Ann Gauger keeps digging

Ann Gauger and her creationist collaborator, Doug Axe, have been swapping amino acid residues in one kind of protein hoping to show that they cannot change it into another. They have deliberately ignored any clues that might be derived from assuming that evolution happened.

They have succeeded in their goal. None of their constructs have a different activity. They conclude that evolution is disproved.

Why fund basic science?

This video was the winner in the 2013 FASEB competition for "Stand Up for Science." The title was "Funding Basic Science to Revolutionize Medicine."

I'm sure their hearts are in the right place but I fear that videos like this are really just contributing to the problem. It makes the case that basic research should be funded because ultimately it will pay off in technologies to improve human health. If you buy into that logic then it's hard to see why you should fund research on black holes or studies of plate tectonics.

Don't we have a duty to stand up for ALL basic research and not just research that may become relevant to medicine? Besides, if the only important basic research that deserves funding is that which has the potential to contribute to medicine, then shouldn't funding be directed toward the kind of "basic research" that's most likely to pay off in the future? Is that what we want? I don't think evolutionary biologists would be happy but everyone working with cancer cells will be happy.

The best argument for basic research, in my opinion, is that it contributes to our knowledge of the natural world and knowledge is always better than ignorance. This argument works for black holes, music theory, and for research on the history of ancient India. We should not be promoting arguments that only apply to our kind of biological research to the exclusion of other kinds of basic research. And we should not be using arguments that reinforce the widespread belief that basic research is only valuable if it leads to something useful.

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A creationist argument against the evolution of new enzymes

Intelligent Design Creationists have found it impossible to make a positive case for intelligent design and the existence of a supernatural designer. Instead, they concentrate on trying to prove that evolution is wrong. Turns out, they're not very good at that either.

The latest attempt is by Ann Gauger posting on the best Intelligent Design Creationist website.¹ She outlines her case at: Is Evolution True? Laying Out the Logic.

On the irrelevance of Michael Behe

Michael Behe is one of the few Intelligent Design Creationists who have come up with reasonable, scientific, defenses of creationism. I give him credit for that and for the fact that it often takes some effort to show why he is wrong.

However, when he has been proven wrong he should admit it and move on. He should instruct his fellow creationists to move on as well. That's not what happened with respect to his book on The Edge of Evolution. Last July he doubled down when a new study appeared that refuted his claims. Amazingly, Behe said that his ideas were vindicated. I questioned his logic in: CCC's and the edge of evolution and Michael Behe's final thoughts on the edge of evolution.

After a thorough discussion, we conclude that Behe is wrong about his edge of evolution. There's nothing in evolutionary theory, or in experimental results, that prevents the evolution of new functions with multiple mutations.

Now Ken Miller has posted an article making many of the same points [Edging towards Irrelevance]. Miller rightly demands an apology from Behe but his main point is that Michael Behe's recent behavior has made him largely irrelevant in the debate over Intelligent Design Creationism. I agree.

What this means is that there is nobody left in the Intelligent Design Creationist community who deserves serious attention from scientists. It will still be fun dealing with them but the game has become more like whac-a-mole than science. PZ Myers¹ makes the same point: Aren’t we all more than a little tired of Michael Behe?.

It's kinda sad.

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1. Unfortunately, PZ weakens his case by misrepresenting Behe's argument. PZ says, The hobby horse he’s been riding for the past few years is the evolution of chloroquine resistance in the malaria parasite: he claims it is mathematically impossible." That's just not true. Behe's entire case rests on the fact that chloroquine resistance is well within the edge of evolution. Behe has no problem with the evolution of chloroquine resistance.

How to revolutionize education

I believe that we need to change the way we teach. But not the way you probably think. Watch this video to see what's really important about teaching.

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Hat Tip: Alex Palazzo, who I hope will help us make the transition to 21st century teaching.

For the King

My son Gordon and his friend Colby are working on a new game called "For the King." It looks really cool. (I'm playing with an early version.)

Check out the website: IronOaks Games. They are also on Facebook: IronOaks Games. Twitter is @IronOakGames where you can make suggestions and follow development.

This is a game that reminds you of Hack and Nethack except with much better graphics. I think all the old people (like me) are going to like it. Ms Sandwalk asked for a carnival and got it (see below) and I'm pumping for a university.

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Nature criticizes science hyperbole and bad science writing

There's a very interesting editorial in the Oct 14, 2014 issues of Nature [see here]. It's about a scientific paper that turned out to be misleading and the role of science writers and journals in promoting that story.

The editors of Nature remind us that ...

Extraordinary claims, as the saying almost goes, demand more scrutiny than usual to make sure they stand up. That is how science works. Claim and counter-claim: intellectual thrust and experimental parry.

They report on an upcoming meeting meeting of the Council for the Advancement of Science Writing in Columbus Ohio. Apparently, this council is composed of scientists and journalists and the goal of the meeting is to search for "lessons learned by scientists and science writers" in light of their publicity campaign promoting the flawed paper.

The Nature editors note that ...

The first thing to highlight is that such a thing as the Council for the Advancement of Science Writing even exists. Too many scientists dismiss the media and journalists as sloppy and unwilling to engage in both detail and ambiguity. In fact, there can be no branch of journalism as self-scrutinizing and anxious about its performance as that which covers science. It is hard to imagine political and sports reporters taking the time to discuss so thoroughly what (if anything) they did wrong after one of their stories went belly-up.

Indeed, that's admirable, but it's another example of journalistic hyperbole. I do not believe that this branch of journalism (science writing) is as "self-scrutinizing" as they would have us believe. I do not believe that science writers usually debate and discuss what they did wrong when a story goes belly-up.

But it may be true that science writers are increasingly "anxious" about their performance. Why are they so "anxious"? It's because they are doing a very sloppy job characterized by parroting press releases written by amateurs whose main goal is to promote their institution or by science journals that want publicity.

Science writers (and journals) used to get away with this but now ...

The (welcome) rise of the science blogger has fuelled this navel-gazing. Some bloggers seem to spend most of their time criticizing other science writers, or at least debunking examples of what they regard as inferior science writing. But they do lots of good stuff too. Although traditionalists lament the decline of science coverage in the mainstream press, a terrific amount of analysis and comment, much of it very technical, is happening online under their noses.

There's an interesting slip of the tongue in that paragraph. If science writers are really interested in self-scrutiny then they should welcome the arrival of a group of bloggers who point out their errors. This should be a "good" thing but the Nature editors clearly contrast this role (criticizing science writers) with other "good stuff" that bloggers do. Apparently the criticism of science writing doesn't count as "good stuff." It just makes science writers anxious—which they weren't before science bloggers came on the scene and pointed out what a bad job they were doing.

Nature then admits its complicity in hyping the event and not doing a proper skeptical analysis of the findings. The editors then get to an important issue.

Some may question the timing of the announcement, made when the paper was released on the Internet, not accepted or published by a journal, but at least the evidence was there to examine. If the scientists and the media both largely acted properly, then what should be discussed at next week’s meeting? It could do worse than start by screening the celebratory online video produced by ... and released to accompany the announcement. Scientists and journalists can include as many academic caveats as they like, but the sounds and images of champagne corks popping tend to render such statements of caution just that — academic.

There is a deeper issue here: science not by press conference but presented as an event. What in reality is a long, messy and convoluted process of three steps forward and two steps back is too easily presented as giant leaps between states of confusion and blinding revelation. At the heart of this theatre is the artificial landmark of a peer-reviewed paper. Fixed print schedules and releases to journalists under embargo (with or without champagne videos) help to lend the impression that the publication of a paper is the final word on a question — the end-of-term report on a scientific project that details all that was achieved.

I bet you're thinking that this is all about the ENCODE publicity campaign and how Nature was totally at fault for misrepresenting the data and hyping the false claims of the ENCODE Consortium.

Nope. It's about the discovery of gravitational waves—a paper that turns out to have been wrong because scientists didn't do the proper controls.

Meanwhile, Nature, and science writers in general, have yet to admit that they failed massively in September 2012 and they have done little to convince us "bad" bloggers that they are capable of self-scrutiny. This is serious because in this case Nature and its editors were very active participants in the making of videos and holding press releases [see How does Nature deal with the ENCODE publicity hype that it created?]. Let me remind you of the video PRODUCED BY NATURE featuring Senior Editor Magdalena Skipper in which she promotes the idea that most of the human genome is functional. [Note: I'm getting error messages when I try to run this video.]


Maybe there are other things that the Council for the Advancement of Science Writing could be talking about? Maybe there are other examples of bad science journalism that the editors of Nature should be addressing?

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Creationists trash Denmark

Denmark present a real problem for many Christians. It appears to be a successful secular society that has all but abandoned extreme forms of religion. These Christians can't figure out how a country could be moral if it's full of nonbelievers.

Vincent Joseph Torley (vjtorley) has found the answer [Is something rotten in the state of Denmark?]. He's responding to claims by Jerry Coyne that Denmark is a successful country.

Perhaps Coyne might be interested to read an eye-opening article by Carol Brown over at American Thinker on what is happening in Denmark. Ms. Brown paints a terrifying portrait of a society which is falling apart under the influence of religiously motivated violence. Crime in Denmark has exploded, and street gangs "have taken over large parts of Danish towns and cities. There are numerous "no go" zones where even the police are afraid to venture. Is this Coyne’s idea of a successful secular society?

Some morals to be drawn from Brown’s article:

1. Not all forms of religion are good; some are toxic.

2. Nature abhors a vacuum. Secularism is powerless to drive out toxic forms of religion.

3. The only proven way to drive out toxic forms of religion, and keep them out, is with wholesome forms of religion.

I was in Denmark for seven days and I never saw any sign of this sort of lawlessness or even heard about it. But maybe I was just in the wrong places? Or maybe it's not true? (Heavens!)

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BREAKING NEWS!!! A creationist doesn't understand evolution

Last March, I dissected the views of James Tour, a chemist who doesn't understand evolution [A chemist who doesn't understand evolution]. Apparently he didn't listen because he's at it again and still being promoted by IDiots [Detective Columbo of Chemistry: "I Don't Understand Evolution"].

I don't know who wrote that post but here's the punchline ...

Tour signed Discovery's Scientific Dissent from Darwinism years ago when the National Center for Science Education asserted that only a handful of scientists doubt Darwin's theory. Our list of dissenters started at 100, then grew to 800. At that point we stopped inviting people to sign it because their names on the list were used by Darwinists to persecute them professionally. Some lost their jobs.

However, Tour doesn't seem to have been hurt. Is that possibly because chemists are more open-minded than biologists? Or is the dirty little secret about Darwinism -- that it has more public advocates in science than private believers -- becoming more apparent?

Maybe we should consider the possibility that that a synthetic organic chemist is not an expert on biology? Naw, that would require the application of skepticism [How to use selective hyperskepticism to debate Darwinists].

You just can't make this stuff up.

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How not to teach biochemistry

One of my friends is teaching introductory biochemistry and he thinks this video (below) is worth posting on his blog [here]. I do not want MY students to think that this is the right way to understand glycolysis and the citric acid cycle.


Theme

Better Biochemistry

1. Accuracy: The top three criteria for effective teaching are; accuracy, accuracy, and accuracy. If what you are saying isn't factually correct then nothing else matters. The citric acid cycle shown in the diagram is pretty good. It avoids the most important error (using FADH₂ as the product of the succinate dehdrogenase reaction) but it commits the three other, less significant, common errors [Biochemistry on the Web: The Citric Acid Cycle].
   
   However, when the song gets to the succinate dehydrogenase reaction (at 1:55) it points to QH₂ and calls it FADH₂. If you are going to teach about these reactions then get them right.
   
   
2. The Evolutionary Approach: There are several ways of teaching biochemistry. The American Society of Biochemistry and Molecular Biology (ASBMB) recommends an emphasis on evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution]. This may seem obvious in the 21st century but very few biochemistry courses are taught this way. Most of them adopt some version of the "fuel metabolism"¹ approach to teaching biochemistry. This approach focuses on human metabolism without putting it into the large context. The video is all about "popping carbs" as though converting carbohydrates (glucose) to energy was the only reason for having these pathways.
   
   This approach caters to the biases of the students and to the pre-meds in the class. It does not take the opportunity to correct some of those biases.
   
   

3. Basic Concepts: ASBMB has come out strongly in favor of teaching core concepts rather than memorize/regurgitate [ASBMB Core Concepts in Biochemistry and Molecular Biology]. While I don't always agree with their core concepts, I strongly support this way of teaching biochemistry. The emphasis in a course should be on understanding the basic principles and not on memorizing the details. When I was teaching this material, I allowed students to bring their notes to the exam so they could refer to the specific reactions of the various pathways. They did not have to memorize them.
   
   The core concepts here are things like the importance of gluconeogenesis and why some species have evolved ways of "reversing" that pathway. It's also important to understand the thermodynamics of the reactions in a pathway and the fact that most reactions are at equilibrium. This leads to an emphasis on flux. With respect to the citric acid cycle, the core concepts are that all of the intermediates are involved in multiple reactions and in most species there's no simple "spinning" of the cycle spewing out CO₂. Once they grasp that, you can teach teach them what happens in active mammalian muscle cells. It's harder to make a rap video about core concepts.
   
   You should never, ever, ask students to memorize these reactions for exam questions. No only is that a waste of time but it detracts from the main goal, which should be learning fundamental principles and concepts.

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1. Also known as "rat liver biochemistry" since most of the information comes from studies on rat livers.

Razib Khan defends old-fashioned evolution theory

Razib Khan writes at Gene Expression. He's a big fan of personal genetics and genome sequencing and, in the past, has been a defender of the Modern Synthesis version of evolutionary theory. In light of the recent Nature discussion on "Does evolutionary theory need a rethink?" (Laland et al. 2014), Razib thought he would re-state his position [Evolution Ever Evolves].

I laid out my position in: Rethinking evolutionary theory. I don't think any of the new ideas like epigenetics, plasticity, facilitated variation etc. are about to change evolutionary theory significantly. However, I do think that the standard version of the 1940s Modern Synthesis was far too rigid and that a modern emphasis on population genetics (including Neutral Theory and more emphasis on random genetic drift) have significantly changed evolutionary theory—something close to a "revolution." The problem is that many scientists, and even many evolutionary biologists, haven't really integrated this change into their way of thinking. This resistance was very well described in a paper by Stephen J. Gould and Richard Lewontin over 45 year ago (Gould and Lewontin, 1978) [What Does San Marco Basilica Have to do with Evolution?]

I think there's already been a "revolution" but most people didn't notice and are still stuck in the 1940s adhering to an old-fashioned version of evolutionary theory that emphasizes adaptation.

Razib Khan doesn't like Gould and doesn't like new-fangled ideas like "neutralism" and "random genetic drift". Let's see what he thinks of the latest kerfluffle.

It seems that rather regularly there is a debate within evolutionary biology, or at least in public about evolutionary biology, where something new and bright and shiny is going to revolutionize the field. In general this does not pan out. I would argue there hasn’t been a true revolution in evolutionary biology since Mendelian genetics and classical Darwinism were fused in the 1920s and 1930s during the period when population genetics as a field was developed, and the famous "synthesis" developed out of the interaction of the geneticists with other domains of evolutionary relevance. This does not mean that there have not been pretenders to the throne. Richard Goldschmidt put forward his "hopeful monsters," neutralism reared its head in the 1970s, and evo-devo was all the rage in the 2000s. Developments that bore scientific fruit, such as neutralism, were integrated seamlessly into evolutionary biology, while those that did not, such as Goldschmidt’s saltationism fell by the wayside. This is how normal science works.

The main point here is whether Neutral Theory and an increased emphasis on random genetic drift "were integrated seamlessly" into the Modern Synthesis view that was popular in the 1960s. Is it true that the way modern population geneticists look at evolution is just a little bit different from the way evolutionary biologists thought about evolution in the 1920s, 1930s, and 1940s? I don't think so. I think there's been a significant shift—so much so that we can no longer refer to the "Modern Synthesis" as the most modern version of evolutionary theory.

Unlike Razib Khan, I am not convinced that most evolutionary biologists have made the shift. At my university, for example, the students must take a first-year course on evolution taught by members of the Dept. of Evolution & Ecology. I see these students in subsequent years and they don't understand the basics of population genetics. Nor do they appreciate the role of neutral alleles and random genetic drift. They are being taught the evolutionary theory of the Modern Synthesis (circa 1960).

Also the debates we are having over junk DNA suggests strongly that most scientists are not familiar with modern population genetics and Neutral Theory.

But every now and then you have a self-declared tribune of the plebs declaring that the revolution is nigh. For decades the late Stephen Jay Gould played this role to the hilt, decrying "ultra-Darwinism," and frankly misrepresenting the state of evolutionary theory to the masses from his perch as a great popularizer. More recently you have had more muted and conventional revisionists, such as Sean Carroll, who promote a variant of evo-devo that acclimates rather well to the climes of conventional evolutionary biology.

I do not believe that Gould misrepresented evolutionary theory to the masses. I believe that Richard Dawkins misrepresented evolutionary theory to the masses.

Like Razib, I'm not a big fan of evo-devo and I don't think it contributes much to fundamental evolutionary theory.

Nature now has a piece out which seems to herald the launching of another salvo in this forever war, Does evolutionary theory need a rethink? It’s written in the form of opposing dialogues. I’m very much in the camp of those believe that there’s no reason to overturn old terms and expectations. Evolutionary biology is advancing slowly but surely into new territory. There’s no problem to solve. The one major issue where I might have to make a stand is that it focusing on genetics is critical to understanding evolution, and dethroning inheritance from the center of the story would eviscerate the major thread driving the plot. The fact that evolutionary biologists have the conceptual and concrete gene as a discrete unit of information and inheritance which they can inspect is the critical fact which distinguishes them from fields which employ similar formalisms but have never made comparable advances (such as economics).

I agree with Razib Khan that genetics (population genetics) is the key to understanding evolutionary theory at the population level. I think we disagree on exactly what version of population genetics we support and on the importance of adaptation.

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Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 205, No. 1161, The Evolution of Adaptation by Natural Selection (Sep. 21, 1979), pp. 581-598. [AAAS reprint] [printable version]

Laland, K., Uller, T., Feldman, M., Sterelny, K., Müller, G. B., Moczek, A., Jablonka, E., Odling-Smee, J., Wray, G. A., Hoekstra, H. E., Futuyma, D. J., Lenski, R. E., Mackay, T. F. C., Schluter, D. and Strassmann, J. E. (2014) Does evolutionary theory need a rethink? Nature 514, 163-165. [PDF]

How to use selective hyperskepticism to debate Darwinists

Gordon Elliot Mullings (kairosfocus) is explaining to his fellow creationists how to debate evolution. His latest post focuses on the techniques of "selective hyperskepticism" and "close-mindedness" [Darwinian Debating Devices # 12: Selective Hyperskepticism, closed-mindedness (and “extraordinary claims require extraordinary evidence”)].

Here's how he describes selective hyperskepticism. He's quoting someone who comment on Uncommon Descent.

... hyper-skepticism (which is certainly not a term we made up … just google it) is virtually never equitable. Rather it is highly selective. Selective Hyper-Skepticism results when one requires a much higher degree of warrant in order to accept things that they prefer weren’t true. It most often comes up when worldview issues are at stake. It’s the application of a double-standard where one demands sufficient evidence to support absolute certainty (which is generally impossible) on certain facts they’d rather not have to believe, but they are willing to accept a much more lax standard of evidence and argumentation on matters of a very similar profile that don’t threaten their worldview. It also happens that someone demonstrating hyper-skepticism on these types of worldview issues often displays hyper-credulity towards arguments and evidence on the matter that is consistent with their own worldview. This isn’t really an accident, because the hyper-skepticism applied on one side of the equation often leaves the person grasping for any contrary evidence or argument at all on the other side of the equation, no matter how implausible or unsubstantiated.

Now, Gordon Elliot Mullings doesn't give any examples of how to use this technique to debate Darwinists but I can think of a few examples.

Let's take the formation of bacterial flagella as a good illustration of how they use selective hyperskepticism. They begin with the unshakeable assumption that gods exist that that they must have created life. They then find an example of something complex where the exact evolutionary pathway hasn't been worked out and declare that the gods made it. They refuse to answer any questions about how, when, where, and why and they refuse to present any evidence that gods did it.

When evolutionary biologists present some evidence that bacterial flagella could have arisen by evolution the creationists turn into selective hyperskepticists by demanding a detailed blow-by-blow account of the historical process complete with reams of scientific evidence. Of course, they would never think of applying these same criteria to their own worldview.

I didn't read the rest of the post or the other ones put up by Gordon Elliot Mullings so I'm not sure why he's exposing this tactic to the public. It makes creationists look bad.

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Do you believe that drinking carbonated beverages containing sugar will cause your telomeres to shorten and hasten your death?

It's very difficult to teach students to be skeptical of the scientific literature and how it's reported. I read this press release from the University of California, San Francisco (San Francisco, USA) and dismissed it as ridiculous but I can't really tell you why. It's from one of the top research universities in the world.

What do you think? Do you believe this study? If not, why not? How do you explain why you are skeptical about this research but not about other research?

Kim Krisberg, who describes herself as "freelance public health writer" writes at The Pump Handle [New research finds that drinking soda may lead to cell aging and disease, regardless of obesity]. She doesn't appear to be skeptical.

UCSF scientists find shorter telomeres in immune cells of soda drinkers

Sugar-sweetened soda consumption might promote disease independently from its role in obesity, according to UC San Francisco researchers who found in a new study that drinking sugary drinks was associated with cell aging.

The study revealed that telomeres — the protective units of DNA that cap the ends of chromosomes in cells — were shorter in the white blood cells of survey participants who reported drinking more soda. The findings were reported online October 16, 2014 in the American Journal of Public Health.

The length of telomeres within white blood cells — where it can most easily be measured — has previously been associated with human lifespan. Short telomeres also have been associated with the development of chronic diseases of aging, including heart disease, diabetes, and some types of cancer.

"Regular consumption of sugar-sweetened sodas might influence disease development, not only by straining the body's metabolic control of sugars, but also through accelerated cellular aging of tissues," said Elissa Epel, PhD, professor of psychiatry at UCSF and senior author of the study.

"This is the first demonstration that soda is associated with telomere shortness," Epel said. "This finding held regardless of age, race, income and education level. Telomere shortening starts long before disease onset. Further, although we only studied adults here, it is possible that soda consumption is associated with telomere shortening in children, as well."

The authors cautioned that they only compared telomere length and sugar-sweetened soda consumption for each participant at a single time point, and that an association does not demonstrate causation. Epel is co-leading a new study in which participants will be tracked for weeks in real time to look for effects of sugar-sweetened soda consumption on aspects of cellular aging. Telomere shortening has previously been associated with oxidative damage to tissue, to inflammation, and to insulin resistance.

Based on the way telomere length shortens on average with chronological age, the UCSF researchers calculated that daily consumption of a 20-ounce soda was associated with 4.6 years of additional biological aging. This effect on telomere length is comparable to the effect of smoking, or to the effect of regular exercise in the opposite, anti-aging direction, according to UCSF postdoctoral fellow Cindy Leung, ScD, from the UCSF Center for Health and Community and the lead author of the newly published study.

The average sugar-sweetened soda consumption for all survey participants was 12 ounces. About 21 percent in this nationally representative sample reported drinking at least 20 ounces of sugar-sweetened soda a day.

"It is critical to understand both dietary factors that may shorten telomeres, as well as dietary factors that may lengthen telomeres," Leung said. "Here it appeared that the only beverage consumption that had a measurable negative association with telomere length was consumption of sugared soda."

The finding adds a new consideration to the list of links that has tied sugary beverages to obesity, metabolic syndrome, type 2 diabetes, and cardiovascular disease, and that has driven legislators and activists in several U.S. jurisdictions to champion ballet initiatives that would tax sugar-sweetened beverage purchases with the goal of discouraging consumption and improving public health.

The UCSF researchers measured telomeres after obtaining stored DNA from 5,309 participants, ages 20 to 65, with no history of diabetes or cardiovascular disease, who had participated in the nation's largest ongoing health survey, called the National Health and Nutrition Examination Survey, during the years 1999 through 2002. They found that the amount of sugar-sweetened soda a person consumed was associated with telomere length, as measured in the laboratory of Elizabeth Blackburn, PhD, professor of biochemistry at UCSF and a winner of the 2009 Nobel Prize in Physiology or Medicine for her telomere-related discoveries.

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Additional study authors include, from UCSF, Nancy E. Adler, PhD, professor of psychiatry and director of the Center for Health and Community, and Jue Lin, PhD, an associate researcher with Blackburn's lab; from UC Berkeley, Barbara A. Laraia, PhD, director of public health nutrition; from the University of Michigan, Belinda Needham, PhD, assistant professor of epidemiology; and from Stanford University, David H. Rehkopf, ScD, assistant professor of medicine.

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Fixing CO2 fixation

How biochemistry students can become multi-millionaires by making plants more efficient. Has someone finally succeeded?

Living organisms need carbon to grow and divide. Many get their carbon atoms from organic molecules such as glucose or acetate that have been synthesized in other species.

Most organisms can fix carbon directly from carbon dioxide by a variety of different reactions but this isn't necessarily the primary source of carbon atoms. (We can fix carbon using pyruvate dehydrogenase, isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, and phosphoenolpyruvate carboxykinase (PEPCK) among others.)

Non-coding half of human genome unlocked

This is another story about press releases. In this case, it's an article published by ScienceDaily: Non-coding half of human genome unlocked with novel sequencing technique. It's almost a direct copy of a press release put out by Texas A&M University (Texas, USA): Texas A&M Biologists Unlock Non-Coding Half of Human Genome with Novel DNA Sequencing Technique.

Let's begin by looking at the actual paper (Aldrich and Maggert, 2014). Here's the abstract.

Heterochromatin is a significant component of the human genome and the genomes of most model organisms. Although heterochromatin is thought to be largely non-coding, it is clear that it plays an important role in chromosome structure and gene regulation. Despite a growing awareness of its functional significance, the repetitive sequences underlying some heterochromatin remain relatively uncharacterized. We have developed a real-time quantitative PCR-based method for quantifying simple repetitive satellite sequences and have used this technique to characterize the heterochromatic Y chromosome of Drosophila melanogaster. In this report, we validate the approach, identify previously unknown satellite sequence copy number polymorphisms in Y chromosomes from different geographic sources, and show that a defect in heterochromatin formation can induce similar copy number polymorphisms in a laboratory strain. These findings provide a simple method to investigate the dynamic nature of repetitive sequences and characterize conditions which might give rise to long-lasting alterations in DNA sequence.