Monthly Archives: June 2008

A Sesquicentennial: Wallace and Darwin at the Linnean Society

One hundred fifty years ago, this date fell on a Thursday. On that Thursday, the meeting of the Linnean Society in London had a reading of an essay by Alfred Russel Wallace and a manuscript chapter extract and a letter from Charles R. Darwin on the topic of tranformism, or the evolution of new species from existing species. This collage of material was presented under a single title, On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection.

The reading itself produced hardly a ripple in the currents of scientific discourse; the Linnean Society president Thomas Bell noted in his journal that nothing of importance took place that dayyear. The real story lay in how it came to be that there was a joint presentation of material from Wallace and Darwin, rather than Wallace alone, and in the course of history that followed on.

Wallace was a naturalist in the field, his field being first the Amazon basin and later the Malay Archipelago. One of the hazards of being a European naturalist out in those regions was disease, and Wallace suffered an attack of malaria. While feverish, Wallace worked out the basics of how natural causes could explain the adaptations that mark different species of organisms. Once recovered, he wrote out an essay on the subject, and sent that on to Charles Darwin, with whom he had previously corresponded on the topic of transformism.

The essay, titled “On the Tendency of Varieties to depart indefinitely from the Original Type”, caught Darwin rather by surprise. While Darwin appreciated Wallace’s previous paper promulgating the “Sarawak Law” that all species are found in geographic proximity to allied species, Darwin had apparently classed Wallace’s views on tranformism as corresponding to progressive creationism. In the essay Darwin read in spring of 1858, though, Wallace clearly laid out the very mechanism of natural selection that Darwin had cogitated over for about twenty years. Clearly, Wallace’s essay deserved publication, but what of Darwin’s own, unpublished, work on the topic? Darwin took the matter to his friends, Charles Lyell and Joseph Hooker. They have a preface to the piece read to the Linnean Society 150 years ago that explains their solution to the problem.

MY DEAR SIR,—The accompanying papers, which we have the honour of communicating to the Linnean Society, and which all relate to the same subject, viz. the Laws which affect the Production of Varieties, Races, and Species, contain the results of the investigations of two indefatigable naturalists, Mr. Charles Darwin and Mr. Alfred Wallace.

These gentlemen having, independently and unknown to one another, conceived the same very ingenious theory to account for the appearance and perpetuation of varieties and of specific forms on our planet, may both fairly claim the merit of being original thinkers in this important line of inquiry; but neither of them having published his views, though Mr. Darwin has for many years past been repeatedly urged by us to do so, and both authors having now unreservedly placed their papers in our hands, we think it would best promote the interests of science that a selection from them should be laid before the Linnean Society.

Taken in the order of their dates, they consist of:—

1. Extracts from a MS. work on Species*, by Mr. Darwin, which was sketched in 1839, and copied in 1844,2 when the copy was read by Dr. Hooker,3 and its contents afterwards communicated to Sir Charles Lyell. The first Part is devoted to “The Variation of Organic Beings under Domestication and in their Natural State;” and the second chapter of that Part, from which we propose to read to the Society the extracts referred to, is headed, “On the Variation of Organic Beings in a state of Nature; on the Natural Means of Selection; on the Comparison of Domestic Races and true Species.”

2. An abstract of a private letter addressed to Professor Asa Gray, of Boston, U.S., in October4 1857, by Mr. Darwin, in which he repeats his views, and which shows that these remained unaltered from 1839 to 1857.1

3. An Essay by Mr. Wallace, entitled “On the Tendency of Varieties to depart indefinitely from the Original Type.”2 This was written at Ternate in February 1858, for the perusal of his friend and correspondent Mr. Darwin, and sent to him with the expressed wish that it should be forwarded to Sir Charles Lyell, if Mr. Darwin thought it sufficiently novel and interesting. So highly did Mr. Darwin appreciate the value of the views therein set forth, that he proposed, in a letter to Sir Charles Lyell, to obtain Mr. Wallace’s consent to allow the Essay to be published as soon as possible. Of this step we highly approved, provided Mr. Darwin did not withhold from the public, as he was strongly inclined to do (in favour of Mr. Wallace), the memoir which he had himself written on the same subject, and which, as before stated, one of us had perused in 1844, and the contents of which we had both of us been privy to for many years. On representing this to Mr. Darwin, he gave us permission to make what use we thought proper of his memoir, &c.; and in adopting our present course, of presenting it to the Linnean Society, we have explained to him that we are not solely considering the relative claims to priority of himself and his friend, but the interests of science generally; for we feel it to be desirable that views founded on a wide deduction from facts, and matured by years of reflection, should constitute at once a goal from which others may start, and that, while the scientific world is waiting for the appearance of Mr. Darwin’s complete work, some of the leading results of his labours, as well as those of his able correspondent, should together be laid before the public.

We have the honour to be yours very obediently,

CHARLES LYELL.

JOS. D. HOOKER.

As solutions to wrangles over scientific priority go, this one is near the lead for deference being paid all around. Wallace and Darwin became, via this joint presentation, co-discoverers of natural selection and its proposed role in the production of new species from existing ones. The reading also forced Darwin’s hand, and the following months saw him discard his long-term project of writing a large monograph on natural selection, and instead hurry to produce an “abstract” of his work. That “abstract” is what we now know as the book, “Origin of Species”, published in November, 1859.

The Lyell-Hooker solution of producing a joint presentation to the Linnean Society has been endlessly argued over. The primary question posed would be, was the solution unfair to Wallace, whose essay lays out the logic of natural selection in graceful and economical prose, preferred by some to Darwin’s own explication? There’s a book length treatment by Brackmann of the argument that Wallace was thoroughly swindled by Darwin and Darwin’s colleagues, set to play a subordinate role to the elder naturalist. Brackmann, though, appears to have been letting a general animus for Darwin determine his approach to the material. The record of continued cordial correspondence between Darwin and Wallace, though strained at times by their varying views of selection with respect to human mental capacity, seems to run counter to various conspiratorial readings of the situation.

I’ll close this post with the final paragraph of Wallace’s Ternate essay, the last part of the presentation given to the Linnean Society 150 years ago today.

We believe we have now shown that there is a tendency in nature to the continued progression of certain classes of varieties further and further from the original type—a progression to which there appears no reason to assign any definite limits—and that the same principle which produces this result in a state of nature will also explain why domestic varieties have a tendency to revert to the original type. This progression, by minute steps, in various directions, but always checked and balanced by the necessary conditions, subject to which alone existence can be preserved, may, it is believed, be followed out so as to agree with all the phenomena presented by organized beings, their extinction and succession in past ages, and all the extraordinary modifications of form, instinct, and habits which they exhibit.

Check out material on this anniversary at the Beagle Project, too.

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Evolution 2008, Day 3: Evolution in the Classroom

There were presentations on Sunday about at least two software packages that allow students to investigate evolutionary processes in the classroom.

Rob Pennock gave a talk about Avida-ED, a version of the Avida artificial life platform that adds a graphical user interface with a number of features useful for interactive use. Typically, running Avida is done in batch mode from a command-line interface. Avida-ED allows the user to specify configuration options from the interface and presents views of populations or individual Avidians as requested. As Avida-ED runs, one also can get graphical indications of population changes in fitness, gestation time, and other measures.

Brian White talked about Aipotu, a simulator that uses genetics and proteomics with evolutionary processes recently added on. (The application is derived from MGX, for Molecular Genetics Explorer.) There are some similarities in the interface for Aipotu and Avida-ED, as White’s group has consulted with the Avida-ED team about ways to display evolution in progress. Aipotu uses an example of genetics of “flower” color as the basis for showing how evolution can change genotype distributions by comparing phenotypes.

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The Practice of Science: Broken

I’m going to make what is likely to be taken as an extreme criticism. I hope to start some discussion by this, and perhaps get people to think about a problem in a somewhat different way. So here goes… Back in graduate school, Diane and I would attend conferences with our advisor, Bill Evans. At several conferences, we would take a look at posters or sit together to listen to presentations. And it was a common occurrence that Bill would tell us that some method or result being reported as new was, in fact, something that had been done or accomplished and duly reported in the literature some decades prior. Bill would be able to give us the appropriate pointer to a citation where we could check that, indeed, a chunk of “new” research happened to be stuff that was (in all likelihood unknowingly) a repetition of what had been done before. And that leads me to the main claim I’m going to make here:

A critical part of scientific practice is identification of prior work and putting current research in context of it. However, this part of scientific practice is not just weak or problematic. It is broken.

Let me explain. First, I will quote a definition of an effective method:

The Turing-Church thesis concerns the notion of an effective or mechanical method in logic and mathematics. ‘Effective’ and its synonym ‘mechanical’ are terms of art in these disciplines: they do not carry their everyday meaning. A method, or procedure, M, for achieving some desired result is called ‘effective’ or ‘mechanical’ just in case

1. M is set out in terms of a finite number of exact instructions (each instruction being expressed by means of a finite number of symbols);
2. M will, if carried out without error, always produce the desired result in a finite number of steps;
3. M can (in practice or in principle) be carried out by a human being unaided by any machinery save paper and pencil;
4. M demands no insight or ingenuity on the part of the human being carrying it out.

Now, consider the problem at issue, that of locating prior scientific work on some topic. We’ll need to establish some points.

A. Except for the very most restricted of topics, the scientific literature is too voluminous to be retained in detail in the memory of any one person. (Even someone with an eidetic memory can only flip pages so fast. Using a repository like a library is thus required.)

B. No repository, collection, or database of scientific literature offers a complete index or better coverage of that literature. (One cannot rely upon any single repository, collection, or database to allow one to survey all the work on a chosen topic. Comparisons of results from separate databases show that upwards of a third of entries present in one may be absent in another.)

C. Systems for search based upon less than full content are inadequate. No information retrieval system known can entirely replace or make up for a lack of supplying appropriate keywords. Keyword identification for indexing can be incomplete or erroneous.

D. Insignificant or negative results are commonly left unreported.

E. Methods that are tried, but fail to meet desired criteria for producing reliable results, are almost never reported.

What I will assert here is that there is no effective method that will, for each and every choice of scientific topic, produce the result that one will obtain a list of the existing publications that bear upon that topic, and cannot produce the complete range of work that has been attempted on the topic. Where one may occasionally obtain a complete result is likely to be where the topic is both recent in origin and where there are yet few relevant published papers.

Certainly, one can apply certain steps and often obtain a partial list of existing publications. Consulting this specific library or that specific database, where library and database are each noted for extensive and general holdings or entries, will likely provide one with some relevant references. But this does not alter the fact that a complete review of relevant literature is not only highly unlikely for any particular topic; it becomes much less likely that for any series of unrelated searches that one would obtain a complete review in every case.

Why should completeness be desirable or desired for this problem? Certainly, completeness has been unobtainable for well over a century, and yet scientific practice continues and has accomplished amazing things. I would argue that scientific practice has succeeded in spite of instead of because of existing methods of reviewing prior work. There are a number of inefficiencies that result from our current methods. First, researchers may unknowingly replicate work. “Reinventing the light-bulb” has entered popular language as the extreme example of this outcome. This problem is not even limited to the natural sciences; it is also endemic to the practice of mathematics, as illustrated by the case of “intelligent design” advocate William A. Dembski re-inventing the Renyi information measure where a=2 in a self-web-published article (see this page for details). Second, researchers are denied the benefit of prior thought and effort in a field of inquiry. Where this does not actually involve “re-invention” scenarios, it will mean that synthetic thinking will be handicapped by keeping prior work obscure. Third, incompleteness implies that the most successful modern researchers are likely to be those who not only have a primary aptitude in their field of specialization, but who also have a high aptitude in being able to mine the current system of literature retrieval for the best available approximation to complete results on specific inquiries. These are the people who will least often find themselves in the position of getting negative comments in peer-review for having overlooked prior work. This secondary aptitude is largely a matter of talent and art rather than application of a straightforward set of techniques, which means that scientific success is a composite of work done using the scientific method and of work done in the tradition of scholarship in the humanities, which is in various aspects not well systematized. This violates item (4) in the list of attributes of an effective method given above.

There are various other drawbacks to incompleteness that could be explicated, but I think that these are enough to show that the problem is real and worthy of our attention. OK, at this point I’ve either convinced you that there is a problem worth considering, or that I’ve gone completely loopy. If the latter, you can drift off to doing something else, and take it as read that I already know that a substantial number of readers will disagree with me on this stuff.

Please note that my list of issues that lead to incompleteness are more inclusive than simply accusing the library sciences of not having delivered a solution. Part of the problem includes what is deemed worth remembering and preserving about effort in the sciences that is not directly fruitful. Just as “hunting” does not mean “catching”, so too does “research” often fail to obtain a desired result. Knowledge about methods that are ineffective or not well-suited to particular problems is useful in the sense that it, if it is published and attended to, can reduce wasted effort on the part of other researchers. There is a lot of jocularity concerning the titles of the humor magazines, “The Journal of Irreproducible Results” and the “Annals of Improbable Results”, but various researchers in conversation will admit that there is something to the notion that our current emphasis on telegraphic reportage of results overlooks the utility of laying out not only what worked in a research project, but also the usually various problems that a research effort encounters and sometimes overcomes.

Given that I have advocated for the existence of a problem, a reasonable concern is whether I have any constructive notion about what to do about it. I think that the problem is certainly difficult, but I do have hopes that it may actually be soluble. What remains to be seen is whether the level of sustained effort that would be necessary to get to a solution that meets several of the properties of an effective method would be worth the very real costs associated with it.

The first cost would be freeing scientific knowledge from the grip of commercial interests. The publication of scientific research is largely done in such a way that the publishing entities expect to retain rights to the work published and be compensated in some way for access to that work over a significant period of time (copyright currently granting something like most of a century of protection). This is a large problem in itself, as current research appears in a bewildering array of thousands of research journals, each applying somewhat differing standards and procedures to the peer-review process. Indexing services themselves add another layer of costs, and any solution to the problem is going to have the side effect of putting these services out of business.

Another cost would be in establishing a comprehensive means of surveying past work. While one may argue that current research is of most value and that a system might be contemplated that would deliver comprehensive and complete results concerning work more recent than some arbitrary date nnnn, this is a bit short-sighted. Once one has the procedural and other concerns taken care of for solving the case of the scientific literature more recent than nnnn, one simply has the finite and diminishing body of surviving work as one expands the system to include earlier values of nnnn. We may as well make a determined effort to incorporate the corpus of human knowledge in the natural sciences in the system.

A further cost lies in making any such system universally accessible. One could argue that, having spent the time, effort, and money to develop a comprehensive system for retrieval of knowledge in the natural sciences that one should attempt to recover part of that cost in direct fees from users. I think that, too, is short-sighted. The benefit of open access to this knowledge lies in fostering work that would in turn be added to the system. Along the way, one would expect that applied results will generate economic benefits that should make the costs discussed so far trivial in comparison. That, though, is simply my expectation and could be a point of argument.

There are the costs of overcoming the technical hurdles in search. I think the progress that was made from 1994 to the present in generating relevant results to natural language queries concerning the unorganized content of the World Wide web indicates that this problem, too, should yield to some concentrated effort, or at least give an approximation to complete results that significantly advances and enhances the progress of scientific research.

There are the costs of changing what gets reported as a scientific result. We need to compensate the time needed to not only briefly report what eventually worked in research (as is done now), but to also report, in sufficient detail to provide a basis for others to benefit without having to travel down false paths themselves, what problems were encountered in technique and methods. This also includes the cost of expanding the volume of reported results to accommodate the extra words needed to do this.

Would a trillion dollars solve this problem? I think so, handily. I suspect that the actual cost would be a small fraction of that figure. (The post just previous reports on how the Encyclopedia of Life project has, as a secondary effort, already digitized about 1% of the available literature on taxonomy for some fraction of their $25 million operating budget.) There are things that are costing us a chunk of a trillion dollars that don’t have anywhere near the potential for economic benefit that solving this problem in scientific practice might offer. In fact, it might be just the thing to do to prepare to pay that outstanding bill.

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Evolution 2008, Day 3: Encyclopedia of Life

I just heard a talk about the Encyclopedia of Life, a project to put up a page for every named species. They already have something like a million pages up, though many are stubs.

Another aspect of their project is to digitize every publication touching upon taxonomy. That reminded me of a draft post I’ve had hanging for a bit over a year now; I’ll put it up shortly. In any case, they estimate that there are some 80 million pages of pre-1923 taxonomic literature, and something near 400 million pages of taxonomic literature total, and that they have already digitized about 1% of the literature in the year or so that they’ve been operating.

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Louisiana: An Open Letter to Gov. Jindal

The Louisiana legislature has passed a bill allowing teachers to insert essentially whatever they want into curricula about evolutionary science. The only thing that remains is for Governor Jindal to either sign it into law or allow it to take effect without his signature, and thus the only thing to stop it is a veto by Jindal. Contact information for Jindal:

Contact Information:

E-mail: http://www.gov.la.gov/index.cfm?md=form&tmp=email_governor

Phone: 225-342-7015 or 866-366-1121 (Toll Free)

Fax: 225-342-7099

And the message I sent:

Please veto SB 733.

This bill does not improve science education. It is backed by groups like the Discovery Institute, whose preferred arguments require revising the definition of science in order to privilege their own account of biological origins. Those arguments also are clearly taken from the religious antievolution movement’s past ensemble of arguments.

That has three implications that you should consider.

1. Parents who do not share exactly the religious views promoted by the Discovery Institute, Answers in Genesis, and the Institute for Creation Research are ill-served by having the State of Louisiana abandon its responsibility in determining what teachers will — and will not — instruct their students about. A substantial proportion of Christians have no problems accepting the results of science; see the Clergy Letter Project at evolutionweekend.org, where over 11,000 US Christian clergy have signed a statement supporting the teaching of evolution and the exclusion of “intelligent design” arguments from science classrooms.

2. Antievolution arguments encourage students to distrust both the scientific process and scientists. A common theme is that mainstream science is covering up information that would point to creationism. This distrust is unlikely to help students fit into a society that is increasingly dependent on constant advancement of technology to remain competitive in the global marketplace.

3. The antievolution arguments are long-rebutted, and represent a misrepresentation of the state of science today. There is no secular purpose to teaching misinformation to students. The antievolution arguments are not in any sense a “state of the art” addition to a curriculum, and are easily linked to their earlier, explicitly creationist, forms. This means that there is no hope that a teacher choosing to use SB 733 as a means of teaching antievolution arguments could defend a challenge in court. This needlessly exposes Louisiana teachers and school districts to significant legal liability.

The religious, sociological, economic, and legal ramifications of SB 733 all require that you veto the bill. I hope that you will do so. The stated cover of improving academic freedom or education generally is a sham.

Wesley R. Elsberry, Ph.D.
Visiting Research Associate
Michigan State University

If you write something to Governor Jindal, please copy it to the comments here.

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Evolution 2008, Day 1

I arrived last night here in Minneapolis. This morning, Weezie Mead from NCSE and I made our way over to the Bell Museum of Science for a K-12 Education workshop. The primary goal was to provide teachers with materials about effective teaching of evolutionary science to students.

This evening, there was a reception at the Bell Museum.

I will be transferring photos and getting those processed. I’ll post more later.

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Things That Make You Go, “Hmmmm.”

For the past several weeks, I’ve been getting email from L. Scott Smith announcing his new blog. I took a look on the first email, but it wasn’t really the sort of thing I’m looking for in reading material. And then there were the repetitions, with as many as three of the identical email announcements coming in within a couple of hours:

A new blog appears at _http://[REDACTED]_
(http://[REDACTED]) .

Here’s the logs showing the same announcement coming in:

1080531 09:44:34 mai From: LSSesq114@[REDACTED]
1080531 09:56:31 mai From: LSSesq114@[REDACTED]
1080531 10:01:10 mai From: LSSesq114@[REDACTED]
1080605 09:04:21 mai From: LSSesq114@[REDACTED]
1080605 09:23:05 mai From: LSSesq114@[REDACTED]
1080605 09:29:52 mai From: LSSesq114@[REDACTED]
1080612 08:06:13 mai From: LSSesq114@[REDACTED]
1080612 08:20:39 mai From: LSSesq114@[REDACTED]
1080612 08:28:52 mai From: LSSesq114@[REDACTED]
1080618 07:28:54 mai From: LSSesq114@[REDACTED]

So this morning I sent what I thought of as a polite note for L. Scott Smith to turn off the verbal diarrhea:

I have already been informed of the existence of your blog some eight
times before. Please remove my email address from your notification
list. The next redundant “New Blog” message I get from you will have
me dropping your email address into the blacklist here.

Wesley

I was going on memory for “eight”. It turns out “nine” would have been more accurate.

Here’s the log entry for the reply: 1080618 07:48:39 mai From: LSSesq114@[REDACTED]

And the content of the reply was that, of course, he would remove my email from his list, as this was the first time that he had heard from me that that was what I wanted. And, he suggested, I should have a cup of coffee and stop being a curmudgeon.

Of course, one would expect that given notice that one’s email announcements were out of control, that one might show some gratitude, or at least some mercy. Smith’s anti-curmudgeon note to me was bracketed with two further redundant announcements:

1080618 07:44:15 mai From: LSSesq114@[REDACTED]
1080618 07:50:12 mai From: LSSesq114@[REDACTED]

So, what do you think? Was I curmudgeonly enough?

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Ohio: The Next Lawsuit Arrives

The Mount Vernon News reports that a civil rights complaint has been filed against “Mount Vernon City School District Board of Education, superintendent Stephen Short, middle school principal William White and science teacher John Freshwater.”

Freshwater, it appears, is a real piece of work, a 21st century Bernardo Gui:

In December 2007, the complaint continues, Freshwater burned an easily identifiable cross into the arm of at least two eighth-grade students with an electric device manufactured by Electro-Technic Products Inc. The complaint states, “Mr. Freshwater knew that the electric device, model BD-10A, could cause harm if placed in contact with human skin. As the eighth-grade science teacher it is Mr. Freshwater’s duty to understand and follow the manufacturer’s advice regarding the proper use of science equipment.”

Nothing like a little torture to advance the faith, eh?

It looks like a defense will be attempted. Maybe Freshwater should call the Thomas More Law Center. It used to be that one would pray to St. Jude. Now, dropping a call to Richard Thompson is almost the equivalent, except that occasionally St. Jude seemed to rescue a lost cause.

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A Wide Experiment

I’m putting a poster together to take to the Society for the Study of Evolution meeting next weekend, and the recommended facility for printing is the MSU library. It turns out they have an HP 4500PS wide-format inkjet printer that prints stuff on 36″ wide rolls of paper. And they charge $6.00 per linear foot, or $2.00 per square foot. That’s a fifth the cost that Kinko’s quoted me.

So I plan to take more than just the poster file with me. I figure I’ll get a couple of other things printed up large.

Diane requested a panorama I did for her back when we lived in San Diego. I went down to Shelter Island and took pictures of the harbor using my trusty 24mm f/2.8 Nikkor. I originally used the Canon PhotoStitch application for putting the pictures together, and it worked out OK. But last night I dug up the originals and put them into the Hugin application. I had some difficulty because I hadn’t gotten the idea that one should overlap about a third to a half from image to image; my panorama shots overlapped just small parts of edges. That meant the Autopano-SIFT function did not find control points automatically on several image pairs, and I had to add those myself. But once I did that, the application put together an 11784×2853 pixel image for me. The Enblend part of Hugin has it all over the PhotoStitch program for making visually seamless joins.

First, the PhotoStitch version:

shelter island pano01 ws

Now, the Hugin version:

DSCF3451 DSCF3458 crop ae ws

That is perhaps not completely fair, because the Hugin and PhotoStitch versions are based on different sequences of photos. I hadn’t realized that when putting the Hugin version together. In any case, I’m planning on splitting the Hugin version in two, and printing both at about 18″ high so as to reduce the linear foot charge. I’ll have one physical join to make between the two images from the printout.

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Ken Miller Was on Science Friday Today

NPR’s Science Friday hosted Ken Miller. Miller is promoting his new book, Only a Theory: Evolution and the Battle for America’s Soul. And he’s doing a good job of it, too. A student called in asking about evolution being forced on children in school, and Miller rebutted that, saying that evolution is no more forced on students than algebra, English, or history. He brought up the point that in schools students should be exposed to the very best thinking on subjects, and not long-discredited objections to topics snuck in via political fiat.

Another caller asked Miller about what he termed as serious criticisms of evolution, such as the improbability of proteins forming by accident and “the fossil record”. He asked why evolution should be exempt from scrutiny. I expected Miller to hand the guy his arse on a platter, and I was not disappointed, though Miller’s arse-ectomies are, characteristically, done with such charm and verve that the victims simply may not feel much sting from it. Miller took the points in reverse order, and started by pointing out that evolution does not escape criticism, which the caller could confirm by attending any scientific conference touching upon evolution. Then Miller took up “the fossil record”, and noted that some of the best evidence for evolution comes from the fossil record, despite the antievolution fondness for saying that there are gaps. Miller recounted how antievolutionists have emphasized the transition from fish to amphibians as one large gap, but that recent evidence has given us about five instances of fossils from this transitional sequence, and the most remarkable of those being Tiktaalik, a fossil whose discoverers predicted where to find it. (Miller plugged Neil Shubin’s book, Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body.) And then Miller took up the protein assembly objection, noting that nobody is proposing that proteins come to have the structure they do by accident, and that students learning this discredited notion would not be hearing about the phenomenal amount of work going on in molecular biology on this topic, all of which supports evolution.

Nice job, Ken, and good luck with the book tour.

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Tom Willis Has a Problem

Remember Lauri Lebo discussing the social costs of confronting religious intolerance in her book, “The Devil in Dover”? Did you think that the problem was confined to rural Pennsylvania?

Here’s Tom Willis, one of the architects of the evolution and cosmology-less science standards in the state of Kansas back in 1999:

The Real Meaning of This Essay

The arrogance displayed by the evolutionist class is totally unwarrented [sic]. The facts warrent [sic] the violent expulsion of all evolutionists from civilized society. I am quite serious that their danger to society is so great that, in a sane society, they would be, at a minimum, denied a vote in the administration of the society, as well as any job where they might influence immature humans, e.g., scout, or youth, leader, teacher and, obviously, professor. Oh, by the way… What is the chance evolutionists will vote or teach in the Kingdom of God? But, of course, I myself, am not deluded. “Kingdom Now” theology notwithstanding, I have no expectations that such a proposal will ever be implemented, for the simple reason that delusion is ordained by God to reign until Christ returns. (2 Thess 2:10)

That’s simply odious. And… he considers theistic evolutionists to be worse, if that is possible.

Religious intolerance of the sort promoted by Willis and various other antievolutionists needs to be confronted and repudiated.

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Lauri Lebo’s “The Devil in Dover”

The Devil in Dover
Lauri Lebo
The New Press
(http://laurilebo.com)

I had been steadily working on analysis of an experiment that I will be presenting later this month, but Sunday afternoon a line of thunderstorms blew through here, and somewhere in there the power went out. My work laptop runs out of juice quickly when running Avida, so that’s closed up. There’s only so much playing with the puppy that I can handle at a time, and somehow I feel a need to do something.

Several of my fellow bloggers at the Panda’s Thumb have been talking about journalist Lauri Lebo’s new book, “The Devil in Dover”. There’s about five who say that they are in various stages of writing reviews to be blogged here, there, or published in the mainstream media. And they all, to a man (yes, all of them are male), love it. About ten days ago, Lauri Lebo even gave me a personally inscribed copy (I contributed a photo for the front of the dust cover design and set up her personal website for the book). I hadn’t gotten around to actually reading the book, though, until the lights and power went out, reducing my options. But I have to say that the book is good enough to wish for a power outage. I have remedied that piece of ignorance with the help of a flashlight and a couple of changes of battery and can now speak to the content in the about two hours that my personal laptop has available in its battery charge.

The first thing to say is that Lauri’s book (and I do hope that I am not unjustly taking liberties in our acquaintance to say “Lauri”) is not just a journalist’s compilation of data, but rather an intensely personal book. There are several threads of personal involvement that Lauri takes up here. Perhaps the most touching is her relationship and estrangement from her father, who converted to fundamentalist Christianity several years ago and persistently searched for signs that Lauri would also be “born again” as he had been. But also there is the personal struggle with those in her profession who misconstrue journalistic “objectivity” perversely as a charge not to speak the truth when a situation indicates that a “side” is plainly in the wrong.

Continue reading

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Powerless

Literally. Bad weather yesterday knocked out power in a variety of spots in and around Lansing. DTE, bless their hearts, still haven’t upgraded their outage reporting phone bank, so while the power went down around 4:30 PM where I was, I didn’t actually get connected to their automated system until about 11 PM. That system took my phone number and promised a service tech would call back.

Yeah. I really believe that one.

So, emergency preparedness… not so hot. We’d be really deeply inconvenienced if we didn’t have the travel trailer, and even that isn’t as useful as it might be. Diane took it to a field trial event and stopped by the Flying J truck stop on the way back. Flying J’s often have RV dump stations, and she used that one, but also used almost all the fresh water in flushing out the tanks. Our main issue is going to be fresh water availability. Our house uses well water and an electric pump. No AC on the mains, no water from the well. We may need to take the trailer out and find a station with a potable water spigot sometime today.

We have the travel trailer refrigerator, which should run for most of a week on the propane that we have. I’ve hooked up an extension cord to run into the house and am currently running the generator to power the inside refrigerator and freezer. I’ll do that periodically today. That’s also why I can get online now, with the laptop charging up and using the Verizon phone card for the laptop. We are OK on basic foodstuffs.

Diane tells me that the power has been out here for a couple of days at a time before, when tornadoes hit Williamston. This is one drawback to a rural location, in that we are pretty much at the bottom of the service list. We’ll get our power back pretty much last.

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Mac OS X and Midnight Commander: The Missing “Insert” Key

I do a lot of work at a Unix command line interface on the MacBook Pro. One of the very handy things I use pretty much all the time is the GNU Midnight Commander (mc) application. This is a text-mode file manager interface that sets up two panels that can show two different directories, and provides most of the file operations one needs to get things done.

One thing that I’ve missed for some time is an “Insert” key, which I have under Windows, FreeBSD, or Linux, but the MacBook keyboard doesn’t have one. In mc, “Insert” tags individual entries for group operations. I had done some Googling before without success, but this morning hit paydirt: <ctrl>-T will tag an individual entry in mc. That made cleaning up after some of the automated processes I’ve been running much more pleasant.

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Welcome to the Pack, Little One

OK, there’s a new critter underfoot here. Follow the link for a “cute” overdose.

But there is some method here… we’re looking for a canine substitute for a weasel or ferret, to pop down rabbit holes and flush the rabbits out where the hawks can have a chance at them. This one should be about ready to hunt come fall. So far, the hawks seem to have no problem recognizing that the new pack member is not a rabbit itself.

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Biologic Institute Releases “Stylus”

The Biologic Institute, the Seattle research arm of the Discovery Institute (not to be confused with the older North American Biologic Institute of Boca Raton, FL, lab for blood chemistry analysis and medical supplier), has a paper on PLOSone announcing a software package, Stylus. Stylus is supposed to do something relative to investigating protein chemistry by simulating evolution of, um, Chinese characters.

The authors, Douglas Axe, Brendan Dixon (he of the Microsoft moneybags), and Philip Lu, know that they are basing their whole effort here on analogy. Given the far-fetched proposition that something useful about evolution of protein chemistry can be learned by examining Chinese characters, one should give them props for making about as forceful an argument by analogy as yet has been seen from religious antievolutionists. You see, certain Chinese characters bear a resemblance to certain protein folds, if one orients the protein in question in just the right way and projects it onto a 2D space. (You knew “METHINKS IT IS LIKE A WEASEL” would be relevant in here somewhere, right?) And since Chinese is a language, and various people have talked about DNA and proteins being language-like, surely it can’t be a stretch to think that there is some deep connection between Chinese character space and protein space… OK, I think that’s enough sarcasm.

The primary fault in this paper, IMO, is that their analogy presumes that protein space is as rugged and, perhaps more importantly, as discontinuous as a Chinese character space. This is by no means established, though they try to give that appearance via citation of Axe’s previous studies.

We have no expectation that Chinese character sets should be evolvable from scratch and represent a spannable set. The significant question for the Stylus team isn’t whether they can do something with Chinese characters, but whether this has any bearing on the issue of whether observed proteomics are in fact spannable given genetic operators. Meaning of Chinese characters doesn’t offhand seem to be a good stand-in for protein function, not least because of the subjective nature of the former and objective nature of the latter.

Now, I have another issue… the Stylus software itself. The Biologic Institute has a SourceForge project set up for this, and one can get the software from there via SVN (sorry, no package for Stylus as of yet):

svn co https://biologicstylus.svn.sourceforge.net/svnroot/biologicstylus

The software is specifically stated to run on FreeBSD, and I have a FreeBSD 6.3 desktop. I should be in good shape.

The README gives some requirements for compiling, and a few “pkg_add” instructions take care of that:

pkg_add -r libxml2
pkg_add -r swig
pkg_add -r python

But the “bootstrap” configuration script provided errors out with a complaint about a bad substitution for “OSTYPE”. The help output for the script doesn’t seem to mention OSTYPE at all. I have an email off to the supplied address at the Biologic Institute to see if someone there has further details to offer.

(Given that Axe is elsewhere critical of Avida, I’ll note that at least one can obtain and compile Avida if one follows the instructions.)

Update: Reed Cartwright pointed out that they have hard-coded “make” in their scripts, and “make” differs between FreeBSD and Linux. So I downloaded Stylus to my Xubuntu, loaded the specified prerequisites, and still got the same set of errors on running “bootstrap”.

Update: I got a very nice note from Brendan Dixon in response to my inquiry on difficulty getting the program going. I’ll see if I can make progress based on that. One thing he notes is that despite what it says on SourceForge, he hasn’t installed Stylus on a FreeBSD system. So I’ll concentrate on getting it running on my Xubuntu install first.

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Flunked, Not Expelled: “Imagine” Use is Fair, Judge Rules

Yoko Ono’s lawsuit went nowhere in Judge Sidney Stein’s courtroom. The judge ruled that “Expelled”‘s brief use of the John Lennon song, “Imagine”, was permitted under “fair use” exceptions to copyright law. [Update: It appears that the ruling was just on the preliminary injunction, which is now lifted. The full case is still pending.]

Hopefully other judges elsewhere will be on that same wavelength when it comes to people criticizing snippets of “Expelled” in video segments.

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