Junk DNA munged

Salvador seems to have successfully hijacked the early embryonic mutations thread and turned it into a discussion of junk DNA. So I thought I’d share my thoughts on the subject of junk DNA. Why care?

Various strains of creationism hold that the earth and life started out perfect, then came the fall, and it all went downhill from there. Both young earth and old earth forms can easily accommodate the presence of junk in DNA. So the presence of junk DNA does not mitigate against the creationist position. But what of it’s absence?

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Miracle of Evolution – The Appendix

In a recent thread here at TSZ the question was raised as to whether naturalism is comfortable with highly typical events. My answer to that question was quite so. Exhibit: the appendix.

Although it is widely viewed as a vestigial organ with little known function, recent research suggests that the appendix may serve an important purpose. In particular, it may serve as a reservoir for beneficial gut bacteria. Several other mammal species also have an appendix, and studying how it evolved and functions in these species may shed light on this mysterious organ in humans.

But wait. There’s more…

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The Glories of Global Warming and the Faint Young Sun Paradox

It is a little known fact that scientists who argue that the paleontological record of life is hundreds of millions of years old, when confronted with astrophysical facts, must eventually rely heavily on the hypothesis of finely tuned, large scale global warming. The problem is known as the Faith Young Sun Paradox. A few claim they have solved the paradox, but many remain skeptical of the solutions. But one fact remains, it is an acknowledged scientific paradox. And beyond this paradox, the question of Solar System evolution on the whole has some theological implications.

Astrophysicists concluded that when the sun was young, it was not as bright as it is now. As the sun ages it creates more and more heat, eventually incinerating the Earth before the sun eventually burns out. This is due to the change in products and reactants in the nuclear fusion process that powers the sun. This nuclear evolution of the sun will drive the evolution of the solar system, unless Jesus returns…
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Virolution

There have been a number of interesting comments lately here at TSZ that referred to viruses.

Are viruses pre-biotic entities, and did they contribute to the origin of life?

Are viruses alive?

Do viruses evolve?

Are viruses an example of what evolution is capable of?

Did viruses contribute to the evolution of life?

Should be fodder for some discussion.

Who’s Skeptical of the Extended Evolutionary Synthesis?

Is anyone here skeptical of the Extended Evolutionary Synthesis (EES) in biology/biological sciences? If so, why? If not, why not?

Background: A couple of days ago I interviewed one of the participants in the Royal Society’s recent ‘New Trends’ meeting (audios now available), who is obviously pro-EES ,as part of a nearly completed research project from the past couple of years.

My interviewee gave the (ahem) ‘brilliant’ answer of a stone when asked to speak about ‘things that don’t evolve’ (one of those interviewer places where it’s really hard to mask a delighted smile with neutrality!) after claiming not to understand the question: “What are the limits of evolution as a scientific theory?” (we had already been discussing its ‘possibilities’ and I explained earlier that I would ask both about the possibilities and the limits of evolutionary theories). Undergrad students around the world chuckle when they hear the Rock answer (as if geological evolution doesn’t exist in the minds of biologists)!

It’s just a ‘play of scales,’ after all, that slips us into the ‘evolution of everything,’ don’t forget 😉

Carl Woese – Evolution Skeptic

Carl Woese

b. July 15, 1928
d. December 30, 2012

“Thus, we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution, because there are other modalities that must be entertained and which we regard as mandatory during the course of evolutionary time.”

“I have concerns about scientists thinking that they’re God when it comes to biology.”

“A future biology cannot be built within the conceptual superstructures of the past. The old superstructure has to be replaced by a new one before the holistic problems of biology can emerge as biology’s new mainstream.”

“I do not like people saying that atheism is based on science, because it’s not. It’s an alien invasion of science.”

  • Carl Woese

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Evolution Skeptics!

In a recent post here at TSZ, participant Alan Fox made some comments and asked some questions which might make for interesting discussion, but first I need to challenge some of his assumptions.

First, his claim that I find evolutionary theory unbelievable.

Second, his claim that I find a naturalistic explanation for the origin of life theory unbelievable.

Third, his his claim that I mock attempts at scientific hypotheses.

Fourth, I thought being skeptical is a good thing.

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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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