The DNA Network

Science vs. Nonscience: Teaching Creation and Evolution is not the Compromise Position, it's the Fundamentalist One [adaptivecomplexity's column]

Posted: 01 Oct 2008 05:14 PM CDT

The argument that we should teach both creationism and evolution in public schools has been the fundamentalist argument since 1968, when the Supreme Court ruled that states can't ban the teaching of evolution. If you can't ban evolution, maybe you can neutralize it with a dose of Biblical literalism in biology class.

Posted: 01 Oct 2008 12:32 PM CDT

via Dienekes, an interesting paper on the temporal origin of disease-related genes.

An ancient evolutionary origin of genes associated with human genetic diseases
Tomislav Domazet-Loo and Diethard Tautz
Molecular Biology and Evolution

Abstract: Several thousand genes in the human genome have been linked to a heritable genetic disease. The majority of these appear to be non-essential genes (i.e. are not embryonically lethal when inactivated) and one could therefore speculate that they are late additions in the evolutionary lineage towards humans. Contrary to this expectation, we find that they are in fact significantly over-represented among the genes that have emerged during the early evolution of the metazoa. Using a phylostratigraphic approach, we have studied the evolutionary emergence of such genes at 19 phylogenetic levels. The majority of disease genes was already present in the eukaryotic ancestor and the second largest number has arisen around the time of evolution of multicellularity. Conversely, genes specific to the mammalian lineage are highly underrepresented. Hence, genes involved in genetic diseases are not simply a random subset of all genes in the genome, but are biased towards ancient genes.

ColoSure™: Stool DNA testing is back! [DNA Direct Talk]

Posted: 01 Oct 2008 12:26 PM CDT

We know that colorectal cancer is the second leading cause of cancer-related deaths in the United States. We also know that when it's caught early, it's curable up to 95% of the time. So why aren't we catching it early? It turns out that at least 60% of Americans age 50 and older have never been screened for colorectal cancer, even though the American Cancer Society (ACS) recommends lifelong screening, including a colonoscopy every 10 years.

At DNA Direct, we think people need better choices. We've found that some people are embarrassed or unwilling to undergo invasive screening—and some would rather go without. Updated ACS guidelines in March of 2008 added both virtual colonoscopy and stool DNA testing to the recommended arsenal of screenings for colon cancer. We thought about how we could help people who know the importance of screening and early detection, but who can't or won't undergo colonoscopy.

Ethnicity, genetic variant at KCNMB1, sex, and asthma [Yann Klimentidis' Weblog]

Posted: 01 Oct 2008 12:17 PM CDT

An african-specific functional polymorphism in KCNMB1 shows sex-specific association with asthma severity.
Seibold MA, Wang B, Eng C, Kumar G, Beckman KB, Sen S, Choudhry S, Meade K, Lenoir M, Watson HG, Thyne S, Williams LK, Kumar R, Weiss KB, Grammer LC, Avila PC, Schleimer RP, Burchard EG, Brenner R.
Hum Mol Genetics 2008 Sep 1;17(17):2681-90.

Abstract: A highly heritable and reproducible measure of asthma severity is baseline pulmonary function. Pulmonary function is largely determined by airway smooth muscle (ASM) tone and contractility. The large conductance, voltage and calcium-activated potassium (BK) channel negatively regulates smooth muscle tone and contraction in ASM. The modulatory subunit of BK channels, the beta1-subunit, is critical for proper activation of BK channels in smooth muscle and has shown sex hormone specific regulation. We hypothesized that KCNMB1 genetic variants in African Americans may underlie differences in bronchial smooth muscle tone and thus pulmonary function, possibly in a sex-specific manner. Through resequencing of the KCNMB1 gene we identified several common variants including a novel African-specific coding polymorphism (C818T, R140W). The C818T SNP and four other KCNMB1 variants were genotyped in two independent groups of African American asthmatics (n = 509) and tested for association with the pulmonary function measure--forced expiratory volume (FEV(1)) % of predicted value. The 818T allele is associated with a clinically significant decline (-13%) in FEV(1) in both cohorts of asthmatics among males but not females (P(combined) = 0.0003). Patch clamp electrophysiology studies of the BK channel expressed with the 140Trp variant of the beta1-subunit demonstrated significantly reduced channel openings, predicted by the loss of pulmonary function observed. African American male asthmatics carrying the 818T allele (10% of population) are potentially at risk for greater airway obstruction and increased asthma morbidity. Female asthmatics may be insulated from the deleterious effects of the 818T allele by estrogen-mediated upregulation in BK channel activity.

Is ethnic self-identification a good predictor of health risks? [Yann Klimentidis' Weblog]

Posted: 01 Oct 2008 12:14 PM CDT

Ability of Ethnic Self-Identification to Partition Modifiable Health Risk Among US Residents of Mexican Ancestry.
Barger SD, Gallo LC.
Am J Public Health. 2008 Sep 17

Objectives. We examined the relationship between ethnic self-identification and the partitioning of health risk within a Mexican American population. Methods. We combined data from the 2000 to 2002 National Health Interview Surveys to obtain a large (N=10044) sample of US residents of Mexican ancestry. We evaluated health risk, defined as self-reported current smoking, overweight, and obesity, and compared the predictive strength of health risk correlates across self-identified Mexican and Mexican American participants. Results. Self-identified Mexican participants were less likely to smoke (odds ratio [OR]=0.70; 95% confidence interval[CI] = 0.60, 0.83; P<.001) and to be obese (OR=0.66; 95% CI=0.56, 0.77; P<.001) than were self-identified Mexican American participants. Within-group analyses found that sociodemographic predictors had inconsistent and even contradictory patterns of association with health risk across the 2 subgroups. Health risk was consistently lower among immigrants relative to US-born participants. Ethnic self-identification effects were independent of socioeconomic status. Conclusions. US residents of Mexican ancestry showed substantial within-group differences in health risk and risk correlates. Ethnic self-identification is a promising strategy to clarify differential risk and may help resolve apparent discrepancies in health risk correlates in this literature.

Gaze into the crystal ball - Nobel Prize Predictions [The Daily Transcript]

Posted: 01 Oct 2008 11:50 AM CDT

This is the third year that I update this list of potential winners. A warning, the list is highly biased towards basic biomedical research. In addition, some of the prizes may be more appropriate for the Chemistry prize.

We'll start with my favorite, Membrane Traffic. This finding is one of the most basic discoveries in cell biology. The two obvious winners would be James Rothman and Randy Schekman.

Last year there was a rumor that intracellular signalling may win. Tony Hunter could get it for phospho-tyrosine, Tony Pawson for protein signalling domains, and Allan Hall for small G-protein switches. Maybe Lew Cantley for modifiable lipid signals.

Structure of the first virus. Steven Harrison and Michael Rossman.

Structure and function of the ribosome. Here the list is long. Some have joked that this prize will only be awarded when some of the candidates have died. Peter Moore, Tom Steitz, Venki Ramakrishnan, Harry Noeller and Ada Yonath. What they could do is give the medicine prize to some and the chemistry prize to others.

Sadly they can no longer give an award for Angiogenesis as ~~Judith~~ Judah Folkman passed away earlier this year. This is really too bad. Dr Folkman labored against conventional wisdom and really opened up a new field of science.

Telomeres. Elizabeth Blackburn, Carol Greider and Jack Szostak. Very important stuff that touches on both cancer and aging. They won last year's Lasker Award.

Major Histocompatibility Complex, structure, maturation etc. Very hard. Don Wiley would be nominated here but he died. There are many others. In addition you could nominate Peter Cresswell.

The discovery of stemcells. Ernest McCulloch and James Till (they took the Lasker in 2006). How come this hasn't been recognized yet???

Transport Motors. Ron Vale for kinesin (they could also throw in Sheetz here too), Ian Gibons for flagellar dynein, and maybe Rich Vallee for cytoplasmic dynein and dynamin ... (there is little chance that this will happen - apparently the major complaint is that motors, i.e. myosin, already got recognized.) On a related note they could give an award for the discovery of AAA ATPases, I'm not sure who would get that but probably Bob Sawer would be on the list. A more appropriate award would be for the proteasome, but that was already the topic for the 2004 Chemistry award. (Who knows, maybe they can use this as an excuse to give it to Fred Goldberg and Alexander Varshavsky )

Chaperones Maybe Hartl, Ellis and Neupert? Maybe Lindquist? I don't know this fild too well, so if you have any more informed opinion, let me know. It would be funny if Neupert got a nobel and Jeff Schatz didn't.

And of course there is p53, one of the most important tumor supressors known. There are about 3 codiscoverers (Arnold Levine, David Lane, and Lloyd Old) so they could get it. There would be a problem with Levine as he had been involved in a small controversy. Bert Vogelstein wasn't one of the p53 discoverers, but he may get it too for demonstrating that it is a tumor suppressor. If it's tumor suppressors they could also give a prize to Robert Weinberg.

Mitosis I would love to see Shinya Inoue get it for the discovery of the mitotic spindle. They could also give it to Mitchison and Kirschner for the discovery of microtubule dynamics. Many others could be listed here.

OK time for some wild guesses ...

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Sarah Palin's Still Dangerous Views on Teaching Evolution [The Tree of Life]

Posted: 01 Oct 2008 10:56 AM CDT

Well, Palin has clearly revised her public position on teaching evolution. In part of her interview with Katie Couric it was addressed (I got the transcript here. )

Couric: Do you believe evolution should be taught as an accepted scientific principle or one of several theories?

Palin: Oh, I think it should be taught as an accepted principle. And, you know, I say that also as the daughter of a school teacher, a science teacher, who has really instilled in me a respect for science. It should be taught in our schools. And I won't ever deny that I see the hand of God in this beautiful creation that is Earth, especially coming from one of the most beautiful states in the Union and traveling around this country also in this last month. My goodness, just seeing, you know, the beautiful landscape of New Mexico recently. That was just breath taking and seeing the rolling hills in Virginia and all … the beauty that is this Earth, I see the hand of God in that. But that is not part of state policy or a local curriculum in a school district. Science should be taught in science class.

Sounds promising right? I mean, previously, she seemed to be wishy washy on the separation of science and religion and now she seems to be trying to do the right thing. But just when you might have thought the anti-science part of her was winning out, look at her response to the next question:

Couric: Should creationism be allowed to be taught anywhere in public schools?

Palin: Don't have a problem at all with kids debating all sides of theories, all sides of ideas that they ever - kids do it today whether … it's on paper, in a curriculum or not. Curriculums also are best left to the local school districts. Instead of Big Brother, federal government telling a district what they can and can't teach, I would like to see more control taken over by our school boards, by our local schools, and then state government at the most. But federal government, you know, kind of get out of some of this curriculum and let the locals decide what is best for their students.

This basically follows the script of the Intelligent Design supporters who have been pushing for changes in the education curriculum by local school boards. And it is pretty dangerous in my mind. There should be separation of church and state. Period. At the federal level. At the state level. And at the local level. And this is clearly an attempt to circumvent that concept. So - Palin is towing the ID line here pretty closely and who knows who havoc she would wreak on science in this country if she were elected. McCain-Palin is starting to look more anti-science than Bush-Cheney, hard as that is for scientists to imagine.

Supporting science by directly funding teachers: DonorsChoose2008 [Discovering Biology in a Digital World]

Posted: 01 Oct 2008 10:42 AM CDT

ScienceBlogs and science bloggers, in general, have enthusiastically supported fund-raising efforts by DonorsChoose for the past two years, and we're doing it once again for 2008.

DonorsChoose works like this: teachers write descriptions of what they want and how they'll use it for teaching, and submit their proposals to DonorsChoose. We pick the projects we like and if you like them, too, you can help get these projects funded.

Donate to schools! Win a prize!

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Luciferase and stem cells #2 [Reportergene]

Posted: 01 Oct 2008 10:02 AM CDT

As previously posted, bioluminescence imaging (BLI) can be helpful to longitudinally monitor stem cells localization, proliferation, and viability. To date, Alessandra Sacco and colleagues from Stanford, illustrate in Nature that reporter genes can be useful also to longitudinally monitor self-renewal and differentiation of luciferase-expressing muscle stem cells (MuSCs) after transplantation in mice. This results has been realized by mating Myf5-nLacZ mice (a reporter mouse for myogenic transcription) with a constitutive firefly luciferase mice (a reporter mouse for assessing cell number).

Bioluminescence by jon.nelson

Of course, that is a technological advance, since it seems now possible to follow the dynamics of stem cell behavior in a manner not possible with retrospective histological analysis. We need now to develop new cognitive skills (and a little bit of statistic also) to understand this unprecedented "real time" picture, since it is quite common for generation 1.0 scientists to wonder only about "end-point" results, without considering the bulk of information revealed by longitudinally imaging in the same experimental subject.

Alessandra Sacco, Regis Doyonnas, Peggy Kraft, Stefan Vitorovic, Helen M. Blau (2008). Self-renewal and expansion of single transplanted muscle stem cells Nature DOI: 10.1038/nature07384

Scale of the debt ... [biomarker-driven mental health 2.0]

Posted: 01 Oct 2008 08:27 AM CDT

Just thought this NY Times graphic nicely captured the outlays of debt taken on during the recent weeks by the US Central Bank. Healthcare spending is usually the big item(s), but the new debt really dwarfs it. Immense new pressure on the financing of healthcare.

Interviews about Medicine 2.0 [ScienceRoll]

Posted: 01 Oct 2008 07:59 AM CDT

Medicine 2.0 is an interesting new field of medicine and focuses on how web 2.0 can change medical education and communication. Two interviews have recently been published about my views on this topic.

DiagnosisPR Blog

Race Talk Blog

If you would like to read more, check the Medicine 2.0 collection out.

Myrl: Connecting virtual lives [ScienceRoll]

Posted: 01 Oct 2008 07:39 AM CDT

Old form of world wide web: We contacted people by e-mail.

Web 2.0: We’re connected to each other by social networks.

Myrl: Our virtual lives (avatars) are connected to each other.

I’m a regular Second Life user but know there are other virtual worlds as well with many different avatars. Why not to connect them to each other? Myrl just does it.

Myrl is a social gateway for virtual worlds that allows you to share your virtual life on the web. Discover, browse and play across multiple worlds with Myrl.

Live report about what you are doing in your virtual life.

You also get a profile for your avatar.

And of course, they have a Second Life residence as well:

I can’t wait to see how many users they will have in some months…

Double Tennis Racquet Racket [Sciencebase Science Blog]

Posted: 01 Oct 2008 07:00 AM CDT

two-racquet-tennis I’m not sure what to make of this, but Don Mueller, of William Paterson University, New Jersey, who goes by the nickname Dr Bones sent me some video clips of what is, essentially, a new sport he invented - two-racquet tennis. Now, my first thought was: “what the flip?” But, apparently his service velocity is higher than that of most tennis professionals, although I don’t think that has anything to do with using a racquet in each hand.

Anyway, he has posted a selection of videos on Youtube to demonstrate his prowess at this new sport:

Tennis Serve (a), Tennis Serve (b), Groundstrokes (a), Groundstrokes (b), Drills-righthand (a), Drills-lefthand (b)

Mueller tells me that he combined his understanding of basic physics to devise the “Whip-Grip”, which gives him the higher velocity. He says there are other advantages of playing tennis with a racquet in each hand: “It’s really great at the net and no more tennis elbow pain from hitting backhands, the cause of most tennis injuries,” he explains, “Where most people say, Why?, I say, Why not?”

Mueller is a teaching adjunct at WPU and this semester he tells me he’s teaching mathematics. “I’ve taught chemistry, physics and math at WPU and that’s the way I like it,” he says, “With a PhD in chemical physics, I enjoy teaching all of these subjects. Not being tied down allows me to do other things, which in my case means performing science and health shows for the public along with my promotion of two-racquet tennis.”

The notion of reinventing a well-known and popular sport by the novel application of physics is not entirely new. Just think of the football (soccer) players on the fields of Rugby School in England, when William Webb Ellis during the early nineteenth century famously made the ball defy gravity and invented the eponymous team sport from which American football was ultimately to evolve. Perhaps in 100 years’ time two-racquet tennis will have its own name, ambibat, perhaps and be just as common. One has to wonder how a McEnroe of the future might cope though, with two racquets to fling at the umpire!

Double Tennis Racquet Racket

Happy birthday, NASA [Mailund on the Internet]

Posted: 01 Oct 2008 01:43 AM CDT

1 Oct 1958, the National Aeronautics and Space Administration (NASA) began operation.

This is shortly after Sputnik 1 and Sputnik 2 (carrying the dog Laika) in 1957. It is in the middle of the cold war. Still, the US makes a civilian agency for space exploration.

Now, 50 years later, we can look back on a truly exciting history of exploration. The first man on the Moon,the Pioneer mission to the outer planets, the Hubble telescope, the Mars rovers…

Of course, NASA didn’t do all the exciting stuff. USSR put the first satelite in space, the first man in space, were the first to land (an unmanned craft) on the Moon, first space station… Still, an impressive list of achivements goes to NASA.

Go visit their anniversary web page and read more about it! Or watch the video here (appropriately the video starts by playing Stairway to Heaven…).

If you are a space buff, it has been an exciting week, even ignoring the anniversary.

A sad goodbye to Seattle Central Community College biotech [Discovering Biology in a Digital World]

Posted: 30 Sep 2008 11:01 PM CDT

I learned via e-mail yesterday that the biotechnology program, that I taught with for ten years during the 90's, is ending due to low enrollments.

I also learned yesterday, via the Seattle Times, that a resurrected version of ICOS called CMC Icos Biologics is planning a $35M expansion of their biotech manufacturing plant in Bothell and talking about hiring lots of students with two-year degrees.

The irony isn't lost on me.

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A bacterium's-eye view of life [adaptivecomplexity's column]

Posted: 30 Sep 2008 10:05 PM CDT

Howard Berg is a physicist turned systems biologist, and he's been a systems biologist long before it was trendy to be one. He's one of the smartest systems biologists around, and a nice guy too (one who was nice enough to sit down for lunch next to an alone, confused, awkward grad student who I'm sure came off as a tremendously boring person...)

Berg has devoted his career to understanding information processing in E. coli, and this week in PNAS he describes a physical model of how E. coli senses food in its environment.

agribusiness

Wednesday, October 1, 2008

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