Open Mike: Cornell OBI Conference Chapter 12—“Can Purifying Natural Selection Preserve Biological Information?”—Excerpt

_{Denyse O'Leary

September 3, 2013

Informatics, Natural selection}

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To facilitate discussion, we are publishing the abstracts and conclusions/summaries/Introduction excerpts of the 24 papers from the Cornell Conference on the Origin of Biological Information here at Uncommon Descent, with cumulative links to previous papers at the bottom of each page. You can get from anywhere to anywhere in the system.

Note: A blow-by-blow account of the difficulties that the authors experienced from Darwin lobby attempts to censor the book by denying it publication with Springer are detailed here. Fortunately, the uproar resulted in an opportunity for readers like yourself to read the book online. That said, the hard cover version is now shipping.

An excerpt from “Can Purifying Natural Selection Preserve Biological Information?” by Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford:

The primary findings of this study are that the selection threshold problem is real and that it is more serious than generally recognized. These findings are very robust. Our basic conclusions do not depend on a narrow range of parameter settings; rather the same picture emerges under all reasonable biological settings, indicating that the basic phenomenon is fundamental. Our most realistic simulations (see Figures 7 and 10) still employed extremely conservative parameter settings, based upon the premise that most mutations are entirely neutral, the premise of partial truncation selection, and the premise of a very high fitness heritability. We do not believe any of these assumptions are reasonable–they were applied only to define the lower range of the deleterious selection threshold for a model human population. Simulations with what we consider to be more realistic parameter settings have indicated an even more serious erosion of genetic information than is presented here.

We suggest that, unlike many phenomena in the realm of physics, the biology of population dynamics is too complex to be reliably reduced to a small set of equations. The primary deficiency we observe in prior mutation accumulation studies is the extreme simplification that has been required both in mathematical formulations and in numerical simulations. Common simplifying restrictions include assuming that all mutation effects are equal and that environmental variance is zero; usually also assuming perfect probability selection or perfect truncation selection. These simplifications may be why previous analytical models have not fully illuminated the phenomenon of mutation accumulation.

Such extreme simplification is no longer required. Today’s rapidly expanding computational resources and much more sophisticated numerical simulations provide the capacity for comprehensive numerical simulations that can address population genetic systems in their entirety, simultaneously considering all the major variables that affect mutation accumulation. Mendel’s Accountant was programmed to be a comprehensive numerical simulation, reflecting biological reality as closely as possible for all the primary variables known to influence selection effectiveness [14, 15]. Mendel empirically and mechanistically tracks the basic biological processes of mutation, meiosis, crossover, gamete formation, mating, zygote formation, and selection. During the course of thousands of generations, millions of individuals are simulated, and hundreds of millions of mutations are tracked individually and continuously — an approach we call genetic accounting.

This approach allows us to observe empirically how different biological factors interact as they influence selection efficiency, requiring far fewer prior assumptions and far less abstraction than the conventional algebraic analysis. We have repeatedly seen that, given parameter settings that correspond to the standard simplifying assumptions, Mendel supports the expectations of classic population genetic theory. However, in simulations that more realistically reflect the complexity of living populations (i.e., multiple sources of noise), Mendel’s Accountant illuminates some fundamental problems in standard theory that were previously clouded by unrealistic simplifications. More.

See also: Origin of Biological Information conference: Its goals

Open Mike: Origin of Biological Information conference: Origin of life studies flatlined

Open Mike: Cornell OBI Conference— Can you answer these conundrums about information?

Open Mike: Cornell OBI Conference—Is a new definition of information needed for biology? (Chapter 2)

Open Mike: Cornell OBI Conference—New definition of information proposed: Universal Information (Chapter 2)

Open Mike: Cornell OBI Conference—Chapter Three, Dembski, Ewert, and Marks on the true cost of a successful search

Open Mike: Cornell OBI Conference—Chapter Three on the true cost of a successful search—Conservation of information

Open Mike: Cornell OBI Conference—Chapter Four: Pragmatic Information

Open Mike: Cornell OBI Conference—Chapter Four, Pragmatic information: Conclusion

Open Mike: Cornell OBI Conference Chapter Five Abstract

Open Mike: Cornell OBI Conference Chapter Five – Basener on limits of chaos – Conclusion

Open Mike: Cornell OBI Conference Chapter Six – Ewert et all on the Tierra evolution program – Abstract

Open Mike: Cornell OBI Conference Chapter Six – Ewert et all on the Tierra evolution program – Conclusion

Open Mike: Cornell OBI Conference Chapter 7—Probability of Beneficial Mutation— Abstract

Open Mike: Cornell OBI Conference Chapter 7—Probability of Beneficial Mutation— Conclusion

Open Mike: Cornell OBI Conference Chapter 8—Entropy, Evolution and Open Systems—Abstract

Open Mike: Cornell OBI Conference Chapter 8—Entropy, Evolution and Open Systems—Conclusion

Open Mike: Cornell OBI Conference Chapter 9—Information and Thermodynamics in Living Systems—Abstract

Open Mike: Cornell OBI Conference Chapter 9—Information and Thermodynamics in Living Systems—Conclusion

Open Mike: Cornell OBI Conference Chapter 10—Biological Information and Genetic Theory: Introductory Comments—Abstract

Open Mike: Cornell OBI Conference Chapter 10—Biological Information and Genetic Theory: Introductory Comments— Excerpt

Open Mike: Cornell OBI Conference Chapter 11—Not Junk After All—Abstract

Open Mike: Cornell OBI Conference Chapter 11—Not Junk After All—Conclusion

Open Mike: Cornell OBI Conference Chapter 12—“Can Purifying Natural Selection Preserve Biological Information?”—Abstract

Comments

I would actually have encouraged the faculty and students to turn out in large numbers to ask questions at every opportunity.
Yes. If you want to promote "critical thinking" then why hide your light under a bushel? Let's all gather in the market place and dicuss the merits of our ideas. But also let's check that claims are supported by evidence. We don't want to be poisoned by sellers of snake-oil, do we? Alan Fox

jstanley01:I have to wonder, had the conference been publicized as you describe, and if, as seems well within the realm of possibility, said publicity stirred up the orthodox among the faculty and students to decry the conference as “creationism in a cheap tuxedo” and throw it off the campus before it could be held, would you be among the cyberspace wags justifying the ouster?
No, I would actually have encouraged the faculty and students to turn out in large numbers to ask questions at every opportunity. Obviously, the conference organizers and attendees wished to avoid anything resembling this at all costs. You have to wonder why all the subterfuge and reluctance to present publicly all their cutting edge research if they have such compelling arguments and data. Well, actually, it doesn't take much wondering at all! I would suggest we let the 'damning' fall where it deservedly belongs right in the laps of all those who made/make the attempt to associate 'one of the most prestigious research Universities' with their secretive conference. franklin

Yeah okay, Franklin. It sounds like Discovery may be guilding the lily by claiming "a scientific conference at a top research university (Cornell)." If the conference was held at a rented room there, why not just say "the conference held at Cornell"? 'Nuff said. I suppose the puffery there could belie an inferiority complex on the part of some IDer's, the lure an anointing at one of the fat-dripping government-funded altars of orthodox academia being what it is. Although I've never noticed a lot of shyness among them -- or creationists for that matter -- when it comes to debating the orthodox. Personally, I don't know why any IDer should have an inferiority complex. When -- in my book anyway as a proud member of that great unwashed mass known as "the general public" and a card-carrying Christian -- the so-called theory of evolution that the ID movement so cogently debunks, by now, has shown itself to be the most laughable load of used horse food ever served up as "science" in the entire history of the endeavor. Like I always say: "Uncommon Descent." You'll come to check on the progress toward science lining up with God's Word. You'll stay for the belly laughs at the antics of the Darwinist clowns. As far as "the couple of things" that you so kindly mentioned, in view of the fact that a rube such as myself "might not have considered" them, viz:
...was the conference advertised on the Cornell campus or anywhere else for that matter? (FYI the answer is no) Was the science faculty from Cornell invited to attend? (FYI the answer is no) secretive affair? (FYI the answer is yes) Do these conditions equate to any other science conference held anywhere else in the world? (FYI the answer is no)...
I have to wonder, had the conference been publicized as you describe, and if, as seems well within the realm of possibility, said publicity stirred up the orthodox among the faculty and students to decry the conference as "creationism in a cheap tuxedo" and throw it off the campus before it could be held, would you be among the cyberspace wags justifying the ouster? Forgive me if I've got you wrong, but somehow I get the feeling that you would be. "Damn them if they do and damn them if they don't." Ha! Gotta love it. Like I said, the "clown antics" are nothing if not comical. jstanley01

franklin:
From the available reports from Springer it sounds more like the submitted papers deviated significantly from the prior accepted prospectus on what the actual deliverables would contain.
evidence? if you have any. Mung

related note: Evolutionary Anthropologist's Advice: Reject Research Papers if Results Come from Discovery Institute Authors - Casey Luskin September 3, 2013 http://www.evolutionnews.org/2013/09/evolutionary_an076161.html bornagain77

Franklin, I take it you hold an atheistic/naturalistic worldview??? If so, can you please tell me how modern science can ground its epistemological basis in naturalism in the first place? "Modern science was conceived, and born, and flourished in the matrix of Christian theism. Only liberal doses of self-deception and double-think, I believe, will permit it to flourish in the context of Darwinian naturalism." ~ Alvin Plantinga Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality? – Stephen Meyer - video – (Notes in description) http://vimeo.com/32145998 Is Life Unique? David L. Abel - January 2012 Concluding Statement: The scientific method itself cannot be reduced to mass and energy. Neither can language, translation, coding and decoding, mathematics, logic theory, programming, symbol systems, the integration of circuits, computation, categorizations, results tabulation, the drawing and discussion of conclusions. The prevailing Kuhnian paradigm rut of philosophic physicalism is obstructing scientific progress, biology in particular. There is more to life than chemistry. All known life is cybernetic. Control is choice-contingent and formal, not physicodynamic. http://www.mdpi.com/2075-1729/2/1/106/ “One absolutely central inconsistency ruins [the popular scientific philosophy]. The whole picture professes to depend on inferences from observed facts. Unless inference is valid, the whole picture disappears… unless Reason is an absolute, all is in ruins. Yet those who ask me to believe this world picture also ask me to believe that Reason is simply the unforeseen and unintended by-product of mindless matter at one stage of its endless and aimless becoming. Here is flat contradiction. They ask me at the same moment to accept a conclusion and to discredit the only testimony on which that conclusion can be based.” —C.S. Lewis, Is Theology Poetry (aka the Argument from Reason) Is Metaphysical Naturalism Viable? - William Lane Craig - video http://www.youtube.com/watch?v=HzS_CQnmoLQ The Unreasonable Effectiveness of Mathematics in the Natural Sciences - Eugene Wigner - 1960 Excerpt: certainly it is hard to believe that our reasoning power was brought, by Darwin's process of natural selection, to the perfection which it seems to possess.,,, http://www.dartmouth.edu/~matc/MathDrama/reading/Wigner.html Etc.. etc... You see franklin, there are more than a few minor problems with naturalism trying to declare itself as the only allowable "scientific" worldview whilst censoring Theism from consideration? bornagain77

jstanley01, here are a couple of things you might not have considered. You might want to pose these questions to the authors of the papers or perhaps the author of the blog post yo copied and pasted: was the conference advertised on the Cornell campus or anywhere else for that matter? (FYI the answer is no) Was the science faculty from Cornell invited to attend? (FYI the answer is no) secretive affair? (FYI the answer is yes) Do these conditions equate to any other science conference held anywhere else in the world? (FYI the answer is no) I've attended and participated in more than a few science conferences where the purpose is to disseminate new research. In all cases the call for abstracts is put out months in advance. Advertisement of the event is widely disseminated in order to get the info out to as many people as possible, This 'sonference' had none of these attributes. franklin

edit: credibility of the conference franklin

jstanley01:But then what happens when us ID proponents do exactly what they say we should do: We present research papers at a scientific conference at a top research university (Cornell) and then seek to have it published by a world-class scientific publisher (Springer)?
Herein lies the problem. The conference was held in a rented hall on the cornell campus. For all the association with Cornell it could have been held at the local Motel 6. So the question is why the need to mention that Cornell is a 'top research university outside of trying to inflate the credibility of the university'. Pretty much everyone can see through the obvious subterfuge in the obvious (and sad) attempt to somehow associate their meeting with a 'top research university'. It's nothing more than credential inflation and it continues to this day. From the available reports from Springer it sounds more like the submitted papers deviated significantly from the prior accepted prospectus on what the actual deliverables would contain. It would be nice if the reviewers comments and communications with Springer were released in full but I suspect that will never happen. franklin

From the "blow by blow" link...
This is a crucial point: How many times have we heard ID critics (like Matzke) say things like "ID shouldn't be taken seriously because it doesn't present research at scientific conferences, or publish scientific papers." But then what happens when us ID proponents do exactly what they say we should do: We present research papers at a scientific conference at a top research university (Cornell) and then seek to have it published by a world-class scientific publisher (Springer)? Does Matzke applaud us for doing what he demanded? No. ID-critics like Matzke work hard to prevent its publication. This is sheer hypocrisy. But Matzke and his cohorts never had any intention of evaluating ID in a serious way, under any circumstances. This episode is a reminder that ID's most vehement critics were never interested in giving ID a fair hearing. Their purpose is, at any cost, to prevent ID from being recognized by anyone as possessing any scientific merit whatsoever. For them, this is not a scientific debate at all. It's an ideological power struggle -- one that, moreover, tells you something important about the would-be censors. No, they don't. People who are confident welcome challenges as opportunities to demonstrate the merit of their case and advance its standing in public opinion. Never forget the origins of Biological Information: New Perspectives. It is a story that reveals exactly what the Darwin lobby is about: its main strategy is viewpoint suppression, but note too the inner weakness and doubt that all its bluster tries to conceal. - See more at: http://www.evolutionnews.org/2013/08/censorship_lose075541.html#sthash.QVir9iI8.dpuf
Re: "Do people who are confident they are right normally behave like this?" No. Startled animals do, however. "Fight or flight" would also represent a plausible alternative explanation for the characteristic verbal and written outbursts that are invariably displayed as something other than Tourette's Syndrome. jstanley01

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