Are there no beneficial mutations?

[rogue06]

Research released earlier this month found genetic mutations that reduce the production of proteins known as tyrosine phosphatases which has been shown to reduce the risk of developing late-onset Alzheimer’s disease (LOAD).

Here's another beneficial Alzheimer's related mutation. This one in a family beset with hereditary Alzheimer's disease.

[rogue06]

It is extremely rare but I actually provided the name of one person who has been confirmed to have it, the artist Concetta Antico. When you Google her she is consistently referred to as "Tetrachromat Artist Concetta Antico."

Gabriele Jordan, a professor at the Institute of Neuroscience, Newcastle University in Britain has been investigating four-color vision or tetrachromacy since the '90s and studying a woman (subject cDa29) who has it that she ran across in 2010. See The women with superhuman vision as well as Scientists find woman who sees 99 million more colors than others. And the paper discussing it can be found HERE.

Jay Neitz, the Bishop Professor of Ophthalmology and a color vision researcher at the University of Washington is even predicting that at some time in the future gene therapy might allow humans with normal color visions to possess tetrachromatic vision.

Here is an interesting article in Psychology Today written by a woman who found out that she has tetrachromatic vision: DNA Results: Positive for Tetrachromacy

[lee_merrill]

Here's another beneficial Alzheimer's related mutation. This one in a family beset with hereditary Alzheimer's disease.

Good news! And both of these seem to be (ala Behe's prediction) degradative mutations.

Source: Science News

The swap prevents the APOE protein from binding to some sugar-dotted proteins called heparan sulfate proteoglycans, or HSPGs, experiments on the isolated proteins revealed.

Source

© Copyright Original Source

Blessings,
Lee

[HMS_Beagle]

Good news! And both of these seem to be (ala Behe's prediction) degradative mutations.

The swap prevents the APOE protein from binding to some sugar-dotted proteins called heparan sulfate proteoglycans, or HSPGs, experiments on the isolated proteins revealed.
Source

Blessings,
Lee

The bad news is Behe is either woefully incompetent, a deliberate liar, or both. Here is a rather scathing review with direct evidence of Behe cherry-picking results and ignoring the huge amount of evidence which directly contradicts his "evolution only degrades" stupidity

Evolution unscathed: Darwin Devolves argues on weak reasoning that unguided evolution is a destructive force, incapable of innovation

The “First Rule” appeared in a 2010 review in the Quarterly Review of Biology (Behe 2010), largely as a critique of the field of experimental evolution, which has grown dramatically in the last 20 years (see reviews by Fisher and Lang 2016; Lenski 2017; Van den Bergh et al. 2018). Collectively, experimental evolution has yielded new insights into the tempo of genotypic and phenotypic adaptation (Barrick et al. 2009), the role of historical contingency in the evolution of new traits (Blount et al. 2008), second‐order selection on mutator alleles (Sniegowski et al. 1997), the power of sex to combine favorable (and purge deleterious) mutations (McDonald et al. 2016), the dynamics of adaptation (Lang et al. 2013; Good et al. 2017), and the seemingly unlimited potential of adaptive evolution (Wiser et al. 2013).

Behe gives a misleading account of experimental evolution by trumpeting each and every loss‐of‐function mutation that provides a selective advantage. In truth, loss‐of‐function mutations are expected to contribute disproportionately to adaptation in experimental evolution, where selective pressures are high and conditions are constant, or nearly so. Systematic studies in yeast and bacteria show that most genes can be deleted singly with little functional consequence (Giaever et al. 2002; Winzeler 1999) and that a number of gene deletions are beneficial in specific environments (Hottes et al. 2004; Pir et al. 2012; Novo et al. 2013). It is important to point out that these mutations are often pleiotropic (Qian et al. 2012) and are not necessarily beneficial outside of the defined conditions of the experiment. No deletion is beneficial in all environments and beneficial loss‐of‐function mutations that arise in experimental evolution are unlikely to succeed if, say, cells are required to mate (Lang et al. 2009), the static environment is disturbed (Frenkel et al. 2015), or glucose is temporarily depleted (Li et al. 2018). Yet, Behe rests his central premise on the weak claim that these data demonstrate the ineffectiveness of random mutation and natural selection in all situations.

After reading Darwin Devolves, one would be forgiven for expecting that loss‐of‐function mutations swamp out all other forms of genetic variation no matter the context. After all, Behe states that “random mutation and natural selection are in fact fiercely devolutionary (p10),” and degrading mutations are “relentless as the tide and as futile to try to resist (p186).” However, the truth is that loss‐of‐function mutations account for only a small fraction of natural genetic variation. In humans only ∼3.5% of exonic and splice site variants (57,137 out of 1,639,223) are putatively loss‐of‐function (Saleheen et al. 2017), and a survey of 42 yeast strains found that only 242 of the nearly 6000 genes contain putative loss‐of‐function variants (Bergström et al. 2014). 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.

Read the whole review to see just what a scam artist Behe really is.

[lee_merrill]

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:

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

And Behe focuses on many real-world examples, not just experiments.

Blessings,
Lee

[shunyadragon]

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:

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

And Behe focuses on many real-world examples, not just experiments.

Blessings,
Lee

No, Behe is very very selective of his examples that justify his religious agenda. As cited his citation is unethical and incomplete, as usual. No his sense of the real world is only therough the eyes of his religious agenda. He only argues through the selective negative and does not real world research.

[rogue06]

The bad news is Behe is either woefully incompetent, a deliberate liar, or both. Here is a rather scathing review with direct evidence of Behe cherry-picking results and ignoring the huge amount of evidence which directly contradicts his "evolution only degrades" stupidity



Read the whole review to see just what a scam artist Behe really is.

I found this paragraph in a book review by Gregory I. Lang and Amber M. Rice (both biologists from Lehigh University) in the International Journal of Organic Evolution to be pertinent here

Source: Evolution unscathed: Darwin Devolves argues on weak reasoning that unguided evolution is a destructive force, incapable of innovation

Behe gives a misleading account of experimental evolution by trumpeting each and every loss‐of‐function mutation that provides a selective advantage. In truth, loss‐of‐function mutations are expected to contribute disproportionately to adaptation in experimental evolution, where selective pressures are high and conditions are constant, or nearly so. Systematic studies in yeast and bacteria show that most genes can be deleted singly with little functional consequence (Giaever et al. 2002; Winzeler 1999) and that a number of gene deletions are beneficial in specific environments (Hottes et al. 2004; Pir et al. 2012; Novo et al. 2013). It is important to point out that these mutations are often pleiotropic (Qian et al. 2012) and are not necessarily beneficial outside of the defined conditions of the experiment. No deletion is beneficial in all environments and beneficial loss‐of‐function mutations that arise in experimental evolution are unlikely to succeed if, say, cells are required to mate (Lang et al. 2009), the static environment is disturbed (Frenkel et al. 2015), or glucose is temporarily depleted (Li et al. 2018). Yet, Behe rests his central premise on the weak claim that these data demonstrate the ineffectiveness of random mutation and natural selection in all situations.

Source

© Copyright Original Source

(Now we can sit back and watch how that gets twisted around into an unrecognizable shape )

Anywho... The entire review is worth a read, especially since I found a copy of it online.

[lee_merrill]

I found this paragraph in a book review by Gregory I. Lang and Amber M. Rice (both biologists from Lehigh University) in the International Journal of Organic Evolution to be pertinent here

Source: Evolution unscathed: Darwin Devolves argues on weak reasoning that unguided evolution is a destructive force, incapable of innovation

Behe gives a misleading account of experimental evolution by trumpeting each and every loss‐of‐function mutation that provides a selective advantage. In truth, loss‐of‐function mutations are expected to contribute disproportionately to adaptation in experimental evolution, where selective pressures are high and conditions are constant, or nearly so. Systematic studies in yeast and bacteria show that most genes can be deleted singly with little functional consequence (Giaever et al. 2002; Winzeler 1999) and that a number of gene deletions are beneficial in specific environments (Hottes et al. 2004; Pir et al. 2012; Novo et al. 2013). It is important to point out that these mutations are often pleiotropic (Qian et al. 2012) and are not necessarily beneficial outside of the defined conditions of the experiment. No deletion is beneficial in all environments and beneficial loss‐of‐function mutations that arise in experimental evolution are unlikely to succeed if, say, cells are required to mate (Lang et al. 2009), the static environment is disturbed (Frenkel et al. 2015), or glucose is temporarily depleted (Li et al. 2018). Yet, Behe rests his central premise on the weak claim that these data demonstrate the ineffectiveness of random mutation and natural selection in all situations.

Source

© Copyright Original Source

Well, see my reply above, Behe focuses on degradative mutations, not loss-of-function mutations so much. And he includes real-world examples, not just experimental evidence.

Blessings,
Lee

[shunyadragon]

Well, see my reply above, Behe focuses on degradative mutations, not loss-of-function mutations so much. And he includes real-world examples, not just experimental evidence.

Blessings,
Lee

You cannot focus one kind of mutations without considering mutations as whole. The problem of the biased unethical way Behe views mutations has already been documented in this thread, and other threads in the past.

[rogue06]

Well, see my reply above, Behe focuses on degradative mutations, not loss-of-function mutations so much. And he includes real-world examples, not just experimental evidence.

Blessings,
Lee

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

[Seeker]

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

But there is still something worth to be learned off of Behe's book, right?

[TheLurch]

But there is still something worth to be learned off of Behe's book, right?

How not to science, maybe?

[rogue06]

But there is still something worth to be learned off of Behe's book, right?

Well, Behe is better than most of his fellow travelers. But that's sorta damning by faint praise since the bar is so low that even an earthworm would have trouble going under it.

[TheLurch]

Well, see my reply above, Behe focuses on degradative mutations, not loss-of-function mutations so much.

What criteria does he use to distinguish between the two?

[lee_merrill]

What criteria does he use to distinguish between the two?

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.

Blessings,
Lee