What I see here though is three conclusions, with no reasons to back them up! Alas…
No, I’m claiming that Axe’s responses, as he said, were to three points Hunt made, and to another point he and Venema made together. And I took it upon myself to address the points Hunt said were his main points, that he said Axe had not responded to.
And the lack of response to Tour’s challenge is more serious, it is specifically a challenge to claims being made by OOL scientists, that progress is being made, substantial progress. None has been forthcoming, either to Tour’s specific challenge, or to his more general claim that “it’s a scam”.
One more point, Axe has responded, in the article I pointed out, and as far as I can see, in publications done later, at PLOS, and at Biologos, though this latter it seems somehow doesn’t count.
Um, saying “You telling us that Axe wrote gibberish is not addressing Art’s point” means to me that I said “Axe wrote gibberish”.
But I repeat, people do reduce a continuous variable to a binary one, when they want to know for example, if an antibiotic is effective enough to go into production. They pick a threshold, which is what Axe did, and it’s quite reasonable.
Actually, Rumraket is responding very specifically to points Axe made. You are apparently not following the discussion…
How strange. I find it so baffling that I as a layman could ever think that I knew better than someone who had the expertise, much less better than the majority of the population of experts. Granted, I was YEC for most of my life, but I at least had the excuse that all these scientists worked—knowingly or otherwise—for Satan himself. Perhaps there’s something similar going on here?
At PLOS?!?! He has published exactly one paper at PLOS, this one, which has no demonstrated relevance for protein folds (or, I think, with anything interesting or useful given that it has been cited [checks notes] ZERO times).
The PLOS ONE paper does not “respond” to anything that anyone has written about the silly 2004 JMB paper. What it does is present an attempt to create a useful tool for exploring protein space. Their proxy for “function” in protein space is human language. Whether their tool works at all, I don’t know, but it has long been rendered obsolete by AlphaFold and its descendants.
I’ve already discussed all three points and the first and second may easily be seen by just reading Axe’s so-called reply. As to the third perhaps you can explain why insisting that the mutant strings perform as well as the start strings is reasonable. The fact that Axe chose a bad method of “scaling up” in his illustrative example certainly doesn’t seem to warrant such a move.
It’s being used by T7 RNA polymerase to make RNA. ATP is one of the four RNA nucleotides (the three others being UTP, GTP, and CTP).
No, it means that you quoted Axe’s gibberish instead of thinking for yourself. I challenge you to think for yourself and express yourself in your own words.
No, they most certainly do nothing of the sort. Repeating a lie doesn’t make it true. You are violating the Ninth Commandment.
No, they don’t; they treat both antibiotic efficacy and beta-lactamase activity as continuous variables. That’s why there’s a cheap beta-lactamase assay available.
I hereby challenge you to name any of the people you are referring to as “they” and document even a single instance of any of them using a binary assay to assess the potency of an antibiotic to approve its production.
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Why not? If two parts can be transferred, then surely three, or four, … or four hundred and forty five. The actual number is arbitrary and irrelevant, the meaning task is the assembly of components.
Let me bring everyone’s attention to this new paper:
What I also find significant and relevant is how common the DNA replication machinery accidentally creates repeats. Relatively short amino acid repeats are surprisingly likely to yield foldable proteins, and the DNA replication process is very prone to create small repeats. It is almost as if the two factors work together to facilitate protein evolution.
Were I a religious man I might have suspected the laws of physics were fine tuned to make evolution unavoidable.
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Yes, so the response I see here would be to provide a way for doing further research, to do further work on the area he worked on in the 2004 paper. I agree that this PLOS paper does not address any specific objections made to the paper.
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Apparently I missed the discussion of the three points, could you point me to them? But let’s discuss Axe’s paper in the thread for that purpose, not here.
But I’m still missing the actual description, can you point me to it?
But I don’t just and only quote Axe, I’m not doing that.
That’s silly, you’re obviously faced with a binary decision, when a company evaluates an antibiotic for production, should it go into production, or not? Then again obviously, a threshold of effectiveness is involved. How is this unclear?
I’m not saying they use a binary assay, though, I’m saying they must set a threshold, to make a binary decision, like Axe did.
And like with another poster, can we move this discussion to the thread on Axe’s paper, and not discuss it here? Thanks.
@lee_merrill, it is not so obvious to anyone involved in the development and approval process. It could go into production, or be shelved due to market demand, side effects, production difficulty, or numerous other factors, or sent back for further development, or scrapped entirely. On the consumer side we see a binary outcome, but the decision and approval process is much more complex.
AND I am still over-simplifying, but you get the idea.
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Yes, but merely moving parts inside does not assemble them, the assembly is still needed. Then again, the interactome is needed, which I think was what Tour was after.
Can we move this to the discussion of Axe’s paper? This is not applicable to the challenges Tour gave. Thanks.
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You think? Was Tour unclear about what may or may not satisfy his challenge, or are you moving the goalposts again?
Biochemistry is not my thing, but since we can assemble DNA to create new proteins and insert it into cells that function, it doesn’t seem like assembly is much of a barrier either.
Have you got another goalpost move in you, or has the fifth challenge been met?