Physicist Lee Spetner weighs in on Adam and Eve controversy

_{Denyse O'Leary

November 14, 2017

Darwinism, Genetics, Human evolution, Intelligent Design}

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Adam and Eve have never been so hot since the days everyone went to church. At least not to judge from the current Bottleneck War in genetics.

Image result for Adam and Eve public domain It was sparked by British geneticist Richard Buggs pointing out in a journal that, strictly speaking, one fertile human pair could survive a bottleneck (Adam and Eve more or less, fig leaves optional). At first, he didn’t get mail. Then he got mail. Yesterday, we reported that Buggs (the Yes guy) was asking geneticist Dennis Venema (the big No guy) to provide sources for some claims. Over to Venema.

Meanwhile, physicist Lee Spetner, author of The Evolution Revolution, writes to say that adaptability is built into organisms by transposable elements and thus assumptions about merely random mutation are wrong:

The arguments about bottlenecks and diversity of alleles are all badly misinformed. The arguments are predicated on the assumption that genetic diversity comes from random mutations in the DNA, which is not true. Most genetic diversity comes not from random point mutations but from the activity of transposable elements (e. g., Kidwell and Lisch 2000, van de Lagemaat et al. 2003, Britten 2010), which are nonrandom. It turns out that environmental stress triggers the endocrine glands to secrete hormones that in turn trigger transposable elements that tend to produce phenotypic changes that relieve the stress yielding an adaptive response to a new environmental condition. This capability is built-in to the organism and is designed to permit the organism to adapt to a variety of environment. Therefore any conclusions about genetic diversity on the assumption that it is produced only by random mutations are wrong.

Image result for Lee peyner Evolution Revolution He offers the following links: Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends in Genetics 19 (10): 530–536. van de Lagemaat, Louie N. et al. (2003) (paywall)

Kidwell, M. and D. Lisch (2000) Transposable elements and host genome evolution. TREE 15 (3): 95-99. (paywall)

Britten, Roy J. (2010) Transposable element insertions have strongly affected human evolution Proceedings of the National Academy of Sciences of the United States of America 107 (46): 19945-19948 (public access)

Keep your scorecard handy.

See also: Are Adam and Eve genetically possible? The latest: Richard Buggs (yes) replies to Dennis Venema (no): I realise that some of your non-biologist readers may think I am being rather pedantic in asking for a citation when you are making what appears to be a very straightforward case from allele numbers. But biologist readers will know that very few things in this area are straightforward, and without a citation I have to treat your claims as unsubstantiated.

Adam, Eve, Richard Buggs, and Dennis Venema: Could Adam and Eve have existed?

Geneticist defends possible Adam and Eve in Nature: Ecology and Evolution

and

Geneticist: Adam and Eve could have existed

Comments

Ha! "Is 1000 greater than 15 million? Who can say! I'll leave it for readers to decide for themselves".mullers_ratchet_{November 18, 2017
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mullers_ratchet @28 I leave it to the unbiased reader to decide, who is trying to find a way to save face and who has provided evidence.Origenes_{November 18, 2017
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Why are you like this? Anyone who reads those quotes can see they never claim most genetic diversity is down to TEs. That claim is laughable. I've already shown you the evidence that there are 15 million SNPs with common alleles and a little more than 1000 TEs like that. So I'm left to wonder, why are you like this? What compels you to keep posting on topics about which you are ignorant? Do even believe the things you post, or are you just trying to find a way to save face?mullers_ratchet_{November 17, 2017
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mullers_ratchet @24 You say about the papers, referenced by Spetner:
mullers_ratchet: “None of them support the claim or anything like it.”
The claim being that most genetic diversity comes not from random point mutations but from the activity of transposable elements. You must be blind as a bat. Let’s look at the paper ‘Transposable element insertions have strongly affected human evolution’ by Britten (2010). On its own the title supports Spetner’s claim — and most certainly ‘anything like it.’ But what does the paper say? An excerpt:
A major source of variation has been the insertion of transposable elements (TEs). They can be identified as catalysts of evolution because their contribution to variation increased the speed of evolution (3–8). TE element insertions increase the rate of recombination (3) and when there are already many copies present nearby as there are for Alu elements the new ones increase the rate of unequal crossover. The insertions affect genes and their expression (8). Humans stand alone in two respects: the speed of evolution and the large number and activity of TEs. This recognition leads directly to the proposal that they are functionally connected. In other words the high frequency of TE insertions is responsible at least in part for the rapid human evolution. It might be due to the increased variation and recombination that certain specific sets of genes were activated or suppressed or the increased total number of opportunities for useful variation.
And here the conclusion in full:
Conclusion TE insertions occur frequently during human lineage evolution. Table 3 shows that the rate of human insertion was larger in the past back to about 3–4.5 Mya and probably much earlier. This observation has led me to speculate that Alu insertions underlie rapid human evolution. There is no doubt about the occurrence of many TE insertions and some of these affected human gene expression. A question is whether there were as many as required and this issue suggests the model is speculative. The proposed model is that the many TE insertions created many potentially effective changes and those changes selected were responsible for the striking human evolution. The number of potential events was effective in the combination selected during human lineage evolution. TE activity has likely been responsible for the speed and exceptional character of human lineage evolution.
You say you've read those papers, but I prefer not to believe you.Origenes_{November 17, 2017
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Cain killed Abel, then ran off with Lilith and her daughter.ET_{November 17, 2017
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"That’s one reason I find the Adam-Eve hypothesis to be so incredible. If humans were anything like they are now, things would have been extremely awkward at the beginning, with all the incestuous relationships. It sounds like a socially untenable situation." thing is where is the evidence Cain or Abel married their sisters? It seems to come down to only one thing - Eve was the mother of all living - but thats out of context. She was certainly not the mother of Adam and he was living. So why this idea of Cain and abel marrying their sisters as a given fact. Why wouldn't Cain and Abel have gotten their wives the same way their father did? Since they would have derived their existence from their husband Eve is still the mother of all living (besides Adam). No incest necessary.mikeenders_{November 16, 2017
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I completely disagree.
Ok then. And what is your opinion on 1000 and 15 million. Which is the larger number?
Again, Spetner argues that SNPs should not be credited for the number of alleles we see in present day
Do you know what a SNP is?mullers_ratchet_{November 16, 2017
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mullers_ratchet @22
I’ve read those papers. None of them support the claim or anything like it.
I completely disagree.
1. Models of bottlenecks etc assume mutations are random
Indeed. And Spetner holds that this is based on the misguided assumption that genetic diversity comes from random mutations in the DNA. So, in Spetner’s view, those models are wrong.
2. Most genetic diversity is from transposons, which are not random 3. Inferences from these models will be wrong because this assumption is not met.
According to Spetner, these models are wrong, simply because they operate under a misguided assumption.
Apart from (2) being laughably wrong, this argument fails because the assumed-random mutations that are used in these analysis are SNPs, and nothing to do with transposons.
Whut? Surely SNPs have nothing to do with transposons. Why do you point that out? Do you think that Spetner wants you to believe otherwise? Again, Spetner argues that SNPs should not be credited for the number of alleles we see in present day — models should not be based on that assumption —, he argues for a different method of analysis which includes a focus on the activity of transposable elements.Origenes_{November 16, 2017
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This is remarkable. First, the point about genetic diversity.
Unlike you, Spetner backs up his claim...
Well, unlike you (or I guess Spetner) I've read those papers. None of them support the claim or anything like it. The claim itself is ridiculous. There are ~1000 transposable elements in the human populations with somewhat common polymorphisms (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647816/). That's probably a slight underestimate for various reasons. But hardly compares to the 15 million SNPs that meet those criteria! https://www.ncbi.nlm.nih.gov/snp/?term=%22Homo+sapiens%22%5BOrganism%5D+AND+(00000.0500%5BGLOBAL_MAF%5D+%3A+00000.5000%5BGLOBAL_MAF%5D) So, Spetner is wrong on that front. Even if he wasn't consider his actual argument (not the one you have decided to defend above).
The arguments about bottlenecks and diversity of alleles are all badly misinformed. The arguments are predicated on the assumption that genetic diversity comes from random mutations in the DNA, which is not true. Most genetic diversity comes not from random point mutations but from the activity of transposable element (eg ...) , which are nonrandom.... Therefore any conclusions about genetic diversity on the assumption that it is produced only by random mutations are wrong.
Pretty simple: 1. Models of bottlenecks etc assume mutations are random 2. Most genetic diversity is from transposons, which are not random 3. Inferences from these models will be wrong because this assumption is not met. Apart from (2) being laughably wrong, this argument fails because the assumed-random mutations that are used in these analysis are SNPs, and nothing to do with transposons.mullers_ratchet_{November 16, 2017
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mullers_ratchet @20
mullers_ratchet: So, be just wrong to say transposable elements are the main source of genetic diversity.
Unlike you, Spetner backs up his claim:
Spetner: Most genetic diversity comes not from random point mutations but from the activity of transposable elements (e. g., Kidwell and Lisch 2000, van de Lagemaat et al. 2003, Britten 2010), which are nonrandom.

mullers_ratchet: But even if he wasn’t, the SNPs that are being used to estimate historical population size are not the result of transposons.
You still don't get it, do you? According to Spetner, the method that uses random point mutations to estimate historical population size is incorrect. He wants, instead, a focus on the activity of transposable elements.
mullers_ratchet: So his argument, that models are misappliy because the variation is non-random because transposons, is obviously irrelevant.
Does not follow. According to Spetner, random point mutations are misapplied as an explanation for the number of alleles we see in present day.Origenes_{November 16, 2017
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So, be just wrong to say transposable elements are the main source of genetic diversity. But even if he wasn't, the SNPs that are being used to estimate historical population size are not the result of transposons. So his argument, that models are misappliy because the variation is non-random because transposons, is obviously irrelevant.mullers_ratchet_{November 16, 2017
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mullers_ratchet @18
mullers_ratchet: H’uh? He knows the studies are about SNPs, so he wrote about transposons?
Yep. According to Spetner the studies should not focus on random point mutations as an explanation for genetic diversity, but, instead, on the activity of transposable elements. For instance, when Venema writes ....
... to generate the number of alleles we see in the present day from a starting point of just two individuals, one would have to postulate mutation rates far in excess of what we observe for any animal.
... he, Venema, seems to focus solely on SNP's. According to Spetner 'the number of alleles we see in present day' can be better explained by the activity of transposable elements. Not that complicated, now is it?Origenes_{November 16, 2017
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H'uh? He knows the studies are about SNPs, so he wrote about transposons?mullers_ratchet_{November 15, 2017
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mullers_ratchet @6
mullers_ratchet: Spetner seems to have missed the fact that these studies almost always use single nucleotide variants, not transposon insertions, as input.
You are mistaken about Spetner. He is well aware of the fact that single nucleotide variants are assumed, that's why he writes:
Spetner: The arguments are predicated on the assumption that genetic diversity comes from random mutations in the DNA, which is not true.

mullers_ratchet: So his comment (in addition to being wrong) is not very relevant.
On the contrary, as shown Spetner is correct and his comment is very relevant:
Spetner: Most genetic diversity comes not from random point mutations but from the activity of transposable elements (e. g., Kidwell and Lisch 2000, van de Lagemaat et al. 2003, Britten 2010), which are nonrandom.
Origenes_{November 15, 2017
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daves- Socially it was just them and their want to reproduce. And as Lilith was already kicked out of Eden her population wouldn't have Adam's sin on their hands but they would have hers. And yes, the existence of Lilith brings in new issues. But I think it is interesting.ET_{November 15, 2017
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ET,
As opposed to one’s half-sister?
I don't know that that would be any better, tbqh. We can of course assume ad-hoc that these people somehow had the capacity (socially) to survive all this inbreeding, but is there any way to test that assumption? Incidentally, if Lilith did exist, and had children, that opens up a huge theological can of worms because now you have a population of humans untainted by Adam's sin.daveS_{November 15, 2017
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daves:
That would make for an interesting arrangement, being in a “relationship” with one’s mother-in-law.
As opposed to one's half-sister? And humans wouldn't have been anything like we are now. Well two eyes, two arms, two legs a head and torso, but that is where it would end.ET_{November 15, 2017
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ET,
If Cain had a choice I would think the answer would be “both”. Then the genetic history becomes a different story.
Both? That would make for an interesting arrangement, being in a "relationship" with one's mother-in-law. That's one reason I find the Adam-Eve hypothesis to be so incredible. If humans were anything like they are now, things would have been extremely awkward at the beginning, with all the incestuous relationships. It sounds like a socially untenable situation.daveS_{November 15, 2017
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Charles, love to hear your take on comment #10.AnimatedDust_{November 15, 2017
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daves- If Cain had a choice I would think the answer would be "both". Then the genetic history becomes a different story.ET_{November 14, 2017
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I've said this before on UD. I see nothing in the Book of Genesis that would cause me to believe that humanity started with a single breeding pair. Genesis is a compilation of stories, genealogies and metaphorical texts. The Adam and Eve that begot Cain and Abel were not the same Adam and Eve of the garden of Eden. Cain himself mentioned being afraid of the ire of the people living in his time. The Adam of the garden of Eden was never called just "Adam" in the Hebrew. The Hebrew text used "The Adam", not just "Adam". It was like saying "The French" or "The Spanish" to refer to a society or group of people. In fact, there is reason to suppose that the original humans (the Adam) were androgynous (male and female). It is impossible to create a male without also creating a female. Jesus also said that male and female were not separate in the beginning, when asked about divorce. They only became so afterwards because God saw that it was not good for the Adam to be alone.FourFaces_{November 14, 2017
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@ daveS 'I’ve been told that since the Mosaic Law did not exist in the time of Adam and Eve, incest between their children was allowed.' I also read that there was a technical reason why such incest would not have caused the damage it has led to in the less than pristine condition of our genetic make-up in later times? Aah, there we are, aarceng just explained it. I was in too much of a hurry to make a cuppa coffee, to read beyond daveS' first post.Axel_{November 14, 2017
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FourFaces @ 3, daveS @ 4 Starting from Adam and Eve alone would have required siblings to marry. Abraham for instance married his half-sister. Since the original created pair would have had zero genetic defects this presents no genetic problems until enough time had passed for defects to accumulate. It wasn't until the time of Moses that incest was banned.aarceng_{November 14, 2017
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I was under the impression that Cain met up with her and they started their own little population.
That would be really twisted, as Lilith was (supposedly) Adam's first wife. Maybe you're referring to Lilith's daughter?daveS_{November 14, 2017
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but, in the second case there would be ZERO “polymorphism.
Well, no. Humans are diploid go through recombination each generation. So, with 2 people there would be four copies of all chromosomes with plenty of evolutionary history recorded in each individual. In reality such a severe bottleneck would likely also involve inbreeding, which would futher reduce teh effective population size. With regards to the main post, Spetner seems to have missed the fact that these studies almost always use single nucleotide variants, not transposon insertions, as input. So his comment (in addition to being wrong) is not very relevant.mullers_ratchet_{November 14, 2017
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Why is Lilith always absent from these discussions? I was under the impression that Cain met up with her and they started their own little population.ET_{November 14, 2017
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I've been told that since the Mosaic Law did not exist in the time of Adam and Eve, incest between their children was allowed.daveS_{November 14, 2017
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It is possible to breed Chihuahuas, Pugs, Greyhounds, French poodles and Great Danes out of a single pair of wolves, right? Still, this does not prove that the human races came from a single breeding pair. Moving to a religious tangent, isn't it forbidden in God's law to marry close siblings?FourFaces_{November 14, 2017
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Ahem: Look who said it first- although I used recombination and not TEsET_{November 14, 2017
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I think Lee Spetner is completely right about this: mutations are mostly directed. If this is so---as evidence suggests---then as a result, few 'non-synonomous' mutations would be expected, while 'synonomous' mutations would be expected to proceed at a normal, 'nearly neural,' rate. This means that w=dN/dS will be low. Population geneticists would interpret this as "purifying" selection, thus undermining the normal neo-Darwinian view of the preponderance of 'positive' selection. The overall result: neutral theory. This is actually the current state of population geneticists: they're almost all neutral theorists. As to the whole notion of "bottlenecks," I also agree with Spetner: this is a very speculative approach for understanding polymorphisms. The formula used for a "bottleneck" involves the harmonic average of population size. This means that if you start with two individuals, building up to 10,000 invidividuals in 25 generations, then keeping this steady for the next 9,975 generations, the equation population geneticists will come up with an answer regarding the level of "polymorphism" found in the population is the VERY SAME as the following scenario: you begin with 10,000 individuals, proceed for 9,975 generations, and then, over the final 25 generations, kill them off until there are just two individuals left. The mathematics are the same. You have a series of fractions that are added together and then rationalized. In doing this, it matters not one iota whether the fraction generated by the large population comes "first," or whether it's last. Likewise with the small population sizes. Thus, you cannot differentiate these two scenarios. Yet, in the first case the level of polymorphism would not be negligible, and possibly somewhat eleveated; but, in the second case there would be ZERO "polymorphism." Are we to use such "mathematical" jiggering to tell us whether or not there was, or was not, an "Adam and Eve." I think not.PaV_{November 14, 2017
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