Zooming in on the Origin of Life Science Foundation

Pharyngula -

I'd been wondering about the credibility of David L. Abel, an Intelligent Design creationist who claims to work in the Department of ProtoBioCybernetics and ProtoBioSemiotics, Origin of Life Science Foundation, Inc. I tried to track down this foundation with the lofty title, the million dollar prize, and the elaborately specific departments, but the best I'd been able to do was find a google satellite image.

Huh. That looks suspiciously like a suburban house.

So then someone from the Evil Atheist Conspiracy's vast network of spies and agents decided to drive by and get a picture.

oolfound.jpeg

Why, it is someone's house at that address! It's a nice but unpretentious little place in a residential suburb. There must be some mistake. This doesn't look like a fantastic institute of advanced science — it's got shady trees and a lawn and a basket of flowers by the garage and it looks like a typical two bedroom house.

But wait…what's that by the hanging basket? It's a sign of some sort. Look closer…

oolsign.jpeg

Yep, that's the place.

That's every intelligent design creationism institute of scientific thinking: a cheap sign tacked up on a garage, with some guy with delusions of competence twiddling his thumbs inside.

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Making excuses

Pharyngula -

The editor of Life, Shu-Kun Lin, has published a rationalization for his shoddy journal.

Life (ISSN 2075-1729, http://www.mdpi.com/journal/life/) is a new journal that deals with new and sometime difficult interdisciplinary matters. Consequently, the journal will occasionally be presented with submitted articles that are controversial and/or outside conventional scientific views. Some papers recently accepted for publication in Life have attracted significant attention. Moreover, members of the Editorial Board have objected to these papers; some have resigned, and others have questioned the scientific validity of the contributions. In response I want to first state some basic facts regarding all publications in this journal. All papers are peer-reviewed, although it is often difficult to obtain expert reviewers for some of the interdisciplinary topics covered by this journal. I feel obliged to stress that although we will strive to guarantee the scientific standard of the papers published in this journal, all the responsibility for the ideas contained in the published articles rests entirely on their authors. Discussions on previously published articles are welcome and I hope that, by fostering discussion and by keeping an open-minded attitude towards new ideas, the journal will spur progress in this little explored, difficult and very exciting area of knowledge.

In particular, the paper "Andrulis, E.D. Theory of the Origin, Evolution, and Nature of Life. Life 2012, 2, 1-105" was published recently online and is due to appear in Issue 1, Volume 2, 2012 of Life, at the end of March this year [1]. So that our readership has as much information as I can divulge without violating the confidentiality of the review process, what follows is the background of these events. Professor Bassez had previously guest-edited a successful special issue titled "The Origin of Life" in another MDPI journal [2]. Although Professor Bassez [3] had also planned to be the Guest Editor of the special issue "Origin of Life - Feature Papers" for Life [4], she was, for personal reasons, unable to do so. I therefore volunteered to take this responsibility on her behalf and to guest edit this special issue and supervise the editorial procedure for the papers. I made the decision of acceptance based on the peer review reports we received and their recommendation in support of publication. As stated earlier, finding reviewers able to cross discipline boundaries as is often needed for multidisciplinary "origin of life" topics [5] is particularly difficult. The publishing process that MDPI manuscripts go through by our in-house editorial staff members is that they choose reviewers from sources like Chemical Abstracts, PubMed, Web of Science or more recently, from Google Scholar. Very often we also ask the Editorial Board members to review papers or ask those of them who have relevant knowledge and expertise to supply possible reviewer names. We also use the reviewer names suggested by the authors, but we do this with great care, checking the background of each potential reviewer and their publication record, as well as ensuring they have no collaborations with the authors that may be construed as a conflict of interest. I should stress that although we try to encourage bold, innovative science, we reject many submissions. In the case of the Dr. Andrulis's long paper, the two reviewers were both faculty members of reputable universities different than the author's and both went to considerable trouble presenting lengthy review reports. Dr. Andrulis revised his manuscript as requested, and the paper was subsequently published.

Regardless of opinion on specific papers that have been published to date, I sincerely hope that all of our articles, most of which are outstanding, will continue to be read and discussed. Our editorial procedure is under scrutiny by the Editorial Board, who wishes to be more closely involved in the editorial process, and we are striving to further improve our editorial service. We welcome comments on the Dr. Andrulis's paper or any other papers that have been published in Life.

The "interdisciplinary" excuse is bogus. I am not a specialist in the fields discussed, but I could see immediately that Andrulis's paper, and Abel's paper as well, were "off" — to any critical, skeptical thinker their flaws are obvious. Are there any scientists in any field — general physics, biology, chemistry, psychology, for instance — who would read either of those papers and think maybe there's something to them? You'd have to be a fellow crackpot or somebody completely unqualified to evaluate any science papers to fail to see the problems in them.

Also, you don't need someone with great interdisciplinary knowledge to be able to screen out this kind of nonsense. I'm reminded of the comment I read on the Velikovsky affair: someone (it might have been Sagan) noted that the astronomers could see that Velikovsky's cosmic billiard game was bad physics, but gosh, his biblical scholarship sure was impressive; while the Bible scholars were all saying his mythology was all terrible literary scholarship, but golly, he sure seemed to know a lot of physics. Evaluating interdisciplinary work does not mean you cherry pick the most favorable interpretations from those most ignorant of a specific subfield, nor does it mean you split the difference and average the opinions of the subfields together. If one part of the mix is bullshit, you throw out the whole thing.

The fact that they're having trouble finding qualified reviewers for the work they're publishing is also ominous. Shouldn't the editorial board consist of people who are competent in this interdisciplinary field who can screen out the wackier submissions? And shouldn't it be setting off alarm bells when they accept suggestions of reviewers from authors, and those are the only people they can get reviews from? It's a situation ripe for selection by crackpots of crackpot reviewers; you just know that the Abel paper was reviewed by fellow travelers in the Intelligent Design creationism movement, and got no critical evaluation at all.

Given the spectacularly poor quality of the Andrulis and Abel papers, though, I am most amused by the claim that the editors and reviewers of Life "reject many submissions". I would love to see the papers that they judged worse than Andrulis's and Abel's.

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More bad science in the literature

Pharyngula -

That sad article on gyres as an explanation for everything has had more fallout: not only has it been removed from Science Daily's site, not only has Case Western retracted the press release, but one of the editors at the journal Life has resigned his position over it. The editorial board of the journal was completely surprised by the wretched content of the paper, which is not encouraging; apparently they exercise so little oversight at the journal that they were unaware of the crap their reviewers were passing through. One board member thinks it is a hoax, and laughed at off. Think about that; your shiny new journal has just published total garbage, and instead of being brought up short and questioning the quality control of the review process, you think it is amusing that what you consider an obvious hoax slipped in? There's something seriously wrong there.

Add this to the list of failures at Life: the paper immediaely after Andrulis's is this one, "Is Life Unique?", by David Abel. Guess what? It's Intelligent Design creationism crap. Here's the abstract:

Abstract: Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity--heat agitation and the cause-and-effect determinism of nature's orderliness--cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical.

It's drivel. The whole thing is one long windy argument from assertion, as in the penultimate sentence above, which is simply the bald claim that higher order functions of human functions like cognition cannot be derived from chemistry and physics. The paper itself contains no data at all — no experiments, measurements, or observations — but it is full of novel acronyms. Apparently, all you need to do to make it as a big time creationist is to make up new words and phrases and string them together. I checked out some of his other papers — he seems to be some kind of computer science guy, and this is all he does, is write impenetrably glib papers full of pretentious acronyms, posing as an expert on biology while saying nothing credible about biology at all.

But he certainly has an impressive address and affiliation!

Department of ProtoBioCybernetics and ProtoBioSemiotics, Origin of Life Science Foundation, Inc., 113-120 Hedgewood Drive, Greenbelt, MD 20770

Whoa. Sounds major. Unfortunately, I've never heard of this foundation, and all I could find out about it is a webpage in which they announce a million dollar prize for "proposing a highly plausible natural-process mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life." This sounds suspiciously like standard creationist dodging — they'll never have to award this prize. So I looked at their judging, and at first glance it seems impressive: they have over 200 judges, including Jack Szostak, Peter Atkins, Paul Davies, and Edward O. Wilson. But then, they mention that judging will be in 5 tiers, and only the ones that pass all other reviews will reach the Nobel prize winners and famous scientists…and the first tier is an "in-house review". I suspect the big names will never be pestered by this prize committee. Actually, I wonder if most of these judges know that their name is on this list. Maybe you should look in case you've been drafted.

I started wondering about this "in-house staff" who would be doing the initial judging, and about the Origin of Life Science Foundation itself. It's awfully hard to track down — its only web presence is the prize page, and its only employee seems to be…David L. Abel. So I looked it up in google maps to see where the foundation's majestic headquarters might be.

olsf.jpeg

It's a house in a residential neighborhood of a Maryland suburb. It made me wonder if maybe the Department of ProtoBioCybernetics was located in the master bathroom, while he Department of ProtoBioSemiotics was in the hall closet, or whether both were consolidated into a sunny corner of the kitchen. At least it seems to be a step above Patriot University, but it's still some guy's house that he's calling a Foundation with multiple implied Departments with fancy titles.

That's not all! Mr Abel seems to be a linchpin of the Intelligent Design movement, who manages to work his rambling, incoherent publications into all kinds of journals. In fact, the Discovery Institute just bragged about all their peer-reviewed scientific publications, and there, in their list of over 70 works published over the last 25 years or so, which includes papers by such famous scientists as William Lane Craig and John A. Davison, and prestigious journals like Rivisti di Biologia and their own in-house pet journal, BIO-Complexity, and also seems to include books that were not peer-reviewed at all, are twelve papers by Mr Fancy-Titled-Suburban-House. 17% of the Intelligent Design creationism movement's 'scientific' output comes out of that dwelling in Maryland.

I'd love to see the gigantic laboratory he must have in there.

For your edification, I've included the official complete list of Intelligent Design creationism's publications below the fold. It's an impressively short list of hackery.

And may I suggest that the journal Life has deeper problems than simply accidentally allowing one bad paper to slip into publication? I think it needs a negative impact factor.

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An open letter to the Indiana legislature

Pharyngula -

The Indiana Senate has approved this bill:

The governing body of a school corporation may offer instruction on various theories of the origin of life. The curriculum for the course must include theories from multiple religions, which may include, but is not limited to, Christianity, Judaism, Islam, Hinduism, Buddhism, and Scientology.

I've heard a few complaints from Hoosiers about this, including teachers. One high school science teacher has asked me to post this open letter on the subject; they've asked that I not include their name, which is sad in itself. Not only is the legislature passing stupid laws, but the environment is so oppressive that the science teachers who are expected to implement it cannot speak out against it, for fear of losing their jobs. Indiana, you suck.

At least I don't have to worry about the politicians of Indiana gunning for my job, so I can post this letter for my correspondent.

Honorable Representatives of the state of Indiana,

I am quite dismayed to learn of the passage of SB 89 which will give Indiana school boards the authority to require the teaching of various origin stories in public schools. There are several reasons I feel this is an inappropriate action for our state to take.

First, the Supreme Court of the United States ruled in 1987 in Edwards v. Aguillard that balanced treatment of creationism and evolution violated the Establishment Clause of the First Amendment. Then in 2005 the U.S. District Court in Pennsylvania ruled against the inclusion of Intelligent Design in the science curriculum. As Judge Jones wrote, "To be sure, Darwin's theory of evolution is imperfect. However, the fact that a scientific theory cannot yet render an explanation on every point should not be used as a pretext to thrust an untestable alternative hypothesis grounded in religion into the science classroom or to misrepresent well-established scientific propositions. The citizens of the Dover area were poorly served by the members of the Board who voted for the ID Policy." Now it appears that the citizens of Indiana are being poorly served. If this becomes law, our citizens will have to foot the bill for the lawsuits that will certainly ensue.

Second, I appreciate Indiana's need to educate our citizens about the beliefs and cultures of our planet's people. Our students would greatly benefit from learning about the multitude of worldviews that exist, in a philosophy or comparative religion class. Such understanding would make our citizens better prepared for international commerce and political discourse. I do not believe that SB 89 was introduced for this reason, however. The implication is that the introduction of various religious beliefs would take place in the science class room. As a biologist and science teacher, I understand the evidence for evolution is as strong as the evidence for any other theory we teach. I also understand that religious belief is based on faith, which by definition requires no evidence. I do not comprehend how exposing my students to ideas based, not on evidence, but faith could constitute good science education. When I read that this bill will allow school boards to require the teaching of "theories from multiple religions", I interpret this to indicate that a school board may specify which religions may be taught. Two constitutes "multiple", so if a school board so chose, they could require teachers to teach Christian and Jewish creation ideas only, which are essentially the same. This would not serve to enlighten students on the diversity of ideas, but to reinforce ideas that either they already hold or that they will find in conflict with their beliefs. In either case, it could set students at odds with each other, while not teaching any science at all.

If I am misinterpreting the spirit of this bill, please change the language to indicate that this is not to be applied to science classes, and/or specify which religions' views must be taught if the local school board chooses to require this. In my opinion, if this is to be done in any way consistent with spirit of the Establishment Clause, all religious views must be taught. In this case, teachers will not be able to cover the state science standards in 180 days and also teach religion.

Third, the misunderstanding of the word theory in the bill is a sad indication of the ignorance of the authors. In science, the word "theory" does not mean an "idea". A theory is an explanation for how something happens, based on a great deal of research which has been reviewed, published, tested, re-tested, accepted by most scientists in the field, and not yet disproven. No religion has a "theory" of the origins of life that meets the criteria we require to give an idea the full weight of the title "theory" in science. I would be happy to speak with any representative who would like to learn more about what the theory of evolution actually says and what evidence supports it.

Sincerely,

Indiana High School Science Teacher

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Your state's report card

Pharyngula -

The Fordham Institute has released their annual evaluation of state science standards. They are very tough graders — Minnesota got a "C". Ack! Mom & Dad are going to be pissed, how will we ever get into a good college at this rate?

state_sci_standards.jpeg

The Institute does a fairly thorough breakdown, so there are some bright spots: Minnesota is doing a good job in the life sciences, but where we got dinged hard was on the physical sciences, which are "illogically organized" and contain factual errors. Here's the introduction to their evaluation of our life sciences standards:

Important life science content is presented quite minimally, but the flow and logic are such as to convey an understanding of the concepts rather than coming across as a list of topics to check off. The inclusion of examples from Kindergarten through eighth grade helps to further explain what students should know and be able to do.

Minimal is OK, as far as I'm concerned; it think it's more important to get across a solid conceptual understanding. Of course, given that some teachers do a very poor job of getting those concepts across, more specific guidelines might be useful.

What's really awful about our C, though, is that that's the same grade Texas got. Oh, the ignominy!

I think we got robbed, though. The detailed breakdown says that a major problem is inconsistency: some bits of the Texas standards are stellar, others are terrible; different grade levels get variable quality of coverage. Texas gets slammed for life science standards that are "woefully imbalanced, with poorly developed material in the early grades and strong, sometimes excellent, content in the upper levels." The major flaws are entirely predictable.

Perhaps the biggest problem with the middle school standards, however, is their coverage of evolution. For instance, the seventh-grade standards mention the Galapagos finches, giving the impression that the Darwinian paradigm is being presented. Unfortunately, it is not. Instead, the example of the finch Geospiza fortis apparently refers to studies by Peter and Rosemary Grant on beak size in this species, made widely known by Jonathan Weiner's Pulitzer Prize-winning book, The Beak of the Finch. Creationists often distort these important findings to argue that Darwinian macroevolution does not occur--instead, microevolution does. In addition, the word "evolution" is never used in any of the middle school standards, and the term "natural selection" is never explained.

What's really telling, though, is the reactions. I just told you I'm disappointed with Minnesota's "C"; we can do better, and I hope the next round of standards will improve ours to an "A". In Texas, creationist kook Don McLeroy was happy with his "C".

McLeroy told the Texas Independent he is "very pleased" with the study and believes it only serves to validate the role he and the conservative bloc played in crafting the standards.

"The work of religious conservatives has been vindicated," he said, pointing to the report's positive review of high school evolution standards. When asked about the poor evaluation of middle school standards, McLeroy said blame could fall on the writing teams and review committees and/or the whole board who could have stepped up to improve them. "In the end, what we wrote was legitimate, sound science and the study proves it."

That is so completely backwards. The weaknesses in the standards are the direct result of the meddling corruption of science pushed by the religious conservatives on the board; everything the Fordham Institute said was bad about their standards were the points the creationists pushed. The strengths are the product of the motivated, hard-working scientists and educators who fought against the religious conservatives. McLeroy can take credit for that "C" in the sense that it could have been an "A" if he and his fellow travellers in superstition had been kicked out of the process…and that's nothing to be proud of.

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Big Charity

Pharyngula -

It must be tough running a charity. You've got a cause you care deeply about, and you're constantly juggling the game of having to spend money (in administration, advertising, staff) to raise money (for the cause!), and worse, of sometimes having to compromise to achieve your goals — you sometimes have to work with your enemies to get where you're going. And if you're really, really good at it, and raise lots and lots of money, it becomes easy to lose sight of the cause while becoming corporate.

So it goes with Susan G. Komen for the Cure, the $400 million/year giant pink gorilla of cancer charities, fighting for the cause of ending breast cancer. As charities go, they're reasonably efficent (about 20% of their budget is overhead, 20% goes to cancer research, and the rest goes to education and health care), and they're certainly effective — they practically own the color pink, it seems, and their little pink ribbons are ubiquitous. If you've donated money to them in the past, you should have no regrets, and you can pat yourself on the back for having done some good.

But it's time to cut the cord to this Big Charity.

Komen has lost sight of the cause, and has become more of a money-raising machine, for one thing. This is one of those awkward compromises they made to tap into corporate interests: they sold their identity and their label to anyone willing to cough up the cash. One correlation with the incidence of breast cancer is dietary fat — yet Komen went into a commercial promotion with KFC, selling big pink buckets of greasy fried chicken.

It was this national nonprofit education and advocacy organization that coined the term "pinkwashing" to describe the situation where a company purports to care about breast cancer by promoting a pink-ribboned product, but manufactures products that are linked to the disease.

This latest campaign between KFC and Komen is "simply pinkwashing at its worst," Barbara A. Brenner, JD, executive director of BCA, told Medscape Oncology. "This is just so wrong on every level. . . . This is so much more about KFC's bottom line than about curing breast cancer," she said.

This is just one example of losing sight of the goal. I would argue that in addition they've been too successful: their marketing has obscured their purpose. We're drowning in a sea of pink every time breast cancer is brought up, and the symbol of slapping a pink ribbon on something has replaced the substance of the cause. I always say that prayer is the very least you can do, but slapping a ribbon on your car is a very close runner-up.

And now, the last straw. Ultimately, breast cancer research is one part of improving women's health; if that narrow slice of concern begins to cannibalize the wider aspects of women's well-being, it does more harm than good. The Susan G. Komen Foundation has reached that point where the money-making machine is being hijacked to benefit organizations that do harm to women.

Specifically, Komen has yanked its support for breast-cancer screenings at Planned Parenthood. That's astonishing. Education and screening for breast cancer is what Komen is all about — it's what they do. It's as if I were to announce that I reject the teaching of evolution at a particular college campus because I really hate their football team (and if I had millions of dollars worth of clout). It makes no sense from the perspective of an anti-cancer charity.

It does make sense if you're a right-wing corporate entity that has funded its growth on a foundation of a universally appreciated cause, but that actually has closer ties to conservative corporate and religious interests. They aren't so much against breast cancer, as they are for protecting "good" girls, and against those fornicating sluts who get abortions, and can go ahead and die horribly. They listen more to the anti-abortion crusaders (some of whom are on their executive staff!) than to women.

So don't give to them anymore. Redirect your charitable giving to organizations that don't have a Puritanical streak, and are a bit less Republican in outlook. There is no shortage; I recommend the Breast Cancer Research Foundation, Breast Cancer Charities of America, CancerCare, and the Cancer Research Institute. So far, they all seem to be dedicated to fighting cancer and helping people, and a lot less concerned about policing people's morality to conform to that of the Religious Right.

But I don't want Susan G. Komen to go away. I think it is an excellent charity for right-wingers and Christian fundamentalists to donate to — their money will go to a cause we can all support, and it's better than filling the coffers of the Mormon or Catholic churches.

P.S. There are some very bad arguments for not donating to the Komen foundation out there, and the very worst are those that selectively cite statistics to argue that cancer research is futile. Some cancers have been refractory and have shown little progress in the last decade; others are showing significantly better statistics. But most importantly, our understanding of cancer has steadily advanced, and even where someone dies of the disease, we glean another piece of the puzzle. And of course, what do you propose to do otherwise? Nothing at all?

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True Science for Boys

Pharyngula -

Ah, the 19th century…when mad scientists were really mad, and not only that, they were popular at parties. In 1818, Dr Ure and Professor Jeffray obtained the freshly killed corpse of Matthew Clydesdale, only an hour from the hangman's noose, and proceeded to experiment on it with a battery in the Glasgow University anatomy theater before a crowd of spectators. In my youth, I had to settle for recent roadkill, a 9 volt battery, and a dark basement, all by my lonesome — my jealousy is acute.

Here is a small portion of the account of that day's fun.

galvanism.jpeg

The supra-orbital nerve was laid bare in the forehead, as it issues through the supraciliary foramen in the eyebrow: the one conducting rod being applied to it, and the other to the heel, most extraordinary grimaces were exhibited every time that electrical discharges were made, by running the wire in my hand along the edges of the last trough, from the 220th, to the 270th pair of plates: thus fifty shocks, each greater than the preceding one, were given in two seconds. Every muscle in his countenance was simultaneously thrown into fearful action: rage, horror, despair, anguish, and ghastly smile united their hideous expression in the murderer's face; surpassing far the wildest representation of a Fuseli or a Kean. At this period several of the spectators were forced to leave the apartment from terror or sickness, and one gentleman fainted.

The account of galvanic experiments on dead bodies is taken from The Young Man's Book of Amusement, which on the cover promises to teach card tricks and how to make fireworks. You'd think an amusement in which the first step is to obtain a dead body would be listed a little more prominently, but I guess playing with cadavers was just commonplace in the year before Queen Vickie was born.

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Death to Elsevier!

Pharyngula -

You already know my feelings about that exploitive science publisher, Elsevier; I'm not the only one, and there's been a long, long history of anger over their publishing model — and it's not just scientists, but scholars in other disciplines who have been peeved.

Now a boycott has coalesced. If you publish, edit, or review Elsevier journal articles, make your opinion known and sign the petition.

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Darwin on the Palouse

Pharyngula -

Time is whipping by, I can tell — Darwin Day is next week! I'm going to have to whip up a talk for this event real soon, I think: it's Darwin on the Palouse, and I'll be talking at Washington State University in Pullman, WA a week from Thursday. They've paired me up with Dan Dennett that evening…which is daunting, since I know which of us people will be lining up to see. On Friday, it'll be Jen McCreight and Fred Edwords speaking, so even more competition.

It should be a couple of good evenings of diverse and interesting talks, so all you folk in Eastern Washington and Idaho should make the trip.

Oh, and if you can't make the February event, you could always drive a bit farther north in May and take another shot at me at Imagine No Religion 2, in Kamloops, BC. There I'll only be standing in the shadow of Lawrence Krauss and a half dozen other luminaries.

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Islamic science has come to this pitiful end

Pharyngula -

The words of the Prophet Muhammad (sallallahu 'aleihi was-sallam) have been tested scientifically, and found hilarious. In work carried out under the direction of Dr. Jamaal Haamid, students at Qassim University examined a saying by the prophet, and have published it in a freely available pdf, The Hadeeth on the Fly, which you can download if you desire. Or you could just read this post, which summarizes entirely the complete content of the short paper, which is pretty much unpublishable and unbelievable anyway.

Here are the holy words.

holywords.jpeg
(Notice that I include the original Arabic so there can be no confusion!)

If a housefly falls in the drink of anyone of you, he should dip it (in the drink), for the one of its wings has a disease and the other has the cure of the disease.

I do find that rather disturbing: so in Arabia, if a fly touches your water, you're supposed to catch it, dunk it in deeper and slosh it around, to prevent disease? Arabian flies buzz around with pathogens segregated to just one wing, while the other one is healthy? How do they do that?

OK, setting aside the sanitary habits of Arabians and the mechanism by which this holy aphorism could be true, our intrepid students do carry out the obvious experiment: they drop a fly in a flask of sterile water, and then they pluck out the fly and immerse it completely in a second flask of sterile water. But then it all goes horribly wrong.

Here is the result of experiment #1.

flydunking.jpeg
Plate 2- Cultured water sample taken from a flask containing sterilized water and where a fly fell (without submersion). Growth of pathogenic (disease causing) bacterial colonies of the E. coli type were identified after taking samples from the water in the flask for culture.
Plate 1- Cultured water sample from the same flask following the complete dipping of the fly. An entire disappearance of the bacterial growth seen in Petri-dish 2 is clear. The new bacteria growing in plate 1 was identified as Actinomyces, the one from which useful antibiotics can be extracted. This explains the complete inhibition of growth in plate 2

Plate 2 on the right is the one from water merely touched by a fly. There is no explanation for how the plate was produced, or how the bacteria were identified; the strange brown sludge suggests poor technique, though, and I've cultured E. coli myself — and that hideous thick fecal-colored glop looks nothing like E. coli.

Plate 1 on the left, made from water in which the fly was fully immersed, looks nasty too. It's a poor photograph, but that looks like a thick lawn of colonies everywhere. How do they know it's Actinomyces? I have no idea, they don't say. It's also a mistake to simply declare it beneficial — Actinomyces are opportunistic pathogens.

Experiment #2 was a different fly, two flasks of water, same result.

Experiment #3 was a third fly, two flasks of water, same result.

Having done the experiment to death, our brave students retired at the third repetition, wrote it up with no methods, no discussion, no literature cited (except for their holy book, of course), and no reliable, believable data. They also didn't do the other obvious experiment, of snipping off the wings and examining the bacterial flora living on the left vs. right, but then, maybe they're leaving that for the advanced students.

Any 10 year olds looking for a quick and easy science fair project, there it is. I'm sure you can replicate this experiment trivially -- but please, talk to a real microbiologist first and learn how to streak a plate. You might also learn something about a control plate, which our U of Qassim students didn't bother to do.

Of course, this work wasn't carried out by 10 year olds. It was done by university students in a "Med 497" (a medical course?) in a department of medical microbiology. I strongly urge anyone visiting Saudi Arabia to avoid getting sick. They might try to treat you by swishing a fly around in your coffee.

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In Indiana, it's not just the lawmakers who are idiots — it's the media, too!

Pharyngula -

The miseducation committee of the Indiana legislature recently approved a bill to allow the teaching of creationism in the schools, and now the Indianapolis newspaper approves, with the usual tepid and illegitimate arguments.

Much would depend on how teachers handle the origins of life in a biology or science class.

No, it doesn't. A bill that inserts garbage into the curriculum is a bill that inserts garbage; it doesn't matter if you think it could be used to make a lovely collage, or as an exercise in recycling, it's still garbage. And if you trust teachers to do their job, let them do it without boneheaded cretins in the legislature telling them how.

And there is no provision in the bill that states creationism must be taught as a science subject.

Let me guess: it would be OK to teach it as "philosophy". How much disrespect are you willing to give to that field? It's bad philosophy, too. What disciplines is Indiana willing to poison with nonsense? Be specific. English? History? I know — how about relegating creationism to the football team.

Courts have ruled that using the Bible as an educational tool is permissible. We see nothing that would change that here, and note the bill stresses "theories" on the origins of life.

Uh-oh. I know what's coming next. I cringe in anticipation.

The march down the slippery slope occurs when theories are presented as facts.

YEEEAAARGH. HULK SMASH!

Scientific theories are explanatory frameworks for integrating a body of facts. Evolutionary theory, cell theory, germ theory, quantum theory, electromagnetic theory, transition state theory, the theory of relativity — these are all theories, and they also represent accurate and useful descriptions of how the universe works. They should be and are taught as facts, provisional explanations that have been tested and evaluated and found successful. "Theory" means something very specific and powerful to a scientist — there is no creation theory to be taught or used, and especially, no creation story that has survived any scientific test.

This bill could act as a safeguard against an educator mentioning creationism, and then possibly getting sued for promoting religion in the classroom. The American Civil Liberties Union has jumped into the fray and says this bill is unconstitutional, and that courts have overturned similar bills from other states.

This makes no sense. Yes, if a teacher peddles creationism in the classroom, they are using a state-supported, public facility to promote a purely religious idea. If a legislator peddles creationism in a bill, they are using the resources of goverment to promote a sectarian religious idea. This is wrong whether it's a teacher or a state rep doing it, it is unconstitutional, and most importantly, it is bad science being used to corrupt education.

Certainly, there is much empirical scientific evidence to support evolution, and some pretty good philosophical arguments to support creationism. It's unfortunate, though, that the latter has to be tagged as a science.

"Pretty good philosophical arguments for creationism"? Name one. Most philosophers are cleverer than that.

We think a thorough education exposes students to different theories, and if schools have done a good job of developing a student's critical thinking skills, there is no harm done.

Oh, great. This is going to be fun. So if they've learned how to fall safely in gym class, I can punch little kids in the nose, and no harm done. If they've learned basic logic in grade school, we can do a crappy job teaching them trigonometry and calculus — they'll be able to derive them for themselves, and no harm will be done. If they've learned playground safety rules, we can turn them loose with random chemicals in the chemistry lab, and no harm done.

This moron is basically saying that if most of the kids' education is decently done, then they can afford to throw a few state-mandated lies at them. Once upon a time, I thought the goal was to excel and provide the best education possible; in Indiana, the dream is a school system that is less than half shitty.

indscience2.jpeg

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Friday Cephalopod: Cuteness!

Pharyngula -

The gang at Skepticon are running a poll to design the World's Most Innocuous Atheist Billboard, and they've settled on the message — "Baby Animals Are Cute" — and they've got some choices for you to pick from. I thought I'd help and offer my own suggestion:

octopus_defilippi.jpeg

See? Far superior to the kittens and puppies they suggest, and it's much more in the spirit of atheism.

DO NOT ARGUE WITH ME. Or Baby Octopus will devour you.

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The comparison to jabberwocky is inevitable

Pharyngula -

Lots of people have been sending me this paper by Erik Andrulis, and most of you have done so with eyebrows raised, pointing out that it's bizarre and unbelievable; some of you wrote asking whether it was believable, at which point my eyebrows went up. Come on people: when you see one grand cosmic explanation that is summarized with cartoons, which the author claims explains everything from the behavior of subatomic particles to the formation of the moon, shouldn't you immediately sense crankery?

It's also getting cited all over the place, from World of Warcraft fan sites to the Discovery Institute (those two have roughly equal credibility in matters of science), so I had to skim through it. I read it with rising concern: Erik Andrulis is a young assistant professor at Case Western Reserve University, and he's published entirely sensible papers on RNA processing. This paper is so weird and out there that it is either an attempt to Sokal the field of origins of life research, or the man is seriously mentally ill. Either way, this is not going to help his career in the slightest.

The paper is titled Theory of the Origin, Evolution, and Nature of Life, and just the sweeping grandiosity of that title should set off alarm bells. Here is the abstract:

Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe.

Having skimmed through all 105 pages of this thing, I can tell you with confidence that it answers none of those questions. Just the fact that it is entirely non-mathematical and non-empirical (there aren't any observations or experiments described at all), and that the entirety of the theory is built around diagrams sketched out by the author, should also tell you that this is not a useful or predictive theory.

It does not have an auspicious beginning. In addition to being constructed around cartoons and being a non-mathematical Theory of Everything, it has to introduce an elaborate collection of neologisms that make the whole paper painful to read.

In the theory proposed herein, I use the heterodox yet simple gyre--a spiral, vortex, whorl, or similar circular pattern--as a core model for understanding life. Because many elements of the gyre model (gyromodel) are alien, I introduce neologisms and important terms in bold italics to identify them; a theoretical lexicon is presented in Table 1. The central idea of this theory is that all physical reality, stretching from the so-called inanimate into the animate realm and from micro- to meso- to macrocosmic scales, can be interpreted and modeled as manifestations of a single geometric entity, the gyre. This entity is attractive because it has life-like characteristics, undergoes morphogenesis, and is responsive to environmental conditions. The gyromodel depicts the spatiotemporal behavior and properties of elementary particles, celestial bodies, atoms, chemicals, molecules, and systems as quantized packets of information, energy, and/or matter that oscillate between excited and ground states around a singularity. The singularity, in turn, modulates these states by alternating attractive and repulsive forces. The singularity itself is modeled as a gyre, thus evincing a thermodynamic, fractal, and nested organization of the gyromodel. In fitting the scientific evidence from quantum gravity to cell division, this theory arrives at an understanding of life that questions traditional beliefs and definitions.

Here's a partial copy of his lexicon. It goes on quite a bit longer than what I've copied here.

Table 1. Gyromodel Lexicon

AlternagyreA gyrosystem whose gyrapex is not triquantal DextragyreA right-handed gyre or gyromodel FocagyreA gyre that is the focal point of analysis or discussion GyradaptorThe gyre singularity--a quantum--that exerts all forces on the gyrosystem GyrapexThe relativistically high potential, excited, unstable, learning state of a particle GyraxiomA fact, condition, principle, or rule that constrains and defines the theoretical framework GyreThe spacetime shape or path of a particle or group of particles; a quantum GyrequationShorthand notation for analysis, discussion, and understanding gyromodels GyrobaseThe relativistically low potential, ground, stable, memory state of a particle GyrognosisThe thermodynamically demanding process of learning and integrating IEM GyrolinkThe mIEM particle that links two gyromodules in a gyronexus GyromnemesisThe thermodynamically conserving process of remembering and recovering IEM GyromodelThe core model undergirding the theoretical framework GyromoduleA dIEM particle in a gyronexus GyronexusA polymer of dIEM particles linked by mIEM particles GyrostateThe potential and/or kinetic state that a particle occupies in its gyratory path GyrosystemA gyromodel with specific IEM composition, organization, and purpose IEMInformation, energy, and/or matter

I can't help myself. You knew this was coming.

Twas brillig, and the slithy toves
Did gyre and gimble in the wabe:
All mimsy were the borogoves,
And the mome raths outgrabe.

Now I know that you are in lexical shock right now, but I'm about to make it worse. Witness the use of these terms in figure 1 of the paper, which will also reveal the kinds of diagrams he's using.

gyrefig.jpeg

"The levorafocagyre, in turn, is antichiral to the dextrasupragyre" is a nice sentence that about sums up the experience of reading this thing. Don't believe me? Here are more excerpts that illustrate the grand, cosmic, and entirely uninformative nature of gyroexplanatory gyrobabble. Andrulis purports to explain everything from learning and memory (learning and memory by gyres, not the poor people trying to understand his paper):

The ultimate state of gyromnemesis is the stably adapted particle or gyronexus in the gyrobase. A particle thus adapts through learning and memory by completing one full cycle--a revolution-- around the singularity. Taken together, gyrognosis defines IEM integration and assessment whereas gyromnemesis defines IEM storage and recovery. Finally, although a diquantal IEM (X'') undergoes gyrognosis as the gyrobase of a primary majorgyre, it undergoes gyromnemesis as the gyrapex of an alternagyre. Thus, gyre learning and memory are relative to the gyradaptive singularity.

To the formation of Earth's moon:

Lunar Formation. The favored hypothesis for the formation of Earth's Moon is from planetesimal impact on a proto-Earth proceeded by matter ejection, accretion, and gravitational capture [189,190]. However, the question of lunar origin has not been settled since there are competing, albeit antiquated hypotheses [191,192]. I also discovered the stunning admission that, "...shamefacedly, [astronomers] have little idea as to where [the Moon] came from. This is particularly embarrassing... [193]." The oxygyre models the Moon as a macroxyon that has a macroelectron within itself; this simple gyrosystem accounts for the known chemical composition of the Moon surface, oxides [194]. Regarding lunar origin, the macroxyon that is the Moon emerges from the macroelectron that is the Earth, concomitant with the emergence of Earth's macroxyon [195,196].

Several additional points can be derived from this gyrosystem. First, the oxygyre explains water on and in the Moon [197-199]. Second, the gyrating effects of the macroxygyre model the rotation of the Moon on its axis. Third, the path of a less exergic macroxyon (Moon) around more exergic one (Earth) follows an ohiogyre path, or lunar orbit. Fourth, this oxygyre provides insight into how tidal cycling is linked to lunar orbit and axial rotation [200] since the Earth's oceans (macroxymatrix) and Moon itself (a macroxyon) exert complementary attractorepulsive forces. Fifth, this theoretical union also helps clarify short-term chronobiological ([201]; see 3.8) and long-term geophysical [202] relationships. Sixth, the craters that cover planetary, lunar, and satellite surfaces [203-205]--most if not all of which are near-perfect circles--bear the signature of the macroelectron singularity and its strong thermodynamic force on the oxygyre [206].

You know what? That doesn't explain anything!

While the strange terminology and nonsensical claims could be clues that this is an elaborate Poe of some sort, the story I've heard from some other sources is that Andrulis is not getting tenure and will be leaving Case next year, and that he seems to have a history of tuning in and out — so what this most like is is a developing personal tragedy. I hope he gets the care he clearly needs; his other work suggests that this is an intelligent mind that is currently going off the rails.

Setting Andrulis aside, though, there are other problems here. How did this paper get published? It's terrible: unreadable, incoherent, bizarre, and completely lacking in evidence or mathematical support. This is from the very first issue of a new journal, Life, which also contains a perfectly reasonable general summary of origins of life research by Stuart Kauffman alongside Andrulis's ghastly dreck. There seems to be a complete lack of editorial discrimination at the journal; this is not the way to build a reputation. Or rather, it is, but not a desirable one.

And then there is Science Daily, which seems to be the source where most of my correspondents found this paper. Science Daily is an incredibly annoying source: all they do is republish, without any kind of intelligent assessment, press releases. They suck. What good is mindless regurgitation?

And finally, there's Case Western Reserve University, which must bear a share of the blame. Where did the press release come from? Why, from the Media Relations office at CWRU. Somebody wrote the press release that begins like this:

The earth is alive, asserts a revolutionary scientific theory of life emerging from Case Western Reserve University School of Medicine. The trans-disciplinary theory demonstrates that purportedly inanimate, non-living objects--for example, planets, water, proteins, and DNA--are animate, that is, alive. With its broad explanatory power, applicable to all areas of science and medicine, this novel paradigm aims to catalyze a veritable renaissance.

It's madness stamped with the Case Western Reserve University School of Medicine seal of approval. If Andrulis did Sokal the journal, he also Sokal'ed the institution that employs him. Who wrote that bullshit? Do they have anyone competent review their press releases before they mail them out to the whole wide world? Was there anyone thinking in all the steps from crank professor to PR department to journal editor to reviewers? There were so many points where this crackpottery should have been detected and rejected, and it didn't happen.

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Indiana fails

Pharyngula -

Indiana is preparing to promote creationism in their science classrooms. A legislative committee has advanced a bill that endorses creationism and "alternative theories" to the vote of the full senate. So it's not a law yet, but it's advancing down the path.

Here's the horrifying part: it was approved 8:2 by the Republican-controlled Senate Education Committee. This is a group that is supposed to be the gatekeeper for good educational practices; you'd think their job was to screen out the random wacky garbage that individual, ideologically motivated members of the senate might poop out. But in the state of Indiana, they've handed that job over to goddamned Republicans in a calculated effort driven by their Republican governor, Mitch Daniels, to overhaul the state's educational system.

It's practically Republican gospel to destroy the system of public education in the US. It's always going to lead to tears when you put those bastards in charge.

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Today is Shawn Otto day at UMM

Pharyngula -

We're having a visit today from Shawn Lawrence Otto, a fellow who has been fighting against the un-American war on science on the web and in a book, Fool Me Twice: Fighting the Assault on Science in America. He's speaking on campus tonight at 7:30 Central, in the HFA Recital Hall — I urge local community members to show up, he has important things to say about education and climate change — and that talk is going to be streamed live, so all you distant strangers can also watch the show.

It was a little strange, though, to get messages from the university administration telling me I'm expected to go to dinner with him. It turns out, I'm in his book — there's actually a substantial 4 or 5 page section in there where he discusses an interview he had with me (I'm getting old, and I've done so many interviews that they all bleed together), so I had to run out and get a copy of the book to find out what I was getting into. It all sounded a bit Chris Mooney-like.

Fortunately, the book is good — if the topic is a bit Mooneyish, it's the Mooney of The Republican War on Science, and not the batty, Nisbet-bespelled Mooney of Unscientific America, and his stuff on me isn't a hatchet job. Otto doesn't come out and declare me the absolutely correct master of all I pontificate on (I'll have to bend his ear and make suggestions for the second edition), but at least he recognizes that there are many different angles to take in fighting ignorance. You are allowed to read the book and listen to the talk without feeling outraged.

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