Spontaneous Reaction Silencing in Metabolic Optimization

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Proteins With 'Cruise Control' Act Like Adaptive Machines

"The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a 'blind watchmaker'?" said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. "Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness."

The paper presents the first quantitative experimental evidence that evolutionary control strategies in the organisms themselves work to maximize their fitness to the environment they inhabit. Chakrabarti calls this an application of "Control Theory," which is basically an appeal to engineering and… design. He of course denies that the findings support the notion of ID, but ID encompasses the notion that design can be entirely 'natural' if one allows for the actual participation of organisms in their own design and evolution. Something biologists have been notoriously reluctant to do for the last 150 years. Looks like now they're going to have to go ahead and admit what the evidence demonstrates to be true.

It's about time.

How old is the oldest evidence for complex life forms? The Science News article Oldest evidence for complex life in doubt discusses that matter. I would hasten to point out that one of the hallmarks of even unicellular organism is intrinsic complexity. It's not as if simple life forms are available to serve as contrasts. Nevertheless there have been attempts to ascertain when it was that ancient organisms related to cyanobacteria first appeared on earth.

In 1999 researchers published a finding indicating that the origin of cyanobacteria was at least 550 million years closer to the time origin of the earth itself. It is believed that single celled organisms were the first life forms followed by cyanobacteria which had photosynthesis capabilities. That in turn is important in assessing when it was that the earth acquired a significant amount of atmospheric oxygen. The article states:

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Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks is authored by Neema Jamshidi and Bernhard Ø. Palsson and appears in PLOS Computational Biology. The paper discusses the development of top-down investigative approaches; the objective being the development of "a “systems” understanding of how networks operate dynamically." The abstract:

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SD published an article entitled Structure of Key Epigenetics Component Identified that hails the reporting of the 3D structure of a key protein, UHRF 1, in ensuring the "epigenetic code" (attached chemicals for methylation) is accurately copied when the DNA is replicated.

A question for those here who claim to understand all these details (and have access to Nature, please. How do chemical attachments to DNA get copied in this process? Does the protein somehow get reverse-engineered into standard DNA code, or does the replicated string come with non-nucleotide chemical 'markers'? Does the DNA now encode this particular protein in this particular spot (standard DNA code)?

Some clarification of what, exactly, is being copied, "proof-read" and reconstructed in the daughter cell would be appreciated. Thanks to anyone who can translate this for me.

Thought Provoker mentioned EAM while talking about FLE in another thread.

Alan Fox requested answers from an EAM point of view to determine if it is just another variation of FLE. As the only resident EAMer, I described it here and expanded here.

That thread has more than 100 comments, meaning I won't be able to keep following if that discussion wants to go anywhere. So this thread will serve that purpose if anyone's got anything they want to discuss about Endogenous Adaptive Mutation.

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Yep. That's the headline. Whole thing reads…

Biology Enters 'The Matrix' Through New Computer Language

Bradford posted about a Protein Folding Game, where scientists are hoping humans turn out to be more efficient than computer modeling programs have been at functional folding. This article is about a new computer language that can mimic the 'mind' of a cell.

Yep. You read that right. Enter "Little b," working off an AI programming language called LISP…

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It's not Yasgur's Farm, but what happens at the Konrad Lorenz Institute in Altenberg, Austria this July promises to be far more transforming for the world than Woodstock. What it amounts to is a gathering of 16 biologists and philosophers of rock star stature – let's call them "the Altenberg 16" – who recognize that the theory of evolution which most practicing biologists accept and which is taught in classrooms today, is inadequate in explaining our existence. It's pre the discovery of DNA, lacks a theory for body form and does not accomodate "other" new phenomena. So the theory Charles Darwin gave us, which was dusted off and repackaged 70 years ago, seems about to be reborn as the "Extended Evolutionary Synthesis".

here

Despite the stunning variety of photoreceptor organs, every animal uses the same kind of light-capturing molecule to do this job. Insects, humans, clams, and scallops all use opsins. Not only can we trace the history of eyes through differences in the structure of their opsins, but we have good evidence that we can thank bacteria for these molecules in the first place.

The bacterial past can be used to our advantage in studying the diseases of mitochondria — in fact, some of the best experimental models for these diseases are bacteria. This is powerful because we can do all kinds of experiments with bacteria that are not possible with human cells… [European researchers] were able to simulate parts of a human mitochondrial disease in a bacterium, with virtually the same change in metabolism. This is putting a many-billion-year part of our history to work for us.

Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body