Biophysics

In recent weeks, we have seen repeated attempts to suggest that Mathematics is essentially a mind game we make up as an aspect of culture. There has been a very strong resistance to the idea that there are intelligible manifestations of structure and quantity embedded in the fabric of the world (and indeed in that of any possible world). And when test cases have been put on the table, they have been consistently brushed aside as cases where our mathematical modelling has been applied; that is it’s all in our heads. So, it is appropriate to put on the table a test case that is quite literally in our heads, hearing and particularly how the cochlea works. Video: We see Read More ›

The mechanome, “the body of knowledge about mechanical forces at work in the molecular, cellular, anatomical, and physiological processes that contribute to the architecture of living structures and their physical properties,” became more prominent this year in discussions of biology (though one story on the physics of biology late last year garnered 354 comments). For so long, the genome ran away with all the interest and publicity but maybe that’s changing. At her blog, science writer Suzan Mazur talks about the way that mechanobiology is becoming mainstream: “When I say mechanobiology is all the rage, I’m not simply referring to lab research and scientific conferences on the subject, although they are, of course, central. But also to: (1) mechanobiology university Read More ›

Here’s a new paper form Nature Communications describing a discovery of a new geometric shape that is apparently found only in curved epithelial cells. I find it intriguing that this shape is entirely new, not found elsewhere in nature, but now coined “scutoids” by the authors, and is proposed as making “possible the minimization of the tissue energy and stabilize three-dimensional packing.” From the abstract: “The detailed analysis of diverse tissues confirms that generation of apico-basal intercalations between cells is a common feature during morphogenesis. Using biophysical arguments, we propose that scutoids make possible the minimization of the tissue energy and stabilize three-dimensional packing. Hence, we conclude that scutoids are one of nature’s solutions to achieve epithelial bending. Our findings Read More ›

From Cassandra Willyard at Nature: Since 2000, estimates have ranged from tens of thousands to hundreds of thousands. The latest attempt to plug that gap uses data from hundreds of human tissue samples and was posted on the BioRxiv preprint server on 29 May1. It includes almost 5,000 genes that haven’t previously been spotted — among them nearly 1,200 that carry instructions for making proteins. And the overall tally of more than 21,000 protein-coding genes is a substantial jump from previous estimates, which put the figure at around 20,000. But many geneticists aren’t yet convinced that all the newly proposed genes will stand up to close scrutiny. Their criticisms underscore just how difficult it is to identify new genes, or Read More ›

From Suzan Mazur at Oscillations, With the ramping up of investigations in various parts of the world into the mechanics of biology, I’ve decided to post my conversation with Institut Curie biophysicist Emmanuel Farge on the role of mechanics in reprogramming the embryo [2010], relating to his work first published in the scientific literature in 2003, which was well received by the science establishment. … Emmanuel Farge:Exactly. Because you need the gene expression to have the germ-band extension. Then after you need the germ-band extension to have the expression of Twist at the anterior pole, which is mechanically induced. What I’m saying is that you always are in a situation where you cannot say that mechanics is more important than genetics Read More ›

Here’s the abstract of a new PNAS article: There’s a new article in PNAS that illustrates the fact that thermodynamics determines the effects of future changes made to a protein molecule. Any one mutation changes the thermodynamic/statistical mechanics of the protein molecule. And these changes in the thermodynamic properties swims around in a giant ocean of statistical possibilities, and consequent improbabilities; so much so, that future mutations following upon any given mutation cannot be ascertained. So, the next time you hear about how they were able to “reconstruct” an ancient protein, allowing the determination of possible pathways, don’t pay any attention to it. Evolutionary prediction is of deep practical and philosophical importance. Here we show, using a simple computational protein Read More ›

From Suzan Mazur at HuffPost, an interview with German biophysicist Dieter Braun, Redford-style good looks have not been enough to divert Dieter Braun from his research interest in nonequilibrium conditions on the microscale, and what is now a central role in the investigation into the origins of life. Braun—-a professor of systems biophysics at Ludwig Maxmilians University in Munich, a Simons Foundation collaborator on the origins of life, and scientific coordinator of the OLIM initiative (Origin of Life Munich)—-says a whole new breed of scientists, “experimentally driven,” have entered the field as funding opens up and that origins of life research is no longer a “side activity,” fishing expedition, or place for dreamy “pet theories.” He tells Mazur, We’re getting Read More ›

Can protein folding complexity be formed by stochastic processes? With 14 intermediate steps?
JILA Team Discovers Many New Twists in Protein Folding

Biophysicists at JILA have measured protein folding in more detail than ever before, revealing behavior that is surprisingly more complex than previously known. . . .
They fold into three-dimensional shapes that determine their function through a series of intermediate states, like origami. Accurately describing the folding process requires identifying all of the intermediate states.
The JILA research revealed many previously unknown states by unfolding an individual protein. For example, the JILA team identified 14 intermediate states—seven times as many as previously observed—in just one part of bacteriorhodopsin, a protein in microbes that converts light to chemical energy and is widely studied in research.
“The increased complexity was stunning,” said project leader Tom Perkins, a National Institute of Standards and Technology (NIST) biophysicist working at JILA, a partnership of NIST and the University of Colorado Boulder. “Better instruments revealed all sorts of hidden dynamics that were obscured over the last 17 years when using conventional technology.”
“If you miss most of the intermediate states, then you don’t really understand the system,” he said.
Knowledge of protein folding is important because proteins must assume the correct 3-D structure to function properly. Misfolding may inactivate a protein or make it toxic. Several neurodegenerative and other diseases are attributed to incorrect folding of certain proteins.

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In this next installment from the Alternatives to Methodological Naturalism (AM-Nat) conference, Salvador Cordova gives us his perspective on epistemology, which he calls “Gambler’s Epistemology,” which intends to be a metaphysically neutral way of analyzing claims based on their costs and payoff possibilities. Cordova shows that naturalism does not have a history of high payoffs, and that the ENCODE and similar projects by the NIH are good gambling bets but have caused consternation for those metaphysically committed to naturalism, which has historically been shown to be impractical.

Rockefeller University researchers

found that part of a DNA repair protein known as 53BP1 fits over the phosphorylated part of H2AX “like a glove,” says Kleiner. This interaction helps bring 53BP1 to the site of DNA damage, where it mediates the repair of double-stranded breaks in DNA by encouraging the repair machinery to glue the two ends back together.

New findings shed light on fundamental process of DNA repair

What are the prospects of a DNA self replicating entity surviving with rapid cumulative DNA mutations until it assembles the DNA repair mechanism – by random stochastic processes? Read More ›

Granville Sewell and Daniel Styer have a thing in common: both wrote an article with the same title “Entropy and evolution”. But they reach opposite conclusions on a fundamental question: Styer says that the evolutionist “compensation argument” (henceforth “ECA”) is ok, Sewell says it isn’t. Here I briefly explain why I fully agree with Granville. The ECA is an argument that tries to resolve the problems the 2nd law of statistical mechanics (henceforth 2nd_law_SM) posits to unguided evolution. I adopt Styer’s article as ECA archetype because he also offers calculations, which make clearer its failure. The 2nd_law_SM as problem for evolution. The 2nd_law_SM says that a isolated system goes toward its more probable macrostates. In this diagram the arrow represents Read More ›

The 2nd law of statistical thermodynamics states that in a closed system any natural transformation goes towards the more probable states. The states of organization are those more improbable, then transformations spontaneously go towards non-organization, so to speak. Since evolution would be spontaneous organization, evolution disagrees with the 2nd law. The tendency expressed in the 2nd law rules all physical phenomena and is clearly evident in our everyday life, where e.g. systems that were ok yesterday, today are ko, while systems that are ko, do not self repair and remain ko until an intelligent intervention. In short, things break down and do not self-repair, to greater reason they do not self-organize. All that can be related to the trend of Read More ›