Category ArchiveAntievolution

Antievolution Wesley R. Elsberry on 10 Feb 2013

Another Uninformed Critique of WIDF Fails

In 2009, Lita Cosner of Creation Ministries International posted a review of the 2004 book “Why Intelligent Design Fails”, claiming in summary that there was nothing in the book to cause discomfort to an “informed creationist”, and that actual problems for “intelligent design” creationism were rare in the book. Here in 2013, let’s have a look at Cosner’s specific critique of the chapter that Jeff Shallit and I contributed.

“Playing Games with Probability”

Shallit and Elsberry, in their essay “Playing Games with Probability”, claim that intelligent design theorists misuse probability in the same way that Bible code pseudo-scientists do. They more specifically argue that Dembski’s use of probability is unjustified and inconsistent (p. 130), and gives “wildly differing results” depending on which method is used (p. 132).

They, along with many of the other authors, use genetic algorithms, and specifically Dawkins’ “weasel” algorithm, to prove that natural selection and mutation are sufficient for evolution to occur. But, as even the authors acknowledge, they do not accurately represent biological evolution, so it is dishonest to use the algorithms as proof for evolution.11–13

It is common for evolutionists to use situations (as Shallit and Elsberry do), such as flipping a coin 50 times to come to an improbable sequence, to demonstrate how improbable things can happen. But in that example, there must be some outcome. But it was not necessary that the universe be suitable for life, or that life would occur even in a universe suitable for it. Since there are many more ways for the universe to be unsuitable for life than suitable for it, and for something to be dead than to be alive, this warrants a sufficient explanation.14

Let’s toss in Cosner’s associated footnotes:

11. Batten, D., Genetic algorithms—do they show that evolution works? , 2008.

12. Truman, R., The weasel returns: Truman replies to Curtis, Journal of Creation 15(2):55– 58, 2001.

13. Abel, D.L., The Capabilities of Chaos and Complexity, International Journal of Molecular Sciences 10:247–291, 9 January 2009 doi:10.3390/ijms10010247 (emphasis added): All too many evolutionary computationists fail to realize the purely formal nature of GA [genetic alogrithims] procedures. GAs are not dealing with physicodynamic cause-and-effect chains. First, what is being optimized is a formal representation of meaning and function. A representation of any kind cannot be reduced to inanimate physicality. Second, “potential solutions” are formal, not merely physical entities. Third, at each iteration (generation) a certain portion of the population of potential solutions is deliberately selected by the agent experimenter (artificial selection) to “breed” a new generation. The optimized solution was purposefully pursued at each iteration. The overall process was entirely goaldirected (formal). Real evolution has no goal. Fourth, a formal fitness function is used to define and measure the fittest solutions thus far to a certain formal problem. The act of defining and measuring, along with just about everything else in the GA procedure, is altogether formal, not physical.

14. Sarfati, By Design, ch. 16.

The first paragraph shows that Cosner read material that makes the second paragraph completely unsupportable. We certainly did note that Dembski’s use of probability was inconsistent, but we stated that this was apparent in an example of something Dembski himself critiqued, and that something was the Dawkins’ “weasel” program. Cosner’s second paragraph claims things that Cosner might wish that we said, but did not. Specifically, we never stated any such thing as genetic algorithms being “proof of evolution”. In dealing with Dembski’s critiques, one has no need of such claims. It is entirely sufficient to note that Dembski is misinformed about, overlooks, or misrepresents the properties of evolutionary computation systems that he criticizes or dismisses out of hand, or even (as we did) demonstrate inconsistencies within the critiques he makes of a single system. Genetic algorithms and evolutionary computation more broadly are useful rejoinders to certain broad claims religious antievolutionists make, but they do not directly bear on the question of a history of evolution and biological common descent as Cosner erroneously asserts we claimed. (Abel’s gobbledygook from footnote 13 is portentous but irrelevant; Dembski remains inconsistent in assigning probabilities, whether one calls the system Dembski critiqued “formal”, “informal”, or “stunning in a mauve chiffon dress”.)

In the third paragraph, Cosner asserts, “It is common for evolutionists to use situations (as Shallit and Elsberry do), such as flipping a coin 50 times to come to an improbable sequence, to demonstrate how improbable things can happen.” This only makes sense if we were attempting to make some sort of apologia for small probabilities. Cosner rather thoroughly misses our point. That’s the charitable reading of Cosner’s critique. On page 122, we noted the central problem that for a given observation of a result such as that of a sequence of coin flips, the likelihood of any possible such sequence is exactly equal to any other such sequence, but we would like to distinguish between those that can be ascribed to chance and those which cannot be ascribed to chance. This is exactly the thing that Dembski claims to have halfway solved, but which we demonstrate he is not even close to doing. Our critique is aimed at showing that Dembski has not sufficiently justified his claims.

Let’s see Cosner’s dismissive conclusion:

To refute all the arguments in this book would require a book in and of itself. Indeed, most of the arguments are addressed in Jonathan Sarfati’s By Design, though it was not written to refute this book specifically. Where Why Intelligent Design Fails does point out a valid weakness in ID theory (which is rare), it is one of the weaknesses which results from ID’s refusal to name the Creator, or from the acceptance of theistic evolution by some ID theorists. These are weaknesses that biblical creation does not share with ID theory, so there is nothing in this book that should challenge an informed creationist.

Our conclusion is entirely overlooked by Cosner:

The bottom line is that Dembski’s specified complexity or complex specified information is an incoherent concept. It is unworkable, is not well-defined, and does not have the properties he claims for it. Even Dembski himself, in attempting to calculate the specified complexity of various events, uses an inconsistent methodology. Most important, specified complexity does not provide a way to distinguish designed objects from undesigned objects.

Biochemist Russell F. Doolittle (1983) once remarked, “The next time you hear creationists railing about the ‘impossibility’ of making a particular protein, whether hemoglobin or ribonuclease or cytochrome-c, you can smile wryly and know that they are nowhere near a consideration of the real issues” (261). That same wry smile might be useful to keep handy when reading Dembski’s claims.

The faults we note for Dembski’s ideas are not due to “failure to name the Creator”, and certainly have nothing to do with Dembski’s thoroughgoing rejection of theistic evolution (the actual case, to be distinguished from Cosner’s inexplicable assertion to the opposite effect). That also means the faults remain the same for those ideas whatever the belief status of the promulgator of them.

“Informed creationists” should know that Dembski’s ideas and more generally those of “intelligent design” creationism didn’t appear as a novelty. No less a personage than Henry Morris of the Institute for Creation Research pointed that out fairly bluntly in “The Design Revelation”:

Our other hesitation to get on this bandwagon is their use of the same arguments and evidences we Biblical creationists have used for years, while simultaneously trying to distance themselves from us. Our adherence to Biblical literalism is ridiculed by evolutionists, and the ID advocates would be embarrassed to be tarred with the same brush.

Morris specifically (!!) noted concordance between ideas Dembski writes about and ideas Morris wrote about long before Dembski appeared on the scene.

Dembski uses the term “specified complexity” as the main criterion for recognizing design. This has essentially the same meaning as “organized complexity,” which is more meaningful and which I have often used myself. He refers to the Borel number (1 in 1050) as what he calls a “universal probability bound,” below which chance is precluded. He himself calculates the total conceivable number of specified events throughout cosmic history to be 10150 with one chance out of that number as being the limit of chance. In a book4 written a quarter of a century ago, I had estimated this number to be 10110, and had also referred to the Borel number for comparison. His treatment did add the term “universal probability bound” to the rhetoric.

The notion that “informed creationists” could rest easy, that “Why Intelligent Design Fails” wasn’t about anything they have an interest in, is complete balderdash. “Intellgent design” creationism is just “creation science” with more Wite-Out, just as “creation science” is simply “scientific creationism”, and both of those are “biblical creationism” with Wite-Out. Dembski is just among the latest to mouth and embellish improbability arguments for religious antievolution. As Morris noted, Dembski modified the rhetoric, not the argument.

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Antievolution &Law and Politics Wesley R. Elsberry on 17 Jan 2013

Final Decision Goes Against Coppedge

The Coppedge v. CalTech and JPL case is done, with a final decision handed down by Judge Hiroshige on Wednesday that confirms his preliminary ruling in favor of JPL. There are news reports here and here about the end of the case. Coppedge had sued, claiming wrongful termination, saying that JPL fired him from his job as a systems administrator because of his religious views. JPL defended itself by bringing to light Coppedge’s personality quirks and also his refusal to get up to speed on the new systems technology that JPL was switching over to. Coppedge was one of about 200 people laid off in a downsizing operation there.

Coppedge’s attorney isn’t letting the press opportunity get away. From the Star News article:

“David was the victim of religious discrimination because a handful of malicious co-workers hated his Christian views, as well as his interest in intelligent design, which they ignorantly perceived to be a religious concept,” Coppedge’s attorney William Becker said in a statement Thursday. “He was demoted and fired for simply being a Christian and someone who believes that nature can be scientifically explained by reference to designs found within it.”

We know that IDC advocates have to deny IDC’s religious character, but that doesn’t make people ignorant for not buying into the deception.

From the La Canada Online article:

Becker — who declined to comment beyond his written statement — contended that by “rubber-stamping” JPL’s proposed judgment, and not issuing a thorough written ruling of his own, it would work in Coppedge’s favor going forward.

“By failing to address the evidence personally, thoughtfully and carefully, [Hiroshige] left the door wide open,” said Becker. “By overruling our objections without giving a reason, the judge has all but handed us a victory on appeal.”

There is a cottage industry of lawyers looking to make their reputation in defending the religious right, and there is some pretty fierce competition for recognition. Becker appears to be participating in that game. As I understand it (and I am not a lawyer), the appeals court will have to take the case with all the findings of fact as they stand; their only review power concerns procedure and findings in law. Contrary to Becker’s statement, it is not clear at all that an appeals court will simply have to overturn the decision. Becker heads into the appeal with the facts as determined by the trial court being that JPL established cause for dismissal of Coppedge and appropriately answered claims of religious discrimination. That puts him behind the eight ball. The appeals court would have to agree that at least one of Becker’s arguments was cogent and revealed an actual difficulty in law rising to reversible error. This, it seems to me, is far from the high probability that Becker assigns to it.

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Antievolution &Computation &Education &Family &Florida &Law and Politics &Science Wesley R. Elsberry on 01 Jan 2013

A New Year

The Mayan apocalypse failed to appear, so I had a nice New Year’s day here in Florida. The temperature got into the 70s here, and not too breezy, so Diane and I worked on various things that all too recently would have been too hot to do comfortably. But here in the evening, I’m reflecting a bit over what has gone by, and thinking about things to be accomplished in the coming year.

I’m still looking to move ahead with various academic publications that have been in process for quite some time. One thing I was doing today was looking through files, which reminds me of just how much of a backlog there is. I did run across my script for my 2002 presentation at the World Skeptic’s Conference, which reminds me of another activity that I’ve deferred: putting my various presentations in video format and putting them online.

And the science education situation in Florida looks like it may get even more interesting in the future. Our new state education commissioner, Tony Bennett, was touted as a featured speaker for a “Creation Evidence Expo” in 2009, then cancelled when it made the news.

There’s the whole issue of data center consolidation for Florida’s state agencies, a process that is supposed to be complete within the next six years or so. The legislative mandate to do this came down some time ago, but it seems to me that the legislature was not properly informed of the downside of data center consolidation: you may save money on personnel, but a frighteningly large proportion of such projects fail outright. Failure of data systems for state agencies is a pretty bad potential downside to have. There are other issues with the implementation of the data centers. The state is aiming to put everything into two data centers, both of them physically located in the state capitol, Tallahassee. That makes it convenient for the state administration, certainly, but anyone who has looked at data bandwidth in high-speed Internet systems would notice that Tallahassee is not in the path of main trunk lines. Data flow, and low latency, is a critical part of client/server and n-tier architectures, and putting the central data repositories at the end of a thin pipe seems an odd choice. Part of the benefit of having multiple data centers is backup and failover capability; these, though, are rather less effective the closer the places are physically. Power outages are more likely to take down both centers when they are in the same geographic locale, and disasters are more likely to effect both, too. Having a data center in Tallahassee makes sense, but having the premier data center elsewhere (somewhere with much better bandwidth access, for one) would make much more sense. There’s lots more to talk about on this topic, and I hope to do some of that later.

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Antievolution &Law and Politics &Science Wesley R. Elsberry on 19 Nov 2012

Florida: Marco Rubio is Not A Scientist, Man

US Senator from Florida Marco Rubio gave an interview to GQ recently. Rubio was asked a question that Republican politicians simply hate to field: How old is the earth? (Hat tip: Talking Points Memo.)

Why is this a difficult question? It isn’t because the science hasn’t been disseminated; this is a part of any middle or high school earth science course. It isn’t because of any ambiguity in the science; an age of about 4.5 billion years has been current for years, with relatively small adjustments for precision. The reason it is a difficult question is that answering it without quibble will annoy the 40 to 45% of the US population who have consistently answered the Gallup poll question on this subject by saying that the earth is about 10,000 years old. That demographic also happens to provide Republican politicians with their consistent voting bloc, so annoying them is the absolutely last thing such a politician wants to do.

So let’s have a look at how Marco Rubio did respond when the question came up in the GQ interview:

GQ: How old do you think the Earth is?

Marco Rubio: I’m not a scientist, man. I can tell you what recorded history says, I can tell you what the Bible says, but I think that’s a dispute amongst theologians and I think it has nothing to do with the gross domestic product or economic growth of the United States. I think the age of the universe has zero to do with how our economy is going to grow. I’m not a scientist. I don’t think I’m qualified to answer a question like that. At the end of the day, I think there are multiple theories out there on how the universe was created and I think this is a country where people should have the opportunity to teach them all. I think parents should be able to teach their kids what their faith says, what science says. Whether the Earth was created in 7 days, or 7 actual eras, I’m not sure we’ll ever be able to answer that. It’s one of the great mysteries.

This is a troubling thing for a powerful politician to say. Its sole purpose can only be to give comfort to the biblical literalist voting bloc. Why is it troubling? Let’s go through the response piece by piece.

I’m not a scientist, man.

This is baloney, pure and simple. You don’t have to be a scientist to answer this question on Jeopardy, or in a GQ interview. It just requires that you actually know what the answer is.

I can tell you what recorded history says, I can tell you what the Bible says, but I think that’s a dispute amongst theologians and I think it has nothing to do with the gross domestic product or economic growth of the United States.

We do not know that Rubio can tell us what history, the Bible, or science says, because he never actually gave any of the different numbers that are used to answer the question. We’re just supposed to accept that Rubio could give those numbers, if he were so inclined. If he can’t do so in the low-pressure context of a GQ interview, though, I doubt that we will hear them from him elsewhere.

The “dispute among theologians” clause is also baloney. Yes, theologians do dispute the age of the earth, but they aren’t the only people who have weighed in on this topic. Rubio’s disclaimer that he isn’t a scientist does indicate that he is aware that science has an answer, but Rubio is here also implicitly disclaiming that science’s answer has any priority in the discussion.

Then there is Rubio’s assertion that the question is without consequences for our economy. This is, of course, hogwash. The manufactroversy over the age of the earth does have consequences. One of the most important consequences is the widespread distrust of scientists and the findings of science that are propagated when religious interpretations are promoted as putting scientific findings into question. Children who are taught that science is in a conspiracy are less likely to accept other things that science discovers and are less likely to themselves take up careers in science and technology. Our gross domestic product, our economic growth, and even our ability to field ever more sophisticated military technology is critically dependent on maintaining an edge in science and technology. How can disputing even the simplest and most basic scientific findings, like that of the age of the earth, possibly do anything but make it less likely that the USA will succeed in its race to keep pace or keep ahead of science progress in the rest of the world?

I think the age of the universe has zero to do with how our economy is going to grow.

The age of the universe has some pretty direct consequences for how scientists view critical cosmological constants. Those constants feed into equations of behavior of matter and energy in the here and now, so, yes, the age of the universe has a part in the operation of science and technology in the here and now, and, yes, it makes a difference for our economy, as explained just above.

I’m not a scientist. I don’t think I’m qualified to answer a question like that.

As noted before, you don’t have to be a scientist to know the answer. It seems that Rubio should not be a contestant on Jeff Foxworthy’s “Are You Smarter Than a Fifth-Grader?”

At the end of the day, I think there are multiple theories out there on how the universe was created and I think this is a country where people should have the opportunity to teach them all.

Senator Rubio should know that people can talk about whatever conjectures they want to. That’s what free speech is for. But Senator Rubio should also know that we teach curricula by subjects for a reason. Accountable science is the only thing that should be taught in science classes. For theological concepts in the public schools, there would need to be a course on philosophy or comparative religion. It has been a consistent feature of evolution versus creation dustups that biblical literalists have no interest in having their concepts compared and contrasted with those from other religions in an even-handed way in comparative religion courses; they want their unevidenced, unaccountable, untestable conjectures taught as if they were science, and as if they had the same scientific stature as accountable science.

I think parents should be able to teach their kids what their faith says, what science says.

They are able to do so, Senator Rubio. Parents can and do teach theological concepts at their churches, their religious private schools, and in homeschooling. They should, but often do not, teach the relevant science in religious private schools and homeschooling.

Whether the Earth was created in 7 days, or 7 actual eras, I’m not sure we’ll ever be able to answer that. It’s one of the great mysteries.

Ignorant people can’t answer it. People committed to obfuscation won’t answer it. But that doesn’t mean that there is not an answer. It is not a mystery. It is a matter of record in a well-developed, accessible scientific literature, with popular treatments readily available, and treatments in textbooks as well.

Rubio is replaying “Roman Catholic Church v. Galileo”. He should refer to that to see how obscurantists have fared. The RCC eventually came to the realization that the anti-scientific interpretation they had committed themselves to was not a necessity to faith. That realization is still in the future for many concerning the age of the earth, but they will eventually have to come to the same conclusion.

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Antievolution &Law and Politics Wesley R. Elsberry on 19 Mar 2012

Time Article on Coppedge v. JPL

Time’s web page has an article up by Jeffrey Kluger. Kluger is a lawyer and relates his reaction to the briefs filed in the case of David Coppedge v. Jet Propulsion Laboratory and Caltech.

Groups like the intelligent design community are not always free to pick their poster children, and it’s unfortunate for them that Coppedge is one of theirs. It’s true enough that employers and colleagues in a science-based workplace might be uncomfortable with the idea of a coworker who believes in intelligent design. But neither the Constitution nor employee-protection laws can regulate feelings — no more than they can or should regulate belief systems. They can, however, circumscribe behavior on both sides of that faith-divide. From the filings at least, JPL appears to have stayed well within those boundaries. Coppedge appears to have jumped the rails entirely.

Yes, even disinterested third parties get it now.

JPL’s brief discusses a lack of self-awareness on Coppedge’s part. The tone-deafness isn’t just Coppedge, though. It permeates the DI and the IDC community. They are so intent on instantiating their myths that they cannot seem to wrap their heads around the idea that one of their own could be in the wrong. You’d think with all those lawyers in their camp that they would be better at this than they are.

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Antievolution &Law and Politics Wesley R. Elsberry on 10 Mar 2012

ID and Science in the Dover Decision

I ran across a link to a blog post from 2007 by Jeff Shallit. One of the commenters there took exception to Jeff’s statement that the KvD case was primarily about religion, noting that a lot of the decision in the case discusses science. I was five years late to the party, but I felt that I needed to put my two cents in:

Sorry to have come across this so late. “analyysi” objects to the idea that the issue in Kitzmiller v. DASD was establishment of religion, saying that the decision discusses the topic of science a lot.

“analyysi” may be unfamiliar with the law here in the USA. The grounds for the complaint in KvD was indeed the establishment clause of the 1st amendment. The legal history will clarify why science is discussed at length in KvD. The Epperson v. Arkansas SCOTUS decision declared that one cannot prevent the teaching of science to privilege particular religious accounts, that science instruction has a valid secular purpose. Since Epperson, the religious antievolution movement has proceeded with a variety of dishonest efforts to characterize the same old arguments they usually make as science and to aid in this they offer new definitions of science. If they could convince a court that what they offer up for inclusion in a classroom is science, they would then have demonstrated a valid secular purpose in having it taught. And so in the KvD case you had the defense present lots of testimony from expert witnesses claiming that “intelligent design” was, indeed, scientific in character, at least as long as you allow them to also tweak the definition of science.

There are people who like to claim that Judge Jones could have completely ignored all the arguments made by the defense that ID was science and by the plaintiffs that, no, it wasn’t. I think the decision would have been weaker if it failed to address an issue that both parties considered central to the suit. The reason that a discussion of the nature of science and whether ID meets criteria to be recognized as science appears in the decision is that both parties made it an issue and prior precedent made whether something is science an issue for determining whether something has a valid secular purpose in being taught. The point in law being addressed is still establishment of religion while the particular instance of argument concerned ID’s lack of status as science.

Hope that clears that up for “analyysi”.

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Antievolution &Education &Florida Wesley R. Elsberry on 09 Feb 2012

Critical Analysis, Critically Analyzed

Dr. Eugenie Scott is giving a public talk Thursday, February 9, 2012, at the University of South Florida in Tampa. The topic is on the “critical analysis” legislative efforts that have popped up in Florida, and how these are part and parcel of the creationism movement.

The location is FAH 101 and the time for the talk is 7 PM. There’s a reception at 6:30 PM, so getting there early would be a good thing. I plan to be there.

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Antievolution &Law and Politics Wesley R. Elsberry on 16 Sep 2011

Educating Casey on Publishing

We’ve known for a long time that Casey Luskin has some very odd ideas about what constitutes a technical publication. Casey’s been good enough to document another deficiency of his in this respect for all to see, but no one is allowed to comment. (I wonder what happened to the Discovery Institute’s grand experiment in interactive commentary, anyway?)

Casey thinks I’m a hypocrite for criticizing Granville Sewell on the topic of self-plagiarism. As evidence, he notes that an essay co-authored by Jeff Shallit and I was published on the web and later in the journal Synthese.

The Case of Wesley Elsberry’s Self-Plagiarism

In 2003, Wesley Elsberry and Jeffrey Shallit co-published a paper, “Information Theory, Evolutionary Computation, and Dembski’s ‘Complex Specified Information,’” on the website TalkReason.org. (I wrote a response to the substance of their 2003 article here.)[*]

In 2011, Elsberry and Shallit co-published a paper in the journal Synthese titled “Information theory, evolutionary computation, and Dembski’s “complex specified information.’”

If you’ll notice, the titles of those two papers are identical. That’s not all that’s identical in the papers. A comparison performed by a colleague using the plagiarism-detection software SafeAssign shows that these two papers are ~94% matching.

(Note: The analysis used text files I had prepared using the original PDFs of the papers. For processing, I had to strip out some numbers and mathematical equations which did not translate well into the text files. Also, my colleague’s name has been redacted.)

Isn’t it just a bit hypocritical that Elsberry harps upon Sewell’s supposed mortal sin of “self-plagiarism” when Elsberry himself has taken previously published work and then republished it in academic journals?

Yeah, I’ll stipulate that the essay is mostly the same. But…

Casey, Casey, Casey… Republishing essentially the same thing multiple times in the technical literature is a bad thing. Getting something that’s been released on the web but not yet published in the technical literature is perfectly fine, with a caveat: the authors should make sure that the editors are aware of the prior release. This was done for the essay that was published in Synthese. (The editors also knew of a similar essay published in 2004′s “Why Intelligent Design Fails”, which Casey hasn’t mentioned yet.) This situation is not what “self-plagiarism” applies to. Nor is converting material from a dissertation into technical articles considered self-plagiarism, which is another process that I’m still working on. For another case in point, some time ago Reed Cartwright blogged a criticism of a paper. Another researcher saw that and invited Reed to contribute to a response letter in the technical literature. Does Reed’s previous web publication of the line of criticism used in the letter establish “self-plagiarism”? That’s a clear “No”. Scientists treat the technical literature as a separate source of knowledge from popular sources like blogs and portal sites. Repetition of material in lay outlets is essentially of no concern to the scientific endeavor. When it occurs in the technical literature, it is perceived as a pernicious problem.

But Granville Sewell doesn’t have a situation analogous to mine, where I converted a lay release into a publication in the technical literature. The Discovery Institute itself counts his shtick about the 2nd Law of Thermodynamics twice already in its list of “peer-reviewed” work on ID. I have no doubt that had AML actually followed through on publication of the essay, the DI would have happily counted it three times over in their list instead of just twice. The DI and its spokes-weasels can’t simultaneously claim that each re-publication counts separately and that self-plagiarism that repeats the same arguments in the technical literature is not happening. Of course, Casey knows how weak his position is, else he wouldn’t have added the following to his screed:

So I personally don’t care if Wesley Elsberry plagiarizes himself, and it doesn’t matter to me one bit if he resubmits material he’s already published to any publication he likes.

My point is simply this: it is hypocritical for Elsberry to attack Sewell for “self-plagiarism,” when Elsberry does the same thing. What Sewell (and Elsberry) have done isn’t a crime. Elsberry’s complaint is both baseless, and hypocritical.

Given that IDC advocates are so unproductive, Casey has to defend the line that if they can manage to sneak the same stuff around to multiple venues within the technical literature, there’s nothing wrong with that. Well, there is something wrong with that. Maybe it isn’t high on the lists of academic sin, but it certainly does goes some way to demonstrating intellectual dishonesty to game the technical literature.

[*] Casey, you did not write a response to the substance of our essay. That would have required reading comprehension on your part. What you wrote was an orgy of strawman gouging and delusional codswallop.

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Antievolution &Law and Politics Wesley R. Elsberry on 02 Sep 2011

Revising Assessment of Clayton Williams, Jr.

Back in 1990, Clayton Williams, Jr. was in the news a lot as he ran for governor in Texas. His campaign famously imploded over insensitive good-ol’-boy comments made to a weekend gathering of media. He was rich, but there didn’t seem to be much else to recommend him. I always thought it odd to go by the “Clayton Williams, Jr. Alumni Center” at the TAMU campus.

But it appears I need to seriously revise my assessment of Williams. The Austin-American Statesman reports that Williams had some extraordinarily good advice for Texas Governor Rick Perry (which Perry obviously and promptly ignored):

Williams, a wealthy Midland oil man, wrote to Perry as the State Board of Education was starting the debate over new science curriculum standards. He warned Perry to stop any effort by the board to include creationism or intelligent design in those standards.
“If Texas enters into a debate on the teaching of fundamental religious beliefs in public schools, it will tarnish our strong academic reputation, set our ability to attract top science and engineering talent to Texas back decades and severely impact our reputation as a national and global leader in energy, space, medicine and other high tech fields,” Williams wrote.
He continued: “Governor, this is a very important issue for Texas. I urge you to quell this issue quietly, firmly and permanently.”

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Antievolution &Law and Politics Wesley R. Elsberry on 22 Jul 2011

Casey Luskin Doesn’t Do It Again

Casey Luskin has an unenviable track record. Pretty much anytime Casey gets going, you can count on him to shoot himself in the foot someway, somehow.

Yesterday evening’s blog post by Casey is no exception. So if Casey has done it again, why would I give the title I have? Well, because of the way Casey shoots himself in the foot. You see, Casey so often goes off half-cocked because he doesn’t bother to figure out what the person he is critiquing actually said, and here we have Casey not listening to the primary source again, therefore Casey “doesn’t do it again”.

Casey’s target this time was Dr. Eugenie C. Scott of the National Center for Science Education. When Casey is up against a strawman he’s constructed, he pulls no punches, thus his post’s title of “Eugenie Scott Misrepresents the Law on Evolution Education”. What does Casey present as evidence of his claim of the title? Let’s let Casey go on a bit:

Uncommon Descent is reporting that National Center for Science Education (NCSE) executive director Eugenie Scott has stated in a talk: “You cannot teach evidence against evolution. There have been some court decisions that have talked about this including Kitzmiller, but there has not been a really clean test of this idea of teaching evidence against evolution.”

Uncommon Descent? Casey trusts them to get anything right? He shouldn’t, because they didn’t. The snippet Casey gives truncates even what UD managed to relate, and UD was missing a pretty critical word in there. Casey doesn’t note that Genie led into to quote by saying that she had an asterisk on this item, “this item” being text on a projected slide on screen. With the critical text restored, we have this instead: “OK, what else can you not do? I have a little asterisk here that you cannot teach evidence against evolution.” Genie goes on to explain the state of the law concerning this point. It has an asterisk because, as Genie ably explains, the law is not yet settled on this particular point. Casey apparently doesn’t know about this, and about the only way that could happen is if he started foaming at the mouth based only on the UD text and failed to actually listen to Genie’s video presentation. Here’s Casey blowing off a piece of his foot:

Isn’t that convenient for Eugenie Scott that she now claims that the courts have insulated evolution from any form of critique in public schools?

First, Casey fails to note the nuanced presentation Genie made concerning the point of law in question. Second, Casey places religious antievolution argumentation within “any form of critique”. A science classroom is not the appropriate venue for “any form of critique”. Only critiques that themselves have passed scientific muster are appropriate there, and that leaves out the old, moldy religious antievolution argumentation.

In any case, Dr. Scott is misrepresenting the law.

Oh, really? Why didn’t you listen to Genie’s video presentation, Casey? If you had, you would have had the opportunity to not misrepresent Genie.

The Kitzmiller v. Dover lawsuit dealt with the teaching of intelligent design, not teaching scientific evidence against evolution. And even if it had, Judge Jones would have been overruled by a much higher court–the U.S. Supreme Court–which has already ruled that it is legal to teach scientific critiques of prevailing scientific theories like evolution. As the U.S. Supreme Court stated in the 1987 case Edwards v. Aguillard, a case that directly dealt with the topic of origins-education in public schools:

We do not imply that a legislature could never require that scientific critiques of prevailing scientific theories be taught. . . . [T]eaching a variety of scientific theories about the origins of humankind to schoolchildren might be validly done with the clear secular intent of enhancing the effectiveness of science instruction.”

(Edwards v. Aguillard, 482 U.S. 578, 593-594 (1987).)

Eugenie can say whatever she wants but she cannot overrule the U.S. Supreme Court refuting her claims.

Genie claimed that the Kitzmiller decision discussed “evidence against evolution”, not that it provided the final word in law prohibiting presenting “evidence against evolution”. Remember the asterisk Genie mentioned? Oh, of course not, since Casey apparently didn’t bother to listen before making up stuff. Can we find Judge Jones doing what Genie said he did? Of course we can:

ID is at bottom premised upon a false dichotomy, namely, that to the extent evolutionary theory is discredited, ID is confirmed. (5:41 (Pennock)). This argument is not brought to this Court anew, and in fact, the same argument, termed “contrived dualism” in McLean, was employed by creationists in the 1980′s to support “creation science.” The court in McLean noted the “fallacious pedagogy of the two model approach” and that “[i]n efforts to establish ‘evidence’ in support of creation science, the defendants relied upon the same false premise as the two model approach . . . all evidence which criticized evolutionary theory was proof in support of creation science.” McLean, 529 F. Supp. at 1267, 1269. We do not find this false dichotomy any more availing to justify ID today than it was to justify creation science two decades ago.

ID proponents primarily argue for design through negative arguments against evolution, as illustrated by Professor Behe’s argument that “irreducibly complex” systems cannot be produced through Darwinian, or any natural, mechanisms. (5:38-41 (Pennock); 1:39, 2:15, 2:35-37, 3:96 (Miller); 16:72-73 (Padian); 10:148 (Forrest)). However, we believe that arguments against evolution are not arguments for design. Expert testimony revealed that just because scientists cannot explain today how biological systems evolved does not mean that they cannot, and will not, be able to explain them tomorrow. (2:36-37 (Miller)). As Dr. Padian aptly noted, “absence of evidence is not evidence of absence.” (17:45 (Padian)). To that end, expert testimony from Drs. Miller and Padian provided multiple examples where Pandas asserted that no natural explanations exist, and in some cases that none could exist, and yet natural explanations have been identified in the intervening years. It also bears mentioning that as Dr. Miller stated, just because scientists cannot explain every evolutionary detail does not undermine its validity as a scientific theory as no theory in science is fully understood. (3:102 (Miller)).

Casey’s strawman is taking a pounding, but he still hasn’t demonstrated Genie misrepresenting anything. Casey, though, is plainly misrepresenting Genie’s talk.

More Casey:

Actually, I’ve heard secondhand that Eugenie doesn’t privately believe it’s really illegal to critique evolution. I’m not going to name names, but I’ve spoken with legal scholars who have collaborated with Darwin lobbyists. They’ve told me that what Eugenie Scott fears more than anything is an army of teachers who WILL teach the scientific controversy over evolution because she knows that under current law, it’s legal to do that. There’s a reason why, as Eugenie puts it, “there has not been a really clean test of this idea of teaching evidence against evolution.” That’s because the NCSE and its allies in the Darwin lobby are afraid to file a lawsuit against a policy that requires or permits scientific critique of evolution because they know they will probably lose that case in court.

After all, if the Darwin lobby feels a policy is unconstitutional, they waste little time in filing lawsuits; it took less than two months for attorneys working with the ACLU to help parents file a lawsuit after the Dover Area School Board passed a policy requiring the teaching of ID.

Uh, no, Casey. In the video handily linked in the post at UD, you could have listened to Genie discussing the difference between a “permissive” act and one that is a demand that something wrong be done. For permissive acts, Genie explains that one cannot simply challenge the law on its own, one must instead wait for someone to use the permissive act to implement a curriculum that infringes rights under the Constitution, find out about the infringement, then find someone within the student body who has standing to challenge it and the willingness to challenge it, and all that is much harder than challenging a law that is wrong on its face. Start around 54:50 into the video to hear it. Of course, Casey should have heard it already, but he either didn’t bother … again … or he is lying about what Genie actually said.

But there have been multiple policies requiring or permitting scientific critique of evolution which have remained on the books for years without any lawsuit. For example:

Texas: Students must “analyze, evaluate and critique scientific explanations . . . including examining all sides of scientific evidence of those scientific explanations so as to encourage critical thinking,” and also “analyze and evaluate” core evolutionary claims, including “common ancestry,” “natural selection,” “mutation,” “sudden appearance,” the origin of the “complexity of the cell,” and the formation of “long complex molecules having information such as the DNA molecule for self-replicating life.”

Minnesota: “The student will be able to explain how scientific and technological innovations as well as new evidence can challenge portions of or entire accepted theories and models including . . . [the] theory of evolution . . . .”

New Mexico: Students will “critically analyze the data and observations supporting the conclusion that the species living on Earth today are related by descent from the ancestral one-celled organisms.”

Pennsylvania: “Critically evaluate the status of existing theories (e.g., germ theory of disease, wave theory of light, classification of subatomic particles, theory of evolution, epidemiology of AIDS).”

Missouri: “Identify and analyze current theories that are being questioned, and compare them to new theories that have emerged to challenge older ones (e.g., Theory of Evolution . . . ).”

Alabama: “[E]volution by natural selection is a controversial theory . . . . Instructional material associated with controversy should be approached with an open mind, studied carefully, and critically considered.”

South Carolina: “Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary theory.”

Louisiana: Louisiana public schools shall “create and foster an environment…that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied including, but not limited to, evolution, the origins of life, global warming, and human cloning.”

Mississippi: “No local school board, school superintendent or school principal shall prohibit a public school classroom teacher from discussing and answering questions from individual students on the origin of life.”

Kansas: “Regarding the scientific theory of biological evolution, the curriculum standards call for students to learn about the best evidence for modern evolutionary theory, but also to learn about areas where scientists are raising scientific criticisms of the theory.”

Ohio: “Describe how scientists continue to investigate and critically analyze aspects of evolutionary theory. (The intent of this benchmark does not mandate the teaching or testing of intelligent design.)”

Each of these policies are still in effect, except for the last two (Kansas’s policy was repealed in 2007 after conservatives lost a majority on the State Board of Education, and Ohio’s policy was repealed in 2006 after its State Board of Education underwent a similar change). The point is this: each of these policies are (or were) on the books for years without any legal challenge from the Darwin lobby. If Eugenie Scott is correct that it’s illegal to teach scientific critiques of Darwinian evolution, why is that?

Genie never said a word about it being illegal to “teach scientific critiques of Darwinian evolution”. What she was discussing was the tendency for religious antievolutionists to present their anti-scientific stuff and try to act as if they have something worth bringing up in a science class. Just because religious antievolutionists call something “evidence against evolution” doesn’t magically change it into something scientific. Scientific critiques have proven to be beyond the capacity of the religious antievolutionists. At best, they present a cargo cult version of critique, adorned with a poor appearance that is, nonetheless, at the limit of what their (mis)understanding of the subject can deliver.

Darwin lobbyists would love to ban scientific critique of evolution in public schools, so why haven’t they filed a lawsuit? It’s simple: They aren’t confident they would win because they know that current law does NOT make it illegal to teach scientific critiques of evolution in public schools.

Sorry, wrong again. Once a bad curriculum turns up and someone with standing to challenge it makes themselves known, then we’ll see how fast off the mark the legal challenge gets going. Casey is trying to equate legal challenges to facially-wrong laws and policies with challenging a law or policy without a facial defect, and that is clearly a misrepresentation of the law. Kinda ironic how Casey ends up doing the bad thing that he claims others do.

What’s most distressing here isn’t just that Eugenie Scott is misrepresenting the law. It’s that in her perfect world, she would apparently prefer that teaching scientific critique of evolution be illegal. What kind of society would we live in if Eugenie Scott and the Darwin lobby had their way, and it was illegal to ask hard questions about scientific theories? Not a good one.

Evolutionary science has a long and distinguished record of asking hard questions about scientific theories. There’s plenty of theories that have been discarded. Casey could read Peter Bowler’s “Evolution: The History of an Idea” to get that background. Or he can continue with not doing it (“it” being due diligence) again… and again.

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Antievolution &Law and Politics Wesley R. Elsberry on 19 Jul 2011

Where Did Jesus Say to Put a Nail in the Tire?

Two vehicles in a Bartram Hall (Zoology department building) parking area at the University of Florida were vandalized, apparently because they displayed “Darwin fish” on them. Besides messing up the Darwin fish, the vandal(s) put nails into tires.

Hat tip to Prof. Betty Smocovitis, whose hand appears in the linked video.

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Antievolution &Law and Politics &Philosophy Wesley R. Elsberry on 07 Jul 2011

Good Reason: A Ouija Board?

There’s an essay by Randal Rauser at “Christian Post” offering what’s termed a rebuttal to a criticism of an earlier essay. Rauser seems to be a run-of-the-mill “intelligent design” creationism (IDC) cheerleader.

Rauser defends Dembski’s ideas early on.

Joseph H. Axell posted a long rebuttal in the comment section of my article “Unintelligent arguments against intelligent design: A Primer”. There are a number of claims I’d like to challenge in the response. For instance Axell writes: “Dembski’s ‘explanatory filter’ for detecting design has been shown to be inadequate (false positives being but one problem)….” That’s like saying that an umbrella is inadequate because it is ineffectual in a windy rainstorm. Dembski’s explanatory filter, like an umbrella, can still be a useful tool even if it is not perfect. Is Newtonian physics tossed out as illegitimate because it doesn’t work at the quantum level?

Joseph Axell is right. Rauser, not so much. Newtonian physics is useful somewhere, which distinguishes it from Dembski’s “design inference” that has never had a fully-worked out example applied to any non-trivial problem. So much of Rauser’s original essay is based upon the conflation of ordinary and rarefied design inferences that it seems that he must not have read The advantages of theft over toil yet. The deficiencies of Dembski’s CSI are detailed in this essay. In the appendix, we introduced the concept of Specified Anti-Information and demonstrated that it formed an upper bound on Dembski’s CSI and disproved Dembski’s proposed “law of conservation of information”. A concerned reader wondered why we would bother repairing “specification”, and I replied:

The existence of a minimal program/input pair that results in a certain output indicates that there exists an effective method for production of the output. Since effective methods are something that are in common between intelligent agents and instances of natural computation, one cannot distinguish which of the two sorts of causation might have resulted in the output, but one can reject chance causation for the output. We haven’t so much repaired specification as we have pointed out a better alternative to it.

SAI identifies an effective method for the production of the output of interest. The result of a design inference is less specific, being simply the negation of currently known (and considered) regularity and chance. The further arguments Dembski gives to go from a design inference to intelligent agency are flawed. On both practical and theoretical grounds, SAI is a superior methodology to that of the design inference.

Back to Rauser:

Second, Axell writes: “So you concede that ID proponents have so far failed to achieve even the preliminary goal of establishing that a causal intelligence has been engaged in creating features of the natural world.”

First of all, whether they have or haven’t suceeded in establishing any particular instance of intelligent design is completely irrelevant to the claim that such a project is, in principle, viable. That’s the point! (And philosopher of science / atheist Bradley Monton makes it much better than I ever could.)

I need to reiterate that ordinary design is not the same as rarefied design, and here we have Rauser explicitly trying to ignore that point.

Now for the relation to the title. Here’s Rauser moving in for the rhetorical kill, at least apparently in his mind:

Finally I turn to the main point. Is it true that a person is obliged to provide “a detailed account of the nature of that intelligent cause and of the time, manner and place in which it has engaged with the natural world” if that intelligent cause is one with which we are not “familiar”?

Axell just invented that stipulation but provided no reasoning for it. He just asserts it. But not only is there no reason to accept it. There is also a good reason not to accept it. Consider the following illustration:

Axell’s friend tells him: “Joseph, I fear that there is some kind of intelligence in my house that doesn’t want me here.”

Axell, being a scientifically enlightened denizen of the twenty-first century is skeptical. “What evidence do you have?” he asks.

Axell’s friend then pulls out a ouija board and sets it on the coffee table. Immediately the planchette begins moving across the board and it spells “Get out of here.” Axell can clearly see that nobody is touching the planchette and immediately he picks it up, inspects it closely. There are no magnets: it is only a piece of wood. There are no wires. There is no draft. He puts it back down. Immediately the planchette begins to move again as it spells out “I said get out of here.”

Good reason? Excuse me, but all I see here is a pathetic fantasy, one in which Rauser ludicrously inserts his critic. There is no reason, and further, no reasoning, going on in Rauser’s response. It is, rather literally, the demon-haunted world being given as a basis for the legitimacy of IDC. We all knew that already, Randal.

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Antievolution &Law and Politics Wesley R. Elsberry on 26 May 2011

Magical Mathematical Metrics: Intelligent Design Hijinks

Over at the “Uncommon Descent” blog, poster “niwrad” decided to dispute claims of high sequence similarity between human and chimpanzee genomes. “niwrad” posted a statistical test of human/chimp genome comparisons in September, 2010, and a follow-up post this week comparing two human genomes using the metric from the earlier post. These were brought to my attention by “CeilingCat” on the AtBC forum. What the pair of posts demonstrates is another instance of “intelligent design” creationism advocates engaging in mathematical hijinks. The “niwrad” performance has more to do with the style of illusionists than it does actual mathematical and statistical practice. What one has to do with these kinds of things is look for the sleight of hand. Because “niwrad” now has a pair of articles based on the same “trick”, it becomes easier to point out exactly where the prestidigitation happened and why it is reasonable to infer that “niwrad” knows full well that it is a trick.

Let’s review some highlights from “niwrad”‘s initial post:

Supporters of the neo-Darwinian theory of evolution have a strong ideological motivation for minimizing the differences between humans and chimps, as they claim that these two species evolved from a common ancestor, as a result of random mutations filtered by natural selection. Now, I don’t personally believe that humans and chimps share a common ancestry, for a host of reasons that would take me too long to explain in this post. Nor do I attach much significance to the magnitude of the genetic differences between these two species, per se, because in my opinion, the fundamental differences between these creatures lie elsewhere. [...]

[...] The comparison I performed was completely different from those usually performed by geneticists, because was purely statistical in nature. In a sense, it could be described as an application of the well-known Monte Carlo method. [...]

[...] While there is only one possible method of comparing identity between strings of characters (the above pairwise comparison), there are many methods of comparing similarity. In other words, there are many measures of similarity, depending on the rules of pattern matching that we choose. [...]

Any final result for a complete statistical similarity test (especially if it is a unique number) is meaningful only if: 1) the distance function is mathematically defined; 2) the rules for pattern matching and the formulas for calculating the result are explained in detail; 3) it is clearly stated which parts of the input strings are being examined; 4) in the event that computer programs were used to perform the comparison, the source codes and algorithms are provided. My explanations below have the goal to meet the three first constraints. To satisfy the fourth condition, the source file of the Perl script used for the test is freely downloadable here.

[...]

For each pair of homologous chromosomes A and B, a PRNG (pseudo-random number generator) generates 10,000 uniformly distributed pseudo-random numbers which specify the offset, or starting point, of 10,000 30-base patterns that are contained in source chromosome A. The 30BPM test involves searching for all 10,000 of these DNA sub-strings of chromosome A in our target chromosome B. Now let F be the number of patterns located (at least once) in chromosome B. The 30BPM similarity is simply defined as F/100 (minimum value = 0%, maximum value = 100%). The absolute difference between 10,000 and F (minimum 0, maximum 10,000) is the 30BPM distance. [...] It can easily be seen that the 30BPM distance will be zero (30BPM similarity = 100%) if the two strings are identical. In an additional test which I performed on two random 100 million-base DNA strings, the 30-BPM distance was 10,000 (i.e. no patterns on A were located in B). [...]

The results obtained are statistically valid. The same test was previously run on a sampling of 1,000 random 30-base patterns and the percentages obtained were almost identical with those obtained in the final test, with 10,000 random 30-base patterns. When human and chimp genomes are compared, the X chromosome is the one showing the highest degree of 30BPM similarity (72.37%), while the Y chromosome shows the lowest degree of 30BPM similarity (30.29%). On average the overall 30BPM similarity, when all chromosomes are taken into consideration, is approximately 62%. Here we have the classic case of the glass which some people perceive as being half-full, while others perceive it as being half-empty. When compared to two random strings which are 0% similar, 62% is a very large value, so nobody would deny that human and chimp genomes are quite similar! On the other end, 62% is a very low value when compared to the more than 95% similarity percentages which are published by bioinformatics evolutionary researchers. Now, I realize that it may seem somewhat arbitrary to choose 30-base-long patterns, as I did in my test, and indeed it is arbitrary to some degree. However, if the two genomes were really 95% similar or more, as is commonly claimed, also a 30BPM statistical test should produce 95% results, and it does not.

The claim is, of course, poppycock. Anyone with the slightest pretension to an understanding of probability or statistics would recognize that the proposed “30BPM” metric is non-linear and not directly comparable to straight-up sequence similarity numbers. What’s truly ironic is that if “niwrad” were slightly more astute, he might have realized that his “30BPM” metric actually confirms the high sequence similarity results that he claims to have rebutted.

And that brings us to “niwrad”‘s second post, the one that aims to apply his “30BPM” metric to intra-specific genome comparisons, this time done as human-to-human comparison.

One reader suggested applying an identical test in order to compare two human genomes. That sounded like a very good idea to me, so I downloaded another human genome dataset from NCBI and performed a test.

[...]

Finally, the average number of pattern matches per chromosome, shown at the bottom of the table, was very different in the two cases: 9616 for human vs. human comparisons, but only 6173 for chimp vs. human comparisons. The average number of patterns without a match for human vs. human comparisons was (10000 – 9616) = 384, or in percentage terms, 384/10000 = 3.84%. The average number of patterns without a match in human vs. chimp comparisons was (10000 – 6173) = 3827, or in percentage terms, 3827/10000 = 38.27%, which is almost ten times greater.

So the bottom-line question is: if, as many evolutionists say, chimpanzee and human genomes are 99% identical, how “identical” are two human genomes?

“niwrad”‘s final question is interesting for the very salient reason that he did not provide an answer for it, even though his whole trick depends on the conceit that he has developed a better metric for quantifying sequence similarity than that used by actual geneticists. There is a reason why “niwrad” failed to answer, though, and that is that trying to claim that there is only 96.16% sequence similarity between two human genomes is manifestly risible. We know that the “trick” involved here is to confuse genetic sequence similarity with the “30BPM” metric, and that when faced with an obviously nonsensical outcome, “niwrad” punted rather than make explicit the full ridiculousness of his claim.

Above, I mentioned that “niwrad”‘s metric actually confirms high sequence similarity values. Here’s how that happens. First, one needs to realize that one doesn’t need “Monte Carlo” techniques to evaluate “niwrad”‘s “30BPM” metric: we can develop its properties with the usual probabilistic equations. The parameters of interest to us are the rate of change (C), the length of the analysis sequence (K), and the probability of a match (p). If we assume a uniform distribution of changes, then our model is simply the probability p that we do not observe a change within our analysis window K at a particular rate of change C. And that is simply expressed as

$p = (1 - C)^{K}$

Besides being simple, it is obviously also nonlinear. Notice that “niwrad” made quite a fuss about how his metric did what everyone expects for the endpoints of the distribution, where complete sequence identity happened and where complete randomness obtained. Notice that “niwrad” did not go anywhere near calibrating his metric against an expectation concerning a sequence with a known amount of similarity. There’s a reason for that, specifically, that one can’t blather about greater-than-expected dissimilarity if one actual calibrates the technique for known amounts of sequence similarity.

For example, what is the expected “30BPM” result when sequence similarity is actually 99%? We just solve the equation above to yield:

$p = (1 - 0.01)^{30} = 0.7397$

Similarly, when sequence similarity is 99.9%, the “30BPM” expected result is:

$p = (1 - 0.001)^{30} = 0.970431$

So, what about “niwrad”‘s “30BPM” numbers that he obtained empirically? We can convert those back into sequence similarity numbers, which are not the same thing as “30BPM” numbers at all. The equation is simply a rearrangement of the one above:

$C = 1 - \exp \left( \ln{p} \over K \right)$

“niwrad”‘s average “30BPM” value for the human-chimp comparison was 0.6173, giving a sequence similarity estimate of 0.984.

“niwrad”‘s average “30BPM” value for the human-human comparison was 0.9616, giving a sequence similarity estimate of 0.9987.

I should note that “niwrad”‘s “30BPM” metric becomes bloody useless at a point far short of completely random sequences. What point is that? I’m glad that you asked. Given a sample of 10,000 analysis windows, the threshold of usability would be when you have a 50% chance of seeing one match out of those 10,000 samples. That sets p at 0.00005 and gives C as 0.28116. That is, any sequence similarity of less than 0.719 will look exactly the same in “30BPM” terms and be ranked as having 0% similarity.

The “30BPM” metric deployment by “niwrad” does exactly what it was designed to do: exaggerate dissimilarity. It’s a magic trick intended to make an inconvenient fact disappear. It is a fundamentally dishonest exercise.

Update: Fixed the discrepancy between the symbols I defined and what I used in the equations. References to R should have been C, and now are.

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Antievolution &Law and Politics &Philosophy Wesley R. Elsberry on 14 May 2011

The Synthese Editors-in-Chief Respond to a Petition

The main petition regarding the Synthese disclaimer published in the January, 2011 issue was signed by 470 academics. It asked for a retraction of the disclaimer and additional information about the circumstances that led the Editors-in-Chief (EiC) to include it.

The EiC have now provided a response to the main petition. I received no direct notice of this response; I ran across a post about it on the “New Apps” blog. Prof. Matthen, author of that blog post, noted:

As far as I can tell, this is a website with one item only. This is clearly a tactic to make the response as obscure and invisible as it can be.

To give some more detail on the apparent desire for obscurity, let me note that the web page as provided has only one piece of content, an image that shows the text of a response letter. Posting an image means that the text of the response is not made easily accessible and it is not indexed by search engines as text. (Interestingly, the page was generated out of Microsoft Word and includes metadata identifying Prof. Hendricks as the author of the piece signed by all three EiC.)

As for the text not being out there recorded for search engines and posterity, that is easy enough to fix. Here it is. I’ve transcribed it from the image at the link above. Any misspellings are likely mine.

In response to the petition sent to Synthese:

We have considered the demands contained in this petition very seriously. We have implemented a moratorium on new special issues and we have begun planning appropriate changes to the editorial procedures of Synthese.

The petition asks for full disclosure of all legal threats. There have not been any communications received from Christian philosophers that constituted legal threats. There was a single email from a member of the public expressing the view that the entire special issue was ‘scurrilous and libelous’. We did not consider this email to be a legal threat. It is important to note that this email was received after our initial contacts with Professor Beckwith.

As far as meaningful legal action is concerned, we have received messages that we take seriously as legal threats but these have not come from Christian philosophers. Our ability to provide detailed responses in the blogs is constrained by these challenges.

Professor Beckwith requested an opportunity to respond to Professor Forrest’s paper. We agreed that this was a fair course of action. As regards the inclusion of our editorial statement and the email correspondence with Professor Forrest, it is true that there was considerable discussion between the editors of all aspects of the special issue. We took these matters very seriously and as is often the case with serious deliberation there were some oscillations prior to our reaching a conclusion. Eventually the editors arrived at a shared position, in consultation with the publisher, based on what we judged to be the offending language in two papers.

With respect to the claim that the guest editors were given assurances that no editorial statement would appear, it is true that the guest editors were privy to internal discussions between the editors-in-chief at earlier stages. We were unable to properly communicate later stages of our decision-making process to the guest editors.

We are ultimately responsible for what appears in the journal and we decided to publish the special issue without amendment to any of its papers. We wish to emphasize that our editorial statement should in no way be interpreted as an endorsement of ‘intelligent design’.

At this point, we have a duty to help create procedures to prevent situations of the sort we saw here from recurring. Thus, in consultation with the publisher, we have begun planning a transition to improved editorial procedures and improved oversight which will be in place in 2012. We will work closely with our board or area editors and our advisory board to make this happen.

Johan van Benthem

Vincent Hendricks

John Symons

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Antievolution &Law and Politics &Philosophy Wesley R. Elsberry on 07 May 2011

Questions, Francis Beckwith, and a Tangible Absence of Answers

Yes, this is yet another bit related to the Synthese flap. One of the issues still outstanding is whether the list of things the Editors-in-Chief have as misconduct includes notifying third-party complainers that the disclaimer was going into the print edition long before the print edition was available. They certainly failed to inform either the guest editors or the authors that any such thing was happening; those people (I’m one of them) had to wait for print copies to appear on their doorstep to find out.

One piece of hard data is that Francis Beckwith, one of the third-party complainers, submitted his “response” to Barbara Forrest on February 7th, 2011, and the response includes in it explicit reference to the disclaimer in the print edition of Synthese 178:2. This sets the latest date at which Francis Beckwith could have been apprised of the disclaimer’s print status. I didn’t hear about it until Glenn Branch emailed me on March 9th, 2011, to say that a disclaimer had been printed. But I’d like to know exactly how much lead time Beckwith had. The Synthese Editors-in-Chief haven’t been very forthcoming when asked questions about this affair, so that leaves Beckwith to be asked about the situation.

So I asked. This is my email to Beckwith’s published Baylor University email address, sent on April 25th, 2011:

I first received notice of the disclaimer in the Synthese special issue printed edition on 2011/03/09. Would you please tell me the date when the Editors-in-Chief informed you that the disclaimer would be printed in the special issue? I know that this had to be prior to 2011/02/07 given the date of submission of your response that refers to the disclaimer, but I would like to be more precise about this matter.

Thanks,
Wesley

That seems pretty straightforward. It isn’t like it is even going against Beckwith’s interests to be forthcoming about answering it. Now, why would I expect an answer, given the context that I’m a known critic of “intelligent design” creationism and its current — and past — advocates? We got on OK at the 2006 Greer-Heard Forum event, for one. Well, and maybe because Beckwith himself has implied as much. Consider his posts over a previous interaction with Barbara Forrest:

[...] Here’s the problem folks: Barbara Forrest is not concerned about truth or justice. For if she were, she would have, at some point in her “unmasking of me,” contacted me to verify or check certain facts. She also would have given a complete account of certain events that when presented in that way do not “prove” anything odd. [...]

[...] Forrest correctly notes that I am no longer a DI fellow. Does she tell you why? No. How come? She never asked me. Why didn’t she ask me? You’ll have to ask her that. But I suspect that if she can’t find by using Google, she doesn’t bother checking.

[...] But did she ask me for the letter? [...]

[...] But she would have known that if….and here’s the clincher…she had asked me. [...]

[...] But Barb would have known this, if…and here’s the clincher… she had just asked.

It sure makes it sound like Francis Beckwith is a open and forthright kind of guy, even when corresponding with trenchant critics.

Which makes it rather puzzling why I don’t have an answer in hand yet, not even one of the “mind your own business” sort.

Maybe Beckwith is snowed under in emails and the first one simply got lost in the shuffle. So I sent a second one on May 4th, 2011:

On 4/25/2011 4:02 AM, Wesley R. Elsberry wrote:
> I first received notice of the disclaimer in the Synthese special issue printed edition on 2011/03/09. Would you please tell me the date when the Editors-in-Chief informed you that the disclaimer would be printed in the special issue? I know that this had to be prior to 2011/02/07 given the date of submission of your response that refers to the disclaimer, but I would like to be more precise about this matter.
>
> Thanks,
> Wesley

http://www.whatswrongwiththeworld.net/2009/05/stove_award_competition_heats.html

you note multiple times that Barbara Forrest could have asked you to clarify particular points, with the implication being that she would have received an answer to her question, had she but posed it.

Let me remind you that the question I asked above is still pending an answer. I would appreciate a response.

Thanks,
Wesley

I thought about other possible excuses, like being on vacation. If so, Beckwith has kept up with his blogging while not checking his email, which doesn’t seem exceedingly likely.

Given the continued lack of response, I am having to re-assess the likelihood that Francis Beckwith doesn’t get asked questions by critics because such questions simply go unanswered.

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Antievolution &Philosophy Wesley R. Elsberry on 27 Apr 2011

Petition for Synthese to Retract the Disclaimer

Just in case there’s any academics who haven’t gotten the word yet, there’s a petition going requesting four things of the Synthese Editors-in-Chief, including the retraction of the vague disclaimer that tarnishes the whole special issue on “Evolution and its rvials”. If you aren’t on board with one or more of the items, that can be noted in a comment when you sign up.

There’s a separate petition requesting that Synthese give Barbara Forrest a chance to respond to Francis Beckwith.

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Antievolution &Law and Politics &Philosophy Wesley R. Elsberry on 25 Apr 2011

Religious Antievolutionists and Civility: Paul Giem

Professor Paul Giem, M.D., of Loma Linda University has a batch of video lectures online. One of them has him discussing the Synthese special issue on “Evolution and its rivals”, with special attention given to Prof. Barbara Forrest’s paper and Prof. Francis Beckwith’s response. Giem really, really doesn’t like Forrest’s article. At 28:49 into the video, Giem delivers a truly stunning bit of incivility:

This lady [referring to Prof. Forrest] needs some Haldol or something. She’s paranoid.

One of the possible defenses against a defamation of character claim concerns the credibility of the defamer. You can’t win a defamation case if the defaming party is not considered credible when stating the defamatory speech. The fact that Giem is an M.D. would work against him in any case concerning the figurative prescription of psychoactive pharmaceuticals. Giem would be held to a higher, not lower, standard in any such instance.

Civility for religious antievolutionists is a one-way street: they can dish out incivility, but they aren’t going to put up with taking any.

I’ve added this instance to the Invidious Comparisons thread, noting that it isn’t an invidious comparison per se.

Update: It’s been noted that I left out a bit of context. Loma Linda U. is a Seventh-Day Adventist institution, and the SDA is committed to a literal Fall of Adam. Giem expresses his young-earth creationist views online here.

Update 2: Following Tom English’s comment, I’ve added the next words from the video where Giem refers to Forrest as paranoid.

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Antievolution &Philosophy Wesley R. Elsberry on 23 Apr 2011

Some of My Best Friends Are Authors…

Over at New APPS, the comments continue. Jeff Shallit, my co-author on the paper in Synthese, weighed in with a brief comment:

Apparently Prof. Laudan thinks it is justified, if editors have a problem with a single paper or two in a special issue, to issue a general disclaimer that potentially impugns the integrity of every single author in the issue under question.

As a co-author of one of the papers in the special issue, I am shocked by both the behavior of the editors and the endorsement of that behavior by Prof. Laudan.

Jon Cogburn took issue with Jeff, expanding at length on his opinion that the EiC disclaimer in no way impugned the integrity of authors in the special issue.

And I replied to a part of Cogburn’s comment:

“I mean the editors did not say that some of the authors abused students or committed plagiarism or that some of the papers were unsound or not deserving of inclusion. They just said they thought some of the papers were too impolite and further clarified that this was an editorial oversight, one that clearly could have been addressed in the revising period of the papers.”

It seems ironic that tender sensitivities must be protected of everyone *except* the authors, who are apparently supposed to simply overlook anything other than outright accusations of high crimes and misdemeanors.

The distinction you make about editorial oversight might arguably be part of the just-released online response from the EiC (though I think it isn’t nearly clear enough to be described in just that way), but it isn’t part of the original disclaimer. I think arguing that it might be implicit in the original disclaimer would not be satisfactory.

We may need to agree to disagree about the scope of effect of the disclaimer on the authors.

Maybe you can touch upon another aspect of this. Given that the EiC felt it necessary to attach a disclaimer that might be applied severally to each and every paper in the volume (and the response in the IDC community shows that this is exactly what is happening, whether justifiable in each case or not), was it appropriate for the EiC to omit notice of their intended action and to deny each of the contributors the opportunity to withdraw their work? As Jeffrey’s co-author, I am in agreement that we would have withdrawn our paper if we had been informed of the nature of the disclaimer that would be published with our work. Maybe that would not have been your choice in the same situation, but I would hope that you would allow that opinions vary, especially with respect to protecting one’s own reputation. We were not notified of any of these concerns and intentions prior to the appearance of the printed issue. I, at least, see that as an irresponsible and unprofessional lapse on the part of the EiC at Synthese.

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Antievolution &Philosophy Wesley R. Elsberry on 22 Apr 2011

Mark Lance makes an excellent point over at “New APPS” concerning the Synthese disclaimer flap. I think it deserves more notice than simply being part of a longish stream of comments.

So, all in all, I’m still looking for anything that is remotely a candidate for exclusion on the grounds of unprofessional rudeness. Again, if the issue is that the arguments are bad, then the paper should have been rejected on those grounds. But if editors start saying that it is unprofessional to draw negative conclusions about people who are engaged in debates with obvious and dire political consequences, then we need to be aware that they are taking a stand in favor of philosophical irrelevancy.

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Antievolution &Philosophy Wesley R. Elsberry on 21 Apr 2011

The Synthese Editors-in-Chief Strike Back

The Synthese Editors-in-Chief issued a joint statement today about the disclaimer in the special issue. The closest approach to an apology was the following:

Of course, there are lessons to be learnt from what happened regarding our internal procedures, and Synthese will do that.

It’s a ‘Nothing to see here, move along’ sort of thing they have there, at least at first sight. On re-reading that, it can be taken not as an indication of a glimmer of recognition that their response might have gotten it wrong, but rather as an implication that they’ll be tightening down on guest editors.

I did my part to set them straight in the comments:

The EiCs also had a responsibility not to tarnish the reputations of contributors whose work did not have “unacceptable content”. Failure to provide authors with the opportunity to revise or withdraw before being smeared with such a disclaimer as employed by the EiCs is irresponsible and unprofessional, in my opinion. As a contributor to the issue in question, I can attest that at no time did the EiCs contact me with respect to that failed “internal resolution”. We would have opted for withdrawal rather than publish under the conditions that actually took place. At a minimum, the EiCs should have specifically identified the papers they believed to be problematic and not turn the issue into a philosophical “Where’s Waldo?” panel. That would have at least not tainted the rest by the vagueness that obtained in the actual disclaimer. I find the vague disclaimer to be itself highly discourteous, let alone the lack of notice provided to affected contributors whether guilty or innocent of the claimed lapses.

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