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From ScienceDaily: Researchers have shown that when parts of a genome known as enhancers are missing, the heart works abnormally, a finding that bolsters the importance of DNA segments once considered “junk” because they do not code for specific proteins. … “The cardiac changes that we observed in knockout mice lacking these enhancers highlight the role of noncoding sequences in processes that are important in human disease,” said study co-senior author Axel Visel, senior staff scientist and one of three lead researchers at the Mammalian Functional Genomics Laboratory, part of Berkeley Lab’s Environmental Genomics and Systems Biology (EGSB) Division. “Identifying and interpreting sequence changes affecting noncoding sequences is increasingly a challenge in human genetics. The genome-wide catalog of heart enhancers Read More ›

MathematicianRoger Penrose recently published Fashion, Faith, and Fantasy in the New Physics of the Universe, reviewed by Richard Dawid in Nature. Dawid is peeved: There are similar issues with Penrose’s claim that fashion is the main reason for string theory’s influential position. His analysis of its problems is not up to the task of debunking proponents’ physics-based reasons for confidence. Penrose’s main complaint about string theory is that it lacks a clear specification of its number of degrees of freedom. He tries to show this in several contexts. However, he tends to omit information that could make the situation less confusing than he takes it to be. For example, he expresses unease about ‘gauge–gravity duality’, the claim that string theory Read More ›

From Alex Berezow at American Council for Science and Health: I first learned about GMOs as a sophomore microbiology major in college. (They weren’t called GMOs then; they were simply referred to as “transgenic crops.”) I remember feeling exhilarated — the sort of thrill that only accountants or geeky academics can usually understand — at how basic knowledge of DNA sequences was leading to a huge technological revolution. The opportunities were limitless. Years later I entered journalism. And I saw breathtaking ignorance and vitriol aimed at scientists like me coming from supposedly educated people. Never in a million years would I have anticipated that our passion for science would be used as a bludgeon or as a scarlet letter. That Read More ›

From Nola Taylor Redd at Space.com: Although planets surround stars in the galaxy, how they form remains a subject of debate. Despite the wealth of worlds in our own solar system, scientists still aren’t certain how planets are built. Currently, two theories are duking it out for the role of champion. The first and most widely accepted theory, core accretion, works well with the formation of the terrestrial planets like Mercury but has problems with giant planets. The second, the disk instability method, may account for the creation of these giant planets. Now, as for Mercury: Like Earth, the metallic core of Mercury formed first, and then gathered lighter elements around it to form its crust and mantle. Mercury, like Read More ›

From Karen Zusi at The Scientist: The genetic code—the digital set of instructions often laid out in tidy textbook tables that tells the ribosome how to build a peptide—is identical in most eukaryotes. But as with most rules, there are exceptions. During a recent project on genome rearrangement in ciliates, Mariusz Nowacki, a cell biologist at the University of Bern in Switzerland, and his team stumbled across two striking deviants. Ciliates, complex protozoans with two nuclei, are known to translate RNA transcripts in unorthodox ways. Nowacki’s team, however, discovered that Condylostoma magnum and an unclassified Parduczia species had gone even further, reassigning all of the traditional “stop” codons (UGA, UAA, and UAG) to amino acids. “It didn’t make sense in Read More ›

Patrick J. Michaels of the Cato Institute asks at Investors Business Daily: “Is modern science polluted?” What constitutes “bad science”? It’s the epidemic of positive results, in which a researcher reports that the data support his or her prior hypothesis. Stanford’s Daniele Fanelli has shown a distressing increase of positive results in recent decades, something that can’t be true in the real world. Think about it — we are not suddenly becoming more intelligent and getting everything right. What’s happening is that scientists are responding to incentives. Usually, hypotheses are put forward in some grant proposal. Financial backers don’t like negative findings, because negative findings don’t support the work that they’ve funded. Supervisors lose face and researchers can lose their Read More ›

In the recently settled soft dino tissue find case, part of the fired prof’s evidence was the following incident: The lawsuit contends that [creationism was] why Armitage’s employment at Cal State Northridge was terminated, with one professor allegedly storming into his office and shouting: “We are not going to tolerate your religion in this department!” More. It strikes me that Prof Stormer thinks that there is a hard and fast distinction to be made between “science” and “religion.” But the distinction falls apart when examined. Here is a hypothetical example: My religion, we’ll say, teaches that killing animals is wrong and therefore eating meat is wrong. It would be easy to come up with a wealth of science information on Read More ›

Armitage settlement: Nuclear chemist Jay Wiles’s thoughts Last evening, we learned frm College Fix: A creationist scholar recently received a six-figure settlement from California State University Northridge, a payout that resolved a 2-year-old lawsuit that alleged the scholar had been fired after discovering soft tissue on a triceratops horn and publishing his findings. … The lawsuit contends that’s why Armitage’s employment at Cal State Northridge was terminated, with one professor allegedly storming into his office and shouting: “We are not going to tolerate your religion in this department!” More. Here’s some of Jay Wile’s further information from his blog: According to Mr. Armitage, his discovery was well-known in the department long before he and Dr. Anderson published their scientific paper. Read More ›

Fired after discovering soft dino tissue. From Jennifer Kabbany at College Fix: A creationist scholar recently received a six-figure settlement from California State University Northridge, a payout that resolved a 2-year-old lawsuit that alleged the scholar had been fired after discovering soft tissue on a triceratops horn and publishing his findings. … Armitage, who has some 30 publications to his credit and is past-president of the Southern California Society for Microscopy, was hired by the university in early 2010 to manage a wide variety of oversight duties for the biology department’s array of state-of-the-art microscopes, court documents state. He also trained students on how to use the complicated equipment. In the summer of 2012, while at the world-famous dinosaur dig Read More ›

Genetics researcher Bruno Lemaitre introduces his book, An Essay on Science and Narcissism at The Scientist: Psychological studies show that narcissistic individuals tend to use human relationships to attain positions of authority or to improve their own visibility, as illustrated by Monod’s strategic mate choice. The Monod case suggests that it would be naive to see scientists as simply seekers of truth. It is likely that the Nobel laureate enjoyed the position of power that science afforded him, and that it suited his personality. After all, a scientist is someone with expert knowledge who can reveal complex secrets to the public. But how does narcissism, a personality trait associated with dominance and short-term mating strategies, influence the scientific process? As Read More ›

Suzan Mazur writes to say that her new book, on the Royal Society rethinking evolution is now available: “The test case for organized science’s ability to deal empirically with evolution.” – Microbiologist James Shapiro (commenting on the Royal Society public evolution summit) Suzan Mazur is the author of three previous books: The Altenberg 16: An Exposé of the Evolution Industry, The Origin of Life Circus: A How To Make Life Extravaganza, and The Paradigm Shifters: Overthrowing ‘the Hegemony of the Culture of Darwin’. Her reports have appeared in the Financial Times, The Economist, Forbes, Newsday, Archaeology, Astrobiology, Connoisseur, Omni, Huffington Post, Progressive Review, CounterPunch, Scoop Media and other publications, as well as on PBS, CBC and MBC. She has been Read More ›

 We’ve written a lot lately about the problems with peer review. So has Nature. The good news is that a number of innovative approaches are being tried. There is doubtless a winner or two entering the field; best clock ’em all. PeerJ offers peer reviewer matching. Its aims & scope: 1 PeerJ is an Open Access, peer-reviewed, scholarly journal. It considers articles in the Biological Sciences, Medical Sciences, and Health Sciences. 2 PeerJ does not publish in the Physical Sciences, the Mathematical Sciences, the Social Sciences, or the Humanities (except where articles in those areas have clear applicability to the core areas of Biological, Medical or Health sciences). 3 PeerJ only considers Research Articles. It does not accept Literature Review Articles, Hypothesis Papers, Read More ›

From Space Telescope.org: The Hubble eXtreme Deep Field— and more The Hubble eXtreme Deep Field (2012) combines all previous observations of the Hubble Ultra Deep Field Published in 2012, the Hubble eXtreme Deep Field is not a new set of observations, but rather a combination of many existing exposures (over 2000 of them) into one image. Combining the Hubble Ultra Deep Field, the Hubble Ultra Deep Field – Infrared, and many other images of the same small spot of sky taken over almost 10 years, the Hubble eXtreme Deep Field pushes the limit even further. It is made up of a total of 22 days of exposure time (and 50 days of observing time, as the telescope can only observe Read More ›

No, says paleontologist and evolutionary biologist Steven Stanley of the University of Hawaii, arguing that the extinction rate was closer to 81% than 96%. From Phys.org: The Permian-Triassic mass extinction lasted for approximately 60,000 years, and was undoubtedly a tough time for the creatures that lived back then—prior research has suggested that there was an unusually large amount of volcanic activity and also possibly multiple large asteroid impacts, which together caused the planet to warm, and also resulted in an increase in ocean acidification—the conditions were so harsh that many species on land and in the sea went extinct. But, Stanley argues, it was not bad enough to wipe out most marine life entirely, as some have suggested. He points Read More ›

From Anna Azvolinsky at The Scientist: Multiple stressful events during childhood may have a greater impact on telomere length in adulthood compared to stressful events faced during adulthood. While the accumulation of stressful events throughout life increases the chance of having shorter telomeres later in life, adversities experienced during childhood appeared to have the greatest effect on these chromosome caps, according to a study published today (October 3) in PNAS. Each additional adverse event during childhood was associated with an 11 percent-increased odd of shorter telomeres—a marker of cellular aging—past age 50, the authors reported. The findings “offer new insights into what types of stressors may potentially be most harmful in impacting biological aging markers,” Judith Carroll, who studies the Read More ›