The most hilarious thing is how this guy still doesn’t understand that ATP is used to make RNA in living cells right now. Imagine if you were to try to explain to him where the energy ultimately comes from?
But hey, we’re talking to a man who appears to believe he’s been possessed by a demon. He’s basically the “delirious” person he kept blathering about in his botched argument against a physical basis for thinking. There is no reason to keep interacting with him.
What goalposts have been moved? I claimed he knows oceanography, I also mentioned specifically hydrothermal vents, so now please examine his points about vents, and explain why he is wrong. I conclude you believe he is wrong, now please back that up.
I did go into more detail, and saw even more detail that I didn’t mention.
Rumraket certainly seemed to, he said it was like nucleotides, which don’t become different molecules when they are incorporated. And ATP is incorporated without change inside living cells? I don’t think so. But maybe you meant something else.
I actually responded to him, as I recall, he left off responding to me, please post a link if I didn’t respond somewhere, and I will respond.
I did look into hydrolysis, and didn’t find anything like ATP being incorporated without change, like a nucleotide.
Apparently you haven’t examined Peltzer’s evidence! And it’s not allowed to be knowledgeable in other areas than your main field? He does mention having an interest in OOL, he was even a student of Stanley Miller, and had many discussions with him about OOL. You may have heard of Stanley Miller. And you implied he was wrong, if you don’t care to defend your claim, you’re not going to convince anyone. And if you don’t care to convince anyone, why do you post in this forum? Why do you respond to me?
I posted that part to show that the molecules of interest do disassemble at the denaturation stage at such temperatures. This refutes your claim that they didn’t. And yes, they then lower the temperature for an annealing phase, but I could point out for one, that hydrothermal vents don’t vary their temperature like that, certainly not in a controlled way and so specifically.
So who is ignoring who here?
But you haven’t refuted any of them! You certainly haven’t investigated what I’ve said.
Actually, what is happening is for the most part, I make points, and you dismiss them.
That’s fine, and that’s quite different than incorporating ATP itself into a chain, like a nucleotide.
Actually, I don’t say that, certainly I say I’ve experienced oppression, pressure from demonic sources, successfully resisting this. That would not be possession, where it’s like a demon takes over.
It’s strange then, that you all point out unreasoning causes for what I say, delirium in this instance, so therefore you can reject my statements. You illustrate my view very well. People recognize this principle, and apply it all the time.
Your lie was:
No. I do evidence, not hearsay.
You believe that you and he are right, now back that up. You never will, because you are lying.
The tiny bit you did mention shows that you don’t have a clue.
That’s because you have trouble with basic English.
That’s not all he wrote. He was perfectly clear:
You don’t understand that, but you pretend to, which is a violation of the Ninth Commandment.
You did not respond to his explanation I quoted above. You just pretended it didn’t exist. An honest Christian who didn’t understand it would ask questions, but you’re not honest.
Lee, stop lying. You obviously don’t understand high-school molecular biology, but you pretend to, which violates the Ninth Commandment.
What evidence? Opinions aren’t evidence.
You have no idea who’s knowledgeable about what, particularly since you claimed a mere postdoc is a 9/10 in his field.
Another lie. I clearly stated that opinions aren’t evidence. OOL research has come a long way since Miller died 18 years ago.
That’s another lie. That wasn’t your claim. PCR can’t amplify DNA if it “goes to pieces,” can it? DNA is locally denatured for every function it mediates. Cooling denatured DNA causes it to renature. So, claiming that denaturation supports your lie is yet another in a firehose of lies you’ve spewed here.
Does the DNA polymerase get denatured?
You could, but that would be dishonest. What happens to the polymerase?
Every single one of them. You, OTOH, supported none of your assertions.
You just made my point by disregarding the OOL papers.
Is this how you believe science works?
I never claimed a scientist had used that analogy. It is utterly baffling that you would think I had, and that this pertains to our discussion at all.
Because it does support the point I was making (as opposed to the point your confused brain led you to believe I was making).
You ought not confuse a situation in which someone has realized the futility of trying to make you understand something and given up in frustration, with one in which you have won the argument. This is a mistake you make repeatedly.
Oh, that’s interesting. So, by your reasoning, when Doug Axe does an experiment on a mutated form of a protein, he should not claim that this tells us anything about the wild form of that protein, never mind about proteins in general.
I suggest you write to Axe at Biola and explain to him how you have disproven his entire argument.
He has been refuted. Many times. And i suspect he knows it, that’s why he has stopped responding to critics.
Here’s another thing you don’t understand: If someone asks you a question, and you write a bunch of words that don’t answer the question, you have not answered the question.
I wonder if this is a problem shared by everyone on the far right. For instance, watch the video below. Dana Bash asks Gregory Bovino a very specific question. In response, Bovino’s mouth certainly moves, and sounds certainly do emit from it. But do those sounds amount to an answer? No, they do not.
I couldn’t just absent-brained go on to ask him further questions as if what just happened was normal interviewing. We saw his “victims” commit murder before our very eyes, he needs to be called a lying sack of shit to his face and I’d donate to the TV station where reporters had the gall to do it.
I some times wonder whether the talking heads on TV truly are robots and not genuine human beings.
Right, silly me. I should have studied more Daemonology I see.
Lee, you should not take intermittent participation on my part as “withdrawal”. You have never - EVER - provided an adequate defense of Axe as it relates to my two main points. Once you come up with something that is more than referring to essays that we already know are either irrelevant or ineffective, I will comment. You haven’t to date. You should stop trying to bluff your way through this. It’s perfectly OK to state that Axe has not addressed my main points (of course - the truth is always preferable). It’s also perfectly OK to start at this point and ask questions about the aspects of this discussion you clearly do not understand.
That’s not moving the goalposts, though! That was my initial claim, my reason for not reading the rest of the paper, which depended on this. But again, you accept nothing on authority? Why did you go to class in school, and take notes, and read books that were assigned to you?
I did mention his view about large molecules disintegrating in vents, and discussed your counterexample, which showed DNA separating due to temperature, though I do recognize a subsequent annealing phase. Your counter example still proves my point. So I presented and defending a claim, now it’s your turn to defend your claim.
Ah. So I did provide evidence?
Rumraket continued:
So the point doesn’t matter, so that’s fine. But I’ve never heard Tour claim diffusion cannot happen, I expect he is aware of that, and instead he points to the extraordinary complexity of living cell membranes, with over 40,000(!) different lipids, he points out that when making synthetic vesicles, mixtures with monoacyl lipids can destablize the system–so how are these avoided? And the outside lipids are different than the inside lipids, nobody knows how that was done. And so on.
Out of curiosity, have you ever taken a post-secondary science course?
Ah, so this statement is just your opinion? I therefore can dismiss it?
You didn’t answer my question. And Axe isn’t just a postdoc any more, he’s the Rosa Endowed Chair of Molecular Biology at Biola University.
Ah. Another opinion. I dismiss what you just said. But I will ask this, what substantial OOL progress has been made in 18 years? And I’m not asking for papers, I’m asking for progress. Such as membrane construction. Tour says they still only use one lipid.
Well, it disassembles, is what I said, which confirms that large molecules don’t hold together in high temperatures. Put a molecule of DNA in a hydrothermal vent, and I think more will happen, it will arguably, go to pieces.
I think more would happen, it wouldn’t hold together in a hydrothermal vent, it would go to pieces, per Ed Peltzer. This is what you need to refute, and even your counterexample shows DNA disassembling due to raising the temperature.
Um, this is what is called an assertion. You do what you accuse me of doing.
So papers are now evidence? I can’t just dismiss them as hearsay? But what OOL papers have I disregarded? I do try and address points people make here, especially if they point to a paper..
To some degree, so in order to keep abreast of the field, you have to read papers, and listen to presentations at conferences, and consult with colleagues. That’s taking things on authority. But certainly scientists also do their own experiments.
All right, I got off track. But you still need to show how OOL has made net progress on homochirality, after claiming they had a good answer for this.
And my reply has been that this shows getting halfway back to where they had claimed to be. Not even halfway back, actually! Only RNA was addressed, there are lots of molecules that need to be homochiral. So no net progress yet.
In a sword duel, if a person withdraws, it’s not typically for the reason you give.
If Axe claims his results only apply for this mutated form of a protein, then yes, he should not claim this applies to proteins in general. But the authors in the paper you pointed to said more work needs to be done for the other nucleotides, implying their results did not apply more generally.
As I always ask, how and where? Please (again) point to one point people have made in the Douglas Axe thread that has gone unaddressed, which has proved unanswerable.
So how does Swamidass’ point not address the question, and so on? So again, please point to a post I did which is just a “bunch of words” that don’t address what someone said?
That means squat. Biola is not a research university. Axe hasn’t published outside of apologetics for decades, so what little claim to expertise he may have once had has now dissipated entirely. That is a sad reflection on the standards at Biola.
Would it matter? He’s getting a free education from many people here, but nothing sinks in.
Which I suppose is somewhat more prestigious than being
Grand Poobah of the Loyal Order of Water Buffaloes. But only somewhat.
I did. It was described in the news article from Science I cited for you. You deny this by making up some weird definition of “progress” that only you seem to follow.
This is where I remind you that you have yet to cite any OoL researcher claiming to have solved homochirality. They seem to exist only in your fervid imagination.
No, but in a street fight it is considered good sportsmanship to stop punching your opponent when he has been reduced to a barely conscious pulp at your feet. Even if he claims he is winning. Or do you think Cool Hand Luke won this fight?
I’m sorry, what? But if he claims that his results for one mutated form of this one protein applies to every form of every protein (which he in fact does), that’s OK?
Does that really make sense to you? Wow.
Exactly.
Hilariously, I suspect you don’t realize you just admitted that I have been right all along.
It beggars belief that you can be this stupid, this ignorant or this dishonest.
Anyway, here is just one example, from just a short while ago, out of many, many others I could have chosen:
The very comment I am responding to know will suffice as an example. Or almost anything you have ever written on this board.
Reading experimental and observational data is not the same as taking things on authority.
Your claim is false. You told another two lies that are falsified by that paper. And “rest of the paper” is really dishonest when you didn’t go beyond the first sentence of the Introduction.
I do, but I don’t pretend to understand those things at the same depth as experts do. I would never conclude that an entire scientific field is wrong based on the claims of a handful of people outside that field. That’s idiotic and mind-blowingly arrogant. That’s what you’re doing here, Gish Galloping from lie to lie.
No, you did not, because you ignored all the other components to blather on about denaturation representing
Which is bogus. For the third time, what happens to the polymerase?
So nothing “went to pieces” at all and you don’t have a leg to stand on.
How so?
No, you showed a lack of understanding of undisputed high-school molecular biology.
Nice Gish Gallop! What happened to your claim that ATP isn’t involved in RNA synthesis? That was the hilariously wrong one we were discussing.
Being a postdoc at Cambridge is far above that.
So what? You’ve dismissed everything to date except my correction of your howler about ATP synthase.
Progress is demonstrated in the papers you are obviously incapable of reading.
OOL research is not an engineering problem. Only ignorant engineers pretend that’s the case.
Then one or more of the following must be true:
I vote for all three being true! In addition, because membranes aren’t limited to lipids, it’s a stupid criticism even if it was correct.
Now, if only someone in this very thread had cited and linked to a full-text version of a lipid-centric OOL paper that shows Tour’s claim to be false! Can you guess which one, Lee?
Which is a lie. And I’m asking you, what happens to the polymerase?
How do the critters that live there possibly survive, then? DNA denaturation temperature is directly proportional to _______ concentration. Simple fact, but you’re not curious enough to look for it.
I don’t. What range of temperatures are present in vents, and what’s the stability of the polymerase? No opinions are involved, just measurements.
“Disassembling” is a lie and you know it.
The primary literature contains evidence by definition. Not all scientific papers are primary. Is this a difficult concept for you?
That’s a lie.
Correct.
It’s anything but, because for real scientists doing real science, all three involve presenting evidence. Pseudoscience depends on the targets not understanding this.
The results of which they present in papers, at conferences, and in consultation with colleagues.
That’s not how ethical people acknowledge false statements they’re called out for making.
Good, then we agree that the paper has zero relevance to proteins in general.
Have you even read the 2004 paper you love so much? Axe isn’t claiming that his results start with a mutated form of a protein, he tells the reader that flat out. But this, as the vast majority of all facts presented here, flies over your head, while you remain far too arrogant to admit it.
Alright, just please leave a note if you have to be away for an extended period, and I will set my timeout interval accordingly. And thanks for resuming discussion!
But I don’t recall posting excerpts or referring to essays in my previous comments to you, I do recall going through your essay and presenting my points in reply.
Alright again, the forum here doesn’t seem to have a good search function, so I’ll just take a fresh run at this.
Now first of all, I think this post depicts more accurately what Axe did than this essay on Panda’s Thumb. Axe wasn’t trying to measure part of the base of the wild-type enzyme, he was trying to evaluate the whole peak of the partially-disabled enzyme, as you depict in the former post. So I’ll address the former post, not the latter article.
Secondly, I don’t see why Axe needed to come up with a conversion factor from the peak in your Figure 3 to the peak in Figure 1. I don’t see what that would accomplish, to get an estimate of the percentage of functional variants generated from the wild-type enzyme, to have this along with the estimate for the disabled enzyme variants. Axe’s aim was to estimate “the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” in general, so having two samples instead of one wouldn’t seem to be helpful or necessary.
Then you write that “Anyone who has plated transformed E. coli on ampicillin or other beta-lactams knows that this isn’t a very quantitative method, and certainly not suited to quantitatively distinguishing enzyme variants with differing activities.” Yet here I read: “Volume Accuracy: Ensuring the precise volume of the sample is critical for certain quantitative analyses.” Which implies you have to be very careful, but it can be done. Similarly here: “The standard plate count is a reliable method for enumerating bacteria and fungi.” They continue: “Accuracy in quantitation is determined by accurate pipette use and adequate agitation of dilution tubes.” Implying quantification can be done accurately.
Then you state: “More to the point of the JMB paper, Axe’s BioComplexity paper shows that, in cases where enzyme activity may be very low, this assay cannot reliably distinguish between low and zero enzyme activity. This is very important – I believe the conditions used by Axe in the 2004 JMB paper cannot distinguish between mutants with low but significant activities and those with no activity. In other words, the accuracy of Axe’s estimates in the 2004 paper cannot be known, and he may be wrong by tens and tens of orders of magnitude or more.”
So I went through this paper, and couldn’t find any statement along the lines of “where enzyme activity may be very low, this assay cannot reliably distinguish between low and zero enzyme activity.” Could you quote the relevant section?
I did find and post a link, but this forum’s search function is not very effective. So here is an excerpt from Wikipedia about this: “Some of these models propose three distinct steps: a mirror-symmetry breaking mechanism to create a minute enantiomeric imbalance (enantiomeric excess or ee) from a racemic mixture, subsequent chiral amplification to achieve a larger ee or full homochirality (i.e., ee=100%), and finally chiral transmission/propagation to transfer chirality from one set of molecules to another.[9][10] “
And here are the references:
Ozturk, S. Furkan; Sasselov, Dimitar D. (2025-08-26). “Life’s homochirality: Across a prebiotic network”. Proceedings of the National Academy of Sciences. 122 (34) e2505126122. doi:10.1073/pnas.2505126122. PMC 12403148. PMID 40828029.
Ozturk, S. Furkan; Sasselov, Dimitar D.; Sutherland, John D. (2023-08-14). “The central dogma of biological homochirality: How does chiral information propagate in a prebiotic network?”. The Journal of Chemical Physics. 159 (6). doi:10.1063/5.0156527. ISSN 0021-9606. PMC 7615580. PMID 37551802.
So it seems your imagination is what is active here?
Well, the reviewers evidently thought it did! And we should also throw out these papers? (referenced here in Uncommon Descent)
”As I noted in my previous post, Axe’s 2004 JMB paper is not an isolated result. I cited a number of papers which attained similar results with respect to the rarity of functional domains within sequence space. In one study, published in Naturein 2001 by Keefe & Szostak, it was documented that more than a million million random sequences were required in order to stumble upon a functioning ATP-binding protein, a protein substantially smaller than the transmembrane protein specified by the gene, T-urf13, discussed by Hunt. In addition, I noted, a similar result was obtained by Taylor et al. in their 2001 PNAS paper. This paper examined the AroQ-type chorismate mutase, and arrived at a similarly low prevalence (giving a value of 1 in 10^24 for the 93 amino acid enzyme, but, when adjusted to reflect a residue of the same length as the 150-amino-acid section analysed from Beta-lactamase, yields a result of 1 in 10^53). Yet another paper by Sauer and Reidhaar-Olson (1990) reported on “the high level of degeneracy in the information that specifies a particular protein fold,” which it gives as 1 in 10^63.”
Eh? If their results did not apply more generally, yes, that was my point, you can’t claim the homochirality problem has been solved, as you seemed to be claiming.
Art Hunt is back! And I am resuming my conversation with him. This does not show that Axe was refuted, the discussion continues.
I assume you meant “now” instead of “know”? But you don’t address how Swamidass’ post does not address the question, nor do I see how asking for “how and where?” does not respond to what you said.