A longer quote helps here: “In the work described in the 2004 JMB paper, I chose to apply the lowest reasonable standard of function knowing this would produce the highest reasonable value for P, which in turn provides the most optimistic assessment of the feasibility of evolving new protein folds. Had I used the wild-type level of function as the standard, the result would have been a much lowerP value which would present an even greater challenge for Darwinism. In other words, contrary to Objection 3, the method I used was deliberately generous toward Darwinism.”
So choosing a lower level of function than the wild-type variant, is more generous.
That doesn’t explain why he thinks that. That is really just him claiming that.
Explain why, based in your understanding of real biochemistry, using TEM-1 would result in a lower percentage of his tested mutant protein enzymes failing to produce colonies on his agar plates.
That’s what a lower P value is, in his experiment. Fewer mutants resulting in colony formation.
Oh and while you’re pondering that question, can you also give some sort of response to this post of mine where I explain your confusions surrounding relative mutation frequencies?
I agree that they are not the same, I’m trying to use Bechly’s view, since that is an essential part of his challenge.
Heat-transfer organs?
Heat-transfer organs? The “melon organ”, for echolocation?
He implies it’s an established conclusion, though the numbers I find on Wikipedia have a time period of about 7 million years.
I agree that this is not saltation, but pointing out intermediates does not answer the challenge, if the starting and ending points are in the 5-10 million year time frame.
The definition I proposed is applicable here, which I think is along the lines of what Bechly meant by a body plan.
No, I claimed flying birds have the same body plan, and penguins have different limbs, and thus different body plans.
Not exactly, Wikipedia says “The flippers of penguins became thicker, denser and smaller while being modified for hydrodynamic properties.”
Yes, basically. “The Beak of the Finch”, and all that.
I did state what I though Bechly’s view amounted to, and this statement did not have a contradiction.
???
I acknowledge that Bechly’s definition is different than Wikipedia’s, though I think new organs would imply substantial changes in nerves, so the definitions would actually be compatible.
A counterargument is an argument. And flat denials aren’t.
I don’t claim that this should always be done. I do claim that it’s mystifying that it wasn’t done by anyone who set out to refute Bechly.
They all are posting in this thread, presumably they can see this and respond to this question now if they wish.
But the problem is “There does not yet appear to be a consensus”, if this is true, and this is not some complicated, hard-to-understand statement, then there is no single tree with some local (minor? insignificant?) exceptions.
This is weird, even with your edit, there is no complete representation by a simple bifurcating phylogeny. That is not the general picture you are painting, the two are different. Can you not see that? And you left out this part of the quote: “The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology.” If what you are saying is true, the challenge is not at all formidable, it is basically done.
Canines!
But so many missing intermediates, that the event is referred to as an “explosion”. I was referring to all the new creatures that appeared suddenly, without intermediates.
Wikipedia says 13-25 million years, so that’s not “considerably longer.”
And biologists still call it that! The best book on the topic that was recommended to me here is called “The Cambrian Explosion” And it is acknowledged now to be real, not just an artifact of incomplete sampling.
The Cambrian Explosion, and the other many explosions is evidence, the lack of an expected, accepted Tree of Life is evidence, the difficulty of evolving irreducibly complex structures is evidence, the conference outlining difficulties with the standard evolutionary theory by the Royal Society is evidence. All this fits the data, and I could go on and on. And I’m not particular about the specific mode of creation, I would prefer separate creation, like the creation of humans. And that’s not silly theologically, it explains how humans are so exceptional, for instance.
And naturalism is actually the view that is silly, it undermines rationality! As John Lennox points out, and C.S. Lewis pointed out. Why do you trust your brain, and your thoughts, if it’s the result of a random process, with no interest in you doing science and so on?
“That peril is that the human intellect is free to destroy itself. Just as one generation could prevent the very existence of the next generation, by all entering a monastery or jumping into the sea, so one set of thinkers can in some degree prevent further thinking by teaching the next generation that there is no validity in any human thought. It is idle to talk always of the alternative of reason and faith. Reason is itself a matter of faith. It is an act of faith to assert that our thoughts have any relation to reality at all.”
“If you are merely a sceptic, you must sooner or later ask yourself the question, ’Why should anything go right; even observation and deduction? Why should not good logic be as misleading as bad logic? They are both movements in the brain of a bewildered ape?’ The young sceptic says, ‘I have a right to think for myself.’ But the old sceptic, the complete sceptic, says, ‘I have no right to think for myself. I have no right to think at all.’” (Chesterton, Orthodoxy)
There’s still some confusion here, the wild-type variant was not used, because “we need the starting sequence to be of the same quality that we intend to require of mutant sequences in order for them to be accepted. Otherwise the mismatch in quality will skew our results.” Then the wild-type variant standard of functionality (note, the variant’s standard, not the variant itself) was not used, in order to be more generous towards Darwinism.
That’s a good point! Now we still need the rate for gene fusion events, only you have said there is no solid result giving a rate for them.
But your comments before and after this do not explain why this isn’t what he’s doing. I think it is, changing a few residues is part of evolution, for instance.
Yes I get his explanation here. He thinks taking wt TEM-1 and testing against a MIC of ~10 ug/ml, using his specific protocol, will show it can tolerate more mutations than it actually can. I don’t buy his analogy for that, but I understand what he means.
But then this is where the chain unhinges. It’s when he says he is being “more generous to Darwinism.” That the P-value would have been lower had he used the wt enzyme. Not just it’s “standard of quality” (by which he apparently means the associated MIC of bacteria carrying that enzyme.) Why not use the wt enzyme AND it’s associated MIC of ~5200 ug/ml?
Is he taking Hunt, Venema, and others to suggest he should use his temperature-sensitive enzyme and test it against the wt MIC? Certainly that would lower P, but who in their right mind would suggest that test to be meaningful? We’re asking why he’s not using the wt ENZYME. Not just the associated MIC.
Do you understand?
Why not the variant itself, too?
Why would that be more generous to Darwinism? Explain it, based in biochemistry.
There isn’t anyone here who doesn’t understand, that Axe’s position here is, that if he had used the wt ENZYME instead of the temp-sensitive version, but against the temp-sensitive MIC of ~10 ug/ml, that would (in Axe’s opinion) have “skewed results” because that would have implied a higher tolerance of mutation that it presumably would have had.
So Axe says he must test a temp-sensitive enzyme against it’s “standard of quality” (aka it’s ~10 ug/ml MIC).
But why not use the wt TEM-1 (the enzyme) against the wt MIC of ~5200 ug/ml (it’s associated “standard of quality”)?
Because, for the purpose of falsifying the claim that new proteins can’t evolve in the history of life, it doesn’t matter what the rate of gene-gene fusions are as long as it is frequent enough to be routinely observed to result in new funcitonal genes in experiments.
What we can then know is that any claim that novel proteins are too rare in protein sequence space to evolve is demonstrably false. It is false by demonstration because we saw it occur, and the claim is that shouldn’t be possible.
Of course, given that it was observed in experiment, what we can at least give is a minimum rate. It must happen at a rate high enough to be observed at least once in an experiment of that duration, right? And since this has happened in numerous experiments, it also can’t be some sort of fluke event.
So, given that in multiple experiments taking place over the course of something like one month, each produced one new functional protein by gene-gene fusion, then mutations resulting in gene-gene fusions must happen at least once per month.
Presumably (by a very reasonable and straightforward inference:) it happens much more often than that, since we’re only seeing those that result in novel functional genes that were beneficial.
No, Axe is only trying to determine a fraction of sequence space. He’s not saying new proteins must, or can only, evolve by amino acid substitutions. Axe is using mutations in his experiment not because he’s trying to mimick some aspect of evolution, but because that’s technologically the simplest and cheapest method we had, at the time, of creating novel sequence variants.
In fact he discusses the possibility of new proteins evolving by the gene-gene fusion method in his paper (and in the response blog post you linked), but he is flatly dismissive of it there.
Here is the totality of what Axe says of that possibility in his 2004 paper:
A commonly accepted view is that new folds are pieced together from small parts of existing folds.32,33,39,40 But to the extent that a new fold is really new, its formation must require the joint solution of at least a considerable number of new local stabilization problems of the kind described above. How likely is it that sequences that carry the hydropathy signatures of other folds and provide joint solutions to the stabilization problems for those folds may be pieced together in such a way that they satisfy a new set of constraints, equally demanding but substantially different? The analysis provided here, bearing in mind the uncertainties, calls for careful examination of such piecing scenarios. The need for caution is underscored by a recent study of the structural and functional consequences of piecing together parts from homologous versions of the same fold.41 Because even close homologues employ substantially different solutions to their local stabilization problems,8 chimeras made by homologous recombination suffer considerable disruption unless the points of crossover minimize intermixing of these local solutions.41 So, if re-creating a fold by ordered assembly of sections of sequences that already adopt that fold is not a simple matter, generating new folds from parts of old ones may be much less feasible than has been supposed.
In other words, he gives verbal arguments for why he considers the probability of that low (“less feasible than has been supposed”). He doesn’t give any numbers, in fact he doesn’t even try to argue the probability is remotely comparable to the number he extracts from his experiment. He is really just totally dismissive of the possibility
So far you are failing even to articulate what Bechly’s view is. And you need to stop talking about the definition you found on Wikipedia, since that has nothing to do with Bechly’s definition.
You have no idea what a counter-current exchange system is, do you? And let’s recall that this is something found in modern whales that is not observable in fossils. So how, again, can you say that Basilosaurus has a novel body plan?
Yes, he does. But it isn’t.
True. I merely point out that the data are incompatible with Bechly’s preferred model.
You proposed no definition other than the common one, with the vague addition of “organs”. Still incompatible with Bechly.
Doesn’t answer the question.
True. Does “thicker, denser, and smaller” equate to a new organ? These seem like minor and gradual differences, less than, say, the difference in beaks among Hawaiian honeycreepers. Note also that many flying, wing-propelled divers, such as puffins, also have thicker, denser, smaller wing bones than most other birds.
You will have to explain what you mean. Clearly. Completely.
You stated several things, and you quoted another source. Some said that Bechly rejected common descent, others that he supported common descent. How are those not contradictory?
No. It’s just that you don’t understand what the standard definition refers to. It’s a nod to the difference between a dorsal, hollow nerve cord, as in chordates, and a ventral set of linked ganglia as in many other taxa. It’s not just the vague claim of “a difference in nerves”, which could be just about anything.
Wasn’t that a flat denial right there? This is going nowhere until you start responding with some clear, relevant point.
You claim that it’s mystifying, but it doesn’t mystify me, and I’ve provided a reason someone might not do what you say. Bottom line: this is not a reason to believe Bechly is correct about anything.
Again, why should we care?
There is not a consensus on the one point that your quote refers to: a basal division among eukaryotes. That is in fact a local exception, corresponding to a single branch of the tree. It may not be a complicated, hard to understand statement, but you seem not to understand it.
No. The point is that the history of life approximates a tree very well. The processes that give rise to exceptions are well known and do not disrupt much of the tree. There are other processes that make some parts of the tree hard to resolve even though the tree still exists at those points. Your claim seems to be that if a tree is not perfect then it doesn’t exist. That makes no sense.
Note that “dated” is part of that bit, and that’s much more difficult than determining the shape of the tree. And “comprehensive” is a problem too, as it seems to require perfection. I don’t claim perfection, just good enough for most purposes and certainly good enough to make common descent the inescapable conclusion.
You would appear, if that one-word response means anything, to be claiming that the dog family is a separate, created kind, unrelated to any other mammals. Is that in fact true? I warn you that this is contradicted by a mass of data.
What new creatures, exactly, are you referring to here? Name a few. This is just you expressing your ignorance of the Cambrian fossil record.
I would suggest that 25 is considerably more than 15.
And yet more complete sampling has extended its length considerably. We don’t abandon convenient terms because they turn out not to be as applicable as they once seemed.
None of these is evidence for fiat creation, if indeed that’s what you’re talking about. You keep waffling.
You could, in a similar vein, but that wouldn’t explain anything. The Cambrian Explosion, as I’ve explained before, shows lots of intermediate forms over a long period of time, not consistent with separate creation. The lack of an accepted tree of life is just a lack of a perfect tree. Some branches are unquestionable, and there are enough like that to make the tree’s existence clear. Difficulties of evolving, even if true, are not evidence against common descent. And a conference isn’t evidence of anything.
I’m afraid that the evidence for common descent of humans and other primates is overwhelming, so it doesn’t matter what you would prefer. If you think humans are exceptional, you need a different reason. Now, separate creation of humans isn’t theologically silly. It’s the separate creation of thousands (millions?) of “kinds” throughout earth history that’s silly.
That’s an entirely separate question from common descent. Are you unfamiliar with theistic evolution?
Bringing up C.S. Lewis is always a sign of intellectual bankruptcy. Evolution isn’t a random process, and it turns out that a mind evolved to aid survival is also good for helping us understand the world, almost as if understanding the world would aid in survival. But again, this has nothing to do with the question at hand, which is about separate creation of “kinds” vs. common descent.
Lennox and Lewis have to be two of the stupidest smart people to have ever lived.
This argument is the equivalent of saying: “Why do you trust a tree branch to support your weight, if trees were not designed for people to climb them?”
To answer your question, we don’t always. That’s why we set up things like peer review, and have to bounce ideas off others to increase our confidence.
You claim naturalism has problem with these things, since there can be reasons why our faculties (cognitive or sensory) could have biases aimed more towards survival than reliability. And yet we do have these biases, demonstrably. Doesn’t that then favor naturalism?
Also, it would be strange if survival and reproduction didn’t correlate with correctly making inferences, and correctly percieving our surroundings.
Sure, we can imagine special situations where we have intuitions that might produce occasional errors (reflexive behavior) because those errors keep us safe (infer predators and flee even if we aren’t sure any are around), but there’s just no reason to think such situations should numerically even remotely approach, never mind outnumber situations where a correct inference, or correct observation, produces better survival outcomes.
However, what about your position? If we were designed by a perfect being that supposedly guarantees the reliability of reason, why do all humans routinely make elementary errors in reasoning? Even on subjects completely devoid of emotional or political content that can bias our thinking, we all will make errors and incorrect inferences when attempting abstract thought.
Something as dry and boring as mathematics, probabilistic reasoning, or symbolic logic will challenge anyone to stay completely accurate.
If we were designed by a perfect being that supposedly guarantees the reliability of the senses, why will we frequently percieve things wrongly? Halluscinate, mishear, misremember, fail to notice things in our surroundings and peripheral vision, lack the ability to distinguish sounds when multiple of them overlap, and so on?
It seems to me the one with a problem is you.
Edit: btw I flagged my own post here as off-topic. I don’t mind discussing it, but it’s a derail from the topic of this thread.
The Fall, of course. But why should we expect a perfect being to guarantee the reliability of reason? Couldn’t he make us to be bad at reasoning and still believe we were good at it? How could you argue he didn’t, unless you already knew the contrary by some process not dependent on reason? And how could you know that process wasn’t also deceptively faulty? Gee, it’s as if not even divine creation can rescue your warrant to believe in human reason from circularity. I guess we have to depend on empirical results.
Again, that’s due to the Fall. Reason only works if you accept Jesus as your personal savior, and I suppose that the saved don’t fall prey to optical illusions either.
One common answer to this is that we can be certain God would not do that because his is perfectly good, and if he did that it would be a bad thing, which goes contrary to his nature. It’s not too difficult to come up with objections to this counter-argument, however.
For example, asking how we know that God is perfectly good. And how we know that a perfectly good God wouldn’t do that, i.e. how we know that it’s a bad thing. And how we know that it hasn’t already happened.
Exactly. Apologists seem to have little problem rationalizing how a perfectly good God could allow innocent little kids to get leukemia, so this should be a doddle.
Whoa. And let this be a warning about a digression from the Bechly digression and about speaking ill of the dead. But looking on his website, I see that Bechly was a supporter of the AFD. Read this and see how insane he was: https://www.bechly.at/world-view/
What’s the point of all this? It does not satisfy a literal take on Genesis. It implies God is unable to create a universe sufficient to achieve His purpose, and demonstrating that God is so incapable seems to be the object of the entire ID project. If God wanted rabbits, plain miracles could produce rabbits without the need for a first eukaryote, first chordate, first tetrapod, first mammal, and onward in a tedious succession of ever closer approximations which look exactly like evolution.