The argument from Upright Biped

I note Barry Arrington, Uncommon Descent’s president, owner and legal defender is promoting a commenter,  the pseudonymous Upright Biped, not unknown to regular participants here. Not one OP but two (so far) glowing posts. Upright Biped has convinced himself, and (let’s be fair) some others, that he has come up with a knock-down argument against origin-of-life theories that take a purely reality-based approach.

The latest OP entitled UB Strikes Again! ends with the rejoinder “AVS, where are you? You’re letting down your side. Come on back and tell UB why he’s wrong!”

This seems somewhat disingenuous. Why should it be left to an anonymous self-described “biochemistry student” to fight against the might of Barry’s moderation and Bipeds weighty argument (that can be summarized as “a miracle happens, therefore design”)?

It’s already been done. Why should AVS need to renvent the wheel? I’d like to remind Barry that there is plenty of material blowing Upright Biped’s argument out of the water but I am unable to comment at Uncommon Descent. Maybe someone who still can would like to draw Barry’s and Biped’s attention to the fact that there are quite a few folks who’d like to tell UB why he’s wrong.

Design Dissimilarity

At Uncommon Descent, Mung makes an assertion that other creationists have raised from time to time:

However, I don’t see why similarity in design necessarily implies common descent. If an architect designs two slightly dissimilar buildings one after the other, where is the common descent in this process? I am assuming that by common descent, one means that the species arose via a long sequence of sexual reproduction events acted upon by random variations.

As a software engineer, I know I don’t use any kind of sexual reproduction mechanism to derive one class of objects from another. Why could not the designers have a huge database of pre-designed genes to choose from and with which to create new species of animals and humans? And why would they need sexual reproduction to accomplish this? Beings that advanced could easily incubate newly designed species outside the womb, no?

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Adam and Eve and Jerry and Bryan and Vincent

Bryan College in Dayton, Tennessee has recently added to its statement of faith, to which faculty members must subscribe, a “clarification” that

We believe that all humanity is descended from Adam and Eve. They are historical persons created by God in a special formative act, and not from previously existing life forms.

Jerry Coyne at his Why Evolution Is True blog has pointed at this with alarm here, and he linked back to the Chattanooga Times Free Press story here. Jerry cites studies showing from the amount of variability in human populations, that effective population size of the individuals leaving Africa in the Out-Of-Africa event cannot have been much less than 2250, and the effective population size in Africa cannot have been much less than 10,000.

VJTorley at Uncommon Descent has published a firm response, saying Jerry was “In a pickle about Adam and Eve” and saying that when he said that “2250 is greater than two”

Evidently math is not Professor Coyne’s forte.

Note: 2,500 isn’t the same as 2,250.

Note: 2,250 + 10,000 = 12,250.

The math lesson is over.

He also quotes a paper by Luke Harmon and Stanton Braude, which notes that effective population sizes can be larger than actual population sizes, and says

It’s rather embarrassing when a biology professor makes mistakes in his own field, isn’t it?

Has Jerry gotten himself into a pickle? I have some background in this area — I have worked on coalescent trees of ancestry of genes within a species, I wrote one of the two basic papers on effective population size of populations with overlapping generations, and I even shared a grant with Luke Harmon two years ago.

A few simple points:

1. 10,000 + 2,250 = 12,250 all right, but in fact that number is even greater than 2.

2. Effective population size can be greater than population size. It can get as much as 2 times higher. That still leaves us with a long way to go.

3. The Bryan College administration does not know how to write a Clarification. Their statement says that all humanity are descended from Adam and Eve, but does not make it clear whether there could have been other ancestors too. I suspect they meant that there weren’t any.

4. According to UD’s own statements, Intelligent Design arguments are supposedly not statements about religion, so that ID arguments do not predict anything about Adam and Eve. ID proponents are being slandered when they are called creationists, we are told repeatedly. So why the concern about Adam and Eve at UD?

So was Jerry wrong? About Adam and Eve, no. Though he is wrong when he says that his “website” is not a blog.

Nullasalus embraces the multiverse

A bizarre new post at UD had me checking the date to make sure it wasn’t April 1st.

In it, commenter ‘nullasalus’ explains that although he doesn’t think the multiverse is plausible, he nevertheless thinks “it’s a good idea, from an ID perspective, to accept and take part in multiverse speculations,” and offers these four reasons, which I have quoted verbatim:

1. If we live in an infinite multiverse, Intelligent Design is no longer a possibility – it is a certainty.

2. While Intelligent Design becomes a certainty (at least somewhere), Darwinism becomes obsolete and obscure.

3. Theism becomes true on the spot – specifically, polytheism.

4. If ID proponents embrace the multiverse, there’s a good chance the scientific community will drop it like a hot potato.

That last one is especially funny. Enjoy!

The capriciousness of intelligent agency

Scordova at UD asks a question that I find interesting.

http://www.uncommondescent.com/philosophy/the-capriciousness-of-intelligent-agency-makes-it-challenging-to-call-id-science/

By way of contrast, intelligent agencies, particularly those intelligent agencies which we presume have free will, cannot be counted upon to behave in predictable manners in certain domains. Even presuming some intelligent agencies (say machine “intelligence”) are deterministic, they can be an unpredictable black box to outside observers. This makes it difficult to make direct experimental confirmation of certain ID inferences.

It has long been my contention that the defining behavior of science is the search for regularity.

Some regularities can be refined into mathematical equations, which we generally call laws of nature.

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Darwin was wrong!!!!!

Stop the presses!

Seriously, are the ID proponents at UD ever going to wonder why Gould and Eldredge remained persuaded that common descent occurred, and that “punctuated equibrium”, although contrary the uniformly incremental pattern that Darwin envisaged, was nonetheless consistent with Darwin’s proposed adaptive mechanism of heritable variation in reproductive success?

Because Darwin was indeed wrong about uniform change.  Unlike us, he didn’t have computers with which to model the predicted output of his mechanism. Indeed he didn’t even know what the vector of heritability was.  We do.  Here’s a sample output from Eureqa, a program that uses Darwin’s proposed mechanism to “evolve” equations to fit data:

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Censorship

There’s a lot of discussion of censorship swirling around the ID/evolution/online world right now, which I find very odd.  Apparently the magazine Nautilus has closed a comment thread (without apparently deleting any comments) on the basis that “This is a science magazine, and our comments section isn’t the place to debate whether evolution is true”.

Accusations of “censorship” by “evolutionists” have been flying around for a while now, at least since the Expelled movie and it resurfaced regarding the withdrawal of the Biological Information: New Perspectives  book from the Springer catalogue. And now, recently, Jerry Coyne has been named “Censor of the Year” by the Discovery Institute.

My own instincts tend against censorship, and although I do not think that all censorship is bad, I would certainly rather err on the side of too little than too much.  Here, as I hope everyone knows, only a very narrow class of material is ever deleted, and only a very narrow class of offenses bring down a ban.

But what is censorship, and who, if anyone, is censoring whom in the ID/evolution debate?

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Ronald Fisher and William Dembski

An odd post by “news” at UD raises yet again the issue of Fisherian p values – and reveals yet again that many ID proponents don’t understand them.

She (I assume it is Denyse) writes:

Further to “Everyone seems to know now that there’s a problem in science research today and “At a British Journal of Medicine blog, a former editor says, medical research is still a scandal,” Ronald Fisher’s p-value measure, a staple of research, is coming under serious scrutiny.

Many will remember Ronald Fisher (1890–1962) as the early twentieth century Darwinian who reconciled Darwinism with Mendelian genetics, hailed by Richard Dawkins as the greatest biologist since Darwin. Hid original idea of p-values (a measure of whether an observed result can be attributed to chance) was reasonable enough, but over time the dead hand got hold of it:

 

Many at UD may also “remember” Ronald Fisher as the early twentieth century statistician who inspired William Dembski’s eleP(T|H)ant.

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A Quiz for ‘Intelligent Design’ Theory Proponentsists

A Quiz for ‘Intelligent Design’ Theory Proponentsists

(Even for those IDist outliers like nullasalus at UD who don’t think IDT is scientific, but who think they are tricking people that logically & responsibly reject IDT)

 Another simple YES/NO exercise.

Acronyms:

IDM = Intelligent Design Movement

IDist = Intelligent Design ideologue

DI = Discovery Institute

IDT = (Uppercase) Intelligent Design theory

USA = United States of America = )

 

Questions:

 1. Is the DI-led IDM making a concentrated, dedicated effort to distinguish good science from bad science by actively and publically rejecting the outdated ‘young Earth’ views of many undereducated, anti-science, evangelical Christians in the USA?

2. Have IDM leaders Michael Behe, Stephen Meyer, William Dembski and Phillip Johnson *all* linked their own version of IDT to their personal Christian faith in public statements, interviews and/or articles?

3. Have several prominent Abrahamic theists (particularly those active in science, philosophy & theology/worldview conversations) openly rejected IDT on the basis of distinguishing Uppercase ‘Intelligent Design’ Theory (the Discovery Institute’s ‘strictly scientific’ theory) from lowercase ‘intelligent design’ (aka the non-scientific, theological/worldview ‘design argument’)?

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A quick question for Dr. Liddle and other skeptics

[Vincent Torley has posted this at Uncommon Descent. As many people who might like to respond, not the least among them Dr. Liddle herslf, are unable to do so directly, I reproduce it here. The rest of this post is written by Vincent Torley]

Over at The Skeptical Zone, Dr. Elizabeth Liddle has written a thought-provoking post, which poses an interesting ethical conundrum about the morality of creating sentient beings. Continue reading

Darwin backwards?

What is it with ID proponents and gambling?  Or rather, what is it that makes people who play p0ker and roulette think that that gives them a relevant background for statistical hypothesis testing and an understanding of stochastic processes such as evolution?  Today, “niwrad”, has a post at UD, with one of the most extraordinary garblings of evolutionary theory I think I have yet seen.  He has decided that p0ker is an appropriate model this time (makes a change from coin tossing, I guess).

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Getting some stuff off my chest….

I don’t think that science has disproven, nor even suggests, that it is unlikely that an Intelligent Designer was responsible for the world, and intended it to come into existence.

I don’t think that science has, nor even can, prove that divine and/or miraculous intervention is impossible.

I don’t think that the fact that we can make good predictive models of the world (and we can) in any way demonstrates that how the world has observedly panned out was not entirely foreseen and intended by some deity.

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Random Mutations: vjtorley

vjtorley, at UD, writes a post entitled It’s time for scientists to come clean with the public about evolution and the origin of life that includes this:

Edward Frenkel, a professor of mathematics at the University of California, Berkeley, recently reviewed a book titled, Probably Approximately Correct: Nature’s Algorithms for Learning and Prospering in a Complex World (Basic Books, 2013) by computer scientist Leslie Valiant, in a report for the New York Times (Evolution, Speeded by Computation, September 30, 2013). The following excerpt conveys the gist of Dr. Valiant’s conclusions:

The evolution of species, as Darwin taught us, relies on natural selection. But Dr. Valiant argues that if all the mutations that drive evolution were simply random and equally distributed, it would proceed at an impossibly slow and inefficient pace.

Darwin’s theory “has the gaping gap that it can make no quantitative predictions as far as the number of generations needed for the evolution of a behavior of a certain complexity,” he writes. “We need to explain how evolution is possible at all, how we got from no life, or from very simple life, to life as complex as we find it on earth today. This is the BIG question.”

Dr. Valiant proposes that natural selection is supplemented by ecorithms, which enable organisms to learn and adapt more efficiently. Not all mutations are realized with equal probability; those that are more beneficial are more likely to occur. In other words, evolution is accelerated by computation.

The criticisms being made here of the Darwinian theory of evolution are pretty devastating: not only is it far too slow to generate life in all its diversity, but it’s also utterly incapable of making quantitative predictions about the time required for a structure of known complexity to evolve, by natural selection. And there’s no reason to believe that the “nearly neutral theory of evolution” espoused by biologists such as Professor Larry Moran would fare any better, in this regard.

 

Dr Torley is a scholar and a gentleman and someone for whom I have a great deal of personal respect. In fact I owe him more than one debt of personal kindness.  But that does not mean that I think his ideas are correct, and I submit he is profoundly wrong here in an extremely useful way.  Unusually, the passage he cites is very specific about the kind of randomness that cannot be the kind of randomness that would produce Darwinian evolution: equally distributed.

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