Has nature ever created a code?

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Sheldon's picture
"replica of a leaf which

"replica of a leaf which benefits the insect is surely beating the odds "

How can the odds be greater against beneficial mutations surviving, than non-beneficial mutations, when the benefit is that they are more likely to survive? Can you really be this stupid by accident?

Sapporo's picture
I must say I have absolutely

I must say I have absolutely zero confidence in the "Intelligent Design" argument.

Sheldon's picture
I'm not even sure ID is an

I'm not even sure ID is an argument, from what I have seen it is nothing more than a duplicitous propaganda machine for creationism.

J N Vanderbilt III's picture
This from a molecular

This from a molecular biologist Michael Behe addressing color patterns , only a 60 sec read

How much can the public trust confident claims by scientists? Especially about morally or politically or philosophically charged topics? Alas, not so much, as The New York Times Magazine reminds us once again in a recent article, “How Beauty Is Making Scientists Rethink Evolution.” The subtitle asks, “The extravagant splendor of the animal kingdom can’t be explained by natural selection alone — so how did it come to be?”

Butterfly Wings
Great question. But wait a second — haven’t we all been told that Darwin’s natural selection has already been shown to explain pretty much everything? Forget about pretty flowers or cute puppies. Whole scholarly books have been written claiming that Darwin’s theory explains mind, law, literature, music, and more. Yet if the theory can explain much more complicated topics that involve even abstract thinking, why does it have trouble with simpler topics that don’t? If it accounts for, say, the Magna Carta, why does it struggle with the colors of butterfly wings?

The author writes that some scientists think it’s not natural selection that accounts for beauty. Rather it’s sexual selection that does the trick. But there’s a big ugly fly in that ointment. The existence of sex itself has stumped Darwinists for 150 years! It’s still a mystery.

What can the theory account for? If it can’t explain even color patterns, how much has it been exaggerated? Quite a bit, it turns out. To see the problem more clearly, let’s first think about studies of human nutrition. For decades the public was told to avoid foods with a lot of cholesterol. Recently, however, a government panel changed its mind, saying there’s no evidence that’s harmful.

Here’s the problem for grand claims about evolution. Science can’t tell if cholesterol is bad for modern humans, who can be studied in great detail. Yet if that’s too hard, then how can science claim to know what affected plants and animals in the distant past? Ones that can’t be studied in real time like people? Ones that encountered myriad environmental influences over millions of years?

That’s easy to answer: Science can’t and doesn’t know.

It’s All a Bluff
So here’s the simple test to tell if scientists are exaggerating wildly. Let’s call it: “The Principle of Comparative Difficulty” (PCD): If an easier task is too difficult to accomplish, then a harder one certainly is too. If a high jumper can’t clear a ten-foot bar, it’s a cinch to know he won’t clear twenty. If nutritionists can’t easily determine how one dietary factor affects human health, evolutionary biologists can’t tell what affected the survival of long dead animals. If Darwin’s theory can’t account for color patterns of animals, it certainly can’t explain the law. Any claim that scientists know Darwin accounts for anything more than color patterns is rank bluster.

Exposing Darwinism
The PCD exposes Darwinian braggadocio to a very much deeper level. I’m a biochemist. Biochemistry is the study of the molecular and cellular foundation of life. Back in Darwin’s day the cell was thought to be a simple jelly called protoplasm. Yet modern biochemists have discovered to their surprise that the cell is chock-full of sophisticated machines — actual machines, made of molecules. Like the machines of our everyday world (say, a lawn mower), cellular machines consist of many parts that have to cooperate with each other to do their tasks.

Yet, as physicist David Snoke and I have shown, Darwin’s mechanism of random mutation and natural selection strains to explain even the very simplest molecular example of cooperation (called a “disulfide bond”). Here’s an analogy. Suppose a lawn mower were stored in a shed that was kept closed by a hook and eye latch. Darwin’s theory struggles mightily to explain even the latch, with just two simple cooperative pieces. So we’re supposed to think it explains the lawn mower? The PCD lets us easily realize that’s ludicrous.

“The extravagant splendor of the animal kingdom can’t be explained by natural selection alone — so how did it come to be?” Great question. One thing we know for sure is that Darwin had little to do with it.

CyberLN's picture
Michael Behe is a proponent

Michael Behe is a proponent of the pseudoscience of ID. I don’t put much stock in any pseudoscience.

Sheldon's picture
Its an appeal to authority

Its an appeal to authority fallacy obviously. Unless the transcript in question has been peer reviewed and the research validated. Then of course evolution through natural selection would have been falsified.

It hasn't though....

It says something about the sheer ignorance of science, and its methods, that vandercreationist III thinks that the creationist bilge in that article has any bearing on the validity of a scientific fact like evolution.

arakish's picture
Well, you know how peer

Well, you know how peer-review goes with pseudoscience. They can only get it at Answer in Genesis, Institute for Creation Research, intelligentdesign.org, etc., etc., etc.

rmfr

arakish's picture
Is it not plagiarism without

Is it not plagiarism without attribution?

rmfr

Sheldon's picture
It certainly is....

It certainly is....

Why he thinks plagiarizing an article by a creationist is relevant to evolution isn't clear.

Sheldon's picture
That's funny I've checked

That's funny I've checked every global news network and not one of them makes any mention of the scientific fact of evolution being falsified???

You also forgot to provide a link for that article you've plagiarized in its entirety.

Do us a favour and link the peer reviewed scientific journal that published the research behind that claim.

When did this news break? It'll involve a Nobel prize obviously, I'd have thought a huge pay out from the Templeton Foundation as well.

I've said it before and I'll say it again, you creatards are funny.

In all the excitement you missed my question about your last claim...

How can the odds be greater against beneficial mutations surviving, than non-beneficial mutations, when the benefit is that they are more likely to survive?

Do take your time...

Calilasseia's picture
Ah, this would be the same

Ah, this would be the same Michael Behe, who had his freshly stir-fried arse cheeks handed to him on a silver platter at the Dover Trial. It's instructive to see how much of an embarrassment that event was to him, courtesy of the trial transcripts, which, hilariously, are all available as free downloads from here. The transcripts of interest being:

[1] Behe Evidence In Chief, Day 10, AM Session

[2] Behe Evidence In Chief, Day 10, PM Session

[3] Behe Evidence In Chief, Day 11, AM Session

[4] Behe Evidence In Chief, Day 11, PM Session

[5] Behe Evidence In Chief, Day 12, AM Session

[6] Behe Evidence In Chief, Day 12, PM Session

Notice that in the following, I provide precise page and line numbers, so that the instances of Behe being completely owned by the cross examining counsel can be located with ease. What follows will be a long post, for which I offer no excuses, simply because of the volume of material to consider, when examining the purported status of Behe as some sort of "authority" on the subject, and because it is also necessary to consider the historical context of Behe's humiliation, coming as it did in via a trial that exposed much of the venality and discoursive criminality that is endemic to professional creationism. So, on to the transcripts, and what they teach us.

Good places to look are:

Day 11, PM session, where Behe is forced to admit under cross examination that his attempt to widen the definition of "science" to admit "intelligent design" would also result in astrology being admitted as a "scientific" discipline. Scroll down the PDF document to Page 36, Line 18 - all pages and lines are conveniently numbered - and read on to Page 39, Line 19 ... take note where he says that "incorrect theories are nonetheless theories" at the end ... then continue reading to Page 41, line 17, where the cross-examining lawyer quips that he didn't taken Behe's deposition in the 16th century.

Day 12, AM session, where Behe is taken apart slowly over flagella and blood clotting. Scroll to Page 101, Line 7, read on, and see Behe admitting that no one in the ID movement ever bothered to put the "irreducible complexity" of the bacterial flagellum to empirical test. He was also forced to accept that 3½ billion years was ample time for the bacterial flagellum to evolve by natural processes at Page 108, Line 23, followed by being forced to admit that the "test" he proposed for invalidating "irreducible complexity" in the case of the bacterial flagellum was as unreasonable as asking a scientist to grow a bird wing in a petri dish. Likewise, Behe is also forced to admit that any demonstration that the flagellum could arise by natural processes would be "a real feather in the cap of people who think Darwinian theory is correct" at Page 112 Lines 13-15. Additionally, Page 112 Line 16 moves on to the blood clotting cascade, and the fact that various Puffer Fishes manage to do without some of the "irreducibly complex" components of Behe's description of the cascade - Page 120, Line 16.

Day 12, PM session, in which the cross examination of Behe continues with respect to the blood clotting cascade, and on Page 6, Lines 5-7, Behe himself says that the Type 3 Secretory System might not be "irreducibly complex" (oh dear, because Nick Matzke later found homologies between the T3SS and - you guessed it - the bacterial flagellum). Behe is then introduced to a particularly awkward question by the cross examiner at Page 8 Line 24 that is well worth savouring. Then, on Page 10, comes the crunch about the immune system, where Behe's statement "the scientific community has no answers to the question of the origin of the immune system" from his book Darwin's Black Box is presented in open session in the court, and from the start of Page 11, the cross examiner begins listing the papers and textbooks that contain precisely the "answers" that Behe claimed didn't exist ... and also demonstrates that Behe, like so many IDiots before, has his knickers in a twist over the meaning of natural selection. On Page 16, line 17, we have the part where Behe claims that the peer reviewed literature on the molecular evolution of the immune system "isn't good enough", whereupon at Page 17, Line 6, the cross examiner reveals that he has fifty eight peer reviewed papers covering the subject, the earliest of which was written in 1971, with the list including new papers that were being prepared for publication at the time of the trial ... then we reach Page 20, where college textbooks on the evolution of the immune system are presented, which Behe is forced to admit he hasn't read, doesn't know the contents of, but he still persists in trying to claim that these texts and these papers aren't good enough because they don't show the entire evolutionary process right down to the atomic level or some such nonsense. Then Behe is hoist upon his own petard on Page 25, Line 23 onwards, when his statement from his book that "if the natural mechanism is to be accepted, then its proponents must publish or perish" is displayed before the court ... read on from this point for some pure comedy gold.

Then of course, we have the little matter that Behe, when he tried to peddle "irreducible complexity" as a purported "problem" for evolutionary biology, was unaware that actual tenured biologists knew he was talking through his arse on the subject, because, wait for it, a real biologist, by the name of Hermann Joseph Müller, alighted upon so-called "irreducible complexity" way back in 1918, NOT as a "problem" for evolutionary biology, but as a natural outcome of evolutionary processes. The scientific paper in which Müller unleashed this concept upon the scientific public for the first time, is this one:

Genetic Variability, Twin Hybrids and Constant hybrids in a Case of Balanced Lethal Factors by Hermann Joseph Müller, Genetics, 3(5): 422-499 (1918)

From pages 464-465 of that paper, we have:

Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect upon which it produced upon the 'reaction system' that had been brought into being by the many previously formed factors in cooperation; thus, a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent upon the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery.

This was placed on a rigorous footing by the 1930s, which means that evolutionary biologists have known Behe's canards about "irreducible complexity" to be canards for over six decades, which means that "irreducible complexity" as posited by Behe was dead in the water among real scientists before Behe was born.

Thence we come to the Müllerian Two Step, which is succinctly encapsulated thus:

[1] Add a component;

[2] Make it necessary.

Which of course means that "irreducible complexity", as well as first being proposed as a concept by an evolutionary biologist, was also proposed not as a problem for evolutionary biology, but as a natural outcome of evolutionary processes. Behe has failed to recognise that he was pre-empted to his "big idea" by an evolutionary biologist, who alighted upon the concept 80 years before Behe started selling his soul to that speciation variant of creationism that has been caught stealing a lab coat.

Even more embarrassing for Behe, he and David Snoke published a paper in Protein Science, claiming that they had produced a simulation establishing the validity of "irreducible complexity" as Behe misuses the term. Unfortunately for Behe, other scientists took a look at the simulation, and found it to be a crock. A subsequent paper that utterly destroys Behe's assertions is this one:

Simple Evolutionary Pathways To Complex Proteins by Michael Lynch, Protein Science, 14: 2217-2225 (2005) [Full paper downloadable from here]

Abstract

A recent paper in this journal has challenged the idea that complex adaptive features of proteins can be explained by known molecular, genetic, and evolutionary mechanisms. It is shown here that the conclusions of this prior work are an artifact of unwarranted biological assumptions, inappropriate mathematical modeling, and faulty logic. Numerous simple pathways exist by which adaptive multiresidue functions can evolve on time scales of a million years (or much less) in populations of only moderate size. Thus, the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions.

Oh dear, look at that. Behe's paper is described as, wait for it:

An artefact of unwarranted biological assumptions, inappropriate mathematical modelling, and faulty logic.

As we delve further into this paper, we find out some other interesting facts, viz:

In a recent paper in this journal, Behe and Snoke (2004) questioned whether the evolution of protein functions dependent on multiple amino acid residues can be explained in terms of Darwinian processes. Although an alternative mechanism for protein evolution was not provided, the authors are leading proponents of the idea that some sort of external force, unknown to today’s scientists, is necessary to explain the complexities of the natural world (Behe 1996; Snoke 2003). The following is a formal evaluation of their assertion that point-mutation processes are incapable of promoting the evolution of complex adaptations associated with protein sequences. It will be shown that the contrarian interpretations of Behe and Snoke are entirely an artifact of incorrect biological assumptions and unjustified mathematical oversimplification.

Before proceeding, a fundamental flaw in the argument of Behe and Snoke needs to be pointed out. Although the authors claim to be evaluating whether Darwinian processes are capable of yielding new multiresidue functions, the model that they present is non-Darwinian (King and Jukes 1969). Contrary to the principles espoused by Darwin, that is, that evolution generally proceeds via functional intermediate states, Behe and Snoke consider a situation in which the intermediate steps to a new protein are neutral and involve nonfunctional products. Although non-Darwinian mechanisms play an important role in contemporary evolutionary biology, there is no logical basis to the authors’ claim that observations from a non-Darwinian model provide a test of the feasibility of Darwinian processes. Moreover, given that the authors restricted their attention to one of the most difficult pathways to an adaptive product imaginable, it comes as no surprise that their efforts did not bear much fruit.

With a priority on being compatible with the conventional framework of population genetics, the following model is the closest possible Darwinian version of the Behe and Snoke model in that the intermediate states of protein evolution involve functional products (in accordance with Darwin) with no immediate positive effects on organismal fitness (consistent with the assumptions of Behe and Snoke). Using conservative biological assumptions, it is shown that the origins of new protein functions are easily explained in terms of well-understood population-genetic mechanisms.

So, Behe engaged in a bait and switch, constructing a NON-Darwinian model, and then attempted to use it to critique Darwinian processes. There's a word for this in the dictionary, beginning with "D".

However, let us move on ...

A major goal of evolutionary theory is to develop a mechanistic understanding of the observed features of molecules, individuals, and populations in terms of universally established principles of mutation, Darwinian selection and descent with modification, Mendelian segregation and recombination (in sexual species), and random genetic drift. To simplify the presentation as much as possible, the focus here is on a nonrecombining haploid genome (as assumed by Behe and Snoke), with the origin of a new adaptive function involving a two-residue interaction, for example, the disulfide bond between two cysteines. As in Behe and Snoke (2004), this adaptation is assumed to be acquired at the expense of an essential function of the ancestral protein, so that the new function can only be permanently established via gene duplication, with one of the copies maintaining the original function. The Behe-Snoke assumption that a selective advantage only results after both participating residues are in place is also adhered to. However, two significant deviations from the model of Behe and Snoke are incorporated.

First, Behe and Snoke start with a duplicate locus that has spread throughout the base population, although they also assume that most gene copies have actually been permanently silenced by previous mutational events, the number of functional copies actually varying arbitrarily among individuals (without upper bound) as a consequence of unknown deterministic mechanisms. In contrast, the model presented here starts with a more realistic base population harboring a single locus in all individuals. A duplicate gene then arises in a single random member of the population, as must always be the case with a mutational change. With many fewer initial targets for mutation, and the vast majority of new duplicates being rapidly lost by genetic drift, this starting condition imposes a much greater challenge for the evolution of a new gene function than that assumed by Behe and Snoke.

Second, Behe and Snoke assume that all mutational changes contributing to the origin of a new multi-residue function must arise after the duplication process. They justify this assumption by stating that the majority of nonneutral point mutations to a gene yield a nonfunctional protein. To stretch this statement to imply that all amino acid changes lead to nonfunctionalization is a gross mischaracterization of one of the major conclusions from studies on protein biology—most protein coding genes are tolerant of a broad spectrum of amino acid substitutions (Kimura 1983; Taverna and Goldstein 2002a,b). For example, in a large mutagenesis screen, Suckow et al. (1996) found that >44% of amino acid positions in the Lac repressor of Escherichia coli are tolerant of replacement substitutions. Axe et al. (1998) found that only 14% of amino acid sites in a bacterial ribonuclease are subject to inactivation by some replacement substitutions, with only one site being entirely nonsubstitutable. For human 3-methyladenine DNA glycosylase, ~66% of single amino acid substitutions retain function (Guo et al. 2004). Even for the highly conserved catalytic core regions of proteins, approximately one-third of amino acid sites can tolerate substitutions (Materon and Palzkill 2001; Guo et al. 2004). Many other studies (e.g., Kim et al. 1998; Akanuma et al. 2002), including all of those cited by Behe and Snoke, have obtained results of this nature. A deeper understanding of the fraction of amino-acid-altering mutations that have mild enough effects to permit persistence in a population comes from observations on within- and between-species variation in protein sequences (Li 1997; Keightley and Eyre-Walker 2000; Fay and Wu 2003), which generally indicate that 10% to 50% of replacement mutations are capable of being maintained within populations at moderate frequencies by selection-mutation balance and/or going to fixation. Because there is strong heterogeneity of substitution rates among amino acid sites (Yang 1996), these average constraint levels should not be generalized across all sites, many of which evolve at rates close to neutrality. Thus, most proteins in all organisms harbor tens to hundreds of amino acid sites available for evolutionary modification prior to gene duplication.

Based on these observations and in contrast to Behe and Snoke, the following model assumes that the intermediate step toward a two-residue adaptation is nondebilitating with respect to the original function but also effectively neutral, with one caveat noted below. Under this assumption, the first step in the evolution of a two-residue function potentially resides at the ancestral locus, where two alternative classes of alleles may be present prior to duplication: those containing a key amino acid at one of the potentially participating sites (type 2), and those with none (type 1) (Fig. 1). Assuming that n amino acid sites can potentially participate in the origin of the new function, the expected frequencies of these two allelic classes are obtained by normalizing the first two terms of the Poisson distribution, as loss of the ancestral protein function renders inviable all single-copy alleles with two or more key residues. The expected frequencies of type-1 and type-2 alleles are then 20/(20+n) and n/(20+n), respectively, under the assumption that all 20 amino acids are equally substitutable in the intermediate neutral state. As a consequence of random genetic drift and mutation, very small populations will generally be monomorphic for one type of allele, with the nature of that allele varying stochastically over time according to the preceding probabilities. In contrast, larger populations will approach a drift-mutation equilibrium, with the two allelic classes following these respective frequencies. In either case, averaging over a long period of time, when a random gene duplicates, it will be of type 1 with probability 20/(20+n) and type 2 with probability n/(20+n). Thus, immediately following gene duplication, there is a single copy of either allelic type 3 or type 5 in the population (Fig. 1), with initial frequency equal to the reciprocal of the population size, 1/N.

Successful establishment of the new function (neofunctionalization of one of the copies) requires the founding pair of linked gene duplicates to (1) initially attain a high frequency; (2) acquire the mutations essential to the expression of the new function (allelic types 6 or 7) while en route or subsequent to fixation; and (3) be preserved by positive selection subsequent to the origin of the new function. All three processes occur in parallel with a background production of null alleles. The two central issues to be resolved are then: (1) How frequently will a duplication event lead to neofunctionalization; and (2) How long will this take? Answers to these questions can be acquired by recursively following the population through the sequential steps of mutation, selection, and random sampling.

So, Behe encapsulated in his so-called "model" a well known fallacy that I myself have exposed as a fallacy both on the Richard Dawkins Forums and elsewhere, namely the "one true sequence" fallacy. His "model" assumes that any mutation in a gene coding for a functioning protein will always result in destruction of function, which is manifest biological nonsense, as my tour elsewhere of the numerous different variations on the insulin theme alone testifies eloquently. I may reproduce that tour of insulin here precisely to reinforce the point in this venue. Indeed, several of the insulin molecules whose structures I examined on the Swiss-Prot database are not even the same length, let alone the same sequence, yet all of them are functional insulin molecules that work in the requisite organisms, ranging from humans to zebrafish. Which means that Behe rigged his so-called "model" in advance with a dishonest and biologically invalid assumption, in order to produce a pre-arranged result, which was then dishonestly presented as a so-called "critique" of Darwinian evolution.

Lynch then goes on to demonstrate in the rest of the paper, that even with conservative assumptions in place that make life hard for evolutionary processes, the sort of product that Behe asserted was impossible for evolution to produce materialises in a relatively short period of time, between 30,000 and 1,000,000 generations. The former value is, of course, entirely consonant with the later experimental results produced by Richard Lenski in his landmark 2008 paper, in which a population of Escherichia coli produced a citrate-metabolising mutant in around 30,000 generations.

From the discussion section, we learn the following:

To support their contention of the implausibility of adaptive protein evolution by Darwinian processes, Behe and Snoke started with an ad hoc non-Darwinian model with a highly restrictive and biologically unrealistic set of assumptions. Such extreme starting conditions guaranteed that the probability of neofunctionalization would be reduced to a minimal level. An alternative approach, adopted here, is to rely on a set of biologically justified premises and an explicit population-genetic framework. When this is done, contrary to the assertions of Behe and Snoke that neofunctionalization events involving multiple amino acid residues require 10 million or more generations and population sizes in excess of 1 billion individuals, it is readily demonstrated that this process can go to completion with high probability on time scales of 1 million yr or less in populations >1 million in size. As is discussed below, this is a highly conservative conclusion with respect to both the time and population-size requirements. To put this into perspective, a span of 1 million yr is small on the total evolutionary time scale (in years) of ~3.8 billion years for all of life, ~2 billion years for eukaryotes, ~700 million years for metazoans, ~400 million years for tetrapods and land plants, and ~200 million years for mammals (e.g., Knoll 2003). In addition, a population size of 1 million is minuscule for most microbes (the species whose genome structure is most compatible with the Behe-Snoke model) (Finlay 2002).

It is difficult to pinpoint the source of the difference between the results of Behe and Snoke and those contained herein, as the latter authors do not explicitly model the evolutionary process, whereas the stochastic computer simulations presented here precisely track the joint dynamics of allele frequencies. In order to maintain a permanent reservoir of potentially neofunctionalizable duplicate genes, Behe and Snoke assume that a new gene copy is produced instantaneously every time an allele is thought to have been silenced. However, the further assumption that duplicate genes are entirely neutral until the final step in neofunctionalization has been achieved leads to a steady-state situation in which almost all alleles residing at the duplicate locus are ‘‘irrecoverably lost.’’ In contrast, the analyses presented here assume that a duplicate gene arises in a single individual in a population in which all other individuals carry a single copy of the gene. This difference in approach, as well as others, is actually expected to reduce the estimated time to neofunctionalization in the Behe-Snoke model relative to that presented here. For example, although Behe and Snoke focus on the time to the first appearance of a neofunctionalizing mutation, the focus here is on the necessarily longer time to achieve the first fixable mutation. In addition, although Behe and Snoke assume that the forward and backward point-mutation rates (per amino acid residue) are equal, it is assumed here that the former is just 1/19 of the latter, which necessarily reduces the likelihood of neofunctionalization.

Uncertainties on these issues aside, there are at least three reasons for the discrepancies between our results. First, for the most part, Behe and Snoke assume that the evolution of a multi-residue function requires the origin of a full set of mutations previously kept absent from the population as a consequence of their lethal pleiotropic effects on ancestral gene functions. However, if the intermediate steps toward the evolution of a selectable multiresidue function are entirely neutral after gene duplication, as Behe and Snoke assume, then there is no compelling reason that ‘‘one-off’’ (type-2) alleles should be absent from the population prior to duplication. In the context of a disulfide bond, for example, the Behe-Snoke assumption implies a situation in which no cysteine residue in an ancestral protein would be capable of participating in a cysteine–cysteine interaction in a subsequently modified copy, which seems highly implausible (e.g., Matsumura et al. 1989). An additional logical problem implicit in the Behe-Snoke model is how an organism producing 50% functional and 50% nonfunctional protein would avoid a reduction in fitness.

Second, Behe and Snoke assume that only two specific amino acid sites within a protein are capable of giving rise to a new selectable diresidue function. Given that the average protein in most organisms contains between ~300 and 600 amino acids, this assumption is also unrealistic. Increasing the number of participating amino acid sites from n=2 to just 10 can magnify the probability of neofunctionalization by more than 10-fold, but the results presented here also demonstrate that even with the restrictive Behe and Snoke assumption of n=2, the probability of neofunctionalization can exceed the neutral fixation probability for populations with effective sizes in excess of 1 million.

Oh dear. So Lynch not only determined that Behe's model was basically dishonest from the start, but that an honest model subject to similiar restrictions yields no problems for evolution. Why am I not in the least surprised about this?

So, we have:

[1] Ample trial testimonies from the Dover Trial, featuring Behe having his arse cheeks handed to him on a plate;

[2] The fact that he didn't even invent the concept of "irreducible complexity" in the first place, but in effect stole it from an evolutionary biologist working 92 years ago, and presented a bastardised version intended as a "problem" for evolution, whilst Müller's original conception from 1918 clearly demonstrates that he erected the concept as a natural outcome of evolutionary processes;

[3] A scientific paper demonstrating that Behe's so-called "model" of protein evolution was dishonestly constructed from the start to produce pre-conceived results in conformity with presuppositions, and contained embedded within its core a known biological fallacy, followed by a demonstration that a real model of evolutionary processes shows none of the problems inherent in Behe's bait-and-switch pseudo-model.

I think that at this juncture, it is entirely fair to characterise Behe as a charlatan, on the basis of the above evidence. consequently, bringing him here does no favours to anyone making the mistake of trying to pass him off as some sort of authority in the field.

Furthermore, the idea that any of the so-called "fellows" of the Duplicity Institute constitute reliable sources of information on evolutionary biology, is quite simply untenable to anyone aware of their history or public pronouncements. They have all given enthusiastic support to the infamous "Wedge Strategy", which was exposed as nothing more than a shill for creationism the moment the internal document was leaked into the public domain, they admitted in that document that the whole business of pretending to be disinterested in the identity of their "designer" was basically a smokescreen, behind which they hoped they could sneak fundamentalist, creationist Christianity into the classroom in violation of the Establishment Clause, and they openly admitted in that document, that the only option they considered to be viable for their "designer", was the invisible magic man of fundamentalist, creationist Christianity.

Indeed, such is the level of rampantly egregious mendacity that is routinely associated with professional creationism (and let's be under NO illusions here, that we're dealing with anything other than a religion-based corporate business), that when Judge Jones was determining the matter of the admissibility of the history of the ID "movement" (complete with such hilarious events as "cdesign proponentsists", possibly THE most embarrassing transitional fossil creationists were ever hit with), he was faced with such a picture of naked skulduggery, that in the interests of honest reportage, he was effectively forced to admit that evidence, in order to avoid being seen to involve the US judicial system in collusion with that skulduggery. Judge Jones' 139 page summation of the trial, as a consequence, not only destroys the IDists' propaganda wholesale, but includes de facto accusations of perjury on the part of the creationism/ID crowd.

Far from being the "Inquisition on Darwinism" that the likes of Dembski were hoping for, the trial was as devastating to their efforts and their reputations as a KT-event sized bolide impact. Now, before any creationist tries peddling the "Expelled" Kool-Aid here, and tries to claim that Judge Jones was chosen specifically to skew the verdict against creationism & ID, the real world facts destroy this nonsense utterly. Judge Jones is a conservative Republican, was appointed by George W. Bush to his post, and is a religious believer, specifically, a Lutheran Protestant. The idea that this man was chosen to be part of some "atheist/evolutionist conspiracy" is laughable. Indeed, Judge Jones also served time as an adviser to Tom Ridge, who at the time was the Republican governor of Pennsylvania. What did Tom Ridge say about this man? Before the trial, Tom Ridge described Judge Jones thus:

"I can't imagine a better judge presiding over such an emotionally charged issue... he has an inquisitive mind, a penetrating intellect and an incredible sense of humor."

Indeed, when it was announced that a conservative Republican was going to sit on the bench during the Dover Trial prior to the trial commencing, many in the IDist camp were rubbing their hands with glee because they thought he would swing the trial their way. But some others were less than happy at having IDist nonsense exposed as such - indeed, three prominent IDists, namely William Dembski, Stephen Meyer and John Campbell, withdrew their depositions before the trial under direct instructions from the Discovery Institute and left Michael Behe to be their stool pigeon. Presumably because they didn't want to be caught out lying on oath. Fortunately for defenders of reality, the various members of the Dover school board were not only unable to escape scrutiny in court, and unable to escape rigorous cross-examination, but were too stupid to realise that lying for Jeebus is still lying, and when done under oath in court, constitutes the criminal offence of perjury. Creationists and IDists have only their own combination of stupidity, arrogance and venal discoursive criminality to blame for their epic failure at Dover.

Now, let's move on to the actual 139 page summing up of the case, shall we, specifically for the purpose of exposing the sham that Behe was an integral part of? We have, for example:

[1] Footnote 7 on page 46:

Throughout the trial and in various submissions to the Court, Defendants vigorously argue that the reading of the statement is not “teaching” ID but instead is merely “making students aware of it.” In fact, one consistency among the Dover School Board members’ testimony, which was marked by selective memories and outright lies under oath, as will be discussed in more detail below, is that they did not think they needed to be knowledgeable about ID because it was not being taught to the students. We disagree.

[2] Top of page 84:

Plaintiffs’ science experts, Drs. Miller and Padian, clearly explained how ID proponents generally and Pandas specifically, distort and misrepresent scientific knowledge in making their anti-evolution argument.

[3] Page 89:

Moreover, ID's backers have sought to avoid the scientific scrutiny which we have now determined that it cannot withstand by advocating that the controversy, but not ID itself, should be taught in science class. This tactic is at best disingenuous, and at worst a canard.

[4] Page 93:

The disclaimer’s plain language, the legislative history, and the historical context in which the ID Policy arose, all inevitably lead to the conclusion that Defendants consciously chose to change Dover’s biology curriculum to advance religion. We have been presented with a wealth of evidence which reveals that the District’s purpose was to advance creationism, an inherently religious view, both by introducing it directly under the label ID and by disparaging the scientific theory of evolution, so that creationism would gain credence by default as the only apparent alternative to evolution, for the reasons that follow.

[5] Pages 96 & 97:

Apart from two consecutive Board retreats, Bonsell raised the issue of creationism on numerous other occasions as well. When he ran for the Board in 2001, Bonsell told Jeff Brown he did not believe in evolution, that he wanted creationism taught side-by-side with evolution in biology class, and that taking prayer and Bible reading out of school was a mistake which he wanted reinstated in the Dover public schools. (8:48-49 (J. Brown)). Subsequently, Bonsell told Jeff Brown he wanted to be on the Board Curriculum Committee because he had concerns about teaching evolution and he wanted to see some changes in that area. (8:55 (J. Brown)). Additionally, Nilsen complained to Jeff Brown that each Board President had a new set of priorities and Bonsell’s priority was that of creationism. (8:53 (J. Brown)). It is notable, and in fact incredible that Bonsell disclaimed any interest in creationism during his testimony, despite the admission by his counsel in Defendants’ opening statement that Bonsell had such an interest. (1:19). Simply put, Bonsell repeatedly failed to testify in a truthful manner about this and other subjects. Finally, Bonsell not only wanted prayer in schools and creationism taught in science class, he also wanted to inject religion into the social studies curriculum, as evidenced by his statement to Baksa that he wanted students to learn more about the Founding Fathers and providing Baksa with a book entitled Myth of Separation by David Barton.

[6] Page 102

After Barrie Callahan asked whether the Board would approve the purchase of the 2002 edition of the textbook entitled Biology, Buckingham told Callahan that the book was “laced with Darwinism” and spoke in favor of purchasing a textbook that included a balance of creationism and evolution. (P-46/P-790; 35:76-78 (Baksa); 24:45-46 (Nilsen); 3:135-36 (B. Callahan); 4:51-52 (B. Rehm); 6:62-63 ©. Rehm); 7:25-26 ©. Brown)). With surprising candor considering his otherwise largely inconsistent and non-credible testimony, Buckingham did admit that he made this statement.

[7] Page 131:

Finally, although Defendants have unceasingly attempted in vain to distance themselves from their own actions and statements, which culminated in repetitious, untruthful testimony, such a strategy constitutes additional strong evidence of improper purpose under the first prong of the Lemon test. As exhaustively detailed herein, the thought leaders on the Board made it their considered purpose to inject some form of creationism into the science classrooms, and by the dint of their personalities and persistence they were able to pull the majority of the Board along in their collective wake.

[8] Page 136 (First part of Conclusion):

The proper application of both the endorsement and Lemon tests to the facts of this case makes it abundantly clear that the Board’s ID Policy violates the Establishment Clause. In making this determination, we have addressed the seminal question of whether ID is science. We have concluded that it is not, and moreover that ID cannot uncouple itself from its creationist, and thus religious, antecedents.

Both Defendants and many of the leading proponents of ID make a bedrock assumption which is utterly false. Their presupposition is that evolutionary theory is antithetical to a belief in the existence of a supreme being and to religion in general. Repeatedly in this trial, Plaintiffs’ scientific experts testified that the theory of evolution represents good science, is overwhelmingly accepted by the scientific community, and that it in no way conflicts with, nor does it deny, the existence of a divine creator.

To be sure, Darwin’s theory of evolution is imperfect. However, the fact that a scientific theory cannot yet render an explanation on every point should not be used as a pretext to thrust an untestable alternative hypothesis grounded in religion into the science classroom or to misrepresent well-established scientific propositions.

[9] Much more damning though is this on page 137:

The citizens of the Dover area were poorly served by the members of the Board who voted for the ID Policy. It is ironic that several of these individuals, who so staunchly and proudly touted their religious convictions in public, would time and again lie to cover their tracks and disguise the real purpose behind the ID Policy.

As if we needed any more examples of malfeasance on the part of creationists from the same trial, we have:

[1] Pages 40-41:

The second paragraph of the disclaimer reads as follows:

Because Darwin’s Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations.

P-124. This paragraph singles out evolution from the rest of the science curriculum and informs students that evolution, unlike anything else that they are learning, is “just a theory,” which plays on the “colloquial or popular understanding of the term [‘theory’] and suggest[ing] to the informed, reasonable observer that evolution is only a highly questionable ‘opinion’ or a ‘hunch.’” Selman, 390 F. Supp. 2d at 1310; 14:110-12 (Alters); 1:92 (Miller). Immediately after students are told that “Darwin’s Theory” is a theory and that it continues to be tested, they are told that “gaps” exist within evolutionary theory without any indication that other scientific theories might suffer the same supposed weakness.

As Dr. Alters explained this paragraph is both misleading and creates misconceptions in students about evolutionary theory by misrepresenting the scientific status of evolution and by telling students that they should regard it as singularly unreliable, or on shaky ground. (14:117 (Alters)). Additionally and as pointed out by Plaintiffs, it is indeed telling that even defense expert Professor Fuller agreed with this conclusion by stating that in his own expert opinion the disclaimer is misleading. Case 4:04-cv-02688-JEJ Document 342 Filed 12/20/2005 Page 41 of 139

In other words, even an expert witness called by the defence in the case agreed, that the disclaimer that the defendants wished to append to textbooks was MISLEADING.

[2] Page 28:

Moreover, in turning to Defendants’ lead expert, Professor Behe, his testimony at trial indicated that ID is only a scientific, as opposed to a religious, project for him; however, considerable evidence was introduced to refute this claim. Consider, to illustrate, that Professor Behe remarkably and unmistakably claims that the plausibility of the argument for ID depends upon the extent to which one believes in the existence of God. (P-718 at 705) (emphasis added). As no evidence in the record indicates that any other scientific proposition’s validity rests on belief in God, nor is the Court aware of any such scientific propositions, Professor Behe’s assertion constitutes substantial evidence that in his view, as is commensurate with other prominent ID leaders, ID is a religious and not a scientific proposition.

[3] Pages 28-30:

Dramatic evidence of ID’s religious nature and aspirations is found in what is referred to as the “Wedge Document.” The Wedge Document, developed by the Discovery Institute’s Center for Renewal of Science and Culture (hereinafter “CRSC”), represents from an institutional standpoint, the IDM’s goals and objectives, much as writings from the Institute for Creation Research did for the earlier creation-science movement, as discussed in McLean. (11:26-28 (Forrest)); McLean, 529 F. Supp. at 1255. The Wedge Document states in its “Five Year Strategic Plan Summary” that the IDM’s goal is to replace science as currently practiced with “theistic and Christian science.” (P-140 at 6). As posited in the Wedge Document, the IDM’s “Governing Goals” are to “defeat scientific materialism and its destructive moral, cultural, and political legacies” and “to replace materialistic explanations with the theistic understanding that nature and human beings are created by God.” Id. at 4. The CSRC expressly announces, in the Wedge Document, a program of Christian apologetics to promote ID. A careful review of the Wedge Document’s goals and language throughout the document reveals cultural and religious goals, as opposed to scientific ones. (11:26-48 (Forrest); P-140). ID aspires to change the ground rules of science to make room for religion, specifically, beliefs consonant with a particular version of Christianity.

In addition to the IDM itself describing ID as a religious argument, ID’s religious nature is evident because it involves a supernatural designer. The courts in Edwards and McLean expressly found that this characteristic removed creationism from the realm of science and made it a religious proposition. Edwards, 482 U.S. at 591-92; McLean, 529 F. Supp. at 1265-66. Prominent ID proponents have made abundantly clear that the designer is supernatural. Defendants’ expert witness ID proponents confirmed that the existence of a supernatural designer is a hallmark of ID. First, Professor Behe has written that by ID he means “not designed by the laws of nature,” and that it is “implausible that the designer is a natural entity.” (P-647 at 193; P-718 at 696, 700). Second, Professor Minnich testified that for ID to be considered science, the ground rules of science have to be broadened so that supernatural forces can be considered. (38:97 (Minnich)). Third, Professor Steven William Fuller testified that it is ID’s project to change the ground rules of science to include the supernatural. (Trial Tr. vol. 28, Fuller Test., 20-24, Oct. 24, 2005). Turning from defense expert witnesses to leading ID proponents, Johnson has concluded that science must be redefined to include the supernatural if religious challenges to evolution are to get a hearing. (11:8-15 (Forrest); P-429). Additionally, Dembski agrees that science is ruled by methodological naturalism and argues that this rule must be overturned if ID is to prosper. (Trial Tr. vol. 5, Pennock Test., 32-34, Sept. 28, 2005). Further support for the proposition that ID requires supernatural creation is found in the book Pandas, to which students in Dover’s ninth grade biology class are directed. Pandas indicates that there are two kinds of causes, natural and intelligent, which demonstrate that intelligent causes are beyond nature. (P-11 at 6). Professor Haught, who as noted was the only theologian to testify in this case, explained that in Western intellectual tradition, non-natural causes occupy a space reserved for ultimate religious explanations. (9:13-14 (Haught)).

In other words, the attempt to present ID as "scientific" was a BARE FACED LIE and KNOWN TO BE SUCH BY ITS PROPAGANDISTS WHEN THEY SET OUT TO DO SO.

Once more, with respect to the Wedge Strategy document cited above, which the IDists themselves published, we have this interesting revelation:

The social consequences of materialism have been devastating. As symptoms, those consequences are certainly worth treating. However, we are convinced that in order to defeat materialism, we must cut it off at its source. That source is scientific materialism. This is precisely our strategy. If we view the predominant materialistic science as a giant tree, our strategy is intended to function as a "wedge" that, while relatively small, can split the trunk when applied at its weakest points. The very beginning of this strategy, the "thin edge of the wedge," was Phillip ]ohnson's critique of Darwinism begun in 1991 in Darwinism on Trial, and continued in Reason in the Balance and Defeating Darwinism by Opening Minds. Michael Behe's highly successful Darwin's Black Box followed Johnson's work. We are building on this momentum, broadening the wedge with a positive scientific alternative to materialistic scientific theories, which has come to be called the theory of intelligent design (ID). Design theory promises to reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions.

In other words, in the highlighted parts above, the "fellows" of the ID movement openly admit that they are seeking to destroy science as currently constituted (first boldface highlight above) and replace it with a bastardised version that is subservient to a particular religious ideology (second boldface highlight above).

It is also interesting to note that William Dembski, one of the "Fellows" of the incongruously named "Discovery Institute" (whose only "discovery" thus far seems to have been the level of gullibility of American religious believers - this organisation certainly hasn't made any scientific discoveries) also blew the cover of the ID movement in his book Intelligent Design: The Bridge Between Science And Theology, whose title alone should be revealing. I'll provide the following quotes, which are apposite with respect to the real agenda of this organisation and its propagandists:

My thesis is that the disciplines find their completion in Christ and cannot be properly understood apart from Christ ... The point to understand here is that Christ is never an addendum to a scientific theory but always the completion.

Not only does intelligent design rid us of this ideology, which suffocates the human spirit, but, in my personal experience, I've found that it opens the path for people to come to Christ. Indeed, once materialism is no longer an option, Christianity again becomes an option. True, there are then also other options. But Christianity is more than able to hold its own once it is seen as a live option. The problem with materialism is that it rules out Christianity so completely that it is not even a live option. Thus, in its relation to Christianity, intelligent design should be viewed as a ground-clearing operation that gets rid of the intellectual rubbish that for generations has kept Christianity from receiving serious consideration.

I think at a fundamental level, in terms of what drives me in this is that I think God's glory is being robbed by these naturalistic approaches to biological evolution, creation, the origin of the world, the origin of biological complexity and diversity. When you are attributing the wonders of nature to these mindless material mechanisms, God's glory is getting robbed. [...] And so there is a cultural war here. Ultimately I want to see God get the credit for what he’s done — and he's not getting it.

That pretty much exposes the real purpose of ID - to drag the developed world kicking and screaming back to the days of Inquisitional religion and its political hegemony over society. In short, Dembski and his ilk are theocrats, and presumably long for the return of politically interfering and muscularly coercive religion, because they think they'll be the ones running the show. Unfortunately, quite a few theocrats have made that mistake in the past, only to discover that when someone else ends up in charge instead, they're the ones being thrown into the dungeons as "heretics". But I've noticed how supernaturalists have a habit of always thinking they'll be dishing it out in a future theocracy, instead of being on the receving end. Typical of the hubris that tends to be a fellow traveller with supernaturalism.

So, Behe's status as some sort of "authority" has been roundly flushed down the toilet by the above, and indeed, the status of the entire professional creationism movement as being in a position to offer genuine, substantive knowledge about relevant biological questions, is also subjected to a one way trip to the sewage treatment plant.

Now it's time to subject to the same treatment, some other assertions that have been brought here, viz:

Yet if the theory can explain much more complicated topics that involve even abstract thinking, why does it have trouble with simpler topics that don’t? If it accounts for, say, the Magna Carta, why does it struggle with the colors of butterfly wings?

Given that I now have thirty peer reviewed papers covering the topic of butterfly wing patterns and their evolution in my collection, and said collection is an incomplete survey of the extant literature, I'll point and laugh at the above assertion, knowing it to be complete horseshit.

But there’s a big ugly fly in that ointment. The existence of sex itself has stumped Darwinists for 150 years!

Ha ha ha ha ha. Hmm, I have 29 peer reviewed papers in my collection on the evolution of sex. Looks like another assertion of yours is seen to be horseshit.

What can the theory account for? If it can’t explain even color patterns, how much has it been exaggerated?

Ha ha ha ha ha ha. Those 30 papers on the evolution of butterfly wing patterns, and all the material I posted earlier, covering which genes have been found to govern pattern element spacing and which genes govern colour filling, stomp on your fatuous assertion above.

Science can’t tell if cholesterol is bad for modern humans, who can be studied in great detail.

Lie. Oh wait, there are numerous scientific papers covering the known effects of the various lipoproteins that are involved in cholesterol transport, low density lipoproteins being the principal implicated agencies in such conditions as atherosclerosis and cardiovascular disease. Do tell us all where you got this drivel from, because whoever fed it to you was taking you for a bigger ride than a 7 foot biker in a prison cell.

Oh, and I've dealt with Snoke above. His paper was a rigged crock.

So, do tell us all, Vanderbilt old bean, do you have any more manifest bullshit of this sort to amuse us with, or are you starting to run out of bullshit to post at long last? Only I gather you've acquired quite a track record for evasion, baits and switches, manifest fabrications, etc., here before my arrival, and now I can add quote mining to your list of instances of discoursive malfeasance. Always amusing to see creationists behave true to type, even if the regularity with which this occurs can become tedious at times.

Now, if you want to complain about the post volume, I have one simple answer for you. Those who paid attention in class won't be complaining, they'll be filing away the information with gusto. They'll appreciate the fact that someone exerted a certain minimum diligent effort in order to expose your vacuous posturings and vainglorious attempts at self-aggrandisement, redolent with the rancid stench of maleficent masquerade, as you try to pretend that your adherence to sad mythological fantasies, purportedly puts you in a position to critique the work of people whose toenail clippings are manifestly more knowledgeable than you.

And with that, I think it's time to take a break, and enjoy something relaxing. JavaScript, here I come ...

arakish's picture
@ Cali

@ Cali

All your links generate "Page Not Found" errors...

rmfr

Old man shouts at clouds's picture
@ Cali

@ Cali

*stands on chair whooping and applauding* *whistles* *cheers until hoarse. * crowd goes quiet as they realise the troll in the corner is mortally wounded....

arakish's picture
Found another location for

Found another location for the transcripts.

https://ncse.com/creationism/legal/kitzmiller-trial-transcripts

rmfr

Calilasseia's picture
Some of those links have

Some of those links have changed since I last used them. Fortunately, the link to the Lynch paper in Protein Science is still valid. :)

arakish's picture
And not a problem for me. If

And not a problem for me. If I find an error, I try to find a solution and post it as quickly as possible.

I have been reading those transcripts all day as I have been here "at the shack" up in Yellowstone. Can get quite boring...

rmfr

Grinseed's picture
I was going to apologise for

I was going to apologise for the length of this....and it might all be superfluous after Cal's superb offering, but I spent too much time typing it up not to post it.

Behe's article is one large strawman. He seems obsessed with Darwin's original theory, which he misrepresents, either ignorantly or maliciously, without any recourse to more recent developments in evo devo and genome research.
It is surprising a biochemist taking his lead from a sub-title in The New York Times Magazine, that 'august scientific peer reviewed journal' (jk) that asks “The extravagant splendor of the animal kingdom can’t be explained by natural selection alone — so how did it come to be?”.

Darwin never argued that natural selection was the only mechanism in his theory. That was Alfred Russel Wallace, who rejected sexual selection outright and fiercely argued that natural selection being the only natural mechanism capable to explain the diversity of life, except for the human brain which he staunchly held to be only possible by the direct intervention of a god which he was flatly unable to evidence.

Darwin stated that sexual selection provided the variation within populations of species on which the pressures of natural selection worked to detemine traits surviving into following generations. He also suggested that concepts of beauty were determined and maintained through sexual selection despite what the author of the magazine article and presumably Behe, thought.

Darwin enlarged on the effects of sexual selection in The Descent of Man and Expression of Emotions in Man and Animals.

And from recent threads here in AR we certainly know that science is not struggling with the colours of butterfly wings. That remains a theist struggle.

Nutritionists and health authorities debating over food has nothing to do with Darwin or his theory. Nutrition claims has more to do with the food industry and its been a see-saw struggle during my 60 years between various vested manufacturing and agricultural interests. Chocolate, red meat, carbo-hydrates were bad for you twenty years ago, and now they are absolutely vital for maintaining and lengthening your life, then bad, then good etc etc. Its a trend that will continue well after I stop eating for good.

True it is that "in Darwin's day" the cell was thought to hold something called "protoplasm" but for a biochemist to insist that "modern biochemists have discovered to their surprise that the cell is chock-full of sophisticated machines — actual machines, made of molecules. Like the machines of our everyday world (say, a lawn mower)" This is a supreme over simplification that beggars belief.
I suggest they were even more genuinely surprised to discover homeoboxes in the genetic makeup of every living organism on the planet.
Behe lost me and I am sure most readers with his lawnmower in the garden shed analogy because Darwin had no recourse to modern biochemistry. None the less his theory has been proven true over and over for nearly 200 years.

“The extravagant splendor of the animal kingdom can’t be explained by natural selection alone" Darwin would have agreed wholeheartedly.
"— so how did it come to be?”
One thing we know for sure is that Behe and his supporters have little understanding of it.

Calilasseia's picture
@Grinseed

@Grinseed

Indeed, one of the aspects of scientific development, which dishonest pedlars of apologetics routinely ignore, is the aspect known as consilience, namely, the manner in which findings arising from one piece of research in one discipline, are repeatedly reinforced by other findings, arising from other research in other disciplines, that appear unrelated to the original findings when viewed by the untrained or superficial eye.

Historically, Darwin never corresponded with Gregor Mendel, as far as I am aware, and likewise, as far as I am aware, Mendel was not made aware in detail of Darwin's ideas. Mendel, in any case, sadly abandoned full time scientific work, as a result of being burdened with the adminiistrative responsibilities of heading a monastery, after the publication of his landmark paper on heredity. That landmark paper, also sadly, did not receive the recognition it was due until some time after Mendel's death in 1884.

Once that landmark paper was recognised on the basis of its merits, however, scientists quickly set to work generating new experimental results, based upon Mendel's ideas. The fun part being, of course, that this new experimental work in genetics, possessed the potential to refute Darwin's ideas. But lo and behold, far from refuting Darwin's ideas, that work reinforced them. The advent of molecular biology, likewise, possessed the potential to torpedo evolutionary theory below the waterline, but instead, its results once again reinforced evolutionary ideas. Indeed, one of the developments arising from the world of molecular biology, was Susumu Ohno's neutral theory, which, instead of being a refutation of evolutionary postulates, constituted an addition to those postulates, extending their remit. Even better, Ohno's work gave us a direct molecular test allowing us to determine whether or not selection processes are active and acting upon a particular gene. Here's how that test works.

Whenever a mutation appears in a gene, scientists can detect that mutation, and determine whether or not that mutation will affect the synthesis product arising from that gene, courtesy of the hard work that's been done beforehand determining the mapping between DNA nucleotide arrangements and amino acids in proteins (the so-called "genetic code"). It so happens that when one examines that mapping in detail, some amino acids are associated with more than one nucleotide arrangement, or "codon". As a corollary, it's possible for a mutation to occur in a gene, but that mutation doesn't result in a change in the amino acid found in the particular location of interest in the protein molecule produced. For example, the codon CTC (corresponding to cytosine, thymine and cytosine nucleotides in sequence along the DNA strand) is associated with the insertion of the amino acid leucine in the protein being synthesised, but this arrangement of nucleotides is not the only one resulting in the selection of leucine during the requisite part of protein synthesis. There are no less than six codons that are associated with the selection of the amino acid leucine - these are TTA, TTG, CTT, CTC, CTA and CTG. Change a CTC codon to a CTA codon in a DNA strand, and the final protein still ends up with a leucine molecule inserted into the requisite position. Mutations of this sort, that don't result in amino acid changes in the target protein, are known as synonymous mutations.

On the other hand, change a TTA to a TTC or TTT codon, and this does result in a change of amino acid in the target protein - namely, a switch from leucine to phenylalanine. Which in turn could exert some interesting effects of its own upon protein folding or the reactive mechanics of the active site, if the protein happens to be an enzyme, and that amino acid is a part of the active site. A mutation of this sort is a non-synonymous mutation, and can, in the right circumstances, result in functional changes.

This is where the fun starts. If you have a population to work with, you can sample the genes of that population, and over several generations, determine how often those genes acquire synonymous or non-synonymous mutations. Let N be the number of non-synonymous mutations found to be appearing, and S the number of synonymous mutations appearing. Now, calculate log(N/S).

If log(N/S) is close to zero, then this means that the mutations affecting the gene are largely neutral. Selection processes are only affecting those genes to a marginal extent. If log(N/S) is a negative value beyond, say -0.5, then what is known as purifying selection is at work on the gene (the larger the magnitude of the value, the stronger the effect), because non-synonymous mutations on that gene are usually deleterious, and as a result, have a habit of being removed from the population over time. If log(N/S) is a positive number beyond, say, 0.5, then positive selection for a new genotype is at work on the gene (again, the larger the magnitude of the value, the stronger the effect), because in this case, non-synonymous mutations are conferring some advantage upon inheritors of the new genotype.

So we not only have corroboration of the effects of selection processes via molecular biology, but that corroboration allows us to subject to direct test, whether or not a given gene is being subject to selection processes, and in addition, determine the type of selection process that is being applied to that gene. When Ohno initially conceived his ideas about neutral theory, he probably did not suspect that those ideas would lead to a direct molecular test for the presence or absence of selection processes active upon a given gene, but that's precisely what happened. Consequently, Ohno's work not only extended our understanding of evolution to encompass neutral mutations (and their role as potential foundations for later positively selectable mutations), but gave us an independent means of detecting selection processes at work, other than population counts.

That's consilience at work. And you'll only find it operating in science.

J N Vanderbilt III's picture
Wow all that posted text from

Wow all that posted text from Calessia and you didn’t accuse him of plagiarism? Here’s some plagiarism vindicating Behe for ya::;;;
(Again you aren’t going to win the numbers game)

A new paper in Proceedings of the National Academy of Sciences USA has vindicated Michael Behe in one of the central controversies over his 2007 book The Edge of Evolution. Behe already reported here on the paper, which found that multiple mutations, at least two, are required to confer resistance to the drug chloroquine on malaria parasites:

A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity. … The findings presented here reveal that the minimum requirement for (low) CQ transport activity in both the ET and TD lineages of CQR PfCRT is two mutations.

(Summers et al., “Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite’s chloroquine resistance transporter,” Proceedings of the National Academy of Sciences USA, Vol. 111: E1759-E1767 (April 29, 2014) (emphasis added).)
behe edge.jpgWhy does it matter? As Dr. Behe explained, this was a major point of contention among critics of his book. They claimed that Behe mistakenly thought chloroquine resistance required multiple simultaneous mutations, when in actuality it could arise through sequential mutations, each conferring a successively greater resistance-advantage. It can no longer be denied that the critics were dead wrong: chloroquine resistance does not arise at all until two mutations or more are present.

(To be precise, the paper found that the two minimum mutations break down as follows: one specific mutation is needed, plus a second mutation that’s also needed which can occur in one of two locations. As the paper puts it, “Given that all known PfCRT haplotypes contain either N75E/D or N326D, these results indicate that PfCRT acquires the ability to transport CQ via one of two main mutational routes, both of which entail the introduction of K76T plus the replacement of an asparagine (N75 or N326) with an acidic residue.”)

From the Beginning, the Critics Mischaracterized Behe
The critics were wrong from the outset. Behe’s argument in The Edge of Evolution didn’t depend on whether chloroquine resistance arose in a stepwise manner, or only after multiple mutations accumulated. His argument was based upon an empirically observed data point from public health studies which found that chloroquine resistance arose in about 1 in every 1020 organisms. He had a strong citation for this empirical observation: Nicholas White, “Antimalarial Drug Resistance,” Journal of Clinical Investigation, Vol. 113: 1084-1092 (2004). He called the mutations (whatever they were) that caused chloroquine resistance a “chloroquine complexity cluster” or CCC. Whatever molecular mechanisms may be behind a CCC, empirical data showed that 1020 cells are required in order to produce one. Behe pointed out that if a trait required the molecular equivalent of two CCC’s before providing any advantage, then that would pose major problems for Darwinian evolution.

It’s a simple calculation. Behe observed that if 1020 organisms were required to obtain one CCC, then the square of that amount — 1040 organisms — would be required to evolve a trait that required two CCC’s before providing any advantage. However, as Behe observed, a total of only 1040 organisms have lived on Earth over the entire history of the planet. As Behe put it:

Recall that the odds against getting two necessary, independent mutations are the multiplied odds for getting each mutation individually. What if a problem arose that required a cluster of mutations that was twice as complicated as a CCC? (Let’s call it a double CCC.) For example, what if instead of the several amino acid changes needed for chloroquine resistance in malaria, twice that number were needed? In that case the odds would be that for a CCC times itself. Instead of 1020 cells to solve the evolutionary problem, we would need 1040 cells. Workers at the University of Georgia have estimated that about a billion billion trillion (1030) bacterial cells are formed on the earth each and every year. … If that number has been the same over the entire several-billion-year history of the world, then throughout the course of history there would have been slightly fewer than 1040 cells, a bit less than we’d expect to need to get a double CCC. The conclusion, then, is that the odds are slightly against even one double CCC showing up by Darwinian processes in the entire course of life on earth.

(Michael Behe, The Edge of Evolution: The Search for the Limits of Darwinism, p. 135 (Free Press, 2007).)
Behe inferred, based upon the great rarity of a CCC evolving, that it was a trait that probably required multiple mutations. Behe’s argument didn’t turn on that inference, but it was a reasonable one. Richard Dawkins himself used exactly the same sort of reasoning in other contexts to infer that a trait required multiple mutations to evolve.

Will Ken Miller, Jerry Coyne, Paul Gross, Nick Matzke, Sean Carroll, Richard Dawkins, and PZ Myers Now Apologize to Michael Behe?
Behe’s critics misread him as saying that a single CCC necessarily required multiple simultaneous mutations, and castigated Behe for allegedly ignoring the possibility of a single CCC arising via sequential mutations. For example:

Kenneth Miller: “It would be difficult to imagine a more breathtaking abuse of statistical genetics. Behe obtains his probabilities by considering each mutation as an independent event, ruling out any role for cumulative selection, and requiring evolution to achieve an exact, predetermined result.” (Nature, 2007)
Paul Gross: “Behe assumes simultaneous mutations at two sites in the relevant gene, but there is no such necessity and plenty of evidence that cumulativeness, rather than simultaneity, is the rule. As Nature‘s reviewer (Kenneth R. Miller) notes, ‘It would be difficult to imagine a more breathtaking abuse of statistical genetics.'” (The New Criterion, 2007)
Jerry Coyne: “What has Behe now found to resurrect his campaign for ID? It’s rather pathetic, really. … Behe requires all of the three or four mutations needed to create such an interaction to arise simultaneously. … If it looks impossible, this is only because of Behe’s bizarre and unrealistic assumption that for a protein-protein interaction to evolve, all mutations must occur simultaneously, because the step-by-step path is not adaptive.” (The New Republic, 2007)
Nick Matzke: “Here is the flabbergasting line of argument. First, Behe admits that CQR evolves naturally, but contends that it requires a highly improbable simultaneous double mutation, occurring in only 1 in 1020 parasites. … The argument collapses at every step.” (Trends In Ecology and Evolution, 2007)
Sean Carroll: “Behe makes a new set of explicit claims about the limits of Darwinian evolution, claims that are so poorly conceived and readily dispatched that he has unwittingly done his critics a great favor in stating them. … Behe’s main argument rests on the assertion that two or more simultaneous mutations are required for increases in biochemical complexity and that such changes are, except in rare circumstances, beyond the limit of evolution. .. Examples of cumulative selection changing multiple sites in evolving proteins include … pyrimethamine resistance in malarial parasites — a notable omission given Behe’s extensive discussion of malarial drug resistance. … [T]he argument for design has no scientific leg to stand on.” (Science, 2007)
Richard Dawkins: “Trapped along a false path of his own rather unintelligent design, Behe has left himself no escape. Poster boy of creationists everywhere, he has cut himself adrift from the world of real science. … If correct, Behe’s calculations would at a stroke confound generations of mathematical geneticists, who have repeatedly shown that evolutionary rates are not limited by mutation.” (New York Times, 2007)
And then of course there’s PZ Myers. He made much the same criticisms, and also wrote:
Behe isn’t just a crackpot who thinks he has a novel explanation for an evolutionary mechanism — he’s a radical anti-evolutionist extremist who rejects the entire notion of the transformation of species by natural processes. … Most of the arguments are gussied up versions of the kind of handwaving, ignorant rationalizations you’d get from some pomaded fundagelical Baptist minister who got all his biology from the Bible, not at all what you’d expect from a tenured professor of biochemistry at a good university — throwing in an occasional technical gloss or mangled anecdote from the literature is only a gloss to fool the rubes.
While these comments were made a few years ago, many ENV readers who follow this debate might remember just how gleefully harsh the critics were towards Behe after his book The Edge of Evolution came out. Even if Behe had been wrong, the critics’ extreme incivility would have been unscholarly and inappropriate. But now it turns out all these critics were wrong. You get no resistance to chloroquine whatsoever unless at least two mutations are present to begin with. You might be able to get some cumulative selection after that, where successive mutations improve resistance up to a certain point. It is, however, by definition a multimutation feature.

Behe reasonably inferred that chloroquine resistance requires multiple mutations. He was right. His critics misunderstood his argument and thought this inference was a crucial plank in his reasoning. It wasn’t.

But it now turns out that the position Behe’s critics attributed to him, and then railed against, was itself correct. Even a single CCC apparently requires multiple mutations before conferring any advantage. In fact, it’s probably very close to the “edge” of evolution that Behe identified in his book.

Is an apology from Behe’s critics then forthcoming? In a world where debates were conducted with the goal of discovering truth rather than scoring points, it sure ought to be. Unfortunately, I’m not sure we live in that world.

What we’ll probably get is nothing more than PZ Myers’s concession, offered in the context of the rant quoted above:

Fair enough; if you demand a very specific pair of amino acid changes in specific places in a specific protein, I agree, the odds are going to be very long on theoretical considerations alone, and the empirical evidence supports the claim of improbability for that specific combination.
Well, that’s more or less what’s required to generate chloroquine resistance. We’ll gladly take this — i.e., simply being proven right — in lieu of an apology.

CyberLN's picture
JNV3, I’ll ask again...are

JNV3, I’ll ask again...are you a biologist? Have you ever had this discussion with an evolutionary biologist?

Sheldon's picture
Here is what the U.S.

Here is what the U.S. National Academy of Sciences thinks of creationism...so your dishonesty in pointing to them validating one of Behe's claims is manifest, as he is a creationist we can be assured they were not vindicating any of his creationist claims.

"The U.S. National Academy of Sciences has stated that intelligent design "and other claims of supernatural intervention in the origin of life" are not science because they cannot be tested by experiment, do not generate any predictions, and propose no new hypotheses of their own."
----------------------------------------------------

Here are some more examples of science giving unequivocal condemnation of creationism and ID as unscientific.

"In September 2005, 38 Nobel laureates issued a statement saying "Intelligent design is fundamentally unscientific; it cannot be tested as scientific theory because its central conclusion is based on belief in the intervention of a supernatural agent." In October 2005, a coalition representing more than 70,000 Australian scientists and science teachers issued a statement saying "intelligent design is not science" and calling on "all schools not to teach Intelligent Design (ID) as science, because it fails to qualify on every count as a scientific theory"."

"In 1986, an amicus curiae brief, signed by 72 US Nobel Prize winners, 17 state academies of science and 7 other scientific societies, asked the US Supreme Court in Edwards v. Aguillard, to reject a Louisiana state law requiring that where evolutionary science was taught in public schools, creation science must also be taught. The brief also stated that the term "creation science" as used by the law embodied religious dogma, and that "teaching religious ideas mis-labeled as science is detrimental to scientific education". This was the largest collection of Nobel Prize winners to sign a petition up to that point. According to anthropologists Almquist and Cronin, the brief is the "clearest statement by scientists in support of evolution yet produced."

arakish's picture
JNV3: "Wow all that posted

JNV3: "Wow all that posted text from Calessia and you didn’t accuse him of plagiarism? Here’s some plagiarism vindicating Behe for ya."

Calilasseia provided links to the articles he quoted. Where as you just plagiarized with no links, but at least you kind of provide some attribution.

rmfr

Calilasseia's picture
Oh dear. Time to remind

Oh dear. Time to remind someone of some elementary concepts at work here.

Elementary concept number 1: when someone provides a full citation for the work they're quoting, and manifestly presents that work as the work of the cited authors, this is NOT plagiarism. Plagiarism proper, consists of presenting the writing of others, as if it were one's own, without attribution of any sort. Do learn this elementary concept before embarrassing oneself further on a globally accessible public medium.

Elementary concept number 2: try reading the content of a scientific paper in full yourself, before trying to pretend that the paper says what your copy-paste apologetics alleges it to say.

Because, wait for it, when we actually look at the full content of the paper in question, we find that the apologetic hyperbole about Behe being "vindicated", is actually so much hot air. Because what that paper actually states, is that an analysis of chloroquine resistance in multiple Plasmodium falciparum strains, demonstrates that the ability of the parasite to avoid the effects of chloroquine is incomplete after two mutations, this only conferring low chloroquine transport activity by the PfCRT, and that full activity of the PfCRT was actually attained after a minimum of four mutations. This is even stated in the abstract you quoted. Furthermore, the paper goes on to demonstrate that parasites with low chloroquine transport activity can still be defeated using chloroquine, simply by increasing the dose.

Meanwhile, I notice how you try to prop up Behe by resorting to the very mechanism you're trying to deny exists, courtesy of this passage:

They claimed that Behe mistakenly thought chloroquine resistance required multiple simultaneous mutations, when in actuality it could arise through sequential mutations, each conferring a successively greater resistance-advantage.

Apparently, you're happy to accept this notion of sequential mutations being capable of producing novelty, when it appears in some apologetics you've copy-pasted from a duplicitous creationist website, but reject the exact same mechanisms being applicable elsewhere, when said applicability destroys your assertions, and resort to infantile parrotting of your tiresome "numbers game" apologetic garbage in response. But I'm used to seeing this level of rampant hypocrisy from mythology fanboys.

So, you're happy to see Behe purportedly "vindicated" by the existence of data demonstrating that an organism won what you sneeringly disparage as "the numbers game", but when data demonstrating that other organisms have also won "the numbers game", in a manner that destroys your worthless assertions, you resort to parroting this apologetic garbage, because you have no real, substantive answer to the data. But then I've yet to meet a creationist that does.

Indeed, the apologetic defence you're attempting to erect here destroys the validity of Behe's own calculations, purportedly demonstrating that too many organisms are required to exist in order for the phenomenon to occur. If all that's required is for one organism to acquire one mutation, followed by the persistence of that mutation in subsequent generations, then the appearance of a second mutation, then Behe's numbers are wildly unrealistic. In short, the actual knowledgeable scientists who dissected Behe's garbage and found it wanting, were entirely correct.

For example, here's how Kenneth Miller dissected Behe's assertions, covered in more detail here:

Behe also falsely claims that a single mutation would always be "strongly deleterious" so would be quickly eliminated from the gene pool, so any accumulative effects of natural selection can be disregarded.

But Behe was dead wrong about it being "strongly deleterious." In fact, it seems to have no effect on transport activity at all. A neutral mutation like this can easily propagate through a population, and field studies of the parasite confirm that is exactly what has happened. In fact, a 2003 study recommended against using the K76T mutation to test for chloroquine resistance since that same mutation was also found in 96% of patients who responded well to chloroquine. Clearly, K76T wouldn't have become so widespread if it were indeed "strongly deleterious," as Behe states it must be. This is a critical point, since Behe’s probability arguments depend on this incorrect claim.

Miller continues, in the same article, with this nice little revelation:

Directly contradicting Behe’s central thesis, the PNAS study also showed that once the K76T mutation appears, there are multiple mutational pathways to drug resistance. In most of these, each additional mutation is either neutral or beneficial to the parasite, allowing cumulative natural selection to gradually refine and improve the parasite’s ability to tolerate chloroquine. One of those routes involves a total of seven mutations, three neutral and four beneficial, to produce a high level of resistance to the drug. Figure 4, taken from the Summers et al PNAS paper, makes this point in graphic fashion, showing the multiple mutational routes to high levels of transport, which confer resistance to chloroquine.

View Figure 4 here

Pathways of this sort, involving sequential mutations, are exactly what Behe had tried to rule out, as I wrote in my own review of his book in 2007:

"Behe obtains his probabilities by considering each mutation as an independent event, ruling out any role for cumulative selection, and requiring evolution to achieve an exact, predetermined result. Not only are each of these conditions unrealistic, but they do not apply even in the case of his chosen example. First, he overlooks the existence of chloroquine resistant strains of malaria lacking one of the mutations he claims to be essential (at position 220). This matters, because it shows that there are several mutational routes to effective drug resistance. Second, and more importantly, Behe waves away evidence suggesting that chloroquine resistance may be the result of sequential, not simultaneous, mutations."

We now know, courtesy of the PNAS paper, that such criticisms were right on target. There are indeed several mutational routes to drug resistance, and they are indeed the result of sequential, not simultaneous mutations. This matters because the assumption of simultaneous mutations is at the very heart of Behe’s math. That’s how he justifies multiplying one probability times another times another to conclude that complex traits are beyond the reach of the evolutionary process. To put it clearly, the problem with the logic of The Edge isn’t the specific figure of one chance in 10^20, but the way in such probabilities are multiplied. In fact, it doesn’t really matter if chloroquine resistance emerges at a probability of one chance in 10^20, one in 10^15, or even one chance in 10^10. The problem is the logic that Behe uses to calculate the chances of evolution producing two or more CCCs. As we will see, that’s the most critical part of his argument — and it’s wrong.

Miller explains (I'll provide the quote in a moment) that Behe has basically committed, in this work what I've known and documented for some time as "The Serial Trials Fallacy". Here's how Miller explains this:

Here’s how it works. Let’s accept Behe’s number of 1 in 10^20 for the evolution of a complex mutation like his CCC. As he admits, CCC’s have arisen multiple times in the malaria parasite population since the drug was first introduced in 1947. In fact, resistance to the drug appeared in the late 1950s and early 1960s, within just 15 years of its widespread use. So it only took a decade and a half for one of Behe’s CCC’s to emerge in the parasite population. Now, suppose that another drug, equal in effectiveness to chloroquine, were to come into wide use. According to Behe, resistance to both drugs would require two CCCs, and the probability of double resistance arising would be a CCC squared. That’s 1 in 10^20 x 10^20 or one chance in 1 in 10^40. According to Behe’s math, that’s such a large number that we can call it impossible:

“…throughout the course of history there would have been slightly fewer than 1040 cells, a bit less than we’d expect to need to get a double CCC. The conclusion, then, is that the odds are slightly against even one double CCC showing up by Darwinian processes in the entire course of life on earth.” (Behe, 2007, p. 63).

Wow! Not even once in the history of life on earth? Pretty impressive. But the math is wrong, and it’s easy to see why. Chloroquine resistance arose in just a decade and a half, and is now common in the gene pool of this widespread parasite. Introduce a new drug for which the odds of evolving resistance are also 1 in 10^20, and we can expect that it will take just about as long, 15 years, to evolve resistance to the second drug. Once you get that first CCC established in a population, the odds of developing a second one are not CCC squared. Rather, they are still 1 in 10^20. Behe gets his super-long odds by pretending that both CCCs have to arise at once, in the same cell, purely by chance. They don’t, and I pointed this out in my Nature review when Behe attempted to apply his reasoning to human genetics:

"Behe, incredibly, thinks he has determined the odds of a mutation “of the same complexity” occurring in the human line. He hasn’t. What he has actually done is to determine the odds of these two exact mutations occurring simultaneously at precisely the same position in exactly the same gene in a single individual. He then leads his unsuspecting readers to believe that this spurious calculation is a hard and fast statistical barrier to the accumulation of enough variation to drive darwinian evolution.

"It would be difficult to imagine a more breathtaking abuse of statistical genetics."

More details can be read on this page, where Miller outlines the bait and switch involved in pretending that evolution can't produce something that it demonstrably produced in a living organism. Basically, Behe's argument consists of assuming that the two mutations have to arise simultaneously in the same cell. This is patent nonsense. Mutation 1 can arise in one cell, be disseminated to other cells in future generations, then mutation 2 can appear in one of those other cells, at which point, that later cell becomes the first to benefit. This assumption is inherent in his use of multiplication of probabilities, which is applied when we're doing serial probability trials. However, when one is performing many trials in parallel, the calculation changes. Asking one person to get 10 heads in a row by tossing 10 coins is pretty unlikely, but if the entire population of China is participating in the trial, all tossing 10 coins simultaneously, then out of those 1 billion people, no less than 976,000 of those people should see 10 heads in a row. Puts a different perspective on matters, doesn't it?

As a corollary, hyperbolic assertions about Behe's "vindication" are not merely hyperbolic, they're outright false. That's before we factor in to the matter, that the copy-pasted apologetics above is plain, flat, wrong for the same reasons as Behe.

But once again, this is all tiresomely familiar creationist mendacity I've been encountering for over a decade. And does NOT address the large amount of data I presented earlier, demonstrating that Behe was utterly humiliated at the Dover Trial, and published a paper with another creationist that was a blatant bait and switch, exposed by another scientist whose work I presented honestly as such. Ah, the heady smell of creationist whataboutery and red herrings is in the air ...

Grinseed's picture
I always find the stories

I always find the stories about the scientist searching for one thing discovering something different and more profound, charming and exciting. Consilience is a new entry for my vocabulary and Ohno is a new science hero.
I did a quick search for Ohno and was surprised to how important his work was particularly in regard to sexual selection in mammilian embryos. Then comes his whismical translation of genetic sequencing into music. "Cute but not profound", as one colleague commented.
I remain disappointed that his name and work is new to me, but happy to have been introduced at last.

You mentioned the expected potential of molecular biology to "torpedo evolutionary theory". That reminds me of Thomas Morgan who, critical of Mendel's theory of inheritance, of chromosonal theory and also of aspects of Darwin's theory, started breeding Drosophila to prove his views. When the first results came in he conceded his error on all three and his continued research method has yielded vast information about genetics during the most of the 20th C.
That's the real appeal of true science; the acceptance of error in the face of obvious evidence. Not a virtue widely practiced in some areas.
Back to my voluminous reading.

J N Vanderbilt III's picture
“Asking one person to get 10

“Asking one person to get 10 heads in a row by tossing 10 coins is pretty unlikely, but if the entire population of China is participating in the trial, all tossing 10 coins simultaneously, .....”

Why only 10 coins, ? try 100 then compute.

CyberLN's picture
JNV3, I’ll ask again...are

JNV3, I’ll ask again...are you a biologist? Have you ever had this discussion with any evolutionary biologists?

arakish's picture
@ CyberLN

@ CyberLN

You know he ain't gonna answer that question. I and others have asked him and he just pulls a John Breezy.

Good luck, though.

rmfr

Calilasseia's picture
“Asking one person to get 10

“Asking one person to get 10 heads in a row by tossing 10 coins is pretty unlikely, but if the entire population of China is participating in the trial, all tossing 10 coins simultaneously, .....”

Why only 10 coins, ? try 100 then compute.

Congratulations on failing to understand anything about the point I was making, namely, that calculations that are valid for serial trials are not valid for parallel trials, especially if the parallel trials involve a large number of participating entities. But please, do continue demonstrating your complete failure of understanding on a globally accessible public forum, so that a large number of people can observe your complete failure of understanding for themselves.

Oh, and don't even bother going anywhere near the "one true sequence" fallacy, which is where you are heading with your latest fatuous substitute for a substantive reply. Because that one is easily destroyed as well. But the mere fact you posted the above comment, once again demonstrates that you didn't even understand the copy-paste apologetics you posted here from your beloved creationist websites, let alone the actual biological realities contained in the papers destroying said apologetics.

Though I'm used to seeing this sort of drivel emanating from people who think that mythology counts for more than actual empirical data, and whose view of the biosphere consists, at bottom, of treating it purely as plunderable and exploitable, instead of being worthy of understanding in its own right. Hardly surprising given the nonsense that is contained in the requisite mythology, such as that farcical piece of cortical excrement in Genesis 30:37-41, in which mutations were purportedly introduced into various livestock animals, simply by arranging for the parents to shag alongside various coloured sticks. Last time I checked the actual science, the only coloured sticks capable of performing this trick would have been fashioned from weapons grade plutonium or high-level nuclear waste, but even if we leave this aside, there's the little matter of how this drivel was tossed into the bin by a 19th century Austrian monk, courtesy of his diligent experiments with peaflowers, and the careful documentation thereof. You might have heard of the monk in question ... his name was Gregor Mendel.

Now, if you really want to go down the road of the "one true sequence" fallacy", I'll enjoy subjecting whatever vacuous apologetic fabrications you present here to try and prop up this fallacy, to much-deserved immolation.

Old man shouts at clouds's picture
@ Cali

@ Cali

Nice to have a Combat Engineer and explosives specialist in our camp...Love your work. Tell me do you teach the SAS to lay minefields in your spare time...??

Love it....

gmoulds's picture
What a completely fatuous

What a completely fatuous post. You provide no proof that DNA is a code. Even if you assume DNA is a code, you also provide no evidence that such a code must be created by intelligence. Of course, your ultimate mistake is the oldest one. You leap to assuming there is such an intelligence without proof begs the question, "How did that intelligence come in being?". I am sorry for your obvious ignorance and lack of rational thought. Next time think before you write.

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