The time scale of the bottleneck?

If you insist. Does their paper need addressed? They imagine that with a bottleneck of 8 4,000 years ago you can end up with the genetic diversity that we have today. That would require at least an increase of the mutation rate of humans of 100x sustained for thousands of years beyond what we observe at the present, not to mention all of the shared ERV and Alu and other insertions that we share with our closest genetic relatives (chimpanzees). If they have a good idea, publish it in a real scientific journal and let it be hashed out there.

Read the thread. I don’t have the expertise or time needed to condense the technical details.

In his final wrap-up post he drops the minimum bound and admits the 95% was a possibility. Something he wasn’t willing to accept at the beginning of the exchange.

Sorry that I can’t point you to the single sentence where he says this.

Well I didn’t find it so I will assume you were mistaken.

@Bill_II Here is @RichardBuggs final post on the topic:

where he concludes:

I would accept 95% as a prediction, but not as a statement of established fact.

But the percent similarity is not really that useful and a nice summary from @DennisVenema:

Where he says,

He is certainly not accepting 95% and I found nowhere where he revised his earlier estimated range of between 84.4% and 93.4%.

I agree. Since humans are mammals then it is to be expected that since we share many tissues, organs, etc., we would have a high degree of genetic similarity.

On the other hand how much genetic difference could have accumulated since the hypothetical split from our common ancestor with the chimp about 7 million years ago? (or is it 5 million, or maybe 13 million?). Can you tell me that? If the genetic difference is less than that figure then perhaps the hypothesis is possible; but what if the genetic difference is greater? Perhaps 95% similarity (5% difference) is already more than can be supported by evolutionary theory.

I’ll leave one explanation up to @glipsnort:
Evolution is a faith because common ancestry doesn't add up

Also from his article I linked earlier the genetic difference in humans that’s due to random mutations looks like this:
image https://biologos.org/files/resources/picture1.png

And this difference between humans and chimpanzees looks like this:
image https://biologos.org/files/resources/picture2.png

The pattern is identical and it mainly just differs in scale. The y-axis is higher in the human-chimpanzee graph than human-human. But because the overall pattern is conserved, that means that the same mechanism of leading to diversity among humans - i.e. random mutations is the main mechanism leading to diversity between the human and chimpanzee lineages. There’s simply just been more time since a common ancestral population.

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@pevaquark

If i have mis-stated some obscure element please let know what or where.

It was my understanding that Buggs and Venema have agreed that there is no indication of a single pair bottlencek any time within 700,000 yrs(though ive read summations that use 500k yrs instead) of the present.

The 700k (or 500k?) represents the wall of noise that makes it impossible to know what could be or couldnt be true further back than 700k years.

@aarceng

My point was there wasn’t a single sentence. You have to read Richard’s final post in the context of the entire conversation that took place. Do you understand the significance of Richard dropping any reference to a lower bound? He has always tried to minimize the % of similarity and is widely quoted on anti-evolution websites as an authoritative source for the smallest % possible. To even admit that 95% was a possibility is a major change in his position.

As @Swamidass eloquently outlines, looking at human variation alone doesn’t grant a miraculous bottleneck anytime in the past 500 kya (looking at TMR4A). But really, the idea of TMR4A is rather ridiculous from a purely scientific perspective. Not that the idea itself is not scientifically sound, it very much is and can be calculated, but you would never have two individuals that have two alleles at every loci that are different from their spouse and thus the timeliness of such a bottleneck (if there was one) would be even further in the past. Hence its more likely that a bottleneck (if there was one) would be closer to the average TMRCA.

But that’s only looking at human variation, not any kind of trans species evidence like shared polymorphisms or incomplete lineage sorting which also provide population estimates of populations and at least the latter do not reveal any bottlenecks at all going back much further.

The point of 500,000 yrs is not that a bottleneck MUST have happened then… but that “noise” prevents science from EXCLUDING a bottleneck prior to 500,000 yrs.

I always thought it odd that Buggs would be so interested in a time-frame well outside of the Biblical limits.

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What are the Biblical limits in an old earth scenario? Most Old Earth concordists are fine with adding ages and finding gaps in the listed geneologies and maybe some place Adam and Eve’s special creation 50,000 some years ago. Ann Gauger though seems perfectly fine going back several million years and finds it consistent with her understanding of essential Catholic doctrines.

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As explained in the other thread, I totally support the conclusion of the scientific community that we have 98.8% similarity of DNA with chimpanzees. However…

  1. This can be a little misleading because small genetic differences do not equal small physiological differences.
  2. This certainly does not mean that chimpanzees are 98.8% human. Our genetics is not where our humanity is to be found. We are primarily meme organisms rather than gene organisms – human minds not primate bodies. It is the information in our linguistic communication which has the more important inheritance for the next generation.

The very concrete difference this makes is actually quite simple. If like the planet of the apes movies, chimps acquired the power of speech and could thus inherit all of our ideas and learning, should they still be considered animals? Surely reasonable people would see that as a terrible mistake.

  1. Our ancestors from 500,000 years ago are not even the homo-sapiens species, which evolved during the period 100,000 to 300,000 years ago. Modern humans are only seen after 100,000 years ago, but the subspecies Neanderthal is found considerably earlier.

Sorry @Bill_II, but you are mistaken. You can find Richard’s final statement on his blog here.

He sticks with his original figures and says “I predict that the 95% figure will prove to be wrong, because (on the basis of my comparison of the PanTro4 and PanTro6 alignments to Hg38) I think that the CNV differences are here to stay, and I doubt that all of the currently unaligned or unsequenced regions of the human genome will prove to all be 95% the same as the chimpanzee genome.” [my emph]

I assume you are referring to where @glipsnort says,

The human genome is ~3.2 billion base pairs so that means 0.72% to 1.22% single-base substitutions when comparing human and chimpanzee genomes. (99.3% - 98.8% similarity)

So, from your reference, the answer to my question is that any less than 98.8% similarity is inconsistent with the evolution hypothesis. 95% is 4 times too much difference (5%/1.22%). Evolution is a faith because common ancestry doesn’t add up.

Chris, as I recall, the percentage is very dependent on the methodology used to calculate it, so whether it is 89% or 98% is really irrelevant, unless you are using those numbers as a tool. In that case, they become useful. For example, it would be of interest to compare human to chimp, and chimp to gorilla, and chimp to orangutan to put it in context, but one isolated comparison tells you very little.

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So a ‘faith’ to you is something that doesn’t have any evidence to support it? Or even worse even despite evidence to the contrary one still proposes their model by ‘faith.’

A special creation model like yours is a faith based model that doesn’t have any mechanisms or predictions beyond God just did stuff. I have showed you now multiple times the types of differences we see can be explained by random mutations among human to human and between human and chimpanzee. Did you not understand the graph that I put above?

So rather than responding to the substance of my post your are picking on a phrase that actually comes from your post. Please respond to the main question; how much difference is too much? From your reference it would seem that 5% difference (95% similarity) is already 4 times more than can be supported by evolution theory.

In which case 98% similarity is not evidence in favour of humans and chimps having a common ancestor within the last ~7 million years. Is that what you’re trying to say?

No, I am saying you have to compare apples to apples. 98% may be evidence, or may not depending on how it is determined, and how it compares to other animals using the same measure.

Skip the genome size and just calculate the rate of difference from the mutation rate and the approximate number of generations. The range is 0.76% to 1.29%.

You seem to have missed something. The range of single base differences is predicted to lie between 0.76% and 1.29% (roughly). The observed rate of single base differences between the species is 1.23%. To predict the total genetic difference between the species requires a good estimate of the mutation rate for insertions and deletions, including large ones, which we do not have. These mutations are less frequent than single-base substitutions but contribute more total sequence change.

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