Pharyngula

Friday Cephalopod: Feasibility trial successful

Category: Cephalopods • Organisms

Next step: lasers mounted on squid mantles.

You puny humans are so screwed.

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Posted by PZ Myers at 12:22 PM • 0 Comments • 0 TrackBacks

Making excuses

Category: Academics • Bad Science

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.

(Also on FtB)

Posted by PZ Myers at 12:05 PM • 3 Comments • 0 TrackBacks

More bad science in the literature

Category: Bad Science • Creationism

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.

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.

(Also on FtB)

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Posted by PZ Myers at 4:07 PM • 31 Comments • 0 TrackBacks

An open letter to the Indiana legislature

Category: Academics • Creationism

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

(Also on FtB)

Posted by PZ Myers at 2:28 PM • 12 Comments • 0 TrackBacks

One Carnival of Evolution, coming right up

Category: Evolution

I've been naughty and neglecting to announce these things, so let's start correcting that: here's the 44th Carnival of Evolution.

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Posted by PZ Myers at 9:30 AM • 2 Comments • 0 TrackBacks

Botanical Wednesday: Walking? No way

Category: Organisms

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Posted by PZ Myers at 9:08 PM • 2 Comments • 0 TrackBacks

Your state's report card

Category: Academics • Creationism

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?

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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Posted by PZ Myers at 7:53 PM • 15 Comments • 0 TrackBacks

Big Charity

Category: Medicine • Politics

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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Posted by PZ Myers at 1:10 PM • 9 Comments • 0 TrackBacks

Mary's Monday Metazoan: the only angel I believe in

Category: Organisms

Aside from Mary, that is.

(via NatGeo)

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Posted by PZ Myers at 9:33 PM • 3 Comments • 0 TrackBacks