Evolution and Functional Information

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Here, one of my brilliant MD PhD students and I study one of the “information” arguments against evolution. What do you think of our study?

I recently put this preprint in biorxiv. To be clear, this study is not yet peer-reviewed, and I do not want anyone to miss this point. This is an “experiment” too. I’m curious to see if these types of studies are publishable. If they are, you might see more from me. Currently it is under review at a very good journal. So it might actually turn the corner and get out there. An a parallel question: do you think this type of work should be published?

 

I’m curious what the community thinks. I hope it is clear enough for non-experts to follow too. We went to great lengths to make the source code for the simulations available in an easy to read and annotated format. My hope is that a college level student could follow the details. And even if you can’t, you can weigh in on if the scientific community should publish this type of work.

Functional Information and Evolution

http://www.biorxiv.org/content/early/2017/03/06/114132

“Functional Information”—estimated from the mutual information of protein sequence alignments—has been proposed as a reliable way of estimating the number of proteins with a specified function and the consequent difficulty of evolving a new function. The fantastic rarity of functional proteins computed by this approach emboldens some to argue that evolution is impossible. Random searches, it seems, would have no hope of finding new functions. Here, we use simulations to demonstrate that sequence alignments are a poor estimate of functional information. The mutual information of sequence alignments fantastically underestimates of the true number of functional proteins. In addition to functional constraints, mutual information is also strongly influenced by a family’s history, mutational bias, and selection. Regardless, even if functional information could be reliably calculated, it tells us nothing about the difficulty of evolving new functions, because it does not estimate the distance between a new function and existing functions. Moreover, the pervasive observation of multifunctional proteins suggests that functions are actually very close to one another and abundant. Multifunctional proteins would be impossible if the FI argument against evolution were true.

Evo-Info: Publication delayed, supporting materials online

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 350 pages. Jan 31 May 1, 2017.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.

I cannot tell you exactly what will be in the forthcoming book by Marks, Dembski, and Ewert. I made it clear in Evo-Info 1 and Evo-Info 2 that I was responding primarily to technical papers on which the book is based. With publication delayed once again, I worry that the authors will revise the manuscript to deflect my criticisms. Thus I’m going to focus for a while on the recent contributions to the “evolutionary informatics” strain of creationism by George D. Montañez, a former advisee of Marks who is presently a doctoral candidate in machine learning at Carnegie Mellon University (advisor: Cosma Shalizi). My advice for George is that if he wants not to taken for a duck, then he had better not walk like a duck and swim like a duck and quack like a duck. Continue reading

Poker as a Proxy Turing Test

I found the recent contest in which an algorithm was able to successfully defeat four professional poker players in a particular version of poker to be very interesting.

What strikes me is not the fact that the algorithm was successful but the way in which it accomplished the task.

check this out it’s all interesting but pay close attention from about the 8 minute mark

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Evo-Info 2: Teaser for algorithmic specified complexity

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 350 pages. January 30, 2017.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.

The introduction to this series ended with a promise of insights into evolutionary informatics that the forthcoming book by Marks, Dembski, and Ewert is unlikely to afford. There will be little doubt at the end of the fourth installment that I have delivered the goods. First I want to assure you that, although I subscribe to the philosophy “Into Each Life, Some Math Must Fall,” the downpour of abstract notions, Greek letters, and squiggly marks will be intermittent, not unrelenting.

1280pxFujRusSunset in the Garden of Id

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Evo-Info 1: Engineering analysis construed as metaphysics

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 350 pages. January 30, 2017.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.

World Scientific is pitching Introduction to Evolutionary Informatics, by Robert Marks, William Dembski, and Winston Ewert, to a general readership, but with particular note of enthusiasts of apologetics. The book features the Conservation of Information Theorem, which was the centerpiece of Dembski’s religio-philosophical treatise Being as Communion: A Metaphysics of Information (2014). So there is no denying that the authors regard their mathematical arguments as support for their religious views. And there is no great surprise in learning that the nonprofit Center for Evolutionary Informatics, operated by Marks and Dembski, has the alternate name Arbor Ministries in public records. The forthcoming book includes a section titled “The Genesis,” and this leads me to hope that the authors, mindful of the canonical teachings of Jesus, have made a clear statement of faith.

No one lights a lamp and hides it in a clay jar or puts it under a bed. Instead, they put it on a stand, so that those who come in can see the light. For there is nothing hidden that will not be disclosed, and nothing concealed that will not be known or brought out into the open. Therefore consider carefully how you listen. Whoever has will be given more; whoever does not have, even what they think they have will be taken from them.

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Chesil Beach is high in algorithmic specified complexity

Winston Ewert, William A. Dembski, and Robert J. Marks II rebranded specified complexity as a measure of meaningful information, at the Engineering and Metaphysics 2012 Conference. In my mind, that was quite a remarkable event in the history of the “intelligent design” (ID) offshoot of “creation science” — particularly in light of the fact that Dembski and Marks changed the meaning of information in the Law of Conservation of Information from specified complexity to active information, back in 2008. But the organizer of that conference, Jonathan Bartlett, seems not to have noticed. He recently undertook to explain algorithmic specified complexity to the unwashed masses, but made no mention at all of meaning.

Jonathan approves of my observation, posted here in The Skeptical Zone, that the “conga lines” formed by hermit crabs are high in algorithmic specified complexity (emphasis added):

Tom English asked about Hermit Crabs forming a line. I agree that this exhibits high ASC for certain things (remember, ASC depends on what you are comparing it to). It gives a high ASC for the line compared to the hermit crabs just walking around. That seems like a success, not a fail, as you have successfully determined that they are lined up intentionally. Even though you don’t have all of the prerequisites for a design inference (at least in your post here), you have at least shown that intentionality on behalf of the hermit crabs is a live possibility. Since they are lining up for a particular purpose, that seems to line up with reality.

He has not responded to my main point (emphasis in original):

Distinguishable entities operating identically by simple rules can form structures high in specified complexity. That is, the crabs in the video differ in size, but not in the “program” they execute. Want more specified complexity? Just add crabs.

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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

An Intelligent Design Turing Test

This is an open challenge to all and sundry!

Can anyone represent the views of someone he disagrees with well enough to pass the “Turing Test” and be mistaken for a real proponent of those views? Barry Arrington has recently issued this challenge for skeptics of “Intelligent Design”. He seems to have overlooked the point that the test should be anonymous and also that most remaining active ID skeptics are unable or unwilling (or both, in my case) to participate at “Uncommon descent”. Continue reading