Informatics

From Mario Aguilera at U San Diego News: Intricate human physiological features such as the immune system require exquisite formation and timing to develop properly. Genetic elements must be activated at just the right moment, across vast distances of genomic space. “Promoter” areas, locations where genes begin to be expressed, must be paired precisely with “enhancer” clusters, where cells mature to a targeted function. Faraway promoters must be brought in proximity with their enhancer counterparts, but how do they come together? When these elements are not in sync, diseases such as leukemia and lymphoma can result. How does this work? Biologists at the University of California San Diego believe they have the answer. Calling it the “big bang” of immune Read More ›

Jeremy England’s origin of life claims have been in the news lately. A friend points us to a paper by Sara Walker: Origins of Life: A Problem for Physics Abstract: The origins of life stands among the great open scientific questions of our time. While a number of proposals exist for possible starting points in the pathway from non-living to living matter, these have so far not achieved states of complexity that are anywhere near that of even the simplest living systems. A key challenge is identifying the properties of living matter that might distinguish living and non-living physical systems such that we might build new life in the lab. This review is geared towards covering major viewpoints on the Read More ›

From Robert Marks II, author (with Dembski and Ewert) of Evolutionary Informatics at Evolution News & Views: On a new episode of ID the Future, CSC Director of Communications Rob Crowther talks with Robert Marks, Distinguished Professor of Electrical and Computer Engineering at Baylor University, about Marks’s new book, Introduction to Evolutionary Informatics, which makes an important but esoteric-sounding field accessible to the general reader. Dr. Marks talks about how he and William Dembski originally connected as researchers, and began working on the subject in 2007, how intelligent design can inform thinking on artificial intelligence, and what a “search for a search” means in evolutionary terms. More. Search for a search?: Needle-in-the-haystack problems look for small targets in large spaces. Read More ›

Don Johnson is the author of Programming of Life and Programming of Life 2: the Earth These vids introduce the ideas.   See also: Don Johnson’s lecture on “Bioinformatics: The Information in Life”

Robert Marks sends these endorsements for Evolutionary Informatics: (Note: It is surprisingly easy to read.) ··············· “An honest attempt to discuss what few people seem to realize is an important problem. Thought provoking!” Gregory Chaitin, Ph.D. Professor, Federal University of Rio de Janeiro Eponyms: Kolmogorov-Chaitin-Solomonov Information Theory Chaitin’s Number Chaitin’s algorithm Author of:The Unknowable Meta Math!: The Quest for Omega The Limits of Mathematics Thinking about Gödel and Turing: Essays on Complexity Algorithmic Information Theory. ··············· “Darwinian pretensions notwithstanding, Marks, Dembski, and Ewert demonstrate rigorously and humorously that no unintelligent process can account for the wonders of life.” Michael J. Behe, Ph.D. Professor of Biological Sciences , Lehigh University Author of: Darwin’s Black Box The Edge of Evolution ··············· “This Read More ›

  The book Introduction to Evolutionary Informatics continues to make waves. The Lab writes to say: A lot continues to happen surrounding the release of “Introduction to Evolutionary Informatics” by Robert J. Marks, William A. Dembski and Winston Ewert: Here’s a quick summary of media. – AI means the topic is Artificial Intelligence hype – EV deals with Darwinian Evolution (AI) Janet Mefford Today – A.I. Hype & Limitations with guest Robert J. Marks (American Family Radio) (AI) “Point of View” with Kerby Anderson. Robert J. Marks talks about AI hype (AI) “The Remnant Road” Raging Against the Machines with guest Robert J. Marks (AI) “Are Super Computers on the Verge of Becoming Our Overlords?’ Terry Lowry interviews Robert J. Read More ›

A friend writes to raise the question of Basener’s ceiling: From Robert Marks II at ENV: We show that no meaningful information can arise from an evolutionary process unless that process is guided. Even when guided, the degree of evolution’s accomplishment is limited by the expertise of the guiding information source — a limit we call Basener’s ceiling. An evolutionary program whose goal is to master chess will never evolve further and offer investment advice. More. William Basener is an artificial intelligence expert. Our friend writes “Complexity in evolutionary algorithms always stops at a certain point and never gets any better, which is predicted by Basener’s ceiling. He also notes that biological evolution seems to have no problem continuously generating Read More ›

Looking for an odd piece of information in the middle of the night (unrelated to controversies around design in nature), I stumbled across a claim from The Skeptical Zone back in June 2015: Uncommon Descent is starving I was naturally curious, as I don’t recall anyone starving at the time. Or anything in particular, really. Post author Tom English seemed to think it odd that one of our authors, Eric Anderson, and Casey Luskin, then a podcaster with the Discovery Institute, had said nice things about UD. Building on that remarkable discovery, English announces, Anderson lives up to Jeff Shallit’s characterization of him, revealing that he is laughably far behind the curve. He’s not worth my time. And there’s something Read More ›

Don’t watch this if you are completely committed to your local End of Science rent-a-riot: See also: Book: Computer simulations yield very minor results for Darwinian evolution Evolutionary Informatics is, despite the math stuff, quite readable. It’s a good look at one part of the real future of discussions around evolution: What can and can’t happen is a stark contrast with the Darwin of the textbooks, where anything can happen, given enough time. Follow UD News at Twitter!

From Brian Miller at Evolution News & Views: In the evolution debate, a key issue is the ability of natural selection to produce complex innovations. In a previous article, I explained based on engineering theories of innovation why the small-scale changes that drive microevolution should not be able to accumulate to generate the large-scale changes required for macroevolution. This observation perfectly corresponds to research in developmental biology and to the pattern of the fossil record. However, the limitations of Darwinian evolution have been demonstrated even more rigorously from the fields of evolutionary computation and mathematics. These theoretical challenges are detailed in a new book out this week, Introduction to Evolutionary Informatics. Authors Robert Marks, William Dembski, and Winston Ewert bring Read More ›

From Kirk Durston at Contemplations: The first mistake is the failure to distinguish between classical forms of information vs. functional information, and is described in a short 2003 Nature article by Jack Szostak.(2) In the words of Szostak, classical information theory “does not consider the meaning of a message.” Furthermore, classical approaches, such as Kolmogorov complexity,(3) “fail to account for the redundancy inherent in the fact that many related sequences are structurally and functionally equivalent.” It matters a great deal to biological life whether an amino acid sequence is functional or not. Life also depends upon the fact that numerous sequences can code for the same function, in order to increase functional survivability in the face of the inevitable steady Read More ›

The first video release from the AM-Nat Biology conference is now available! In this video, Salvador Cordova talks about the possibility that many things that are commonly considered errors in biology actually have identifiable purposes. Cordova confronts what is both a theological and a scientific critique of design, and shows its limitations. As Sal points out at the beginning of this video, this talk was a special request of mine. Sal has posted on these topics here on UD, but I thought they got less attention than they should, as I think they are really important concepts. If you are interested in the Alternatives to Methodological Naturalism series, you should pick up our book, Naturalism and Its Alternatives in Scientific Read More ›

In an interview with Suzan Mazur at Huffington Post. Mazur explains, Plug certain information into SUPERFAMILY and it can analyze a vast assortment of genomes and assist you in building a Tree of Life using superfamilies — i.e., domains with an evolutionary relationship — and the conserved part of thousands and thousands of protein structures called protein domains. … Suzan Mazur: Do protein Superfamilies represent the current limits of our ability to identify common ancestry? Julian Gough: Yes. That is exactly what their definition is. So if you want to group two protein structural domains into the same Superfamily, the question that you ask is whether there is structural sequence and functional evidence for common evolutionary ancestry. So they’re classified 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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From Progress in Biophysics and Molecular Biology: Abstract: (paywall)The background of this study is that models of the evolution of living systems are based mainly on the evolution of replicators and cannot explain many of the properties of biological systems such as the existence of the sexes, molecular exaptation and others. The purpose of this study is to build a complete model of the evolution of organisms based on a combination of quantum-like models and models based on partial directivity of evolution. We also used optimal control theory for evolution modeling. We found that partial directivity of evolution is necessary for the explanation of the properties of an evolving system such as the stability of evolutionary strategies, aging and death, Read More ›