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Zachriel

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Starting with an isogenic population distorts the initial behavior of the system. If you don't wait long enough, you will reach erroneous conclusions. Consider this example, defaults except numP = 1000 and favMuts = 0.0002.

We see our now well-expected decline. Continuing for 100 turns, we see a bit of an improvement, then stagnation.

Stagnation is good. Eventually, we'll see significant, favorable mutations. Here after 200 turns.

This is the same settings only favMuts = 0.0001 and a thousand turns.

It reaches a minimum of 0.12 after 51 turns, then rises to 0.64 after 135 turns. That's five times the minimum. It recrosses fitness of 1 at 402 turns before retreating a bit. Then takes off.

The key is that there has to be a certain amount of diversity in the population to enable the recombinatorial possibilities. If we just consider the fitness from it's minimum, then the closeup of the previous image looks quite different.

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Dr.GH

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So, how does Mendel's Accountant compare under the same conditions? Which variables control the difference in output?

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"Science is the horse that pulls the cart of philosophy."

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Zachriel

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 Quote (Dr.GH @ July 12 2009,16:40) So, how does Mendel's Accountant compare under the same conditions? Which variables control the difference in output?

Leaving aside their choice of defaults, Mendel's Accountant is seemingly broke due to a faulty calculation of "working fitness". The resulting fitness signal is very feeble. I'm not even sure why they decided on using the "divide by random" method, though it is a lot faster and somewhat easier to program than Roulette. Two consecutive posts from here:

http://www.antievolution.org/cgi-bin....y147439

DIFFERENCES between Gregor's Bookkeeper and Mendel's Accountant:

* Multiplicative fitness.
* Roulette Wheel mating, rather than the odd "divide by random" method.
* Can handle very large populations and generations—if you're willing to wait.
* Raised limit on the effect of favorable mutations. Adjusted some other settings.

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You never step on the same tard twiceâ€”for it's not the same tard and you're not the same person.

Dr.GH

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So, you have basically followed Wesley's suggestion of writing your own program.

I still see the same problem as I did before- how do you reply to the creationist challenge that YOU faked the result and not they?" This needs to be explained to someone with no programing experience, nor any sophistication in genetics.

Otherwise, Sanford et al will continue to promote their "refutation" of evolution with out any useful response.

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Zachriel

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Joined: Sep. 2006

 Quote (Dr.GH @ July 12 2009,17:44) So, you have basically followed Wesley's suggestion of writing your own program.I still see the same problem as I did before- how do you reply to the creationist challenge that YOU faked the result and not they?" This needs to be explained to someone with no programing experience, nor any sophistication in genetics.Otherwise, Sanford et al will continue to promote their "refutation" of evolution with out any useful response.

Mendel's Accountant should have replicable results. Gregor's Bookkeeper is relatively simple and open source. That Gregor's Bookkeeper differs should indicate a problem with one or the other. By pointing to a single line of code that apparently breaks Mendel's Accountant, that should satisfy most with open minds.

work_fitness(i) = work_fitness(i)/(randomnum(1) + 1.d-15)

Most IDers, though, wallow in fallacies  (of categorization, of argument, of the scientific method; liberally sprinkled with equivocations), so there is rarely a way to convince them.

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You never step on the same tard twiceâ€”for it's not the same tard and you're not the same person.

Zachriel

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Joined: Sep. 2006

 Quote (Zachriel @ July 13 2009,07:16) work_fitness(i) = work_fitness(i)/(randomnum(1) + 1.d-15)

Even if someone were to justify this line of code, it would merely demonstrate the somewhat arbitrary nature of such models. Why ÷Rnd^1? Why not ÷Rnd^½ or ÷Rnd^¾? These models still need to be compared to real biological systems. Any strong conclusion that they debunk evolution is not supported.

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You never step on the same tard twiceâ€”for it's not the same tard and you're not the same person.

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The press releases for the Lenski experiment assert that the E.coli populations underwent every possible mutation during the course of the experiment. I fail to see how this kind of scenario could lead to extinction.

Except, as noted, in a very small population. But we already know from field observations that population declines can result in extinction. But after mass extinction events, there are always fast breeders of some kind lurking in the wings. Fast breeders never seem to melt down.

Am I wrong?

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

keiths

Posts: 2195
Joined: Jan. 2006

Quote (Zachriel @ July 13 2009,05:16)
 Quote (Dr.GH @ July 12 2009,17:44) So, you have basically followed Wesley's suggestion of writing your own program.I still see the same problem as I did before- how do you reply to the creationist challenge that YOU faked the result and not they?" This needs to be explained to someone with no programing experience, nor any sophistication in genetics.Otherwise, Sanford et al will continue to promote their "refutation" of evolution with out any useful response.

Mendel's Accountant should have replicable results. Gregor's Bookkeeper is relatively simple and open source. That Gregor's Bookkeeper differs should indicate a problem with one or the other. By pointing to a single line of code that apparently breaks Mendel's Accountant, that should satisfy most with open minds.

work_fitness(i) = work_fitness(i)/(randomnum(1) + 1.d-15)

Most IDers, though, wallow in fallacies  (of categorization, of argument, of the scientific method; liberally sprinkled with equivocations), so there is rarely a way to convince them.

I haven't been following this thread closely, but if that single line of code is the culprit, it seems that you could make a devastating case by:

1. Compiling Mendel's Accountant as is.
2. Running it on a small but interesting suite of test cases.
3. Changing that line of code and recompiling.
4. Running the same suite of test cases.

By doing so, you would prove:

1. That you haven't faked your results.  Anyone could reproduce them by changing just that one line of code in MA.
2. That MA depends crucially on that line of code.

Anyone (including non-programmers) should be able to see the force of this demonstration.

All that would be left for Sanford et al would be to attempt to justify their version of that single line of code against yours.

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And the set of natural numbers is also the set that starts at 0 and goes to the largest number. -- Joe G

Please stop putting words into my mouth that don't belong there and thoughts into my mind that don't belong there. -- KF

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My reading is that the one line of code would be replaced by a function

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Richardthughes

Posts: 11175
Joined: Jan. 2006

Would this be useful in teaching about GAs?

http://www.mathsisfun.com/games/mastermind-game.html

Watch out for the quasi latching.

I like the fitness function part, but sadly no RM - It's directed.

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keiths

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 Quote (midwifetoad @ July 13 2009,09:47) My reading is that the one line of code would be replaced by a function

The point is the same either way.  If you publicly specify a small set of changes to the MA code, justify those changes, and demonstrate that MA produces radically different outcomes when those changes are implemented, then you have made a persuasive case against Sanford et al while at the same time proving that you have not rigged the code to get a desired outcome.

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And the set of natural numbers is also the set that starts at 0 and goes to the largest number. -- Joe G

Please stop putting words into my mouth that don't belong there and thoughts into my mind that don't belong there. -- KF

Posts: 4003
Joined: Mar. 2008

I'm not disagreeing, but perhaps the MA programmers chose a method because it was easier to program.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Zachriel

Posts: 2717
Joined: Sep. 2006

Discovered that that Gregor's Bookkeeper is implementing genetic dominance consistent with Mendel's Accountant.

c...     We assume deleterious alleles behave in a recessive manner
c...     and when heterozygous have an effect given by the allele
c...     fitness effect multiplied by recessive_hetero_expression.
c...     Similarly, we assume favorable alleles behave in a dominant
c...     manner and when heterozygous have an effect given by the
c...     allele fitness effect times dominant_hetero_expression.  The
c...     full allele fitness effect is realized only when the same
c...     version of the allele occurs on both instances of its linkage
c...     block, that is, is homozygous.

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You never step on the same tard twiceâ€”for it's not the same tard and you're not the same person.

Dr.GH

Posts: 2279
Joined: May 2002

Quote (keiths @ July 13 2009,09:34)
Quote (Zachriel @ July 13 2009,05:16)
 Quote (Dr.GH @ July 12 2009,17:44) So, you have basically followed Wesley's suggestion of writing your own program.I still see the same problem as I did before- how do you reply to the creationist challenge that YOU faked the result and not they?" This needs to be explained to someone with no programing experience, nor any sophistication in genetics.Otherwise, Sanford et al will continue to promote their "refutation" of evolution with out any useful response.

Mendel's Accountant should have replicable results. Gregor's Bookkeeper is relatively simple and open source. That Gregor's Bookkeeper differs should indicate a problem with one or the other. By pointing to a single line of code that apparently breaks Mendel's Accountant, that should satisfy most with open minds.

work_fitness(i) = work_fitness(i)/(randomnum(1) + 1.d-15)

Most IDers, though, wallow in fallacies  (of categorization, of argument, of the scientific method; liberally sprinkled with equivocations), so there is rarely a way to convince them.

I haven't been following this thread closely, but if that single line of code is the culprit, it seems that you could make a devastating case by:

1. Compiling Mendel's Accountant as is.
2. Running it on a small but interesting suite of test cases.
3. Changing that line of code and recompiling.
4. Running the same suite of test cases.

By doing so, you would prove:

1. That you haven't faked your results.  Anyone could reproduce them by changing just that one line of code in MA.
2. That MA depends crucially on that line of code.

Anyone (including non-programmers) should be able to see the force of this demonstration.

All that would be left for Sanford et al would be to attempt to justify their version of that single line of code against yours.

I am hoping Zac thinks this two, because that would make me three!

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Henry J

Posts: 5537
Joined: Mar. 2005

Quote
Zachriel, posted 7/13/09 5:48 PM
Discovered that that Gregor's Bookkeeper is implementing genetic dominance consistent with Mendel's Accountant.

 Quote We assume deleterious alleles behave in a recessive manner [...]

Why would that be an assumption? I'd expect that a dominant deleterious allele would be selected against, but that should be a direct consequence of the logic, no additional assumption needed.

Similarly, I see nothing to prevent a recessive advantageous allele, except that it wouldn't be spread by selection unless already in a large enough fraction of the population (unless its only partially recessive).

Henry

Zachriel

Posts: 2717
Joined: Sep. 2006

Quote (Henry J @ July 13 2009,22:08)

Quote
Zachriel, posted 7/13/09 5:48 PM
Discovered that that Gregor's Bookkeeper is implementing genetic dominance consistent with Mendel's Accountant.

 Quote We assume deleterious alleles behave in a recessive manner [...]

Why would that be an assumption? I'd expect that a dominant deleterious allele would be selected against, but that should be a direct consequence of the logic, no additional assumption needed.

Similarly, I see nothing to prevent a recessive advantageous allele, except that it wouldn't be spread by selection unless already in a large enough fraction of the population (unless its only partially recessive).

Henry

Some deleterious mutations are dominant. More commonly, you have a pair of alleles that perform some function. If one becomes defective or just less than optimized, as long as the other functions properly, it can pick up the slack, hence dominant. But your point is well-taken. That's why I haven't been happy with the feature, and have it turned off by default (Dominant = 50%).

One alternative is just to have allele-zero be dominant by default. Or a sliding scale. The "natural" alternative is having a variety of different types of allele relationships. That may be beyond what we need here to verify Mendel's claim to have "debunked" evolution.

 Quote (keiths @ July 13 2009,11:34) All that would be left for Sanford et al would be to attempt to justify their version of that single line of code against yours.

They need to do that regardless of any independent implementation.

Mendels' Accountant takes genetic fitness, then adds noise resulting in phenotypic fitness. Then divides this by random to produce "working fitness" before truncating. Presumably, this represents the effect of chance on mating success. As shown previously, it cripples the fitness signal and results in a ranking very close to random. An explanation from Mendel's creators would be helpful.

There are many such arbitrary assumptions built into Mendel. That's why I gave up on a direct parallel. It would help if the code was built modularly so that it was easier to read and reconstruct. This is Gregor's basic algorithm.

For T = 1 To numT
Mutate
GeneticFitness
PhyloFitness
Selection
Stats
Roulette
Extinction?
Next T

Mendel's ÷Rnd seems to replace Gregor's Roulette.

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You never step on the same tard twiceâ€”for it's not the same tard and you're not the same person.

dvunkannon

Posts: 1377
Joined: June 2008

KF is hoist on his own FCSI
 Quote 102Nakashima07/16/20097:13 amMr KairosFocus,For practical purposes, once an aspect of a system, process or object of interest has at least 500 – 1,000 bits or the equivalent of information storing capacity, and uses that capacity to specify a function that can be disrupted by moderate perturbations, then it manifests FSCI, thus CSI. So if I write a GA system where the population members are competitors in an iterated prisoners dilemma with competitions running up to 1000 iteratioins, then you are satisfied that FSCI is being created by the GA? Each member is 1000 bits long, each bit stands for the action to take (cooperate=1, defect=0) in the current iteration. Fitness is the score of the individual at the end of an iterated competition with another member of the population.

Granted, that is a crappy way to write an IPD system, but it makes the case.

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

oldmanintheskydidntdoit

Posts: 4999
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Quote (dvunkannon @ July 16 2009,07:27)
KF is hoist on his own FCSI

 Quote 102Nakashima07/16/20097:13 amMr KairosFocus,For practical purposes, once an aspect of a system, process or object of interest has at least 500 – 1,000 bits or the equivalent of information storing capacity, and uses that capacity to specify a function that can be disrupted by moderate perturbations, then it manifests FSCI, thus CSI. So if I write a GA system where the population members are competitors in an iterated prisoners dilemma with competitions running up to 1000 iteratioins, then you are satisfied that FSCI is being created by the GA? Each member is 1000 bits long, each bit stands for the action to take (cooperate=1, defect=0) in the current iteration. Fitness is the score of the individual at the end of an iterated competition with another member of the population.

Granted, that is a crappy way to write an IPD system, but it makes the case.

He came back with "yeah, but the program itself was written by a intelligent designer therefore ID!"

Pathetic.

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I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
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if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
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dvunkannon

Posts: 1377
Joined: June 2008

Quote (oldmanintheskydidntdoit @ July 16 2009,11:47)
Quote (dvunkannon @ July 16 2009,07:27)
KF is hoist on his own FCSI

 Quote 102Nakashima07/16/20097:13 amMr KairosFocus,For practical purposes, once an aspect of a system, process or object of interest has at least 500 – 1,000 bits or the equivalent of information storing capacity, and uses that capacity to specify a function that can be disrupted by moderate perturbations, then it manifests FSCI, thus CSI. So if I write a GA system where the population members are competitors in an iterated prisoners dilemma with competitions running up to 1000 iteratioins, then you are satisfied that FSCI is being created by the GA? Each member is 1000 bits long, each bit stands for the action to take (cooperate=1, defect=0) in the current iteration. Fitness is the score of the individual at the end of an iterated competition with another member of the population.

Granted, that is a crappy way to write an IPD system, but it makes the case.

He came back with "yeah, but the program itself was written by a intelligent designer therefore ID!"

Pathetic.

Which reply was duly anticipated by Nakashima! Now he is pushed into agreeing with GilD. You can tell KF is out of his comfort zone because his follow-up reply is short. As soon as he figures out how to fit this question into his system, he'll be back to multipoint posts.

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

keiths

Posts: 2195
Joined: Jan. 2006

Quote (dvunkannon @ July 16 2009,09:42)
Quote (oldmanintheskydidntdoit @ July 16 2009,11:47)
Quote (dvunkannon @ July 16 2009,07:27)
KF is hoist on his own FCSI
 Quote 102Nakashima07/16/20097:13 amMr KairosFocus,For practical purposes, once an aspect of a system, process or object of interest has at least 500 – 1,000 bits or the equivalent of information storing capacity, and uses that capacity to specify a function that can be disrupted by moderate perturbations, then it manifests FSCI, thus CSI. So if I write a GA system where the population members are competitors in an iterated prisoners dilemma with competitions running up to 1000 iteratioins, then you are satisfied that FSCI is being created by the GA? Each member is 1000 bits long, each bit stands for the action to take (cooperate=1, defect=0) in the current iteration. Fitness is the score of the individual at the end of an iterated competition with another member of the population.

Granted, that is a crappy way to write an IPD system, but it makes the case.

He came back with "yeah, but the program itself was written by a intelligent designer therefore ID!"

Pathetic.

Which reply was duly anticipated by Nakashima! Now he is pushed into agreeing with GilD. You can tell KF is out of his comfort zone because his follow-up reply is short. As soon as he figures out how to fit this question into his system, he'll be back to multipoint posts.

Here's a link to the exchange.

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And the set of natural numbers is also the set that starts at 0 and goes to the largest number. -- Joe G

Please stop putting words into my mouth that don't belong there and thoughts into my mind that don't belong there. -- KF

dvunkannon

Posts: 1377
Joined: June 2008

Quote (dvunkannon @ July 16 2009,08:27)
KF is hoist on his own FCSI
 Quote 102Nakashima07/16/20097:13 amMr KairosFocus,For practical purposes, once an aspect of a system, process or object of interest has at least 500 – 1,000 bits or the equivalent of information storing capacity, and uses that capacity to specify a function that can be disrupted by moderate perturbations, then it manifests FSCI, thus CSI. So if I write a GA system where the population members are competitors in an iterated prisoners dilemma with competitions running up to 1000 iteratioins, then you are satisfied that FSCI is being created by the GA? Each member is 1000 bits long, each bit stands for the action to take (cooperate=1, defect=0) in the current iteration. Fitness is the score of the individual at the end of an iterated competition with another member of the population.

Granted, that is a crappy way to write an IPD system, but it makes the case.

Just for giggles, I tried to think through what kind of solution this GA would find. Each iteration is actually independent, there is no use of memory. The population should have 50% of each of Cooperate and Defect at each locus. That should be enough to sweep towards Cooperate at every locus.

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

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 Quote In abiogenesis, there is no fitness function, there are only reaction rates and products. The ‘fitness’ of a molecule depends entirely on its enviroment, which is why a GA like the IPD scenario I proposed is closer to that reality than silly Weasel style functions.

Regardless of how complex or "realistic" the fitness function, it all boils down to its effect on the probability of reproduction.

Rather than saying there is no fitness function, it might be better to say that it is difficult to construct a function that is equivalent to chemistry, or to an ecosystem.

http://www.uncommondescent.com/intelli....-327292

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Henry J

Posts: 5537
Joined: Mar. 2005

 Quote (midwifetoad @ July 22 2009,10:05) Rather than saying there is no fitness function, it might be better to say that it is difficult to construct a function that is equivalent to chemistry, or to an ecosystem.

Yeah, when the ecosystem includes thousands of other species* that are also evolving (and changing their population sizes) all at the same time, that does "slightly" increase the number of variables the program would have to keep track of.

*Some of which are trying to eat the subject of the experiment (and each other as well), and some of which are trying to avoid being eaten by that subject (and each other).

Henry

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Joined: Mar. 2008

Well you could try coating the computer with honey and running your sim near an ant bed.

Alternatively, I hear Squirrels are fond of wire insulation.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

dvunkannon

Posts: 1377
Joined: June 2008

Nakashima whips it out.

 Quote 246Nakashima07/23/200912:45 pmPopSize = 1000IndSize = 1000MaxTime = 1000mutationRate = 0.05allocate Pop[PopSize, IndSize], Fitness[PopSize]for i = 1, PopSizefor j = 1, IndSizePop[i, j] = rnd(0, 1)next jFitness[i] = evaluate(Pop[i, *])next iallocate NewInd[1, IndSize]for t = 1, MaxTime * PopSizefor j = 1, IndSizep1 = rnd(1, PopSize)p2 = rdn(1, PopSize)if Fitness[p1] > Fitness[p2]then newBit = Pop[p1, j]else newBit = Pop[p2, j]if rnd(0,1) < mutationRatethen newBit = not(newBit)NewInd[1, j] = newBitnext jp3 = rnd(1, PopSize)Pop[ p3, *] = NewInd[1, *]Fitness[p3] = evaluate(Pop[p3, *])next tevaluate( Ind ){}

Not the best code in the world, but ok for lunch time.

 Quote 252Nakashima07/23/20099:39 pmMr Jerry,I did not know that God was writing comments on this site. Did He also write the code that Nakashima gave us.While I think you are expressing it somewhat jokingly, this question of where to assign credit (or blame) for FSCI is key. Do we give credit to the first cause or to the last cause? If the first cause, then I understand naming God as the author of the FSCI. If the last cause, then the GA itself is the author of the FSCI, not of itself, but of the Pop data array inside it. (Note that the bits in Pop come from the random function or copied from other places in Pop. The ultimate source of every bit in Pop is random.

I will be interested to see how the UD crowd react to that last observation.

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

Zachriel

Posts: 2717
Joined: Sep. 2006

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You never step on the same tard twiceâ€”for it's not the same tard and you're not the same person.

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Between you folks and the people at Theology Web, I think you've scared off Sanford completely.

I salute you.

I'm impressed at the speed that "Mendel's Accountant" got dismembered and turned into pea-potting soil.

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AtBC Award for Thoroughness in the Face of Creationism

Dr.GH

Posts: 2279
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 Quote (deadman_932 @ July 24 2009,06:21) Between you folks and the people at Theology Web, I think you've scared off Sanford completely. I salute you. I'm impressed at the speed that "Mendel's Accountant" got dismembered and turned into pea-potting soil.

I agree, congratulations. What has yet to be done is to produce a coherent reply for general readers to the claim that, “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.”

Larry Vardiman
2008. “The "Fatal Flaws" of Darwinian Theory” Acts & Facts. 37 (7): 6. Institute of Creation Research
http://www.icr.org/article/fatal-flaws-darwinian-theory/

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

JonF

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I agree. While I don't know of anyting I can do to help, I think that a general-audience explanation is important.

I can does HTML ...

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The broad form that a reply to Sanford should take -- to give the fullest possible refutation of Sanford -- would be to eventually demonstrate how Mendel's Accountant is a deceptive product of Sanford's overall views.

Because Sanford believes that all life on Earth is between 5,000-100,000 years old, Mendel's Accountant essentially cooks the books to arrive at output which is intended to bolster Sanford's claims set out in his book "Genetic Entropy and the Mystery of the Genome."

I think everyone here is aware of that. Mendel's Accountant and Sanford's "Genetic Entropy" book go hand-in-hand

Over at TalkRational, Febble, Vox Rat and others are going through Sanford's book. This can be useful in the future. See here,  here and here keeping in mind that the last two are currently less useful because the discussion really hasn't begun yet -- due to "AF Dave" serving as a foil for Febble. He's really putting off any in-depth discussion because (1) he's an idiot and (2) he's doing what he usually does; use a discussion for propaganda purposes rather than anything difficult like, y'know...learning. Then there's the good discussion at Theology Web. I'll look around and see what else I can find at other BB's

Anyway, all of this has to be brought together at some point to show the pattern of pseudoscience and deception inherent in Sanford's efforts. It's a largish task, but manageable when broken down into parts.

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AtBC Award for Thoroughness in the Face of Creationism

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