Does this study strongly confirm "De novo" creation?

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In a 2011 article called “Evangelical Questioning the existence of Adam and Eve”, an outspoken critic of the biblical story, named Dennis Venema, who is also a theistic evolutionist and scientist made a profound prediction about how the story could be true. To get down to just two ancestors, Venema said,

“You would have to postulate that there’s been this absolutely astronomical mutation rate that has produced all these new variants in an incredibly short period of time. Those types of mutation rates are just not possible. It would mutate us out of existence.”

In 2013, a group of scientists, however, seem to have confirmed this prediction in its exact form and much more: “Mutations have fostered the great variety of traits seen among modern humans, according to the researchers, who added, ‘They also may have created a new repository of advantageous genetic variants that adaptive evolution may act upon in future generations.’”

The study also shows how most of the harmful mutations in people arose in the past 5,000 to 10,000 years. Moreover, the study observed that the older the genetic variant, the less likely it was to be deleterious. This means that the harmful genetic mutations that would normally extinct a population today was apparently not the case during Adam and Eve’s time and, thus, a breeding population of two would not fail for, at least, ancient humans.

But, I am not an expert so what do you guys think? Does this study actually confirm Denis Venema’s prediction. Here is the study and secondary source:

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants . Nature , 2012

Most of the harmful mutations in people arose in the past 5,000 to 10,000 years -- ScienceDaily

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More precisely, they saw a negative correlation between age of the variant and likelihood of being deleterious.

That is not what “this means.” I don’t see anything in their findings that suggests such a bizarre conclusion.

The answer to the question in the title of this thread is “no, not even close.” Moreover, the explanation for the recent birth of so many deleterious mutations is given in the paper and I find it overwhelmingly compelling. The explanation is explosive population growth, and not any hint of a difference in how mutations arose.

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First off, I specifically said “apparently” when I made that conclusion and then afterwards said “BUT, I am not an expert so what do you guys think…”

Second, you did not explain scientifically or logically how the study does not confirm Venema’s prediction. Until then, I can’t take your answer seriously and will wait for a more well thought out answer to come.

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The keyword there is “most”. 86.4%. The rest are older - up to 800,000 years old. You have to explain both the old and young variants, not just focus on the young ones.

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Source Paper:
Analysis of 6,515 exomes reveals a recent origin of most human protein-coding variants

the recent dramatic increase in human population size, resulting in a deluge of rare functionally important variation, has important implications for understanding and predicting current and future patterns of human disease and evolution. For instance, the increased mutational capacity of recent human populations has led to a larger burden of Mendelian disorders, increased the allelic and genetic heterogeneity of traits, and may have created a new repository of recently arisen advantageous alleles that adaptive evolution will act upon in subsequent generations.

Population growth is the principle driver. I might also speculate that selection may be harsher among hunter gatherers than agriculturally based societies, but I have not read anything which supports that notion.

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Oh, gosh darn it! Bye!

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I think there’s an important distinction to be made here. Population growth explains why there is an enormous number of young, rare alleles. It doesn’t explain why likely deleterious alleles are younger than likely neutral alleles; that’s explained by purifying selection, which slowly but steadily removes the deleterious alleles from the population.

Also, I see they used my (now very creaky) model of human demographic history. So yay.

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Can you please explain scientifically or logically how the study does NOT confirm Venema’s prediction in its exact form, which was what I referenced first to show how the study confirmed De novo creation but NOT suggest that God created the first humans? But then again, I might have used the wrong title for my post.

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Can you please explain scientifically or logically how the study does not confirm Venema’s prediction in its exact form?

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Oh geez, let’s not bring Venema into this. I’ve already gone on record disputing much of his scientific case, and several scientists have endorsed my critique. He is claims were overblown and poorly supported.

That doesn’t mean other people haven’t made more trustworthy cases of more measured claims. Just because Venema was wrong doesn’t mean everyone else was too.

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It seems also that this is evidence of negative selection, right @Joe_Felsenstein ?

We expect that selection weeded out most the ancient deleterious. I suspect this study might give us insight into the time it takes for negative selection to work on mildly deleterious alleles.

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I think it’s critical you understand that Venema’s assessment in 2011 was incorrect in several ways. He himself has backed off them as has BioLogos, in large part (though not exclusively) due to my work.

Here are a couple lay summaries:

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@Meerkat_SK5 I see this as saying what no one else would say. Yes, the study confirms Venema’s prediction about two ancestors, but he is saying Venema shouldn’t be taken seriously because he’s been wrong in other areas about two ancestors, therefore his prediction has no merit in the first place. Correct me if I’m wrong.

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Yes, as glipsnort (Steve Schaffner) has already noted.

The classical theory of population genetics shows that a deleterious mutation will hang around longer, the less deleterious it is. In the case where it is not recessive, the descendants of a single mutation will hang around long enough to appear in, on average,  1/s  copies before they disappear, where  s  is the selection coefficient against the mutant. So a mutant that has fitness lower by 0.01 appears in about 100 individuals before it disappears, and a mutant that has fitness lower by 0.001 hangs around 10 times longer on average and appears in about 1,000 individuals.

It is not, of course, that there were mostly wonderful and beneficial mutations before 7,000 years ago but lately things have been kind of depressing.

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Venema wasn’t making a prediction.

He was claiming the number of alleles as evidence against a bottleneck of 2 going back 18 million years ago. That was a false claim, both because the number of alleles don’t put bounds on a bottleneck, and the evidence doesn’t tell us much going back before 500,000 years ago.

He was also claiming that YEC models that have a recent bottleneck for AE (e.g. Jeanson’s model), make use of mutation rates orders of magnitude higher than what we are known to have. In that point, Venema is correct, even though the evidential problem that arises for a recent bottleneck has nothing to do with the number of alleles we observe.

As for dating Adam and Eve with genetics, central to the question is whether or not a genetic bottleneck is even needed. Just about every camp makes space for interbreeding between Adam and Eve’s lineage and others. In that case, we would not expect to see a bottleneck. That obviates the whole debate in a totally different way.

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For the most part, yes. I am actually arguing that Denis was right in regards to his prediction NOT his personal opinion on the subject.

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He was not making a prediction. That is not what a prediction looks like.

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The quote in the OP seems to be about mutation rates, and the paper in question does not in any way suggest that there has been an elevated mutation rate in humans. So, @thoughtful, I would say that you do have it wrong.

(edited to clarify who was saying what)

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You guys make one’s head spin because the topic always gets changed. All I see is Venema’s insistence on the evolutionary interpretation that all variation arises from mutations. The study later showed that isn’t the case, and gave the interpretation of population growth instead. Yes or no?

I don’t really understand what @swamidass is saying in his reply. But Jeanson didn’t have a model back in 2011 as far as I know. Did any creationist have specific models based on what we knew then? I think we’re applying anachronisms.

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The quote does not refer to a specific model:

You would have to postulate that there’s been this absolutely astronomical mutation rate that has produced all these new variants in an incredibly short period of time. Those types of mutation rates are just not possible. It would mutate us out of existence.

In that statement, Venema was entirely right (if we confine ourselves to AE in the very recent past with no interbreeding). Jeanson then went on to postulate exactly just this, an astronomically high mutation rate to make sense of the data. Jeanson certainly tries to justify this high rate, and most of us think he fails in that justification.

No. Sorry.

As population grows (and our sampling of the population grows), you expect more rare variants. There is nothing surprising about this, and it doesn’t mean most mutations aren’t arising by random processes, though Venema seemed to be unaware of this relationship at the time.

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