Random Genetic Drift: a controversy?

Over my time as a dilettante observer of the science blogging community, I have noticed a certain frisson of controversy over the idea of random genetic drift. Sewall Wright, who with Ronald Fisher and J. B. S. Haldane (Bill Bryson’s observations on Haldane’s research into diving and decompression are entertaining) established the science of population genetics, is credited with coining the phrase in 1929. Thanks to Professor Joe Felsenstein for pointing out his seminal paper. Continue reading

CSI-free Explanatory Filter…

…Gap Highlighter, Design Conjecture

Though I’ve continued to endear myself to the YEC community, I’ve certainly made myself odious in certain ID circles. I’ve often been the lone ID proponent to vociferously protest cumbersome, ill-conceived, ill-advised, confusing and downright wrong claims by some ID proponents. Some of the stuff said by ID proponents is of such poor quality they are practically gifts to Charles Darwin. I teach ID to university science students in extra curricular classes, and some of the stuff floating around in ID internet circles I’d never touch because it would cause my students to impale themselves intellectually.
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Circularity of using CSI to conclude Design?

At Uncommon Descent, William Dembski’s and Robert Marks’s coauthor Winston Ewert has made a post conceding that using Complex Specified Information to conclude that evolution of an adaptation is improbable is in fact circular. This was argued at UD by “Keith S.” (our own “keiths”) in recent weeks. It was long asserted by various people here, and was argued in posts here by Elizabeth Liddle in her “Belling the Cat” and “EleP(T|H)ant in the room” series of posts (here, here, and here). I had posted at Panda’s Thumb on the same issue.

Here is a bit of what Ewert posted at UD:

CSI and Specified complexity do not help in any way to establish that the evolution of the bacterial flagellum is improbable. Rather, the only way to establish that the bacterial flagellum exhibits CSI is to first show that it was improbable. Any attempt to use CSI to establish the improbability of evolution is deeply fallacious.

I have put up this post so that keiths and others can discuss what Ewert conceded. I urge people to read his post carefully. There are still aspects of it that I am not sure I understand. What for example is the practical distinction between showing that evolution is very improbable and showing that it is impossible? Ewert seems to think that CSI has a role to play there.

Having this concession from Ewert may surprise Denyse O’Leary (“News” at UD) and UD’s head honcho Barry Arrington. Both of them have declared that a big problem for evolution is the observation of CSI. Here is Barry in 2011 (here):

All it would take is even one instance of CSI or IC being observed to arise through chance or mechanical necessity or a combination of the two. Such an observation would blow the ID project out of the water.

Ewert is conceding that one does not first find CSI and then conclude from this that evolution is improbable. Barry and Denyse O’Leary said the opposite — that having observed CSI, one could conclude that evolution was improbable.

The discussion of Ewert’s post at UD is interesting, but maybe we can have some useful discussion here too.

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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Counting generations of M&Ms

Allan Miller’s post Randomness and evolution deals with neutral drift in the Moran model applied to a bag of M&Ms. Much of the discussion has focused on the question of counting generations in a situation where they overlap. I think it’s a good idea to divert that part of the discussion into its own thread.

Here are the rules. Start with a population of N M&Ms. A randomly chosen M&M dies. Another randomly chosen M&M gives birth to a child M&M. Repeat.

Because the focus of this thread is generation count and not fixation, we will pay no attention to the colors of M&Ms.

How do we count generations of M&Ms?

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Randomness and evolution – An Interactive toy

Lizzie Allan Miller said:

Here’s a simple experiment one can actually try. Take a bag of M&M’s, and without peeking reach in and grab one. Eat it. Then grab another and return it to the bag with another one, from a separate bag, of the same colour. Give it a shake. I guarantee (and if you tell me how big your bag is I’ll have a bet on how long it’ll take) that your bag will end up containing only one colour. Every time. I can’t tell you which colour it will be, but fixation will happen.

I’ve written an interactive browser based version you can explore this idea with.

http://mandmcounter.appspot.com/emeniem.html

color

 

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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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Randomness and evolution

Here’s a simple experiment one can actually try. Take a bag of M&M’s, and without peeking reach in and grab one. Eat it. Then grab another and return it to the bag with another one, from a separate bag, of the same colour. Give it a shake. I guarantee (and if you tell me how big your bag is I’ll have a bet on how long it’ll take) that your bag will end up containing only one colour. Every time. I can’t tell you which colour it will be, but fixation will happen.
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Lizzie asked me a question, so I will respond

Sal Cordova responded to my OP at UD, and I have given his post in full below.

Dr. Liddle recently used my name specifically in a question here:

Chance and 500 coins: a challenge

Barry? Sal? William?

I would always like to stay on good terms with Dr. Liddle. She has shown great hospitality. The reason I don’t visit her website is the acrimony many of the participants have toward me. My absence there has nothing to do with her treatment of me, and in fact, one reason I was ever there in the first place was she was one of the few critics of ID that actually focused on what I said versus assailing me personally.

So, apologies in advance Dr. Liddle if I don’t respond to every question you field. It has nothing to do with you but lots to do with hatred obviously direct toward me by some of the people at your website.

I’ve enjoyed discussion about music and musical instruments.

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Proof: Why naturalist science can be no threat to faith in God

I’m going to demonstrate this using Bayes’ Rule. I will represent the hypothesis that (a non-Deist, i.e. an interventionist) God exists as H_G, and the evidence of complex life as L_C.  What we want to know is the posterior probability that H_{G} is true, given L_C, written

    \[P(H_{G}|L_N)}\]

which, in English, is: the probability that God exists, given the evidence before us of complex life.

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Chance and 500 coins: a challenge

My problem with the IDists’ 500 coins question (if you saw 500 coins lying heads up, would you reject the hypothesis that they were fair coins, and had been fairly tossed?)  is not that there is anything wrong with concluding that they were not.  Indeed, faced with just 50 coins lying heads up, I’d reject that hypothesis with a great deal of confidence.

It’s the inference from that answer of mine is that if, as a “Darwinist” I am prepared to accept that a pattern can be indicative of something other than “chance” (exemplified by a fairly tossed fair coin) then I must logically also sign on to the idea that an Intelligent Agent (as the alternative to “Chance”) must inferrable from such a pattern.

This, I suggest, is profoundly fallacious.

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Barry gets it wrong again….

Here.

 

The null hypothesis in a drug trial is not that the drug is efficacious. The null hypothesis is that the difference between the groups is due to chance.

No, Barry.  Check any stats text book.  The null hypothesis is certainly not that the drug is efficacious (which is not what Neil said), but more importantly, it is not that “the difference between the groups is due to chance”.

It is that “there is no difference in effects between treatment A and treatment B”.

When in hole, stop digging, Barry!

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Yes, Lizzie, Chance is Very Often an Explanation

[Posted by Barry at UD]

Over at The Skeptical Zone Elizabeth Liddle has weighed in on the “coins on the table” issue I raised in this post.

Readers will remember the simple question I asked:

If you came across a table on which was set 500 coins (no tossing involved) and all 500 coins displayed the “heads” side of the coin, how on earth would you test “chance” as a hypothesis to explain this particular configuration of coins on a table?

Dr. Liddle’s answer:

Chance is not an explanation, and therefore cannot be rejected, or supported, as a hypothesis.

Staggering. Gobsmacking. Astounding. Superlatives fail me.

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Getting from Fisher to Bayes

(slightly edited version of a comment I made at UD)

Barry Arrington has  a rather extraordinary thread at UD right now, ar

Jerad’s DDS Causes Him to Succumb to “Miller’s Mendacity” and Other Errors

It arose from a Sal’s post, here at TSZ, Siding with Mathgrrl on a point,and offering an alternative to CSI v2.0

Below is what I posted in the UD thread.

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Siding with Mathgrrl on a point,and offering an alternative to CSI v2.0

[cross posted from UD Siding with Mathgrrl on a point, and offering an alternative to CSI v2.0, special thanks to Dr. Liddle for her generous invitation to cross post]

There are two versions of the metric for Bill Dembski’s CSI. One version can be traced to his book No Free Lunch published in 2002. Let us call that “CSI v1.0”.

Then in 2005 Bill published Specification the Pattern that Signifies Intelligence where he includes the identifier “v1.22”, but perhaps it would be better to call the concepts in that paper CSI v2.0 since, like windows 8, it has some radical differences from its predecessor and will come up with different results. Some end users of the concept of CSI prefer CSI v1.0 over v2.0.
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