Thank you. I’ve been posing similar questions for a long time. What is it about IDcreationism that somehow entails that functional protein sequences should be rare and isolated in sequence space? If a designer created a flagellum, or intervened in the history of life to deliberately create an animal body plan or something, why does this have to come packaged with the conviction that the evolution of new protein structures and functions is essentially impossible?
I also wonder why so many IDcreationists spend so much time trying to argue that the origin of life is impossible, as if that is somehow an essential entailment of the idea that life was intelligently designed. It can’t be only me to whom it is completely obvious that there is no necessary contradiction between these ideas? It seems to me it could both be true that life could relatively easily originate naturally, yet in some particular instance it was intelligently designed. I don’t see what supports the conviction that there has to be a mutually exclusive dichotomy at work here.
To me these strange assumptions reveals that the purpose behind these IDcreationist arguments aren’t actually based on something scientific, but instead are evangelical and apologetic. They are intended to be tools for compelling conversion to theism (or at least to keep believers believing) - rather than anything you’d “naturally expect” from an understanding of the laws of chemistry and physics.
I would agree that it may have evolved form a similar enzyme. Especially given the nature of single celled prokaryotes.
I would argue if you traced its origin back to the first enzyme of a similar type the design inference becomes a viable explanation for the origin of catalytic activity in an enzyme containing hundreds of amino acids.
I don’t see why that nature has anything to do with it.
Why “single celled”? Are there multicellular prokaryotes?
While you offer only arguments, I would point you to the actual evidence that beta-lactamase activity is present in much smaller proteins that falsifies your argument.
And BTW, proteins don’t contain amino acids, because the acid moiety was lost during the condensation reaction of protein synthesis, catalyzed by the ribozyme peptidyl transferase. They are properly called residues.
What ID hypothesis is consistent with peptidyl transferase being a ribozyme?
What ID hypothesis is consistent with the polymorphism of human MYH7?
It may be true or it may enhance the design argument as what you are pointing too could be evidence of independent designs. Similar function with a different configuration.
I see ID more as a method more than a hypothesis. A method of detecting design in nature.
@Chris_Falter, I think the proposition that functionality is rare in sequence space connects to Dembski’s ideas about complex specified information. CSI is supposed to be a calling card of intelligent design, thus … (I believe you can fill in the rest).
Oddly enough, Demski’s CSI is supposed to measure the simplicity of computer code to reproduce a given sequence (shorter code, more CSI). Rare function is more likely to be harder to describe, requiring longer code, rather than be short and simple.
I never said that hypothesis was intrinsically connected to ID. Rather that it is a hypothesis held by a ID.
It is a testable hypothesis too, and most of us here come to different conclusions about the result of testing that hypothesis. Axe thinks it is clearly demonstrated by his work, so much so that he and the rest of ID treat it like a fact. We think there is a mountain of evidence which he ignores that demonstrates it false, and his reasoning is flawed in his own work too.
Regardless, this still demonstrates that ID has scientific hypotheses.
I think that you give them too much credit. It’s not a mere subjective belief on the part of others – it’s not that you “think” there’s a mountain of evidence which demonstrates it to be false. It’s actually false. Science may not deal in certitudes, but while this is perhaps a level of certitude below, say, the Second Law of Thermodynamics, nobody really expects that there’s any conceivable way in which Axe turns out to be right. The data to the contrary are already there and there is no effort underway to deal with those data because the problem cannot be resolved in ID’s favor.
When one has a scientific hypothesis which has already been comprehensively falsified, I’m not sure one can really go about saying that one has a scientific hypothesis. There is a certain strict sense in which one does, of course. I can hypothesize that walruses are a variant of the Monarch butterfly, and this is a “scientific hypothesis” because it makes testable predictions. But after somebody goes to the trouble of pointing out how gravely and completely wrong my hypothesis is, how much credit do you really wanna give me, after I spend the next forty years advancing it while ignoring all the data, for having a “scientific hypothesis”?
I know you don’t like to go there, but frankly, ill motive explains all of this so very well. It is such a parsimonious and superb explanation. It’s not that these people are trying to do scientific work but merely happen to be very, very bad at it and merely happen, by some unhappy accident, to always fail in the direction of misunderstanding the world in ID terms. They are liars. They are propagandists. And you won’t get anywhere in dealing with that reality by trying to concede, in the spirit of good faith argument, that, well, they DO have something which is a scientific hypothesis. Their “scientific hypothesis” is as good and as robust as my hypothesis that walruses are butterflies.
So would a shorter sequence coding for the same protein function that does the job equally well or better should be a refutation of the “design” hypothesis, n’est ce pas?
Hi Chris
I think it depends on the protein, function and measurement method. This is from my reading of of @Art critique of Axe’s work and other comparative sequence data where there can be high animal to animal variation of protein types certain cases in almost no variation in other cases.
If a hypothesis is not intrinsically linked to ID, then its vindication or refutation has no probative value in evaluating ID.
If Axe has a hypothesis that one of his kids stole a cookie from a cookie jar, a trail of cookie crumbs leading from the cookie jar to the kid’s bedroom is not of any probative value in assessing ID. IT just means that Axe’s hypothesis about the thief’s identity was correct.
It really doesn’t, in this case, and it’s an inference, not a guess – one supported by decades of damning evidence that demonstrates that the entire affair of “ID” is a culture-war campaign of deception. And if you mean to throw them a bone by admitting that a comprehensively-falsified hypothesis which they can in no way defend and which they frankly do not even attempt to defend in any credible manner is a “scientific hypothesis,” I think the same deference is owed to the “walruses are butterflies” camp. The two are equivalent cases; and if the one would be a case of contemptible dishonesty, the other is as well.
And I think you do them an injustice. They’re too careful and crafty for this to be cognitive bias. Far better to admire the comprehensive web of dishonesty they’ve spun, and to understand the extraordinary snow job they’ve pulled on the rubes, than to dismiss their sole accomplishment. Perhaps one might learn, from the way lies are sold, how to promote the truth. But first one’s got to face the facts and understand that we are dealing with a movement whose central principle is that the truth is never allowed to be an obstacle to the project.
Anyone who doesn’t think the DI is entirely, maliciously and purposefully dishonest hasn’t read the DI’s marvelous books. I would recommend the following recent four:
Darwin’s House of Cards, Tom Bethell;
Foresight, Marcos Eberlin;
Zombie Science, Jonathan Wells;
Heretic, Matti Leisola.
Read those four and you will be done – done with making excuses for ID and the DI forever.
I don’t see that he thinks that. If he behaved as a scientist and not a propagandist, he would still be testing this hypothesis instead of writing a book.
I see the latter, but not the former. I think that Axe is much cagier than the others.
No, we know that and we definitely know that he ignores most of the evidence; neither is a mere matter of opinion. His behavior is perfectly consistent with his knowing that too.
No, it really doesn’t. The hypothesis of cognitive bias is completely inconsistent with their behavior.
Yet that’s exactly what you did:
You’re the one claiming to know Axe’s state of mind, not us!
I’m not seeing how. The facts don’t support your claim about the size of the protein needed, which appears to have flowed directly from your version of “the design argument.” Walk me through it, please.
Wouldn’t that also mean independent designers?
Interesting. I see methods as things one does. I see ID as an absence of doing anything, just talk.
Still, where are the designs you have allegedly detected with your ID method that address my questions?
There doesn’t appear to be any need of that hypothesis.
While I think Axe’s estimate of frequency of sequences that adopt the structure and function of beta-lactamases is an extremely skewed underestimate (in part because of numerous shortcomings of his experimental approach), there does appear to be some evidence that comparatively speaking enzyme sequences are considerably more rare in protein sequence space, than things like ligand/molecule binding proteins, transmembrane transporters, or transcriptional regulators and the like.
In this respect I don’t think it would be wrong to say that you’d expect de novo protein evolution (from non-coding DNA) to yield enzymes much more rarely than, for example, proteins with structural or regulatory roles.
However, I think it is a mistake to take this to imply that de novo enzyme evolution is so rare as to be essentially impossible. One problem is there are numerous ways to get a de novo enzyme sequence than just the spontaneous emergence of an ORF in some stretch of non-coding DNA. And while on the subject of non-coding DNA, even this is more likely to yield something functional, than the sort of spontaneous polymerization “tornardo-in-a-junkyard” picture one gets from reading IDcreationist material. We have to be mindful that a lot of non-coding DNA is actually previously functional, protein coding DNA that has been carried along by selfishly expanding transposable elements. That means a lot of non-coding DNA is actually quite near in sequence space to DNA encoding significant secondary structural elements of proteins. Much nearer than just completely random.
That said, I think a more holistic view of protein evolution implies that enzyme functions are most likely to emerge in already existing, stably folding proteins, or (less often) from gene fusion events where pieces of already existing genes are copy-pasted as insertion vents, resulting in shuffled and recombined protein coding gene fragments. Folding proteins are largely modular structures consisting of secondary structural elements, which can in principle be moved around and combined into new structures.
This makes much more sense to me, because pieces of already existing proteins are of course much nearer in protein sequence space to “something potentially functional”, than some arbitrarily picked non-coding DNA sequence that has been blindly accumulating mutations for eons. So when it comes to explaining the ultimately origin of novel catalytic functions, I would rank (from more to less likely) the order of likelihood of explanations like this:
Emergence of new catalytic function in an already existing catalytic scaffold (divergence of duplicate enzymes).
Emergence of new catalytic function in a non-catalytic scaffold (structural/ligand binding protein becomes an enzyme).
Domain or subdomain sized fragments(exon shuffling, insertions, or just gene-gene-fusion) combine to yield a new protein with a catalytic function. (see this and this and this)
Oligomerization of smaller protein fragments result in a new protein (repeat-proteins).
De novo gain of an open reading frame that codes for a functional enzyme sequence, from non-coding DNA.
I think the vast majority of enzyme function gains in the history of life owe to 1 and 2, with the diversity of all known chemical reactions catalyzed by enzymes reducing to a smaller set of enzyme superfamilies. There’s a nice article showing exactly this here:
Now these families in turn have to have originated somehow, and here I think 3 and 4 provide the best, most likely explanations for the reasons already stated. Pieces of already existing, stably folding proteins are much closer in protein sequence space to something potentially functional, so their shuffling/recombination and fusion into larger structures constitutes a much more efficient, and biased-towards-functional-and-folding “search process” than spontaneous gain of an enzyme fold from non-coding DNA does. And there’s a lot of good evidence that stably folding tertiary structures can be gained by repeating duplications (oligomerization) of smaller fragments.
This is, again, what I consider a more holistic view of protein evolution over the history of life on Earth. It’s the sort of picture I’ve come to hold after 13 years of reading the literature, and trying to follow the evidence and arguments from different camps. To sum up, I think you put too much trust in Axe’s work, and when considering evolution I don’t think you really appreciate the many different “search strategies” are available to evolution besides the sort of “randomly hook amino acids together into longer chains” pop-out-of-a-soup-of-amino-acids view.
therefore functional protein sequences will be rare.
The rarity of functional sequences is not an expectation of ID; in fact, it may make more sense for a designer to design a system where functional sequences are common, and can be easily traversed by evolution.
So while the rarity of functional sequences may be a hypothesis, it’s not an ID hypothesis.
I don’t actually know anyone involved in the ID movement (research, teaching, advocating, whatever they do), but I do know plenty of regular folk, outside the academy, working, raising families, going to church, who believe either YEC or something like ID.
These folks seek truth in the Bible. And then assume that if science affirms something that disagrees with their understanding of the Bible then science must be incorrect on that point. They are then happy about proposals that present “science” that, in their minds, lines up with the Bible. And these folks are generally not interested enough in science to really dig into the evidence themselves. And if they did dig in to it, they might not really understand how strongly the evidence affirms evolutionary science.
I know none of this is ground breaking. But here’s the point, or question that I’m leading up to…
Is it possible that ID proponents, those heavily involved in the movement, are coming from a similar place as the regular folks I describe? Do they seek truth from their understanding of the Bible and then search for explanations of the natural world that do not conflict with their understanding of the Bible?
In other words, could they be decieved by their own take on how the Bible relates to science, biased based on their participation in the culture war, and so invested in their world view that they are blind to what the evidence affirms, rather than being intentionally dishonest?
I’m not making the argument that this is the case. I’m honestly asking the question. Like I said, I don’t know folks who are heavily invested in the ID movement. But I do know the church culture that they may come from.
In general, no, it’s not possible. A great deal of their misuse of sources is very clearly intentional: to have misunderstood their sources so badly, always just happening to err in the direction of some bizarre misconstruction that happens to support an ID notion, just would have to be the worst run of bad luck for the witless in the history of all intellectual endeavor. And their omissions are plainly tactical, too: they bear, as the ID people like to argue in regard to other things, the clear hallmarks of design.
Why would Stephen Meyer, for example, omit reference to the small shelly fauna in a book about the Cambrian explosion? How could he possibly have endeavored to understand the Cambrian and still managed to come up with an entire book that does not contain ONE reference to oceanic oxygen levels during the period? How could he completely misread a Doug Erwin paper, cite it for the proposition that thirteen new phyla appear in a six-million year window when it says no such thing, and then ignore requests that he correct the “error” (Ha!) for years? And Meyer is just one example – the whole crew are this way, through and through.
Incompetence has a signature and it’s very different from this. Jerry Bergman is incompetent (though that should not be taken as an endorsement of his honesty!). An incompetent boob does things like make reference to the Cambrian taxon “Waxia haluigenia” (yeah, I know. I kid you not.). But the rhetorical structure and approach of a work like Darwin’s Doubt shows that it is VERY well written and VERY carefully crafted, with a very specific purpose: wowing the booboisie with the claim that science now demonstrates the existence of the very god whose idols they’ve spent all these years tonguing.
Let’s look at the sincerity of the DI. I can never, it seems, convince people to read the horrifying garbage which the DI actually puts out to the public, and this, it seems to me, sometimes leads to people imagining that the DI is a bunch of deluded fools rather than a bunch of compulsive, willful liars. But just READ some of this nonsense. Take, for example, one of their particular favorites, Douglas Axe, as he comments upon the views of most evolutionary biologists:
“The current stance is that evolution was so successful that it perfected life to the point where modern forms no longer evolve, making the whole process even further removed from the category of observable phenomena.”
Or, if you would like not to know whether to laugh or to cry, take Marcos Eberlin, on the cervix:
“One might posit that cervix ripening was a selective advantage acquired over many generations of blind evolution, but notice the problem. If in the first-ever baby delivery, the cervix was not able to hold the baby in place and then open at the right time, this poor pioneer infant would have been expelled too early or been trapped inside the mother’s womb, leading to the death of both child and mother. No first baby, no chance for gradual evolution over many generations. Proper dilation at the right time of the cervix is a prerequisite for human reproduction.”
Or, if the dishonesty of Darwin’s Doubt isn’t enough to slake your thirst, take Stephen Meyer, on adaptive radiations:
“Although the Cambrian explosion of animals is especially striking, it is far from the only ‘explosion’ of new living forms. The first winged insects, birds, flowering plants, mammals, and many other groups also appear abruptly in the fossil record, with no apparent connection to putative ancestors in the lower, older layers of fossil‐bearing sedimentary rock.”
And on, and on, and on.
If we do not call these people liars, we are not being honest.