Adam and Eve had Perfect Genomes (The Genetic Entropy Argument)


(Matthew Pevarnik) #1

Moving these posts over here for a separate topic. @aarceng has made the genetic entropy argument that aims to demonstrate the human genome must have been made perfect and very recently (specifically 6,000 some years ago) because of the accumulation of many mutations each generation would have built up too much for our species to have been older.


(Matthew Pevarnik) #2

Are these all genetic defects? Many that are harmful don’t end up getting passed down as natural selection is a real thing. Outside of many of these being neutral mutations, how would you explain these positive mutations:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791022/

Is this a reasonable inference? Given that again, natural selection is a real thing you would not accumulate such defects at such high rates. @Chris_Falter could confirm if this is a legitimate computer model, but this video outlines nicely how again natural selection eliminates many negative mutations:

It is? How did you come to this conclusion? Unfortunately they must have also been created with many many indications of common descent as well- from pseudo genes, to gene location on chromosomes, to ERV insertions and beyond. To suggest that any and all of these came after our human lineage split is an unreasonable position to have. I highly recommend spending some time on the main BioLogos site and learning at least what the scientific evidence says and has been saying for the past decades to century.


Pregnancy: too badly designed? Zygotes not implanted, miscarriages... where's God?
(Chris) #3

Yes I believe these are genetic defects. Even the synonymous mutations that code for the same amino acid can affect protein folding or production rates, so there are probably no truly neutral mutations. The vast majority would be mildly detrimental. Natural selection is a real thing but from my reading can only remove about 1 mutation per generation; hence the question “why aren’t we dead 100 times over?”. Most of the mutations would be mildly deleterious but below the selection threshold. The significantly deleterious mutations are probably those that cause spontaneous abortion and never get born.

According to Keightley P, Lynch M (2003) “Toward a realistic model of mutations affecting fitness”. Evolution 57:683–685. “In summary, the vast majority of mutations are deleterious. This is one of the most well-established principles of evolutionary genetics, supported by both molecular and quantitative-genetic data.”

Based on this I think it is a reasonable inference to estimate that the genetic load has increased by 10,000 defects over the last 2,500 years. (OK so you could allow for 1/100 mutations being removed per generation and get 9,900 defects)

I watched the video and I think it is quite superficial. It seems to be attacking a strawman version of YEC. Since I don’t have Matlab I can’t check the program itself. From what I can see in the video the program is about as superficial as the video. I suggest a better reference would be “The fundamental theorem of natural selection with mutations” Journal of Mathematical Biology, June 2018, https://link.springer.com/article/10.1007/s00285-017-1190-x


(Jay Johnson) #4

100% successful pregnancies is not a reasonable assumption, under any scenario. Did Adam and Eve have children before or after the Fall? If after, then their “perfect genes” were capable of combining and replicating imperfectly, generating defects. As well, childbirth itself has inherent dangers for both mother and child. Assuming 100% success is a non-starter.


(Chris) #5

Incorrect. Pre-fall, with perfect genomes and replication working perfectly, 100% successful pregnancies is reasonable. It was, remember, Very Good. However as far as I know there were no children before the fall so this remains hypothetical.

Post-fall however, replication would have been imperfect and consequently there would have been defects, even for Adam and Eve, possibly even some failed pregnancies. However even if their offspring started accumulating genetic defects at today’s rate; about 100 per person per generation; because they were starting with zero genetic load the effects would probably not have been anywhere as severe. Remember it was only in the time of Moses that laws relating to incest were introduced, since the accumulating genetic load made marriage to close kin increasingly likely to produce birth defects.

Since we live in a post fall world our only experience is with imperfect reproduction, miscarriages, defects, and risks to mother and child. This is normal for us.


(Jay Johnson) #6

But it was also normal for Adam and Eve. Their only experience with childbirth was post-Fall, according to the literalist interpretation. In any case, the more that people hypothesize and speculate about the perfection of this “original pair” of human beings, the farther and farther they are removed from anything resembling normal human experience.


(Matthew Pevarnik) #7

I’m sorry, did you click the first link I sent you? It’s a factual list of positive mutations that certain humans have. It also gets in to why is it so difficult to monitor mutations that have a selective advantage over others. And if 100 mutations occur, certainly it is well simply not true even begin to suggest that all 100 are ‘negative.’

Or perhaps Sexual Selection Helps Clear this Mutation Load much More than You Imagine

Or another neat paper concerning the spontaneous mutation accumulation in selection free- vs. competitive environments.

There is markedly a very large role that sexual selection plays and note that this is a very challenging topic to work on- especially given that there are individual mutations and then population level mutations. I think it is a really interesting topic that I don’t know too much about though so I can’t speak too much more just yet.

Okay- let me see what this paper is about and perhaps what kind of work have the authors worked on since. Here is Keightley’s publication list:
http://www.homepages.ed.ac.uk/pkeightl//pkpubs.html

My thoughts: holy cow- he’s been publishing multiple papers every year on the same types of topics.

Here’s one paper just randomly grabbed where 1-2% of new mutations in this study were positively selected-
http://www.homepages.ed.ac.uk/pkeightl//publications/schneider-etal-2011.pdf

Here’s a 2012 review paper discussing deleterious and mutations that are positively selected for here: http://www.homepages.ed.ac.uk/pkeightl//publications/keightley-genetics-2012.pdf

Needless to say I don’t think that your quote from his 2003 paper truly summarizes how geneticists might phrase things today.

Okay this is now at least completely debunk from what I’m seeing and not sustainable as any reasonable inference. Given all that I just presented, let me know what you think.

I agree knowing a little more than I did yesterday. My apologies for having you sit through the video though I do think at least the basic ideas can help serve as an introduction for how natural selection can impact negative mutational load.

I do if you’d like me to try and do something with this though I’d prefer to just defer to the large array of literature on the topic since the video and 2003 paper.

I kind of like this paper as it is at least one strictly YEC author (Sanford) and another I’m not sure on the age of the earth issue but who has obvious ties to the ID movement. Not a problem though as what I like is these two very obviously anti-evolution advocates actually went and published a peer-reviewed scientific paper in a real journal! That is incredibly rare and I certainly want to take the time to celebrate that.

But what is the paper arguing for and what is its significance?

Evolution news seems to think that this paper falsifies well the entire theory of evolution. That sounds a bit… well… um… wrong.

The entire premise of Fisher’s Theorem is obviously not true and I would imagine that all biologists kind of already knew this. As Wikipedia notes:

the theorem was widely misunderstood to mean that the average fitness of a population would always increase, even though models showed this not to be the case

So unfortunately the entire premise of the paper and Evolution News article seem to be based upon a strawman. Their paper appears to show not much of anything and naturally is picked up on by anti-evolution websites and paraded around as if it is somehow relevant to anything.


(Chris) #8

I hadn’t but I have now. (I was focusing more on the video clip I addressed earlier). A lot of the article is fairly vague but I think it is worth noting the sentence in the third paragraph.

A mutation that disables a gene is clearly a defect, even if it has some beneficial effects. In this case it appears to have beneficial effects for “elderly, overweight individuals” but we don’t know if it has detrimental effects for other people.
I know of several cases of a defect that can be beneficial in certain circumstances; adult lactose tolerance, sickle cell trait, black fur in desert mice; but we must distinguish between the effect a mutation has on the genome and benefits that might accrue in certain circumstances.
Clearly evolution by breaking, disabling, or deleting genes is a downhill path that might give some immediate benefits at the cost of long term detriment. But theoretically, I suppose, it could explain how microbes evolved from mammals.


(Chris) #9

Yes, but remember they were starting from scratch. Even at current rates their immediate descendants would each have had an average of 100 defects in the entire genome. Even with brothers marrying sisters the chance of their offspring having 2 copies of the same defective gene would be negligible. Today however there would be significant risk of a brother-sister marriage producing offspring with 2 copies of defective genes and hence birth defects or genetic disease. This is why from the time of Moses such marriages were banned, since it was a problem even then. I recall several documentaries that attributed ill health in some Pharaohs to inbreeding.


(Steve Schaffner) #10

Most intergenic mutations have less effect even than synonymous mutations. In any case, it doesn’t matter: mutations with very slight effect on fitness will not be selected against, but they also were never selected for, so most sites in that class will be more or less at equilibrium, with as many very slightly deleterious mutations as very slightly beneficial, all of them meaning nothing in the long run.

Nah, that’s quite incorrect. Natural selection can remove an arbitrarily large number of deleterious mutations every generation. The limiting factor is how large a burden of deleterious mutations an individual can carry. Suppose the average number of deleterious mutations carried by people is 1000. That’s just the average, though. Some will be carrying 800 and some 1200, for example. The ones with 1200 will be a lot less likely to reproduce than those with 800. For every 800er that reproduces in the place of a 1200er, effectively 400 deleterious mutations have been removed.

The only assessment they make in that paper of neutral mutations is for amino-acid altering ones, which is a tiny fraction of the total. The paper has no relevance to the discussion at hand.

A 6000 year long history of humanity, starting with a single couple, is completely inconsistent with observed genetic variation in current humans. You cannot get the genetic variation we see, in the patterns we see it, in less than about half a million years. We’ve been over this at excruciating length here previously, in this thread


(Chris) #11

There is a new post on youtube for The Fundamental Theorem of Natural Selection with Mutations - Conference Presentation. here


(Steve Schaffner) #12

It’s worth reading Joe Felsenstein’s comments here and here on this issue. It’s pretty much a lot of hoo-ha about nothing.


#13

That seems to be a rehash of Sanford’s “Mendel’s Accountant” that others have mentioned. There was a forum back in the day that delved deep into this program and population model, and the results were quite entertaining. They plugged in some conservative mutation rates and generation times for rabbits, and the program spit out a result where rabbits should have gone extinct from genetic entropy in just a few hundred years. Obviously, that hasn’t happened. Therefore, these claims are refuted by reality itself.

I tried to find the forum and thread, but my Google-fu is weak today. I will see if I can’t dig it up at some point in the future.


(Chris) #14

Please note, I didn’t come here for a long debate. If you expect me to still be discussing this in a month’s time you’ll be disappointed.


(Chris) #15

As shown in the video I linked the vast majority are slightly deleterious and swamp the slightly beneficial. Look at ~27mins where they show the Current Gamma Model, Kimura 1977.

Nah, that’s quite incorrect. In your scenario 400 deleterious mutations will have been removed IFF (if and only if) those mutations are unique to that person. It is far more likely that those 400 mutations will be shared by many within the population. You have removed one person but the alleles remain.

Edit: On second thoughts they are likely to have close to 100 mutations that they didn’t inherit from their parents so as an approximation say they have 100 unique mutations and 300 shared mutations.

The theory of genetic drift already assumes that most of the effectively neutral mutations in each generation will be lost by drift. In a population of 10,000, of the 1 million mutations that occur in that generation 999,900 are expected to be lost and 100 will eventually be fixed.


(Steve Schaffner) #16

Oh criminy. That’s a model, a mathematical expression someone made up as a guess at what the real distribution might look like. In 1977, when we knew next to nothing about the actual distribution. There is no empirical data at all that says that the majority of mutations in humans are very slightly deleterious.

There are also excellent grounds for thinking that mutations of slight effect in humans are not strongly skewed toward being deleterious. For example, one class of slightly deleterious mutations are synonymous substitutions, in which a preferred codon is replaced by a slightly less efficient codon, both coding for the same amino acid. This is exactly the kind of thing you’re talking about – tiny but real effect in fitness, too small to be weeded out by purifying selection. And there are millions of sites where this could occur. So are humans experiencing a constant rain of mutations that are degrading our fitness this way? No – because human genes don’t preferentially use the more efficient codon (in technical terms, codon bias is not seen in humans). Our codon usage is already haphazard and random, and as likely to be inefficient as efficient. So synonymous changes are as likely to make things slightly better as to make them slightly worse.

The entire idea of a flood of slightly deleterious mutations reflects a significant misunderstanding of molecular evolution.

You misunderstand. By “mutations” I meant copies of mutant alleles. Realistically, each new human birth introduces roughly 2 new deleterious allele copies (effectively deleterious, in that they will eventually be removed by natural selection). A single preferential reproduction by one of the lightly loaded individuals (relative to a heavily loaded individual) removes 400 deleterious allele copies. Extrapolate that to the whole population, and you will find that there is an equilibrium mean number of deleterious alleles carried in the population for which the number removed every generation equals the number introduced.

This is all standard population genetics. The equilibrium is known as ‘mutation-selection balance’. Look it up.


(Matthew Pevarnik) #18

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