Category Archives: Evolution

Some Questions on Genetic Algorithms

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vjtorley:

I was very struck by Glenn Williamson’s [vjt meant GlenDavidson] remark that creativity is not the same thing as complexity. Very deep. Glenn seems to think that people are good at the former, but the blind processes can outdo them in the latter. That’s an interesting view, but I’d want to see evidence that blind processes are actually capable of producing systems with a high degree of functional complexity, of the kind Axe described in his book. Even a computer simulation would be something.

What with all the experts in writing GA’s here at TSZ I was hoping VJT would have elicited more of a response.

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Vincent Torley’s Disappearing Book Review

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I guess many folks here are familiar with Dr (of philosophy) Vincent Torley as a contributor of many posts at Uncommon Descent now operated by one Barry Arrington.

Vincent strikes me as a genuinely nice guy whose views are very different from mine on many issues. Possibly one of his most remarked-upon idiosyncracies is his tendency to publish exceedingly long posts at Uncommon Descent but (leaving Joseph of Cupertino in the air for a moment) lately Vincent has become a little more reflective on the merits of “Intelligent Design” as some sort of alternative or rival to mainstream biology. Continue reading →

Evolution’s Search Problem

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Tom English: (If Mung does not know that authors at Evolution News and Views often disagree with one another, but never point out their disagreements, then I’ve given him way too much credit. For instance, Dembski told us that “evolutionary search” really does search for targets. But Meyer and Axe have both gone out of their ways to explain that “evolutionary search” actually does not search.)

Did Tom ever reveal his sources?

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Mung, a theistic evolutionist who disagrees with some of his kind

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Mung: What I Believe

I am neither YEC nor OEC, so don’t really know of a label I can give you.

I accept that the universe is old, that the earth is old. No problem with dating as provided by the latest science.

I am a theist and a Christian. I am not a deist. I am not a naturalist. I reject the idea of “nature acting alone.”

I believe the universe is created and sustained by God I believe the same of all living beings. I accept common descent or descent with modification as the best explanation for the history of life on earth, but reject the idea that this happens without God (by a random undirected process).

I’ve not identified myself as a theistic evolutionist because I find myself in disagreement with theistic evolutionist authors.

So the best description I can offer is “intelligent design” proponent.
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Did Patrick Matthew prove natural selection is just a line of reasoning in its conclusions.

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I recently found Patrick Matthew , some 20 years before, had some important conclusions about how natural selection can lead to new species. Darwin agreed he had come to like conclusions, on main points, as he did. This is not known well and indeed they emphasis wAllace as a co discoverer of evolution but say nothing about Matthew.

This brings up a good YEC creationist point.

Matthew did do just what darwin did. he observed the seeming hand of selection controling survival/reproduction of individuals and so new environments bring new controls and so new species.

this is fine for creationism. its minor changes in types/kinds of biology. Yet matthew, a little, and darwin, a great deal,  then went on to extrapolate from this the entire creation of biology. Its entire complexity and diversity as from selection on traits. Yet Matthew did no more investigation then his idea of selection. So it follows the both men ‘s conclusions on evolutions story in biology are just lines of reasoning from simple raw data points.

Both desperately embrace the fossil record, geology concepts for deposition, to make thier lines of reasoning.

I say Matthew’s existence in these matters proves Darwins idea was mostly lines of reasoning from a minor trivial observation of selections ability to determine success in creatures survival.

So evolutionism really is based on a real selection truth and then is wild extrapolation.

Micro does not equal Macro after all. Macro needs to cross boundaries beyond selection on traits. It needs these mutations desperately  and thats the great error in the lines of reasoning.

 

Dynamics of genome evolution in E. coli

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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?

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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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“Species”

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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

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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

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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

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

http://www.theatlantic.com/science/archive/2016/06/how-consciousness-evolved/485558/

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

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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

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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

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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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Biology as viewed through 19th Century Lenses

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Most modern readers have difficulty appreciating the resilience of spiritual or metaphysical overtones to 19th Century scientific thought, alternatively referred to as “vitalism” & “teleology”. At this point, a quick historical digression is in order.

What exactly is life?”! Traditional education systems were well-grounded in the classics, and many 19th Century naturalists could relate to an ancient Greek philosopher named Aristotle who was convinced no real boundary existed between “living” and “non-living”. According to Aristotle, non-living matter could give rise to living things because our universe possesses some vital life force or soul, “anima”, which could “animate” non-living matter. In Aristotle’s view: the universe, as a whole, had its own soul. In modern terms the universe could be considered as some giant fractal and we are all but elements therein. Even today, various mystical traditions hold similar ideas.

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What did Lamarck and Darwin really say?

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Historically and conceptually, modern Genetics and modern Evolutionary Theory are closely intertwined. Mendel and Darwin both published their masterpieces in the mid-1800s and both were promptly misunderstood and discounted for half a century. Both theories required several more “kicks at the can” before final acceptance. Put simply: the Theory of Evolution itself evolved in response to an emerging understanding of Genetics.

Some quick questions:

Question: Name the scientist that first suggested “the effects of use and disuse” were passed from one generation to the next?

Answer: Charles Darwin and NOT Jean-Baptiste Lamarck who actually had a somewhat different theory.

Question: Name the scientist who first to employed the term evolve/evolution while also suggesting human beings had “evolved” from apes?

Answer: That would be Jean-Baptiste Lamarck. (Lamarck in fact invented the word “evolution”, a word which never appeared in Darwin’s Book “Origin of the Species”). Continue reading →

Impractical Naturalism of Dan Graur vs. the NIH

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I’ll be making a presentation at AM-NAT 2016, and Dan Graur will be the poster boy of impractical naturalism. Below are some things I collected from his websites, some of which I view as highly anti-science. The aim of my presentation isn’t to settle the question of God or no God or ultimate questions of whether godless naturalism is the best description of reality. The goal is to suggest there are some unspoken naturalistic creeds that often take priority over experiments and observations. In a manner of speaking, there are some interpretations of naturalism that actually go against dispassionate examination of how the natural world actually operates.
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Miracles of Evolution

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From time to time, when I am not actively engaged in “dishonest quote-mining” of materialists and evolutionists, I take time to actually read their writings. Today I was reading John Maynard Smith.

I now want to take a great leap forward in time, and suppose that not only has a modern protein-synthesizing machinery evolved, but that specific enzymes exist catalysing specific reactions, and that the organism has a cell membrane which prevents the products of catalysis from diffusing away.

– p. 115

This isn’t a great leap forward in time, it’s just a great leap. Poof! A cell membrane! I love how that just magically appeared. Let’s assume a fully functional cell membrane.

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Tetrapod Evolution and the Evolution of Consciousness

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It is here proposed that the evolution of life was destined to produce self consciousness out of physical matter just as surely as self-consciousness is destined to be produced by the build up of matter from the human zygote.

Our external vantage point allows us to see the process whereby an individual human matures from the point of conception  We are in a position to witness all the stages in the life of individual humans. Activities such as birth, death, growth and decay go on all around us. Conversely on the grand scale of things, taking life as a whole, we are in the middle of evolving life and so we don’t have an overall, clear picture of the process.

In this video Sean B. Carroll states that:
…living things are occupying a planet whose surface is always changing. Hurricanes, earthquakes, volcanoes, tectonic movement, ice ages, climate changes whether local or global, all of these keep changing the environments that species are in, they are running to keep up and most of the time they fail. So we have to think about earth’s history to understand life’s history. We have to understand what’s going on at any particular place to appreciate what’s going on with any particular species.

The same could be said for the cells in your body. Their environment is always changing and most of them do not survive as you change from embryo to adult. From an individual cell’s point of view there may not seem to be any direction.Some live some die, some change slowly, others change dramatically. But from the higher perspective of the whole body there certainly is direction.

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