Yes, I’m familiar with attractors in dynamical systems theory. But an attractor is not a mechanism that values one state over another; it merely describes where a system will stabilize under fixed parameters. A pendulum cannot act against its lowest entropic state; it must settle there. A bird, however, can. It applies ordered energy toward an outcome not required by the underlying law that constrains the function of the pendulum. That distinction defines the boundary between lawful necessity and intelligent preference.
An attractor dictates what must occur, not what should occur. It describes convergence, not choice. Biological systems behave in the latter mode: they actively preserve and restore their own informational integrity, opposing decay rather than submitting to it. The bird is a physical machine, but in its operation it displays the unmistakable signature of intelligence embedded in its design.
You’re mistaken — that is precisely the question Axe was asking. His 2004 Journal of Molecular Biology paper was explicit: “The aim here is to estimate how frequently functional folds occur among random amino-acid sequences.” (Axe, 2004, J. Mol. Biol., 341:1295–1315)
He wasn’t testing variation within life. He was measuring how rare functional proteins are in the total space of possible sequences, which directly addresses the likelihood of such a sequence appearing without any preexisting informational or cellular framework.
Axe later clarified this himself:
“My experiments with enzymes were designed to see how rare functional protein sequences are in the space of all possible sequences, because this tells us how plausible it is for new functional proteins to arise by chance.” (Axe, 2016, Undeniable, p. 166)
And again, in a 2010 Biologic Institute discussion:
“We weren’t studying evolution within living systems; we were studying the fundamental question of how likely it is for any random sequence to produce a working protein fold. The fact that I used a living cell to run the test doesn’t change that it was just the hardware for the assay.”
Even critics of ID have acknowledged that his study’s scope is the rarity of functional sequence space, not evolutionary drift. For example: “Axe’s study estimates the rarity of stable, functional protein sequences in total sequence space.” (Hunt, 2014, Trends in Biochemical Sciences, 39(9):405–407)
So when I say, “We are not asking about variation within life,” that isn’t a reinterpretation of Axe, it’s a direct reflection of what he himself stated was the purpose of his work.
Not at all. We don’t actually know who made the statues on Easter Island — it could have been humans, another hominid species, or, for all we know, spacefaring visitors. The point isn’t who carved them, it’s that they were carved. Whatever the source of the Intelligence, we both agree it wasn’t wind and water, it was a creation of Intelligent design. Dan and I both stand shoulder to shoulder on this point: “wind and water” origination theories are laughably out the window.
Citation needed, non-sequitur, and borderline ridiculous. No one in ID had made claim the rabbit burrows are evidence of a Design capable of anything more complex than a rabbit hole. Even if they do make that claim, rabbits clearly do not have an intelligence capable of creating complex life, which would just be silly.
Are you using AI to write this stuff?
Now, your postulation of a Leprechaun is curious, we have about as much evidence it could make those statues as we do for unguided nature, perhaps more… who knows what forms of intelligent life preexisted our records.
Exactly! The Intelligent Designer could be a leprechaun, or a unicorn, aliens from Alpha Centauri, or a hyper-intelligent shade of the color blue. Without a hypothesis about Design or the Designer, ALL of those conclusions are equally valid as an inference to, for example, the God of Abraham.
Without a hypothesis ID is scientific nonsense, AND it’s theologically bankrupt too, because it makes faith in God equivalent to any (and every) other belief. ID makes a mockery of faith.
BUT you still can and should have faith in God, if you think that is the right thing to do; faith is not the problem. The problem lies in thinking that faith can be science.
I haven’t brought this up before, because I didn’t think you were ready for it, but “small probability” claims like this are just wrong - that is not how the mathematics of statistical inference works. I do this sort of thing for a living, and I know the math very well. I won’t expound at length here, not enough time today, but I can point you to several discussions on this topic if you like.
Briefly: Everything you claim here hinges on this “small probability” argument. It is an invalid claim because inference requires TWO probabilities, one calculated under a null hypothesis and the under calculated under an alternative. The ratio of these (a Likelihood Ratio or a Bayes Factor) is a test statistic used to make an inference about the two hypotheses. ID has no hypothesis, therefore we cannot calculate a “probability of design”, and there is no inference about a Designer. We got mathematical proofs that this is the best way of making inference too - the methodology is not in question.
No, let’s drill into the hypothesis for ID. Axe’s inference is committing a fallacy whether or not he has a valid hypothesis, because he is going from a specific example to a general conclusion. The only important question (from a standpoint of statistical inference) is the hypothesis about Design, and there isn’t any here.
Yes it is. That’s exactly what it is. The fact that the sysem will return to that state even if disturbed to some extent, the attractor state, is such a mechanism.
Really? Please detail the experiment that showed birds don’t function according to the laws of physics.
It’s not clear choice in the sense you describe it here actually is something that ever occurs anywhere, much less in birds.
A polite suggestion, @Thacker - try to resist the temptation to use AI for composing your arguments. While I may have made this statement, it certainly wasn’t in an issue of TIBS.
Which isn’t the same as asking how “how likely it is for a functional protein such as β-lactamase to arise without any preexisting informational or cellular framework.” Now granted the two questions have overlapping domains, and I’m sure Axe would agree his paper also somehow magically disproves the origin of life. But that changes nothing about how Axe and the DI have spun his results and their purported implications for biological evolution.
Axe is purporting to undermine Darwinian evolution. It’s what the DI constantly tell his adoring fans that he has done. It’s what Stephen Meyer wrote in his book “Darwin’s Doubt” that Axe accomplished. The context of that book is the Cambrain explosion, not the origin of life.
Axe later wrote a followup paper in the ID vanity journal “Bio-Complexity”, with the title “The Case Against a Darwinian Origin of Protein Folds”, basing his arguments there largely on his 2004 paper.
True but irrelevant. What he did made no sense.
He wasn’t actually doing that either. He certainly makes claims to that effect, but his methods do no such thing.
It doesn’t, really, because that would require knowing the processes by which the proteins emerged. At best what Axe does in that respect is try, with a very flawed experimental setup, to estimate the probability of finding a particular structure-function relationship if you imagine proteins first arose by completely blindly and randomly polymerizing amino acids.
Of course there’s no good reason think this truly represents how the first proteins had to originate.
And since Axe is a creationist, he likes to characterize Darwinian evolution as “chance.”
That Axe didn’t employ evolution in his experiment (that’s what he means by not studying evolution within living systems) doesn’t mean he hasn’t claimed that his results are intended to undermine evolution. What they like to call “Darwinism”, or “chance.”
Who the hell brought up evolutionary drift? When I say that Axe’s paper was intended to show problems with evolution, I am not claiming that Axe somehow tested the process of evolution in his experiments. Merely that the results he got has been spun, by him and the other cronies at the Discovery Institute, as if they undermine evolution (with all the pre-existing informational stuff you love to stuff your posts with.)
Who did (insofar as a generalized “who” referring to the human species) is relevant though. We know that humans a) exist, b) have means of transportation to travel the world and visit islands, and c) carve rocks into various shapes. That humans are the likely source of the carvings on Easter Island is a reasonable conclusion. If you think there is another species (including aliens) that could have made the carvings instead, then by all means present evidence to support the existence of said species and that they also have traversed the globe and have the means to produce rock carvings.
Otherwise your assertion is about as silly as wondering whether my house was built by humans, crafted by aliens, or conjured into existence by an inter-dimensional wizard.
Balderdash. Before I try correct your misunderstanding, a few preliminary questions:
Do you accept universal common descent?
If not, do you have an alternative explanation for the observed nested hierarchy that occurs at multiple levels in biology, from molecular genetics, to protein structure, and to gross anatomy?
Actually, no, that is not what I am saying at all. And, TBH, it seems to me that you are just pasting boiler plate responses that you have already prepared, without taking the time to actually understand what you are responding to and ensuring the response is actually apt. So I will simply request that you re-read my comment and try coming up with something germane to my argument.
Untrue. We know that they were made by the inhabitants of Rapa Nui between 1000 and 1500 AD. We know how they were made, and we even have some idea of why. Contrast with ID, which claims to know only that life was designed (not made), but nothing about who, how, or why. There are arguments about when too, and even about what, since apparently some features of various species were designed but others weren’t, and nobody has suggested how to tell which.
In all reality, recognition of design is associated with the identification of the designer, even hypothetically aliens. This is clear thinking, and thus reasonable, notwithstanding your raft of purported fallacies.
If a designer is capable of designing anything, then anything could be designed, including things that have no hallmarks of design, so hallmarks of design are evidence against that designer, since they wouldn’t be expected to leave any.
RumRaket: He wasn’t actually doing that either. He certainly makes claims to that effect, but his methods do no such thing.
It’s odd then, that a respected journal published his paper, and hasn’t published a rebuttal in 21 years. And mere assertions are not convincing.
Rumraket: At best what Axe does in that respect is try, with a very flawed experimental setup, to estimate the probability of finding a particular structure-function relationship if you imagine proteins first arose by completely blindly and randomly polymerizing amino acids.
Again, how was the setup flawed, and how did the reviewers not see this? And this applies to evolution, as well as to a protein arising at first, the search is essentially random, until you get a significant difference in fitness, either improving or degrading it.
And Joshua Swamidass is on record as stating in an interview that he has seen problems with Axe’s paper, I would love if he would chime in here and state the problems he was referring to.
I was considering returning here to discuss Axe’s paper and James Tour’s challenges to OOL researchers, and lo! Here it is.
John Mercer: Then it’s utter nonsense that he went backwards, beginning with an already unstable temperature-sensitive (ts) mutant and changing 10 residues at once, no?
Well, from Uncommon Descent here: “And, indeed, Axe did begin with an extremely weak (temperature sensitive) variant, entailing that an evolving new fold would be expected to be poorly functional. And why would Axe do this? Because he saught (sic) to detect variants operating at the lowest level — the threshold, if you will — of detectability.”
John Mercer: Axe’s binary assay is not an accurate measurement of enzymatic function; I suspect that this was by design.
I do wonder, as I did with RumRaket, why the reviewers of his paper didn’t catch this. Would you be willing to publish your refutation in a note to the Journal of Molecular Biology? I’m sure many in this world would be interested in seeing this paper refuted.
John Mercer: If this was so groundbreaking, why didn’t Axe follow it up in the last 21 years? He’s had plenty of money provided by the DI to do so.
No less odd than the fact that none of the hundreds of articles the DI claims to have refuted have ever been retracted. Are you, then, admitting that the DI has never been correct?
(To be clear, it is pretty much the case that they have never been correct. But that is not based on the fact that the articles have not been retracted.)
How often has Axe’s article been cited and discussed in the mainstream biology literature? That’s probably a better measure of its soundness and significance. If he had actually disproven evolution, it would be among the most cited articles ever written.
So one paper 17 years ago, and nothing since (Articles in the fake DI “journal” BIO-complexity don’t count). Not exactly Nobel Prize level productivity, is it?
Most of your other questions have already been addressed in the preceding discussion, so why not read that first including the relevant links.
I have to assume that even you don’t genuinely think that every paper ever published that has not received a direct rebuttal or response paper, must therefore assumed to be true and accurate. Right? Because otherwise you’re going to have to accept a lot conclusions in support of evolution that you presumably reject. As such, this response of yours is entirely ineffective and I think you can see why.
Let me give you a significant hint here. The way Axe characterizes the results and implications of his experiment are very different between what he writes in his paper, and what he writes in books, blog posts, says in interviews or presentations to creationist audiences. Axe makes claims to the public he doesn’t make in his paper. That’s one among several reasons why Axe can get a paper published that don’t support his conclusions. Because he doesn’t state those conclusions in the paper.
Assuming peer review functioned like it should, had Axe stated in his paper what he has said in blog posts, books, interviews, and public presentations, the reviewers would have told him why he can’t extract that conclusion from his experiment and sent his paper back to him to rewrite it.
Neither thing is “odd.” The paper is poor, and it’s a shame that it was published in a moderately good journal, but that’s not unusual. I don’t know what you mean by a “rebuttal” but the absence of anything called a rebuttal is not even remotely odd. Or even interesting.
The weaknesses of this paper, which has long since been shown wrong and silly, have been extensively discussed here on the forum and written about by Art Hunt.
[Shrug] Reviewers miss stuff all the time. In this case, the problem was that the author made claims unjustified by his simplistic data, and speculated in ways that are just silly. This is frustrating to scientists who know the field, but it is far from the kind of error that merits retraction or official correction.
