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


(Vlad K. I'm an Agnostic Atheist) #1

http://creation.com/historical-adam-biologos

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). I have written about the predictions of a straightforward biblical model several times, including my articles on Adam, Eve, and Noah vs. Modern Genetics, The Neutral Model of Evolution and Recent African Origins, and Does Genetics Point to a Single Primal Couple?

There are two issues at hand. The first is their a priori exclusion of the biblical model from any and all consideration—following ardent atheists like Richard Lewontin. The second is their appeal to mutation as the sole source of genetic diversity. Of course there has not been enough time to accumulate all the diversity we see in people today if Adam was homozygous at all loci.15 But that is a straw-man argument. Why would anyone believe Adam had no genetic diversity built into his genome from the beginning?

Question - IF we assume Adam had genetic diversity built into his genome, what would it say for his off spring? And how would it affect the diversity among human population today, even if we assume a 6000 year time span?

As we will see, the amount of genetic diversity within people alive today, coupled with the distribution of alleles among world populations, is strong testimony to an original Adam. Add this to the genetic effects of the biblical Flood (with its severe but short population bottleneck) and the Tower of Babel (with its subsequent partitioning of the genes that were formerly on board the Ark) and we can go a long way to explain human genetic history, from a biblical perspective, while using the genetic data available to date.

When I began to analyze the data, I was at first struck by several things that appeared to support the evolutionary model. For example, Figure 1 displays the relative proportions of the alleles analyzed by HapMap. One can easily see that the bulk of allelic variants are transitions18 (A/G or C/T). These are chemically (thus statistically) more likely than the transversions (A/C, A/T, C/G or G/T). Why are the two types of transitions evenly balanced? Because an A to G change on one strand creates a G to C change on the reverse strand of DNA, and vice versa. Given millions of years of random mutation, one might expect to find 1) more transitions than transversions and 2) equal levels of the reverse complements, because mutations should appear randomly on either strand. This second rule is followed in all the variant classes except between A/T and C/G, and could be interpreted as functional conservation of C and G position in the genome. This is not evidence against the creation model, however, as I do not believe the creation model makes any specific prediction about these ratios

Now, when we get to the modeling, I think I see where his problem may be (but I am no expert)

At this point, we need something more powerful to model allele frequency changes in human history under the biblical parameters. To do this, I wrote a program in Perl that starts with a founder (Adam) and assigns him 1,000 heterozygous alleles. I assume Eve is a clone26 and give her the same set of variations. As they start having children, the children will be assigned a spouse after reaching a user-defined age of maturation. Spouses are chosen at random from all available unmarried people of the opposite sex. I assume mating for life. Also, unlike many other modeling programs that use discrete generations, I use overlapping generations. Thus, a person can marry anyone of the opposite sex, regardless of age (although an old, unmarried person is unlikely to exist) or relational status (with the exception of ancestors). Because I am tracking individuals, not averages, there is a greater demand on memory allocation, so the size of the population I am able to model is limited. However, this does allow me to model something that should more or less reflect biblical history.

I’m not sure sure how many RANDOM unmarried people of opposite sex can be, when they are all children of the same parents,ultimately.

The evolutionary models espoused by BioLogos and others depend on genetic drift and natural selection to influence allele frequencies. Because drift occurs so slowly in a large population, millions of years are needed to account for the allele frequency spectrum of modern man. The biblical model, however, starts with the smallest population possible (two individuals) and expects rapid drift in the antediluvian population. What would occur at the Flood, over a millennium and a half later, when the world population was reduced to eight people, with only three reproducing couples, of whom the three men are brothers? Using the same parameters as in Figure 11, I ran the model to simulate 1,500 years of marriage and birth, stopping every 500 years to reduce the population to three founding couples made up of three brothers (full siblings) and three women selected at random from the available unmarried women (Figure 12). From Figure 11, I knew that drift would effectively stop in any exponentially growing population prior to 500 years, so this seemed like a fair strategy.

What can we learn from Figure 12? First, as before, drift occurs from Adam and Eve (horizontal blue line) to the first sampling at 100 years (jagged brown line) and nearly no drift is noticeable 400 years later (smooth green line). A bottleneck occurred after year 500. One hundred years later, the population has drifted even farther (jagged dark blue line). In fact, each bottleneck drives the allele frequency distribution closer and closer to the modern average.

I’m confused. Biologos argues that genetic diversity shows no bottlenecks smaller than a few thousand individuals at it’s lowest, where as this guy has multiple bottlenecks and still arrives at a distribution closer to the modern average? How can this be?

As detailed above, one of the arguments from BioLogos is that there has not been enough time to accumulate the mutations found among people today if we came from Adam and Eve. A corollary to that is, we could not survive that kind of mutation load. As I said above, however, this is assuming Adam had no heterozygosity, which is ridiculous. How much created diversity might we assume? One way of estimating this is to look at the number of alleles shared among all world populations.

It is disingenuous for Biologos to claim no evidence for Adam and Eve for several reasons. First, their conclusions are based on evolutionary assumptions. One cannot legitimately claim something to be proven without testing the assumptions behind that claim. To do otherwise amounts to circular reasoning and question begging, and a rejection of any alternative theory following from this is thus reduced to nothing more than a straw man argument. Second, the majority of data fit nicely into the straightforward biblical model, including a single starting couple a mere 6,000 years ago. While there are several unresolved issues with the biblical model as it relates to the data at hand, the same can be said about every evolutionary model, so one cannot conclude that the Bible has been invalidated by the available evidence. Albert Einstein is rumored to have opined, “A thousand experiments cannot prove me right. A single experiment can prove me wrong.” This is sound logic. Francis Collins and BioLogos would do well to heed his advice.

Can someone provide a detailed response? I’m a total newb when it comes to the theory of evolution and DNA.

Thanks.


Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1)
Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1)
(James McKay) #2

Not being a geneticist I can’t comment on it in detail, but here are one or two observations anyway.

My first impression is that it’s not an easy article to understand. It uses a lot of technical terms that are unfamiliar to non-geneticists, and it doesn’t define them all that clearly. I’ve found this with other articles on creation.com as well – they tend to get a bit tough going when you try to follow them through and drill down into the details.

Secondly, it mentions that the author wrote a Perl script, but the script itself isn’t provided, so it’s not possible to review it for correctness. Having said that, it turns out that it’s quite common for scientific papers in mainstream journals not to include source code – a fact that those of us in the software development industry find quite astonishing, given that open source collaboration on GitHub is pretty much the lifeblood of computer programming these days, and that the correctness of computer code can make or break your conclusions.

It also mentions a computer program called Mendel’s Accountant, but it doesn’t explain clearly what it does. It turns out that it’s some kind of evolution simulator written by a team of YECs. The footnote links to a paper in a mainstream peer reviewed journal referred to as simply SCPE. Turns out that SCPE stands for “Scalable Computing: Practice and Experience” – in other words, it’s a journal about research into techniques for building high performance web applications.

Mendel’s Accountant is open source after a fashion – you can download it here. It probably needs a geneticist with programming experience to look at it and see what to make of it.


(Roger A. Sawtelle) #3

If you want to know how human beings evolved, you do not look to Darwin’s Theory, you look to the geological record.

Darwinian theory of genetic change tells how things might change, not how things did change. Natural history gives us that information and it indicates that genetic change comes with ecological change. Unfortunately natural history does not confirm YEC.


(James McKay) #4

Just to be clear, the issue being addressed here isn’t the age of the earth or evolution in general – it’s about something more specific, namely, the possibility of the whole human race having descended from just two people.

I’m told that genetic evidence contradicts this, but personally I don’t quite understand how.


#5

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(James McKay) #6

Thanks Eddie. I’ve no doubt about Sanford’s competence as a geneticist. However, speaking as a software developer, I know for a fact that it’s very, very easy to get computer software wrong without even realising that you’ve done so – even for seemingly very simple code written by very competent developers.

That’s why we place so much value on things such as unit tests and code reviews. It’s also why so much software is developed in the open these days – sites such as GitHub are designed to make the process of reviewing code and contributing changes as low-friction as possible. The whole principle of open source software is “Given enough eyeballs, all bugs are shallow.”

What bugs me here is that the citation they give for Mendel’s Accountant is to a paper in a journal about scalable computing – in other words, building high performance web services. It also bugs me that they abbreviate the name of the journal in the citation, which effectively obfuscates the fact. I would have expected a paper such as this to have been published in a journal which deals specifically with computational genetics or computational biology – of which, it seems, there are several.


#7

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(Roger A. Sawtelle) #8

@jammycakes

This is a perfect example of what I said above. The answer is not that humans could not have been created from an original pair, but the evidence shows that that they were not.

First of all we share most of the genes of apes and other creatures, so humans were not created de novo.

Second of all the evidence shows that a new species is created when a branch breaks off from the mainstream and develops differently in response to a different ecological conditions.


(Andrew M. Wolfe) #9

Like many others here, I’m not a geneticist, so I can’t reply to those details. Since the article’s been around for five years, I’m sure someone has picked it apart somewhere, but Google wasn’t very helpful to me in finding it.

I just wanted to say briefly that “BioLogos” doesn’t “argue” anything. Or, very little, at least. People affiliated with BioLogos sometimes do. BioLogos also offers their platform to non-affiliated scholars who argue things. I’m not playing some kind of clever semantics game. It’s important to note that BioLogos — and you could take this to refer to (1) people officially connected to BioLogos, who are very few, (2) scholars and thinkers given the BioLogos platform to share their views for consideration (a larger circle), and (3) BioLogos Forum participants and fans more generally — is very diverse. The only thing they have in common (for the most part) is a belief in common descent and a general ethos that (most aspects of) mainstream science and Christian faith can peacefully coexist. On the Adam question in particular, there are a variety of views.

I hope someone else will reply fruitfully on the other matters at hand.


(George Brooks) #10

@SuperBigV

This is definitely the Best of the short answers! Thanks, @Relates


(George Brooks) #11

@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.


(Amy Chai) #12

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.


#13

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.


(Andrew M. Wolfe) #14

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


(Peaceful Science) #15

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


(Steve Schaffner) #16

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.


Joshua and Cornelius get to know each other
(Steve Schaffner) #17

I just gave it a go.


(Peaceful Science) #18

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.


(Andrew M. Wolfe) #19

@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: )


(Vlad K. I'm an Agnostic Atheist) #20

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