February 2011 Archives

Scientific American has posted what you might call a compendium of articles on evolution – some from the archives, some brand new.

The featured articles include a new article by Lauri Lebo, who details the manner in which creationists hide their true intentions by using code words such as “helping students understand, analyze, critique and review in an objective manner the scientific strengths and scientific weaknesses of existing scientific theories covered in the course being taught.” Indeed, in a display that gives chutzpah a bad name, they invoke the name of John Scopes, because he stood up for academic freedom.

Hole-punch cloud

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IMG_0743_HolePunchCloud.JPG

Hole-punch cloud, Westmann Islands, Iceland, 2010.

Asserting that the Second Law of Thermodynamics (2LoT) means that evolution is false is a perennial favorite out of the ensemble of religious antievolution arguments. It takes a subsection of the Index to Creationist Claims to cover the various ways it most often gets presented by a religious antievolutionist. The TalkOrigins Archive has a series of longer responses to the sometimes bizarre range of 2LoT folderol coughed up by religious antievolutionists. Even “Answers in Genesis” notes that one variant, that 2LoT started with “The Fall”, is among arguments that should never be used.

So what can one make of a recent attempt to publish a batch of 2LoT religious antievolution as if it were a genuine scientific contribution? E. Granville Sewell, a mathematician at the University of Texas at El Paso and “intelligent design” creationism (IDC) advocate, submitted a manuscript to Applied Mathematical Letters (AML) titled, “A second look at the second law”. AML apparently indicated acceptance of the manuscript to Sewell, leading to gloating on an IDC blog. That in turn led to action by David vun Kannon from the “After the Bar Closes” forum, who wrote the editors at AML to point out the problem. AML responded to vun Kannon, saying that they were withdrawing the manuscript.

More below the fold.

by Joe Felsenstein,
http://evolution.gs.washington.edu/felsenstein.html

Granville Sewell is a mathematician at the University of Texas, El Paso, who is an expert on numerical solution of differential equations. He is also the author of repeated arguments that the Second Law of Thermodynamics makes it impossible for evolution to improve living organisms.

The obvious reply is that the biosphere is not an isolated, closed system, that to come near having one, we must also include the sun which undergoes a huge increase of entropy as it radiates energy, that more than compensates for the much smaller decrease of entropy involved in the evolution of life.

William Dembski, at Uncommon Descent, has announced that a paper by Sewell is in press at Applied Mathematics Letters. Sewell makes available a preprint version here. It is the same argument Sewell has been making lately:

Thus the equations for entropy change do not support the illogical “compensation” idea; instead, they illustrate the tautology that “if an increase in order is extremely improbable when a system is closed, it is still extremely improbable when the system is open, unless something is entering which makes it not extremely improbable”.

And Sewell does not think that anything has entered the Earth that explains the decrease of entropy by evolution of life because, as he said in a paper in The Mathematical Intelligencer in 2001:

if all we see entering is radiation and meteorite fragments, it seems clear that what is entering through the boundary cannot explain the increase in order observed here.

We should be grateful to Sewell: he has apparently proven something astonishing.

A year ago, I pointed out here at Panda’s Thumb that if true, Sewell’s arguments showed that weeds could not grow in a garden – that a few weed seeds could not turn into weed plants bearing many of the same seeds. All we see entering the weeds is (mostly) radiation from the sun, carbon dioxide, water, and a few minerals. Following Sewell’s logic, this is not enough to explain the decrease of entropy involved in the growth of the weeds.

Sewell continues to make the same arguments. If not only the Discovery Institute, but also William Dembski and, now, Applied Mathematics Letters [1] validate Sewell’s arguments, who are we to resist? We must get the word out, especially to gardeners. Sewell’s formulation of the Second Law proves conclusively that:

* Weeds can’t grow in your garden

and for that matter

* Flowers can’t grow either.

Granville Sewell may have saved gardeners a huge amount of wasted effort.

Notes

  1. Editor: Reports indicate that the Applied Mathematics Letters has rescinded the acceptance.

Free documentary, Kansas vs. Darwin

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According to NCSE, in honor of Darwin Day, 2011, the documentary movie Kansas vs. Darwin is available free on the web through March 14 – that is, for the 30 days following Darwin’s birthday.

Thanks to Karen Spivey for the tip!

A high-school student’s activity spearheading a grass-roots movement to repeal Louisiana’s inaptly named Louisiana Science Education Act is “a profile in (evolutionary) courage,” according to Michael Zimmerman, writing in the Huffington Post.

According to Professor Zimmerman, the student, Zack Kopplin, has already succeeded in influencing the Board of Elementary and Secondary Education to adopt a new biology textbook, in the face of opposition from the powerful Louisiana Family Forum. More recently, State Senator Karen Carter Peterson announced her intention to introduce legislation repealing the LSEA, which promotes the use of “supplemental materials” in the classroom. Supplemental materials is a code term for literature that promotes creationism and attacks evolution.

Wesley Elsberry reported briefly on Mr. Kopplin’s campaign here. Please do not rehash that discussion on this thread.

Instead, please help make sure that Professor Zimmerman’s article gets the widest possible readership.

Kelvin-Helmholtz wave in clouds

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Photograph by Deanna Young

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Unusual cloud formation showing Kelvin-Helmholtz waves, Boulder, Colorado, 2010. Thanks to Kelly Chipps for providing the link.

I talked to Bill Dembski in person about my work on using Genetic Algorithms to solve Steiner’s problem way back in 2001. He didn’t “get” it then, and he still doesn’t!

Reacting to this news story, “Supercolony trails follow mathematical Steiner tree”, Dembski writes today that

Some years back, ID critic Dave Thomas used to tout the power of genetic algorithms for their ability of solve the Steiner Problem, which basically tries to minimize distance of paths that connect nodes on a two-dimensional surface (last I looked, he’s still making this line of criticism - see here). In fact, none of his criticisms hit the mark – the information problem that he claims to resolve in evolutionary terms merely pushes the design problem deeper … In ID terms, there’s no problem – ants were designed with various capacities, and this either happens to be one of them or is one acquired through other programmed/designed capacities. On Darwinian evolutionary grounds, however, one would have to say something like the following: ants are the result of a Darwinian evolutionary process that programmed the ants with, presumably, a genetic algorithm that enables them, when put in separate colonies, to trace out paths that resolve the Steiner Problem. In other words, evolution, by some weird self-similarity, embedded an evolutionary program into the neurophysiology of the ants that enables them to solve the Steiner problem (which, presumably, gives these ants a selective advantage).

Kudos to Dr. Dembski for this classic Goal-Post movement! The purpose of my original article was simply to move the discussion of Genetic algorithms beyond the ID “Dawkins Defense,” namely that all genetic algorithms suffer the “Weasel” flaw of needing the solutions to be incorporated directly into the fitness function.

Dembski’s response is remarkable in that it totally avoids the issues I raised. Just because ants can find ways for colonies to make efficient paths has no bearing on whether genetic problems can be applied without having solutions in hand already.

My original article on Steiner (Target? TARGET? We don’t need no stinkin’ Target!) showed that there are also physical methods for solving Steiner’s problem, including minimal-surface soap films.

If soap films can solve Steiner problems, why not ants? And this bolsters the Weasel defense, how?

My Skeptical Inquirer article from last year, “War of the Weasels: An Evolutionary Algorithm Beats Intelligent Design” has a nice summary of these Weasel Wars, including the marvelous story of UD’s software engineer, Sal Cordova, getting whupped by a Genetic Algorithm on an open-book design problem. The article posting is courtesy of Southern Methodist University’s Critical Thinking/Physics Class!

More: Panda’s Thumb’s “EvoMath” category.

New Mexico Creation Bill Tabled

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After a series of very strange stories on New Mexico’s proposed House Bill 302 (see my earlier report for bill text and comments), Rep. Thomas Anderson’s House Bill 302 was tabled on a 5-to-4 vote in the NM House Education committee this morning.

Why were the stories strange?, Well, sponsor Anderson told the Santa Fe New Mexican that the bill was written by him, and not by the local Intelligent Design group (Measure clears way for teaching of ‘intelligent design’ by Steve Terrell, The New Mexican, Tuesday, February 08, 2011):

Both Newton [of the National Center for Science Education] and Thomas[president of New Mexicans for Science and Reason] said they believe Anderson’s bill is based on model legislation from a Seattle-based intelligent-design think tank called the Discovery Institute. Anderson said he’d heard that accusation, but says the bill is his own. Though Anderson insisted the bill is not focused on evolution, it is being backed enthusiastically by an anti-evolution group in the state. …

Then, Anderson told the Albuquerque Journal (“Sponsor: Bill Is About Teachers, Not Creationism,” Dan Boyd, Feb. 16th) that

“My bill has been hijacked by people who want to talk about religious issues.”

The local Intelligent Design group wasn’t nearly as humble, having posted text almost identical to HB 302 for years on their “OriginsEducation” website.

Oh yeah - there was also IDNet’s full-page ad in Monday’s Albuquerque Journal.

The word from Santa Fe is that sponsor Anderson is now regretting getting involved with the bill - and perhaps is feeling he was “left in the lurch” by IDNet-NM.

NMSR’s page has links to stories and news videos here, and a chart of the bill’s five-year-long evolution here.

Discuss!

There is a grassroots movement afoot to repeal the Louisiana law privileging creationism and other dreck under a false banner of “academic freedom”. Check out the site and lend what aid you can.

Enallagma civile

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Photograph by Greg Goebel.

GregGoebelDamselfly.jpg

Enallagma civile – familiar bluet – damselfly, Loveland, Colorado, 2009.

You may be sniffing at the end of this one. That, or making out.

Kevin Cryderman - The Only Thing (country pop) (4:25)

On Fits and Starts: Volume Two

Answers in Genesis hosted a “date night” last night at their Kentucky Kreationism Komplex, where couples could attend a talk by Ken Ham, dine in the main hall, and attend a concert. Talk about romance! And since AiG has pledged to not discriminate in order to obtain government subsidies, we all expect them to welcome gay couples to their event, right? Wrong.

Unfortunately, we were told at the door that we would not be allowed entry.

They explained to us that the Creation Museum Date Night was a “Christian environment”, therefore the presence of two men eating dinner together would not be allowed. The very sight of this would “add an un-Christian element to the event” and “disrupt the evening for everyone”.

But Answers in Genesis didn’t send them packing without a dessert; they refused to refund the tickets. We knew they were a bunch of scholastic frauds, but now we know they are a bunch of criminal frauds as well.

Freshwater files Notice of Appeal (Updated already!)

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See update at the end of the post.

John Freshwater, the Mt. Vernon, Ohio, middle school science teacher recently terminated by the Board of Education, has filed a Notice of Appeal (search by name for “Freshwater”) in the Knox County Court of Common Pleas. A Notice of Appeal is just that: It notifies the court (and public) that the plaintiff intends to appeal a decision of some other body to that court–it essentially reserves the option to file an appeal but does not require filing. Thereafter the plaintiff has a set period, typically 20 or 30 days (though I don’t know if teacher terminations have a different deadline), to file the appeal document itself detailing the respects in which the decision being appealed was allegedly faulty and therefore warrants overturning by the court.

Freshwater was terminated on two basic grounds outlined by the administrative hearing referee in his final report, violating the establishment clause of the First Amendment to the Constitution by teaching creationism and advocating for his fundamentalist Christian beliefs in school, and insubordination.

Freshwater filed the Notice of Appeal pro se, meaning that he is acting as his own attorney in the action. I have no information on whether he will seek professional legal advice in preparing the actual appeal document.

I do not presently have links to copies of the documents Freshwater submitted with the Notice of Appeal except for Hamilton’s final brief, which is the Closing Statement Brief (4Mb PDF). The most interesting documents appear to be “Complaint Filed with Resolution”, “Letter,” “John Freshwater’s Reply Brief to the Employer’s Post-Hearing Brief,” and “John Freshwater’s Closing Statement Brief.” As much as I can obtain will all be online soon on the relevant NCSE page.

If the Court of Common Pleas denies the appeal, the next (and last!) step would be for Freshwater to appeal that rejection to the state appellate court.

=======================

Update: I heard late this afternoon that Freshwater has gone ahead and actually filed his appeal, including the various documents and thousands of pages of the hearing transcript. I hope to have more information tomorrow.

HHMI to produce TV science films

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Two weeks ago Sean B. Carroll, evo-devo researcher, author, and new Vice President for Science Education of the Howard Hughes Medical Institute, visited Kenyon College where I used to profess. Our dinner conversation touched on the recent Freshwater fiasco in the local public schools, and the Q&A following his talk about Darwin, Wallace, and Bates (based on his book Into The Jungle) turned to the sorry state of general science knowledge in the U.S. I pressed him about it, asking whether in his new role with HHMI he proposed to do anything about it. His answer was “Wait for a press release on February 4.” Well, that press release is out now. It promises that HHMI will commit $60m “… to bring high-quality, compelling science features to television.”

Libellula quadrimaculata

Photograph by Andrew Freeman.

Photography contest, Honorable Mention.

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Libellula quadrimaculata – four-spotted skimmer.

ResearchBlogging.orgA couple of months ago we started looking at the concept of fitness landscapes and at some new papers that have significantly expanded our knowledge of the maps of these hypothetical spaces. Recall that a fitness landscape, basically speaking, is a representation of the relative fitness of a biological entity, mapped with respect to some measure of genetic change or diversity. The entity in question could be a protein or an organism or a population, mapped onto specific genetic sequences (a DNA or protein sequence) or onto genetic makeup of whole organisms. The purpose of the map is to depict the effects of genetic variation on fitness.

Suppose we want to examine the fitness landscape represented by the structure of a single protein. Our map would show the fitness of the protein (its function, measured somehow) and how fitness is affected by variations in the structure of the protein (its sequence, varied somehow). It's hard enough to explain or read such a map. Even more daunting is the task of creating a detailed map of such a widely-varying space. Two particular sets of challenges come to mind.

Over the past few years there have been increasing numbers of calls for governments to properly fund systematics and taxonomy (and a number of largely molecular-focused biologists insisting they can do the requisite tasks with magic molecule detectors, so don't fund old-school, fund new-fangled-tech). But I think that there is considerable confusion about what systematics and taxonomy are.

Now the usual way a philosopher resolves such questions, apart from interrogating their intuitions relying upon what they learned in grade school, is to go find a textbook or some other authoritative source and quote that. If it is someone they already know, all the better, like Mayr or Dawkins. This is problematic, so I thought I'd do a slightly better job at reviewing what people think. And then I will of course give my own view.

Science fairs in decline

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An article in today’s Times notes that participation in high-school science fairs is declining. At fault?

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Another antievolution bill has just been introduced in the New Mexico House:

AN ACT RELATING TO PUBLIC EDUCATION; PROVIDING FOR PROTECTION OF TEACHERS AND STUDENTS REGARDING THE TEACHING OF CONTROVERSIAL SCIENTIFIC TOPICS.
BE IT ENACTED BY THE LEGISLATURE OF THE STATE OF NEW MEXICO: SECTION 1. A new section of the Public School Code is enacted to read: “[NEW MATERIAL] TEACHING OF CONTROVERSIAL SCIENTIFIC TOPICS.–
A. The department, school district governing authorities and school administrators shall not prohibit any teacher, when a controversial scientific topic is being taught in accordance with adopted standards and curricula, from informing students about relevant scientific information regarding either the scientific strengths or scientific weaknesses pertaining to that topic. A teacher who chooses to provide such information shall be protected from reassignment, termination, discipline or other discrimination for doing so.
B. This section only protects the teaching of scientific information and specifically does not protect the promotion of any religion, religious doctrine or religious belief.
C. Public school teachers may hold students accountable for knowing and understanding material taught in accordance with adopted standards and curricula, but public school teachers shall not penalize a student in any way because that student subscribes to a particular position on the controversial scientific topic being taught.
D. For purposes of this section:
(1) “controversial scientific topic” includes biological origins, biological evolution, causes of climate change, human cloning and other scientific topics that are often viewed by society as controversial; and
(2) “scientific information” means information derived from observation, experimentation and analyses regarding various aspects of the natural world conducted to determine the nature of or principles behind the aspects being studied. “Scientific information” may include information that coincides or harmonizes with religious tenets, but does not include information derived from religious writings, beliefs or doctrines.”

Analysis below the fold.

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