Are you incapable of looking it up for yourself?
In what way is correctly noting that there is a lot of variation, including the reasons, not an answer?
It would appear that “mutations such as Axe investigated” are pretty much nonexistent. Perhaps you should read the paper you’re trying to defend? Maybe you could explain how he produced those mutants in your own words.
If it’s clear to you, explain it in your own words.
Creation! But I see your point now, and no, there is no inherent assumption in ID that there is a constant rate of creation. And Bechly’s assumption of a basically constant probability of a new body plan emerging is taken when he assumes the evolutionary perspective. I think it’s an appropriate assumption then, molecular clocks being an indication that people do think that.
Yes, that would be uniformity, which is generally accepted nowadays in scientific circles, as far as I have seen: “Though an unprovable postulate that cannot be verified using the scientific method,[6] some consider that uniformitarianism should be a required first principle in scientific research.” (Wikipedia, “Uniformitarianism”)
“But of course, even if such a single example were to be found, it would not be sufficient to remove the general problem of a clear pattern of big changes in short time being ubiquitous in the fossil record but not in the present fauna. This pattern is undeniable and requires an explanation.” (Bechly here)
So evidently Bechly believes this pattern happened frequently enough to call it “ubiquitous”, thus not just and only after extinction events. Bechly again, here:
“Some examples of abrupt body plan transitions are the origin of photosynthesis; the origin of eukaryotes; the origin of the Ediacaran biota (Avalon Explosion) and Cambrian animal phyla (Cambrian Explosion) such as the origin of trilobites from worm-like ancestors in less than 13 million years (Daley et al. 2018, Bechly 2018); the origin of efficient eyes in arthropods, cephalopods, and vertebrates; the terrestrialization of plants (embryophytes), arthropods (tracheae), and vertebrates (tetrapod limbs); the origin of wings in insects, pterosaurs, bats, and birds (including the origin of pennaceous feathers from filamentous precursors); the origin of secondarily marine vertebrates such as ichthyosaurs, mosasaurs, manatees, and whales; the origin of echolocation in bats and whales; the origin of complex new reproductive systems (angiosperm flowers, dragonfly secondary copulatory apparatus, holometabolic insect metamorphosis, amniote egg, and eutherian placenta); the origin of distinct new body plans in vertebrates (e.g., snakes, turtles, bats, and whales); and even the origin of our own genus Homo and of a globular braincase correlated with the “Creative Explosion” of symbolic thinking within Homo sapiens.”
Well, it is actually an area of study, in relation to the fossil record! Here is a 2018 article excerpt::
“Early studies of taxonomic richness through deep time (e.g. Benton, 1985; Sepkoski, Bambach, Raup, & Valentine, 1981; Valentine, 1969) interpreted the fossil record literally using face-value (=raw or observed) counts of taxa. However, because fossil record sampling varies considerably among clades, geological time-intervals and geographic regions, direct comparisons of face-value richness can be misleading (e.g. Alroy et al., 2001, 2010a, 2010b; Peters, 2005; Raup, 1972; Smith & McGowan, 2011). To infer genuine patterns of deep-time biodiversity, we need methods that successfully standardise samples of unequal sizes and permit direct comparisons of richness among assemblages.”
Then they mention rarefaction work by Sanders, and then investigate other methods.
But Wikipedia references it as lasting about 13-25 million years. Maybe you should edit the article? I’m sure they would want the most accurate estimate, with references. But scientists do indeed seem to have abandoned the artifact hypothesis in regard to the Cambrian explosion, which means that in one significant area of diversity, we have a reasonably good picture of what it was like.
That’s fine, but I need support for these conclusions. For example, why do you mention the Cambrian explosion, after acknowledging that it was indeed real, implying we have sufficiently sampled it to make that conclusion?
Well, I missed that, but then I also quoted Bechly’s summary of a body plan, which I think would be the one relevant to his challenge. But I don’t think the two definitions are entirely different:
“This term, usually applied to animals, envisages a ‘blueprint’ encompassing aspects such as symmetry, layers, segmentation, nerve, limb, and gut disposition.” (Wikipedia)
And I can’t seem to find the post where I quoted Bechly’s definition, but I as I recall he did mention nerves and guts.
I don’t think what I said has no meaning, though, nor is it circular. Molecular clocks show that people do think they can get an idea of the rate at which mutations such as those Axe investigated, occur.
This statement is unclear to me, certainly I’m not saying a mutation rate is rare, that can’t be what you mean.
I have no idea! And I’m not sure how faith is going to help give me an answer here, nor do I see how this challenge has anything to do with this discussion.
I did do a search, and came up with nothing. It doesn’t seem to be an area of major interest, unlike the rate of small-scale mutations such as point mutations.
Well, this implies there is no ready answer, or no good answer. So there can be no conclusion that gene-fusions occur often, producing new function “in our lifetime”, or at any given rate.
“Four sets of residue positions in the reference sequence (coloured in Figure 6) were chosen for separate randomization experiments. Each set comprises ten residues in close proximity in the native large-domain fold (Figure 7b).” (Axe)
So, randomized residues, or point mutations.
Yes, I did, twice.
If you have faith in Axe, you certainly do. Why won’t you predict?
Doesn’t Axe’s work give you an idea?
Are they point mutations? What does the modifier “point” mean?
Assertions are not explanations.
Nope. The molecular clock has nothing to do with any supposed morphological clock, much less a new body plan clock. You have to know that we are very far outside any area of competence you may possess.
No. Count the principle of uniformity as another thing about which you have no real notion. Again, it’s irrelevant to anything we’re discussing here.
And yet he presents zero evidence, merely listing a few major transitions, some of them at odds with his notion of a uniformly distributed history; for example, the Cambrian explosion, during which a great many new body plans emerged, to level not seen before or since. Many more of those examples are nonsensical in context, and very few of them fit his definition of “new body plan”. I’ll point out a few.
No fossil record of how long this transition took, or any idea what it has to do with a body plan.
His source, Daley et al., makes no such claim. And it also refers to evidence that this wasn’t an abrupt event, given the many fossil intermediates between “worms” and trilobites.
Fossil record is very sparse for this and consists mostly (in its early stages) of spores.
We aren’t even sure how many times arthropods became terrestrial or how long it took in any case.
Another gradual transition with many intermediates. Not clear how long it took.
Insects: unclear from the fossil record. Pterosaurs and bats: transition pretty much unknown, which I suppose is nice for Bechly, but is there really any evidence that it was quick? Birds: many millions of years of intermediates, depending on what you count. Are any of these new body plans even under Bechly’s definition?
Where’s the fossil record of any of that?
But I grow tired of all this. Bechly isn’t here to defend himself, and you are clearly incapable. But I hope you can see that there are problems with his claims.
Yes, but not any aspect of the record that concerns us here. Your little quote shows that, if you read for comprehension.
Not interested. But note that even their minimum interval is much longer than Bechly allows for modern species pairs.
No, it doesn’t mean that at all. You have a talent for non sequitur.
I’m afraid I have no idea what you’re asking for here, but it seems to contain another non sequitur.
You are very wrong, but again you lack the competence in this subject to judge. Absent a long period of education, you might credit the statements of people who have that competence. Me, for example. And you might, again, consider actually reading what I say. I’m not trying to be rude here, but you must realize how out of your depth you are.
Yes, it is. Acknowledging that nature is more complicated and nuanced than you personally would prefer may fail to satisfy you, but that’s the price of integrity people of science like us at times must pay. Confuse not for allies those who would choose the other path. To seize the opportunity to finally dump my favourite quote from the ancients (Cicero, in this case): Nulla est igitur haec amicitia, cum alter verum audire non vult, alter ad mentiendum paratus est.
No. Uniformitarianism does not propose that all processes in nature have an unchanging rate, or all events of a type a constant frequency. A thesis saying something so obviously wrong would not be accepted by any respectable researcher of nature either. Fundamental laws are assumed to be uniform (and so called in part because of that)[1], general principles tend to hold, too, but particular high-level emergent effects in systems so far away from equilibrium as life cannot be expected to be this simple. This is quite like suggesting, after having understood a simple pendulum, not only that an entire clockwork reduces to a single parameter in much the same way, but that an entire global computer network would not be any more intricate than a mass on a spring, even accounting for it interfacing with human users in various ways on an ever varying number of nodes.
Ironically, the one contributor to mutation rates and therefore to evolution which is constant by all accounts – the decay rate of unstable nuclei, which (correct me if I’m wrong) could in principle damage or otherwise interact with either a nucleotide or a replication enzyme enough to trigger an error – is the one whose uniformity throughout the ages many creationists actually insist might yet be an open question.
And they are assumed so for practical reasons, one should stress, not philosophical or ideological ones: Without assuming that the past can tell us something about the present and the future, we’d have literally nothing to go on whatsoever. The reliance on experience predates not only the scientific revolution, but our species altogether. ↩︎
Hi, Lee.
I don’t want to distract you from the intellectual pummeling you are receiving from the other members here. However, I am still interested in hearing how you decided that this article, written in 2011, was a response to this article, that was not written until 2018.
Please explain.
Well, his work was about fitness landscapes, and your challenge was not about that, so no.
Yes, I think so, and “point” means changing a residue.
No, I did explain myself twice, and I think what I said was clear. And so this was not a mere assertion.
Well, I don’t claim that people propose specific morphological clocks, or body plan clocks. I do claim that people think it’s reasonable to investigate rates of evolutionary change, and that we can get an idea of such rates, whatever they might be.
How is your statement not an expression of uniformity, though? “This requires that they are common enough that some are expected in any 5-million-year period and that those events are distributed fairly evenly through earth history.”
That’s fine, Bechly’s point is that body plan changes happened quickly and frequently in the past, a period of even more rapid change does not refute that.
Well, I agree, I don’t think those belong in the list.
Here is Bechly’s comment on this, which you somehow skipped: “since the authors refute the existence of stem group arthropods in the Ediacaran period before 550 million years, and euarthropods are documented already for the Lower Cambrian at 537 million years, there remains a window of time of only 13 million years to evolve the stem arthropod body plan from unknown ecdysozoan worm-like ancestors and to make the transition from lobododian pro-arthropods to the fully developed euarthropod body plan, with exoskeleton, articulated legs, compound eyes, etc.”
But a sparse record is still a record, no? All that needs to be established is the time span of the change.
Bechly’s specialty was dragonflies, so I think if he was still available, he could give some reasons for this being in the list.
Intermediates implies a fossil record, though. How is it that the timeframe is unclear?
Certainly insect and bats and birds would seem to fit Bechly’s definition of different body plans. But I agree that there are problems in his list, but that doesn’t seem to overturn his point that new body plans (by his definition, or by Wikipedia’s definition) frequently arose in the past, in short geologic timeframes, and that doesn’t appear to be happening now, as demonstrated by living species pairs.
But that would be an interval for the entire Cambrian explosion, what Bechly is interested is in the timeframe of the development of new, individual body plans.
Speaking of non sequiturs! You make a claim, without any explanation of why we should believe it.
I’m not sure how I can be any clearer, Darwin subscribed to the artifact hypothesis, saying we just haven’t sampled enough, and with more sampling, the expected gradual intermediates would appear. People used to say this about the Cambrian explosion, and now this has been abandoned, and scientists believe we have sampled enough of this era, to be able to conclude that there was a real, sudden appearance of many animal forms. As shown by the book title you mentioned, titled (wait for it!) The Cambrian Explosion. You said “New samples of what, exactly? New Cambrian organisms? Sure.” As if to say, we’re still finding new Cambrian organisms, enough to say we haven’t sampled enough yet, there may still be intermediates we haven’t seen. Enough to revive the artifact hypothesis about this event?
Um, again, why? Please defend all your points.
But you are not saying anything, when you just say “Non sequitur” and so on, and leave it at that.
But the claim was made that gene fusion events have created new functions in our lifetime. That implies we know a rate of such changes.
Well, yet again I point to people who study and propose molecular clocks. This implies they hold to a view of some level of uniformity, though I agree, everyone agrees that rates can vary some. But the point being made is that we can also get an idea of what the rate of evolution might be.
A pop-sci book is not a literature review or the reflection of a consensus. A book title, one that correctly captures the way the topic is referenced in common parlance among both professionals and lay folk, is not a literature review either. Whether or how much the artifact hypothesis was ever in doubt pertaining to the cambrian period is best addressed by the biologists here, but certainly a book for the likes of you and I shall not settle that question, no matter how dull or appealing, appropriate or misleading any of us find its title, or, indeed, its contents.
Regardless, the expectation that novel body plans should appear at any particular and static rate is as absurd as expecting fair dice to reliably loop through all its faces. So the point is moot either way. It is no mystery why body plans haven’t been popping out at a constant rate between the Cambrian and now, regardless of how quickly or how gradually they came about at the time, and regardless of how well or poorly we’ll ever come to reconstruct Cambrian biohistory.
It does? How? If we have observed fusion events, and if we have observed these fusion events to produce new functions, how does any statement about the rate of such events follow from the acknowledgement of such observations?
Though I disagree with the point you make, I appreciate the legitimacy of the question. But here too I must wonder how the reference to molecular clocks is actually relevant to your point. Mutations, rare though they may be, are in the end numerous enough to where one could run some statistics and come up with a number to characterize the rate of their occurrence. In order to be fair about this, one would have to do it on a fairly low cladistic level, of course, because lineages that are far apart may be subject to very different environments, internal chemistries, genome sizes, and reproductive cycles, to where their molecular clocks would tick at vastly different rates, but nevertheless, one could have some semblance of a measure here.
The problem of course is that mutation is not the same as evolution, and when we are talking about such macroscopic features as body plans, simply accounting for how the distribution of alleles changes in a population over a time period far too short to see any changes at all to their body plans by any definition of that term, is not going to supply us with any useful intuitions regarding that.
It is a problem of scale, and the fact of the matter is, attempting to understand all of biology by principles of chemistry or physics alone is not going to be productive. There are good reasons these are different fields with very different languages and methodological minutia. As much as I sympathize with a reductionist sentiment regarding the operations of nature, ultimately the goal of science is to build models with predictive capabilities, not merely to tell a satisfactory story about how the pieces work. And to that end, molecular clocks measured for one environment in one lineage are just an insufficient basis to build expectations about long-term developments of all populations in an entire ecosystem.
Ah, I disagree. Several of said members have punted, and withdrawn from this discussion. One of them claiming victory! While neglecting to mention that they did not respond to my latest point I made to them in reply, at all.
Well, Art’s article, he said, was a response to a paper by Axe published after the 2004 paper. And Axe in the (2011? I don’t see a date on it) article said he was responding to an email request from Art, about his 2004 paper: “In August of 2004 I received an email inquiry from plant biologist Art Hunt. He had written a draft for a blog piece aimed at reviewing a research article of mine that had just appeared in the Journal of Molecular Biology”. But Axe’s comments are still relevant today, since Art seemed to be unaware of them, when I mentioned them to him. And Art basically just reiterated his original objections, and did not respond to any of Axe’s points for some reason. Nobody responded to any of Axe’s points! Very strange, while people continue to state that Axe has been refuted, and has not responded to criticism.
Pretty safe claim. Whatever does that hafe to do with anything you have said previously or anything we’re talking about here?
It is. But it’s not an appeal to uniformitarianism, which you brought up for no discernible reason. You persist in throwing random words at me, apparently in an attempt to make it look as if you understand something.
I will point out, once more, that he presents very little data to make that point, and the few instances he does present are flawed in many ways.
Notice that this quote makes no mention of trilobites, which was the original claim. And note that 13 million years, whatever it refers to, is much longer than the time allotted for his challenge.
A sparse record is a record with little constraint on duration, so it can’t be used to claim a rapid transition.
Perhaps, but I can’t think of what they would be. Since he’s not available, there seems no point.
Because The fossil record, as usual, is fragmentary. You are, I think, imagining a linear series of ancestors and descendants, which the fossil record seldom if ever delivers.
How? What’s his definition and how do they fit it?
No, it completely overturns his point, by showing that his premise has no support.
If you had a point to make there, it’s opaque. I’m not sure you understand what you meant to say.
It should be obvious. Abandonment of the artifact hypothesis doesn’t mean we have a reasonably good picture of what the Cambrian explosion was like. Why should it?
They did, you know. Not, mostly, in the Precambrian, but the lower boundary of the Cambrian has moved since Darwin’s time to encompass parts of the former Late Precambrian, now Cambrian Stages 1 and 2. And there are quite a few intermediates in that interval. There are also a few still in the Precambrian. Once might point to Kimberella or Namacalathus.
Which you clearly have not even looked at, or you wouldn’t be talking about “sudden appearance”. This is your personal ignorance talking again.
There are plenty of intermediates we have seen. The Burgess and Chengjiang faunas are full of them, as well as the earlier small, shelly fauna and a variety of ichnofossils. And the latter show that the first appearance dates of many taxa in the Chengjiang and other deposits of similar age are indeed artifacts of preservation.
I did that previously, and you ignored it. Again, Bechly’s notion of a body plan gives whales a different body plan from other artiodactyls. The standard notion gives them the same body plan as all other vertebrates. Do you not see the huge gulf there? This is why I say you lack the competence to judge.
Once more, you might consider actually reading what I say.
Oh, I am sure you do. Blind denial seems to be the only debate tactic at your disposal. To wit:
This really is not complicated. The Axe article was, indeed, written in 2011. The date is at the bottom.
@Art’s article was written in 2018.
Therefore, Axe’s article could not be a response to Art’s.
Do I need to explain why? I hope not.
This, of course, should have been evident even without the dates, since Axe clearly did not respond, and has not responded, to the specific criticisms Art made in 2018. That is, it should have been evident to anyone who read and understood both articles.
But reading and understanding, you don’t do that, do you? It’s just not your thing.
Keep it up, Lee. You’re providing in object lesson in the kind of dishonest and intellectually lazy person who keeps the DI afloat.
Um, this book was said by the scientist person here to be the best book on the subject. And are you saying there is no consensus that the Cambrian explosion was a real event? That we have not yet sampled enough to know this? And the biologist who recommended the book did not dispute the point that the Cambrian explosion is now thought to be a real event. And I even quoted a scientific article, that said the same thing.
Why is this analogy a good one? I don’t think it is, nobody claims that evolution somehow must loop through its various possibilities.
But I need to see your evidence for this conclusion. Why is this not a mystery?
Saying an event should have occurred in our lifetime implies the rate of occurrence is high enough for it to have occurred in that interval. Implying we know the rate.
My point is that work in this area implies some level of a subscription to the principle of uniformity, in evolution. Which would then indicate that some level of uniformity would apply to the development of new body plans, too.
Well, we had this discussion already, and I pointed to an article that shows that indeed, molecular clocks are applied over the whole fossil record. I did another search, here is an excerpt from another article, from Science News Today: “Beneath the surface of every living thing—beneath skin and muscle and cell membranes—there lies a molecular code written over millions of years. It is not etched in stone or preserved in amber, but instead flows quietly through the spiraling strands of DNA, replicated with every cell division, passed from parent to offspring. This code is not static. It mutates, shifts, evolves. And remarkably, within these changes lies a method of telling time—not with gears or ticking hands, but with patterns of genetic differences. These are the molecular clocks of evolution: the biological timepieces that allow us to peer back through eons and trace the shared ancestry of life on Earth.”
You’re right about that, and @Gisteron is wrong. The Cambrian Explosion is not a pop-sci book (though it should be quite accessible to the lay reader). But you haven’t looked at it, have you?
Sorry, I’m missing that. What scientific article did you quote? Are you talking about the review of a creationist textbook? Not exactly a scientific article.
But yes, the Cambrian explosion was a real event. A great many eumetazoan phyla seem to have originated somewhere in the 30 million years or so from the latest Precambrian to the end of the Early Cambrian; call it 550-521ma. Not all phyla. Some are likely a bit older and some have no fossil records or so little as to be useless. (The earliest nematode fossil, for example, is Jurassic.)
This is of course bad for Bechly’s challenge. If the origins of new body plans are clustered in time rather than uniformly distributed, we have no reason to expect the last 5 million years to contain one of those clusters, and the challenge is pointless.
Well of course it is. There are many hypotheses for why the Cambrian explosion happened when it did and why no similar event has happened since. The book I mentioned to you covers some of them. I personally like the arms race theory: the invention of macropredation was a major selective force on the animal biota. This explains, for example, why so many lineages independently developed sclerotized or mineralized integument. And of course this invention could happen only once. Later ecological changes were on a smaller scale, but we see bursts of evolution after each mass extinction, as another example of an explanation for clustering of events.
Urk. Science “journalism”.
No, for the claim that “gene fusion events have created new functions in our lifetime” it just requires that we have observed at least one. We have, I gave some examples.
We’ve observed many, not that we can extract anything like a rate across the history of life for that, or whatever it is you want.
Edit: Incidentally the fact that we have directly observed them in experiments lasting mere weeks to months seem to throw a massive spanner in the works of Axe’s case against new proteins evolving.
That means Axe now has to push his argument all the way back to the very origin of the first proteins in the entire history of life (these can’t have evolved from fusions of other existing proteins of course)*, but his argument is completely ineffective when it comes to the entirety of the history of evolution since then.
He can’t invoke his (extremely poorly supported) 10-77 number to cast doubt on any major transitions in the history of animals, for example, since these would definitely be subject to mutations that result in gene fusions.
Because it captures the specific character it is set out to capture: It is absurd to expect very regular patterns out of highly sensitive and profoundly chaotic systems.
It is not a mystery, because competition is one of the strongest forces of evolution, both driving and stabilizing it. When, for example, multicellularity appeared on the scene, along with it opened a new possibility: Re-distributing the functions necessary fo the survival of the organism. Instead of every cell being self-sufficient, it was now possible to have cells take over and specialize in some functions to the detriment of others, said detriment being compensated by other cells in the organisms. What began as amorphous blobs could spontaneously develop structure, and, if the structure was viable, its emergence would mark the beginning of a new species, different from its brethren in having that structure. And with all competitors being structure-less at the time, it was a free-for-all for developing all sorts of structures, like external shells or internal skeletons, or lots of flexible limbs, or food processing or stimulus processing. If I were to guess, I’d reckon more such experimental body plans went extinct than survived to leave a mark in the fossil record. But those that did stay for the long term would now improve on their type. The reason nothing like this many body plans have been emerging eversince is because it’s never been quite such a free-for-all ever again. The environment changed permanently, because now all manner of highly specialized critters are around either hunting or competing for resources, and something new starting from scratch now would in all likelihood go extinct before it got going anyplace else. It’s the same reason life in general does not emerge again on earth. In the beginning it might have emerged multiple times, but once one sort got good enough at it to dominate the planet, potential new arrivals were destroyed before they could even remotely hope to share the space.
Seeing an event did occur does not imply knowledge of the rate at which events like it occur. Maybe you misspoke in the former message. In that case, fair enough, and point granted. However, going by what you said, as I did when I replied to you, no, the claims are not equivalent, and what follows from one may not follow from the other.
Well, you are incorrect, and for several reasons:
For one, what applies to the whole may not apply to all parts, or vice versa. This is called a compositional fallacy.
Secondly, molecular clocks are not dependable for all of time. What works for a hundred thousand years, or even for a million will not work for a hundred million years. The emergence of a new body plan is not the kind of point-mutation-by-point-mutation drift that molecular clocks are a vague measure of the rate of. Just because some periods where the environment is stable lends itself to uniformitarian treatments does not mean that all of history does, just like the accuracy of a yard stick to measure the dimensions of a room is no indication that the distance to the moon can be measured to the inch, let alone by a yard stick, were it only sized appropriately.
Very well, happy to retract my dismissal.
I still refrain from addressing the “is the Cambrian Explosion a real event” question, because, frankly, I do not understand it:
Did a large number of novel body plans emerge over a duration the likes of which have never since yielded so much fundamental diversification? Yes. Does that mean it is a real event? I don’t know.
Are we talking about a process that unfolded over something like a week of time? No. Does that mean it is not a real event? I don’t know.
To be clear, what I claimed was no mystery is why new body plans have not been emerging at the same rate since the Cambrian. The “of course this could only happen once” part is the one that I say is unsurprising. I articulated the reasoning behind my intuition on this matter earlier in this message. I’m sure there are factors I neglected. Though if I was grossly incorrect in some of the basic assumptions, I’ll be happy to hear of such mistakes and know better afterward.
I’d say that we have a number of hypotheses to explain two things: that it happened when it happened and not earlier, and why nothing similar has happened since. But it would be difficult to test any of these hypotheses. All we can really say is that some hypotheses make sense given what we know and others don’t. But I don’t see that we can confidently narrow it down to one.
Dead wrong.
My challenge is about function. You don’t know what you are talking about. His work was not about fitness landscapes. The title of the paper is:
Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds
Keywords: functional constraints; sequence-function relationship; sequence-structure relationship; function landscape; sequence space
The only modifer in front of “landscape” is function, Lee. The word “fitness” isn’t even in the paper.
That’s why your claim that determining a threshhold had something to do with fitness was incoherent, and why my challenge is an accurate measure of your faith in Axe’s work.
Might it help you to summon the courage to make a prediction if I told you that the enzymatic activity was beta-lactamase?
No, it doesn’t. But I am impressed that you used the term “residue.”
So you don’t know what a point mutation is, but you understand this work better than I do, yet you lack the faith to make a single prediction based on Axe’s extrapolation from experiments that I say are bad, but you claim are good. Is that an accurate summary?
Your assertions were about fitness, which was not mentioned in Axe’s paper, so they were anything but clear.
So, again, in your own words,
How does converting a cheaply assayed continuous variable into a binary one help here?
What was the meaning of my hint: diffusion?
How many other papers in this field have you read?
If one screens a library of immunoglobulin sequences from an unimmunized mouse, what fraction of them do you predict will have measurable beta-lactamase activity?