Has nature ever created a code?
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"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?
I must say I have absolutely zero confidence in the "Intelligent Design" argument.
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.
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.
Michael Behe is a proponent of the pseudoscience of ID. I don’t put much stock in any pseudoscience.
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.
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
Is it not plagiarism without attribution?
rmfr
It certainly is....
Why he thinks plagiarizing an article by a creationist is relevant to evolution isn't clear.
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...
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:
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]
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:
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 ...
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:
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:
[2] Top of page 84:
[3] Page 89:
[4] Page 93:
[5] Pages 96 & 97:
[6] Page 102
[7] Page 131:
[8] Page 136 (First part of Conclusion):
[9] Much more damning though is this on page 137:
As if we needed any more examples of malfeasance on the part of creationists from the same trial, we have:
[1] Pages 40-41:
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:
[3] Pages 28-30:
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:
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:
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:
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.
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.
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.
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 ...
@ Cali
All your links generate "Page Not Found" errors...
rmfr
@ 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....
Found another location for the transcripts.
https://ncse.com/creationism/legal/kitzmiller-trial-transcripts
rmfr
Some of those links have changed since I last used them. Fortunately, the link to the Lynch paper in Protein Science is still valid. :)
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
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.
@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.
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.
JNV3, I’ll ask again...are you a biologist? Have you ever had this discussion with an evolutionary biologist?
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."
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
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:
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:
Miller continues, in the same article, with this nice little revelation:
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:
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 ...
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.
“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.
JNV3, I’ll ask again...are you a biologist? Have you ever had this discussion with any evolutionary biologists?
@ 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
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.
@ 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....
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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