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

@SuperBigV

As you can see, I am highlighting one of the last paragraphs from the article you have submitted for discussion.

The problem with this topic is that it is probably one of the arguable topics one could have selected.

It would be like trying to disprove “string theory” in physics by starting with the question: could the universe really be made of strings?!?!?

We cannot simply the discussion by starting with the most dubiously complex of questions.

I would propose focusing on just two things:

  1. Can we rely on the YEC interpretation of Genesis if geologists can confidently and convincingly use multiple methods to show that the Earth is billions of years old… instead of 6000 years old?

and

  1. Even if we assume that dinosaurs were wiped out by the Great Flood, geologists can show that there were no large horses, or rhinos or elephants or whales (or any other large mammals) in existence until AFTER dinosaurs became extinct.

There is no YEC explanation for this reality.

Well, I have to say that I refute both because of a lack of grace and humility.
I am not going to lie, I also find Biologos proponents to be, at times, aggressive and overly sure of themselves. Yet at the same time, I find the creationists to be equally aggressive and sure of themselves.

I guess I will say it again. We are carbon based life forms, with five rather primitive senses, who are limited to three dimensions. I just think we need a bit more humility all around. I can only imagine Satan laughing at us as we tear one another down and waste our time in science smackdowns. How about we think about unity, humility, and the limits of our understanding? I am not “anything.” I am not YEC, I am not ID, I am not Biologos. All of the above or none of the above may be or may not be correct. Because I am trained in science, I have learned to be skeptical of everything, and to reject surety. I have lived long enough to see many things proven wrong. It isn’t really that long ago that Watson and Crick published the double helix paper. And now we are talking about the genetics of Adam and Eve? I’m sorry, I am just not feeling it. We don’t know. Anything is possible. I believe the Bible. The Bible is not a science textbook. I am not going to look down my nose at anyone for thinking differently from what I think. I am not pleased when Christians use up their precious time to denigrate the views of other Christians. Sorry, that wasn’t the answer you were looking for.

The Mendel’s Accountant program was discussed on Theology Web and on After the Bar Closes at Panda’s Thumb. I think this was around 2009. Here’s a link to the start of discussion from the Panda’s Thumb board. 2-3 people in that discussion dissected the code and analyzed whether the coding and assumptions made in the program were reasonable as there were several test cases where aberrant results were found. Some of the issues were traced to a ‘broken’ implementation of the fitness function. Then they created a more realistic version. Follow Zachriel’s commentary in that thread.

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Hi Amy,

Greetings in Christ.

I’m sorry you’ve found (some) proponents of EC to be so brash. I suppose every group has folks that give the rest a bad name.

I can only speak for myself but as an EC proponent my modest goal is to have a seat at the table alongside YECers without being told I’m a heretic, a sell-out, or not a real Christian. Unfortunately, while ECers rarely state that “you can’t be a strong, Bible-believing Christian and a YEC proponent,” the reverse is stated only far too often.

Many EC proponents, myself included, are passionate about this issue because we see that young educated folks are turned away from the beauty of our Lord because they were taught from a very young age that evolution and Christianity just don’t go together. So when they find out evolution is true, they figure, well, Christianity must not be. So do we think it’s important to lobby for a “bigger tent” with respect to this issue within Evangelicalism? You betcha. Because young souls are on the line.

And yes, that includes the Adam issue. I think few would say they know with 100% certainty that the human race didn’t descend from a single Adam and a single Eve, but most of us EC folks are busy trying to figure out what it would mean for us if science does continue to amass evidence in that direction. How can we all agree that we “believe the Bible,” as you so simply put it, while we explore the implications of all this? Unfortunately in the process of trying to make space for this sort of important theological reflection, we get called out for not just “believing the Bible” and for trying to sow disunity.

When you say “I am not going to look down my nose at anyone for thinking differently from what I think,” I’m not sure I believe you, to be honest. I know your comments are directed primarily at the original poster, but from where I sit, your comments come across as a bit patronizing to folks that believe as I do. There’s a reason we’re passionate about this issue, and (for many of us, at least) it’s not because we love to put on airs and tell everyone how backwards and stupid they are. It’s because we care about science-minded kids who believe in Jesus, and we’re tired of them being treated like second-class citizens in the Kingdom.

Respectfully,
your brother
AMW

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Did you get your question answered? If not, I might give it a shot…

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There are three questions we can ask about what genetic variation would look like if we come from a recent Adam and Eve: what is the total number of genetic variants present today, what is the distribution of their frequencies (e.g., take A/G variants – how often is the A seen in 50% of chromosomes vs. in 5% of chromosomes or 0.1%?), and what are the relative numbers of different kinds of mutation. As Carter notes, the first question turns out to be uninformative: If Adam and Eve were created with different genomes, there could have been any amount of variation already present in the first couple. The mutation model also cannot make a prediction without an independent estimate of the ancestral population size, and so this one is a wash.

When it comes to the third question, about the different kinds of mutations, Carter kind of waves his hands trying to make it go away. He does concede that transitions – which we know occur more often in mutations than transversions – make up the bulk of genetic variants in the human population. This certainly sounds like evidence that the variants are the product of mutation. Actually, the situation is worse for Carter’s model than he acknowledges. There are other ways of classifying mutations than transition vs transversion, and some of them have different mutation rates. In particular, the combination of bases ‘CG’ (that is, a C followed by a G on the chromosome) mutates like crazy, with the C usually mutating into a T. (The reason for this high mutation rate is well understood, by the way.) When we look at genetic variation in humans, we do indeed see a greatly increased rate of C/T variants in the human population when the C is followed by a G – once again what we would expect if all variation originally started out as mutations.

What is disturbing about Carter’s treatment of the question, though, is his logic: “This is not evidence against the creation model, however, as I do not believe the creation model makes any specific prediction about these ratios.” In short, he has the mutational model, which predicts very specific things about genetic variation, and the creation model, which predicts nothing. When we see the predictions come true, we are not allowed to conclude anything, though, because one of the models didn’t make a prediction. To this I can only say, “Huh?”

(On this last point, a parable: There was a town in which the police were trying to bring a criminal gang to justice. One evening, a man appeared at the police station and told detectives that he had inside information on the gang, and that he could supply it to the police in exchange for cash. “Prove it,” the detectives responded. So the man told them, “That murder last week – I know who did it. I don’t know his name, but he’s a left-handed man in his late forties, balding and with a beard and he’s got a tattoo of a star on his left bicep. Oh, and he speak Lithuanian.” Well, the next day the police happened to catch the murderer, and he did indeed turn out to be a star-tattooed left-handed Lithuanian etc. When the informant returned, though, the police told him this: “We have two theories. Theory 1 says you don’t have inside information, while theory 2 says you do. If theory 2 is correct, then your information about the murderer will be accurate. If theory 1 is correct, then we wouldn’t know anything about the murderer despite what you told us. Since theory 1 doesn’t make any predictions about the murderer, we have no way of judging whether you knew who he was or not.” And so the reign of terror continued.)

It is on the second question, though – the frequency distribution of genetic variants – that Carter really screws the pooch(*). There’s nothing obviously wrong with his simulation of what to expect from accumulated mutation: we really should find lots more rare variants than common ones. In an ideal, constant-sized population, in fact, the number we find would drop off as 1/f, where f is the frequency of the new, mutated variant (in technical language, of the “derived allele”). That is, if we find 1 variant occurs in 40% of the population, we would find 2 that occur in 20% of the population, 4 that occur in 10% of the population, 8 in 5% and so on, down to very low frequency variants, of which there will be very many.

Carter’s problem lies not in the simulation but in the data he is contrasting with it (see his Figure 2). What he is using is HapMap data for a European population; he finds that the distribution is nearly flat. There are two problems here. First, while humans as a whole haven’t been through a substantial population bottleneck in our recent genetic history, European populations have been through one or more, including a pretty tight one when humans left Africa before ending up in Europe. Bottlenecks have the effect of flattening out allele frequency distributions. So no fair comparing this to the simulattion.

More importantly, what he is plotting is not the frequency distribution of all variants in the European population. Instead, it is the frequencies of variants that the HapMap project chose to study. They chose the variants by identifying them in a small ascertainment sample (which greatly favors higher frequency variants) and selected them for being present in multiple populations (same effect). This guarantees major distortions to the frequency distribution. (This also means that the HapMap data were very hard to use for inferring population history or other population genetics purposes. I was part of the HapMap project when these decisions were being made, and the population geneticists were not happy.)

What he should be doing is looking at all variants found in a sample of an African population, which requires determining the full sequence of each individual. Fortunately, this has been done as part of the 1000 Genomes Project. I happen to have a spreadsheet with data from early in the project on my laptop. (Better data are probably available now, but this set is fine for this purpose.) Here’s the actual frequency distribution for the 1000 Genomes sample from the Yoruba, a West African population:

As you can see, the real distribution does indeed fall off quickly at higher frequencies – as we would expect if the human population had been large for a long time. (Note: the little sag at the very left of the plot is because the 1000 Genomes sequencing was not very good at finding really rare variants. The odd blip at the far right are variants where I have picked the wrong variant as the derived allele: they belong all the way on the left end instead. Their loss from that end also contributes to the flattening out there.)

In fact, we can see how similar the actual distribution is to that perfect, 1/f distribution for a constant-sized population I mentioned before. Dropping the first bin and the last two bins (for the reasons noted above), and fitting a simple power curve, I find this:

Instead of falling as 1/f, that is, f to the power -1, it falls slightly faster, as f to the power -1.078. Not bad at all, especially since there is no reason to thing the ancestral human population was actually constant in size.

In short, had Carter examined a suitable data set, he would have found that his model was completely untenable.

(*) Probably not suitable language for a 5 yo. Tough titty.

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I just gave it a go.

This is great. Can you show what the Adam/Even model predicts on the same graph? And make the data/code available? That is really helpful.

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@BradKramer, I’m trying to find that post where I can flag a contribution as worthy of being featured by you on the website, but I’m coming up empty. At any rate, this is golden*!

(*except for the bit about the pooch. :smiley: )

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To be honest, I’m a total newb. The more answers, the better

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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