Information

Biochemist James Shapiro told Suzan Mazur in The Paradigm Shifters: Overthrowing “the Hegemony of the Culture of Darwin,” Genome change is not the result of accidents. If you have accidents and they’re not fixed, the cells die. It’s in the course of fixing damage or responding to damage or responding to other inputs—in the case I studied, it was starvation—that cells turn on the systems they have for restructuring their genomes. So what we have is something different from accidents and mistakes as a source of genetic change. We have what I call “natural genetic engineering.” Cells are acting on their own genomes in a large variety of well-defined non-random ways to bring about change. p. 15 This is consistent Read More ›

From H. Allen Orr in “DNA: ‘The Power of the Beautiful Experiment,’” in a review of Matthew Cobb’s Life’s Greatest Secret: The Race to Crack the Genetic Code (Basic Books)New York Review of Books: The “information” that is “encoded” in DNA gets “read” by cells. You likely didn’t notice because this is now a nearly reflexive way of talking about DNA, even in popular culture. It’s just obvious to us that DNA stores information—for curly hair or blue eyes—and it’s natural to think of it as an information storage device much like the hard disk of a computer. Yet one of Cobb’s main points is that this is a remarkably recent way of thinking about biology. True Then it gets Read More ›

We are told, Running a brain-twisting thought experiment for real shows that information is a physical thing – so can we now harness the most elusive entity in the cosmos? … Recently came the most startling demonstration yet: a tiny machine powered purely by information, which chilled metal through the power of its knowledge. This seemingly magical device could put us on the road to new, more efficient nanoscale machines, a better understanding of the workings of life, and a more complete picture of perhaps our most fundamental theory of the physical world. More. That hardly makes information physical; if anything it would show that the universe in which we live is not ultimately controlled by physical forces. But we Read More ›

A friend sends this gem from the literature;, it sounds totally oblivious of the information requirement for life: It is now generally accepted that the emergence of increasingly complex eukaryotic life forms was accompanied by a corresponding increase in genome complexity, entailing both an expansion in gene number and more elaborate gene regulation.(22–24) Only DNA recombination in the form of gene or segmental duplications, exon shuffling, insertions, deletions, and chromosomal rearrangements can adequately account for this massive increase in gene number and the complexity of their regulation.(22–24). – Oliver, Keith R. & Wayne K. Greene (2009) Transposable elements: powerful facilitators of evolution BioEssays 31:703–714. Kirk Durston, picking on the theme, offers a translation from the Darwinspeak: The authors are blowing Read More ›

Or something like that. From Priceonomics: The Independent Discovery of TCP/IP, By Ants After years of watching ant colonies in the Arizona desert, Stanford biologist Debra Gordon made a discovery: harvester ants, the species she was studying, had a very particular foraging technique. … Theydidn;twaste a lot of ants in hard times. But when Gordon showed her data to Prabhakar to model computationally, he had a revelation. “The algorithm the ants were using to discover how much food there is available is essentially the same as that used in the Transmission Control Protocol,” he said. … If we consider that the ant colony’s goal is to collect more food and expend fewer ants, and a server’s goal is to send Read More ›

. Cells are the fundamental units of life. The genome sequence of a cell may be thought of as its operating system. It carries the code that specifies all of the genetic functions of the cell, which in turn determine the cellular chemistry, structure, replication, and other characteristics. Each genome contains instructions for universal functions that are common to all forms of life, as well as instructions that are specific to the particular species. The genome is dependent on the functions of the cell cytoplasm for its expression. In turn, the properties of the cytoplasm are determined by the instructions encoded in the genome.  – Venter Institute, 2016   Sixty-three years ago Francis Crick wrote a letter to his 12 Read More ›

From ScienceDaily: A new study suggests that ravens can be as clever as chimpanzees, despite having much smaller brains, indicating that rather than the size of the brain, the neuronal density and the structure of the birds’ brains play an important role in terms of their intelligence. … The large-scale study concluded that great apes performed the best, and that absolute brain size appeared to be key when it comes to intelligence. However, they didn’t conduct the cylinder test on corvid birds. (For some reason, humans were not tested for the ability to get food out of the end of a tube instead of striking at the middle… ) Can Kabadayi, together with researchers from the University of Oxford, UK Read More ›

Recently, we’ve seen some rather abrupt shifts: The Royal Society is suddenly rethinking the importance of Darwinism in evolution—which will have huge ramifications even if they lose heart and flee the scene. It’s enough that they even considered such grave apostasy. For most people who grew up in the English-speaking world, evolution (indeed, all of biology) is Darwinism. The American Darwin-in-the-schools lobby, for example, has no similar interest in horizontal gene transfer, hybridization, epigenetics, or other ways evolution can happen. No one is suing the school board over chromosome doubling or getting their pants in a knot over convergence. But then these demonstrated ways evolution can happen do not add up to a grand naturalist scheme either. It’s more like Read More ›

From ScienceDaily: Researchers discover sophisticated alarm signaling in a primitive insect Many insect species respond to danger by producing chemical alarm signals, or alarm pheromones, to inform others. In a recent study, investigators found that their alarm may be even be context dependent. The researchers discovered that larvae of the Western Flower Thrips produce an alarm pheromone whose composition of 2 chemicals, decyl acetate and dodecyl acetate, varies with the level of danger they face. When pheromone is excreted with a predator present but not attacking, the percentage of dodecyl acetate increases, whereas when a predator does attack, the percentage of dodecyl acetate is low. “This type of communication was so far only known from vocal alarm calling in mammals, Read More ›

For those who are unfamiliar with The Royal Society, it’s an academic organization whose membership includes many of the world’s most eminent scientists, and is “the oldest scientific academy in continuous existence”. In loose terms, they are a British forbearer to many of the various Academies of Science sprinkled throughout the nations of the world. From their mission statement: The Society’s fundamental purpose, reflected in its founding Charters of the 1660s, is to recognize, promote, and support excellence in science and to encourage the development and use of science for the benefit of humanity. This article isn’t necessarily about the Royal Society, except for the fact that it serves as the genesis of the story, and also a proper backdrop Read More ›

We asked physicist Rob Sheldon: “Front-loading” is something I picture as an elaborate “Rube Goldberg” machine. Here’s a sampling of real-life front-loading by brilliant engineers with too much time on their hands. Okay, if engineers could do that, couldn’t God make the flagellum out of spare parts by a properly front-loaded machine? I think the answer here is “yes”. But of course that begs the question, “doesn’t the machine show much more design than the thing it makes?” Of course. But our goal wasn’t to minimize design effort, our goal was to create a “front-loaded” machine, which is what was asked. Now we have another problem. Isn’t the “front-loading machine” a lot more fragile than the thing it made, the Read More ›

Richard Mabey, author of The Cabaret of Plants: Forty Thousand Years of Plant Life and the Human Imagination, was interviewed recently by National Geographic: There Is Such a Thing as Plant Intelligence … We tend to judge plants not as autonomous organisms but in terms of what they can do for us. But they’re astonishing in their own right and deserve to be given the same ethical status as animals. … It’s long been known that the trees in a forest are connected by mycorrhizal fungi. This means fungi that live symbiotically with the roots of forest trees. The forest trees can’t grow without them because they haven’t got enough access to the minerals in the soil, and the fungi Read More ›

Prof. Robert Marks, Editor-in-Chief of Bio-Complexity, offers the following vids, featuring computer scientist Winston Ewert’s work: (Part I, Part II, and Part III:   Part I: Paper. Dr. Winston Ewert, a Senior Research Scientist at both Biologic Institute and the Evolutionary Informatics lab, discusses the mathematical foundation for why we know Mount Rushmore is designed and Mount Fuji isn’t. The mathematical theory of algorithmic specified complexity is introduced and illustrated. A single complex snowflake, for example, displays essentially zero algorithmic specified complexity whereas two identical snowflakes earns a high algorithmic specified complexity. The model discussed by Dr. Ewert can also measure algorithmic specified complexity in units of bits in the context of poker. Dr. Ewert explains how a Royal Flush Read More ›

According to computer scientist Leslie Valiant. From John Pavlus at Quanta: Valiant’s self-stated goal is to find “mathematical definitions of learning and evolution which can address all ways in which information can get into systems.” If successful, the resulting “theory of everything” — a phrase Valiant himself uses, only half-jokingly — would literally fuse life science and computer science together. Furthermore, our intuitive definitions of “learning” and “intelligence” would expand to include not only non-organisms, but non-individuals as well. The “wisdom of crowds” would no longer be a mere figure of speech. … How can a theory of learning be applied to a phenomenon like biological evolution? Biology is based on protein expression networks, and as evolution proceeds these networks Read More ›

From ScienceDaily: Comparing notes boosts cells sensing accuracy To decide whether and where to move in the body, cells must read chemical signals in their environment. Individual cells do not act alone during this process, two new studies on mouse mammary tissue show. Instead, the cells make decisions collectively after exchanging information about the chemical messages they are receiving. Every cell in a body has the same genome but they can do different things and go in different directions because they measure different chemical signals in their environment. Those chemical signals are made up of molecules that randomly move around. “Cells can sense not just the precise concentration of a chemical signal, but concentration differences,” Nemenman says. “That’s very important Read More ›