November 2015

From his blog: On Saturday, November 21, I had the privilege of hearing Zach Throckmorton of Lincoln Memorial University speak on Homo naledi at the Gray Fossil Site just outside of Johnson City, TN. Dr. Throckmorton is an expert on feet, and he was part of the research team that studied the fossils of Homo naledi after they were excavated from the Rising Star Cave. … I was quite struck by his candid discussion of the burial of these creatures. He was careful to note that they preferred the burial hypothesis because they could not find another credible explanation for why the bones would be in that remote chamber. At the same time, he admitted that these hominins not only Read More ›

From a Top Rated journal TM: ‘Seek Funding’ Step Added To Scientific Method PARIS—In an effort to modernize the principles and empirical procedures of examining phenomena and advancing humanity’s collective knowledge, the International Council for Science announced Thursday the addition of a “Seek Funding” step to the scientific method. More. The friend who contributed this tip notes, This is what would happen if philosophers of science really looked at the process of science as currently practiced 🙂 A conference in tht? this time, Marseilles? Note: Top Rated journal:   See also: Retraction Watch and If peer review is working, why all the retractions? Follow UD News at Twitter!

A new study is out here. They were studying epigenetic effects in planaria flatworms. Same planaria, three different “species”-level “heads” were regenerated. Of course, everything must have an “evoltuion-did-it” explanation; so, for the record, here it is: The ease with which a particular shape could be coaxed from a G. dorotocephala worm was proportional to the proximity of the target worm on the evolutionary timeline. The closer the two species were related, the easier it was to effect the change. This observation strengthens the connection to evolutionary history, suggesting that modulation of physiological circuits may be one more tool exploited by evolution to alter animal body plans. However, there is more to mull over: Working with Girardia dorotocephala – free-living Read More ›

Mantis shrimps use it to avoid already occupied hiding places. From ScienceDaily: Researchers from the Queensland Brain Institute at The University of Queensland have uncovered a new form of secret light communication used by marine animals. … Dr Yakir Gagnon, Professor Justin Marshall and colleagues previously showed that mantis shrimp (Gonodactylaceus falcatus) can reflect and detect circular polarising light, an ability extremely rare in nature. Until now, no-one has known what they use it for. The new study shows the shrimp use circular polarisation as a means to covertly advertise their presence to aggressive competitors. “In birds, colour is what we’re familiar with; in the ocean, reef fish display with colour. This is a form of communication we understand. What Read More ›

From The Atlantic: The toughest animals in the world aren’t bulky elephants, or cold-tolerant penguins, or even the famously durable cockroach. Instead, the champions of durability are endearing microscopic creatures called tardigrades, or water bears. They live everywhere, from the tallest mountains to the deepest oceans, and from hot springs to Antarctic ice. They can even tolerate New York. They cope with these inhospitable environments by transforming into a nigh-indestructible state. Their adorable shuffling gaits cease. Their eight legs curl inwards. Their rotund bodies shrivel up, expelling almost all of their water and becoming a dried barrel called a “tun.” Their metabolism dwindles to near-nothingness—they are practically dead. And in skirting the edge of death, they become incredibly hard to Read More ›

“using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes” From Nature Reviews Genetics:, should feature many useful examples: Here’s the abstract: Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent–offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that Read More ›

No, we didn’t come up with that phrase but it is certainly worth considering, considering almost all alternatives. If you doubt that, see “Maybe if we throw enough models at the origin of life… some of them will stick?” From Quanta: The polymath Christoph Adami is investigating life’s origins by reimagining living things as self-perpetuating information strings. … Life, he argues, should not be thought of as a chemical event. Instead, it should be thought of as information. The shift in perspective provides a tidy way in which to begin tackling a messy question. In the following interview, Adami defines information as “the ability to make predictions with a likelihood better than chance,” and he says we should think of the Read More ›

Quasars. From Scientific American: A dozen quasars in the early universe appear to have shut down in just a few years, baffling astronomers … Last year Stephanie LaMassa from NASA Goddard Space Flight Center (then at Yale University) discovered the greatest change in luminosity ever detected in a quasar. She was digging through data from the Sloan Digital Sky Survey when she found that a quasar had dimmed in brightness by a factor of six in just 10 years. Its spectrum changed, too, from that of a classic quasar to a regular galaxy. … There is nothing controversial about the idea that active galactic nuclei can become inactive. What LaMassa and her colleagues doubted was that a quasar could go Read More ›

From ScienceDaily: Researchers decode patterns that make our brains human … Despite the anatomical complexity of the brain and the complexity of the human genome, most of the patterns of gene usage across all 20,000 genes could be characterized by just 32 expression patterns. While many of these patterns were similar in human and mouse, the dominant genetic model organism for biomedical research, many genes showed different patterns in human. Surprisingly, genes associated with neurons were most conserved across species, while those for the supporting glial cells showed larger differences. … “The human brain is phenomenally complex, so it is quite surprising that a small number of patterns can explain most of the gene variability across the brain,” says Christof Read More ›

Not exactly, but computer use can, they say, distort it in unexpected ways. From RealClearScience: How Computers Broke Science For most of the history of science, researchers have reported their methods in a way that enabled independent reproduction of their results. But, since the introduction of the personal computer – and the point-and-click software programs that have evolved to make it more user-friendly – reproducibility of much research has become questionable, if not impossible. Too much of the research process is now shrouded by the opaque use of computers that many researchers have come to depend on. This makes it almost impossible for an outsider to recreate their results. Recently, several groups have proposed similar solutions to this problem. Recent Read More ›

EL invites me to post comments at The Skeptical Zone:  “I will take this opportunity of inviting him over here, where he can post freely.” Yeah, but no.  I tried to post at The Skeptical Zone once.  KN promptly trashed everything I wrote.  Fool me once . . .  

Over at The Skeptical Zone Elizabeth Liddle quotes me regarding the circular reasoning that would be necessary to suppose that cladistics establishes common descent: It does not take a genius to know that cladistic techniques do not establish common descent; rather they assume it.  But I bet if one asked, 9 out of 10 materialist evolutionists, even the trained scientists among them, would tell you that cladistics is powerful evidence for common descent.  As Johnson argues, a lawyer’s training may help him understand when faulty arguments are being made, sometimes even better than those with a far superior grasp of the technical aspects of the field.  This is not to say that common descent is necessarily false; only cladistics does Read More ›

From Natural History Magazine: Pigs possess complex ethological traits similar to dogs and chimpanzees. … Pigs’ ability to differentiate each other, part of what is termed social cognition, provides evidence that pigs are as socially complex as other intelligent mammals, including primates. This capacity forms the basis for all pig social relationships, including the establishment of dominance hierarchies. Dogs can discriminate between barks recorded in different contexts from the same individual, and also from different individuals in the same context. Elephants are well known for their sophisticated recognition of other individual elephants even over long distances. Pigs have the ability to discriminate between individuals, even closely-related individuals, by smell and by auditory cues, a finding that suggests pigs vocalize in Read More ›

As some might hope? Where would that leave evangelicals now that Darwin is being re-evaluated in so many other places? Dragging in here late, with the last of the religion coverage for the week: Further to: “Karl Giberson? But at this point who cares what Darwin’s Christian huffs at Huffpo? (We all rate a better informed class of critic. Especially now.) There we looked at Nazarene process theologian Karl Giberson’s fact-free claims about the Discovery Institute, sponsor of ID theorists … Sounded odd, but he had been in the files for years. So I went back to see what else one might learn about a figure on the Christian lecture circuit who wants to “save Darwin.” From my notes: – Read More ›

A new PNAS paperpublished last week on the dark proteome has some interesting implications for the theory of evolution. The paper presents a survey of protein sequences, focusing on the many sequences for which the corresponding three dimensional protein structure is not known, and cannot be inferred from any remotely similar sequence. Why is this so-called “dark proteome” is so large? The survey finds that the various hypotheses to explain this—that the dark proteins are intrinsically disordered, or their sequences are compositionally biased, or they are transmembrane proteins, all reasons that can confound structure determination—don’t work very well. The paper concludes that “a surprisingly large fraction of dark proteins … cannot be easily accounted for by these conventional explanations.” And Read More ›