Mouse Utopia, Mutational Meltdown, Extinction by Natural Selection

The National Institute of Mental Health (NIMH) of the National Institutes of Health (NIH) sponsored the work of John Calhoun on social behaviors. Here were the results of one of his experiments:

On July 9th, 1968, eight white mice were placed into a strange box at the National Institute of Health in Bethesda, Maryland. Maybe “box” isn’t the right word for it; the space was more like a room, known as Universe 25, about the size of a small storage unit. The mice themselves were bright and healthy, hand-picked from the institute’s breeding stock. They were given the run of the place, which had everything they might need: food, water, climate control, hundreds of nesting boxes to choose from, and a lush floor of shredded paper and ground corn cob.

This is a far cry from a wild mouse’s life—no cats, no traps, no long winters. It’s even better than your average lab mouse’s, which is constantly interrupted by white-coated humans with scalpels or syringes. The residents of Universe 25 were mostly left alone, save for one man who would peer at them from above, and his team of similarly interested assistants. They must have thought they were the luckiest mice in the world. They couldn’t have known the truth: that within a few years, they and their descendants would all be dead.
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Take the Evolutionary Turing Test!

The challenge, for all and sundry but especially for “Darwin doubters”, should you wish to take it, is to submit a one-paragraph summary of the theory of evolution. The idea is to see if you understand it well enough to fairly summarize the theory so that you pass as a proponent of evolution. We also need some examples from proponents to test the null hypothesis!

To ensure anonymity, please submit your paragraph by private message to me or another admin and we will add it in edit. (Or email it to me at alanfox@free.fr if you prefer.) Continue reading

Evolution’s Puzzle & Trans-Evolutionary Change

In lead-up to the recent Royal Society’s “New Trends in Evolutionary Biology: Biological, Philosophical and Social Sciences Perspectives” meeting in London, which courted the terms ‘extension,’ ‘replacement’ and ‘amendment’ in regard to the (neo-)Darwinian evolutionary ‘Modern Synthesis’ in biology, as presented by active and leading members of the (mainly Anglo-American) biological scientific community as well as philosophers (and a couple of largely physical rather than cultural anthropologists), including several members of The Third Way of Evolution, this was one of a few trans-evolutionary change preparations aimed at liberating the social sciences and humanities from positivist, reductionist, evolutionist, atomist & naturalist (PREAN) ideologies (none of which, of course, refers to a single soul at TSZ because almost everyone here is – by definition of being a ‘skeptic’ – skeptical about even their own admittedly personal ideologies that are often so easily identifiable by their words made in public?), which display hegemonic tendencies by capital-capture political positioning scholars & dehumanising ‘public understanding’ gurus coming from oftentimes highly specialised natural-physical sciences fields that have become an unfortunate burden in collaborative science, philosophy and theology/worldview discourse, to everyone.

Cheers to moving beyond (neo-)Darwinian evolutionism with trans-evolutionary li-ber-a-tion!

Solving Wallace’s Problem and Resolving Darwin’s Doubt

I want to consider, in light of fairly new philosophical and scientific research, two long-standing conceptual objections to evolutionary theory: Wallace’s Problem and Darwin’s Doubt.

It is well-recognized that Wallace saw the need for some supernatural intelligence in explaining human evolution, in contrast to Darwin’s naturalistic speculations in Descent of Man. What is less recognized is that Wallace was, in an important sense, right. He squarely faced the problem, “can natural selection alone account for the unique cognitive abilities of human beings, such as abstract thought, self-consciousness, radical reshaping of the environment (e.g. clothing, building), collective self-governance by ethical norms, and the symbolic activities of art, religion, philosophy, mathematics, logic, and science?”  Whereas Darwin thought there was continuity between humans and non-human animals, his evidence is primarily amount emotional displays, rather than the genuinely cognitive discontinuity.

A closely related problem, however, was squarely faced by Darwin: the question, nicely phrased in his famous letter to Asa Gray, as to whether it is plausible to think that natural selection can have equipped a creature with a capacity for arriving at any objective truths about the world.  (It is not often noted that in that letter, Darwin says that he believes in an intelligent creator — what is in doubt is whether natural selection gives him reasons to trust in his cognitive abilities.)

These two questions, Wallace’s Problem and Darwin’s Doubt, are two sides of the same coin: if natural selection (along with other biological processes) cannot account for the uniquely human ability to grasp objective truths about reality, then we must either reject naturalism (as Wallace did) or question our ability to grasp objective truths about reality (as Darwin did).

Call this the Cognitive Dilemma for Naturalism. Can it be solved? If so, how?

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Does Puncuated Equilibrium actually destroy evolutionary biology? Yes!

I just read, skimmed, struggled with Stephen Gould’s ” Structures of Evolution theory”  Its really one long argument for Punctuated Equilibrium.

Aside from many interesting observations on the substance and style the surprising thing i note is how PE actually disproves all of evolutionary biology if you think about it. No wonder Dawkins and the rest smelled it as trouble and resisted. Wikipedia also resists it on this subject. Continue reading

The Sternberg-Collins Paradox for non-random SINE insertion mutations

One of the most brilliant evolutionary biologists of the present day, Richard Sternberg, PhD PhD was ousted and permanently blacklisted by the National Institutes of Health and the Smithsonian Museum for his ID sympathies.

Sternberg is neither a Creationist nor Darwinist but classifies himself as a Process Structuralist which means he is not much involved in the ultimate questions of how things came to be, he just appreciates the amazing patterns of similarity and diversity in biology.

He was labelled by some of his former supporters as an intellectual terrorist after he used his position as editor of a journal to publish an ID-friendly article by Stephen Meyer in 2004. He paid dearly for that decision, and his subsequent dismissal from the NIH and Smithsonian precipitated special investigations by members of Congress and the White House a decade ago. Unfortunately, nothing of consequence was done for Sternberg and he was destroyed professionally and personally.

Despite his circumstances, he continued to publish excellent essays such as the one that highlights the non-random patterns of SINES (presumed by some to be junkDNA) which are present in mice and rats (link below).
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Cumulative Selection Explained!

The battle over cumulative selection and Dawkins’ Weasel program has raged on for some months [years?] here at TSZ and across numerous threads. So can it possibly be that we now, finally, have a definitive statement about cumulative selection?

Mung: And whether or not my program demonstrates the power of cumulative selection has not been settled…

To which keiths responded:

keiths: Anyone who understands cumulative selection can see that it doesn’t, because your fitness functions don’t reward proximity to the target — only an exact match. The fitness landscapes are flat except for a spike at the site of the target.

So there you have it. You need a target and a fitness function that rewards proximity to the target.

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A One Line GA

Please post your software implementation of a GA that can be expressed in a single line of executable code.

Here’s mine:

#

A minimalist GA – Inspired by Allan Miller at TSZ

#
pop = Array.new(10) {“I AM APE-ISCH”}.map! {|ape| ape.dup}

The original population is copied and eliminated.

Further Thoughts on the Evolution of Consciousness

Continuing a discussion I and one or two others were having in the thread vincent-torleys-disappearing-book-review it is of little surprise that those responding to what I said, along with many of the posters here, regard consciousness as a product of matter. I believe that it is the other way round. As with Owen Barfield and John Davy, I came to this conclusion many, many years ago, and for me like them, Rudolf Steiner was a big influence in solidifying this view. Here is an extract from an article about Owen Barfield from Richard A. Hocks

Barfield’s precoccupation with the history of consciousness is different from even the most saturated analyses of the past, such as Erich Auerbach’s Mimesis. Barfield maintains that, in any thoughtful consideration of evolution, it is both more reasonable and more illuminating to hold that mind, or consciousness, precedes matter rather than the reverse–though not individualized mind or self-consciousness. Not only does the origin of language point toward this supposition but also the content of the great myths, indeed even the very archetypes that a thinker like Jung explores so deeply yet without ever considering that that they might inhabit the world “outside” the human head–or a vast collection of human heads. In other words, evolution for Barfield begins with mind as anterior to matter, as a given “field” out of which, as it were, matter compresses. Barfield’s thesis herein does not merely challenge the Darwinian argument; in a sense it turns that argument on its head: for not only does mind precede and bring matter into being, and a form of intentionality replace chance-ridden natural selection, but the very same physical evidence used in support of the received position is never directly challenged or discredited, but interpreted differently…

Here are some words from John Davy (pseudonym, John Waterman) who gives an overview of Steiner’s thoughts on the evolution of physical life better than I ever could:

John Davy:

The evolution of man, Steiner said, has consisted in the gradual incarnation of a spiritual being into a material body. It has been a true “descent” of man from a spiritual world into a world of matter. The evolution of the animal kingdom did not precede, but rather ;accompanied; the process of human incarnation. Man is thus not the end result of the evolution of the animals, but is rather in a certain sense their cause. In the succession of types which appears in the fossil record-the fishes, reptiles, mammals, and finally fossil remains of man himself-the stages of this process of incarnation are reflected. Continue reading

Some Questions on Genetic Algorithms

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

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

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

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.

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

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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“Species”

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