Are there no beneficial mutations?

[lee_merrill]

This does not show any research just a claim. I want to see independent peer reviewed science research that demonstrates Behe's conclusions.

Well, then, read the book, his pages contain many references to research that supports his conclusions!

Blessings,
Lee

[TheLurch]

The computer models give a pretty clear idea as to function, and to whether it has been impaired.

What computer model? And how is it applied to different proteins? And again, Roy says that Behe doesn't use computer models.

Well, that's what Behe does, he examines evidence in genomes. What he finds is that most often, evolution selects degradative mutations.

No, he chooses examples that are present in the genomes. That's different from examining evidence in the genome. The latter would involve compiling a comprehensive list of every damaged protein in several genomes of closely related species, and then cross-species comparisons - it has to be done that way to avoid cherry picking.

Can you point to an instance of Behe doing that? If not, he has not even bothered to test his own hypothesis.

Now we don't see this in speciation (is my view) since speciation events such as the massive radiations require supernatural invention.

Most speciation events do not occur during radiations. And in any case, we could examine speciation events that don't occur during radiations if you'd prefer. It gives the same answer: there aren't that many inactivated or damaged genes, and their presence doesn't correlate with speciation.


Edited to add: Why have you suddenly dropped talking about fixation without comment? Do you accept that you were wrong about that? If so, why do you not acknowledge it?

[shunyadragon]

Well, then, read the book, his pages contain many references to research that supports his conclusions!

Blessings,
Lee

I read the book and it is most atrocious unethical selective editing of sources to justify a religious agenda I have ever seen in my life, and of course o research by Behe corraborated by independent peer reviewed scientific sources.

[lee_merrill]

What computer model? And how is it applied to different proteins? And again, Roy says that Behe doesn't use computer models.

Model PolyPhen-2:

Source: Evolution News

Does the program examine biochemical damage? We pointed out that the computer program is precisely designed to detect biochemical damage. The technical documentation for PolyPhen-2 explains that it predicts when a mutation is “likely to destroy the hydrophobic core of a protein, electrostatic interactions, interactions with ligands or other important features of a protein,” and predicts when a mutation is “affecting protein stability or function.” That’s biochemical damage.

Source

© Copyright Original Source

And Behe discusses papers that use computer models, he doesn't do modeling himself, as Roy pointed out.

No, he chooses examples that are present in the genomes. That's different from examining evidence in the genome. The latter would involve compiling a comprehensive list of every damaged protein in several genomes of closely related species, and then cross-species comparisons - it has to be done that way to avoid cherry picking.

I'm not sure what you mean here, look at every damaged protein to see if it is selected?

... there aren't that many inactivated or damaged genes, and their presence doesn't correlate with speciation.

Which fits with my view that speciation generally requires supernatural intervention.

Edited to add: Why have you suddenly dropped talking about fixation without comment? Do you accept that you were wrong about that? If so, why do you not acknowledge it?

It seemed to be a side issue, so I dropped it.

Blessings,
Lee

[lee_merrill]

I read the book and it is most atrocious unethical selective editing of sources to justify a religious agenda I have ever seen in my life, and of course o research by Behe corraborated by independent peer reviewed scientific sources.

So you should be able to point out why you disagree with Behe, specifically. You should be able to engage his arguments, instead of all this rending of your garments!

Blessings,
Lee

[TheLurch]

Model PolyPhen-2:

Source: Evolution News

Does the program examine biochemical damage? We pointed out that the computer program is precisely designed to detect biochemical damage. The technical documentation for PolyPhen-2 explains that it predicts when a mutation is “likely to destroy the hydrophobic core of a protein, electrostatic interactions, interactions with ligands or other important features of a protein,” and predicts when a mutation is “affecting protein stability or function.” That’s biochemical damage.

Source

© Copyright Original Source

And Behe discusses papers that use computer models, he doesn't do modeling himself, as Roy pointed out.

Ok, have you looked into the documentation of this software, and understood whether it can do what Behe says it does? Because the researchers who actually used it seem to think that Behe is misinterpreting its output. What reason do you have to think that they're wrong and Behe is right other than your personal preference?

I'm not sure what you mean here, look at every damaged protein to see if it is selected?

Scan the genomes of related species, identify all mutations that appear to lead to non-functional or reduced function in proteins, and see if there are patterns to them. If Behe is correct, then you'd see a pattern where speciation always involves a number of damaged genes, with the number increasing with evolutionary distance. And you should be able to identify that some of these damaged genes produce the phenotypic differences between the species.

We don't see any sort of pattern. To take the human/chimp example, the vast majority of damaged genes between the two are inactivated olfactory receptors in humans. There is no similar pattern of damage in chimps, or following the chimp/bonobo split. And it's safe to say that the key phenotypic differences between humans and chimps do not include our ability to smell things.

Which fits with my view that speciation generally requires supernatural intervention.

I'm sure you don't realize this, but you've just admitted that every possible situation is consistent with your belief. If you do see a pattern of inactivated genes, then (in your view) intelligent design is right. And if you don't, it's because supernatural intervention happened.

You can never possibly be wrong. And therefore this isn't science.

Which is fine. Just stop pretending it is, and i'll leave you alone.

It seemed to be a side issue, so I dropped it.

Considering it's an indication that you don't even understand your own argument, it's not a side issue. It's rather central to this discussion.

[lee_merrill]

Ok, have you looked into the documentation of this software, and understood whether it can do what Behe says it does?

Source: Harvard

Here we present a new method and the corresponding software tool, PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/, Supplementary Software), for predicting damaging effects of missense mutations.

Source

© Copyright Original Source

This seems to be what Behe was expecting.

Because the researchers who actually used it seem to think that Behe is misinterpreting its output.

That was a review, right? Not the original researchers. But I addressed this in my last reply to Roy, I believe.

If Behe is correct, then you'd see a pattern where speciation always involves a number of damaged genes, with the number increasing with evolutionary distance.

Well, again, I hold that speciation is generally something nature cannot do, but we can look within a species for damaged genes, which Behe does.

I'm sure you don't realize this, but you've just admitted that every possible situation is consistent with your belief. If you do see a pattern of inactivated genes, then (in your view) intelligent design is right. And if you don't, it's because supernatural intervention happened.

No, my view could be falsified if someone shows that nature can produce all types of speciation.

[Fixation is] rather central to this discussion.

But how so? All I maintain is that we will generally see changes that are fixed, not those that appeared for a while and then vanished. This would seem rather indisputable.

Blessings,
Lee

[shunyadragon]

So you should be able to point out why you disagree with Behe, specifically. You should be able to engage his arguments, instead of all this rending of your garments!

Blessings,
Lee

We all have in the past and specifically I have detailed his bogus unethical use of statistics, and provided detail academic sources on the problems with the statistics. You tend side step these responses and repeat your assertions based your sources that share your religious agenda.

[TheLurch]

I've not had time to reply here, because i spent the last three days chasing down all the ideas that are being considered for developing therapies for coronavirus. All of these are based on what we know about the evolutionary relationships among the coronavirus family (where - surprise - no gene damage is involved), and in some cases the evolutionary relationships among the normal hosts of viruses that have recently jumped to humans.

Doing that against the background of this thread has made me acutely aware that the charlatans like Behe who try to replace biology with magic via a cherry picked presentation of work done by actual biologists aren't just some harmless distraction. They're positively dangerous. It makes me very angry at them, and very angry at people like Lee, who can't seem to even comprehend what taking a critical view of Behe's garbage might look like.

I don't think it's helpful for anyone for me to talk from a position of anger. And i suspect that, as the weeks go on, and the death toll rises as it certainly will, my anger's not going to subside very much. The fact that i have a number of dear family members who are older and at-risk isn't going to help in that regard.

So, i'm going to disengage for a bit. If anybody has any questions about actual biology, i'll be happy to answer them. But otherwise, i'm taking a break from trying to correct willful ignorance about it.

[rogue06]

I've not had time to reply here, because i spent the last three days chasing down all the ideas that are being considered for developing therapies for coronavirus. All of these are based on what we know about the evolutionary relationships among the coronavirus family (where - surprise - no gene damage is involved), and in some cases the evolutionary relationships among the normal hosts of viruses that have recently jumped to humans.

Doing that against the background of this thread has made me acutely aware that the charlatans like Behe who try to replace biology with magic via a cherry picked presentation of work done by actual biologists aren't just some harmless distraction. They're positively dangerous. It makes me very angry at them, and very angry at people like Lee, who can't seem to even comprehend what taking a critical view of Behe's garbage might look like.

I don't think it's helpful for anyone for me to talk from a position of anger. And i suspect that, as the weeks go on, and the death toll rises as it certainly will, my anger's not going to subside very much. The fact that i have a number of dear family members who are older and at-risk isn't going to help in that regard.

So, i'm going to disengage for a bit. If anybody has any questions about actual biology, i'll be happy to answer them. But otherwise, i'm taking a break from trying to correct willful ignorance about it.

Keep up the good work

[TheLurch]

Keep up the good work

All i'm doing is collecting information and organizing it where other people can use it. It's the grad students and biotech workers - the highly educated "elites" that get so much garbage dumped on them of late - who are really doing the good work here.

[rogue06]

All i'm doing is collecting information and organizing it where other people can use it. It's the grad students and biotech workers - the highly educated "elites" that get so much garbage dumped on them of late - who are really doing the good work here.

Don't sell yourself short. Thanks.

[lee_merrill]

Sorry to see you bow out, Lurch, best wishes on your work.

Blessings,
Lee

[shunyadragon]

Sorry to see you bow out, Lurch, best wishes on your work.

Blessings,
Lee

The Lurch already has responded to all bad science of Behe and you. What else could he do?

[HMS_Beagle]

Doing that against the background of this thread has made me acutely aware that the charlatans like Behe who try to replace biology with magic via a cherry picked presentation of work done by actual biologists aren't just some harmless distraction. They're positively dangerous. It makes me very angry at them, and very angry at people like Lee, who can't seem to even comprehend what taking a critical view of Behe's garbage might look like.

^^^^ This, in spades. Liars and charlatans like Behe and the rest of the DI's clown circus aren't just minor annoyances. They actively damage our society by pushing their pseudo-science horsecrap on ignorant laymen like Lee who are too clueless to realize what tools they are.

Thanks and keep up the good work on SARS-CoV-2.