradative mutations will rapidly, relentlessly, unavoidably, outcompete beneficial constructive mutations at every time and population scale.

So, in order to refute Behe's rule, the best and the brightest Darwinists offer: unproven examples which assume the very thing in question (lol), imagination in place of science (lol), distractions which Behe addressed years ago (lol), and a complete dodge of Behe's central point (lol).

These are the best and the brightest defenders of Darwin, and they are grade-A morons.


Moving on, we have Jerry Coyne continuing to be a moron (surprising, I know), and Behe continuing to put him in his place. Coyne offers nothing of substance, choosing to go with the empty rhetoric of "Darwin did it, but no one knows how, now stop asking questions we can't answer!" strategy. It's a rather boring exchange. Coyne's human garbage, and so I'll link to Behe owning him and then move on to better things.

Article #4: Bullet Points for Jerry Coyne


Continuing on, Behe offers up rebuttal to Lenski's extended review of Darwin Devolves. I have to say, Lenski seems like a halfway decent guy, at least when compared to the average Darwinist. I get the feeling he knows Behe is right, but can't admit it. Unfortunately, he's wasted his life away on a badly-outdated, Victorian view of biology, which he has no choice but continue defending. He's so deep in the Darwin cult that there's no turning back. Poor guy.

Article #5: Lessons from Polar Bear Studies

Article #6: For Dreams of Darwinian Evolution, First Rule of Adaptive Evolution Is an Insuperable Problem

Behe again offers some quick and easy bulletpoints for the skimmers. I've combined the bullets from both articles below, for simplicity's sake.

Although it was not the topic of his first post, I will begin with Lenski’s discussion of the example with which I open my book — the polar bear genome — because it illustrates some principles that will be useful going forward. For readers who don’t have time to read to the end, here are a couple of take-home lessons:

• Experimental evidence strongly supports my conclusion (disputed without good reason by Lenski and others) that highly selected mutations in the polar bear genome work by breaking or blunting pre-existing functions.
• A “function” of a protein is a lower-level molecular feature or activity, such as being a gear or a tether; it should not be confounded with higher-level phenotypic effects, such as “lowers cholesterol” or “makes the organism happy.” Ignoring the distinction leads to much confusion.
• Professor Lenski’s contrasting of the frequency versus importance of evolutionary changes is misconceived and his illustrations are inapt.
• Mindless evolution works only in the short term. That is an insuperable problem for long-term Darwinian progress.

Lenski avoids the science altogether, and instead appeals to hopes and wishes:

But then, without benefit of supporting data, Lenski waxes strongly optimistic. He quotes an author of the study and then stresses his own view in bold face:

In a news piece about this research, one of the paper’s authors, Rasmus Nielsen, said: “The APOB variant in polar bears must be to do with the transport and storage of cholesterol … Perhaps it makes the process more efficient.” In other words, these mutations may not have damaged the protein at all, but quite possibly improved one of its activities, namely the clearance of cholesterol from the blood of a species that subsists on an extremely high-fat diet.

Lenski is almost certainly wrong about the bolded text. Here’s why. In 1995 researchers knocked out (destroyed) one of the two copies of the APOB gene in a mouse model — the same gene as has been selected in polar bears. Although APOB is itself involved in the larger process of the transport of cholesterol, mice missing one copy of the APOB gene actually had lower plasma cholesterol levels than mice with two copies. (Mice missing both copies died before birth.) What’s more, the researchers noted that “When fed a diet rich in fat and cholesterol, heterozygous mice were protected from diet-induced hypercholesterolemia.”

Lenski also shows a deep misunderstanding of the distinction between low-level function and high-level purpose (I've noticed others in this thread have done the same), which Behe illustrates with some wonderful analogies:

I’d like to highlight one final critical point. Let me set it up with a homey analogy. When I was 14 I worked weekends at McDonald’s, and sometimes I’d be assigned to operate the milkshake machine. The machine was broken down each night for cleaning. One of my tasks early in the morning before opening was to reassemble its parts. There were maybe a dozen parts to put together — sprockets, clamps, gaskets, and such. Shakes were very popular back then (mid 1960s) and made many customers happy for a while. Nonetheless, the function of the parts of a shake machine is not “to make people happy.” The function of a sprocket or a clamp isn’t even “to make a milkshake.” Rather, they have lower-level mechanical duties that are subservient to the overarching higher purposes of the systems.


The same is true of APOB. Its function is not “to help polar bears survive,” nor even “to clear cholesterol.” Rather, it has one or more lower level functions that are subservient to those higher purposes. Thus the fact that cholesterol might be cleared more efficiently in polar bears does not at all mean that APOB hasn’t been degraded, any more than breaking the off-switch of a shake machine so that it works continuously throughout lunch hour means some new improved function was added.


In both Darwin Devolves and my Quarterly Review of Biologypaper on which it is based, I repeatedly stressed the need to look beneath higher-level, phenotypic changes to associated underlying molecular-level mutations. Did they help by constructing or by degrading what I termed Functional Coded elemenTs (FCTs)? Helpful higher level changes can often be misleading, because they might actually be based on degradative molecular changes. There is every reason to think that’s what occurred in the evolution of the examples I cite in Darwin Devolves, definitely including the magnificent Ursus maritimus. The more effective clearance of its cholesterol allows the polar bear to thrive on a diet of seal blubber, but it is the result of a mutation that breaks or blunts APOB.

That's the entire point of Behe's rule: beneficial adaptation can be found much easier by breaking than by constructing. If Lenski can't grasp this point, even if he doesn't accept it, then he's a lost cause.


Finally, here's the first part of Behe's rebuttal to his collegues at Lehigh University:

Article #7: A Response to My Lehigh Colleagues, Part 1

The article teaser says all you need to know: "Their review pretty much completely misses the mark. Nonetheless, it is a good illustration of how sincere-yet-perplexed professional evolutionary biologists view the data."

I did find one part of this artice interesting, though. The Leheigh collegues agree with Behe's rule when it comes to laboratory evolutionary research, but take issue with it when it's used outside of the lab, in nature. Why? Because laboratory research, according to them, doesn't accurately mimic nature. in other words, these idiots just cut off their own nose to spite their face. Behe's superior science has them so trapped, that in order to try to refute it, they're willing to delegimize the whole field of evolutinary lab research. God, what an embarassment. I feel bad for Behe for having to associate with these clowns.


This has been total dominance by Michael Behe. He's singlehandedly answered every one of his critics' issues, and he's done so clearly and thoroughly, with dozens of citations, and eloquent writing. Oh, and he's done it all while being polite. What a scientist, and more importantly, what a man!

[DayOneish]

Behe doesn't look at gene duplications at all - he essentially pretends they don't exist.

Except for that whole chapter titled "Evolution by Gene Duplication Revisited."

But, hey, let's not let those pesky facts get in the way of a good bad argument.

[TheLurch]

Except for that whole chapter titled "Evolution by Gene Duplication Revisited."

But, hey, let's not let those pesky facts get in the way of a good bad argument.

Look, i'll readily acknowledge i have not read the book. I'm going based on the articles brought into this discussion. If there are things not in this discussion that are relevant, give me links and i'll read them.

[Roy]

You should have stopped after identifying haemoglobin as a protein.

Source: Brittanica

Hemoglobin, also spelled haemoglobin, iron-containing protein in the blood of many animals...

Source

© Copyright Original Source

Excellent. You've got the same thing right twice.