The IDiot Version of Reality

 
It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).

Richard Dawkins
Check out this posting by Barry Arrington on Uncommon Descent [Peppered Moth Idolatry].

The venerable peppered moth (Biston betularia) has popped up a couple of times in recent posts. It seems that some of our Darwinian commenters (see, e.g., qwerty017 in comment [2] here) have not gotten the memo – the peppered moth myth has been completely exploded. Don’t take our word for it. Uber-Darwinist Jerry Coyne says in the November 1998 edition of Nature: “For the time being we must discard Biston as a well-understood example of natural selection in action.” Why else would the popular school text Biology pull its discussion of Biston as an example of “evolution in action”?

Here are some examples of scientists who have not heard message from the IDiot's.

Douglas Futuyma in his textbook Evolution published in 2005 (p. 293).

Until the 1930s, most evolutionary biologists followed Darwin in assuming that the intensity of natural selection is usually very slight. By the 1930s, however, examples of very strong selection came to light. One of the first examples was INDUSTRIAL MELANISM in the peppered moth (Biston betularia). ...

There are many scientific papers on the "myth" as well. Here's the abstract from Saccheri et al. (2008).

Historical datasets documenting changes to gene frequency clines are extremely rare but provide a powerful means of assessing the strength and relative roles of natural selection and gene flow. In 19th century Britain, blackening of the environment by the coal-fired manufacturing industry gave rise to a steep cline in the frequency of the black (carbonaria) morph of the peppered moth (Biston betularia) across northwest England and north Wales. The carbonaria morph has declined across the region following 1960s legislation to improve air quality, but the cline had not been comprehensively described since the early 1970s. We have quantified changes to the cline as of 2002, equivalent to an interval of 30 generations, and find that a cline still exists but that it is much shallower and shifted eastward. Joint estimation of the dominant fitness cost of carbonaria and dispersal parameters consistent with the observed cline change indicate that selection against carbonaria is very strong across the landscape (s approximately 0.2), and that dispersal is much greater than previously assumed. The high dispersal estimate is further supported by the weak pattern of genetic isolation by distance at microsatellite loci, and it implies that in addition to adult dispersal, wind-dispersed first instar larvae also contribute to lifetime dispersal. The historical perspective afforded by this study of cline reversal provides new insight into the factors contributing to gene frequency change in this species, and it serves to illustrate that, even under conditions of high dispersal and strong reverse selection acting against it, complete erosion of an established cline requires many generations.

Wow, this is a tough call. Who are you going to believe, evolutionary biologists like Futuyma and Sacheri et al., or an IDiot like Barry Arrington?

There's no rush. Take a microsecond or two to make up your mind.

See Revenge of the Peppered Moth. Ohmygod! These photographs are faked!, and Peppered Moths and the Confused IDiots for some insight into why one textbook got cold feet in 2000.

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Saccheri, I.J., Rousset, F., Watts, P.C., Brakefield, P.M. and Cook, L.M. (2008) Selection and gene flow on a diminishing cline of melanic peppered moths. Proc. Natl. Acad. Sci. USA 105:16212-16217. [doi:10.1073/pnas.0803785105]

On the Origin of Species

 
Yesterday (Nov. 24, 2008) marked the 149th anniversary of the publication of On the Origin of Species by Charles Darwin. Ms. Sandwalk just bought me an illustrated edition by David Quammen and I highly recommend it. The text is from the first edition of Darwin's work and the illustrations cover a wide range of topics including copies of Darwin's letters and letters from his friends. This is an excellent way to get people interested in one of the most important books ever published.

I was prompted to re-read Origin and I discovered some things I had long forgotten. Most importantly, the style of Darwin's writing is impressive. He takes the time to argue his point by highlighting the most relevant objections to his ideas. While we all recognize that this is the appropriate style for a scientific work, we also recognize (unfortunately) that it may be a lost art. There are too many papers these days that ignore anything that weakens one's case.

In the four succeeding chapters, the most important and gravest difficulties on the theory will be given: namely, first, the difficulties of transitions, or in understanding how a simple being or a simple organ can be changed and perfected into a highly developed being or elaborately constructed organ; secondly, the subject of Instinct, or the mental powers of animals; thirdly, Hybridism, or the infertility of species and the fertility of varieties when intercrossed; and fourthly, the imperfection of the Geological Record.

The second thing I re-discovered is the clarity and forcefulness of Darwin's writing, given the style of the Victorian era. Also his foresight and originality.

Although much remains obscure, and will long remain obscure, I can entertain no doubt, after the most deliberate study and dispassionate judgment of which I am capable, that the view which most naturalists entertain, and which I formerly entertained—namely, that each species has been independently created—is erroneous. I am fully convinced that species are not immutable, but that those belonging to what are called the same genera are lineal descendants of some other and generally extinct species, in the same manner as the acknowledged varieties of any one species are the descendants of that species. Furthermore, I am convinced that Natural Selection has been the main but not the exclusive means of modification.

Thomas H. Huxley read an advance copy of On the Origin of Species and sent a letter to Darwin, which he received on the day before the book went public. Huxley knew what was coming ...

I trust you will not allow yourself to be in any way disgusted or annoyed by the considerable abuse and misrepresentation which, unless I greatly mistake, is in store for you. Depend upon it you have earned the lasting gratitude of all thoughtful men. And as to the curs which will bark and yelp, you must recollect that some of your friends, at any rate, are endowed with an amount of combativeness which (though you have often justly rebuked it) may stand you in good stead.

I am sharpening my claws and beak in readiness.

The letter is published in the illustrated edition by David Quammen.

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Deceptive Science?

 
I was recently taken in by a paper where the authors implied that they were the first to identify one of Gregor Mendel's original genes [see Identity of the Product of Mendel's Green Cotyledon Gene (Update)].

The reason I was sensitized to this issue is because of a similar incident involving a paper published in Cell. Here's an outline of the issue as reported in The Times Higher Education.

It appears that the Cell paper is very misleading. It does not give appropriate credit to the work of other labs.

Peter Lawrence asked if he could publish a letter in Cell but he was told to post comments on the website instead. This is not appropriate. Nobody reads those comments. The author of the suspect Cell paper, Jeffrey Axelrod of Stanford School of Medicine (Palo Alto, CA USA) stands by his publication. The editors of Cell use the common excuse when a journal is caught with it's pants down.

After being sent four of the letters of complaint, Professor Axelrod added on the 6 November: "Our paper (Chen et al, June 2008) underwent a strict process of peer review prior to publication. Concerns about the review process should be directed to Cell. We stand by our conclusions as stated in the paper, as well as by our use of citations."

Cell declined to respond to questions put by Times Higher Education. However, in a response to the complaint from Professor Lawrence, Cell's senior scientific editor Connie Lee said: "I can only assure you that the reviewers were experts in planar cell polarity and the consensus decision was that the model presented by Chen et al was thought-provoking, well supported and provided a sufficient conceptual advance beyond the existing literature."

The incident raises a serious question. Is the pressure to publish so great that authors are tempted to deceive editors and reviewers by making their work seem more original and novel than it really is?

This is not a new problem. A few years ago Nature was pressured into publishing an editorial defending its policies against the charge that they were publishing bad science in order to be the first journal to publish "breakthroughs" (Adam and Knight, 2002). The Nature editorial denies that the popular journals are promoting sensationalism.

Editors of leading journals reject the suggestion that standards are slipping in the face of heightened competition. "Nature has nothing to gain by the pursuit of glamour at the expense of scientific quality, considering, not least, the criticisms, corrections and retractions we would then habitually be forced to publish," argued this journal in an editorial comment earlier this month5. And many researchers who were interviewed for this article agree that the system is still working tolerably. If it ain't broke, they say, don't try to fix it.

Speaking of the pursuit of glamour, Nature continues its policy of hiring science writers to promote and hype papers that have recently been published in its journal [Human genes are multitaskers].

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Adam, D. and Knight, J. (2002) Journals under pressure: Publish, and be damned... Nature 419: 772-774. [doi:10.1038/419772a]

Identity of the Product of Mendel's Green Cotyledon Gene (Update)

Last year I drew your attention to the identification of one of Gregor Mendel's original seven mutants [Identity of the Product of Mendel's Green Cotyledon Gene]. At the time, I thought that a recent 2007 paper by Sato et al. was the first publication to make this identification. Now I realize that I slighted the original discoverers Armstead et al. (2007) and earlier publications. The Armstead et al. paper is referenced in the later Sato et al. paper but the reference does not give appropriate credit to the work done by Armstead et al. in identifying the Mendelian gene. It was easy to get the impression that the Japanese group was the first to make the definite connection between Mendel's gene and work done in other species. I suspect that this was deliberate.

Here's a revised version of my original posting. Thanks to a reader who alerted me to the proper credit.

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Another of Mendel's seven genes has been identified. This one is described in his 1865 paper Experiments in Plant Hybridization [MendelWeb] as character number 2.

2. To the difference in the color of the seed albumen (endosperm). The albumen of the ripe seeds is either pale yellow, bright yellow and orange colored, or it possesses a more or less intense green tint. This difference of color is easily seen in the seeds as their coats are transparent.

Mendel's reference to the color of albumin, or endosperm, is inaccurate. He was actually observing the color of the cotyledons—the "seed leaves" that surround the embryo in the pea seed. These tiny leaves are covered by a seed coat that is partially transparent.

In wild-type peas the seeds turn yellow as they mature (I) but certain mutants exhibit a "stay-green" phenotype where the peas retain their green color (i). The figure shows seeds from a plant with the II genotype (top) and the ii genotype (bottom). The seed coat has been removed from the lower pair of each group of four peas.

A paper published in Science identifies the "stay-green" gene that Mendel worked with (Armstead et al. 2007). This work is based on several decades of study of the "stay-green" phenotype by Howard Thomas and his colleagues at the Institute of Grassland and Environmental Research, Aberystwyth, UK (Armstead et al. 2006; Thomas, 1987; Thomas et al. 1996; Thomas and Stoddart, 1975).

It turns out that the gene, called sgr (stay-green), encodes an enzyme that is localized to chloroplasts and plays a role in the degradation of chlorophyll during senescence and maturation of seeds. When the enzyme is defective chlorophyll isn't broken down and the tissue stays green.

This brings to three the number of Mendel's genes that have a known function. The wrinkled pea phenotype is caused by a defect in the gene for starch branching enzyme (Bhattacharya et al., 1990) [Biochemist Gregor Mendel Studied Starch Synthesis]. The tall/short phenotypes are caused by defects in the gene for gibberellin 3β-hydroxylase (Martin et al., 1997). Gibberellins are plant growth hormones.

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[Photo Credit: The photograph of mutant and wild-type pea seeds is taken from Figure 1 of Sato et al. (2007)]

Armstead, I., Donnison, I., Aubry, S., Harper, J., Hörtensteiner, S., James, C., Mani, J., Moffet, M., Ougham, H., Roberts, L., Thomas, A., Weeden, N., Thomas, H., and King, I. (2007) Cross-species identification of Mendel's I locus. Science 315: 73. [DOI: 10.1126/science.1132912]

Armstead, I., Donnison, I., Aubry, S., Harper, J., Hörtensteiner, S., James, C., Mani, J., Moffet, M., Ougham, H., Roberts, L., Thomas, A., Weeden, N., Thomas, H., and King, I. (2006) From crop to model to crop: identifying the genetic basis of the staygreen mutation in the Lolium/Festuca forage and amenity grasses. New Phytologist 172: 592-597.

Bhattacharyya, M. K., Smith, A. M., Ellis, T. H., Hedley, C., and Martin, C. (1990) The wrinkled-seed character of a pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell 60:115-122.

Martin D.N., Proebsting W.M., Hedden P. (1997) Mendel's dwarfing gene: cDNAs from the Le alleles and function of the expressed proteins. Proc. Natl. Acad. Sci. (USA) 94:8907–8911.

Sato Y., Morita R., Nishimura M., Yamaguchi H., and Kusaba M. (2007) Mendel’s green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway. Proc. Natl. Acad. Sci. (USA) 104: 14169-14174. [doi: 10.1073/pnas.0705521104].

Thomas, H. (1987) Sid: a Mendelian locus controlling thylakoid membrane disassembly in senescing leaves of Festuca pratensis. Theoretical and Applied Genetics 73: 551 555.

Thomas, H., Schellenberg, M., Vicentini, F., Matile, P. (1996) Gregor Mendel's green and yellow pea seeds. Botanica Acta 109: 3-4.

Thomas, H., and Stoddart, J.L. (1975) Separation of chlorophyll degradation from other senescence processes in leaves of a mutant genotype of meadow fescue (Festuca pratensis). Plant Physiology 56: 438-441.

Monday's Molecule #98

 
Name this molecule. This time we need the common name and the systematic (IUPAC) name. A Nobel Prize was awarded for discovering this molecule and showing how it is involved in cell metabolism.

The first one to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are only three ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin, Dale Hoyt from Athens, Georgia and Ms. Sandwalk from Mississauga, Ontario, Canada. Dale and Ms. Sandwalk have offered to donate the free lunch to a deserving undergraduate so the first two undergraduates to win and collect a free lunch can also invite a friend.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the "molecule" and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: The molecule is azathioprine [6-(3-methyl-5-nitroimidazol-4-yl)sulfanyl-7H-purine]. The Nobel Laureates are Gertrude B. Elion and George H. Hitchings. Alex Ling of the University of Toronto beat everyone else so he gets another free lunch only this time he can invite a friend. There were a dozen people who got this one—that's a surprise to me since I had never even heard of the Nobel Laureates unitil last week.

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A Fondness for Beetles

 
By now everyone has heard the story. There are almost as many species of beetle as all the rest of the insects put together. This is what prompted J.B.S. Haldane to say that God has "an inordinate fondness for beetles."

Now that's fine if you're an ordinary person, but if you're into taxonomy the huge diversity of beetles presents some really tough problems. Christopher Taylor describes one of the problems of classifying beetles in The Diversity of Ground Beetles.

Apparently God isn't the only one who likes beetles.

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Best Canadian Sci/Tech Blog

 
The Canadian Blog Awards are for "Celebrating the best in the Canadian blogosphere." Here are the nominees for Best Sci/Tech Blog.

• AmberMac.com
• Climate Audit
• Sync, the Tech & Gadgets Blog
• Synchro Blogue
• 9th Sphere
• Post Darwinist
• Bad Astronomy
• DeSmogBlog
• Eco-Can News
• A View from the Isle
• Serendipityoucity
• Techvibes
• Column 2
• Colliding Universes
• Mindful Hack
• Dusan Writer
• The Tyrannosaur Chronicles
• XsampleX

I'm not sure why Bad Astronomy is on a list of blogs that celebrate the best in the Canadian blogosphere but that's who I voted for. I'm hoping that Phil Plait is NOT a Canadian 'cause that would point out how silly these awards really are.

Wouldn't it be funny if Mindful Hack or Post Darwinist won? That would say a lot about the people who vote for these things.

I support Canadian Cynic who refuses to participate ...

Another year, another incarnation of the Canadian Blog Awards, and another request to please delete CC HQ from any and all categories in which we've been nominated for a fairly simple reason -- we're not interested in any popularity contest in which voters seriously have to choose between CC HQ and batshit crazy, racist, white supremacist, Nazi sympathizer loons like Kate McMillan and Kathy Shaidle for "best blog."

I wish I could take the same stance but nobody nominated me for anything. Damn, I don't even get to withdraw my nomination.

BTW, I'm not familiar with most of these blogs. Can anyone point me to the wheat among all the chaff?

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Canada's New Minister of State (Science and Technology) Is a Chiropractor

 
It's true. Checkout the Stephen Harper website, which incidentally, is supposed to be the Prime Minister's website.

The Honourable Gary Goodyear
Minister of State (Science and Technology)

Cambridge (Ontario)

Gary Goodyear was first elected to the House of Commons in 2004 and re-elected in 2006 and 2008.

Prior to entering federal politics, Dr. Goodyear practised chiropractic medicine and worked as an advisor to investment firms in the biomedical industry.

Dr. Goodyear was a co-designer of a three-year post-graduate sports fellowship program. He also co-authored “Practice Guidelines” and was Public Relations Director and Past President for the College of Chiropractic Sports Sciences in Toronto. Dr. Goodyear has taught at the Canadian Memorial Chiropractic College and the University of Waterloo. He has worked with many athletes, both amateur and professional, including serving as medical services chair for the Ontario Special Olympics.

Dr. Goodyear is a graduate of the University of Waterloo and the Canadian Memorial Chiropractic College.

It's bad enough that we have a chiropractor advising the government about science but this particular one seem especially unqualified. He also practiced acupuncture when he was actively seeing patients. Dr. (sic) Goodyear is strongly supported by evangelical christians (e.g. Christian Conservatives). That may not have anything to do with his ability to understand modern science. Gary Goodyear was endorsed by Vote Marriage Canada, a group that opposes gay marriage.

The website of the Canadian Memorial Chiropractic College has a lengthy article praising the 4 MPs who are chiropractors (3 Conservatives, 1 Liberal) [Chiros on the Hill].

“The single biggest criticism of politicians,” explains Dr. Colin Carrie, Class of ’89 and Member of Parliament for the electoral district of Oshawa, Ontario, “is that they don’t listen.” Chiropractors, he says, are educated to be exceptional listeners. “Regardless of our political stripes, we want to do what’s right for our patients and our constituents.”
It’s people skills, agrees his colleague and fellow Conservative Dr. Gary Goodyear (MP for Cambridge, Ontario). “Every chiropractor has to be a people person, that’s what we were taught at CMCC.”

Goodyear, Class of ’83, and Chair of the Committee of Procedure and House Affairs, adds with a laugh that his advisors have had occasion to remind him not to be quite so hands-on when dealing with his constituents. “My election team has actually told me to stop touching people so much, but I can’t help it. It’s just natural to me. As a chiropractor, you automatically love people. Chiropractic is a touchy-feely profession—that transfers.”

Interestingly, all four chiropractic MPs tell similar stories about how—for each in his or her own way—they have come to view their constituents in much the same light as chiropractors perceive their patients: “You can’t be a successful chiropractor without good interpersonal skills,” explains Dr. James Lunney, (Class of ’83, Nanaimo-Alberni, BC). “Our job as chiropractors is taking complicated issues, and finding ways of explaining them—interpreting X-rays, for example—you have to be able to communicate to your patient what needs to be communicated.” The job requirements are strikingly similar, he says, on Parliament Hill. “Any chiropractor who deals with patient issues successfully has the skills to make the transition into politics. If you can manage a practice, you have an aptitude for politics.”

I'm beginning to see the parallels between being a politician and a chiropractor. This is not complimentary to politicians.

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Good IDEA?

 
The Discovery Institute is promoting the IDEA Center.

As part of our efforts to support academic freedom on evolution, we are teaming up with the IDEA Center (Intelligent Design and Evolution Awareness) to help students in starting an IDEA chapter on their campus. Such campus clubs are a fun and educational way for students to examine all sides of the debate over evolution.

IDEA Clubs are student-initiated clubs that foster academic freedom as students learn about scientific evidence that supports intelligent design and also learn about modern evolutionary theory. IDEA Clubs are a growing network of student-led clubs on university and high school campuses around the United States with thirty new chapters formed to date. (my emphasis)

Here's a challenge for everybody no matter which side you are on. Finding anti-evolution articles on the IDEA Center website is trivial. All the standard lies are there, sometimes in multiple articles. But can anyone find a single bit of evidence that supports Intelligent Design Creationism?

What about modern evolutionary theory? Is there anything on the website that comes remotely close to explaining modern evolutionary theory?

I didn't think so? How many campus have clubs of IDiots like this?

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Riding in the Car to Get Cherries

 
Riding in the Car to Get Cherries is a painting by Kanzi who also gave it the title. The painting is part of Apes Helping Apes.

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Were Neanderthals stoned to death by modern humans?

 
Were Neanderthals stoned to death by modern humans? is the provocative title of a press release reported in New Scientist. The author of the study is interviewed,

Human aerial bombardments might have pushed Neanderthals to extinction, suggests new research. Changes in bone shape left by a life of overhand throwing hint that Stone Age humans regularly threw heavy objects, such as stones or spears, while Neanderthals did not.

"The anatomically modern humans would have this more effective and efficient form of hunting," says Jill Rhodes, a biological anthropologist at Bryn Mawr College in Pennsylvania, who led the new study. A warmer Europe would have opened up forests, enabling longer range hunting, she says.

Rhodes and a colleague studied changes to the arm bone that connects the shoulder to the elbow – the humerus – to determine when humans may have begun using projectile weapons.

"If we're trying to understand whether anatomically modern humans had projectiles, then why not read the signature that it can imprint in the skeleton," Rhodes says.

The paper by Jill Rhodes of the Department of Anthropology, Bryn Mawr College and Steven E. Churchill of the Department of Evolutionary Anthropology, Duke University appears in The Journal of Human Evolution under Article in Press.

Rhodesa, J.A. and Churchill, S.A. (2008) Throwing in the Middle and Upper Paleolithic: inferences from an analysis of humeral retroversion. [doi:10.1016/j.jhevol.2008.08.022M]

Here's the complete text of the conclusiosn from that paper.

Clinical evidence from professional and college-level throwing athletes reveal differences in the humeral retroversion angle both between athletes and comparative (non-throwing) samples and between the dominant (throwing) and non-dominant limbs in the athletes. Comparative analysis of humeral architecture, specifically the humeral retroversion angle, in Pleistocene fossil humans has the ability to contribute new insights into the origins of projectile weaponry by examining the individuals who would have wielded those weapons. While the data is equivocal (in part because of confounding variables that affect humeral retroversion and in part because of small fossil sample sizes), we can reach two conclusions. First, while Neandertals tend to have high amounts of humeral retroversion, the overall pattern between limbs and between sexes strongly suggests that it is not due to habitual throwing behavior. The humeral retroversion data is largely consistent with other lines of evidence pertaining to projectile weaponry; the preponderance of evidence, ranging from fossil spears and Mousterian lithics to the articular and diaphyseal morphology of upper limb bones, suggests that Neandertals did not habitually employ long-range projectile weapons ([Churchill et al., 1996], [Schmitt et al., 2003], [Shea, 2003a], Shea, 2006 J.J. Shea, The origins of lithic projectile point technology: evidence from Africa, the Levant, and Europe, J. Archaeol. Sci. 33 (2006), pp. 823–846. Article | PDF (774 K) | View Record in Scopus | Cited By in Scopus (15)[Shea, 2006] and [Churchill and Rhodes, in press]). It is worth noting that earlier hominins also lack humeral torsion, further demonstrating that the increased retroversion found in Neandertals is unlikely to be linked to throwing. Second, we cannot reject the suggestion of projectile weapon use in the European Upper Paleolithic. The patterns seen in bilateral asymmetry in humeral retroversion angle suggest a variable use of throwing in the middle Upper Paleolithic (and thus great inter-individual variation in asymmetry), perhaps related to regional differences in hunting practices or the importance of projectile-based hunting. The levels of asymmetry seen in late Upper Paleolithic males are consistent with the regular use of projectile technology by this time.

Is it just me, or does there seem to be a disconnect between what's in the paper and what's in the press release? Why would the author allow the press release to say something that cannot be found anywhere in the paper?

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Creationists Fight Dirty, Scientists Don't

 
Martin at The Atheist Experience has been posting about the Texas State Board of Education hearings on science standards. Several members of the board want to "teach the controversy," which means teaching the creationist lies about evolution in an attempt to discredit it. His latest posting (Crippled dogs and one-trick ponies) is quite interesting.

Martin points out that when creationist board members use the standard lies and misconceptions to make their point about flaws in evolution, the pro-science witnesses should be prepared to hit back just as hard. They lose credibility if they waffle.

This is not a scientific dispute. Creationists don't care about science.

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This Is Ridiculous

 
The New York Times has an article by Nicholas Wade on Regenerating a Mammoth for $10 Million. It outlines a possible method for re-creating extinct organisms from a knowledge of their DNA sequence. The idea is to produce a mammoth.

I suppose there's nothing wrong with this kind of speculation. After all, we all did it back when Jurassic Park first came out. But there's a time to be serious as well. Why in the world would we want to spend $10 million of valuable research money to bring back the mammoth? I can see the importance of resurrecting the dodo or the sabre tooth tiger, but mammoths? Who need them? Do they even taste good?

Wait a minute ... there's even more exciting news in the New York Times article. George Church, a "genome tecchnologist" at Harvard Medical School was interviewed. He describes out a way to resurrect Neanderthals.

The full genome of the Neanderthal, an ancient human species probably driven to extinction by the first modern humans that entered Europe some 45,000 years ago, is expected to be recovered shortly. If the mammoth can be resurrected, the same would be technically possible for Neanderthals.

But the process of genetically engineering a human genome into the Neanderthal version would probably raise many objections, as would several other aspects of such a project. “Catholic teaching opposes all human cloning, and all production of human beings in the laboratory, so I do not see how any of this could be ethically acceptable in humans,” said Richard Doerflinger, an official with the United States Conference of Catholic Bishops.

Dr. Church said there might be an alternative approach that would “alarm a minimal number of people.” The workaround would be to modify not a human genome but that of the chimpanzee, which is some 98 percent similar to that of people. The chimp’s genome would be progressively modified until close enough to that of Neanderthals, and the embryo brought to term in a chimpanzee.

“The big issue would be whether enough people felt that a chimp-Neanderthal hybrid would be acceptable, and that would be broadly discussed before anyone started to work on it,” Dr. Church said.

What a clever way to get around all the ethical issues (not)! However, aren't we missing the point here? Why would we want to clone a Neanderthal in the first place? (BTW, you need two of them.)

What if the Neanderthals turn out to be smarter than us—a distinct possibility? Wouldn't they take over all the good jobs, like university professors? And what if they turn out to be stupider than the average human? Don't we already have enough creationists?

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[Hat Tip: john hawks weblog: Clone your own Neanderchimp baby?]

Closed for the Winter

 
We've just had our first significant snowfall in Toronto and the campus maintenance people have sprung into action. The main ramp leading into my building from the subway station has been closed for the winter. You may recall that this is the entrance where the expensive stone walkway is useless [If you build it, will they follow?].

Toronto is in Canada. In Canada we have real winters, with snow and ice. You may be asking yourself why anyone would build an entrance that has to be shut down for five months of the year. That's a very good question.

This entrance was constructed a few years ago when the Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) was built. The ramp consists of wood slats with about one centimeter spaces between them. I'm told that a special kind of wood was used and it's very expensive.

Here's the problem as it was explained to me. First, it is difficult to clean ice and snow from a wooden walkway without damaging it. Second, when this kind of wood gets wet it becomes very slippery. That means you can't use salt to get rid of the ice without creating dangerous conditions in the winter.

I'm told that the university and the architects have been unable to reach agreement on who should fix this problem.

CCBR was designed by the architectural firms of Alliance & Behnisch Architekten. The architects won the Royal Institute of British Architects Awards (RIBA) in 2006 for this building [RIBA 2006]. They also won the Governor General's Medal in Architecture for 2008 for this building.

Here's part of the press release from the University of Toronto.

The Governor General's Medals in Architecture recognize outstanding achievement in recently built projects by Canadian architects. These awards are administered jointly with the Canada Council for the Arts, which is responsible for the adjudication process and contributes to the publication highlighting the medal winners. The recipients of the 2008 Governor General's Medals in Architecture were selected by a jury of distinguished architects.

Elizabeth Sisam, assistant vice-president (campus and facilities planning), said buildings like the Donnelly CCBR are very complex and boast many notable features.

"The CCBR is a very clever design that knits the Medical Science Building to the CCBR while being respectful of the heritage buildings and at the same time maintains and enhances pedestrian routes and entrances through to the campus," Sisam said. "Below grade, there are research laboratories that extend all the way to the sidewalk. The inside of the building in the area of the laboratories is a flexible design allowing the research teams to expand and contract. The exterior has a very unique treatment, a 'double façade' which is an excellent example of sustainable design."

The original design did not "knit the Medical Science Building to the CCBR." That was only added after many of us complained about the original design and the Dean of Medicine (David Naylor) intervened to provide extra funding to build the proper connection. In the original plan the buildings would have been quite separate.

The end product does not "maintain and enhance pedestrian routes and entrances through to the campus." The entrance off College St. requires that you climb up an annoying two flights of steps inside the building before gaining access to the lobby where the cafeteria is located. The direct entrance to this lobby from the other side (see photo above) could only be considered an "enhancement" by someone with a wicked sense of humour.

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Science 2.0

 
You may have heard of Science 2.0. It's the latest "revolution" in science. You can read a nice summary from the Howard Hughes Medical Institute [Science 2.0 You Say You Want a Revolution?].


Personally, I think blogging is going the become part of the culture in the same way that newsgroups did in the past except that more people are going to read the blogs. I don't think it's going to be a revolution. I don't think the majority of scientists and students are going to become regular readers of blogs. The blogosphere culture is not for everyone. Many of my colleagues are completely turned off. Blogging is going to be just one more way of communicating science and sharing ideas.

I'm skeptical of OpenWetWare (OWW) and other software that allows you to put all your notes and protocols on the web. Right now, most labs don't make shared electronic versions of protocols and notes even though we've been able to do that for 25 years. I don't see why that's going to change. My notebooks have lots of comments that I've scribbled in the margins (F**k - forgot to add magnesium!). I don't know why I'd want to share that with everyone on the planet.

I've done lots of "secret" experiments in my lifetime just to check out some crazy idea. So have the graduate students and post-docs in my lab. Does this sort of thing never go on in the labs that have adopted open access lab books? That doesn't sound like any kind of lab that I'd like to be in. Too much control for my liking. (According to the article it's "where the cool people are." I don't think so.)

Open-Access Journals are here to stay and will only increase in popularity.

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[Hat Tip: A Blog Around the Clock]

Reprogenetics and Genetic Variants

 
Reprogenetics is a company that offers the following service.

Preimplantation Genetic Diagnosis consists of the biopsy of a single cell per embryo, followed by its genetic diagnosis through different techniques (FISH, PCR, or CGH), and the subsequent replacement to the patient of those embryos classified by genetic diagnosis as normal.

Reprogenetics provides PGD analysis to IVF centers, including diagnosis of aneuploidy for advanced maternal age (such as Down's syndrome), repeated IVF failure, recurrent spontaneous abortions, chromosome translocations and inversions, as well as for gene defects such as Cystic fibrosis, fragile X, Myotonic Dystrophy, Thalasaemia, Tay Sachs, and others. We can also provide an experienced embryologist to perform embryo biopsy and cell processing.

Other tests may be offered soon including predisposition for diabetes and other genetic diseases.

The research director of Reprogenetics was interviewed for an article that appeared today on the Nature website [Gene testing of embryos needs guiding]

Last week, at a meeting of the American Society for Reproductive Medicine in San Francisco, California, researchers cautioned that they do not yet advocate this use of genetic tests. But as the technology advances, consumer demand is likely to overwhelm societal ethical qualms. "If people think they can make their babies healthier at year one, year two, or in utero, they will do it," says Jacques Cohen, research director at Reprogenetics, a genetic-testing company in West Orange, New Jersey.

...

Cohen says that as the understanding of disease genetics progresses, use of tests that seem controversial now may become more acceptable in the future: "If you had the chance to decrease your child's risk of a disease like diabetes and you didn't, society would blame you."

I assume this is a profit-making company. I wonder why Nature chooses to rely on the opinion of someone who has a vested interest in the technology? Especially someone who has an opinion like that?

What can he be thinking? Does he think that the average American in the future will be forced to undergo in vitro fertilization to avoid being sued by their children?

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[Hat Tip: The Sciphu Weblog: This pisses me off a little]

Nobel Laureate: Sinclair Lewis

 


The Nobel Prize in Literature 1930.

"for his vigorous and graphic art of description and his ability to create, with wit and humour, new types of characters"

Sinclair Lewis (1885 - 1951) won the Noble Prize in Literature for his novels about average Americans doing non-average things. The prize committee specifically mentions Main Street, Babbitt, Arrowsmith, Elmer Gantry, and Dodsworth.

Sinclair Lewis was the first American to win a Nobel Prize in Literature.

Arrowsmith is a novel about a scientist. It is one of the first works of the 20th century to describe the realities of being a scientist and really should be required reading for all science students. Lewis relied heavily on his scientific adviser, the microbiologist Paul de Kruif, and the novel is based loosely on Félix d'Herelle. Here's how the novel is described in the presentation speech on the Nobel Prize website.

THEME:
Nobel Laureates

Arrowsmith (1925) is a work of a more serious nature. Lewis has there attempted to represent the medical profession and science in all its manifestations. As is well known, American research in the natural sciences, physics, chemistry, and medicine ranks with the best of our age, and it has several times been recognized as such from this very platform. Tremendous resources have been placed at its command. Richly endowed institutions work unceasingly on its development.

That even here some speculative persons want to take advantage of their opportunities may be regarded as inevitable. Private industries are on the alert for scientific discoveries and want to profit from them before they have been tested and finally established. The bacteriologist, for instance, searches with infinite care for vaccines to cure widespread diseases, and the manufacturing chemist wants to snatch them prematurely from his hand for mass production.

Under the guidance of a gifted and conscientious teacher, Martin Arrowsmith develops into one of the idealists of science. The tragedy of his life as research worker is that, after making an important discovery, he delays its announcement for constantly renewed tests until he is anticipated by a Frenchman in the Pasteur Institute.

The book contains a rich gallery of different medical types. We have the hum of the medical schools with their quarrelling and intriguing professors. Then there is the unpretentious country doctor, recalled from Main Street, who regards it as an honour to merge with his clientele and become their support and solace. Then we have the shrewd organizer of public health and general welfare, who works himself into popular favour and political power. Next we have the large institutes with their apparently royally independent investigators, under a management which to a certain extent must take into consideration the commercial interests of the donors and drive the staff to forced work for the honour of the institutes.

Above these types rises Arrowsmith's teacher, the exiled German Jew, Gottlieb, who is drawn with a warmth and admiration that seem to suggest a living model. He is an incorruptibly honest servant of science, but at the same time a resentful anarchist and a stand-offish misanthrope, who doubts whether the humanity whose benefactor he is amounts to as much as the animals he kills with his experiments. Further we meet the Swedish doctor, Gustaf Sondelius, a radiant Titan, who with singing and courage pursues pests in their lairs throughout the world, exterminates poisonous rats and burns infected villages, drinks and preaches his gospel that hygiene is destined to kill the medical art.

Alongside all of this runs the personal history of Martin Arrowsmith. Lewis is much too clever to make his characters without blemish, and Martin suffers from faults which at times seem obstructive to his development, both as a man and as a scientist. As a restless and irresolute young man he gets his best help from a little woman he encountered at a hospital where she was an insignificant nurse. When he begins to drift about the country as an unsuccessful medical student, he looks her up in a little village in the Far West, and there she becomes his wife. She is a devoted and simple soul, who demands nothing and who patiently waits in her solitude when, bewitched by the siren of science, her husband loses himself in the labyrinths of his work.

Later she accompanies him and Sondelius to the plague-infected island where Arrowsmith wants to test his serum. Her death in the abandoned hut, while her husband listens distractedly to another and more earthy siren than that of science, seems like a poetically crowning final act to a life of primitive self-sacrificing femininity.

The book is full of admirable learning, certified by experts as being accurate. Though a master of light-winged words, Lewis is never superficial when it comes to the foundations of his art. His study of details is always as careful and thorough as that of such a scientist as Arrowsmith or Gottlieb. In this work he has built a monument to the profession of his own father, that of the physician, which certainly is not represented by a charlatan or a faker.

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Gene Genie #40

 
The 40th edition of Gene Genie has been posted at Human Genetics Disorders [Gene Genie Edition 40].

NSGC Conference exibit and MBA thesis poster presentation videos from the October 24-28 2008 AEC Conference by Chavonne Jones

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life
30. Gene Expression
31. Adaptive Complexity
32. Highlight Health
33. Neurophilosophy
34. ScienceRoll
35. Microbiology Bytes
36. Human Genetic Disordrs
37. The Genetic Genealogist
38. ScienceRoll
39. Genetics & Health
40. Human Genetics Disorders

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My Desk

 
Eva re-starts another meme.

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I Hate Ironing

 
But these guys seem to like it. What am I missing?

I've been following this sport for several years and I still don't get how they do it. Maybe I need a new iron?

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[Hat Tip: Canadian Cynic, of course.

They're Coming to Your Town!

 
The American Family Association sells Christmas crosses that remind you of something evil [Hide it under a bushel? NO!]. But the website has lots more stuff as pointed out by one reader who commented on my earlier posting.

You really need to see They're Coming to Your Town DVD.

Residents of the small Arkansas town of Eureka Springs noticed the homosexual community was growing. But they felt no threat. They went about their business as usual. Then, one day, they woke up to discover that their beloved Eureka Springs, a community which was known far and wide as a center for Christian entertainment--had changed. The City Council had been taken over by a small group of homosexual activists.

The Eureka Springs they knew is gone. It is now a national hub for homosexuals. Eureka Springs is becoming the San Francisco of Arkansas. The story of how this happened is told in the new AFA DVD “They’re Coming To Your Town.”

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Arwen

 
This is Arwen. Ms. Sandwalk tells me there's a connection between her and Monday's Molecule #97. I didn't know that.¹ Did you?

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1. This is really just an excuse to post the photo.

Monday's Molecule #97

 
Today we're taking a bit of a break from boring old biochemical molecules and fruit flies to look at some specific individuals of the species Homo sapiens. Your task for today is to identify these men. I need all of their names and the name that collectively identifies them.

The answer is indirectly related to this week's Nobel Laureate. See if you can make the connection.

The first one to correctly identify the individuals and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are only three ineligible candidates for this week's reward: Bill Chaney of the University of Nebraska, Dima Klenchin of the University of Wisconsin and Dale Hoyt from Athens, Georgia. Dale has agreed to donate the free lunch to a deserving undergraduate so the first undergraduate to win and collect a free lunch can also invite a friend.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the "molecule" and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

The band is Aerosmith and this should remind you of the book "Arrowsmith" by Sinclair Lewis who won the Nobel Prize for Literature in 1930. Arrowsmith is a book about scientists.

Three people knew who the band was—one of them was Ms. Sandwalk! Only one person saw the connection between Aerosmith and a Nobel Laureate but that person (Dima) is ineligible. I decided to award the free lunch to Ms. Sandwalk, making her ineligible for any more lunches for one month!!!

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Hide it under a bushel? NO!

 

This is the latest in Christmas decorations from the American Family Association.

Let Your "Light" Shine For Christ This Christmas Season!

Looking for an effective way to express your Christian faith this Christmas season to honor our Lord Jesus? Now you can.... with the "Original Christmas Cross" yard decoration.

Light up your front yard, porch, patio, driveway, business, organization or church this holiday season with a stunning Christmas cross.

Can't you just picture these five and-a-half foot crosses in the middle of front yards all across America?

What in the world are they thinking?

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[Hat Tip: LuLu at Canadian Cynic]

Be Afraid

 
There have been some changes on Uncommon Descent. Bill Dembski won't be posting as often (Boo!) and the chief web person will be Barry Arrington [What’s New At UD].

Here's a warning from the new chief IDiot.

We live in exciting times. The Darwinist/materialist hegemony over our culture has definitely peaked, and we are privileged to watch the initial tremors that are shaking the Darwinist house of cards. These are only the beginning of woes for St. Charles’ disciples, and I look forward to one day watching the entire rotten edifice come crashing down. I am persuaded that just as when the Soviet Union went seemingly overnight from “menacing colossus astride the globe” to “non-existent,” the final crash of the House of Darwin will happen with astonishing suddenness. You can be sure that we at UD will be there not only reporting on events, but also lending our intellectual pry bars to the effort.

Hmmm ... "intellectual pry bars" ... that's an image that's going to be hard to shake.

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Why do we blog and other important questions

 
OK, so I'm not a Nature Network blogger, but I thought I'd answer the questions anyway.

1. What is your blog about?
   It's about science, religion, universities, politics, and almost everything else I'm interested in. Mostly science and science education.


2. What will you never write about?
   Aha! A trick question! You almost got me!


3. Have you ever considered leaving science?
   No.


4. What would you do instead?
   I dunno, what do other people do? (Eva has a much funnier reply to this question)


5. What do you think will science blogging be like in 5 years?
   Pretty much the same as it is now. Which is pretty much the same as it's been for the past five years. Which isn't a lot different than the newsgroups were for the previous 20 years before that.


6. What is the most extraordinary thing that happened to you because of blogging?
   I've made dozens of new friends. (For me, that's extraordinary.)


7. Did you write a blog post or comment you later regretted?
   Yes.


8. When did you first learn about science blogging?
   I don't recall exactly. It was probably sometime around 2002 when I first learned that people were actually reading them.


9. What do your colleagues at work say about your blogging?
   Most of them don't understand the blogging culture. They think it's bizarre. They think I'm bizarre—but they thought that even before I started Sandwalk

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Be the First in Your School

 
Be the first in your school, or church, to have one of these T-shirts—or others like it. (It also comes in red and black.) Go to Evo-Ts.

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Making Sense in Biology

When I teach students how to read the scientific literature, I caution them not to believe everything they read. Science is, by it's very nature, tentative and exploratory. Much of what is published doesn't get confirmed and is quietly ignored. Many of the ideas and speculations that are published never amount to anything. Some experiments are flawed. Many skim over hidden assumptions so that the conclusions aren't valid.

How do you tell the difference between the wheat and the chaff? Well, for one thing, you ask yourself whether the results "make sense" in light of what you already know. Are there any basic principles of biology that conflict with the conclusions? You always have to be on the lookout for papers that just don't fit in with your current model of how things work.

There are two potential problems with this approach. First, your model may not be correct. Maybe you don't know enough to make a judgment. Second, it prevents you from recognizing truly novel results that may change your idea of what makes sense.

The first problem is curable. The second is more serious. Science is basically conservative in its acceptance of new ideas. This may seem like a bad thing but, in fact, it's the only way to do good science. You simply can't afford to believe in several paradigm shifts every day before breakfast because most of them will turn out to be wrong. Today, when scientists want to convince their colleagues of something new that may not "make sense", they are obliged to present solid evidence that will convince the skeptics. It's an uphill fight. And it should be.

One of my colleagues has been following the discussion about alternative splicing and he directed my attention to a paper he just published in Nature Genetics. He pointed out that far from being an overestimate of alternative splicing, the EST data actually underestimates the extent of alternative splicing.

The paper by Pan et al. (2008) makes two extraordinary claims.

1. Their data indicates that about 95% of all multiexon human genes undergo alternative splicing.
2. They estimate that there are, on average, seven (7) alternative splicing events per multiexon human gene.

Neither of these claims make sense. It's not reasonable to assume that most conserved housekeeping genes produce variants by alternative splicing yet that's exactly what would have to happen if 95% of all genes undergo alternative splicing. It means that most most genes for things like metabolic enzymes, RNA polymerase, ribosomal proteins and transport proteins will have variants due to alternative splicing. This doesn't make sense from an understanding of biochemistry and it doesn't make sense in light of evolution.

That's good reason to be skeptical.

But surely the data must be convincing? Surely the proponents of these extraordinary claims have extraordinary data to back their cease?

Frankly, I don't know. I can't evaluate the Pan et al. (2008) paper because I have no idea how they actually do their experiments and whether those experiments are reliable. Part of the problem is that the authors don't tell me enough and part of it is that this is unfamiliar technology (to me).

All I know is that it doesn't make sense. I've asked the author to give me some specific examples of alternative splicing predictions for common genes, like those in the citric acid cycle. By looking at specific, rather than global, data it might be possible to see whether the results make sense.

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Pan, Q., Shai, O., Lee, L.J., Frey, B.J. and Blencowe, B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics, published online Nov. 2, 2008. [DOI:10.1038/ng.259]

Students and a Sense of Entitlement

 
A recent study by Greenberger et al. (2008) looked at student's sense of entitlement in order to see where it comes from. Here's the abstract ...

Abstract Anecdotal evidence suggests an increase in entitled attitudes and behaviors of youth in school and college settings. Using a newly developed scale to assess ‘‘academic entitlement’’ (AE), a construct that includesexpectations of high grades for modest effort and demanding attitudes towards teachers, this research is the first to investigate the phenomenon systematically. In two separate samples of ethnically diverse college students comprised largely of East and Southeast Asian American, followed by Caucasians, Latinos, and other groups (total N = 839, age range 18–25 years), we examined the personality, parenting, and motivational correlates of AE. AE was most strongly related to exploitive attitudes towards others and moderately related to an overall sense of entitlement and to narcissism. Students who reported more academically entitled attitudes perceived their parents as exerting achievement pressure marked by social comparison with other youth and materially rewarding good grades, scored higher than their peers in achievement anxiety and extrinsic motivation, and engaged in more academic dishonesty. AE was not significantly associated with GPA.

I don't put a lot of credence in these studies but I thought it was interesting that the problem was at least being investigated. The survey results, below, are interesting.

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[Hat Tip: Musings of the Mad Biologist]

Greenberger, E., Lessard, J., Chen, C. and Farruggia, S.P. (2008) Self-Entitled College Students: Contributions of Personality, Parenting, and Motivational Factors. Journal of Youth and Adolescence 37:1193-1204 [Springerlink]

Tangled Bank #118

 
The latest issue of Tangled Bank has been published on Submitted to a Candid World [Tangled Bank #118: Yes We Did Edition].

It’s my pleasure to bring you this edition of Tangled Bank, a biweekly collection of posts on important issues of biology and science. How I managed to secure the first post-election Tangled Bank for this little politics blog is beyond me: far be it for me to complain, but it really makes you wonder about PZ Myers’ processes for vetting new hosts… I’ll try my best not to play Sarah Palin to his John McCain.

Common readers of this site will know from experience that I, like all the co-writers of this blog, pushed hard for Obama’s election, and new visitors will guess as much from the site’s browser icon (surprise!). Now that the man’s elected, though, there’s a lot of work to be done - especially because, over the past eight years, scientific integrity somehow became a Democrats-only issue. America’s science community has a lot of ground to recover and, until Obama decides to restore the office to its pre-Bush grandeur, we, the concerned netroots, are the closest thing he has to White House science advisers. Thus, I present to you President-Elect Barack Obama’s first science briefing -

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Send an email message to host@tangledbank.net if you want to submit an article to Tangled Bank. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger.

Nobel Laureate: Edward Lewis

 

The Nobel Prize in Physiology or Medicine 1995.

"for their discoveries concerning the genetic control of early embryonic development"

Edward B. Lewis (1918 - 2004) won the Noble Prize for his studies on the genetics of Drosophila melanogaster, especially the homeotic mutants in the bithorax complex. These are the mutations that cause transformation of the 3nd thoracic segment into the 2nd, giving rise to a fly with four wings instead of two.

The significance of this work can't be underestimated. It led to our modern understanding of development and evolution. Thanks to Lewis, we now know that small changes in the regulation of gene expression can have large effects on phenotype. It means that the number of mutations required to make the difference between mice and humans, for example, may be far less that what people imagined 50 years ago.

Edward Lewis shared the prize with Christiane Nüsslein-Volhard and Eric Wieschaus. Here's what the press release said about Lewis.

THEME:
Nobel Laureates

The fly with the extra pair of wings

Already at the beginning of this century geneticists had noted occasional malformations in Drosophila. In one type of mutation the organ that controls balance (the halteres), was transformed into an extra pair of wings (Fig. 2). In this type of bizarre disturbance of the body plan, cells in one region behave as though they were located in another. The Greek word homeosis was used to describe this type of malformations and the mutations were referred to as homeotic mutations.
Figure 2.

Fig. 2. Comparison of a normal and a four-winged fruit fly. The third thoractic segment has developed as a duplicate of the second due to a defectic homeotic gene. In the normal fly only the second segment develops wings.

The fly with the extra pair of wings interested Edward B. Lewis at the California Institute of Technology in Los Angeles. He had, since the beginning of the forties, been trying to analyze the genetic basis for homeotic transformations. Lewis found that the extra pair of wings was due to a duplication of an entire body segment. The mutated genes responsible for this phenomenon were found to be members of a gene family ( bithorax-complex) that controls segmentation along the anterior-posterior body axis (Fig. 3). Genes at the beginning of the complex controlled anterior body segments while genes further down the genetic map controlled more posterior body segments (the colinearity principle). Furthermore, he found that the regions controlled by the individual genes overlapped, and that several genes interacted in a complex manner to specify the development of individual body segments. The fly with the four wings was due to inactivity of the first gene of the bithorax complex in a segment that normally would have produced the halteres, the balancing organ of the fly (Fig 3). This caused other homeotic genes to respecify this particular segment into one that forms wings.

Edward Lewis worked on these problems for decades and was far ahead of his time. In 1978 he summarized his results in a review article and formulated theories about how homeotic genes interact, how the gene order corresponded to the segment order along the body axis, and how the individual genes were expressed. His pioneering work on homeotic genes induced other scientists to examine families of analogous genes in higher organisms. In mammalians, the gene clusters first found in Drosophila have been duplicated into four complexes known as the HOX genes. Human genes in these complexes are sufficiently similar to their Drosophila analogues they can restore some of the normal functions of mutant Drosophila genes.

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[The book is a tribute to Edward Lewis, edited by my colleague Howard D. Lipshitz.]

[Image Credit: California Institute of Technology]