That seems to be the primary criticism being made here, over and over.
Glad you agree it’s fair. What is left then? What exactly is the problem?
The problem is the inconsistency. One purported evolutionary expert here, John Harshman, says Shapiro is a nut, implying incompetence. Others say that his problem is not incompetence, but self-aggrandizement. And it’s not just this website that is relevant, Joshua. I am thinking of judgments of Shapiro (and of others) that I’ve seen elsewhere. The point is that the self-declared spokespersons of evolutionary theory on the internet (and elsewhere) appear to have inconsistent standards. And this has been going on for a long time, e.g., Margulis saying that John Maynard Smith “doesn’t understand evolution” and Dawkins angrily denying it. The question is: Why aren’t the standards (for what counts as good or bad science) as consistent in evolutionary theory as they are in engineering physics or electrochemistry or many other branches of science? Why is it that the engineering physics and electrochemistry fields aren’t constantly holding meetings like the Wistar Conference, the Altenberg conference, the Royal Society conference, etc., where the fundamentals in the field are thrown open for debate? There has to be a reason for this difference between scientific fields.
Notice that I didn’t mention ID once in the above paragraph. 
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These are mutually consistent claims. What is the disagreement exactly? Self aggrandizement that puts oneself unnecessarily in conflict with the field is incompetence. We have been saying the science is accepted already, so a Crusade to get it accepted is in error. Some would call that incompetence.
It is pretty similar. You may not be up to date on the similar controversy there 
.
This is what we see a lot from supporters of Shapiro. They clutch at their pearls when Shapiro is criticized, but they never tackle the actual science. Here you are arguing about nonsense like “standards of criticism” while ignoring the most fundamental scientific criticisms that people are making.
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That would be my criticism of Shapiro.
I’ll note that you labeled your two parts as “(a)” and “(2)”.
Ignoring that labeling, I have seen no reason to believe that Shapiro is incompetent. Of course, I’m not a biologist, so not really in a position to judge that. From my perspective, the only objection I have to Shapiro is that he hypes things up a bit too much for my liking.
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Shapiro came to my attention, because I saw a pattern of creationists quoting Shapiro, and using those quotes to attack evolution. And this was usually followed by biologists pointing out that Shapiro actually agrees with evolution and that they are misunderstanding what he is saying.
I don’t know why @John_Harshman calls Shapiro a nut, but that could be due to Shapiro providing ammunition to creationists.
T. aquaticus:
I have Shapiro’s book, and have read it, though it was a while ago. If you would like to specify the incompetent or erroneous scientific claims in the book, I might know better what you object to – beyond the commonly-made criticism that Shapiro is too concerned with making himself seem daring and original. I’m actually quite open to the claim that he has done this, but I’m interested in knowing whether he is guilty of bad science as well as inflated rhetoric. So far, no one here has shown any bad science. That he boasts too much, that he is too attention-seeking, or that some think he is a “nut”, does not establish that he has produced bad science. I assume that when the University of Chicago gave him tenure to research and teach molecular biology that they thought he produced pretty good science, so there is need to show where he fell off the wagon later on.
I disagree. That is not the normal meaning of the English word “incompetence”. It might be professional bad manners, or the like.
I remember back at university - in social psychology - my supervisor saying that “Thomas Bowlby, like most innovators, overstated his own case.” (Note to non-sociologists - Bowlby discovered maternal deprivation syndrome). So Shapiro wouldn’t be the first scientists to engage in hype, and it would be orthogonal to the value of the work.
I do remember, though, that a researcher well known to most of us here did his last work off the back of reading Shapiro, and thanked me for introducing me to his work. But maybe that’s his ticket out of the mainstream. so I won’t name him.
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The most obvious error is the way in which Shapiro misrepresents what is stated in the mainstream theory of evolution. When biologists say that mutations are random they mean that the processes that produce mutations are blind to how these changes will affect fitness. Nowhere do biologists say that:
- random mutations are only substitution mutations caused by copying errors.
- random mutations must have an equal chance of occuring at every base in the genome 3
- random mutations are not caused by complex mechanisms.
So what does Shapiro claim? That mutations are not random because they are not simply copy errors, there are mutational hotspots, and that they are caused by complex mechanisms. Shapiro ignores the one way in which biologists do say that mutations are random. From this misrepresentation he claims that the mainstream theory of evolution is wrong even though he doesn’t even address the claims the actual mainstream theory of evolution makes.
To use a specific example, Shapiro likes to talk about mutations caused by transposons. As it turns out, when transposons jump around the genome they cause neutral, beneficial and detrimental mutations. The mechanisms that cause transposons to jump around have no way of knowing which changes will improve fitness. Transposon mutations are random with respect to fitness. Shapiro falsely claims that they are not random mutations even though he can’t point to a single instance where transposon activity only produces beneficial changes.
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Your reply is on-point. I like the format of it. It would help me, though, if you could tie your answer to some passages of his book, so I can look them up and follow in more detail where the problems lie. Your comments sound plausible to me, but I would like the accused’s own words to give him a fair hearing.
Have their been public exchanges, orally or in print, where Shapiro has been asked about these points, and if so, what have his responses been?
Fixed; thank you.
Thanks for your other comments as well. I now see how your position is distinct from that of some others. And there is nothing wrong in principle for criticizing a scientist for “hyping” too much. But if I may plead for consistency here: has no one noticed that “hyping” is found elsewhere, e.g., in paleontology? In recent years we have seen some cases regarding ancient hominids where overclaims were made about the significance of some fossil find for human evolution, and eventually were shown to be exaggerations and, if memory serves, in one celebrated case an outright error. (I’m speaking here of the judgment of secular scientists, not creationists.) Those overclaims seemed to have drawn less ire from the “atheists and agnostics blogging about evolution and creation” community than Shapiro’s overclaims, and one is led to wonder why.
I agree that a number of creationists seem to seize on any criticism of any aspect of evolutionary theory and try to turn it into evidence against “evolution.” I think this is a lamentable habit, but I don’t know how to change it. I’m in a difficult position regarding the creationists, because they think that evolution itself is inherently un-Christian, regardless of the proposed causes of evolution, whereas I don’t think that. I think that evolution is only a problem for Christianity if it is conceived of as wholly explicable without any reference at all to design, plan, or purpose.
I can give you quotes from some of his papers:
and this one
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Hype is everywhere. I expect that every science is affected by it.
I don’t go out of my way to criticize Shapiro. I only mention when his name has come into the discussion for other reasons. His book is intended for the general public, and a bit of hype can help get him some attention.
I notice it, because I find people quoting the hype in mistaken arguments. And that’s possibly the general rule – we complain about hype that causes problems for us, but we don’t make a fuss about other examples of hype, even though we may have noticed them.
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Now this is an interesting stance.
Its my interpretation of ID principles that anyyhing God does - - because natural law by itself will take too long or isnt possible at all - - is, by definition, miraculous.
So how do you conceive of any ID positions that dont somehow require miracles?
George, you have already had this question answered by me many times, and you’ve seen the same questioned answered by other people many times. Is your memory that bad, that you need to have it answered again?
How many times do I have to suggest that you read Michael Denton’s Nature’s Destiny, for a conception of design in which future changes are programmed at the beginning, into a lawlike evolutionary process, and appear over time naturally, without any need for divine intervention? A crude analogy (very crude, and not to be taken as Denton’s actual conception of the subtlety of chemical, geological and biological nature) would be the setting up of a complex pattern of dominoes, in which, after the first domino is tipped over, the whole elaborate pattern of domino-falling ensues, without any intervention by subsequent tippers. Every fall of every domino is planned from beginning, i.e., designed, but no law of physics is ever observed to be violated (except the meta-violation, as it were, of the creation of the initial domino pattern and the first tip).
For ID, natural law alone cannot explain the complex order of the organic world, but natural law set up by a far-sighted intelligence could. At least, some ID followers believe that. Others don’t. They (e.g. Meyer) think there would have to be at least a few subsequent interventions. And before you go on to point out that those others are the majority of ID proponents, don’t bother – I already know. But it doesn’t make the minority view any less an ID view. It’s an ID view if it affirms the possibility of detectable design in nature. Miracles aren’t required.
If you are willing to stop making generalizations about ID, and limit yourself to discussing individual ID proponents, and want to say, “According to Meyer, miracles are required” – that’s fine. I’d agree with you. It’s only the sweeping generalizations I object to.
Who in science says that natural law alone can explain the complex order of the oragnic world? Clearly initial conditions and unexplained contingencies matter too.
If this is what ID argues, it boxes a shadow.
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No, it’s because he’s a nut. He turns Hox genes into magic and gene duplication into some kind of conscious tool. Etc.
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There are Nobel prize winners in science who had wacko ideas. Linus Pauling thought vitamin C cured everything. Roger Sperry thought the the 2nd law of thermodynamics didn’t apply to organisms. Tenure, likewise, is no assurance of reason.
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I would probably call that hype. But I may be giving him too much benefit of the doubt.
I seem to recall that he also says the genome is a read-write random access memory.
I didn’t know that; do you suppose that’s where Sal Cordova got the notion?