Did Douglas Axe Disprove Evolution? Spoiler: No

[Rumraket (Mikkel R.)]

@lee_merrill

@Rumraket

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.

Yes, and he said why, 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.”

That doesn’t answer my question. Why not use the wt enzyme and it’s associated MIC?

@lee_merrill

@Rumraket

Why not the variant itself, too?

Why would that be more generous to Darwinism? Explain it, based in biochemistry.

Well, again, because using the wt variant would skew the results.

Against the temp-sensitive MIC, but why would it skew results against the wt MIC?

@lee_merrill

@Rumraket

But why not use the wt TEM-1 (the enzyme) against the wt MIC of ~5200 ug/ml (it’s associated “standard of quality”)?

Axe does actually address this: “But there’s another problem with Objection 3, having to do with the choice of a quality standard. We now know that the same standard has to be applied consistently if our results are to be meaningful, but we are still free to set that standard at any level. So, what difference does the level make?” Did you read his comments? It seems you may be just shooting from the hip.

Yes I read it and it doesn’t make sense.

@lee_merrill

Here is how Axe sums up his response to this: “Notice two things. First, both of these P values are far more favorable than one in 10^60, and second, lowering the standard always increases the P value. This makes perfect sense—it has to become easier to meet the standard as the standard is lowered.”

This isn’t an answer to why he’s not testing the tw ENZYME against the MIC of bacteria carrying the wt enzyme. The wt enzyme being tested against the wt MIC isn’t mentioned anywhere in his entire purported response.

Yes, lowering the standard to test against, but using the same enzyme would necessarily raise P. But raising the standard while also raising the quality of the enzyme does… what, to the P value?

Why are you quoting me Axe not answering this?

@lee_merrill

@Rumraket

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.

Um, those new genes were generated as part of the experiment, by the researchers, and not by evolutionary processes used in the lab.

No, in the second paper spontaneous deletions resulting in gene-gene fusions occurred during the course of the evolution experiment. In fact they show eight independent deletions roughly occurring across the same locus, resulting in gene-gene fusions.

So it isn’t a rare occurrence at all.

@lee_merrill

@Rumraket

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.

But we didn’t see new function evolve, is the problem, neither in the gene-fusion experiment

False. Transport of a gene carrying the cytosolic di-guanylate cyclase activity to the membrane resulting in an adaptive phenoty is a novel function (that’s why they’re called cytosolic di-guanylate cyclases, they’re not memebrane proteins). In the second paper I linked, that is the function that evolved by gene-gene fusion. Evolved, wasn’t created by the researchers.

@lee_merrill

, or in Axes. work.

… waaaait. You claim it’s a problem for inferences from the gene-gene fusion experiments when the function didn’t evolve. Wouldn’t that also be a problem for inferences from Axe’s paper, then? You’re going to have to make up your mind.

If Axe can purport to undermine evolution despite not employing the evolutionary process to try to estimate his frequency of sequence space that constitute functional proteins, then one can obviously also support evolution by experiments that also produces some frequency of functional proteins.

@lee_merrill

And the claim is that it’s improbable, not impossible, because Axe was seeking to know how rare such folds are, so if they’re very rare, then the rate doesn’t actually matter much, if it’s inordinately improbable. But with your claim, that we see such events in the wild in our lifetime, that implies we know both the probability and the rate.

Another straightforward non-sequitur. The claim is that X is an event with such a low probability we should not expect to see it in the entire history of life. If we then observe that X happens numerous times in a series of experiments, it obviously follows that X is false even if we cannot from those experiments alone determine what the true rate is.

@lee_merrill

@Rumraket

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.

No, that doesn’t follow at all, nature is not in a lab, with experimenters.

That’s deeply confused. All of the physical world is part of nature, including laboratories. Nature very much is in a lab. It’s in hospitals, in your kitchen, in your bathroom, in your mouth, in your food, under your fingernails, etc. All of it is part of the natural world.

As with many environments “out there” in the wild, laboratories are definitely their own unique environments in many respects, and often come with changes to the selective pressures organisms might see in the wild. But of course there is no such thing as just “nature” outside, as if it is just one thing. Different environments are different. You’re going to experience radically different selective pressures on the arctic compared to in the jungle. A laboratory is just another environment. They’re not magical places that defy the operations of the natural laws.

And to be sure, researchers can deliberately put mutagens in their experiments, or subject organisms to radiation-levels they normally don’t experience. It’s just they didn’t do that in this experiment. There’s no good reason to think that something radical has happened to the rate of genomic deletions resulting in gene-gene fusions in the experiments I have referenced. That’s a very silly, ad-hoc excuse to deny the results.

@lee_merrill

@Rumraket

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.

Agreed, though I would add that small-scale mutations do seem to be considered predominant.

For reasons already explained, they don’t have to strictly outnumber point mutations to have high relevance to evolution.

@lee_merrill

Imagine what our genome would look like if gene-fusion events were predominant!

Yeah could you imagine? Then we’d probably have a lot of multi-domain proteins, and something like 65% of Eukaryotic proteins would be multi-domain proteins. And different proteins could be identified by sequence-similarity searches has having segments that appear to have been copy-pasted from other proteins.

Haha, that would be so weird.

Anyway…

@lee_merrill

@Rumraket

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.

Yes, he gives arguments, and he gives references to support the points he is making. But now if you are arguing that he is wrong, do you now need to give numbers to support your conclusion? It seems by your standard, you do. And I note your reply doesn’t give any references. So are you being dismissive?

I gave a reference that directly tried to establish a frequency by which gene-gene fusions would result in adaptive functions when tested against 107 different functions. The number found was ~3x10^-5.

Axe doesn’t give any numbers at all. The dismissal is his, not mine.

[lee_merrill]

@AnEvolvedPrimate

@lee_merrill

No, I claimed flying birds have the same body plan, and penguins have different limbs, and thus different body plans.

Penguins have different limbs? Really?

What is your criteria for determining what is different versus what is the same?

Well, in a previous post, I quoted a description where flippers are said to be “thicker, denser, and smaller”, as well as “modified for hydrodynamic properties”. It’s a judgement call, certainly, but this does seem different.

[lee_merrill]

@Rumraket

@lee_merrill

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?

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.

As I said to someone else, the question is more fundamental, it’s not a question of practicality. Yes, we need others to review our reasoning, but if we’re all just ultimately reflecting motions of atoms in our brains, how can we trust anyone’s reasoning? And biases towards survival instead of reliability would be an indication we can’t trust our reasoning, that would tend to uproot naturalism, or any conclusion, as a result. That’s the point Lewis and Lennox and others are making, if our reasoning is ultimately due to unreasoning causes, we can’t really trust it. Lennox does get asked sometimes where he first saw this issue raised, and he says he saw it first, in all places, in a letter written by Darwin!

@Rumraket

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.

So the theist view is that we are indeed flawed beings, but our reason has a source which also reasons, so reliability is not guaranteed, but validity of reasoning, is. So if reason comes from reason (this is Lewis’ point) we accept it, but if say, a madman says there is a lion in the streets, we do not even bother to go look for it. We never make any exception to this rule, he adds.

[RonSewell (RonS)]

@lee_merrill

if we’re all just ultimately reflecting motions of atoms in our brains, how can we trust anyone’s reasoning?

My own reasoning is fallible, and in view of this thread, I do not trust yours.

Anyways, why should uncertainty be uncomfortable? So what if reason springs from millennia of pragmatic development and survival.

[lee_merrill]

@John_Harshman

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.

Well, as I said to Rumraket, the theist view, and I would add here, the Christian view is that we are flawed, as you said, and also that God is a reasoning being, and if he is good, we can trust him to give us good reasoning abilities. So Christianity has evidence for both, and you kind of have to start with reasoning being valid as a fundamental principle, and proceed from there.

Again, as I mentioned to Rumraket, we do accept reason coming from reason, but not from unreasoning causes. If you have evidence that we (with our reason) were created by a reasoning cause, we can make progress. But naturalism ends all this, empirical results, practical considerations, don’t help, if our reasoning is all ultimately the result of an unreasoning cause, both in our history, and the immediate ultimate cause being simply the movement of atoms in our brains.

[lee_merrill]

@Mercer

@lee_merrill

I’ve explained again and again why a binary assay does seem reasonable,

You’ve explained nothing. You’ve merely asserted that again and again. Do you not understand the difference?

I said if you need a conclusion, like “is the antibiotic effective enough to be produced?” then a threshold is needed. This is not a mere assertion.

@Mercer

@lee_merrill

and calling his assay silly is not a refutation.

It’s silly because enzyme activity is a continuous variable, typically over multiple orders of magnitude

And I also said that saying “we measured variants, and here are the numbers, and we have no conclusion” is not very useful.

@Mercer

@lee_merrill

So choosing a lower level of function than the wild-type variant, is more generous.

No, not true. Assertions are not explanations.

But I showed how Axe explained why. So again, this is not a mere assertion. Saying “No, not true”, is, though.

[lee_merrill]

@John_Harshman

@Faizal_Ali

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.

Well, “taste and see” is one way, getting to know God in his creation, in his revelation, in establishing a relationship with him, is the way. How do you know a person is trustworthy? By getting to know them. “Faith is based on evidence”, says John Lennox. People do think faith is belief without any evidence. Dawkins believes this, and Lennox asked him if he has faith in his wife. “Lots of evidence!” replied Dawkins. Oops…

@Faizal_Ali

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.

Lennox responds to the problem of evil by pointing to a God who died on a cross. That’s not a complete answer, but it does give reason to hope, if God is good, and he is not apart from pain, that it’s not meaningless. In naturalism, however, it is. So the problem is one for naturalism as well, and it has no reply to make, at all.

[AnEvolvedPrimate]

@lee_merrill

Well, in a previous post, I quoted a description where flippers are said to be “thicker, denser, and smaller”, as well as “modified for hydrodynamic properties”. It’s a judgement call, certainly, but this does seem different.

That doesn’t answer my question as to the criteria you are using to determine what is different. If it’s just a subjective judgment call, then it’s not an objective criteria we can apply across the board.

[Gisteron]

@lee_merrill

So the problem is one for naturalism as well, and it has no reply to make, at all.

If we assume that a being exists who dislikes suffering and has the choice of making there not be any, then the presence of suffering – meaningless and meaningful – is an actual conundrum. One that there’s been millennia of attempts to address, and how effective any of them were is something best debated among theologians, but still, there is an actual question there to ponder.

On the other hand, nothing about naturalism would suggest that we should expect kids to not get leukemia. Your appeal would be a tu quoque fallacy even if it actually applied, but in this case it does not.

[Rumraket (Mikkel R.)]

@lee_merrill

As I said to someone else, the question is more fundamental, it’s not a question of practicality.

It is also a question of practicality. Since your point being that God is necessary to make us able to trust reason, the evident fact that we still cannot blindly do that creates an issue for your position.

@lee_merrill

Yes, we need others to review our reasoning

And why would that be the case, if our being designed should make our reasoning trustworthy?

@lee_merrill

but if we’re all just ultimately reflecting motions of atoms in our brains, how can we trust anyone’s reasoning?

Exactly for the reason that we should expect that survival correlates with correct inferences.

Think about what it would mean if it was the opposite. We would have to believe that for every possible survival/reproductive challenge an organism could potentially face, it is more likely than an incorrect inference about that challenge is adaptive, than it is that a correct inference about it is adaptive.

To be more specific, when you your foodstock diminishes each day (and innumerable other possible surival situations where reasoning can contribute to survival), we’d have to posit that making incorrect inferences about whether and when that means you should go and collect some more would be more likely to increase your survival, than correct inferences about whether/when you should go and collect some more.

There just isn’t any good reason to think incorrect inferences are generally more biased towards survival than correct inferences are. It just seems to me logically obvious that the opposite should generally be the case. That incorrect inferences being adaptive should be exceptions and not the other way around.

@lee_merrill

And biases towards survival instead of reliability would be an indication we can’t trust our reasoning

But for reasons just explained, I think the distinction of reliability versus survivability is actually exaggerated, because in the vast majority of cases they should strongly correlate.

You haven’t given us any reason to think the two should be expected to be anti-correlated.

So, given that our reasoning appears to be mostly reliable, yet we do have some biases that can lead us astray, but that those biases are in fact adaptive in certain situations we are likely to have faced in our evolutionary past. It just seems to me this picture is actually perfectly in line with what we should expect from evolution.

@lee_merrill

That’s the point Lewis and Lennox and others are making, if our reasoning is ultimately due to unreasoning causes, we can’t really trust it.

I think I have given intuitively obvious reasons for why the claim is untrue, and in fact that evolution would tend to strongly bias cognitive processes towards correct inferences exactly because those are in the majority of situations, more likely to be adaptive than incorrect inferences are.

@lee_merrill

So the theist view is that we are indeed flawed beings, but our reason has a source which also reasons, so reliability is not guaranteed, but validity of reasoning, is.

That’s just a circular argument.

[John_Harshman]

@lee_merrill

I did do what I thought would show what that would be.

Did you? When? Where? And what exactly did you do?

@lee_merrill

Because whales seem to need it? So probably creatures like Basilosaurus needed them, too.

So you can decide this in the absence of evidence, and the whole argument for “different body plan” depends on a conclusion you draw without evidence. Do you really think that’s a good idea?

@lee_merrill

And intermediates in such a timeframe make the problem worse!

What do you mean by “such a timeframe” and how do they make the problem worse?

@lee_merrill

I wish I could fish up the description I posted earlier, because as I recall, it is compatible.

I have no idea what description you’re talking about here, but you don’t show much ability to determine what’s compatible and what isn’t. There will be a case in point a little later in this post.

@lee_merrill

But you left out the “modified for hydrodynamic properties” somehow. This is not as simple as you are making it sound.

You know nothing on this subject. Remember that there are many flying birds that use their wings to swim too. Do they lack those “hydrodynamic properties”?

@lee_merrill

I meant the book by that title, and Darwin and his finches. Beak differences, well, for one, they were still finches.

So from that you draw that any beak modifications are no big deal, even though honeycreepers have much greater differences than Galapagos finches do. And “they were still finches” is the sort of thing the most ignorant creationists say. A greater irony is that Galapagos finches are actually tanagers, Thraupidae, while Hawaiian honeycreepers are actually finches, Fringillidae. And of course Indohyus and Basilosaurus are still artiodactyls.

@lee_merrill

I stated how you could have a view with both statements, in a way that was not inconsistent.

You may have thought you did, but you were wrong. You can’t both reject and support common descent without being contradictory. Remember that thing I said above about a case in point? This is that case.

@lee_merrill

I can be more specifiic, “more nerves” is not what we find in new organs, they certainly are adapted to and part of the new function. And following Wikipedia, in their reference to “nerve disposition”, I read elsewhere that “Nerve disposition typically refers to the anatomical arrangement of nerves in the body, particularly in relation to conditions like ulnar nerve compression.”

No, this is just you finding a snippet you can use by taking it out of context. These are the same phrase used with two separate meanings. But where was “elsewhere”? You don’t say. You’re just wrong about this.

@lee_merrill

And a counterargument, well, the very term contains the word “argument”, was my point.

I sincerely believe you didn’t have a point, and you seldom do. One problem is that you seldom manage to say what you mean. Another is that you don’t understand the science well enough to talk about it.

@lee_merrill

And I provided a reason to expect that they would.

But your reason was just that you thought they would. That’s not a reason.

@lee_merrill

This sounds like an important branch! Like in the Wikipedia article: “Trees have been proposed with either four[25][26] or two supergroups.” Supergroups! But are you saying that is specifically what they mean? Why then didn’t they say so?

Sure, it’s an important branch if you’re interested in the basal divergences within eukaryotes. But it’s still local. And yes, that’s what they meant. They were talking specifically about the basal divergences in eukaryotes, mostly one-celled organisms. They actually did say so. Unlike some, they said what they meant.

@lee_merrill

Well, as long as people are postulating “ghost lineages” to explain problems of descent

I’m not sure you know what ghost lineages are, and I can’t tell why you brought them up. You seem to feel that they’re important and relevant, but you don’t say why. None of the other stuff you mention is relevant to universal common descent either. Why do you think Bechly was wrong about this one issue when you take his word for all the others?

@lee_merrill

I’m claiming that in Biblical parlance, creatures reproduce “after their kind”, so canines produce canines, so they are a “kind”.

But isn’t every species therefore a “kind”? Were all species separately created? And if you’re agnostic about the relations of canines to felines, then you can’t know if they’re a “kind”. Also, how can you be agnostic? Is it because you know nothing about the relevant data?

@lee_merrill

Well, I’ve read books on this, actually, trilobites come to mind, as do crabs.

Trilobites have transitional forms connecting them to other arthropods and to other ecdysozoans. Crabs have transitional forms, and they’re also not Cambrian. This is relevant because you were making a claim about “all the new creatures that appeared suddenly, without intermediates” in the Cambrian, and I’m doubting that you have any idea what you’re talking about. That much seems clear.

@lee_merrill

But the problem is not so much one of terminology, there are no known intermediates for so many of the creatures that appear at the start of the Cambrian, that is what needs explaining.

Notice that the start of the Cambrian is 20 million years before we see most of the creatures that constitute the Cambrian explosion. And I asked you to name any of those creatures, but you didn’t, probably because you couldn’t. My point is that you’re wrong: there are plenty of intermediates for Cambrian taxa.

@lee_merrill

I mentioned that “I’m not particular about the specific mode of creation”, though, and so there is actually evidence for a Designer, is the conclusion.

That’s an entirely different question, demanding entirely different evidence. Your thinking on this is so muddled it’s impossible to clearly understand what you’re proposing. And you are particular: you reject common descent in favor of separate creation. You’re on record as claiming that every species was separately created, though I don’t think you realized what you were saying.

@lee_merrill

But the Bible has no problem with similar creatures, and no one is requiring a perfect tree, just resolve basic problems such as supergroups.

Why are you bringing the bible into it? This is, I believe, your first mention. Do you consider Genesis relevant data on earth history? And let’s add “supergroups” to the list of words I doubt you understand. These supergroups may not be entirely clear, but we can be confident about the reality of Opisthokonta, which includes all animals, fungi, choanoflagellates, and several other protists.

@lee_merrill

And difficulties of evolving are indeed evidence against common descent, if the difficulties are only resolved by invoking remote sequences of improbable events, then such descent is unlikely too.

No, you could resolve all those problems, if you thought they were problems, by involving God in the process. Thus you have a model that keeps the Jesus you want to be responsible but, unlike separate creation, actually is compatible with the data.

@lee_merrill

Chesterton has a quote that applies here:

I really don’t care whether you want to think that humans are exceptional or whether Chesterton is your justification. I only say that you needed something other than what you said the first time.

@lee_merrill

But I don’t see why, if for example, we see new creatures popping up all over the fossil record.

Are you again claiming that every species was separately created, with no ancestors? And it’s silly for the reasons I mentioned, which you have not addressed.

@lee_merrill

Yes, I am, and I do have problems with the deistic version of theistic evolution, it also undermines rationality.

Whether it does or not, why attack a version of theistic evolution that I didn’t mention? (Though it does seem to be Bechly’s version. Again, you accept many things just because he says so, but you reject this. Why would that be.) I, however, was talking about the idea that God intervenes to introduce particular mutations during the process of descent. Why don’t you like that?

@lee_merrill

I should perhaps have said “unguided” instead of “random”, a need for survival doesn’t solve the problem, people with a phobia of snakes may be more likely to survive, but not all snakes are venomous, some snakes are relatively harmless.

But if you say “unguiedd” rather than “random”, that changes the meaning of what you said completely. And since some people have an irrational phobia of snakes, doesn’t that kill your claim that our minds are rational in a way that can’t be explained by evolutionary advantage?

[John_Harshman]

@lee_merrill

Well, as I said to Rumraket, the theist view, and I would add here, the Christian view is that we are flawed, as you said, and also that God is a reasoning being, and if he is good, we can trust him to give us good reasoning abilities.

That was gibberish. There is no evidence that reason can only come from reason, whatever you mean by that. There is no evidence that a reasoning cause can only give rise to an entity whose attempts at reason are valid. Even if we suppose that entity is good. Maybe it’s good to give us bad reasoning abilities. And of course we can’t believe that God is good unless we can first believe that our reasoning is valid. CIrcular. And no, Christianity doesn’t have evidence for both, and if you think it does, you have to depend either on reason or on something more basic than reason to decide that. Again, you have to trust your reason prior to deciding that you can trust your reason.

@lee_merrill

you kind of have to start with reasoning being valid as a fundamental principle, and proceed from there.

True. And it doesn’t matter for that purpose where reason comes from. Unreasoning nature is just as good (or as bad) as God for that purpose.

@lee_merrill

we do accept reason coming from reason, but not from unreasoning causes

Who is “we”?

@lee_merrill

But naturalism ends all this, empirical results, practical considerations, don’t help, if our reasoning is all ultimately the result of an unreasoning cause, both in our history, and the immediate ultimate cause being simply the movement of atoms in our brains.

Here you conflate two separate questions: creation by God, or not; and whether reason happens in our brains or in some magical, immaterial entity attached to them. These questions are unrelated. And you haven’t said (or apparently thought about) anything meaningful about either of them.

@lee_merrill

How do you know a person is trustworthy? By getting to know them.

That assumes your judgment in such matters is reliable. But you’re trying to prove that your judgment is reliable. Still circular. You haven’t addressed any of the questions. Can you even read and understand them?

@lee_merrill

“Faith is based on evidence”, says John Lennox.

How do you know John Lennox is trustworthy?