Dynamics of genome evolution in E. coli

Hi All,

The Lenski lab has just published a new paper in Nature that looks at the dynamics of genome evolution in E. coli populations over the course of the LTEE.  Here is the abstract:

Tempo and mode of genome evolution in a 50,000-generation experiment

Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. Here we analysed 264 complete genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The populations that retained the ancestral mutation rate support a model in which most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to mutation-accumulation lines evolved under a bottlenecking regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions and deletions are overrepresented in the long-term populations, further supporting the inference that most mutations that reached high frequency were favoured by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.

I’m assuming the whole thing is pay-walled, but a pre-print copy (which may or may not be identical to the final version) is freely available here.

I’ve only read the abstract thus far, but the paper seems likely to touch on a variety of topics that folks here like to discuss. Have at it!

What is the Plan?

A prominent ID supporter at UD, gpuccio, has this to say:

My simple point is: reasoning in terms of design, intention and plans is a true science promoter which can help give new perspective to our approach to biology. Questions simply change. The question is no more:

how did this sequence evolve by some non existent neo darwinian mechanism giving reproductive advantage?

but rather:

why was this functional information introduced at this stage? what is the plan? what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?


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On the thread entitled “Species Kinds”, commenter phoodoo asks:

What’s the definition of a species?

A simple question but hard to answer. Talking of populations of interbreeding individuals immediately creates problems when looking at asexual organisms, especially the prokaryotes: bacteria and archaea. How to delineate a species temporally is also problematic. Allan Miller links to an excellent basic resource on defining a species and the Wikipedia entry does not shy away from the difficulties.

In case phoodoo thought his question was being ignored, I thought I’d open this thread to allow discussion without derailing the thread on “kinds”.

Thorp, Shannon: Inspiration for Alternative Perspectives on the ID vs. Naturalism Debate

The writings and life work of Ed Thorp, professor at MIT, influenced many of my notions of ID (though Thorp and Shannon are not ID proponents). I happened upon a forgotten mathematical paper by Ed Thorp in 1961 in the Proceedings of the National Academy of Sciences that launched his stellar career into Wall Street. If the TSZ regulars are tired of talking and arguing ID, then I offer a link to Thorp’s landmark paper. That 1961 PNAS article consists of a mere three pages. It is terse, and almost shocking in its economy of words and straightforward English. The paper can be downloaded from:

A Favorable Strategy for Twenty One, Proceedings National Academy of Sciences.

Thorp was a colleague of Claude Shannon (founder of information theory, and inventor of the notion of “bit”) at MIT. Thorp managed to publish his theory about blackjack through the sponsorship of Shannon. He was able to scientifically prove his theories in the casinos and Wall Street and went on to make hundreds of millions of dollars through his scientific approach to estimating and profiting from expected value. Thorp was the central figure in the real life stories featured in the book
Fortune’s Formula: The Untold Story of the Scientific Betting System that Beat the Casino’s and Wall Street by William Poundstone.
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Boltzmann Brains and evolution

In the “Elon Musk” discussion, in the midst of a whole lotta epistemology goin’ on, commenter BruceS referred to the concept of a “Boltzmann Brain” and suggested that Boltzmann didn’t know about evolution. (In fact Boltzmann did know about evolution and thought Darwin’s work was hugely important). The Boltzmann Brain is a thought experiment about a conscious brain arising in a thermodynamic system which is at equilibrium. Such a thing is interesting but vastly improbable.

BruceS explained that he was thinking of a reddit post where the commenter invoked evolution to explain why we don’t need extremely improbable events to explain the existence of our brains (the comment will be found here).

What needs to be added is that all that does not happen in an isolated system at thermodynamic equilibrium, or at least it has a fantastically low probability of happening there.  The earth-sun system is not at thermodynamic equilibrium.  Energy is flowing outwards from the sun, at high temperature, some is hitting the earth, and some is taken up by plants and then some by animals, at lower temperatures. Continue reading

Evolution of Consciousness

Seems like this new thing in the Atlantic’d be up y’all’s alley:


A New Theory Explains How Consciousness Evolved

Michael Graziano

Ever since Charles Darwin published On the Origin of Species in 1859, evolution has been the grand unifying theory of biology. Yet one of our most important biological traits, consciousness, is rarely studied in the context of evolution. Theories of consciousness come from religion, from philosophy, from cognitive science, but not so much from evolutionary biology. Maybe that’s why so few theories have been able to tackle basic questions such as: What is the adaptive value of consciousness? When did it evolve and what animals have it?

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Non-DNA Structural Inheritance

If the DNA codes primarily for proteins and helps regulate protein quantities, then where is the developmental or structural information? I’ve never gotten a straight answer from most evolutionists I’ve encountered, for that matter anyone on planet Earth. Maybe no one really knows. I think Creationist biologist Arthur Jones is right about Non-DNA inheritance.
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Wistar Day

Koprowski and I, the only biologists present, were confronted by a rather weird discussion between four mathematicians – Eden, Schutzenberger, Weisskopf, and Ulam – on mathematical doubts concerning the Darwinian theory of evolution. At the end of several hours of heated debate, the biological contingent proposed that a symposium be arranged to consider the points of dispute more systematically, and with a more powerful array of biologists who could function adequately in the universe of discourse inhabited by mathematicians.

– Martin Kaplan

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Design by Evolution

Evolution is Nature’s design process. The natural world is full of wonderful examples of its successes, from engineering design feats such as powered flight, to the design of complex optical systems such as the mammalian eye, to the merely stunningly beautiful designs of orchids or birds of paradise. With increasing computational power, we are now able to simulate this process with greater fidelity, combining complex simulations with high-performance evolutionary algorithms to tackle problems that used to be impractical.

Design by Evolution: Advances in Evolutionary Design

I was like great! A book that will finally tell me how Evolution designs such magnificent designs. But there’s that “problem” word again. Is Evolution faced with design problems that it then solves? And I wonder if, over time, Evolution has learned how to make better designs, advances in evolutionary design. Some folks certainly seem to think so.

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