How can you tell whether two species have different body plans? “They’re obviously all birds” doesn’t illuminate anything. If penguins arguably have a different body plan, please make that argument.
We’re trying to figure out how to tell if honeycreepers all have the same body plan, and, if so, where that body plan ends. I’m coming to the conclusion that you have no idea.
How do you know? What is the definition of body plan you want to use? By the only one you have quoted so far, lampreys and honeycreepers share the vertebrate body plan.
Ah, you don’t understand the concept of assuming for the sake of argument. They were trying to answer the challenge in its own terms.
Still don’t understand “for the sake of argument”, eh? Do you understand anything I say to you? It seems doubtful based on your non-responsive response.
What follows seems to display a failure of your ability to use the “quote” function. It’s hard to tell which parts are yours, which are new, and which are old. Please, please try harder. But I don’t see that you have actually responded to anything I said.
Irrelevant. Nobody disputes that there can be utility in doing this. You assert that setting a threshold is the only way any conclusion can be drawn.
“The field of comparative anatomy” is not a statement. I’ll leave it to those involved in it to express how amused they are, however, by your suggestion that what they do is not rooted in measurement.
Nobody actually made that claim, but do carry on…
No. Once again you are struggling to string together the simplest of logical structures, and “realize” nonsense as a result.
If it is true, that “the only statements that can be believed are those that are established by measurement”, and if that claim itself is not established by measurement, then the only conclusion is that it is a statement which is not among those that can be believed. At no point did we agree that believability and truth were synonyms. For the time being, a statement can be both unbelievable and true at the same time. There is no contradiction here.
And, of course, nobody made that claim anyway, so it’s an entirely moot point. I’ll still waste my time on it, because I’m not qualified to debate the matters at hand seriously with you anyway, and because it amuses me to see and to expose your fumbling of logical inferences of even the simplest sort like this modus ponens.
That is not quite my objection to lee’s argument. I don’t think he is saying it is the only way to measure function. He only says it is one of, possibly, several ways that are “effective.” But who knows what he means by “effective”?
Continuing with my analogy, it could be argued that having people stand on crates and seeing whether the crates can withstand their weight is an “effective” means of determining obesity. But is it an appropriate method to obtain an accurate measure of the prevalence of obesity? I would say not. Lee’s opinion remains unclear. He seems to have his doubts, but then is unable to articulate why those doubts do not equally apply to the method Axe used in his experiment.
True, lee did not say that it was the only way to measure function, though I’m not sure that it was about measuring it effectively, what ever, indeed, that means. What I am contesting are his statements like this:
In my interpretation – and by all means, @lee_merrill, do correct me if I am mistaken – the claim is that for the purposes of making conclusions it is necessary that fitness and function be treated as binary variables. If it so happens that measurement of such things yields a spectrum of possible values, then a threshold must be set to map the actual values to something binary, else conclusions cannot be drawn regarding these things, or at least not as well as they could with binary values so obtained.
Come to think of it, it is somewhat ironic that the suggestion of a binary mapping making it at least easier if not outright enabling the drawing of conclusions, should come from someone who so consistently commits non sequitur errors as lee.
No, I made a point, you told me I have to respond to it. Odd…
I seem to have lost track of Bechly’s definition of a body plan, but I found this: “This is very different from cases where an entire new body plan or system appears, such as the countercurrent heat exchange found in whales. It’s these dramatic innovations that modern evolutionary theory needs to explain, and it’s precisely the kind of change we don’t see in any modern species pairs, according to Bechly.” So I would say flippers in penguins is a new system. And again I ask how is the statement “honeycreepers are all birds”, disputable? This seems obvious.
I’m quoting Bechly, and Wikipedia, and basing conclusions on how evidently qualified people define this concept. Glad to hear your definition!
I would say the lamprey mouth parts are “new systems”, as opposed to beaks on birds, using Bechly’s comments on new body plans.
I do understand the concept, I’m saying they didn’t do this. Again, why not take the simple approach of correcting Bechly’s definition of a body plan? End of discussion.
Yes, something got gummed up, I noticed that and was too tired to correct it. It was Christmas Eve! Feliz Navidad…
Well, I deduce that Bechly also holds to external input, apart from natural processes, in the arrival of new body plans. Kind of like Michael Behe, who believes God can act within nature, such as at the quantum level, to provide needed input for new structures. So every organism can have a parent, and God can intervene.
I don’t subscribe to either of these views, they seem to be positing miracles, so I just believe new creatures could be plain miracles, without God working in ways we couldn’t detect.
No, I would agree that posting a distribution, and computing the average and the standard deviation could be another way.
Well, it is a field, if as you say, there are people “involved in it.”. You are getting incoherent. And I need a refutation, I think it’s a clear and understandable point. Saying “other people could refute you” won’t do.
I’m not saying they are, I would say that we can know true things, by evaluating them by different kinds of evidence, and making conclusions, by finding what is reasonable to believe.
No, I disagreed with you implying that. I even said a crate cannot replace a scale. But my point was that the chosen procedure doesn’t have to be as sensitive, it just has to be effective as a measurement.
Please reply to what I said.
I did give reasons to believe Axe’s method was reasonable, this has got to be standard procedure in evaluating antibiotics, to determine whether a remedy should be put into production, and the reviewers of his paper evidently thought what Axe did was reasonable, and adequate.
I would correct what I said, and say that’s the simplest way to draw conclusions, and an effective and reasonable way to proceed. You all seem to say this is false, but are not telling me why.
Appeals to obviousness, much like appeals to intuition, are invoking a subjective assertion.
The real challenge is to objectively characterize something (such as defining body plans) in situations where you feel they are obvious. Only then can you apply such definitions or characterizations to things that are not so obvious.
Glad we can agree that the field of comparative anatomy is, in fact, a field, and not a statement that can be true or false, established or refuted by argument. I never said that other people could or would refute you. Just being outside the field I find it not my place to take offense at your suggesting that measurement is not a way by which people in the field substantiate some of their claims about measurable quantities.
Only to someone who could not read what was written and made up what was meant instead. If you can produce one quote from any of my messages that even remotely seems to suggest anything like that “the only statements that can be believed are those that are established by measurement”, by all means, let’s see it. Otherwise I feel rather comfortable calling this a lie, since an honest mistake I shall charitably assume you would not double down on like that.
Yes, you are. Feel free to go back and read what you said. In your argument “Something is believable only if it is established by measurement” implies “Something that is not established by measurement is false”. You are saying that being unbelievable and being false is the same. Either that, or you Think that \left[\left(A\to B\right)\wedge A\right]\to C which is just embarassing.
For what it’s worth, I did not say it was false. Thresholding otherwise more nuanced values into a binary form can be helpful for some purposes. Whether anything fruitful is still to be gained from this operation when it comes to discussing function and fitness, that’s something the present biologists shall best opine over. My objection was to the idea that this was necessary to draw any conclusions at all, because it depends entirely on context whether this is so, and it is trivial to imagine any number of problems where such binarization would actually prevent making correct conclusions.
For example, suppose the debate is over which of two variants of an enzyme is more functional than the other in a given environment, and suppose that one of them actually makes more of the product than the other over the same length of time, or perhaps it uses less energy per cycle to do that. Or maybe one of them is faster, but the other is more efficient. If we just set a threshold, we may end up concluding that both are equally non-functional, or that both are equally functional, or that one is functional and the other is not. All of the nuance of the situation will be lost, the conclusion reduced to a very crude binary outcome that does not correctly reflect what was experimentally observed.
Of course, in some other situations all that finer detail may be uninteresting and muddy an otherwise very simple decision. And that’s fair enough. There is use and merit to this technique, all I objected to was that it was a necessary or the only way to make progress. If this is no longer your position, I’m glad, and we have little disagreement on this issue anymore.
You didn’t make a point. I want to know what you think Bechly’s definition of “body plan” is, and you won’t say and can’t even seem to find where he states it.
Note, that this is second hand, and as we have seen you can’t count on the DI to accurately represent what someone says. Still, better than nothing. But what’s “entirely new”? Flippers on penguins are just wings put to a different use, one that even many flying birds employ them for too. So we are left with a definition that relies on more undefined terms, difficult to apply in any real case. And of course the countercurrent heat exchange is not visible in fossils, so there’s no way to determine if it arose within 5-10 million years.
It’s not disputable. What’s at issue is its relevance to the question at hand, of whether they display new body plans or innovations.
But you aren’t quoting Bechly. And the Wikipedia quote gives the standard definition, the one I would use, but not at all what Bechly means; by that definition whales and hippos (and fish, and birds) have the same body plan. We are getting nowhere because you refuse to provide the definition you and/or Bechly are using.
Why are lamprey mouths new systems but beaks aren’t? What criteria are you using to judge this?
What’s your argument?
OK, if you like. Behe’s definition is non-standard and vague. Nobody uses it. Therefore his challenge is invalid. Happy?
Probably, though this is not clear, and it isn’t clear for Behe either. Sometimes they have both said that there may be no actual divine intervention during earth history, only a careful setup of the initial conditions in the first cell that would naturally result in a desired outcome. From Bechly’s web site https://www.bechly.at/anti-darwinism-1/:
“Intelligent Design is instantiated not by supernatural interventions within spacetime but by fine-tuned initial conditions, fine-tuned laws of nature, and a fine-tuned fitness landscape.”
Obviously. But that’s still common ancestry. Also obviously.
Could be, perhaps. But the evidence supports common descent. You can’t believe in separate creation and accept the evidence at the same time. So why do you reject the evidence? Your buddy Bechly accepts it.
No, I’m seeing that Axe was responding to a request for comments on 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 [1], and he wanted to know whether he had understood my work correctly. He clearly aimed to refute claims that were beginning to surface that my paper supported intelligent design, but he also wanted to make sure he wasn’t misconstruing my work in the process. He didn’t expect me to oblige—’I will understand if you decline; in fact, I would probably do the same…’—but I did.”
Then we read: “Here I summarize what appear to be the four most common objections to using my 2004 paper in support of ID, three of which trace back to Hunt’s blog entry, the fourth perhaps originating with Steve Matheson, who joined Art Hunt last summer for critical dialog with Steve Meyer in front of an audience at Biola University.”
So maybe you say this because you are thinking Axe was responding to your later article. Do please read what Axe said he was responding to, I presume you did send him a request for comments, and then address the reply he made.
As far as your 2007 article is concerned, glad to discuss that, too.
“Recall that Axe did not work with the native TEM-1 penicillinase, but rather with a variant that had a lower activity. The assay system made this necessary.”
Actually that’s not what Axe said about his choice, he describes why he made his choice of a variant with lower activity in his response, this therefore needs a response from you.
“In addition, Axe deliberately identified and chose for study a temperature sensitive variant. In altering the enzyme in this way, he molded a variant that would be exquisitely sensitive to mutation.”
Well, ditto, Axe explains why he did this, as mentioned above, and his counterpoint is what needs a response now.
You continue, “One of these, the metallo-beta-lactamases (Daiyasu et al., 2001), is quite unrelated to the TEM-1 enzymes. Axe’s study does not “count” these families of enzymes (or their neighbors), nor does it acknowledge that many more such structures are at least hypothetically possible.”
But I think it’s quite appropriate to pick one enzyme, and see how far away other functional enzymes might be. Why he needs to examine all possible enzymes that could have such a function is a mystery to me.
Then we have “To give the reader a sense of the higher end (10^-10) of this range, it helps to keep in mind that 1000 liters of a typical pond will likely contain some 10^12 bacterial cells of various sorts. If each cell gives rise to just one new protein-coding region or variant (by any of a number of processes) in the course of several thousands of generations, then the probability of occurrence of a function that occurs once in every 10^10 random sequences is going to be pretty nearly 1.”
But you don’t get a new variant in every cell. Your argument doesn’t work, if variants can be duplicates, which they can be.
Back to your post here!
But I don’t see this in your essay, which was just examined here. And I thought that Axe was sampling variants, to see how often functional variants occurred. Nothing about measuring parts of the bases of peaks.
I’ve been trying to diligently respond to objections in this thread, actually, thanks for your additional reply here. Glad to discuss this point in detail, why does Axe’s method not reliably distinguish between functional and non-functional variants?
Well, you did: “I’ll leave it to those involved in it to express how amused they are, however, by your suggestion that what they do is not rooted in measurement.” That’s pretty plain, people are only amused by a silly statement that can easily be refuted.
I did quote you! “I might suggest that a statement which is not a tautology nor can be verified by measurement may be one whose truthfulness would be impossible to demonstrate to a sincere and rational interlocutor.” I think the meaning is clear, only arguments that can be resolved by measurements can be resolved.
No, I’m saying according to this view, something that is not established by measurement is unknowable. I disagree.
Glad to agree!
Well, I did correct my comment, and mentioned another way of making conclusions that doesn’t involve a binary threshold. So I don’t insist that a binary threshold is the only way.
I am having trouble finding the definition I found (and posted!) before, but I did find a sort of summary of his definition elsewhere. And I did speak about what he said. How can you claim I’m not saying anything?
I agree that it’s a judgement call, but again, I say the term “body plan” refers to a real concept which can be discussed and even defined. Though I agree that the definitions are not identical, and are not as precise as measurements.
Well, that’s saying what sort of change he meant, I think that’s clear. So it would not be a claim of an example we can find in the fossil record.
And I claim that don’t, based on the similarity of all flying birds.
But I did quote Bechly, or a report of what he said, which does seem to differ from Wikipedia’s definition.
I meant lamprey mouths and beaks are different enough to say that creatures with them, respectively, have different body plans. Again, I agree that this is a judgement call, but I do insist this is a real concept, that biologists use.
I gave an argument, asking why those who responded to him didn’t simply correct his view of a body plan.
I assume you meant Bechly, not Behe. Now as mentioned previously, any definition of this is going to be somewhat imprecise. And again I ask why those who proposed their counterexamples didn’t simply do what you suggest, and correct his view of body plans?
I agree, this has been one of the views within ID.
There actually is evidence against common descent, such as the inability of biologists to come up with a tree of life, for instance. There’s broadbrush pictures, but the genetic evidence seems to give unclear results. Contrary to expectations. Then there’s the sudden appearance of new forms in the fossil record, such as the Cambrian explosion.
Yes, in the sense that an orange is not identical to an octopus.
We are then left to wonder why whales are used an example of a new body plan evolving in 5 million years. Can you explain?
So you’re saying that all flying birds have the same body plan and display no innovations? Why then do you consider penguin flippers to be an innovation? Until you can define “innovation”, there’s no way to say what is or isn’t.
You understand that those two things are different, right? We have already seen that one report of what he said, denying common ancestry, is at odds with something he actually did say.
Seem? Are you that unsure about what language means?
Please try to say what you mean the first time. Saves effort.
No, it is not. The real concept that biologists use is the one you found on Wikipedia, in which vertebrates share a body plan. For vertebrates, that would be notochord, dorsal hollow nerve cord, post-anal tail, segmented musculature, 3-part brain, and probably a few others that I’m not thinking of. Note, again, that all vertebrates have the same body plan.
That’s not an argument. A question isn’t an argument. Try again.
Yes, Bechly. I made no such suggestion. And as to others’ motives, we can only speculate. I’ve made my suggestion, which seems perfectly reasonable: they were playing along so as to refute the claim in its own terms. Why is this unlikely?
And it’s apparently Bechly’s view, according to his own words. Would you agree?
Don’t believe everything you read on a creationist web site. We have a quite good tree of life, and it’s improving all the time.
You have no idea what you’re talking about here. Do you understand that I’m a molecular phylogeneticist?
Not sudden, and showing clear phylogenetic relationships to boot. And even if it were sudden, that would support Bechly’s idea of saltation, not separate creation.
You misunderstand. That is exactly the point I am arguing against. Sensitivity DOES matter. In the example I gave, Axe greatly underestimates the prevalence of obesity, because he fails to account for the poor sensitivity of his test.
So if Axe’s extrapolation has even the slightest validity, if one samples 10^8 immunoglobulin variable regions (each about 100 amino-acid residues) for beta-lactamase activity, how many do you predict will be positive?
Note that the function is the same. The fact that all of these proteins adopt the immunoglobulin fold shows Axe’s rhetoric about folds to be a joke.
Because the threshhold is absurdly high. Obviously by design. It also has zero relevance to the evolution of beta-lactamase in nature. That’s why I offered the hint of diffusion to help you think about how it would work in nature.