From The Scientist: Of 441 randomly selected biomedical research papers analyzed in a new study, none provided access to all the authors’ data. And only one of these papers shared a complete protocol. The results of this analysis, which could shed light on science’s reproducibility problem, were published today (January 4) in PLOS Biology. “What was most surprising to me was the complete lack of data-sharing and protocol availability,” said study coauthor John Ioannidis, a professor of medicine and health research and policy at the Stanford University School of Medicine. “That was worse than I would have predicted.” “This study confirms what most of us already know—that the current clinical research enterprise is set up in a way that researchers Read More ›

In 2010, Lynch and Abegg claimed in a widely cited journal article that neutral evolutionary processes could generate complex adaptations much more rapidly than was previously believed. Their article contained a mathematical flaw, which was pointed out by Dr. Douglas Axe, but Axe’s critique continues to be ignored by senior evolutionary biologists, including the article’s authors, Professor Joe Felsenstein and Professor Larry Moran. Want proof? Read on. For those readers who don’t know him, Michael Lynch is an eminent scientist: he is Distinguished Professor of Evolution, Population Genetics and Genomics at Indiana University, Bloomington, Indiana. He has also written a two-volume textbook with Bruce Walsh, which is widely regarded as the “Bible” of quantitative genetics. In 2009, he was elected Read More ›

Recently, I (O’Leary) raised the question whether epigenetically triggered dominance behaviour in fish was rightly considered a struggle for “social status”: The concept of social status presupposes not only a society but a relationship to that society consciously recognized by most actors within it. It is not only the behaviour, but also the consciousness—evident in human affairs, as people strive for social status, even from something as apparently abstract as area codes and zip codes. Purely virtual territory. Some may argue that the term social status “shouldn’t” mean what human beings generally understand it to mean. But the term was invented by and for human beings, to describe a situation we experience. Part of that experience is knowing one’s status Read More ›

From Washington Post: Startling new finding: 600 million years ago, a biological mishap changed everything Zounds. Most mishaps don’t change everything by introducing vast new realms of complexity. As in: Bill Gates stumbled in his garage one day, and behold, Windows! In a paper published in the open-access journal eLife this week, researchers say they have pinpointed what may well be one of evolution’s greatest copy mess-ups yet: the mutation that allowed our ancient protozoa predecessors to evolve into complex, multi-cellular organisms. Thanks to this mutation — which was not solely responsible for the leap out of single-cellular life, but without which you, your dog and every creature large enough to be seen without a microscope might not be around Read More ›

Further to: Falsifiability only gained traction as anti-creation move? philosopher (and photographer) Laszlo Bencze writes to say,   The passage you quote from “Newton’s Apple and Other Myths of Science” is terribly misguided: “Part of the appeal of the falsification axiom (if it could never be disproved, it can’t be science) was that it was simple enough for nonscientists to grasp. Yet, when we look at history, falsification simply does not work as a definition of science. As Gordin explains, most historians and scientists accept a sociological definition: Science is what the scientific community says it is (e.g., peer-reviewed work in reputable journals). It’s not a perfect definition, nor a stable one, but it has the virtue of being the Read More ›

(A friend advises, this ran a decade ago.  No one who matters in Canada would have the guts to say it today, not if they are boffins or part of legacy media. National Post was  freer then, as I remember. ) From a no-byline article in Canada’s National Post, 2005: … the theory of intelligent design holds that there are tell-tale features of living systems and the universe that are best explained by an intelligent cause. The theory does not challenge the idea of evolution defined as change over time, or even common ancestry, but it does dispute Darwin’s idea that the cause of biological change is wholly blind and undirected. Either life arose as the result of purely undirected material Read More ›

Commenting on a recent PLOS paper, Ann Gauger writes at Evolution News & Views, A recent paper in PLOS Genetics considers the origins of new “genes” in humans and chimps. By comparing RNA sequences, researchers identified over 600 transcriptionally active “genes” that appear to be present only in humans and not in chimps or the other mammal species tested. They claimed that these “genes” were the product of evolution from previously non-coding, untranscribed DNA. They argued that some of the “genes” are made into proteins and perhaps may be subject to selection, meaning that they are evolving. I put genes in quote because this is not what the term gene typically means. It used to be that a gene was Read More ›

Not smell? At Scientific American blogs, animal behaviour researcher Julie Hecht asks, Does a dog know, merely by sight, that an approaching being is a fellow dog? Before you answer, remember this: Canis familiaris is the least uniform species on the planet. Members of this species come in a wide range of body shapes and sizes from itty bitty teeny weeny to absolutely ginormos. Adult members of this species appear as tight little packages, huge weightlifters, lean ballerinas, elongated hotdogs and everything in between. Of course the obvious response is, “How do humans manage it?” The old canard about the gullible couple buying a chihuahua that turns out to be a yappy rat* is funny precisely because it is not likely Read More ›

Denyse’s recent post here on falsifiability tells me that we need more thought on this creature we call science and what it means for all of us, and especially the enterprise of knowledge.
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Odd, and it speaks very poorly of the science of the day. But one historian says that the historical data demonstrate that view. Further to the new science mythbuster book, Newton’s Apple and Other Myths About Science, a reader kindly notes that we also learn from the paywalled review in Science: Michael Gordin … [debunks] the widely accepted belief that science can be easily differentiated from pseudoscience simply by determining whether a particular theory is falsifiable. In addition to the philosophical shortcomings of this approach, he notes that if a negative result is sufficient to falsify a theory, then high-school science students manage to “falsify” most of Western science each week in their lab classes. Gordin goes on to analyze Read More ›

“How real is reality?” asks theoretical physicist Adam Frank at NPR: … throughout the past 100 years, physicists have proposed a lot of different ways to interpret their mathematics and, in the process, explain what quantum theory tells us about the fundamental nature of “The Real.” These interpretations tend to fall into one of two camps. For the first camp, the mathematics directly describes a reality that is independent and objective. In this view, quantum mechanics is an ontological theory (ontology is the branch of philosophy dealing with what truly exists). For the second camp, however, the mathematics of quantum mechanics describes only our knowledge of the world. For these folks, quantum physics is an epistemological theory (epistemology is the Read More ›

The parable of Plato’s Cave in The Republic — vid: [youtube d2afuTvUzBQ] . . . is a classic point of departure for discussions of true vs false enlightenment, education, worldviews, liberty and manipulative sociocultural agendas or power games that open up marches of folly. ( I think Acts 27 still has the best classical case study on how democratic polities and/or decision makers can all too easily be led into such ill advised marches.) March of folly? Yes: Of course, with a US Election cycle in full swing as the number one media story for the year, such is obviously highly relevant to anyone interested in public policy or geostrategic issues. But, these issues are also highly relevant to the Read More ›

Learn how. Or so they say. From Mashable: It’s an age old question: Can cutting pizza ever be truly equal? … But mathematicians Joel Haddley and Stephen Worsley at University of Liverpool in England believe they have cracked the code for perfect equality at the dinner table by cutting somewhat complex, curved slices — also known as monohedral disc tiling. More. From Phys.org: “I’ve no idea whether there are any applications at all to our work outside of pizza-cutting,” said Haddley in New Scientist. He has tried slicing a pizza in this way for real. But the results are “interesting mathematically, and you can produce some nice pictures.” In short, the math is beautiful, but the pizza was probably a Read More ›

Science historian Michael Flannery kindly contributed this review: When I started reading Perry Marshall’s book, Evolution 2.0: Breaking the Deadlock Between Darwin and Design, I must confess to some consternation almost from the beginning. While Marshall was quick to point out the shortcomings of the neo-Darwinian approach of common descent by means of natural selection through the undirected processes of chance and necessity, he oddly went on to claim that ID, while recognizing many truths about biology that old-school Darwinism denies, ultimately abdicates its responsibility by jumping directly to ‘God did it’. At least in its most simple forms, ID halts scientific inquiry by dismissing too easily the possibility that God may have used a process to develop life on Read More ›