Sunday, 17 July 2016
(Not so)Civil war?
When Atheists Attack (Each Other)
David Klinghoffer
The squabble between Darwin lobbyists who openly hate religion and those who only quietly disdain it grows ever more personal, bitter and pathetic. On one side, evangelizing New or "Gnu" (ha ha) Atheists like Jerry Coyne and his acolytes at Why Evolution Is True. Dr. Coyne is a biologist who teaches and ostensibly researches at the University of Chicago but has a heck of a lot of free time on his hands for blogging and posting pictures of cute cats.
On the other side, so-called accommodationists like the crowd at the National Center for Science Education, who attack the New Atheists for the political offense of being rude to religious believers and supposedly messing up the alliance between religious and irreligious Darwinists.
I say "supposedly" because there's no evidence any substantial body of opinion is actually being changed on religion or evolution by anything the open haters or the quiet disdainers say. Everyone seems to seriously think they're either going to defeat religion, or merely "creationism," or both by blogging for an audience of fellow Darwinists.
Want to see what I mean? This is all pretty strictly a battle of stinkbugs in a bottle. Try to follow it without getting a headache.
Coyne recently drew excited applause from fellow biologist-atheist-blogger PZ Myers for Coyne's "open letter" (published on his blog) to the NCSE and its British equivalent, the British Centre for Science Education. In the letter, Coyne took umbrage at criticism of the New Atheists, mostly on blogs, emanating from the two accommodationist organizations. He vowed that,
We will continue to answer the misguided attacks [on the New Atheists] by people like Josh Rosenau, Roger Stanyard, and Nick Matzke so long as they keep mounting those attacks.
Like the NCSE, the BCSE seeks to pump up Darwin in the public mind without scaring religious people. This guy called Stanyard at the BCSE complains of losing a night's sleep over the nastiness of the rhetoric on Coyne's blog. Coyne in turn complained that Stanyard complained that a blog commenter complained that Nick Matzke, formerly of the NCSE, is like "vermin." Coyne also hit out at blogger Jason Rosenhouse for an "epic"-length blog post complaining of New Atheist "incivility." In the blog, Rosenhouse, who teaches math at James Madison University, wrote an update about how he had revised an insulting comment about the NCSE's Josh Rosenau that he, Rosenhouse, made in a previous version of the post.
That last bit briefly confused me. In occasionally skimming the writings of Jason Rosenhouse and Josh Rosenau in the past, I realized now I had been assuming they were the same person. They are not!
It goes on and on. In the course of his own blog post, Professor Coyne disavowed name-calling and berated Stanyard (remember him? The British guy) for "glomming onto" the Matzke-vermin insult like "white on rice, or Kwok on a Leica." What's a Kwok? Not a what but a who -- John Kwok, presumably a pseudonym, one of the most tirelessly obsessive commenters on Darwinist blog sites. Besides lashing at intelligent design, he often writes of his interest in photographic gear such as a camera by Leica. I have the impression that Kwok irritates even fellow Darwinists.
There's no need to keep all the names straight in your head. I certainly can't. I'm only taking your time, recounting just a small part of one confused exchange, to illustrate the culture of these Darwinists who write so impassionedly about religion, whether for abolishing it or befriending it. Writes Coyne in reply to Stanyard,
I'd suggest, then, that you lay off telling us what to do until you've read about our goals. The fact is that we'll always be fighting creationism until religion goes away, and when it does the fight will be over, as it is in Scandinavia.
A skeptic might suggest that turning America into Scandinavia, as far as religion goes, is an outsized goal, more like a delusion, for this group as they sit hunched over their computers shooting intemperate comments back and forth at each other all day. Or in poor Stanyard's case, all night.
There's a feverish, terrarium-like and oxygen-starved quality to this world of online Darwinists and atheists. It could only be sustained by the isolation of the Internet. They don't seem to realize that the public accepts Darwinism to the extent it does -- which is not much -- primarily because of what William James would call the sheer, simple "prestige" that the opinion grants. Arguments and evidence have little to do with it.
The prestige of Darwinism is not going to be affected by how the battle between Jerry Coyne and the NCSE turns out. New Atheist arguments are hobbled by the same isolation from what people think and feel. I have not yet read anything by any of these gentlemen or ladies, whether the open haters or the quiet disdainers, that conveys anything like a real comprehension of religious feeling or thought.
Even as they fight over the most effective way to relate to "religion," the open atheists and the accomodationists speak of an abstraction, a cartoon, that no actual religious person would recognize. No one is going to be persuaded if he doesn't already wish to be persuaded for other personal reasons. No faith is under threat from the likes of Jerry Coyne.
David Klinghoffer
The squabble between Darwin lobbyists who openly hate religion and those who only quietly disdain it grows ever more personal, bitter and pathetic. On one side, evangelizing New or "Gnu" (ha ha) Atheists like Jerry Coyne and his acolytes at Why Evolution Is True. Dr. Coyne is a biologist who teaches and ostensibly researches at the University of Chicago but has a heck of a lot of free time on his hands for blogging and posting pictures of cute cats.
On the other side, so-called accommodationists like the crowd at the National Center for Science Education, who attack the New Atheists for the political offense of being rude to religious believers and supposedly messing up the alliance between religious and irreligious Darwinists.
I say "supposedly" because there's no evidence any substantial body of opinion is actually being changed on religion or evolution by anything the open haters or the quiet disdainers say. Everyone seems to seriously think they're either going to defeat religion, or merely "creationism," or both by blogging for an audience of fellow Darwinists.
Want to see what I mean? This is all pretty strictly a battle of stinkbugs in a bottle. Try to follow it without getting a headache.
Coyne recently drew excited applause from fellow biologist-atheist-blogger PZ Myers for Coyne's "open letter" (published on his blog) to the NCSE and its British equivalent, the British Centre for Science Education. In the letter, Coyne took umbrage at criticism of the New Atheists, mostly on blogs, emanating from the two accommodationist organizations. He vowed that,
We will continue to answer the misguided attacks [on the New Atheists] by people like Josh Rosenau, Roger Stanyard, and Nick Matzke so long as they keep mounting those attacks.
Like the NCSE, the BCSE seeks to pump up Darwin in the public mind without scaring religious people. This guy called Stanyard at the BCSE complains of losing a night's sleep over the nastiness of the rhetoric on Coyne's blog. Coyne in turn complained that Stanyard complained that a blog commenter complained that Nick Matzke, formerly of the NCSE, is like "vermin." Coyne also hit out at blogger Jason Rosenhouse for an "epic"-length blog post complaining of New Atheist "incivility." In the blog, Rosenhouse, who teaches math at James Madison University, wrote an update about how he had revised an insulting comment about the NCSE's Josh Rosenau that he, Rosenhouse, made in a previous version of the post.
That last bit briefly confused me. In occasionally skimming the writings of Jason Rosenhouse and Josh Rosenau in the past, I realized now I had been assuming they were the same person. They are not!
It goes on and on. In the course of his own blog post, Professor Coyne disavowed name-calling and berated Stanyard (remember him? The British guy) for "glomming onto" the Matzke-vermin insult like "white on rice, or Kwok on a Leica." What's a Kwok? Not a what but a who -- John Kwok, presumably a pseudonym, one of the most tirelessly obsessive commenters on Darwinist blog sites. Besides lashing at intelligent design, he often writes of his interest in photographic gear such as a camera by Leica. I have the impression that Kwok irritates even fellow Darwinists.
There's no need to keep all the names straight in your head. I certainly can't. I'm only taking your time, recounting just a small part of one confused exchange, to illustrate the culture of these Darwinists who write so impassionedly about religion, whether for abolishing it or befriending it. Writes Coyne in reply to Stanyard,
I'd suggest, then, that you lay off telling us what to do until you've read about our goals. The fact is that we'll always be fighting creationism until religion goes away, and when it does the fight will be over, as it is in Scandinavia.
A skeptic might suggest that turning America into Scandinavia, as far as religion goes, is an outsized goal, more like a delusion, for this group as they sit hunched over their computers shooting intemperate comments back and forth at each other all day. Or in poor Stanyard's case, all night.
There's a feverish, terrarium-like and oxygen-starved quality to this world of online Darwinists and atheists. It could only be sustained by the isolation of the Internet. They don't seem to realize that the public accepts Darwinism to the extent it does -- which is not much -- primarily because of what William James would call the sheer, simple "prestige" that the opinion grants. Arguments and evidence have little to do with it.
The prestige of Darwinism is not going to be affected by how the battle between Jerry Coyne and the NCSE turns out. New Atheist arguments are hobbled by the same isolation from what people think and feel. I have not yet read anything by any of these gentlemen or ladies, whether the open haters or the quiet disdainers, that conveys anything like a real comprehension of religious feeling or thought.
Even as they fight over the most effective way to relate to "religion," the open atheists and the accomodationists speak of an abstraction, a cartoon, that no actual religious person would recognize. No one is going to be persuaded if he doesn't already wish to be persuaded for other personal reasons. No faith is under threat from the likes of Jerry Coyne.
Enzymes v.Darwin.
When Enzymes Don't Lie
Evolution News & Views
New research published in Bio-Complexity calls into question some fundamental assumptions of neo-Darwinian theory and enzyme evolution.
Enzymes are proteins that catalyze reactions that are necessary for life. Enzymes play such a fundamental role in life that many researchers are interested in how they originated and how they have evolved. They are composed of strings of amino acids, and the particular sequence of amino acids determines what three-dimensional shape each protein has, and what enzymatic function it carries out. Biologists categorize enzymes into families based on similarity of structure. The more similar the structure, the closer the evolutionary relationship is presumed to be.
It is generally believed that these enzyme families arose by a process of gene duplication followed by divergence of the extra copies over time. If accumulating mutations in an extra gene led to a beneficial change in enzyme function, the gene encoding that enzyme would tend to be preserved. Over time, then, repeated rounds of duplication and divergence would produce the large multi-functional families we see today. Yet for this explanation to be true, converting enzymes to new functions must require only a few mutations in order for the process to be within reach of neo-Darwinian evolution.
Doug Axe and Ann Gauger from Biologic Institute recently published a paper that addresses this pervasive assumption about the ease of enzyme conversion :
Here, we explore this question by asking how many mutations are needed to achieve a genuine functional conversion in a case where the necessary structural change is known to be small relative to the change commonly attributed to paralogous divergence.
As the authors report, they focused "not on minor functional adjustments, like shifts in substrate profiles, but rather on true innovations -- the jumps to new chemistry that must have happened but which seem to defy gradualistic explanation." Their aim was not to establish ancestry between two particular enzymes, but to identify a functional innovation that should be relatively straightforward within a superfamily and then evaluate how evolutionarily feasible this modest innovation would be.
They began by looking at a large "superfamily" known as the pyridoxal-5'-phosphate (PLP) dependent transferases. This is a well-characterized family of enzymes that share a common fold (shape) but catalyze distinctly different reactions. They identified a pair within that superfamily with very close structural similarity but no functional overlap. Kbl2 is involved in threonine (a type of amino acid) metabolism, and BioF2 is part of the biotin biosynthesis pathway. They then used a three-stage process to identify the sequences mostly likely to confer a functional change.
The experimental question is: How many mutations are required to convert Kbl to BioF function?
Experimental Results:
There are about 250 different amino-acid differences between Kbl and BioF. This is a huge number, and probably many more than the minimum number of amino acids that are needed to convert one enzyme's function to the other's. In order to determine the minimum number of amino acid changes necessary for functional innovation to occur, Gauger and Axe followed a three stage process. First they used sequence and structural comparisons of the two enzymes to identify candidate amino acids most likely to be significant for function. Second, they mutated those amino acids in BioF, making them like Kbl, and checked for loss of BioF activity. They identified three groups of amino acids, each consisting of six or seven individual amino acids, and one single amino acid, H152, that were essential for BioF function. Finally, they tested whether changing these groups in Kbl to look like BioF would enable the mutated Kbl to substitute for BioF.
The experiment ended up showing that no functional conversion could be achieved, even when all identified changes were made, including every amino acid in the enzyme's active site (the place where the enzyme's chemistry is carried out). Gauger and Axe estimate that seven or more mutations would be required to convert Kbl to BioF function.
So what does this all mean?
Two major implications need to be noted from the results of this experiment. In a second post, we will have a further discussion on implications of this research for neo-Darwinism.
The first finding was that H152 was vital to the functionality of the BioF. Perhaps what is most interesting about this finding is that H152 is not within the active site but is on the enzyme surface away from the active site. It is generally believed that the active site is the area of interest for enzymes within a family and the rest of the enzyme (the "scaffold") just holds the active site. However, these experimental findings seem to indicate that the non-active site differences, however minimal they may be, need to be considered, and that these differences may be more important than the apparent similarities.
The second implication from this failure to convert functionality is the question of whether a neo-Darwinian process of step-by-step conversion from one enzyme to another is actually feasible. The two enzymes in this study were very similar enzymes, yet even with generous estimates for mutation rate, gene duplication rate, and no fitness cost for carrying the extra gene, there does not seem to be enough time for mutations of this sort to occur:
"...seven is a reasonable lower-bound estimate of the specific nucleotide substitutions required for conversion...this places the Kbl [to] BioF conversion outside the bounds of what can be achieved by the Darwinian mechanism." When using the established mechanisms and estimates, it would require 10^30 or more generations to elapse before any type of BioF-like conversion could be established. There is not enough time to accomplish this relatively small innovation! As Axe and Gauger aptly summarize:
This places the innovation well beyond what can be expected within the time that life has existed on earth, under favorable assumptions. In fact, even the unrealistically favorable assumption that kbl duplicates carry no fitness cost leaves the conversion just beyond the limits of feasibility.
These are not large leaps or large-scale changes, but small-scale changes. And other research, cited in this paper, have shown the same difficulty in achieving enzyme conversions. This calls into question a fundamental assumption in the neo-Darwinian paradigm, that similarity of structure or form means ease of conversion, and implies that a different paradigm is necessary to account for enzymatic functional conversion.
Evolution News & Views
New research published in Bio-Complexity calls into question some fundamental assumptions of neo-Darwinian theory and enzyme evolution.
Enzymes are proteins that catalyze reactions that are necessary for life. Enzymes play such a fundamental role in life that many researchers are interested in how they originated and how they have evolved. They are composed of strings of amino acids, and the particular sequence of amino acids determines what three-dimensional shape each protein has, and what enzymatic function it carries out. Biologists categorize enzymes into families based on similarity of structure. The more similar the structure, the closer the evolutionary relationship is presumed to be.
It is generally believed that these enzyme families arose by a process of gene duplication followed by divergence of the extra copies over time. If accumulating mutations in an extra gene led to a beneficial change in enzyme function, the gene encoding that enzyme would tend to be preserved. Over time, then, repeated rounds of duplication and divergence would produce the large multi-functional families we see today. Yet for this explanation to be true, converting enzymes to new functions must require only a few mutations in order for the process to be within reach of neo-Darwinian evolution.
Doug Axe and Ann Gauger from Biologic Institute recently published a paper that addresses this pervasive assumption about the ease of enzyme conversion :
Here, we explore this question by asking how many mutations are needed to achieve a genuine functional conversion in a case where the necessary structural change is known to be small relative to the change commonly attributed to paralogous divergence.
As the authors report, they focused "not on minor functional adjustments, like shifts in substrate profiles, but rather on true innovations -- the jumps to new chemistry that must have happened but which seem to defy gradualistic explanation." Their aim was not to establish ancestry between two particular enzymes, but to identify a functional innovation that should be relatively straightforward within a superfamily and then evaluate how evolutionarily feasible this modest innovation would be.
They began by looking at a large "superfamily" known as the pyridoxal-5'-phosphate (PLP) dependent transferases. This is a well-characterized family of enzymes that share a common fold (shape) but catalyze distinctly different reactions. They identified a pair within that superfamily with very close structural similarity but no functional overlap. Kbl2 is involved in threonine (a type of amino acid) metabolism, and BioF2 is part of the biotin biosynthesis pathway. They then used a three-stage process to identify the sequences mostly likely to confer a functional change.
The experimental question is: How many mutations are required to convert Kbl to BioF function?
Experimental Results:
There are about 250 different amino-acid differences between Kbl and BioF. This is a huge number, and probably many more than the minimum number of amino acids that are needed to convert one enzyme's function to the other's. In order to determine the minimum number of amino acid changes necessary for functional innovation to occur, Gauger and Axe followed a three stage process. First they used sequence and structural comparisons of the two enzymes to identify candidate amino acids most likely to be significant for function. Second, they mutated those amino acids in BioF, making them like Kbl, and checked for loss of BioF activity. They identified three groups of amino acids, each consisting of six or seven individual amino acids, and one single amino acid, H152, that were essential for BioF function. Finally, they tested whether changing these groups in Kbl to look like BioF would enable the mutated Kbl to substitute for BioF.
The experiment ended up showing that no functional conversion could be achieved, even when all identified changes were made, including every amino acid in the enzyme's active site (the place where the enzyme's chemistry is carried out). Gauger and Axe estimate that seven or more mutations would be required to convert Kbl to BioF function.
So what does this all mean?
Two major implications need to be noted from the results of this experiment. In a second post, we will have a further discussion on implications of this research for neo-Darwinism.
The first finding was that H152 was vital to the functionality of the BioF. Perhaps what is most interesting about this finding is that H152 is not within the active site but is on the enzyme surface away from the active site. It is generally believed that the active site is the area of interest for enzymes within a family and the rest of the enzyme (the "scaffold") just holds the active site. However, these experimental findings seem to indicate that the non-active site differences, however minimal they may be, need to be considered, and that these differences may be more important than the apparent similarities.
The second implication from this failure to convert functionality is the question of whether a neo-Darwinian process of step-by-step conversion from one enzyme to another is actually feasible. The two enzymes in this study were very similar enzymes, yet even with generous estimates for mutation rate, gene duplication rate, and no fitness cost for carrying the extra gene, there does not seem to be enough time for mutations of this sort to occur:
"...seven is a reasonable lower-bound estimate of the specific nucleotide substitutions required for conversion...this places the Kbl [to] BioF conversion outside the bounds of what can be achieved by the Darwinian mechanism." When using the established mechanisms and estimates, it would require 10^30 or more generations to elapse before any type of BioF-like conversion could be established. There is not enough time to accomplish this relatively small innovation! As Axe and Gauger aptly summarize:
This places the innovation well beyond what can be expected within the time that life has existed on earth, under favorable assumptions. In fact, even the unrealistically favorable assumption that kbl duplicates carry no fitness cost leaves the conversion just beyond the limits of feasibility.
These are not large leaps or large-scale changes, but small-scale changes. And other research, cited in this paper, have shown the same difficulty in achieving enzyme conversions. This calls into question a fundamental assumption in the neo-Darwinian paradigm, that similarity of structure or form means ease of conversion, and implies that a different paradigm is necessary to account for enzymatic functional conversion.
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