Oh, that reminds me:
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56 of them are mine, but that includes my thesis and meeting abstracts.
My middle initial is A. There’s another John A Mercer at UNLV.
It mostly runs out of me by the end of page 2. I didn’t know there were so many Harshmans in science. The only one I was familiar with was Larry Harshman, a fruit fly geneticist. I’m assuming that they’re all related to me.
Didn’t know the difference between an ion channel and ion pump; didn’t know about fatty acid membranes or related primitive cell models; didn’t know ATP was an RNA nucleotide; didn’t know the energy for the elongation reaction came from NTPs; still doesn’t seem to understand that is what extant cells do during transcription.
One could go on and on.
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So here’s a question: Why do some authors have google sholar profiles/pages, and others don’t?
You can set your own page up, picking out your own publications from the much larger group produced by a search.
They are associated with Paradigm, which has high ethical standards that it provides training in, and enforcement, see the pertinent FAQ entries about ethics.
Again I refer you to the FAQ, which discusses the peer review process, and mentions how to ask questions if people have concerns. Also, conflicts of interest are a concern, and are addressed in the FAQ.
I’m not sure what you mean by “broad recognition”, they should have famous editors? What on earth? Let’s try for competent editors, with good integrity. But they list the members of their editorial board, almost all professors, let’s look at the editors-in-chief: Professor Anthony Futerman, Weizmann Institute, Israel, in the Department of Biomolecular Sciences, he has a lab called “Futerman Lab”. Then there’s Professor Siegfried Scherer, Technical University of Munich, Germany, he has a Wikipedia page! He is a proponent of intelligent design, and he does real science.
And “lack of significant citation” (where is your evidence?), “Lack of indexing” (what does that mean?), “Lack of published impact factor” (eh? what is an impact factor?), “Limited publication history” (well, it started in 2021, I don’t if we can fault it for that).
You can sort articles in that journal by number of citations. The most cited article, Post-genomics, Evo-Devo and the Recurrence of Teleologic Thought (published May 2022), only has 5 citations.
That is not a lot.
Your confusion about such very basic terminology and metrics concerning a journal’s quality should be an indicator to you, that perhaps you are less than ideally prepared to render a judgement on a particular journal’s reputableness, much less to defend it competently against detractors. Of course, it could be that you think Tim is just making stuff up, and that these aren’t real things one might review in an effort to find out how much trust one should put into a journal. But the point is you don’t know, and the reason you don’t is that you never actually looked into it. Perhaps, then, since you are so unprepared to discuss a journal’s reputableness, a more effective strategy than to openly admit that you have no clue how to evaluate a scientific source whatsoever, would be to try and defend the paper in question on substance instead, insisting that the journal’s track record may not necessarily reflect on a paper’s veracity.
Unfortunately, of course, you already tried that, and exposed just as clearly that you are just as incompetent when it comes to the actual subject matter.
You say you are here to “defend” Axe’s paper. Yet you are clearly unprepared to have a discussion on basically any point of any relevance. Is it that you think yourself enough of a genius that putting in zero work should be enough to keep up with professionals? Or is it that you do not believe in professionalism at all, and that in your opinion everyone starts out on equal footing basically, just as incompetent as you are, so there is no point learning anything about anything before engaging? How do you reckon an approach this insultingly arrogant (in either case!) could possibly do your cause any good?
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Hilarious.
It’s too bad @lee_merrill is so clueless. He’s missing a good joke.
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Here again are some papers listed with similar results:
“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 Nature in 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.”
A “yes” or “no” is all that’s required, sir.
I can tell the results are different, that’s plain. And you changed topics, my point was that “I’m sure though that you don’t think the results are the same”.
Again, a simple “yes” or “no”, please.
As I said, function implies and requires working folds. So measuring the incidence of function also shows the incidence of working folds.
Ah, so now you think I have a valid point? Axe studied folds? And let’s check Wikipedia on protein folding: “Protein folding is the physical process by which a protein, after synthesis by a ribosome as a linear chain of amino acids, changes from an unstable random coil into a more ordered three-dimensional structure. This structure permits the protein to become biologically functional or active.”
So there certainly are a number of types, different types of structures, but they are all required for the protein to be functional. That’s the point I was making. So I’m not sure what you mean when you seem to be saying folds have function, the enzyme has function, right? And each fold helps provide that. And yes, Axe studied one domain, and as far as globalizing his results, he gives his reasoning here: “Although the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution. First, given the importance of hydrophobic interactions to protein folding, it seems likely that the sample space can be restricted to sequences carrying the hydropathic signature of a known fold. Second, because folds are stabilized by the cooperative action of many local interactions distributed throughout the structure, the overall problem of fold stabilization may be viewed reasonably as a collection of coupled local problems. This enables the difficulty of the whole problem to be assessed by assessing the difficulty of several smaller problems.”
But Axe claims his results apply to beta-lactimase domains in general: “Using these simplifications, the difficulty of specifying a working beta-lactamase domain is assessed here.”
Less than a page 
.
But I did find a reference to steamship design from the 1880s, probably by my great-great-grandfather.
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IIRC it’s already been pointed out that 10^24 is vastly different to 20^77.
Just keep swimming, swimming, swimming…
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AHAHAHHAHAHAHAHAHHAHAHAHAHAHA
deep breath
AAAahahahahAhahahahahahahahaaaaaah!
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So you are admitting that you lack the basic computer literacy to do a search for yourself, instead running to the safety of hearsay. Got it.
That is not even close to Axe’s extrapolation. Do you not understand how exponents work?
Calling it a “result” is a lie, and again, not even close.
Closer, but still more than a million million fold away.
A Google search is all that is required.
Good. So Axe’s work done under a Nobel laurate’s supervision gives a very different answer. That’s telling.
No, in reality, much of protein function involves transitions between metastable states, which in isolation no one in their right mind would describe as the same fold. One of them is doing so with every beat of your heart as you read this.
Fat chance.
Not very good from my perspective as a biochemist. And your confusion is showing in looking up the gerund instead of the noun.
Of course, as that’s not what I said. I said that the same function (including beta-lactamase) can arise from completely different folds. Axe is succeeding at confusing you. So particular folds do not map to particular functions.
Which is simply ridiculous. What would happen to you if we somehow increased “fold stabilization” (an absurd term) on your very own PrPC protein, Lee?
And it’s objectively, empirically false. Do you remember what I challenged you with in one of my very first responses to you?
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Why do you think that’s an important thing to note, Lee? What else would Futerman’s lab be called?
Any one with minimum computer literacy can look these things up with ease, but you either lack basic literacy, are afraid of what you’ll find, or both. Which is/are true? You’re clearly not looking to learn anything here.
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@lee_merrill: You need to look up “amino acid side chain” in order to find out why he’s laughing so hard. I googled it myself just now to make sure it works, and it does. You really need to learn just a little bit about what proteins are, what they’re composed of, and such.
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I already told him what they are. He just goes on as if nothing happened.
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Yeah, I forgot to mention that. He’s not a reader.
The ‘association’ is solely commercial. Paradigm is a provider of “publishing services” and The Israel Biocomplexity Center buys publishing services off them.
It would be more accurate to state that they offer training services, and offer assistance with enforcement, rather than that they impose either unless requested by their clients.
I would also note that this is a mere FAQ, not a statement of binding Terms and Conditions.
It offers services in managing the peer review process or reporting conflicts of interest. This provides no guarantee whatsoever that the peer review will be rigorous, or that conflicts of interest that the editors choose to ignore will be reported.
I therefore conclude that neither Paradigm nor its FAQ is relevant to the issues I raised.
No Lee. If I had meant “famous”, I would have said “famous”.
It would seem that ‘recognition’ is another term that you are unfamiliar with. Do I need to start writing in only one syllable words?
By "broad recognition … in the journal’s core disciplinary domain (evolutionary biology, origin-of-life research, and related), I meant that they would be widely recognised as being experts in the fields of evolutionary biology and/or origin-of-life research, by others in those fields. Fame doesn’t enter into it. Having such experts ‘on the masthead’ adds credibility to the journal.
That they are “almost all professors”, is far less relevant than what their actual fields are.
And do either of them have any expertise (let alone “broad recognition” as experts) in evolutionary biology and/or origin-of-life research? Futerman,'s expertise seems to be in in lipid biochemistry and metabolic disease. Scherer’s seems to be in food-borne bacterial pathogens.
Of the rest of the board, there are a sociologist, a physicist, a public health expert, two mathematicians, and a philosopher, working in unrelated fields. A couple of the others (Ardern & Carlson) could probably be described as evolutionary biologists, but I’m seeing little indication that they have achieved any substantive recognition within that field (explicitly not talking about fame that would extend outside that field). A couple more others (Garte & McMenamin) could be claimed as having expertise tangential to evolutionary biology.
But I will leave it to those with greater expertise in biology than I have, to demarcate exactly how much, or how little, “broad recognition … in the journal’s core disciplinary domain” they have.
Don’t you mean where’s the lack of evidence? The evidence is that I could find no papers in that journal with more than a handful of citations. If you want more, then either (i) read @AnEvolvedPrimate’s post above, or (ii) do your own research.
“Eh?” Lee’s too ignorant to know what an impact factor is, and too apathetic to bother looking it up on Wikipedia.
Why the hades should anybody give a rat’s arse about anything Lee has to say about whether this is a “respectable journal”, when he displays this level of willful ignorance?
And it has published only 28 articles in that time – around six per year.
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