Bounded Science

Install Ubuntu Linux alongside OS X Tiger

2011-12-19T12:40:00.000-08:00

Setting up a Mac to boot either OS X (10.7.2) or Ubuntu Linux (11.10, 64-bit) is easy. (The complicated procedures that turn up in Web searches are outdated.)

Download the ISO image of the installation CD.

Use Disk Utility to burn the image into a CD.

Use Disk Utility to partition the hard drive.

[Plug in USB mouse/keyboard.]

Boot the “live” version of Ubuntu from CD.

[Connect to wireless router.]

Click the “install” icon on the desktop.

Warnings. Don’t do this to install more than one operating system alongside OS X. There’s a question as to whether installing Linux voids the Apple warranty, and I haven’t found a credible answer online. Ubuntu crashes when I tell it to hibernate.

If you use a wireless router, make sure, before starting, that you know its name, security method, and password (key). To get the first two, click on the wi-fi icon, select “Open Network Preferences…,” and click “Advanced…”

In step 3, select the hard drive in the pane on the left, click the “Partition” button, and then drag upward the bottom border of the picture of the disk partition. This will create an empty block at the bottom. If I recall correctly, the minimum size for an Ubuntu installation is 20 gigabytes. (Don’t be a disk miser. I had 440GB of disk space available, and didn’t think twice about allocating twice the minimum size.) Be sure to click “Apply” before exiting Disk Utility.

Step 4 is necessary if your keyboard and mouse/trackpad are wireless. Here is information on use of the Magic Trackpad with Ubuntu.

In step 5, hold down the c key while rebooting.

Step 6 is necessary if you use a wireless router for Internet access. Ubuntu will prompt you to provide what it needs to connect to the router.

After installation, hold down the option key while booting to run Ubuntu. The bootstrap procedure will indicate that you have a choice between OS X and Windows. Click on “Windows” to select Ubuntu.

Accidentally American: A better example

2011-10-04T17:00:00.000-07:00

Forgive a second ad for my other blog, Accidentally American. The post I previously linked to does not give a good idea of why I consider myself to be a citizen of the world, and an American by accident of birth. In “More American Lawlessness in the ‘War on Terror,’” I object to the Predator assassinations of criminal suspects.

“Intelligent design” creationists never define “intelligence”

2011-09-17T19:22:00.000-07:00

Long ago, commenting on a post at Uncommon Descent, I called on William Dembski to explain what intelligence is. He responded with his standard evasion — something like “If SETI is searching for intelligence, then intelligence must have scientific legitimacy.” Unsurprisingly, the “Expelled” expelled me from his site for raising a question he didn’t want to address again.

In ethology and scientific psychology, intelligence is a hypothetical construct, not a physically real entity. You can’t cut open an organism and find intelligence, any more than you can thirst. Studies that address intelligence always define it operationally. Just as the thirst of a rat may be defined as the number of hours it has been deprived of water, the intelligence of a person may be defined as his or her score on a paper-and-pencil test. Although we know that there is a physiological basis for thirst, thirst is itself hypothetical. Similarly, density of neural connections is correlated with performance on “intelligence” tests, but intelligence remains hypothetical.

I’ve spent a fair amount of time perusing SETI documents. The use of “intelligence” is entirely casual. Some in the project have preferred “civilization” to “intelligence.” SETI scientists explicitly assume that ET thinks as they do about how to contact a distant civilization. There’s implicitly an operational definition of intelligence in that.

In contrast, intelligence does some mighty heavy lifting in ID creationism. IDCists believe that non-material intelligence, and nothing else, creates special kinds of physical information. But what is intelligence? Ruling out matter and energy, we’re left apparently with information. So information creates information ex nihilo? That’s a nonstarter. Intelligence must have a special ontological status.

Gee, what could this entity that creates physical stuff out of nothing be? Do you suppose that IDCists believe that creative intelligence is spiritual in essence? There is, of course, no way for it to be anything but in the belief systems of almost all of them. Far be it from me to criticize personal belief in creative intelligence. But I have huge problems with people who pretend to have raised a challenge to evolutionary theory that is scientific, when they know that it is at core spiritual.

Impugning randomness convincingly?

2011-09-12T07:20:00.000-07:00

I haven’t finished reading “Impugning Randomness, Convincingly” [pdf], by Yuri Gurevich and Grant Olney Passmore, but I’ll go ahead and share its remarks about our old pal William A. Dembski.

The idea that specified events of small probability do not happen seems to be fun- damental to our human experience. And it has been much discussed, applied and misapplied. We don’t — and couldn’t — survey here the ocean of related literature. In §2 we gave already quite a number of references in support of Cournot’s principle. On the topic of misapplication of Cournot’s principle, let us now turn to the work of William Dembski. Dembski is an intelligent design theorist who has written at least two books, that are influential in creationist circles, on applications of “The Law of Small Probability” to proving intelligent design [TDI, NFL].
We single out Dembski because it is the only approach that we know which is, at least on the surface, similar to ours. Both approaches generalize Cournot’s principle and speak of independent specifications. And both approaches use the information complexity of an event as a basis to argue that it was implicitly specified. We discovered Dembski’s books rather late, when this paper was in an advanced stage, and our first impression, mostly from the introductory part of book [TDI], was that he ate our lunch so to speak. But then we realized how different the two approaches really were. And then we found good mathematical examinations of the fundamental flaws of Dembski’s work: [Wein] and [Bradley].
Our approach is much more narrow. In each of our scenarios, there is a par- ticular trial T with well defined set Ω_T of possible outcomes, a fixed family F of probability distributions — the innate probability distributions — on Ω_T , and a particular event — the focal event — of sufficiently small probability with respect to every innate probability distribution. The null conjecture is that the trial is governed by one of the innate probability distributions. Here events are subsets of Ω_T, the trial is supposed to be executed only once, and the focal event is supposed to be specified independently from the actual outcome. By impugning randomness we mean impugning the null hypothesis.
Dembski’s introductory examples look similar. In fact we borrowed one of his examples, about “the man with a golden arm” [i.e., Nicholas Caputo]. But Dembski applies his theory to vastly broader scenarios where an event may be e.g. the emergence of life. And he wants to impugn any chance whatsoever. That seems hopeless to us.
Consider the emergence of life case for example. What would the probabilistic trial be in that case? If one takes the creationist point of view then there is no probabilistic trial. Let’s take the mainstream scientific point of view, the one that Dembski intends to impugn. It is not clear at all what the trial is, when it starts and when it is finished, what the possible outcomes are, and what probability distributions need to be rejected.
The most liberal part of our approach is the definition of independent specification. But even in that aspect, our approach is super narrow comparative to Dembski’s.There are other issues with Dembski’s work; see [Wein, Bradley].

I’ve changed the reference numbers to tags that are meaningful to many of you. TDI and NFL are Dembski’s The Design Inference and No Free Lunch, respectively. James Bradley wrote “Why Dembski’s Design Inference Doesn’t Work” [pdf] for BioLogos, and Richard Wein wrote Not a Free Lunch But a Box of Chocolates for TalkOrigins.

Accidentally American

2011-09-10T18:30:00.000-07:00

I’ve started a new blog, Accidentally American, for posts that don’t have anything to do with creationism. A number of you who stop by are not American, and you might find my perspective interesting at times. I consider myself American by accident of birth, and I see much of what goes on around me as insane.

Much of the world is concerned with America’s inability to manage its debt. So I’ll point you to my new post, Exploding Myths About Disparity in Taxation. Progressive federal taxation is largely offset by regressive state and city taxation. When all taxes are taken into account, effective tax rates do not vary much for taxpayers in the top 40 percent of income. The wealthy have a very sweet deal in America.

I was wrong about the Ninth Circuit opinion

2011-09-04T15:32:00.000-07:00

In my last post, I exhibited a knee-jerk response to language in an opinion of the Ninth Circuit Court of Appeals. I’ve edited it to indicate my errors. I’m not terribly embarrassed to have forgotten Edwards v. Aguillard, and failed to recognize it as the source of various creationist watchwords. However, I have no excuse for failing to see that the court addressed the behavior of a history, not science, teacher.

I apologize for the errors, and thank Glenn Branch and Robert Luhn of the NCSE for gently setting me straight.

Scary Ninth Circuit opinion [NOT]

2011-08-30T16:58:00.000-07:00

[I was wrong. I’ve edited to indicate my errors.]

The National Center for Science Education is celebrating the vindication of James Corbett, a California high-school teacher who characterized creationism as “[religious,] superstitious nonsense.” A federal district court found that he had engaged in “improper disapproval of religion in violation of the Establishment Clause.” But a three-judge panel of the Ninth Circuit Court of Appeals has ~~reversed~~ [vacated this part of] the decision.

[Mindful that there has never been any prior reported case holding that a teacher violated the Constitution under comparable circumstances, we affirm the district court’s conclusion that the teacher is entitled to qualified immunity. Because it is readily apparent that the law was not clearly established at the time of the events in question, and because we may resolve the appeal on that basis alone, we decline to pass upon the constitutionality of the teacher’s challenged statements.]

So what’s scary about this? ~~The panel has taken language from the creationist legislation of several states, and inserted it into federal case law~~:

But teachers must also be given leeway to challenge students to foster critical thinking skills and develop their analytical abilities. This balance is hard to achieve, and we must be careful not to curb intellectual freedom by imposing dogmatic restrictions that chill teachers from adopting the pedagogical methods they believe are most effective.

~~This is a very bad turn of affairs~~. [Glenn Branch, Deputy Director of the NCSE, gently explained to me that there’s similar language in Edwards v. Aguillard (1987), and that the creationists have been trying to exploit it.] However, the offended student reportedly is appealing the decision. If the full court accepts amicus briefs, then I would recommend that the NCSE and/or some legal organization submit a brief suggesting more appropriate language. [What I had in mind here is that critical thinking is more heavily constrained in science than in all other disciplines, with the exception of math. However, the courts ruled on Corbett’s behavior in a college-level history class. There’s no reason for them to comment on science education, or for any science organization to get involved.]

Potted corpses impassively reciting old rants

2011-07-25T18:35:00.000-07:00

It's seemed for some time that the nonstop propaganda at Uncommon Descent was like something I'd seen before. I've finally put my finger on it.

By the way, this is a brilliant performance of one of the finest plays of the 20th Century. But you're probably not going to follow it well unless you read the script.

Tolstoy on church “hypnotism”

2011-06-29T23:57:00.000-07:00

In his last book, The Kingdom of God is Within You (1894), Leo Tolstoy insists that Jesus taught nonviolence, and argues that only nonviolent responses to evil can remedy evil. Gandhi said that the book was one of the three most important influences on his life.

More germane to this blog is Tolstoy’s description of how churches manipulate “so-called believers.” In the following excerpt, I’ve added emphasis to a passage that speaks volumes to what we see constantly in the ID movement — conflicted, frightened Christians foisting on children the lie that there is no conflict between Biblical literalism and scientific realism.

A man of the present day need only buy a Gospel for three copecks and read through the plain words, admitting of no misinterpretation, that Christ said to the Samaritan woman "that the Father seeketh not worshipers at Jerusalem, nor in this mountain nor in that, but worshipers in spirit and in truth," or the saying that "the Christian must not pray like the heathen, nor for show, but secretly, that is, in his closet," or that Christ's follower must call no man master or father — he need only read these words to be thoroughly convinced that the Church pastors, who call themselves teachers in opposition to Christ's precept, and dispute among themselves, constitute no kind of authority, and that what the Churchmen teach us is not Christianity. Less even than that is necessary. Even if a man nowadays did continue to believe in miracles and did not read the Gospel, mere association with people of different forms of religion and faith, which happens so easily in these days, compels him to doubt of the truth of his own faith. It was all very well when a man did not see men of any other form of religion than his own; he believed that his form of religion was the one true one. But a thinking man has only to come into contact — as constantly happens in these days — with people, equally good and bad, of different denominations, who condemn each other’s beliefs, to doubt of the truth of the belief he professes himself. In these days only a man who is absolutely ignorant or absolutely indifferent to the vital questions with which religion deals, can remain in the faith of the Church.

What deceptions and what strenuous efforts the churches must employ to continue, in spite of all these tendencies subversive of the faith, to build churches, to perform masses, to preach, to teach, to convert, and, most of all, to receive for it all immense emoluments, as do all these priests, pastors, incumbents, superintendents, abbots, archdeacons, bishops, and archbishops. They need special supernatural efforts. And the churches do, with ever-increasing intensity and zeal, make such efforts. With us in Russia, besides other means, they employ, simple brute force, as there the temporal power is willing to obey the Church. Men who refuse an external assent to the faith, and say so openly, are either directly punished or deprived of their rights; men who strictly keep the external forms of religion are rewarded and given privileges.

That is how the Orthodox clergy proceed; but indeed all churches without exception avail themselves of every means for the purpose — one of the most important of which is what is now called hypnotism.

Every art, from architecture to poetry, is brought into requisition to work its effect on men's souls and to reduce them to a state of stupefaction, and this effect is constantly produced. This use of hypnotizing influence on men to bring them to a state of stupefaction is especially apparent in the proceedings of the Salvation Army, who employ new practices to which we are unaccustomed: trumpets, drums, songs, flags, costumes, marching, dancing, tears, and dramatic performances.

But this only displeases us because these are new practices. Were not the old practices in churches essentially the same, with their special lighting, gold, splendor, candles, choirs, organ, bells, vestments, intoning, etc.?

But however powerful this hypnotic influence may be, it is not the chief nor the most pernicious activity of the Church. The chief and most pernicious work of the Church is that which is directed to the deception of children — these very children of whom Christ said: "Woe to him that offendeth one of these little ones." From the very first awakening of the consciousness of the child they begin to deceive him, to instill into him with the utmost solemnity what they do not themselves believe in, and they continue to instill it into him till the deception has by habit grown into the child's nature. They studiously deceive the child on the most important subject in life, and when the deception has so grown into his life that it would be difficult to uproot it, then they reveal to him the whole world of science and reality, which cannot by any means be reconciled with the beliefs that have been instilled into him, leaving it to him to find his way as best he can out of these contradictions.

If one set oneself the task of trying to confuse a man so that he could not think clearly nor free himself from the perplexity of two opposing theories of life which had been instilled into him from childhood, one could not invent any means more effectual than the treatment of every young man educated in our so-called Christian society.

It is terrible to think what the churches do to men. But if one imagines oneself in the position of the men who constitute the Church, we see they could not act differently. The churches are placed in a dilemma: the Sermon on the Mount or the Nicene Creed—the one excludes the other. If a man sincerely believes in the Sermon on the Mount, the Nicene Creed must inevitably lose all meaning and significance for him, and the Church and its representatives together with it. If a man believes in the Nicene Creed, that is, in the Church, that is, in those who call themselves its representatives, the Sermon on the Mount becomes superfluous for him. And therefore the churches cannot but make every possible effort to obscure the meaning of the Sermon on the Mount, and to attract men to themselves. It is only due to the intense zeal of the churches in this direction that the influence of the churches has lasted hitherto.

Let the Church stop its work of hypnotizing the masses, and deceiving children even for the briefest interval of time, and men would begin to understand Christ's teaching. But this understanding will be the end of the churches and all their influence. And therefore the churches will not for an instant relax their zeal in the business of hypnotizing grown-up people and deceiving children. This, then, is the work of the churches: to instill a false interpretation of Christ's teaching into men, and to prevent a true interpretation of it for the majority of so-called believers.

The “intelligent design” creationists are hardly focused on the Sermon on the Mount.

The worst in statistical reasoning, from Climategate scientist Phil Jones

2011-06-13T13:14:00.000-07:00

According to the BBC News, Phil Jones declared global warming since 1995 statistically insignificant last year, and statistically significant this year. Why? Last year, the probability that “ordinary” variation of global temperatures yielded warming as extreme as that observed was .1, and this year it is .05.

I clearly recall the day my statistics professor railed against categorical response to the 95% confidence level as “statistically significant.” It is hard to believe that Jones, who is younger than I, did not hear something similar in school. Suppose that when next year’s data are processed, the confidence level goes down to 94%. Will Jones revert to saying that the observed warming is not statistically significant?

It is impossible to decide absolutely whether human activity is causing global warming. Scientists in general, and climate scientists in particular, should explain that their research leads to degrees of belief.

Furthermore, what policymakers need is Bayesian processing of climate data, not the Fisherian silliness of Phil Jones. That is, the possibility of anthropogenic global warming calls for sophisticated risk management rather than a true-false decision. We are gambling on the future of the world, and the only reasonable response, given present information, is to hedge our bets.

[Thanks to jivlain for his comment. I'm presently having to use an outdated browser, and cannot enter a comment of my own. So I'll respond here. From the infamous BBC Q&A with Jones in February 2010:

B - Do you agree that from 1995 to the present there has been no statistically-significant global warming

Yes, but only just. I also calculated the trend for the period 1995 to 2009. This trend (0.12C per decade) is positive, but not significant at the 95% significance level. The positive trend is quite close to the significance level. Achieving statistical significance in scientific terms is much more likely for longer periods, and much less likely for shorter periods.

Jones should have known to respond that the trend was statistically significant at the p% confidence level.]

[Bob O'H, it's great to see a statistician call for such a straightforward interpretation. But you're apparently looking at different numbers than Jones is:

C - Do you agree that from January 2002 to the present there has been statistically significant global cooling?

No. This period is even shorter than 1995-2009. The trend this time is negative (-0.12C per decade), but this trend is not statistically significant.

I'll hazard a guess that your data have been adjusted to take radiative forcing into account — as they should be. Total solar irradiance (TSI, plotted here) contributes substantially to global temperatures, and cycles up and down with a quasi-period of about 11 years. The most recent downswing in TSI began in 2002, was more pronounced than usual, and lasted longer than usual (until 2009). The BBC question is utterly ill-posed, because it calls for analysis of cherry-picked data.]

Revised ID thesis describes plagiarism in originally accepted version

2011-06-07T22:11:00.000-07:00

The response at Baylor University to my report of plagiarism has been extraordinary, though not entirely perfect. The thesis of Winston Ewert, Studies of Active Information in Search, now includes a preamble that, while somewhat evasive, describes what was wrong with the originally accepted version.

Before going into the details, I want to emphasize again that I am not reveling in the academic misconduct of a young master’s student. The villains are the members of the thesis committee, who have not, to my knowledge, had to acknowledge their misconduct publicly. I hope that Baylor administrators censured Gregory J. Hamerly, the assistant professor of computer science who served as thesis chairperson despite the fact that Robert J. Marks II directed and contributed to the research, for negligence in oversight. And I hope that they put Marks on a short leash for approving plagiarism of his own publications with William A. Dembski. In particular, Marks, who is an electrical engineer, should not be allowed to direct the research of graduate students in computer science.

Here is the preamble, with my responses interspersed.

This thesis is a replacement of a previous version. The replacement is necessary because of a number of serious challenges. Some of the contents of the first version were taken from previously published work of the author. As was done in the original version, copyright notices are included at the end of the thesis. Although using previously published work in a thesis is common practice, the document itself did not make clear that this was the case.

The replacement is necessary because of defects, not challenges. You did not indicate in any way that William A. Dembski was a coauthor of text you copied into your thesis. You excluded his name from the copyright release forms, and those forms are unchanged in the revised thesis. Are you showing us the forms you actually submitted to the IEEE Press?

Additionally, and more seriously, the introduction was constructed by drawing passages from previous papers including some which the author of thesis was not a coauthor. This was clearly an inappropriate usage.

You copied more than half of the introduction from publications by William A. Dembski and Robert J. Marks II.

The work for this thesis was done in collaboration with others in Dr. Marks’ research group. All of content in the thesis including the sections from the introduction were produced by members of the research group including Dr. Marks who was a member of the thesis committee.

Dembski and Marks wrote the papers you plagiarized before you joined the group. You contributed in no way to that effort. And you seem not to understand that it is scandalous for a thesis committee member to condone plagiarism of his own work. As for the chapters which you generated collaboratively, I doubt highly that you can explain all of the math (e.g., Markov chain analyses). What sort of thesis defense is it in which the committee agrees not to question the candidate on certain parts of the document?

Within the group, we use tools such as LaTeX and Dropbox which make collaboration very easy. Unfortunately this also made it easy to reuse existing text in an inappropriate manner. This is not an attempt to excuse the content of the original thesis, but rather to explain how the mistake was made.

The technology is a red herring. You did not collaborate in the preparation of the papers by Dembski and Marks, so why should you possess the LaTeX source for them? People have mentioned on this blog that they stapled together photocopies or reprints of published papers to generate theses. Obviously, complete lists of authors appeared in their documents. You went out of your way to avoid mention of Dembski, and continue to do so even here.

In future all members of the lab, especially the author of this thesis, will be careful about the reuse of collaborative work.

It is hardly your place to offer a guarantee that Marks will behave appropriately in the future. He should step forward and acknowledge his own misconduct.

This version of the thesis remedies these problems. The introduction has been rewritten by the author and those sections drawn from previous work of the author have been appropriately cited in the thesis body.

The revisions are indeed appropriate.

Grumblings about the preamble aside, I have to say that it is remarkable to see any admission of wrongdoing at all. My hat is off to Baylor for dealing with the thesis as judiciously as it has. I can only hope that my report to EthicsPoint also triggered an investigation of Marks.

Plagiarism at a glance

2011-03-23T01:26:00.000-07:00

I reported yesterday on a thesis, Studies of Active Information in Search, I retrieved from the BEARdocs archive at Baylor. If the document is authentic, then Distinguished Professor of Engineering Robert J. Marks II, a.k.a. the "Charles Darwin" of intelligent design, approved extensive plagiarism of publications he coauthored with William A. Dembski.

Here are images, purposefully low in resolution, of pages 1-7 of the 8-page introduction. Passages plagiarizing papers by Dembski and Marks are highlighted in color. Those copied from papers by the thesis author (with Dembski and Marks as coauthors) are "lowlighted" in gray. The gray areas are hard to see, and some of you have suggested that they should be white. But I emphasize that the bibliography does not include the papers, and that Dembski's name is omitted from the copyright release forms in the appendix. I call shenanigans.

There are also comment boxes in my annotation of the document. They indicate the sources of the copied passages, and I include that content here to cover myself legally. Most of you will want simply to glance at the images, and gauge the scale of the plagiarism.

YELLOW: I give a reference list below.
PURPLE: Begin at first sentence of [1].
YELLOW: Begin at paragraph 2 of [1]. A period has been changed to a colon, and "no free lunch theorem" has been capitalized.

GRAY: First sentence of [4].
RED: Begin at third complete paragraph of second page of [1].

GRAY: Points (a-c) here come from the third sentence of [3].
GREEN: Begin about midway in the second column of [1], with "can" changed to "often" in the last sentence.

BLUE: Begins with the third sentence on the second page of [1].
PURPLE: Skip 3 sentences, arriving about midway in the first column of second page of [1].
GRAY: First 3 paragraphs of [4], with one awkward sentence rewritten. This gray passage runs to the end of the thesis section.

PURPLE: Opening of Sect. II-A of [2], with a period changed to colon, and with a reference deleted. Note that the copied period in the equation should have been changed to a comma.

YELLOW: The fourth sentence in column 2 of [2], with one reference removed. Note that the period at the end of the equation is copied, and that the "bits" should have been inserted ahead of the period.
RED: Skip two sentences following Equation (3) [(1.3) here] in [2].
GREEN: Begin with second sentence, third paragraph of Sect. II of [2]. The colon prior to the equation is changed to period here.
BLUE: Begin with third sentence following Equation (2) in Section II-A of [2], eliminating initial clause, and changing "for" to "of."
PURPLE: Begin with last paragraph of first column of page 2 [2].
YELLOW: Begin with the second sentence of footnote 3 of [2].

RED: Begin with second sentence, column 2, second page of [2]. Note that exogenous information is given above (1.2), so the copy here of the definition in [2] is redundant.
GREEN: Begin with last sentence of first full paragraph in column 2 of page 2 of [2], and move footnote 4 into the body.
BLUE: [blue highlighting, yellow box by mistake] Second full paragraph in second column, second page of [2]. Here "dB" is changed to "decibels," and "instead" is changed to "rather."

Conclusion

It seems to me that 4+ pages are highlighted. In other words, at least half of the introduction is copied from papers by Dembski and Marks. If Marks in fact approved this, then he has suffered a serious lapse in ethics.

References

[1] William A. Dembski and Robert J. Marks II "Conservation of Information in Search: Measuring the Cost of Success" IEEE Transactions on Systems, Man and Cybernetics A, Systems & Humans, vol.5, #5, September 2009, pp.1051-1061, http://evoinfo.org/publications/cost-of-success-in-search/

[2] William A. Dembski and Robert J. Marks II, "Bernoulli's Principle of Insufficient Reason and Conservation of Information in Computer Search," Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics. San Antonio, TX, USA - October 2009, pp. 2647-2652, http://evoinfo.org/publications/bernoullis-principle-of-insufficient-reason/

[3] Winston Ewert, William A. Dembski and Robert J. Marks II, "Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism," Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics. San Antonio, TX, USA - October 2009, pp. 3047-3053, http://evoinfo.org/publications/evolutionary-synthesis-of-nand-logic-avida/

[4] Winston Ewert, George Montañez, William A. Dembski, Robert J. Marks II, "Efficient Per Query Information Extraction from a Hamming Oracle," Proceedings of the 42nd Meeting of the Southeastern Symposium on System Theory, IEEE, University of Texas at Tyler, March 7-9, 2010, pp.290-297, http://evoinfo.org/publications/efficient-per-query-information-extraction-from-a-hamming-oracle/

“Charles Darwin” of intelligent design condones plagiarism at Baylor?

2011-03-22T02:50:00.000-07:00

Last year, “intelligent design” creationist William A. Dembski, Research Professor of Philosophy at Southwestern Baptist Theological Seminary, said of one of his coauthors at Baylor University, “Winston Ewert — With pro-ID graduate students like this, Darwinian profs don't stand a chance.” Well, Ewert evidently went on to defend a master’s thesis, Studies of Active Information in Search, in the Fall semester of 2010. I downloaded it from Baylor’s document archive, and had only to read to the bottom of the first page to discover plagiarism.*

Almost half of the first chapter is copied, without citation or sign of quotation, from

William A. Dembski and Robert J. Marks II, Conservation of Information in Search: Measuring the Cost of Success, 2009
William A. Dembski and Robert J. Marks II, Bernoulli's Principle of Insufficient Reason and Conservation of Information in Computer Search, 2009

[Edit 3/24: Actually, at least half is copied, as you easily can see in my markup of the text.] According to the signature page, Marks, who holds the rank of Distinguished Professor of Engineering at Baylor, served on the thesis committee. Yes, I am referring to one of the twenty most influential Christian scholars — the “Charles Darwin” of intelligent design.

Most of the thesis is copied from two published conference papers, and from an article that had been accepted for publication:

Winston Ewert, William A. Dembski and Robert J. Marks II, Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism, 2009
Winston Ewert, George Montañez, William A. Dembski, Robert J. Marks II, Efficient Per Query Information Extraction from a Hamming Oracle, 2010
George Montañez, Winston Ewert, William A. Dembski, Robert J. Marks II, A Vivisection of the ev Computer Organism: Identifying Sources of Active Information, accepted August 27, 2010; published December 15, 2010

Not only are these papers not cited, but they also are not listed in the bibliography.

Chapter 2 is essentially (2), beginning with the fourth paragraph, and skipping Section II. (The first three paragraphs are in Chapter 1.) It corrects errors that I identified here at Bounded Science. More than half of the paper is mathematical analysis that is beyond most master’s students in computer science. I would guess that Ewert’s contributions were programming, data gathering and visualization, and paper preparation. If I am right, then it is inappropriate for the thesis to give the impression that Ewert did the math.

Chapter 4 is (1) with Section I eliminated, and with several small changes. It haplessly ends with “we have not explored in this paper.” (For those of you who are not scholars, I should explain that theses are not referred to as papers.)

Chapter 3 is not so simply related to its source, presumably because its author is not the lead author of (2). Almost all of its text is present in the article. But the chapter reorders passages of the article. Most notably, it moves empirical results ahead of theoretical analysis, and introduces awkward forward references to the analysis. Also, there are occasional replacements of words with synonyms, as well as deletions and insertions of short phrases. All in all, the chapter looks like the work of someone who was trying, pathetically, to make copy-and-paste pass for original writing. (Seventeen years of teaching experience are talking here.)

Chapter 5 is a double-spaced, one-page conclusion.

Some universities limit how much of a thesis may come from published work, but I can find no indication that Baylor is one of them. Yet the thesis does not state that the chapters are excerpted from published and forthcoming papers. Instead there is an appendix entitled ”Copyrights” that gives, without explanation, copyright release forms bearing the titles, but not the complete lists of authors (required by the publisher), of (1) and (2). Guess which author is missing? Yes, that would be William A. Dembski. I suspect that the forms on file with the publisher bear his name.

To get a hint that Dembski deserves credit for contributions to the thesis, you have to click the Show full item record button of the entry for the thesis in the BEARdocs system, and then figure out the meaning of the identifier.citation fields providing full citations of (1) and (2). In my opinion, burying this information in the metadata of the document retrieval system is unethical.

The copyright release forms indicate that the authors retain the right to use the published material in derivative works, “provided that the source and any IEEE [Institute of Electrical and Electronic Engineers] copyright notice are indicated.” So the thesis perhaps does not violate the copyrights of the publisher. But there is much more to academic integrity than not breaking the law. When you draw on a source, you cite it, even if you are one of the authors. When you copy from a source, you indicate clearly what you are copying. It would have been so easy to end the introduction of the thesis with an indication that Chapter 2 is excerpted, with emendations, from (2), and that Chapter 4 is excerpted from (1). As for Chapter 3, the author should have written it from scratch, and should have cited (3) in all places where the work was not his own.

Now, should you believe that self-citation and self-quotation are optional in scholarly writing, go back to the beginning of this post. It is unethical for a thesis committee member to condone plagiarism, even if it is plagiarism of his own work. The unacknowledged use of (3) in the thesis is egregious. It is clearly wrong to draw on the work of others, and not indicate that you are doing so. (For those of you who are not scholars, I should mention that references to forthcoming publications are common.) There is no wiggle room here. If the document is authentic, then both Ewert and Marks are out-of-bounds ethically. And one really must wonder what was going on with the chairman of the thesis committee, associate professor of computer science Greg Hamerly. Was Marks the de facto chairman? Had Hamerly even bothered to read the handful of papers on active information? If he had, then he is complicit. If he had not, then his performance was shabby, to say the least.

The contact information below should come in handy for any journalist who wants to work on the story. And I encourage readers to let Baylor administrators know what a blight on the reputation of the school the thesis is. Click here now to open your default email application and address the dean of the graduate school, J. Larry Lyon. You will CC the executive vice president and provost, the dean of engineering and computer science, and the chairman of the computer science department.

Thesis author:
Winston Ewert, M.S.
evoinfo@winstonewert.com

Thesis committee member:
Robert J. Marks II, Ph.D.
Distinguished Professor of Engineering
(254) 710-7302
Robert_Marks@baylor.edu

William A. Dembski, Ph.D.
Research Professor of Philosophy and Director of the Center for Cultural Engagement
Southwestern Baptist Theological Seminary
817-923-1921 ext.4435
wdembski@designinference.com

J. Larry Lyon, Ph.D.
Dean of the Graduate School
Baylor University
(254) 710-3588
Larry_Lyon@baylor.edu

Elizabeth Davis, Ph.D.
Executive Vice President and Provost
Baylor University
(254) 710-7803
Elizabeth_Davis@baylor.edu

Benjamin S. Kelley, Ph.D., P.E.
Dean of Engineering and Computer Science
Baylor University
(254) 710-3871
Ben_Kelley@baylor.edu

Signed to approve thesis as department chairman:
Donald L. Gaitros, Ph.D.
Professor and Chairman of Computer Science
Baylor University
(254) 710-3876
Don_Gaitros@baylor.edu

Thesis committee chairperson:
Greg Hamerly, Ph.D.
Associate Professor of Computer Science
Baylor University
(254) 710-6846
hamerly@cs.baylor.edu

Thesis committee member:
[completed Ph.D. and joined Baylor in 2009]
Young-Rae Cho, Ph.D.
Assistant Professor of Computer Science
Baylor University
(254) 710-3385
Young-Rae_Cho@baylor.edu

* I emphasize that my remarks are contingent on the authenticity of the document residing in Baylor’s BEARdocs archive on March 19, 2011. When possible, I assess the thesis I retrieved, and not persons. I have verified that Baylor requires entry of theses into BEARdocs. A metadatum indicates that the thesis was added on January 5, 2011, which is consistent with December 2010 graduation. I contacted Ewert by email to ask if the document were the final draft of his thesis, and he responded, “I have not verified the document, but it should be the final draft.”

The most dangerous innovation of ID creationism

2011-01-11T02:13:00.000-08:00

At the Panda's Thumb, Richard B. Hoppe posts a link to a 1981 debate between Henry Morris and Ken Miller, and asks, "What arguments, if any, do contemporary ID proponents offer that Morris does not?" The overall response is that there's really nothing in "intelligent design" creationism that was not present in overt creationism. Unsurprisingly, everyone focuses on matters of science. I must say that this reflects a dangerous indifference to the role of philosophy in judicial tests of creationism.

Any test of the legality of teaching a form of creationism as science in public schools will hinge on demarcation of science and religion. My reading of the Kitzmiller decision is that demarcation was much more important than the specifics of science and pseudoscience entered into evidence. For instance (pp. 67-68),

It is notable that defense experts’ own mission, which mirrors that of the IDM [ID movement] itself, is to change the ground rules of science to allow supernatural causation of the natural world, which the Supreme Court in Edwards and the court in McLean correctly recognized as an inherently religious concept. Edwards, 482 U.S. at 591-92; McLean, 529 F. Supp. at 1267. First, defense expert Professor Fuller agreed that ID aspires to “change the ground rules” of science and lead defense expert Professor Behe admitted that his broadened definition of science, which encompasses ID, would also embrace astrology. (28:26 (Fuller); 21:37-42 (Behe)). Moreover, defense expert Professor Minnich acknowledged that for ID to be considered science, the ground rules of science have to be broadened to allow consideration of supernatural forces. (38:97 (Minnich)).

Prominent IDM leaders are in agreement with the opinions expressed by defense expert witnesses that the ground rules of science must be changed for ID to take hold and prosper. William Dembski, for instance, an IDM leader, proclaims that science is ruled by methodological naturalism and argues that this rule must be overturned if ID is to prosper.

By the way, we all laugh at Behe now, but he is really no worse a philosopher than the majority of scientists. I shudder to think how the trial would have gone if Pennock and Forrest had dropped out, and a couple of "philosophy is bullshit" scientists had testified that science proves naturalism true.

So what is the most dangerous innovation of ID creationism? The movement stopped trying to overturn methodological naturalism, and adopted a new perspective on the nature of nature. The physical Universe is now comprised not just of matter and energy, but also of information. There is conservation of mass-energy, but not of information, which is created (only) by non-material intelligence. Six years ago, the design inference was to non-natural (i.e., supernatural) cause, and mainstream scientists were denigrated as naturalists. Now intelligent design is a non-material, though natural, cause, and mainstream scientists are denigrated as materialists.

The change in ontology makes IDC much more slippery than it was in Kitzmiller. On a verbal level, IDC has stepped entirely within naturalism. It does not obviously appeal to supernatural explanations. Many physicists accept the notion that information is in some sense physical. Thus it is much harder today than it was six years ago to argue that IDC is not science and that teaching of IDC as science does not serve a secular purpose.

Of course, most of us regard an unobservable entity that creates physical stuff, whatever it may be, out of nothing as supernatural. But we really should worry about a judge who is disposed to accept intuitively that people are creative, and that what they create by virtue of intelligence is not matter, but the information that gives form to matter. On the face of it, this does not seem a religious claim. And when IDCists say they can measure the information created by intelligence, citing the peer-reviewed publications of Dembski and Marks, it does not seem an unscientific claim. I believe that it is of the utmost importance to develop a simple explanation of why such a seemingly innocent notion of creation of information must be regarded as supernaturalism.

A chuckle from William Lane Craig

2010-12-21T14:37:00.000-08:00

Some of you know William Lane Craig as the evangelical Christian theologian from Biola University who often speaks favorably of “intelligent design” creationism. It happens that I just read one of his criticisms of the Jesus Seminar, a large group that gauged the historicity of the sayings and acts of Jesus reported in the four canonical gospels and the Gospel of Thomas:

Of the 74 [scholars] listed in their publication The Five Gospels, only 14 would be leading figures in the field of New Testament studies. More than half are basically unknowns, who have published only two or three articles. Eighteen of the fellows have published nothing at all in New Testament studies. Most have relatively undistinguished academic positions, for example, teaching at a community college.

Prof. Craig, you really should spend some time with Confucius. Not one leading figure in the field of biology has ever contributed to the “theory” of intelligent design.

Whatever the Jesus Seminar got wrong, something it got right was to place the burden of proof on those who would claim historicity of a gospel passage. Obviously, most scholars delving into the matter are Christians seeking to demonstrate the truth of what they believe. Sound familiar? This is not to suggest that traditional New Testament scholars are no better than ID creationists. The New Testament scholars truly know the subject matter, while ID creationists demonstrate time and again their execrable ignorance of the relevant science.

The three Isaac Newtons of Ypsilanti

2010-12-17T17:07:00.000-08:00

Back on August 5, Clive Hayden, the moderator at Uncommon Descent, exclaimed, “Robert Jackson Marks II is THE CHARLES DARWIN OF INTELLIGENT DESIGN!” The occasion was the inclusion of Marks among The 20 Most Influential Christian Scholars at Superscholar.org:

Robert J. Marks II (b. 1950), Baylor University’s leading research professor, has emerged as the public face of intelligent design. As the movement’s premier scientist, he has been dubbed “the Charles Darwin of intelligent design.”

That hyperbole is old news. But the site’s list of 15 Professors Who Were Also Criminals just caught my eye:

Alan Turing was the Isaac Newton of the 20th century, and is seen by many to be the father of the Information Age.

Given that Superscholar.org is the absolute authority on such matters, what are we to make of the claim that Bill Dembski is the Isaac Newton of Information Theory?

The superabundance of Isaac Newtons has me thinking of The Three Christs of Ypsilanti:

To study the basis for delusional belief systems, Rokeach [a psychiatrist] brought together three men who each claimed to be Jesus Christ and confronted them with each other's conflicting claims, while encouraging them to interact personally as a support group. Rokeach also attempted to manipulate other aspects of their delusions by inventing messages from imaginary characters. He did not, as he had hoped, provoke any lessening of the patients' delusions, but did document a number of changes in their beliefs.

I suspect that, although he occasionally retreats from particular errors with “not-pologies,” Dembski will never give up the delusion that he is the Isaac Newton of his day.

The talk that could have killed me

2010-12-09T20:42:00.000-08:00

Presentations seem to be hit-or-miss affairs for me.

My first talk on evolutionary computation, which I gave during the opening session of the Third Annual Conference on Evolutionary Programming (1994), was a hit. Hans-Paul Schwefel, one of the inventors of the evolution strategy, joined me for lunch that day. Prior to the conference banquet, I was buttonholed by a guy whose name I did not recognize from the EC literature. He was obviously very bright, and he complimented me on my work. Furthermore, he seemed to know a lot about directed evolution. I kept stealing glances at his name tag, wondering, "Who is this guy?" To be honest, if I had known how to break away politely, we’d have spoken for 5 minutes instead of 20. In the end, one of the conference organizers approached him to say, “We’re about ready to start now.” And he walked to the table at the front of the room with the “reserved” placard. After dinner, he gave the most brilliant talk I’ve ever heard. His name was Gerry Joyce. Many of you know of the sensational result, “Self-Sustained Replication of an RNA Enzyme,” that he and his student Tracey Lincoln published last year (see PZ Myers' explanation). The conference got even better for me on the last day, when David Fogel, last year’s president of the IEEE Computational Intelligence Society, asked me to serve as co-chair, with Thomas Bäck and Pete Angeline, of the technical program for the following year’s meeting. (Unfortunately, I had to resign that position due to illness.)

The “disbelief discourse” I recently gave to the Oklahoma Atheists was a miss, no matter that I put a huge amount of time into preparing it. Driving to the venue, I took two wrong turns. I arrived at precisely the time I was supposed to begin, with my anxiety sky-high. It turned out that the guy with the projector and screen showed up just when I did, but that didn't make me feel any better. Then it turned out that my Apple laptop would not connect to the projector. So I converted my presentation to PDF and, with two tries, got it onto a thumb drive. I plugged the thumb drive into a backup laptop that was perched on a chair, rather than the podium where I was supposed to stand (and where there was a microphone, as well as a voice recorder for the planned podcast). At that point, I was totally discombobulated. I needed to stand in front of the podium to deal with the laptop. The screen, to which I wanted to point, was well behind me, and I caught myself talking over my shoulder several times. The microphone stand was directly behind my foot, and I bumped into it several times. Worst of all, I occasionally dared to look into the faces in front of me, and saw clearly that things were not going well. “Must press on” was all that I could think. The bright side of the experience was the Q&A. There were some good questions, and I had a lot of fun answering them. I hope that some of you who were there will believe that I’m usually the guy you saw in the end. It was an embarrassing experience for me.

So how could this have killed me? Well, the following day, I felt some pain behind my right knee. I thought I had sat wrong while finishing my slides. Indeed I had, but there was more to the story than that. Several days later, I was admitted to the hospital with extensive clotting in my leg, and with three pulmonary emboli. At present, it appears that an autoimmune response is making my blood sticky (i.e., antibodies are attaching to hemoglobin cells).

Perhaps you can understand now why I started by reminiscing about a time when everything went well.

The identity of the Designer

2010-11-08T12:41:00.000-08:00

The elusive Kilroy has left his mark in exceedingly improbable places, all around the world. The only reasonable inference is....

Image copyright: Patrick Tillery

What is the probability of life in the physical universe?

2010-11-03T19:19:00.000-07:00

I’ll be giving a “Disbelief Discourse” to the Oklahoma Atheists and the Channing Unitarians on Tuesday, November 16, at 7:30 PM.

Channing Unitarian Universalist Church
2800 West 15th Street
Edmond OK 73012

The event is open to the public.

What Is the Probability of Life in the Physical Universe?

The question posed in the title has no objective answer, and creationists avoid confronting it directly. They instead give mathematically dandified arguments that particular features of life are objectively so unlikely to have arisen by natural processes that they must reflect supernatural intervention. Their conclusions imply that life is physically improbable, and thus their claims of objectivity are false. This simple rebuttal may seem unsatisfying to laypeople who believe incorrectly that scientists use math to prove the properties of nature. Consequently, the presentation will begin with an explanation of mathematical modeling in science.

Biosketch

Tom English flirted with creationism in his teens, and went so far as to deliver an anti-evolution talk to his biology classmates. What led him to abandon his naive beliefs about the truth and reconcilability of scripture and science, and to embrace methodological naturalism in scientific investigation, was a combination of studies in the Bible and the philosophy of science. After earning bachelor’s and master’s degrees in psychology and English, respectively, at Mississippi College, and master’s and doctoral degrees in computer science at Mississippi State University, he began investigating evolution in computational processes. He independently proved what came to be known as the “no free lunch” theorem for optimization, and subsequently published six papers related to it. In empirical research, he obtained by computational evolution a predictor of annual sunspots activity that was far more accurate than any previously reported. Tom is a senior member of the Institute of Electrical and Electronics Engineers, and has served as an associate editor of the IEEE Transactions on Evolutionary Computation. His most recent scholarly publication, coauthored by Garry Greenwood, is “Intelligent Design and Evolutionary Computation,” Chapter 1 of Design by Evolution.

“Dover II”: Forensic science is not engineering

2010-11-01T12:31:00.000-07:00

It is no secret that William A. Dembski, who filed a brief before withdrawing as an expert witness for the defense in Kitzmiller et al. v. Dover Area School District, is looking ahead to “Dover II.” I just wrote the following in a response to “Conservation of Information in Search: Measuring the Cost of Success”:

The article is the first in a series of publications that makes no positive contribution to the design of search procedures, but instead develops and applies a formal approach to arguing that success in search evidences design. That is, Dembski and Marks have disguised as engineering what is actually an attempt at forensic science, appropriate to making cases in courts of law and public opinion.

I’d point out to anyone who might serve as an anti-IDC expert in Dover II that Dembski and Marks have not subjected their work to scrutiny as forensic science. They have done their damnedest to avoid calling attention to the fact that their engineering papers are really not about engineering. Thus they’ve evaded whatever appropriate scrutiny they might have gotten within an inappropriate community. You can count on it, nonetheless, that the defense will present their publications as peer-reviewed science when the next legal battle comes along.

My comments are also relevant to those of you who face in the court of public opinion the (few) IDC rhetoricians who have managed to write off complex specified information and move on to active information.

Of “bad boys” and insipid women

2010-10-13T15:16:00.000-07:00

This morning I had breakfast in Midwest City, Oklahoma, home of Tinker Air Force Base. It seems that many military retirees live there. Sitting in the booth next to mine was a one-armed man who might well have been a Vietnam vet. After some time he was joined by a young couple and an infant child. The husband was a brawny guy with a buzzcut. He had a cowboy hat in one hand, the infant carrier in the other, and cowboy boots on his feet. His T-shirt, which looked brand new, was tucked ever-so-neatly into his bluejeans. On the back was an image of a bottle of beer emptying over the silhouette of a shapely woman. Here’s the text that went with it:

Why beer is better than women...
A beer is always wet.
Beer always looks the same in the morning.
Beer is always happy to ride in the trunk.
Beer always goes down easy.
A beer doesn't change its mind after you've gotten the top off.
When you change beers, you don't have to pay alimony.
You can enjoy beer all month long.
You can share a beer with friends.
Things turned utterly surreal when I heard the server ask, “How old is she?” Yes, she.

Grandpa did not seem thrilled to have the company. Eventually Daddy went out to his immaculate, humongous, white pickup truck and moved Baby Girl’s bag to Grandpa’s car. Then he left alone to do whatever manly stuff he was going to do in that T-shirt.

Perhaps I am making too much of this. For all I know, a buddy gave him the T as a tasteless gag when he was getting married, and he was off to visit the buddy… at 8 a.m. on a Wednesday.

Long ago, I’d have expressed disgust at the “bad boy” making a big display of his indomitability. I would have regarded both the mother and daughter as victims. But there’s nothing secret anymore about attraction to bad boys — I’ve seen first-hand that it runs high among feminist intellectuals, whom you would expect to be least susceptible — and I have to say that women are responsible for dealing with it. After all, we are talking here about guys who do not deceive women. The mother allowed the sexually exciting male she has snagged and foolishly expects to change to degrade and humiliate not only her, but her daughter and women in general.

Archive critiques of ID creationism

2010-10-04T17:37:00.000-07:00

It is easy to forget, here in our echo chamber, that most of the world’s researchers care little about “intelligent design” creationism. When Dembski and Marks submit a paper like “The Search for a Search” to online journals founded and edited by Poles and Japanese, there is a good chance that the reviewers are unsuspecting of shenanigans.

Much of the online criticism of IDC could, with little modification, be packaged as rough drafts of scholarly papers, and uploaded to archives such as arXiv.org. What makes this worthwhile is that Google Scholar, and not just Google, indexes these archives. A Scholar hit with a title such as “Errors in ‘The Search for a Search’ of Dembski and Marks” stands a good chance of catching the attention of reviewers of future work by the authors. Of course, archiving a critique does not preclude linking to it from blogs.

Rob recently gave a response [PDF] to “The Search for a Search” that strikes me as a prime example of what should be uploaded to arXiv.org. (In any case, I recommend it to those of you who can deal with math.)

I intend to follow my own advice. Provided that the lead author does not object, I’ll soon archive a brief paper, and notify you of it.

Perfectionism and writer's anxiety

2010-09-13T00:03:00.000-07:00

I used to think that I could learn to toss off remarks on the Internet. This post is my 20th at Bounded Science. But I have 24 un-posted drafts.

I recall ever-so-clearly copying sentences from the board when I was in the first grade. The other students had finished all ten, and I was on my fifth. The anxiety and shame I felt were incredible. I’ve since studied psychology and had some counseling. But I cannot begin to explain what was going on with that little guy.

I took the Scholastic Aptitude Tests back when there was no penalty for wrong answers. Although I knew to stop agonizing and start guessing when time was running out, I could not bring myself to do it. I left fairly large numbers of questions unanswered, and ended up with high (“DaveScot”) scores anyway.

Please don’t take this as backhanded bragging. My birthday is coming soon, and how little I’ve produced is weighing heavily on me. “To those whom much is given, much is expected.” I might have another 20 or 30 years in which my brain works well, and I’m wondering how to turn my life around.

The greater the scrutiny I expect a piece of writing to receive, the greater the problems I have with it. Writing for a journal ties me in knots. No matter that I see mediocre stuff in journals all the time, I can’t let go the notion that my own submission has to be absolutely fabulous.

The more I struggle to make my work fabulous, the worse it gets. The best prose I’ve turned out is, unfortunately, my dissertation (1990). What made it different? After gathering data compulsively, I had only a month to do the writing. There was a job in the offing, and my wife and son were depending on me. So I forced out a certain number of pages each day, revising little. Every now and then, I flip the book open, and find myself asking, “Is that really my work?”

I get annoyed when people like Dembski weigh my c.v. I’m well aware of my horribly low output. But anybody who attempts to diminish me when I speak about the area of research I’ve focused upon for 15 years has problems greater than my own.

I’ve begun writing a special post — a highly accessible presentation of my current understanding of “no free lunch” in optimization. Dembski and Marks are pushing an interpretation of the classic NFL theorem that is precisely backwards, and my goal is to get most of you to understand it better than they do. But let’s plan on my post being far from perfect, and on its improving with feedback from you.

Too late to be a Sooner...

2010-09-03T00:05:00.000-07:00

... but here I am, living in Oklahoma City (profile updated). Yes, every county in Oklahoma was red in the last presidential election. What can I say? I got a totally refurbished house at a fantastic price. My brother and his wife, with whom I get along famously, are just 5 miles away. The National Weather Center is about 20 miles away… for good reason. And, of course, there's Abbie, aka ERV. We have yet to meet, but I'm sure we will, Sooner or later.

Abbie and I disagree on the size of the hail that hit the area back in May. She says that it was baseball-sized (see the incredible video she posted), but I insist that it was softball-sized. Here’s my sister-in-law with a specimen of lesser diameter than some of the holes in her roof.

One hailstone not only passed through the roof, but also cratered the attic deck. My neighborhood was spared. But I am rethinking the deductible of my homeowner’s insurance.

Wasted days and wasted nights?

2010-08-18T18:44:00.000-07:00

On his blog Deep Thoughts and Silliness, Bob O'Hara recently linked to this bulletin-board thread devoted to recording “banninations” at the intelligent-design blog Uncommon Descent. It happens that I've been reflecting on my “wasted days and wasted nights” at UD, and I've just gone through the 23 pages of comments on the thread. Now I'm in a confessional mood:

Tom English
Thom English
Thomas English
T M English
austin english
Turner Coates
Cloud of Unknowing
Semiotic 007
Liz Lizard
Sal Gal
Mystic
Oatmeal Stout
Atticus Finch
CEC09
Hamlet
Sooner Emeritus

Those are my UD identities I can remember. Most of what I wrote was good stuff. I often did a lot of reading and thinking before posting. My comments changed considerably over the years, and that was because I was learning. But I also indulged my anger at people who indoctrinate children with simplistic "the Bible tells the truth, and so does science" garbage. And I succumbed to the temptation to jerk the ever-so-accessible chains of Gil Dodgen and Gordon Mullings aka kairosfocus.

Three or four of my alter egos were undeservedly booted by Dembski for posting stuff that made him squirm. I feel good about getting one of the stars of Expelled to reveal himself as the censorial hypocrite that he is. And various of me were killed off capriciously by the notorious blog-czar David “DaveScot” Springer. Some others committed virtual suicide by butting heads with that egotistical jerk. There was some entertainment value in it, but I can’t say that it was a particularly good use of my energies. Some of my personae ranted, and some of them treated Gil and Gordo badly — definitely a waste.

In the end (?), I wish that I'd been a lot more like Bob O'Hara, Mark Frank, David vun Kannon, Allen MacNeill, Seversky, and R0b. (There have been others with a combination of brilliance and good blogosphere manners that I do not have, and I’ve just listed the ones that spring immediately to mind.) Josh Rosenau recently got me thinking with his post on the backfire effect in presenting people with information that contradicts their beliefs. “In your face” confrontation is really not the way to encourage independent thinking in someone leaning toward conservative acceptance of what they hear about science in religious contexts.

By the way, all of admirable individuals I listed above have been banned under some name, if I’m not mistaken. I point this out not to rationalize my occasional online ugliness, but to emphasize the chronic unfairness of the moderation at Uncommon Descent.

I want to mention that I’m gentle, and perhaps effective, in face-to-face conversation with people who’ve heard that intelligent design is the latest, greatest thing in Bible-consistent science. I feel compassion especially for kids who are where I was 35-40 years ago. It comes to me quite naturally to find out what they believe and how they believe, and to proceed on their terms, rather than mine. I am not an ogre in the real world.

Feeling charitable toward Baylor’s IDC cubs

2010-07-29T16:50:00.000-07:00

The reason I come off as a nasty bastard on this blog is that I harbor quite a bit of anger toward the creationist bastards who duped me as a teenager. The earliest stage of overcoming my upbringing was the worst time of my life. I wanted to die. Consequently, I am deadly serious in my opposition to “science-done-right proves the Bible true” mythology. William A. Dembski provokes me especially with his prevarication and manipulation. He evidently believes that such behavior is moral if it serves higher ends in the “culture war.” My take is, shall we say, more traditional.

When Robert J. Marks II, Distinguished Professor of Engineering at Baylor University, and Fellow of the Institute of Electrical and Electronics Engineers (IEEE), began collaborating with Dembski, I did not rush to the conclusion that he was like Dembski. But it has become apparent that he is willing to play the system. For instance, Dembski was miraculously elevated to the rank of Senior Member of the IEEE, which only 5% of members ever reach, in the very year that he joined the organization. To be considered for elevation, a member must be nominated by a fellow.

Although Marks was the founding president of the progenitor of the IEEE Computational Intelligence Society, which addresses evolutionary computation (EC), he and his IDCist collaborators go to the IEEE Systems, Man, and Cybernetics Society for publication. He is fully aware that reviewers there are unlikely to know much about EC, and are likely to give the benefit of the doubt to a paper bearing his name. I would love to see him impugn the integrity of his and my colleagues in the Computational Intelligence Society by claiming that they don’t review controversial work fairly. But it ain’t gonna happen.

I’ve come to see Marks as the quintessential late-career jerk, altogether too ready to claim expertise in an area he has never engaged vigorously. He is so cocksure as to publish a work of apologetics with the title Evolutionary Computation: A Perpetual Motion Machine for Design Information? (Chap. 17 of Evidence for God, M. Licona and W. A. Dembski, eds.). He states outright some misapprehensions that are implicit in his technical publications. Here’s the whopper: “A common structure in evolutionary search is an imposed fitness function, wherein the merit of a design for each set of parameters is assigned a number.” Who are you, Bob Marks, to say what is common and what is not in a literature you do not follow? Having scrutinized over a thousand papers in EC, and perused many more, I say that you are flat-out wrong. There’s usually a natural, not imposed, sense in which some solutions are better than others. Put up the references, Distinguished Professor Expert, or shut up.

Marks and coauthors cagily avoid scrutiny of their (few) EC sources by dumping on the reviewers references to entire books, i.e., with no mention of specific pages or chapters. This is because their EC veneer will not withstand a scratch. The chapter I just linked to may seem to contradict that, given its references to early work in EC by Barricelli (1962), Crosby (1967), and Bremmerman [sic] et al. (1966). [That's Hans-Joachim Bremermann.] First, note the superficiality of the references. Marks did not survey the literature to come by them. The papers appear in a collection of reprints edited by David Fogel, Evolutionary Computation: The Fossil Record (IEEE Press, 1998). Marks served as a technical editor of the volume, just as I did, and he should have cited it.

Although Marks is an electrical engineer, he has been working with two of Baylor’s graduate students in computer science, Winston Ewert and George Montañez. I would hazard a guess that there is some arrangement for the students to turn their research with Marks into masters’ theses. I’ve been sitting on some errors in their most recent publication, Efficient Per Query Information Extraction from a Hamming Oracle, thinking that the IDC cubs would get what they deserved if they included the errors in their theses. Well, I’ve got a soft spot for students, and I’m feeling charitable today. But there’s no free lunch for Marks. He has no business directing research in EC, his reputation in computational intelligence notwithstanding, and I hope that the CS faculty at Baylor catch on to the fact.

First reading

On first reading the paper, I was deeply annoyed by the combination of a Chatty-Cathy, self-reference-laden introduction focusing on “oracles,” irrelevant to the majority of the paper, with a non-survey of the relevant literature in the theory of EC. Ewert et al. dump in three references to books, without discussion of their content, at the beginning of their 4-1/2 page section giving Markov-chain analyses of evolutionary algorithms. It turns out that one of the books does not treat EC at all — I contacted the author to make sure.

As I have discussed here and here, two of the algorithms they analyze are abstracted from defective Weasel programs that Dawkins supposedly used in the mid-1980's. It offends me to see these whirlygigs passed off as objects worthy of analysis in the engineering literature.

Yet again, they express the so-called average active information per query as

$$I_\oplus = {{I_\Omega} \over Q} = \frac{\log N^L}{Q} = {{L \log N} \over Q},$$

where Q is not the simple random variable it appears to be, but is instead the expected number of trials (“queries”) a procedure requires to maximize the number of characters in a “test” string that match a “target” string. Strings are over an alphabet of size N, and are of length L. Unless you have something to hide, you write

$$I_\oplus ={{L \log N} \over {E[T]}},$$

where T is the random number of trials required to obtain a perfect match of the target. This is a strange idea of an average, and it appears that a reviewer said as much. Rather than acknowledge the weirdness overtly, Ewert et al. added a cute “yeah, we know, but we do it consistently” footnote. Anyone without a prior commitment to advancing “intelligence creates active information” ideology would simply flip the fraction over to get the average number of trials per bit of endogenous information I_Ω,

$$\frac{1}{I_\oplus} = E\left[{T \over {I_\Omega}}\right] = {{E[T]} \over {L \log N}}.$$

This has a clear interpretation as expected performance normalized by a measure of problem hardness. But when it’s “active information or bust,” you’re not free to go in any sensible direction available to you. I have to add that I can’t make a sensible connection between average active information per query and active information. Given a bound K on the number of trials to match the target string, the active information is

$$I_+ = \log \Pr\{T \leq K\} + {L \log N}.$$

Do you see a relationship between I₊ and I_⊕ that I’m missing?

By the way, I happened upon prior work regarding the amount of information required to solve a problem. The scholarly lassitude of the IDC “maverick geniuses” glares out yet again.

Second reading

On second reading, I bothered to do sanity checking of the plots. I saw immediately that the surfaces in Fig. 2 were falling off in the wrong directions. For fixed alphabet size N, the plots show the average active information per query increasing as the string length L increases, when it obviously should decrease. The problem is harder, not easier, when the target string is longer. Comparing Fig. 5 to Figs. 3 and 4, it’s easy to see that the subscripts for N and L are reversed somewhere. But what makes Fig. 3 cattywampus is not so simple. Ewert et al. plot

$$I_\oplus(L, N) = \frac{L \log N}{E[T_{N,L}]}$$

instead of

$$I_\oplus(L, N) = \frac{L \log N}{E[T_{L,N}]}.$$

That is, the matrix of expected numbers of trials to match the target string is transposed, but the matrix of endogenous information values is not.

The embarrassment here is not that the cubs got confused about indexing of square matrices of values, but that a team of four, including Marks and Dembski, shipped out the paper for review, and then submitted the final copy for publication, with nary a sanity check of the plots. From where I sit, it appears that Ewert and Montañez are getting more in the way of indoctrination than advisement from Marks and Dembski. Considering that various folks have pointed out errors in every paper that Marks and Dembski have coauthored, you’d think the two would give their new papers thorough goings-over.

It is sad that Ewert and Montañez probably know more about analysis of algorithms than Marks and Dembski do, and evidently are forgetting it. The fact is that

$$E[T_{L,N}] = \Theta(N L \log L)$$

for all three of the evolutionary algorithms they consider, provided that parameters are set appropriately. It follows that

$$I_\oplus = \Theta\left(\frac{L \log N}{N L \log L}\right) = \Theta\left(\frac{\log N}{N \log L}\right).$$

In the case of (C), the (1, λ) evolutionary algorithm, setting the mutation rate to 1 / L and the number of offspring λ to N ln L does the trick. (Do a lit review, cubs — Marks and Dembski will not.) From the perspective of a computer scientist, the differences in expected numbers of trials for the algorithms are not worth detailed consideration. This is yet another reason why the study is silly.

Methinks it is like the OneMax problem

The optimization (not search) problem addressed by Ewert et al. (and the Weasel program) is a straightforward generalization of a problem that has been studied heavily by theorists in evolutionary computation, OneMax. In the OneMax problem, the alphabet is {0, 1}, and the fitness function is the number of 1's in the string. In other words, the target string is 11…1. If the cubs poke around in the literature, they’ll find that Dembski and Marks reinvented the wheel with some of their analysis. That’s the charitable conclusion, anyway.

Winston Ewert and George Montañez, don’t say the big, bad evilutionist never gave you anything.

Creeping elegance, or shameless hacking?

2010-07-28T14:47:00.000-07:00

In my previous post, I did not feel great about handling processes in the following code for selection, but I did not see a good way around it.

from heapq import heapreplace

def selected(population, popSize, nSelect, best = None):
    if best == None:
        best = nSelect * [(None, None)]
    threshold = best[0][0]
    nSent = 0

    for process in processes:
        if nSent == popSize: break
        process.submit(population[nSent], threshold)
        nSent += 1

    for process, x, score in scored(popSize):
        if score > threshold:
            heapreplace(best, (score, x))
            threshold = best[0][0]
        if nSent < popSize:
            process.submit(population[nSent], threshold)
            nSent += 1

    return best

What I really want is for selected to know nothing about parallel processing, and for the generator of scored individuals to know nothing about selection. The problem is that threshold changes dynamically, and the generator needs a reference to it. As best I can tell, there are no scalar references in Python. Having taught LISP a gazillion times, I should have realized immediately that I could exploit the lexical scoping of Python, and pass to the generator a threshold-returning function defined within the scope of selected.

def selected(self, population, nSelect, best = None):
    if best is None:
        best = nSelect * [(None, None)]

    threshold = lambda: best[0][0]

    for x, score in evaluator.eval(population, threshold):
        if score > best[0][0]:
            heapreplace(best, (score, x))

    return best

Perhaps I should not be blogging about my first Python program. Then again, I’m not the worst programmer on the planet, and some folks may learn from my discussion of code improvement. This go around, I need to show you the generator.

def eval(self, population, threshold):
    popSize = len(population)
    nSent = 0

    for process in self.processes:
        if nSent == popSize: break
        process.submit(population[nSent], threshold())
        nSent += 1

    for unused in population:
        process = self.processes[self.isReady.recv()]
        yield process.result()
        if nSent < popSize:
            process.submit(population[nSent], threshold())
            nSent += 1

This is a method in class Evaluator, which I plan to release. No knowledge of parallel processing is required to use Evaluator objects. The __init__ method starts up the indexed collection of processes, each of which knows its own index. It also opens a Pipe through which processes send their indexes when they have computed the fitness of individuals submitted to them. The Evaluator object’s Connection to the pipe is named isReady.

The first for loop comes from the original version of selected. Iteration over population in the second for loop is just a convenient way of making sure that a result is generated for each individual. In the first line of the loop body, a ready process is identified by receiving its index through the isReady connection. Then the generator yields the result of a fitness evaluation. The flow of control stops flowing at this point, and resumes only when selected returns to the beginning of its for loop and requests the next result from the eval generator.

When execution of the generator resumes, the next unevaluated individual in the population, if any, is submitted to the ready process, along with the value of a call to the threshold function. (The rightmost parenthesis is outside the meager Blogger column, and I don’t care to diddle with my code.) The call gives the current value of best[0][0], the selection threshold.

By the way, the Pipe should be a Queue, because only the “producer” processes, and not the “consumer” process, send messages through it. But Queue is presently not functioning correctly under the operating system I use, Mac OS X.

Efficient selection with fitness thresholds, heaps, and parallel processing — easier done than said

2010-07-26T23:34:00.000-07:00

The obvious approach to selection in an evolutionary algorithm is to preserve the better individuals in the population and cull the others. This is known as truncation selection. The term hints at sorting a list of individuals in descending order of fitness, and then truncating it to length nSelect. But that is really not the way to do things. And doing selection well is really not that hard. After providing a gentle review of the considerations, I’ll prove my point with 18 lines of code.

A principle of computational problem solving is not to waste time determining just how bad a bad solution is. Suppose we’re selecting the 3 fittest of a population of 10 individuals, and that the first 3 fitness scores we obtain are 90, 97, and 93. This means that we’re no longer interested in individuals with fitness of 90 or lower. If it becomes clear in the course of evaluating the fourth individual that its fitness does not exceed the threshold of 90, we can immediately assign it fitness of, say, 0 and move on to the next individual.

Use of the threshold need not be so simple. For some fitness functions, a high threshold reduces work for all evaluations. An example is fitness based on the Levenshtein distance of a string of characters t from a reference string s. This distance is the minimum number of insertions, deletions, and substitutions of single characters required to make the strings identical. Fitness is inversely related to distance. Increasing the threshold reduces the number of possible alignments of the strings that must be considered in computing the distance. In limited experiments with an evolutionary computation involving the Levenshtein distance, I’ve halved the execution time by exploiting thresholds.

A natural choice of data structure for keeping track of the nSelect fittest individuals is a min heap. All you need to know about the heap is that it is stored in an indexed data structure, and that the least element has the least index. That is, the threshold element is always heap[0] when indexing is zero-based. The heap is initialized to contain nSelect dummy individuals of infinitely poor fitness. When an individual has super-threshold fitness, it replaces the threshold element, and the heap is readjusted.

Evolutionary computations cry out for parallel processing. It is cruel and immoral to run them sequentially on computers with multiple processors (cores). But I have made it seem as though providing the fitness function with the selection threshold depends upon sequential evaluation of individuals. There are important cases in which it does not. If parents compete with offspring for survival, then the heap is initialized at the beginning of the run, and is reinitialized only when the fitness function changes — never, in most applications. Also, if the number of fitness evaluations per generation exceeds the number of processors, as is common with present technology, then there remains a sequential component in processing.

The way I’ve approached parallel processing is to maintain throughout the evolutionary run a collection of processes dedicated to fitness evaluation. The processes exist when fitness evaluation cum selection begins. First an individual is submitted, along with the threshold, to each process. Then fitness scores are received one by one. For each score received, the heap and threshold are updated if necessary, and an unevaluated individual is submitted, along with the threshold, to the process that provided the score. In the experiments I mentioned above, I’ve nearly halved the execution time by running two cores instead of one. That is, the combined use of thresholds and two fitness-evaluation processes gives almost a factor-of-4 speedup.

The Python function

I’m going to provide an explanation that any programmer should be able to follow. But first look the code over, considering what I’ve said thus far. The heap, named best, is an optional parameter. The variable nSent registers the number of individuals that have been submitted to evaluation processes. It steps from 0 to popSize, the size of the population.

from heapq import heapreplace

def selected(population, popSize, nSelect, best = None):
    if best == None:
        best = nSelect * [(None, None)]
    threshold = best[0][0]
    nSent = 0

    for process in processes:
        if nSent == popSize: break
        process.submit(population[nSent], threshold)
        nSent += 1

    for process, x, score in scored(popSize):
        if score > threshold:
            heapreplace(best, (score, x))
            threshold = best[0][0]
        if nSent < popSize:
            process.submit(population[nSent], threshold)
            nSent += 1

    return best

If no heap is supplied, best is set to an indexed collection of nSelect (unfit, dummy) pairs represented as (None, None). This works because any (fitness, individual) pair is greater than (None, None). The expression best[0][0] yields the fitness of the least fit individual in the heap, i.e., the threshold fitness for selection.

The first for loop submits to each of the waiting processes an individual in population to evaluate, along with threshold. [My next post greatly improves selected by eliminating the direct manipulation of processes.] The loop exits early if there is a surplus of processes. The processes are instances of a subclass of multiprocessing.Process that I have defined, but am “hiding” from you. I am illustrating how to keep the logic of parallel processing simple through object-oriented design. You don’t need to see the code to understand perfectly well that process.submit() communicates the arguments to process.

The second for loop iterates popSize times, processing triples obtained from scored. Despite appearances, scored is not a function, but a generator. It does not return a collection of all of the triples. In each iteration, it yields just one (process, x, score) to indicate the process that most recently communicated an evaluation (x, score). This indicates not only that the fitness of individual x is score, but that process is waiting to evaluate another individual. If the new score exceeds the selection threshold, then (score, x) goes into the best heap, and threshold is updated. And then the next unevaluated individual in the population, if any, is submitted along with the threshold to the ready process.

When the loop is exited, each individual has had its chance to get into the best heap, which is returned to the caller. By the way, there’s an argument to be made that when the best heap is supplied to the function, an individual with fitness equal to that of the worst in the heap should replace the worst. Presumably the heap contains parents that are competing with offspring for survival. Replacing parents with offspring when they are no better than the offspring can enhance escape from fitness plateaus.

Sure mutation in Python

2010-07-13T04:04:00.000-07:00

In Python, “lazy” mutation goes something like this:

for i in range(len(offspring)):
    if random() < mutation_rate:
        offspring[i] = choice(alphabet)

The random() value is uniform on [0, 1), and the choice function returns a character drawn uniformly at random from alphabet.It follows from my last post that this can be made right within the implementation of an evolutionary algorithm by defining

adjusted_rate = \
    len(alphabet) / (len(alphabet) - 1) * mutation_rate

and using it in place of mutation_rate. “And that’s all I have to say about that.”

If you want a mutation operator that surely mutates, the following code performs well:

from random import randint

alphabet = 'abcdefghijklmnopqrstuvwxyz '
alphaSize = len(alphabet)
alphaIndex = \
    dict([(alphabet[i], i) for i in range(alphaSize)])

def mutate(c):
    i = randint(0, alphaSize - 2)
    if i >= alphaIndex[c]:
        i += 1
    return alphabet[i]

Here alphaIndex is a dictionary associating each character in the alphabet with its index in the string alphabet. The first character of a string is indexed 0. Thus the expressions alphaIndex['a'] and alphaIndex['d'] evaluate to 0 and 3, respectively. For all characters c in alphabet,

alphaIndex[c] == alphabet.index(c).

Looking up an index in the dictionary alphaIndex is slightly faster than calling the function alphabet.index, which searches alphabet sequentially to locate the character. The performance advantage for the dictionary would be greater if the alphabet were larger.

The function mutate randomly selects an index other than that of character c, and returns the character in alphabet with the selected index. It starts by calling randint to get a random index i between “least index” (0) and “maximum index minus 1.” The trick is that if i is greater than or equal to the index of the character c that we want to exclude from selection, then it is bumped up by 1. This puts it in the range alphaIndex[c] + 1, …, alphaSize - 1 (the maximum index). All indexes other than that of c are equally likely to be selected.

The roly poly and the cockroach

2010-07-12T16:05:00.000-07:00

You may have noted in my post on Dembski's Weasel-whipping that I gave .0096 as the mutation rate of the Dobzhansky program, a conventional (1, 200) evolutionary algorithm (EA), while Yarus indicates that “1 in 100 characters in each generation” are mutated. Well, the slight discrepancy is due to the fact that the program uses the “lazy” mutation operator that I slammed as a bug in the algorithms analyzed by Ewert, Montañez, Dembski, and Marks [here]. I should explain that what is a roly poly in one context is a big, fat, nasty cockroach in another.

To mutate is to cause or to undergo change. That is, mutation is actual change, not an attempt at change. The lazy mutation operator simply overwrites a character in a phrase with a character drawn randomly from the alphabet, and sometimes fails to change the character. For an alphabet of size N, the mutation rate is (N − 1) / N times the probability that the operator is invoked. For the Dobzhansky program, N = 27, and

26 / 27 × .01 ≈ .0096.

The difference between .01 and .0096 is irrelevant to what Yarus writes about the program.

Correcting an EA implementation that uses a lazy mutation operator is trivial. Set the rate at which the operation is performed to N / (N − 1) times the desired mutation rate. Goodbye, roly poly.

No such trick exterminates the cucaracha of Ewert et al. Their algorithms (A) and (B), abstracted from the apocryphal Weasel programs, apply the lazy mutation operator to exactly one randomly selected character in each offspring phrase. The alphabet size ranges from 1 to 100, so the probability that an offspring is a mutant ranges from 0 / 1 to 99 / 100. As I explained in my previous post, it is utterly bizarre for the alphabet size to govern mutation in this manner. The algorithms are whirlygigs, of no interest to biologists and engineers.

Ewert et al. also address as algorithm (C) what would be a (1, 200) EA, were its “mutation” always mutation. The rate of application of the lazy mutation operator is fixed at 1 / 20. It is important to know that the near-optimal mutation rate for phrases of length L is 1 / L. With 100 characters in the alphabet, the effective mutation rate is almost 1 / 20, and the algorithm is implicitly tuned to handle phrases of length 20. For a binary alphabet, the effective mutation rate is just 1 / 40, and the algorithm is implicitly tuned to handle phrases of length 40. This should give you a strong sense of why the mutation rate should be explicit in analysis — as it always is in the evolutionary computation literature that the “maverick geniuses” do not bother to survey.

Regarding the number of mutants

I may have seemed to criticize the Dobzhansky program for generating many non-mutant offspring. That was not my intent. I think it’s interesting that the program performs so well, behaving as it does.

With the near-optimal mutation rate of 1 / L, the probability of generating a copy of the parent, (1 − 1 / L)^L, converges rapidly on e^-1 ≈ 0.368. Even for L as low as 25, an average of 72 in 200 offspring are exact copies of the parent.

It would not have been appropriate for Yarus to tune the mutation rate to the length of the Dobzhansky quote. That’s the sort of thing we do in computational problem solving. It’s not how nature works. I don’t make much of the fact that Yarus had an expected 109, rather than 73, non-mutant offspring per generation.

Edit: Yarus possibly changed the parameter settings of the program from those I’ve seen. I really don’t care if he did. I’m trying to share some fundamentals of how (not) to analyze evolutionary algorithms.

Dembski haplessly admits to plagiarism?

2010-06-28T10:55:00.000-07:00

In “Efficient Per Query Information Extraction from a Hamming Oracle” Winston Ewert, George Montañez, William A. Dembski, Robert J. Marks II do not cite the sources of the algorithms they analyze. Yet Dembski trumpeted at Uncommon Descent, “New Peer-Reviewed ID Paper — Deconstructing the Dawkins WEASEL.”

The algorithms (A) and (B) are implemented, respectively, by the programs WEASEL1 and WEASEL2 that Dembski said were supplied to him by the pseudonymous “Oxfordensis.” Dembski announced, “[W]e shall… henceforward treat the programs below as the originals,” i.e., as those used by Richard Dawkins. Any way you slice it, the programs and the algorithms they implement are due to someone other than Ewert et alia.

If you abstract an algorithm from a program, you are ethically obligated to cite the program, just as you are ethically obligated to cite a book from which you get an idea, even if you do not copy words from the book. Algorithms are intellectual property, and are in fact patentable.

Has Dembski not tagged himself and his colleagues as plagiarists?

Willie can’t stop whipping the Weasel

2010-06-28T09:08:00.000-07:00

William Dembski recently projected his obsession with the Weasel program onto evolutionists. His rationalization? Origin-of-life researcher Michael Yarus reuses the 1986 pop-sci illustration of evolution in a new pop-sci book, Life from an RNA World.

Dembski has misunderstood Richard Dawkins’ description of the program for at least a decade. He and Bob Marks falsely attributed partitioned search — not only the algorithm, but also the term — to Dawkins in a September 2009 article. As soon as the article appeared, he vested faith in two programs implementing different algorithms, explaining vaguely that the pseudonymous “Oxfordensis” supplied them. The story goes that Dawkins used one in preparing The Blind Watchmaker, and the other as a demo in a television show. Dawkins no longer has his code, and does not recognize the apocrypha. Yet Dembski announced that he would pin it on Dawkins anyway.

The kicker is that the programs share a bug. They attempt to mutate exactly one character in each offspring phrase, but instead create a perfect copy of the parent in 1 of 27 attempts, on average. The implemented mutation rule is bizarre, with relevance neither to biology nor to engineering. Yet Dembski, Marks, and IDCist cubs recently published analyses of algorithms abstracted from the buggy programs. (Of course, they went once again to the IEEE Systems, Man, and Cybernetics Society, where reviewers are unlikely to know much about evolutionary algorithms.)

Now the clown-scholar Willie has the temerity to write,

Some internet critics have urged that we are beating a dead [weasel], that this example was never meant to be taken too seriously, and that if we were “serious scientists,” we would be directing our energies elsewhere. Let me suggest that these critics take up their concerns with Yarus.

Ironically, Yarus explains that pedagogy trumps biology:

To fully appreciate this particular [example], you must be aware that it is an idealization, not a realistic model of evolution. But its power comes from its precise aim — directly at the heart of the difficulty many people have with the concept of evolution.

Dembski’s subconscious no doubt screams, “Deny! Deny! Deny!”

Yarus sees this simulation as underwriting the power of evolutionary processes.

Underwriting? Yarus says that it “should give intelligent designers (and the rest of us) a reflective moment or two.”

Poor Willie. Imagine how conflicted he must be, to have a “serious scientist” like Yarus invoke his name, but put the Weasel in its place.

No more exegesis of apocrypha

Rob Knight kindly supplied me with the code of what Yarus calls the “Dobzhansky program.” Rob and I agree that it implements a (1, λ) evolutionary algorithm (EA). In each generation, one parent phrase reproduces λ = 200 times. The characters in the offspring mutate independently at a rate of .0096. One offspring of maximal fitness survives as the parent of the next generation, and all other phrases “die.” This matches Wikipedia’s algorithm, except that the mutation rate is lower. The consequence of the lower rate is that the program performs well with phrases of length considerably greater than 100.

No more blogorrheaic Mullings

The (1, λ) EA is distinguished from the (1 + λ) EA, in which the parent competes with offspring for survival. With the PLUS algorithm, it is impossible for parental fitness to decrease from one generation to the next. Under certain conditions, it is nearly impossible for the COMMA algorithm. Some elementary calculations — not prolix, overwrought exhortations to the beloved onlookers [inside joke] — make this clear. For generality, let’s refer to the phrase length as L and the mutation rate as μ.

The probability of no mutation in a particular position of an offspring phrase is 1 − μ. The probability of no mutation in all L positions, i.e., no difference from the parent, is (1 − μ)^L. Subtract this quantity from 1, and you get the probability that the offspring differs from the parent,

m = 1 − (1 − μ)^L.

The expected number of mutants among the λ offspring of a generation is λm, and the probability that all of the offspring are mutants is m^λ.

For Yarus’ illustration, with L = 63 and μ ≈ .0096, m ≈ .4554. Of the λ = 200 offspring in a generation, only λm ≈ 91 are mutants, on average. The probability of generating 0, rather than the expected 109, copies of the parent is

m^λ ≈ .4554²⁰⁰ ≈ 10⁻⁶⁸.

It follows that the (1, 200) EA performs identically to the (1 + 200) EA with overwhelming probability. Even for a phrase of length 300, which the Dobzhansky program will converge upon poorly — the ideal mutation rate is about 1 / 300, and μ is almost 3 times too large — only 1 in 100 thousand generations lacks a copy of the parent.

Profligate evolution

The computational waste is striking. But I believe that it is entirely appropriate to illustrate rapid evolution on a generational basis, i.e., assuming simultaneous evaluation of offspring. It is progress on the generational time scale that matters in biological evolution. And we know that biological evolution is profligate in its own ways. Dembski, Marks, and cubs focus on how many fitness evaluations, rather than how many generations, are required to obtain the fittest phrase. They essentially force a sequential model onto a process characterized by parallelism.

That’s not a feature — it’s a bug

The apocryphal TV demo almost implements what theorists of evolutionary computation call randomized local search (RLS). You can think of RLS as a (1 + 1) EA modified to ensure that there is exactly one mutation in each offspring. This eliminates evaluations of copies of the parent (and also multiply mutated offspring).

The apocryphal TV demo does not surely mutate the character in a randomly selected position, but instead assigns a randomly drawn character to the position.

Right: x_i := Random(ALPHABET - {x_i})
Wrong: x_i := Random(ALPHABET)

The incorrect version fails with probability 1 / N, where N is the size of the alphabet. The de facto mutation rule is very weird: With probability (N - 1) / N, mutate a randomly selected position of the phrase. Ewert, Montañez, Dembski, and Marks consider alphabet sizes ranging from 1 to 100. For the important case of a binary alphabet, 1 in 2 offspring is a copy of its parent, and the bug doubles the expected running time. All the authors can say is that they’re analyzing an error they suspect Dawkins of making a quarter-century ago.

The apocryphal TBW program implements a (1, 100) EA modified to use the weird mutation rule. As I just explained, the probability of mutation in an offspring phrase is m = (N - 1) / N. Here, for several interesting alphabet sizes N, are the the expected numbers of mutants in a generation (100 m) and the probabilities that all offspring in a generation are mutants (m¹⁰⁰).

N	100 m	m¹⁰⁰
2	50.0	1 / 10³⁰
27	96.3	1 / 44
100	99.0	1 / 3

It is simply crazy for alphabet size to govern mutation as it does here. For the Weasel-Dobzhansky case of N = 27, about 1 in 44 generations has no copy of the parent. Convergence usually requires more than 44 generations. So, with irony that can be appreciated only by folks who follow Uncommon Descent...

There is no latching or ratcheting or locking of any sort in the program that Dawkins putatively used in preparing The Blind Watchmaker.

And I repeat that there is no scholarly value in formal analysis of idiosyncrasies arising from faulty implementation of mutation. If Dembski, Marks, and cubs want to investigate two buggy programs as artifacts of possible “historical significance,” let them openly tell the story of Oxfordensis.

BIO-Complexity: Manufacturing the controversy

2010-05-05T22:18:00.000-07:00

BIO-Complexity bills itself as a peer-reviewed journal of science. However, close inspection of its policies reveals it to be a website for slapdash dissemination and discussion of articles that have not been vetted by editors and reviewers. And very few scientists would agree that the scope is scientific.

It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life.

The gist of intelligent design is that an immaterial, and hence unobservable, intelligence creates physical information for a purpose. Scientists are virtually unanimous that such godlike action has no place in scientific explanations.

As long as scientists reject ID as supernaturalism, there will be none of the "scientific controversy over ID" referred to at BIO-Complexity. It seems that the forum is designed to get scientists, identified by their real names, to engage in highly restricted exchanges on ID that create the impression of genuine controversy. This could aid the Discovery Institute in its "teach the controversy" campaign, the objective of which is to get ID into the science curricula of public schools.

I'm not spinning a silly conspiracy theory here. The Discovery Institute supports the Biologic Institute, which in turn supports BIO-Complexity. The editorial board of BIO-Complexity is dominated by affiliates of the Biologic Institute and fellows of the Discovery Institute. Douglas Axe, the director of the Biologic Institute, and an editor of the forum, tries to induce debate with a taunt in The Debate Over Design Gains Momentum with a New Peer-Reviewed Science Journal: BIO-Complexity:

[I]f you examine the way scientists on both sides of the ID debate are conducting themselves, which side would you say is generally doing a better job of inviting critical scrutiny? Which side is earnestly seeking the strongest critique that the other side can offer? The answer should be obvious. It has to be the side that is promoting the debate, right? Or conversely, which side has little tolerance for dissent? That’s equally obvious. It’s the conflicted side—the one that is constantly switching between denying that the debate exists, trying to win it, and trying to shut it down.

The Biologic Institute also offers "Our take on the ID controversy", cherry-picking the writing of ID adversaries to create the false impression that they regard ID as scientific. ID propagandists have a long history of turning scientists' remarks on ID into evidence of ID's scientific legitimacy. Scientists stirred to comment at BIO-Complexity should keep this in mind.

I cannot imagine how an adversary of ID could win by submitting a research article to BIO-Complexity. It would say implicitly that scientists believe that the claims of ID can be falsified on naturalistic grounds, contradicting the crucial fact that the claims are intrinsically supernatural. And it would suggest that science is advancing due to the "controversy," even if ID does not explain life on Earth.

Journal publishing without the tears (and blood and sweat)

The ~~conveniently redefined~~ "innovative" peer-review process of BIO-Complexity is much less stringent than is the norm in scientific journals.

The most significant form of peer review begins when a completed work is made publically available for examination and response. The goal of pre-publication peer review should therefore be to decide whether the work in question merits the attention of experts, rather than to predict the final result of that attention. BIO-Complexity uses an innovative approach to pre-publication peer-review in order to achieve this goal.
[...]
Two or more reviewers will be consulted for each reviewed manuscript. Authors are encouraged to suggest suitable reviewers, though the Editor may elect to use other reviewers.
Reviewers are asked to comment in fair terms on the work’s limitations, but also on whether they think the expert community would benefit from considering both the merits and the limitations. Taking into consideration the manuscript and the reviewers’ comments, the Editor will use this criterion of benefit to decide whether to take the manuscript forward.
[...]
BIO-Complexity aims to communicate decisions to authors within six weeks of submission.

In short, this is a slapdash approach to getting articles posted on a website for debate. There is no requirement that the editor act as advised by the reviewers. At the same time, the editor does not take personal responsibility for the quality of an accepted article.

R - E - S - P - E - C - T, oh, what it means to me

For each published article, the journal publishes one critique, accepted at the sole discretion of the editor of the article. The authors of the article will respond just once to the critique. There are also online comments on articles:

Respectful, open dialog is the most productive way to approach matters of controversy. [emphasis added]

(Watch to see if a double-standard for "respect" emerges at yet another creationist website. Do you think Doug Axe will restrain himself any more than he did in the taunt I quoted above?) If an adversary comments, he or she does so under constraints that lend to the impression that there is a legitimate scientific controversy:

Only people willing to use their real names are allowed to post comments.
Comments that fail to respect others will be removed (repeat or flagrant offenders being blocked).
Comments need to stay on point.
To be registered for posting comments, first register as a reader or author, then send an email from an institutional or corporate account (to establish your identity) with a brief description of your areas of interest to our support address

My point will never be on point according to BIO-Complexity. An intelligent designer is a god by another name, and is outside the scope of scientific investigation. There is no scientific controversy over intelligent design.

Errors in "Conservation of Information in Search"

2010-03-15T18:00:00.001-07:00

William A. Dembski is a senior member, and Robert J. Marks II is a fellow, of the Institute of Electrical and Electronics Engineers (IEEE). The IEEE Code of Ethics requires members "to see, accept, and offer honest criticism of technical work, to acknowledge and correct errors, and to credit properly the contributions of others."

A correspondent tells me that he has notified Dembski and Marks of obvious mathematical errors in Conservation of Information in Search: Measuring the Cost of Success. The errors are identified and explained here.

My opinion, as a senior member of the IEEE, is that it is unethical for Dembski and Marks to continue disseminating the article online without correcting its known errors. Some researchers, including me, emend online versions of their publications by adding footnotes. I do not know why Dembski and Marks would not follow suit. Of course, they must "credit properly" the source of the corrections.

Section III.E of the article begins, "Partitioned search [12] is a 'divide and conquer' procedure. . . ." The combination of emphasis and citation falsely indicates that the term "partitioned search" comes from [12], Richard Dawkins' The Blind Watchmaker (TBW). Furthermore, categorical attribution of the procedure itself to Dawkins is unwarranted.

TBW describes a program that models an aspect of biological evolution (pp. 47-48). The program searches for a target phrase by iteratively "'breeding' ... mutant 'progeny'" from a parent phrase. The parent of the next generation is the progeny that "most resembles the target." Partitioned search would require additional information as to where the parent matches the target, along with exemption of matching characters from "mutation" in "breeding." There is no mention in TBW of these necessary elements of partitioned search.

The following now appears on the anonymously authored WeaselWare page of the website for Marks' Evolutionary Informatics Lab:

In an Evolutionary Search such as the one proposed by Dr. Dawkins [in TBW]*....

The footnote reads,

* Dr. Dawkins no longer possesses the original source code for his algorithm. Feeback and reflection have led the authors to conclude that an Evolutionary Search is the more likely interpretation for the type of search presented in TBW. Although Partitioned Search was the original interpretation, we have now expanded our analysis to include Evolutionary Strategies, thus covering all reasonable interpretations.

I'm calling on Dembski and Marks to acknowledge in the online version of the article that the term partitioned search does not appear in TBW, and that they "probably" interpreted TBW incorrectly.

Dembski and Marks should not dodge responsibility for the misinterpretation. As a computer scientist, I find the phrase "Dawkins no longer possesses the original source code for his algorithm" utterly bizarre. One starts with an algorithm, selects a programming language, and then expresses the algorithm in the particular programming language to obtain "source code." Dawkins need not have source code to tell us his algorithm. Dembski publicized a communication with Dawkins immediately after the publication of the article. Clearly he could have contacted Dawkins to ask about the algorithm while writing the article. If he doubted that the algorithm produced the results shown in TBW, all he had to do was implement the algorithm and check to see if worked as advertised.

Please join me in asking Dembski and Marks (their email addresses are at the bottom of the first page of the article) to fulfill their obligations under the IEEE Code of Ethics. Feel free to link to this text, which appears both at my blog, Bounded Science, and on the Sidewiki here at the website of the Evolutionary Informatics Lab.

Granville Sewell discovers YouTube

2010-01-18T16:39:00.000-08:00

Mathematician and creationist Granville Sewell mangles thermodynamics for the UncommonDescent crowd yet again in Can ANYTHING Happen in an Open System–Video. I really don't have time to respond at the moment, but attached the following to the UD page as a Sidewiki comment, simply because it annoyed the hell out of me that he did not allow comments. I'd appreciate "helpful" votes from those of you set up to use Google's Sidewiki.

----------------------------------

Don't waste your time.

Believe it or not, the "unpolished" video is a sequence of still shots, mostly of text that Prof. Sewell is reading aloud. The only exceptions are images of 1) the cover of a book he reads from and 2) a computer motherboard. Sewell says nothing that he has not posted here on multiple occasions.

Professors who go to class unprepared and read from the textbook get fried in student evaluations. It amazes me that Prof. Sewell would do essentially that in a YouTube presentation. It should surprise no one that he allows comments neither at UncommonDescent nor at YouTube.

Ironically, Sewell's colleagues in the Evolutionary Informatics Lab, William A. Dembski and Robert J. Marks II, lionize a physicist and pioneer of information theory, Leon Brillouin, who answered Sewell more than 50 years ago in Science and Information Theory. Brillouin emphasized that large amounts of information can be gained through expenditure of small amounts of negentropy in physical observation, with overall increase in entropy of the physical system including the observer and the observed. He also emphasized that the negentropy costs of information processing would decline with advances in technology. There is no contradiction of thermodynamics in the growth of human knowledge and the attending advances in complexity of artifacts.

Work is not information

2009-12-16T04:10:00.000-08:00

Suppose you are searching for a DNA sequence that translates to a protein with certain properties. To simplify matters, let's say you know magically that the sequence is 300 bases in length. You might roll a fair four-faced die 300 times to guess a sequence, and then conduct an experiment to see if the guess is correct. Clearly, there is no knowledge of the specific problem manifest in the die-rolling procedure.

Now let's say you do 1000 repetitions of the die-rolling procedure, and conduct 1000 experiments to check the randomly generated DNA sequences. The probability of "hitting the target" with a "query" of nature increases. But does this mean that you exploited more knowledge about the problem than you did previously? Of course not. It means only that you did more work.

In their recently published article, Conservation of Information in Search: Measuring the Cost of Success, Bill Dembski and Bob Marks sometimes measure work and call it active information. They claim,

Active information captures numerically the problem-specific information that assists a search in reaching a target.

But in Section III.A they demonstrate otherwise:

Multiple queries clearly contain more information than a single query. Active information is therefore introduced from repeated queries.

Now wait just a gol-dern minute, Billy Bob! The first sentence says that a procedure doing more work yields more information about the solution to the problem than a procedure doing less work. The second says that the procedure doing more work has more more information about how to solve the specific problem than a procedure doing less work. The error here is not just equivocal use of the word information. The authors go on to calculate a gain in active information for repetition of an utterly uninformed procedure.

Dembski and Marks commit the same errors in Section III.F.1, where they show that increasing the number of offspring in an evolutionary search increases the probability of obtaining an offspring more fit than the parent. To make this probability gain into active information, they redefine the search as just one generation of the evolutionary search they originally considered.

The fact that you can gain information by doing work does not imply that work is itself information.

[1/2/2010: I contradicted myself in saying "repetition of an utterly uninformed procedure" after predicating that "you know magically that the sequence is 300 bases in length." In a forthcoming post, I will explain that what Dembski and Marks call the endogenous information of a search problem seems endogenous only if one ignores magical circumscription of the solution space.]

Blunder in the new Dembski-Marks paper

2009-12-10T07:53:00.000-08:00

The recently published conference paper of Dembski and Marks, Bernoulli’s Principle of Insufficient Reason and Conservation of Information in Computer Search contains an enormous, undebatable, and embarrassing error in the argument regarding the so-called "search for a search."

Search algorithms explore a finite space of solutions Ω. An algorithm basically selects a solution in Ω, examines the solution, and decides which solution to select next. It repeats this until it has made Q selections. It is crucial to the arguments of Dembski and Marks that search algorithms have the capacity for randomizing their decisions. To randomize a decision is to base it, at least in part, on inputs from a random source. (Think of flipping a fair coin repeatedly and feeding the sequence of outcomes into a computer program. The inputs would permit the program to randomize its decisions.)

Dembski and Marks believe that people search for search algorithms in a higher-order space Ω₂. They write,

Let Ω₂ be the finite space of all search algorithms on the search space Ω.

The word I've emphasized is wrong, wrong, and wrong. The set of all randomized search algorithms is infinite, not finite. Section III.A and the "proof" of Equation (7) in Appendix B are based on a false premise.

Consider making just one randomized decision between alternative solutions ω₁ and ω₂ in Ω, with the probability of choosing ω₁ equal to p. The set of all possible values for p is infinite, and therefore the set of all randomized algorithms for making the decision is infinite.

Some technical details

For a fixed representation of randomized algorithms (e.g., probabilistic Turing machines reading i.i.d. uniform bits from an auxiliary tape), the set of probabilities p possible in a randomized dichotomous decision is countably infinite. There is no upper bound on the size and running time of the randomized decision algorithm.

The set of probabilities [0, 1] is uncountably infinite. Thus, while every randomized search algorithm implements a random search process, vanishingly few random search processes correspond to randomized search algorithms. Relatively few randomized search algorithms are fast enough and small enough to solve a problem in practice. We humans necessarily prefer small randomized search algorithms that make decisions rapidly.

Bad theology and bad science

2009-10-12T13:10:00.000-07:00

[Now on the Sidewiki at Uncommon Descent:]

The founder of this blog, William A. Dembski, has proclaimed that "intelligence creates information" [source]. He and other proponents of intelligent-design creationism (IDC) hold that information is physical, like matter and energy, and that intelligence is purposeful and natural, though immaterial and unobservable. IDC calls for science to consider the possible physical existence of something immaterial and unobservable that purposefully creates physical stuff out of nothing.

It is remarkable that proponents of IDC, most of whom believe in a supernatural Creator, attribute the design of living things to natural intelligence. Until recent years, a more coherent IDC held that intelligence was "non-natural." The view was unlikely, however, to make its way into science curricula of public schools, given that federal case law prohibits instruction in the supernatural. Evidently IDC strategists realized this, and shifted to intelligence is natural, but not material as a matter of expedience. No leading proponent stepped forward to announce the change in stance and offer an explanation. It makes a muddle of IDC, both logically and theologically.

All who oppose IDC, be they theistic, non-theistic, anti-theistic, deistic, or agnostic, agree that scientific explanations cannot include the famous "then a miracle occurs" step — even those who believe that miracles really do occur. And a claim that an invisible, immaterial entity has created something physical with evident purpose is indeed a claim of a miracle.

Scientists work to explain the wonders of nature, not "unexplain" them by accepting that they are miracles due to purposeful intervention of something invisible. The history of science is full of cases in which the seemingly unexplainable was explained. As a practical matter, scientists can never give up trying to show that the wondrous is not miraculous.

Source bluffing by Dembski and Marks

2009-10-10T11:45:00.000-07:00

In their September 2009 article in IEEE SMC-A, Dembski and Marks cite a book outside the literature on evolutionary computation as their source for the (1,2)-EA [evolutionary algorithm] which they do not identify as a (1,2)-EA. I had guessed that they had googled to locate a source with a title that would not telegraph to editors and reviewers, "This is an evolutionary algorithm."

It turns out that my guess was not so bad. DiEb has located the book online. Furthermore, s/he has found that the evolutionary algorithm it presents is quite different from the one that Dembski and Marks analyze. Is it "by chance or by design" that Dembski and Marks neglect to specify where in the book the algorithm is presented?

DiEb slyly points out that Dembski and Marks demonstrate in another book-reference that they know to give the range of pages... though they give the wrong range.

Join together to report scholarly misconduct?

2009-10-06T05:30:00.000-07:00

Edit (9 Oct 2009): Friends and respected acquaintances have persuaded me to rebut the article of Dembski and Marks in the peer-reviewed literature, and not to fuel the "Expelled" propaganda campaign of the intelligent design movement by lodging complaints of scholarly misconduct.

In my opinion, Dembski and Marks engaged in scholarly misconduct in their article Conservation of Information in Search: Measuring the Cost of Success. I will respond by lodging complaints with the academic institutions that employ the authors. I had planned on supplying readers with contact information and encouraging them to send their own letters of complaint. Now I believe that letters with many signatories would command more respect.

At most academic institutions, there are established procedures for responding to credible allegations of scholarly misconduct by faculty members. Allegations are typically reviewed by committees comprised mostly of ordinary faculty members — people who generally want to make fair decisions. Perhaps Dembski is safe. It would be nonetheless interesting to see a "secularized" Baptist university sanction one author, and a Baptist seminary let the other off the hook.

I must emphasize that the issue is not ID per se. Deceptive manipulation of a scholarly forum to advance any socio-political agenda whatsoever is wrong. As some of you know, I actually protested Baylor University's refusal to let Bob Marks display his "Evolutionary Informatics Lab" webpages with the standard disclaimer promulgated by the American Association of University Professors. What animates me to demand academic freedom is precisely what animates me to demand academic integrity.

Technical language goes nowhere with administrators and academic integrity committees. Furthermore, people may have a hard time seeing that Dembski and Marks misconstrued Dawkins. Here are some transgressions that are relatively easy to establish:

The authors analyze two closely-related computational methods without giving their conventional names, without indicating that they have been analyzed many times in the literature, and without citing prior analysis. This is egregious in light of the fact that their analyses did not appear in the paper until I explained one of the methods to Marks, provided its name, suggested analyzing it, and indicated that there were many analyses of it in the literature.
The authors mathematically formalize a computational method described informally in a popular-science book by Richard Dawkins, and attribute their formal method to Dawkins. That is, they mention neither that they are disambiguating an ambiguous text, nor that their disambiguation is highly controversial. This is egregious in light of the fact that Dembski has offered elsewhere several distinct interpretations of the text, and has emphasized its ambiguity.
The authors falsely attribute the term partitioned search, an apt name for their own formalization, to Dawkins. The attribution heightens the impression that they are relating straightforwardly Dawkins' precise meaning.

Speaking to motivation is tricky, but necessary, I think:

The authors submitted the article to a broad-scope journal with editors unlikely to recognize methods coming from the field of evolutionary computation. They evidently did not want to draw attention to the fact that parts of the paper needed the scrutiny of specialists in evolutionary computation. One of the analyses is a rehash of old results, and the other has no apparent utility in engineering.
Dembski has engaged in what he calls "cultural war" for many years, and the prominent atheist and evolutionary biologist Dawkins is his arch enemy. Dembski's socio-political ends take precedence over academic honesty in the article. He could not score a categorical hit on Dawkins without unequivocally representing Dawkins' work as something he and Marks knew how to analyze. In fact, the dubious interpretation makes for a very simple analysis. Following publication of the article, Dembski revealed his agenda on the Web:
Our critics will immediately say that this really isn’t a pro-ID [intelligent design] article but that it’s about something else (I’ve seen this line now for over a decade once work on ID started encroaching into peer-review territory). Before you believe this, have a look at the article. In it we critique, for instance, Richard Dawkins METHINKS*IT*IS*LIKE*A*WEASEL (p. 1055). Question: When Dawkins introduced this example, was he arguing pro-Darwinism? Yes he was. In critiquing his example and arguing that information is not created by unguided evolutionary processes, we are indeed making an argument that supports ID.
But soon after that, Dembski emphasized the ambiguity of Dawkins' description of his computational method, and decided that Dawkins used a method other than the one he and Marks analyzed — a method much harder to analyze. He also reported that he had communicated recently with Dawkins on the matter, and this brings to the fore the question of why he did not ask Dawkins for clarification prior to publication of the article. Evidently getting an unqualified "critique" of Dawkins through peer review was more important than honestly reporting that he and Marks had analyzed a mathematically convenient interpretation of Dawkins.

Some rumination

Dembski and Marks write, "Partitioned search [12] is a 'divide and conquer' procedure best introduced by example." Italicizing the term and placing a reference immediately after it is significant. By convention, this indicates that the term comes literally from the indicated source. There is, of course, no instance of "partitioned search" in reference [12], The Blind Watchmaker. Students might claim plausibly that they did not know the convention, but not a pair of highly experienced scholars.

There is utterly no way to warp Dawkins' description of how his Weasel program operated into D&M's partitioned search. Perhaps I'm underestimating the academic integrity committees. If they saw Dawkins' description of the Weasel program juxtaposed with D&M's description of partitioned search, they might sense that something's rotten in Texas.

How would an honest and responsible scholar go about disambiguating an algorithm in a popular science book? Obviously he would contact the author, if possible. Dembski has communicated with Dawkins plenty of times in the past, and has communicated with him about the Weasel program since publication of the article. Considering the controversy over the Weasel program, there was absolutely no justification for excluding Dawkins from the loop. This lends credence to the claim that Dembski and Marks chose to engage in false attribution because it served an ulterior purpose.

D&M did not know how to analyze the active information of Dawkins' algorithm, so they pinned on Dawkins an algorithm they felt was "close enough," and that they knew how to analyze. (I am sure that they did not know how to analyze Dawkins' algorithm because the article includes an analysis of a restricted form of it.) Whether partitioned search was "close enough" or not is irrelevant. The issue is that D&M had no justification for flat declaration that it was Dawkins' algorithm.

Back to the task

It would be good, I think, to mail a cover letter, a synopsis of the allegations like that I provided above, and somewhat detailed evidence. For instance, I would quote from my email to Marks, as in my last entry. It would be nice if Wesley were to provide a synopsis of Dembski's weaseling on the Weasel. I can give a succinct and simple explanation that D&M analyzed the (1,2)-ES and the (1+1)-ES, as well as a demonstration that they needed to keep reviewers from looking at prior analyses of ES's.

What I have in mind is to prepare the materials, put them on display for comments, revise, and then solicit signatures. I'd like to hear if you think many people would join in if I prepared something along the lines of what you've seen here. Should I just go it alone?

ADDENDUM

See Jeffrey Shallit's remarks on acknowledging priority at Recursivity.

Resolving a moral dilemma

2009-10-05T15:38:00.000-07:00

I made a promise to Bob Marks that I would not divulge my correspondence with him regarding drafts of the paper that IEEE SMC-A published last month. But I did not know that he and Dembski would resort to trickery to get the paper through peer review, and, after considerable agonizing, I've decided that the better course is to break my word.

(Bob has done a great deal of admirable work in computational intelligence, and I don't count him as a personal enemy. In fact, I recently joined with him in recommending an IEEE member for elevation to a higher rank.)

This is from a July 31, 2008, note that went, at his request, to his Yahoo address rather than through the (no doubt archived) Baylor email system:

Dawkins' weasel program implements a (1, λ)-ES, not partitioned search. In each generation, there are λ offspring. All points in the parent string are subject to mutation in all generations. The fittest of the offspring replaces the parent. Fitness is the number of positions containing correct letters. It is possible for fitness of the parent to decrease from one generation to the next. The mutation probability is "low," so offspring are concentrated in the neighborhood (naturally defined in terms of Hamming distance) of the parent, not uniformly distributed on a subspace of the solution space as you indicate.

I think your analysis of partitioned search makes for a good example, but you should not suggest in any way that you're analyzing Dawkins' algorithm. I would like to see you change the target sentence. In any case, the Bard (and Dawkins) wrote "methinks" as one word, not two.

It would be interesting to see an analysis of the active information of the (1, λ)-ES Dawkins used. There are plenty of published analyses of the (1, λ)-ES as a Markov process for λ = 1 [actually 2]. I'm not sure about greater values of λ. What you need is the probability that the process enters the state corresponding to the target string in Q or fewer time steps, expressed as a function of mutation probability and λ. Of course, you could fall back on simulation.

Marks did not respond to this particular note, but "ME*THINKS" turned into "METHINKS" in later drafts, and section III-F-2 of the published article addresses a (1,2)-ES [evolution strategy; sometimes it's instead "EA" for "evolutionary algorithm"] solving a restricted form of the problem solved by the Weasel program. Furthermore, section III-F-3 deals with the closely related (1+1)-ES.

It's not plausible, I think, that Marks ignored my note - he's responded to others since - and that he and Dembski subsequently happened to think of analyzing the evolutionary algorithms. The article neither gives the established names of the algorithms nor cites prior analyses in the literature. You have a good idea now of why I consider this to be academic misconduct.

Never look a gift weasel in the mouth

2009-10-01T17:56:00.000-07:00

At least ten years ago, William Dembski misunderstood the description of the Weasel program in Richard Dawkins' 1986 book The Blind Watchmaker. (Take it from an experienced teacher of computer science: Some mathematicians cannot think algorithmically.) Many people have tried to persuade him that there is only one reasonable reading in the context of a book on biological evolution. His response has been to ignore context, and to play up ambiguity in his attempts to save face.

Now Dembski reports that "Oxfordensis" emailed him two Weasel programs, claiming that Dawkins ran Weasel1 in preparing the book, and Weasel2 for a demonstration in a 1987 TV show based on the book. The programs accord well with Dembski's misconceptions, so he has posted gelatinous "analysis" leading to the conclusion that "unless further evidence is presented, ... the single-mutation algorithm implemented by WEASEL1 is the one used by Dawkins in TBW."

I will save for another day the details of how Dembski got himself speared by looking a gift weasel in the mouth. Suffice it to say that both programs are easy to model formally as Markov chains, and that I, unlike Dembski and his colleagues at the Evolutionary Informatics Lab, actually bothered to do the math. (Furthermore, I translated the Weasels from Pascal to C++, and cross-checked my models and programs.) Dawkins gives an example run in which the number of correct characters in the parent goes from 3 to 22 in 19 generations. Dembski is perfectly happy to say that this is what we would expect from Weasel1. In fact, the probability that the program improves the parent so quickly (as quickly as it possibly can) is just .037.

It is quite unlikely that Dawkins used Weasel1 in preparing his book. The probability that a Weasel program like that described in Wikipedia (200 offspring per generation, mutation rate of .05) goes from 3 to 12 correct characters in generations 1 to 10, and from 12 to 22 correct characters in generations 10 to 20, is in the range of .05 to .06. (I am working on a Markov model that will yield a precise probability.) The likelihood of the conventional Weasel program, though low, is greater than that of the apocryphal Weasel1.

We cannot regard "Oxfordensis" as a reliable source of information on the program(s) Dawkins used. Thus, even though 32% of Weasel2 runs obtain the target sentence as quickly as the run in the TV show does, we must worry about a hoax. I will have more to say later as to whether a conventional Weasel program is more likely than Weasel2 to yield the run in the TV show.

Technical Details

Markov model source code: main.cpp. Modify constants according to comments, compile, and run. IOU a LaTeX document explaining the math behind the code.

Output files: weasel1.txt, weasel1-TBW.txt, weasel2.txt [8 MB]. The long lines of numbers give the probabilities of having 0 characters correct, 1 character correct, ..., and 28 characters correct after the specified number of transitions. In the "TBW" output, the initial state corresponds to generation 1, not generation 0 as in the other outputs. Thus 9, 19, and 42 transitions yield the probability distributions for generations 10, 20, and 43, respectively.