Can someone explain like I'm 5 yo, what's wrong with this refutation of Biologos?

I should be able to, with a large caveat: when I have time. I’ll have to rework an existing forward simulator, modeling Adam and Eve not being one of my usual research areas. I’ll see if I can get to it.

Oh, c’mon. That was the best part.

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The problem, is that there are Creatinist PHD’s, such as Dr Georgia Purdom, Answers in Genesis, who holds to a Biblical view. My young earth Creatinist family thinks that they have a reason to reject biologos because of Georgia Purdom and similar scientists.

@SuperBigV

I was checking out some of Dr. Purdom’s research. I found this to be a good benchmark of for just about any ID researcher!:

[A] "Concerning natural selection, Purdom’s argument is that, while it does occur and causes changes in organisms, natural selection always results in a loss of information, not the addition of new information. "

**Has Dr. P ever worked with random numbers? If it wasn’t for the random number generator, some problems could never be solved. When reptiles with legs lost their legs in a crowded terrain … was that a loss of information? We could say so … but the snake is still in an evolutionary process! **

**And when a terrestrial mammal starts hunting fish in the water, and exchanges its limbs (that allowed it to run 25 mph) for fins (which can’t run 25 mph on land) allowing this land animal to return to the primordial waters - - is that a loss of information? Does it matter if the whale is still in the process of evolution? **

Semantically speaking, doesn’t Any change mean something is lost? When humans gained our vertical stance . . . we also lost our more robust spinal column - - and we have the back aches to show for it!

[B] “On the subject of Intelligent Design, Purdom believes that the movement has many good points, but she has a problem with the fact, while it insists there must be a designer, it does not identify the designer.”

Dr. P. seems to be playing along with the ID folks here. She argues that they are doing the wrong thing … when politically their position is exactly the one to try to disarm the public!

[C] "In an article on the subject, Purdom says, “…the major problem with the ID movement is a divorce of the Creator from creation. The Creator and His creation cannot be separated; they reflect on each other. In today’s culture, many are attracted to the ID movement because they can decide for themselves who the creator is—a Great Spirit, Brahman, Allah, God, etc.” "

^^^ This is the silliest thing I’ve ever heard anyone say about Intelligent Design…

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I am a theistic evolutionist, and part of the BioLogos Voices program. So I am going to do something surprising here. I am going to explain why the referent article by Dr. Carter (http://creation.com/historical-adam-biologos) is actually correct on several important points. This does not mean he is right on everything, but he is right on quite a bit.

  1. He is right to protest that science cannot rule out an idea it has not tested. This is completely correct. Scientists never considered the model he proposed, and so it cannot rightly claim to rule it out. This is the same argument I make when I say the science cannot rightly claim to rule God out, because it never actually considers the possibility. He is right, and I agree with everything but the italics portion…

Needless to say, I take great exception to the dogmatism of the BioLogos spokespeople. I do not believe the data support their conclusions and I believe it is entirely unfair to exclude the creation model without ever considering what the implications of the model would be (in scientific terms, they failed to propose a null hypothesis that could be ruled out by the evidence).

  1. I think he is right to complain about Collin’s and @DennisVenema’s statements about variation and Adam and Eve. As well intentioned as they are, I do not think science can claim to rule out something it never considered. That being said, I do not think it correct to claim that this is the official BioLogos position. BioLogos itself does not stake out a position on Adam and Eve (@jpm and @BradKramer please comment here).

  2. I entirely support his effort to build a testable model that determine if his theory matches the data. I will more creationists and ID people would do just this. Even if he is wrong, I enthusiastically welcome work like this. We can all learn from it, whether it ultimately does or does not pan out. People who do this should not be demeaned for their efforts. I really appreciate he is doing more trying to “poke holes” in evolution, but is building a quantitative model of his own. That doesn’t necessarily make him right, but this is certainly respectable. In fact, I would even argue that careful studies like this should be published in the mainstream scientific literature.

  3. I think @glipsnort’s analysis is interesting and it does explain the problem that Carter points to with the HapMap data being too flat (Figure 2). In defense of Carter, that is a very subtle error that takes very special knowledge to detect (and I’m not even sure if 1000 Genome data was out). Even if Carter is wrong here (which it looks like he is) I think this looks like an honest error, and not anything like the distortions (rightly or wrongly) some of us have come to expect. If Carter can revise his assessment of the data, I would be doubly impressed.

  4. I am also appreciate that he honestly explain that there is no reason that the creation model would prefer a specific distribution of nucleotide specific variation. I totally respect that more than silly confabulations that might have tempted others. I think he also makes a fair counter point to @glipsnort in saying that the data shows a bottleneck, even though evolution does not require this, but their creation model (because of Adam/Even and Noah) requires it. So there is some symmetry on this point. The key way to resolve this is to exhaustively list all patterns we see in the data, and catagorize them along several dimensions (a) consistency with evolution or YEC, (b) predicted by evolution or YEC, © unknown how to make consistent with evolution or YEC. Of course, there are several patterns I thinking of here, and I believe that in the genetic data evolution would win in spades, but I do not think that has been done yet.

So what do I disagree with?

  1. He seems to think that @DennisVenema and Collins’ speaks for all of BioLogos on these points. They don’t. I, for one, am a theistic evolutionist (evolutionary creationist) that beleives in a historical adam and eve. So does John Walton too.

  2. He thinks he has shown clear evidence against evolution. This is not the case. The more interesting thing he is doing is actually building a compelling quantitative creation model.

  3. He faults us all for not considering his model, but has it ever been published before? I think the real problem is that this type of work is not being done enough. I would welcome more of it, and even wish him success in his efforts. Don’t fault us, however, for not evaluating a model we have not been presented with.

  4. Even if his model is correct, because it directly invokes God I do not think it is part of mainstream science. This doesn’t make it false though. It could be true, and science could be wrong.

So there you have. I just defended a YEC. =)

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@Eddie

Yes… that would be fine… if I could even take more than one ID proponent seriously. I find it a much more efficient use of my time to let someone else (like you?) tell me how these anecdotes, or my interpretation of them, are wrong.

Have at it, dear sir.

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I have read papers that model genetic variation based on ToE, stochastic modelling based on an initial pair with historic populations growth and migration patterns, and now thanks to the mention by Joshua, the model proposed by Dr Carter. I have previously noted that models may be used to account for various data bases, but in themselves are based on assumptions that, by the nature of the exercise, may not be subject to rigorous testing.

I welcome the fact that people are willing to discuss strengths and weaknesses in modelling approaches - in a semi-humorous approach, I may mention a very complicated model (chemical kinetics) that I and my group developed over more than 5 years. One portion of the model required treatment that could involve 3-, or 4-body gas phase reactions. It is beyond our capabilities to deal with such chemistry, especially within the constraints and limitations of our software and hardware at that time. Yet I had a great deal of data, which preceded the particular chemistry, and also after the chemistry (products). To cut a very long story short, I found that I could reproduce the products formation using the data available, by using (what amounts to theoretically) a “made up” chemical scheme. The simulation proved extremely useful, but I made it very clear that portions had no valid theoretical basis - it simply accounted for data available at that time.

The lesson from my experience is straightforward - computer models are based on assumptions and theoretical considerations, but ultimately, they are meant to account for available data. In themselves, they can easily consist of a mixture of what is known, and what may need to be "made up’. Scientists accept this ONLY WHEN it is clearly stated, and the areas in question are identified and discussed fully.

IMO it is unwise for Christians to change theology because people have made some models.

This is not strictly true. While no scientist is likely to have considered a creationist model as part of their professional work, I’ve certainly spent some time trying to come up with scenarios that would be consistent with both a recent Adam and Eve and human genetic variation. That includes the basic idea he presented in his article, which is having a lot of genetic variation built into the first couple. (The allele frequency distribution can actually be dealt with, I believe, if you allow arbitrary changes to the mutation rate over time. That in turn raises a new set of problems.)

I do applaud the effort to come up with a quantitative model, though.

Here I’m a little less sympathetic than @Swamidass. The details of the HapMap ascertainment scheme were indeed complex, not well advertised and pretty much impossible to model. On the other hand, the mere fact that it was genotype data rather than sequence data would immediately tell any population geneticist that you shouldn’t be trying to naively read off the frequency distribution from the data. Not knowing that fact doesn’t make Carter a bad person, but it does mean he shouldn’t be doing this kind of analysis without getting help from those with more experience in the field. There’s just too much background knowledge that goes into scientific studies.

I have noticed a tendency for creationists to ignore that kind of knowledge, and often to assume mainstream scientists are basically stupid. It can be a little annoying. Not that they’re alone in that regard. . .

http://imgs.xkcd.com/comics/physicists.png

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Does that caution apply to heliocentric models as well?

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@Swamidass @glipsnort

Hi Steve and Josh,

It’s been a while since I’ve read that article, and time does not permit me to do so again at the moment, but how does Carter hypothesize that Adam and Eve carried this vast excess of variation? Presumably he thinks they were 2n (i.e. diploid), and that means a max of two alleles per locus each, to a maximum of 4 alleles in the population for any given locus. It also means a max of four haplotypes for any given combination of alleles. Anything beyond this would arise from mutation and recombination, and then he would have to account for that within his timeframe to explain current diversity at both the allele and haplotype levels. No, one cannot rule out miraculous rates of mutation and recombination within 4000-odd years, but then neither can one formally rule out miraculous radioisotope decay to match YEC expectations.

Or does he think Adam and Eve were polyploid? Again, I haven’t looked at his paper in a few years.

@Eddie,

If you don’t care enough to prove me wrong … then you just don’t care enough.

Leave people alone, ok? I’m a people.

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I was independently talking to John Sanford about some of this (who is smart and thoughtful, even if we might disagree with him. I think this model says that there was initially 4 separate alleles, but each allele has several different mutations in it. Recombination of these alleles (even without new point mutation) in this model elaborates many many more alleles in the children.

My instinct tells me…

  1. This could work with biologically realistic mutation rates for genomic data, but its the recombination rate need to be very different than we currently think in evolutionary theory. Now, I am not sure about this, and its not clear in the blog post, but I think they have to use higher recombination rates than currently imagined to get this to work. Of course, this is instinct talking, and I could be totally wrong. That, again, is the value of getting this stuff published. We can get it fixed, down on paper, and move from there.

  2. If this model requires a very different recombination rate, it could make an interesting prediction. @glipsnort (who works at the Broad) can correct me here, but this might fall into a technical blindspot of current sequencing methods. Right now, we are getting tones of new data about the prevalence of point mutations, but many (most?) sequencing methods have difficulty detecting recombination (because of challenges in detecting phasing and because parent/child triads are not usually sequencec). It is possible the data is out there to distinguish the two predictions, but I am not sure (and of course my bets are on evolution at the moment).

  3. This model would probably not work for mitochodria (or Y chromosomes?), even it works well for genomic data, because it relies heavily on recombination which is not a capability of mitochondria. Once again @glipsnort can comment, but I there is probably data here that catalogues mitochondria variants. How would themodel handle that? I do not know. I am still curious what they can come up with.

  4. Another place where they might be able to descriminate is that the difference in X, Y, and mitochondria recombination should produce a marked signature in the variation of these regions. That could help determine how much of the variation is recombination (even if the rates were different in the past) and how much would have to be new mutations.

  5. I think the final place where I’d like to see this model checked out is in how it fits Neanderthal and Denisovan sequences into the picture. These are all supposed to be members of the “human” group in YEC models, so how do they account for the variation they see there that is not seeing in any modern humans? Perhaps that is bottleneck predicted, but I’d like to see some real numbers behind this about (for, example) the percentage of variants expected to be neanderthal unique under this model.

Now this is all my instinct. I’m a computational biologist, not a population geneticist, so I do not ferociously defend any of these points. I could be wrong. This is just my informed instinct.

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The recombination issue is actually, in my opinion, worse than the mutation issue. Especially if you’re talking about recombining point mutations within genes (!). Their model only allows for about 200 human generations, total. That number does not allow for the needed recombination - not even close.

You very well may be right. I think you are.

It would be good to see explicit evidence of this in their modeling, and to compare it directly with measured data. I think that is the best argument against it. IMHO

Can you explain why you think it is a worse issue than the mutations? These seem pretty equivalent to me.

I’d need to actually think about it a bit more, but the general idea is that the main driver of variation in populations is not de novo mutations, but recombination of standing variation. Some of the best evidence for large ancestral population sizes in humans is based on paired SNP haplotype distributions - i.e. not raw allele counts at a given locus, but the number of combinations of those alleles in haplotypes in populations. Even if you assume miraculous mutation rates, you’d have to assume even more miraculous recombination events to get all that variation within 200 generations.

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Also, I would say that these types of experiments do allow for very small bottlenecks as a (null?) hypothesis. So, contra Carter, “evolutionists” have tested his ideas, and found them not to be consistent with what we observe.