Are there no beneficial mutations?

[lee_merrill]

His "focus[ing] on" has led to the cherry-picking of data.

It seems however that it's a lot easier to degrade or disable a function than it is to provide new function. So that would not be cherry-picking.

Blessings,
Lee

[lee_merrill]

You cannot focus one kind of mutations without considering mutations as whole.

Behe considers all kinds of mutations, though, and concludes that most selectable mutations are degradative.

Blessings,
Lee

[shunyadragon]

It seems however that it's a lot easier to degrade or disable a function than it is to provide new function. So that would not be cherry-picking.

Blessings,
Lee

Not true, when you consider the whole scheme mutations in life and evolution.

[shunyadragon]

Behe considers all kinds of mutations, though, and concludes that most selectable mutations are degradative.

Blessings,
Lee

Again, this is not true and an ethical claim by Behe based on his religious agenda and not science. This has been addressed previously.

[TheLurch]

I'm taking loss-of-function to mean complete loss of function, since they are talking about gene deletion in the quote above. Behe doesn't actually use the term "loss-of-function", but it should be clear when he means complete loss of function versus degradation of function.

FYI, the correct terminology is that loss of function means loss of any function. The complete loss of function is termed a null mutation.

In any case, what criteria does he use to figure out which category the mutation fits in?

[TheLurch]

It seems however that it's a lot easier to degrade or disable a function than it is to provide new function.

That is true from the perspective of new mutations. But it may not be true when it comes to which mutations survive selection and persist in the genome. In that context, the vast majority of mutations are neutral, followed by altered function. Nulls are relatively rare.

Therefore this statement:

So that would not be cherry-picking.

Is only true when talking about newly arisen mutations, rather than talking about those that persist following selection.

[HMS_Beagle]

Source: Evolution unscathed

Compared to the vast majority of natural genetic variants, loss‐of‐function variants have a much lower allele‐frequency distribution (MacArthur et al. 2012). Still, Behe fixates on beneficial loss‐of‐function mutations, drawing heavily from situations where one expects such mutations to be favored—such as experimental evolution—and generalizes to all situations this one mechanism writ large.

© Copyright Original Source

I think Behe is fixing on degradative mutations more that loss-of-function mutations, though:

Lee

Yes. That's called cherry-picking and is quite dishonest.

[HMS_Beagle]

Behe considers all kinds of mutations, though, and concludes that most selectable mutations are degradative.

Which is pretty stupid since science has known for 70 years evolution works by modifying existing features. Behe dishonestly calls this "degrading" even when the new variation provides an increase in reproductive fitness.

Behe is nothing but a scam artist using weasel words to attack evolution and push his religious agenda. He counts on ignorant fools like you Lee because no one who knows any genetics swallows his BS.

[Roy]

Source: Darwin Devolves, p. 151, emphasis in the original

So what do those changes do to the protein? The authors write that “[computer] analysis classified both as damaging.”

Damaging. In other words, as in the case of the polar bear discussed in the first chapter, the mutations are predicted (based on computer modeling, not yet on actual experiments) to impair the normal function of the protein.

© Copyright Original Source

If you look up what the authors Behe is citing actually mean by "damaging", rather than blindly accepting Behe's interpretation, you'll find that "damaging" refers to any change that affects the protein's shape or chemical properties, because that is all can be determined, and does not rule out the possibility that the change has a negligible or even a positive effect in practice.

Behe is using a limitation of the computer modelling to make unwarranted claims.

[lee_merrill]

FYI, the correct terminology is that loss of function means loss of any function. The complete loss of function is termed a null mutation.

Though this reference calls them synonyms. It seems the review is using "loss-of-function" to mean "null mutation", since they talk about gene deletion. But Behe does not restrict himself to talking about null mutations, this review seems to be mistaken.

In any case, what criteria does he use to figure out which category the mutation fits in?

I'm not sure why you are asking this, any mutation that only degrades function is damaging (in Behe's terminology in the quote I gave), and any mutation that disables a gene would be a null mutation.

In that context, the vast majority of mutations are neutral, followed by altered function. Nulls are relatively rare.

After selection, Behe argues (I commend to you reading the book) that most selectable mutations are degradative, given that the raw material selection has to work with (we need not consider neutral mutations here) is predominately degradative, and selection can often use such mutations advantageously.

Blessings,
Lee

[lee_merrill]

Yes. That's called cherry-picking and is quite dishonest.

Not if you can argue that degradative mutations predominate in selection.

Which is pretty stupid since science has known for 70 years evolution works by modifying existing features. Behe dishonestly calls this "degrading" even when the new variation provides an increase in reproductive fitness.

No, Behe doesn't call any modification "degrading". He says that most variations that increase fitness are degradative.

Blessings,
Lee

[lee_merrill]

If you look up what the authors Behe is citing actually mean by "damaging", rather than blindly accepting Behe's interpretation, you'll find that "damaging" refers to any change that affects the protein's shape or chemical properties, because that is all can be determined, and does not rule out the possibility that the change has a negligible or even a positive effect in practice.

Behe is using a limitation of the computer modelling to make unwarranted claims.

In various cases Behe does rely on computer modeling, that determines that a mutation is probably damaging.

But why do you say that "damaging" refers to any change that affects the protein's shape or chemical properties? What specific references do you mean?

Blessings,
Lee

[TheLurch]

I'm not sure why you are asking this, any mutation that only degrades function is damaging (in Behe's terminology in the quote I gave), and any mutation that disables a gene would be a null mutation.

Because it's not a simple question. Even an incredibly simple mutation like the one for sickle cell anemia is complicated. It is:
A neutral change in terms of hemoglobin's ability to carry oxygen.
A harmful loss of function in terms of the activities of the circulatory system.
A beneficial gain of function in terms of disease resistance.

So, what category do you lump that into? The answer isn't at all obvious to me - and that's a simple mutation in an equally simple gene. Changes in proteins involved in something like a signaling network have far more complicated consequences.

So, i'd hope if he's intending to make any kind of scientific argument, Behe's laid out clear criteria for the appropriate use of his terminology. If he hasn't, well, that should tell you something.

After selection, Behe argues (I commend to you reading the book) that most selectable mutations are degradative, given that the raw material selection has to work with (we need not consider neutral mutations here) is predominately degradative, and selection can often use such mutations advantageously.

But, as we've seen in earlier discussions—and as anyone could see if they bothered to compare genomes—that's simply not true in general. (I could go into some exceptions if anyone were interested.) So i don't see the value of reading a book with a central argument that consists of misinformation. Why would you commend such a thing?

[shunyadragon]

Not if you can argue that degradative mutations predominate in selection.

Which they do not degradtative mutations only have short term effect, and othe mutations have long term effects.

No, Behe doesn't call any modification "degrading". He says that most variations that increase fitness are degradative.

Which is not true.

[Roy]

In various cases Behe does rely on computer modeling, that determines that a mutation is probably damaging.

Behe doesn't rely on computer modelling, he relies on other people's work, which he lies about.

But why do you say that "damaging" refers to any change that affects the protein's shape or chemical properties?

Because I've read the background information on the results Behe lies about, rather than blindly swallowing Behe's lies because I like his conclusions.

You should try that sometime.