Mendel's Accountant

ICR has just announced a new free tool called, “Mendel’s Accountant”.I plan on downloading it and trying it out.Larry Vardiman said,

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“Evolutionary genetic theory has a series of apparent "fatal flaws" that are well known to population geneticists, but that have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades--based upon logic and mathematical formulations. However, population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue.”

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Seeing that the program contains,

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data including: deleterious and beneficial mutation counts per individual

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and other types as output, I was wondering if the output to Mendel’s Accountant is intended to alleviate the flaws claimed for evolutionary theory.What I am wondering is, is if the new program will really help population genetics better divide environmental variance, but perhaps this is not what the flaws were seen to be.For me the complaint against Darwin has to be that he dismissed special creation so I am uncertain as to how this program really is to make changes in the way the concept of evolution itself has been thought.Any thoughts on this new work from Sanford, Baumgardner, Brewer, Gibson and ReMine?Can it be used to challenge Neo-Darwinism?Can it become useful for instance in developing Waddington’s critique of Neo-Darwinism??

Thread moved here from the Proposed New Topics forum.

The ICR claim ... Which makes me wonder how good their grasp of the concept of empirical evidence is. They may mean statistical empiricism if they based their parameters specifically on observed values of some particular population, otherwise I'm not sure how a computer simulation fits the bill.As is so often the case, a lot is going to depend on what numbers you plug into the simulation. The ICR argue ... As far as I can tell there is no way to know what parameters they did in fact use to reach this conclusion, or how realistic they were. I'm especially cautious as to what they consider biologically realistic or reasonable when they argue ... It might be an interesting tool to play with, it may well work perfectly well as a simulator of population genetics. However, I doubt that it can provide empirical proof of any flaw in evolutionary theory.As far as what flaws they are talking about, I think it is pretty clear from the article that it is another way of re-iterating Sanford's theories on 'Genetic Entropy' through the accumulation of deleterious mutations leading to continual reductions in fitness.Reading through the original paper on the software (Sanford et al., 2008) one point that strikes me is that they only use population sizes of 1000 in all of their examples. If the ICR claims are based on similarly small population numbers then it is not surprising that they saw mutational meltdown occurring. As I say the value of conclusions drawn from such software rests entirely on how well the parameters used actually correspond to the real world.TTFN,WKEdited by Wounded King, : Updated with comments on original paper.

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The ICR claim ...

Mendel's Accountant provides overwhelming empirical evidence that all of the "fatal flaws" inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified--with a degree of certainty that should satisfy any reasonable and open-minded person.

Which makes me wonder how good their grasp of the concept of empirical evidence is. They may mean statistical empiricism if they based their parameters specifically on observed values of some particular population, otherwise I'm not sure how a computer simulation fits the bill.

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It does seem odd to me that one might be able to find statistical empiricism of the program’s output adequate to conclude real “falsification" as there are different “philosophies” at interpreting probabilities (not only that but Kant differentiated "versimultude" and probability). If ”Mendel’ is for biology what the YECFlood model was for geology my guess would be that the claim of fitting a YEC system of thought replaces the discussion of Bayesian vs other probabilistic opinion views. But I will give them the benefit of the doubt for now.The algorithm(s) in the program seem to computationally inhibit the use of large structured populations, but because they do have island, one and two-way step models of migration already written in, it seems that different conclusions may be reached on suitable hardware and perhaps with some man-made changes to the source code added.In the PDFmanual they do say,

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“A planned future improvement is to allow a user-specified degree of dominance in the initial heterozygous alleles. This would allow more direct investigation of the role of dominance in the expression of heterosis and inbreeding depression”

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Aside from my own interest in sustaining a view point which deprecates a generalization of Fisher’s, I have not discounted that by using the program and possibly changing it in some ways, one might be able to help discuss Gould’s feeling that Mayr was wrong when he said that neutral changes (third position point mutations) would be energetically affecting changeable natural selection pressures.If the work of these computer program writers helps to discuss Gould’s and Provine’s assertion that the evolutionary synthesis was divided into two phases secondarily hardening around adaptationism then I think it could have claims of merit even if privately someone thinks the system supports a particular religious belief structure.This would mean there would have to be a consensus about what neo-Darwinism was vs the history of the evolutionary synthesis. There is not. Perhaps the program writers’ purpose is directed toward an obsolete goal. I don’t have an opinion on this yet.Later, I will write about Sanford's work beyond the simple issue of "primary axiom" we already started on EvC.Edited by Brad McFall, : missing word

It's a mathematical model based on assumptions. No mathematical model can challenge reality. If the model does not end up with realistic results it is the model and the assumptions that are at fault, not reality. Some of these are entered by the person operating the system but some are built in to the software.What it can do is test the validity of the assumptions used in running the model, by seeing how well they match real observations.As an interesting side note, not all of Mendel's data fit his strict hereditary predictions, but could only come close to those numbers. The reason for the deviations is mutations that occurred during the experiments. Geneticists have known this "fatal flaw" in Mendel's theory for years.Enjoy.Edited by RAZD, : .

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I asked

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Can it be used to challenge Neo-Darwinism?

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because the announcement contained:

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Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. At the 6th International Conference on Creationism in Pittsburgh on August 3-7, 2008, two papers will be presented on the results of tests that utilized numerical simulation of mutation and natural selection. They are entitled "Mendel's Accountant: A New Population Genetics Simulation Tool for Studying Mutation and Natural Selection" and "Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory." The primary authors of these two papers are Dr. John Baumgardner and Dr. John Sanford, respectively.

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You said,

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No mathematical model can challenge reality. If the model does not end up with realistic results it is the model and the assumptions that are at fault, not reality. Some of these are enteredby the person operating the system but some are built in to the software.

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But if one thinks about the difference WK made (message 3 above) possible, by the difference of/among and between, a and one makes a fine discrimination between referents for/to “neo-Darwinism” and evolution as a statistical phenomenon (as Wright for instance made divergent with Lamarkianism in his 30s paper rather than as one based on Gitt information notions or HootMan’s interest in entropy and molecular biology etc etc)then one need not decide necessarily, that the reality the flaws connote or confute is either the particular that Fisher doubted Mendel’s data nor the particular mutations that show Mendel might have fudged the stuff himself or simply got approximate rather than rational numbers.I am a long way from admitting that numerical simulation is the “tool” to help dissipate the supposed expert known “cloud” because the applied math may help to show what pure math may afford a more elegant devise to change minds with.Perhaps you did not mean to sufficiently hang the notion of mutational deviations as for denoting what the “flaw” is.I will try to do some digging in the creationist literature to see if the isn’t a more obvious reading. It is possible the focus for us will have to be on Mendel himself but this does not seem to me to be the targetable intention.I do know that Henry Morris wrote to me that neither mathematical manipulation nor simulation could prove creation any more than evolution. I had written to him to suggest that creationists ought attempt to ”predict’ morphological shaped gaps while I had suggested this in the context of interesting a mathematician at Cornell in helping me with affine transforms saying to Henry, that, these re-drawings I was suggesting where gaps were, was to have been thought from “a mathematical proof point of view” but by that I had merely meant, most reductionistically, that algebra was always submitted to ocular evidence.“Mendel” as a program is visible rather than merely conceptual and whether viewing output from it can change minds as to Neo-Darwinism seems possible to me if it is able to capture in our more modern distributed computer environment an agreement not possible with less use of simulations as has been our past time so far.I plan on working out my own position slowly and I hope you will continue to respond to this thread. I would hope that it will not require me to reflect back on what baraminology may be about after Mendel (either person or program). What will make the possible versimulte probable is if one can adequatly reinterpret what is going for "history" in biology. It would not be thought easy to be able to do this as it must be paid contingently as one goes etc.Here is the visible matter on the first page of from the Cornell Server: Edited by Brad McFall, : links added

There seem to be a few obvious flaws with the model used in Mendel's Accountant. To illustrate one that comes to mind, I'll outline a hypothetical system.Imagine a genome with two possible alleles for each variable gene. By "variable gene", here i mean any gene which can vary and not be fatal to the organism's development or reproduction. One allele is the "good" version and one is the "bad" version.If you start with the perfect "good" genome (111111...) then 100% of the mutations of variable genes will be bad, conversely if you have 100% of the "bad" alleles (00000....), then any non-fatal mutation will be good (flipping a 0 to a 1). If you are in the middle, then a good mutation will be as likely as a bad mutation (remember i'm talking only mutations which do not remove you from the gene pool). And that's before even adding any effect of natural selection.So, picking a completely good set of starting genomes will lead to a drop to the middle, and picking a completely "bad" starting genome will lead to a rise to the middle.The developers of Mendel's Accountant picked a huge genome size (3 billion in their screenshot), a small population size (1000) and do not run the simulation for long enough to see any stabilizing level of mutations (only 5000 generations). They also seem to assume a starting population with zero genetic variation, and then add "mutations" on the basis that beneficial mutations are much rarer than good mutations, but wouldn't a real starting population fall in the middle of the "allowed" varations within it's species? With the middle as the starting point good mutations would be as likely as bad. eg if a specific 'G' flipping to an 'A' was detrimental (but not fatal), then a subsequent flip of that 'A' to a 'G' would be beneficial by an equal amount, so in reality within the range of a species non-reproductively-fatal mutations, there'd be as many beneficial flips, inserts/deletes etc as harmful ones (because there's as many actions as there are reversals).The rarity of beneficial mutations is in reality because existing species are already near the top of their "range" of fitnesses. With almost all the best genes in your species range already, any mutation is likely to take you away from "perfection" (for your current environment), but mutations leave the gene pool at a steady rate due to chromosome recombination and also natural selection. Even without these two factors, the level of mutations will level out not drop forever.Edited by jasonlang, : No reason given.

There's been some discussion of this program at Theology Web and After the Bar Closes. It look as if Mendel's Accountant is not a realistic simulation of evolutionary processes. There's a group trying to understand better how it works and whether or not it's overly biased, perhaps leading to a talokorigins FAQ. See Evolutionary Computation and A chance for input ... Dr. John Sanford (starting near the bottom of the page).

Thanks for the links! I'm starting to read the "chance for input" one now. I'll just put down my last observtions here for now.Mendel to me seems to (deliberately or ignorantly) mix apple and oranges. it has 3 billion "genes" which i assume to represent the 3 billion or so base-pairs of the human genome (this is to maximize their plausible search space). Base-pairs have only 4 different expressions, ACGT, so only a finite amount of variation, (2 bits of data per base-pair). Mendel's Accountant seems to use a continuous random variance of "benefit", heavily scaled for negative benefit, and making no account of the fact that when one mutation occurs it can change the benefit/cost of many other mutations, even making mutations which were beneficial before harmful, or vice-versa.Like i said above, the good/bad balance of their program has to stabilize at some point ("good" mutations become more likely than "bad" mutations), but they refuse to run it for long enough to see this behavior develop. 5000 generations for humans is enough (750000-100000 years or so) they might say, otherwise where did the "balance" come from, but they assume a huge search space, small pop and time, and starting genomes not in equilibrium, even for their flawed model.The answer is that the population which modern humans developed was already at their "balanced" point, due to 100 of millions of years of continuous generations. Further mutations or environmental challenges change this balance point, hence pulling development in another direction.