Scheherezade would be envious.
1 Like
I’m not here to argue that with you. I was simply trying to tell you how you can check for citations of articles.
2 Likes
This claim is problematical on a number of levels:
-
Lee has already exhibited extreme ignorance of, and lack of interest in, how academic journals actually work. Therefore, rather than being an informed opinion, this is simply him ‘throwing everything at the wall and hoping that something sticks’.
-
At five years old, Biocosmos isn’t particularly new.
-
It wasn’t called a “crap journal” because it was new.
-
It ignores how newer journals can garner attention, and thus citations.
These ways would include:
-
Getting the journal indexed in major bibliographic databases. This would likely mean convincing the database compilers of a combination of (i) the reputation and probity of the publisher, (ii) the rigor of the journal’s processes (not merely services that the journal’s publication services provider offers), and (iii) the degree to which its editorial board are recognised experts within the field.
-
Having recognised experts on the editorial board.
-
The editorial board using their reputation and contacts to encourage other prominent experts in the field to publish there.
Biocosmos has none of these things, which is why it garners so few citations, and these are also among the reasons why it could accurately be characterised as “a crap journal”.
4 Likes
Here is the relevant quote: “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).”
So the “who” is Jonathan McLatchie, and the “why” is to scale the Taylor et al result from a 93 amino acid enzyme to the 150-amino-acid section analysed from beta-lactamase.
Well, here we read: “A protein fold refers to a general aspect of protein architecture, like helix bundle, beta- barrel, Rossman fold or other ‘folds’ provided in the Structural Classification of Proteins database.” Nothing mentioned here about fold transitions between different folds, where one fold can turn into another. Similarly here on Wikipedia on helix bundles: “A helix bundle is a small protein fold composed of several alpha helices that are usually nearly parallel or antiparallel to each other.” Nothing about different folds appearing due to transitions.
Your challenges, as I recall, were all about biological minutiae, how much I know about such specifics is irrelevant, if they are not pertinent to the topic at hand, and they haven’t been. You’ve given a number of such challenges, I don’t remember the first one, and this last one is again avoiding the issue, how is Axe’s statement objectively and empirically false? And how did the reviewers miss the main point of the paper being invalid? They all missed it, according to your claim, this was not an obscure point, I therefore deem a failure of peer review unlikely.
Another dodge? You claim to know this, but you don’t speak up and give evidence for your conclusion.
I can quote from it well enough to answers objections people make here. And people don’t reply that “this is not what Axe meant.” So again I ask, how is posing me technical questions in biology in any way an answer to Axe?
I just quoted Axe! “Using these simplifications, the difficulty of specifying a working beta-lactamase domain is assessed here.” And your response is not that I misunderstood him, you reply instead with yet another technical challenge to me, in biology…
Tour’s challenges were based on the hypothesis that OOL is not something we can reasonably approach in the lab at this time. To refute this, OOL researchers need to demonstrate that they can meet the challenges.
Axe went in expecting his results to be similar to previous results by others, that is a hypothesis, and it was confirmed.
Tour and Stadler proposed a limit of about 2 mutations, if the mutations were not selectable individually, then they examined various attempts to prove or disprove this, that’s evaluating a hypothesis.
Bechly was actually evaluating a hypothesis that is the opposite of his view, that species pairs should occur about every 5-10 million years, this is testable if paleontologists can provide counterexamples.
That was a meaningless garbling of Bechly’s challenge. I don’t think you have any clear idea of what you just said there. And of course it wasn’t paleontologists who were supposed to provide counterexamples, because the challenge was to find living species that fit the criterion.
I believe that just before you lost interest it had become clear that the great auk answered that challenge. Do you remember?
2 Likes
It is irrelevant when it comes to the actual merits of a paper you had no part in writing. However, none of your criticisms or defenses, if they are ever yours to begin with instead of just mindless quotations, are rooted in any actual data, but rather in your own intuitions. To point out that said intuitions are in turn also rooted in total ignorance even of high school biology is entirely fair here. You are in no position to defend or criticize much of any work on the subject. How much you think something is plausible or absurd, how much you think someone might be qualified or respected in a field you have zero clue about, are questions you invite, when the entirety of your case is built upon such proclamations and none of it is backed up empirically.
You are not Axe. Indeed exposing that you have no clue what Axe or anyone else wrote on the subject is not a response to Axe or said anyone else. It’s a response to you.
Oh, so when you said you were here to “defend” Axe’s paper, what you meant was not an actual discussion of what it said or its implications, not an actual defense of the technical correctness of his conclusion or thoroughness of his methods. By “defense” all you meant was that you were willing to “quote it well enough”? To just regurgitate individual phrases out of it, as if the question was merely whether or not some claim was made, rather than whether or not any claim was accurate. The moment anyone actually challenged any of the paper’s contents you commit to “defending”, rather than whether or not some statement was made in it at all, that was to be technical minutia a “defender” such as yourself needn not further address?
This is what I meant by another recent post of mine. You came embarassingly unprepared, and seem to think putting in zero work like you did may yet be good enough to accomplish what ever it is you seek here. It is like you think everyone else is just as clueless as yourself, or that your charisma is all it takes to keep up with actual study. I should conjecture that is because you do not know what studying is actually like or what difference it makes, because you never did it. You don’t know what putting work in means, and thus you have no respect for people who do.
4 Likes
And nowhere does it say that, as a fold transitions, it is a fold in a different state, as opposed to a different fold.
F for fail. Try again.
Here’s what “people” in the field actually say:
This as unambiguous as it is going to get(my bold):
Lymphotactin
Lymphotactin is one of the most dramatic examples of a protein that undergoes conformational switching. Under physiological conditions it exists in two forms in approximately equal amounts, a monomeric chemokine fold (Ltn10), and a novel dimeric β-sandwich fold (Ltn40) [8,20]. The equilibrium between these two species can be shifted completely from one form to the other by varying salt and temperature conditions.
3 Likes
I notice that McLatchie doesn’t present any derivation or calculation, only the final number.
So Dory is citing a number he doesn’t understand from a forum post which doesn’t explain it.
3 Likes
Ahh cool, so McLatchie simply makes up a new number based on a completely baseless extrapolation that fold-rarity directly scales exponentially with protein length. An idea literally based on nothing in the entire world.
It’s also still off from Axe’s number by an extraordinarily large TWENTY FOUR ORDERS OF MAGNITUDE.
McLatchie’s baseless extrapolation from L=93 to L=150 is still 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 × 10 times more frequent in protein sequence space than Axe’s 10-77 number.
Do you comprehend the magnitude of discrepancy between these two numbers?
3 Likes
'Nuff said.
3 Likes
No, that doesn’t work. It would give a different number: ~10^39, not 10^53. Whatever McLatchie did, it wasn’t that.
1 Like
Your recall is defective. I’m citing a single challenge from the beginning. You did not respond. It is about the whole point of the paper you don’t understand, not minutiae.
It wasn’t about how much you know about a specific. Please stop lying.
It was highly pertinent to the extrapolation of the Axe paper. Another lie.
Then why are you making multiple false claims about what you recall?
What you deem has no basis in experience.
That’s insane, because the fact that you quote from it screams that you don’t understand it. If you understood it, you would discuss in your own words. You can’t do that.
And you obviously don’t understand what you’re quoting.
2 Likes
But you don’t understand what you claim to read. We do. None of that supports Axe’s misuse of the term or your misunderstanding of it.
BTW, the challenge you allegedly can’t recall, yet posted paragraphs of misrepresentations of, was about a specific fold.
3 Likes
Yes, I cannot for the life of me figure out how he got that number. It’s literally made up. You’re right, scaling the 10-24 number for L=93 to L=150 gets us 10-39. Not 10-53.
He’s making it up. He’s literally making it up. And he’s still off by 24 orders of magnitude.
Edit: It gets even worse. The protein estimated to have a frequency of about 10-63 that Axe has invoked as ballpark substantiating his own number of 10-77 is the 236 amino acid long Lambda repressor protein. That’s close to 100 amino acids longer than the ~150 aa beta-lactamase, and 143 amino acids longer than the 93 aa chorismate mutase.
They’re just making shit up.
1 Like
I meant that a laptop with a working theorem-proving program is doing reasoning, so “reason” in that sense. And yes, a reasoning agent isn’t reason, here is what I mean: “reason: the power of comprehending, inferring, or thinking especially in orderly rational ways : intelligence” (Merriam-Webster), so a reasoning agent has this, they have reason.
Yes, to be and to come from are different, and to say that thinking is motions of atoms in your brain is odd, to say the least. Not every motion of atoms in your brain is a thought, right? These two are not somehow equivalent.
If I carry out an action, like driving to the grocery, I can be said to have produced that. And if thoughts are not produced, that would mean they have no source, I think. So they just pop out of thin air, or something. So I don’t think you are making coherent statements here.
They do both! As you acknowledge:
But a verdict is a decision about what the person did or did not do, as a matter of fact. You are denying the obvious.
Why do you trust you laptop, then? I must ask again, would you ride in a plane, that you knew was the product of a mindless, unguided process? With no interest in producing a flying machine?
And this does substantiate my claim, if we trust various objects, because we know they were intelligently designed and assembled, if they come from a reasoning source.
That’s why Habermas and Moreland in “Beyond Death” present NDE accounts where the patient gives details that they could not have known, in the ways like you describe, “veridical NDEs”, they call them.
How do you know they don’t try and control this?
Wait, now you say they do control this at times? And how do you mean the magical ghost is blinded? We have reports, how is the soul somehow blinded?
Well, here we read: “Scientists have pinpointed a special part of the brain that, when stimulated, appears to produce out-of-body experiences.” That’s one experience that can apparently be replicated. But NDEs would not be expected to be replicated, though such reports are coming to light, more and more.
“How have naturalists responded to this research? In an older article in the journal The Humanist, John Beloff argued that the data in favor of life after death was already significant enough that even humanists should admit an afterlife and should attempt to interpret it in naturalistic terms. Beloff declared that the evidence indicates a ‘dualistic world where mind or spirit has an existence separate from the world of material things.’ He also conceded that this could ‘present a challenge to Humanism as profound in its own way as that which Darwinian Evolution did to Christianity a century ago.’ Therefore, naturalists ‘cannot afford to close our minds … to the possibility of some kind of survival.’” (John Beloff, The Humanist)
But why does interacting with nature mean it’s part of nature? Christians for example have always believed that “God is spirit” (John 4:24), and omnipresent, and yet not physical. So I need to know why interacting with nature means it must be part of physical nature. I interact with my kitty, but I’m not part of my kitty. Mere interaction doesn’t mean I must be part of what I interact with.
Relativity, with Einstein, that took some time to verify and be accepted. I believe that’s why he got his Nobel Prize for photovoltaics, instead of relativity. And Einstein himself did not like entanglement, which he called “spooky interaction at a distance”.
Well, people made a bunch of money off of books about “The Jupiter Effect”, but after it became apparent that they had no good points, and no supporting evidence, the whole thing collapsed.
This is actually general knowledge, do you deny that Bechly lost his post because he subscribed to ID views? And Axe lost his position for similar reasons? And I have heard only Tour make the claim that he lost funding from NSF, because he signed “A Scientific Dissent from Darwinism”, but this is quite believable.
But the fact remains that various prominent ID people have been set back financially, for their views on ID. They’re certainly not doing this for the money. And not everyone in ID can be president of the Discovery Institute! And $164,200 (the max listed, for the president) is indeed a nice salary, by comparison, Deborah Haarsma, president of Biologos, makes $173,914 a year, a comparable salary, so the Theistic Evolutionists are in it for the money?
I’m not sure what your point is here…
So again, please look for one point that has proven unanswerable here. Just one. And then come back and tell me who is who in your video.
No it wasn’t. That’s just you making up this ad-hoc framing to his challenge.
You’re making that up. It’s not stated anywhere in the introduction to Axe’s paper that he expected some particular value, and he does not propose any sort of observation that would disprove or otherwise seem out of agreement with any hypothesis.
In fact compared to the other numbers Axe reports, from studies on other proteins by other authors, Axe’s stand out as the lowest among them by a very large margin.
They didn’t propose anything as a hypothesis. Rather Stadler lied to Tour about what the papers said (this was Stadler’s framing of it all) and Tour just sat there nodding along, being utterly clueless about evolution that he is. And none of the papers constituted anyhing like an attempt to disprove any hypothesis about a two mutation limit to evolution.
Dude this is getting increasingly ridiculous.
No, he wasn’t. Bechly actually set up a strawman of evolution that he refers to as “Darwinism”, which he proposes to be the idea that there is “no conceivable reason” we should’nt be able to find a pair of extant species that diverged (by some degree he doesn’t define) from a common ancestor within the last 5-10 million years.
And if we can’t give him an example that satisifies his unspecified/undefined criterion, he will declare Darwinism false (again because, he wrote, there is “no conceivable reason” why we shouldn’t observe the same high rates of morphological evolution at any point in time on “Darwinism”).
What’s most ironic about it all is the human-chimp split is suggested by Bechly himself to meet the challenge, yet he tries to excuse his way out of that by claiming that if we go that route it would support “human exceptionalism” (presumably to discourage us from suggesting the chimp-human split?). You know what, I’ll just agree to that. The human-chimp split having occurred within the last 7 million years meets Bechly’s challenge, and yeah humans are exceptional.
1 Like