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Self-Org. Theory

SwiftKey co-founder: Computers can’t just “evolve” intelligence; cites James Shapiro’s self-organization

In a still-interesting 2017 paper, Ben Medlock talks about the way life forms self-organize: (which computers don’t, really). Read More ›

Dr Selensky on a Tour vs Cronin debate on OoL

He writes: >> Participants: From the naturalists’ camp: chemist Lee Cronin (University of Glasgow, UK). From the skeptics’ camp: chemist James Tour (Rice University, USA). Okay, origin of life research. Like in any other research, there should be no magic: garbage in — garbage out. Between 25:00 and 26:00 Lee said something like this: We found in a laboratory how chemicals can be steered towards decision making. (emphasis mine). This is already telling. I am fine with experiments in a test tube. But as soon as naturalists need to explain something non-trivial like the alleged naturalistic emergence of decision making or information translation, they use imagination. Closer to the end of the debate, Cronin gives way to it: in 5 Read More ›

What? Mutations not random? An “enigmatic in-built self-preserving organization”?

Researchers: Our calculations reveal an enigmatic in-built self-preserving organization of the genetic code that averts disruptive changes at the physicochemical properties level. Read More ›

Scutoids: a New Geometric Shape found in Epithelial Cells

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 ›

Guest Post — Template-Assisted Ligation: A New OOL Model

Dr E. Selensky occasionally requests that UD posts an article on his behalf. What follows is his latest: ______________ Arguably, the RNA world model is excessively complex: it operates too complex structures and involves too complex interactions. The origin of life, some researchers believe, must have been simpler.In an attempt to close the gap between chemistry and life by naturalistic means a new model has been proposed recently, yet another one of many, that seeks to explain the rise of RNAs. This model is called template-assisted ligation. It has been proposed by Alexey Tkachenko and Sergei Maslov at American Institute of Physics. They hope it can help shed light on what could have preceded the RNA world.The crux of the Read More ›

Origin of life researchers: RNA World can’t produce genetic code

From ScienceDaily: Life on Earth originated in an intimate partnership between the nucleic acids (genetic instructions for all organisms) and small proteins called peptides, according to two new articles from biochemists and biologists. Their ‘peptide-RNA’ hypothesis contradicts the widely-held ‘RNA-world’ hypothesis, which states that life originated from nucleic acids and only later evolved to include proteins. … Co-author Peter Wills, PhD, professor of physics at the University of Auckland, said, “Compared to the RNA-world hypothesis, what we’ve outlined is simply a much more probable scenario for the origin of life. We hope our data and the theory we’ve outlined in these papers will stimulate discussion and further research on questions relevant to the origins of life.” The two scientists are Read More ›

Self-organization: New James Shapiro paper on the Read-Write genome

From U Chicago’s James Shapiro at Pub Med: Biological action in Read-Write genome evolution. Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular Read More ›

Self-organization paper of interest: Biological regulation: controlling the system from within

Friends note, from Biology & Philosophy (Springer): Biological regulation is what allows an organism to handle the effects of a perturbation, modulating its own constitutive dynamics in response to particular changes in internal and external conditions. With the central focus of analysis on the case of minimal living systems, we argue that regulation consists in a specific form of second-order control, exerted over the core (constitutive) regime of production and maintenance of the components that actually put together the organism. The main argument is that regulation requires a distinctive architecture of functional relationships, and specifically the action of a dedicated subsystem whose activity is dynamically decoupled from that of the constitutive regime. We distinguish between two major ways in which Read More ›

Knockout gene study shows “beautiful hierarchical structure” underlying cell’s biology

From Veronique Greenwood at Quanta: In a monumental set of experiments, spread out over nearly two decades, biologists removed genes two at a time to uncover the secret workings of the cell. And what did they find?: In all, they found 550,000 pairs that, when removed, result in sickness or death. This network of genetic connections reveals a previously hidden scaffolding that underlies the operation of the cell. “The complete picture,” Boone said, “clearly shows a beautiful hierarchical structure.” Over here are the genes involved in taking out the cell’s garbage, and over there are the genes responsible for its metabolism. Zoom out from one cluster of genes, and you’ll find the ones involved in the larger process the cluster Read More ›

Stochastic or Intelligent Teleology?

Former Templeton Fellow John Fellow asserts: Why Teleology Isn’t Dead

Conway Morris argues that in the grand scheme, evolution will not be reduced to chance: constraints built into life at the most fundamental level guarantee that life is going to follow the same evolutionary pathways to achieve limbs, respiration, vision, balance, an immune system, indeed all the remarkable features we associate with living things across the great spectrum of life.

Morris begs the question by assuming a stochastic origin of these “constraints built into life”. Read More ›

Basketball games a form of evolution?

From Eurekalert: Behind the apparent randomness of a basketball game, a process of self-organisation is actually taking place amid the teams. The interactions between team mates and opponents are constantly influencing each other while the game itself allows for creative behaviours to emerge. This phenomenon, detected by Spanish researchers after analysing over 6,000 NBA games, resembles the way in which living things must continually evolve in order to survive in nature. More. Hmmm. If the basketball players are evolving as a result of their strategies, they are keeping it a secret. In a predator-prey system, for instance, or in a natural changing environment with limited resources, species evolve in their arms race by adapting. They continuously fight and give it Read More ›

Complex eye coordinates own development

Entirely at random, or so the theory runs… From ScienceDaily: While study has long been conducted on vertebrates with sight-sensory systems involving a lens, retina and nervous system, new research reported by the University of Cincinnati and supported by the National Science Foundation is the first to examine how the complex eye system of an invertebrate – the Sunburst Diving Beetle – coordinates the development of its components. Despite the complexity of their eyes, including a bifocal lens, extremely rapid eye growth of the Sunburst Diving Beetle occurs during the transitions between larval stages. In addition, they temporarily go blind as the eye is quickly redeveloped. The findings by Shannon Werner, a recent University of Cincinnati master’s degree graduate in Read More ›

Emergence as an Explanation for Living Systems

Yesterday I watched a re-run of a Star Trek: The Next Generation episode. There. I said it. I love Star Trek. Notwithstanding the many absurd evolution-based plotlines. In this specific episode, Data referred to a particular characteristic of a newly-developing lifeform as an “emergent property.” I’ve looked into the “emergence” ideas in the past, and the related self-organization hypotheses, and have never been too impressed. But it has been a while, so I thought I’d quickly navigate over to the Wikipedia page on the subject to see what it says. Now I’m a big fan of the general concept behind Wikipedia and it is a very useful tool, if used properly. Yet everyone knows that Wikipedia is a questionable source Read More ›