Invited responses to my nylonase research and the question of “New Proteins Without God’s Help”

Susumo Ohno (who coined the term “junkDNA”) published a paper in 1984 through the National Academy of Sciences that was used by the NCSE, Ken Miller and Dennis Venema to claim “proteins can evolve without God’s help”. At the request of John Sanford, a courtesy associate research professor at Cornell, I was recruited to write a paper to refute Ohno’s evolutionary hypothesis on nylonases. I wrote it under John’s guidance based on his intuitions about genetics, his life-long specialty of 40 years and for which he became famous as attested by the fact he is one of the few geneticists who had their work featured in the Smithsonian National Museum of American History.

The actual paper is now in review, but it is not intended to be published in any journal, but will be released in a variety of channels shortly. It is hoped the material can be used by others to actually create papers that enter peer review. The motivation for releasing the paper in this way is to counter Venema’s book while it is still hot off the press.
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Where is the scientific evidence that arguments change minds?

There is considerable scientific evidence that arguing with people about their beliefs usually has an effect opposite of what you would hope (assuming, generously, that you care more about the effect your arguing has on others than the effect it has on you). I’m sure that most of you have seen reviews of the relevant literature. In any case, I have not the least interest in arguing about the evidence that arguing hardens, rather than changes, beliefs. Why? I insist that, as obviously negative as arguments are, the burden is on the arguer to provide strong evidence that arguing is, on balance, more beneficial than harmful.

It would be entertaining to observe the arguing of the most compulsive of arguers that they actually do not argue. But let’s make that a wee bit harder for them to do, and require that, whatever they regard their not-arguing to be, they present scientific evidence that it generally benefits the people with whom they not-argue. And, no, I have not overlooked the fantasy that the benefit is to the silent Onlookers, and that you are their Champion. Either provide us with evidence that there exists such an effect, or entertain us with your Kairosfocus imitation.

The Arrival of the Fittest: a book review

Andreas Wagner’s book,The Arrival of the Fittest has been mentioned many times (just try a site search as I’ve just done) since it was published. Petrushka pointed it out in a comment

For anyone interested in whether RMNS can create stuff, I recommend a relatively new book, Arrival of the Fittest. I just bought the Kindle version an haven’t finished, but it has a lot to say about how goldilocks mutations occur.

Much later Mung writes:

Reminds me of petrushka, who is always plugging Andreas Wagner’s Arrival of the Fittest, but will never post an OP on it for discussion.

So I’ve taken the hint and bought the book at last. I can see why people have recommended it. Continue reading

Jerry Falwell Jr, a Trump appointee.

I’m sure the name Jerry Falwell Jr means more to US members than it does to me. A friend passed on a link where I read:

Donald Trump appoints creationist college president to lead higher education reform taskforce

According to Salon:

The focus will be on “overregulation and micromanagement of higher education,” according to university spokesman Len Stevens. This would be consistent with Falwell’s past positions, in which he has opposed federal regulations on funding and accreditation for American schools of higher learning.

Following the appointment of (Calvinist?) Betsy DeVos as Education secretary, should we be concerned for the future of public education in the US?

Darwin’s House of Cards

In this provocative history of contemporary debates over evolution, veteran journalist Tom Bethell depicts Darwin’s theory as a nineteenth-century idea past its prime, propped up by logical fallacies, bogus claims, and empirical evidence that is all but disintegrating under an onslaught of new scientific discoveries. Bethell presents a concise yet wide-ranging tour of the flash points of modern evolutionary theory, investigating controversies over common descent, natural selection, the fossil record, biogeography, information theory, evolutionary psychology, artificial intelligence, and the growing intelligent design movement. Bethell’s account is enriched by his own personal encounters with of some our era’s leading scientists and thinkers, including Harvard biologists Stephen Jay Gould and Richard Lewontin; British paleontologist Colin Patterson; and renowned philosopher of science Karl Popper.

Darwin’s House of Cards: A Journalist’s Odyssey Through the Darwin Debates

Of course, no real skeptic will want to read this book.

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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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Climate Change: myth or reality?

There’s no question in my mind the “Intelligent Design” movement has lost all its arguments with Science. Unfortunately, post Trump-it, that fact is now an irrelevance. With Trump’s appointment of Betsy de Vos as Education Secretary, it looks like religious fundamentalism no longer needs its figleaf. What concerns me much more is that a similar fate awaits climate research if his appointment of Rex Tillerson as Secretary of State is any indication of future policy on combating climate change. Continue reading

Knowledge As Articulated Insight

The standard definition of knowledge, canonized in epistemology textbooks, is that knowledge is “justified true belief.”

I think that this is badly wrong, and to put it right, we should return to where this idea comes from: Plato’s argument (“argument”) in Meno. I suggest, based in part on Plato, that we should reject the JTB definition of knowledge in favor of knowledge as articulated insight.

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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!

Some evidence ALUs and SINES aren’t junk and garbologists are wrong

Larry Moran, Dan Graur and other garbologists (promoters of the junkDNA perspective), have argued SINES and ALU elements are non-functional junk. That claim may have been a quasi-defensible position a decade ago, but real science marches forward. Dan Graur can only whine and complain about the hundreds of millions of dollars spent at the NIH and elsewhere that now strengthens his unwitting claim in 2013, “If ENCODE is right, Evolution is wrong.”

Larry said in Junk in Your Genome: SINES
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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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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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Impractical Naturalism of Dan Graur vs. the NIH

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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Philosophy and Complexity of Rube Goldberg Machines

Michael Behe is best known for coining the phrase Irreducible Complexity, but I think his likening of biological systems to Rube Goldberg machines is a better way to frame the problem of evolving the black boxes and the other extravagances of the biological world.
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How and Why: questions for scientists and philosophers?

The late John Davison often remarked that science could only answer “how” questions, not “why”. It seems to me philosophers, perhaps I’m really thinking of philosophers of religion rather than in general, attempt to find answers to “why” questions without always having a firm grasp on how reality works. Perhaps this is why there is so much talking past each other when the explanatory power of science vs other ways of knowing enters a discussion. Continue reading

Christiantoday.com sides with UMC against the DI / ID.

Here’s the article in full:

Christian Today Article

The best bit?:

….However, the UMC has taken the view – expressed though it is in dusty legalese – that in allowing the promotion of intelligent design at its conference would to connive at something which is, not to put too fine a point upon it, not true.

In this respect, it is surely right. It’s always possible to find things about life and its development that evolutionary theory has not yet succeeded in explaining. To argue from this that the answer must be “God did it” is ultimately self-defeating. Science advances, the number of unknowns diminishes, and God is driven into a smaller and smaller space accordingly. This “God of the gaps” approach has long been discredited.

The UMC appears to have taken the view that giving a platform – no matter how small – to a view as mistaken as this undermines the credibility of the gospel because it encourages people to believe things that aren’t true. Building a faith around falsehood is putting people’s souls in peril. The Discovery Institute may not like it, but the UMC is surely right to stand its ground.

(format not the same as the original). Thoughts?

Excilience and Contextomy

consilience. : the linking together of principles from different disciplines especially when forming a comprehensive theory.

contextomy. : an informal fallacy and a type of false attribution in which a passage is removed from its surrounding matter in such a way as to distort its intended meaning. Quote mining.

excilience. : the linking together of Contextomies from different disciplines especially when forming a comprehensive theory. Thought mining.

The Quote Mine Project provides excellent examples of contextomy. Uncommondescent provides excellent examples of excilience.

The practices lend themselves to all kinds of humorous incongruities. Among them are:

1. free will vs predestination
2. deism vs interventionism (Michael Denton vs Michael Behe)
3. front loading vs twiddling (Mike Gene vs gpuccio, etc.)
4. ascentism vs degenerationism (Chardin vs Sanford)
5. old earth vs young earth
6. realism vs last thursdayism
7. biblical literalism vs inspirationism

There are probably a lot more, but these come up frequently. The humor comes from observing that the armies of ID clash by night, without ever mentioning or discussing their differences and their contradictory assumptions and conclusions.

Food for discussion.