Why is evolution so controversial?

It's presumable ultimately derived from the 1993 Takahata paper and it's a broadly quoted figure. Other more recent estimates have been a bit lower.It's certainly the case that there have been significant bottlenecks in human population history and, accordingly, humans have a low effective population size.

Additionally they estimated the effective population size of the common ancestor of humans and chimpanzees to be ~100,000. This was somewhat surprising since the present day effective population size of humans is estimated to be only ~10,000. Human evolutionary genetics - WikipediaI used the wiki here, estimates do vary somewhat. I will have to go deeper for further conformation... Let us just accept a reasonable number to further our discussion.

You answered your own question. The reason for the low effective population is genetic bottlenecks. Since the acceptance of indels? We have known about indels since we were able to sequence DNA which has been decades.Also, why do 5 million indels in addition to 35 million substitutions pose a problem for the 5 million year estimated time since divergence?

Got it, thanks.But, that is neither evidence for a young genome nor that our DNA denies common descent.It is evidence of a bottle neck in the human population.We're aware of that.

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It is evidence of a bottle neck in the human population.

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So when and how did your bottleneck happen?

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Also, why do 5 million indels in addition to 35 million substitutions pose a problem for the 5 million year estimated time since divergence?

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Simple Instead of being 1.33% divergent from chimps, we are now found to be 5% divergent from chimps. There are simply not enough beneficial mutations to explain a divergence from the chimp. As a side note, most mutations are either neutral or deleterious. Both are added to that genetic loading number in humans under soft selection and eventually have to be purged from a population to maintain a acceptable fitness in that population.Explain how you can account for the high U that would be imparted if mutation rates were met for a human chimp divergence of 5.6 million years? I can quantify that number but you would not like the result.

If you would have kept reading after where you cut off your quote, you would have seen the following in the wiki page you linked to:

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Additionally they estimated the effective population size of the common ancestor of humans and chimpanzees to be ~100,000. This was somewhat surprising since the present day effective population size of humans is estimated to be only ~10,000. If true that means that the human lineage would have experienced an immense decrease of its effective population size (and thus genetic diversity) in its evolution. (see Toba catastrophe theory)

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That wiki link goes to:

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The Toba supereruption was a supervolcanic eruption that occurred some time between 69,000 and 77,000 years ago at the site of present-day Lake Toba (Sumatra, Indonesia). It is one of the Earth's largest known eruptions. The Toba catastrophe hypothesis holds that this event caused a global volcanic winter of 6—10 years and possibly a 1,000-year-long cooling episode.

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and:

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The Toba eruption has been linked to a genetic bottleneck in human evolution about 50,000 years ago,[29][30] which may have resulted from a severe reduction in the size of the total human population due to the effects of the eruption on the global climate.

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According to the genetic bottleneck theory, between 50,000 and 100,000 years ago, human populations sharply decreased to 3,000—10,000 surviving individuals. It is supported by genetic evidence suggesting that today's humans are descended from a very small population of between 1,000 and 10,000 breeding pairs that existed about 70,000 years ago.

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That's one theory. There's another that says:

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On the other hand, in 2000, a Molecular Biology and Evolution paper suggested a transplanting model or a 'long bottleneck' to account for the limited genetic variation, rather than a catastrophic environmental change. This would be consistent with suggestions that in sub-Saharan Africa numbers could have dropped at times as low as 2,000, for perhaps as long as 100,000 years, before numbers began to expand again in the Late Stone Age.

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You can read the paper on that one here: Population Bottlenecks and Pleistocene Human Evolution | Molecular Biology and Evolution | Oxford AcademicWhat makes you think that the human effictive population size means that the genome is young and that we can't have common decent?

The molecular data suggests a recent bottleneck, not a recent origin. See Heng and Durbin (2011). In this study, the researchers used bioinformatic approaches to date the time of the bottleneck. If there were a recent origin, we wouldn't see things like:"Both populations experienced a severe bottleneck between 10—60kya while African populations experienced a milder bottleneck from which they recovered earlier."There's plenty of evidence in the literature -- utilizing different methods -- that suggest a bottleneck, rather than a recent origin. So this argument for a recent origin doesn't really stand up well in the light of scrutiny. Uh, you haven't explained why the theory of common descent is not compatible with the amount of indels that separate our genomes from the genomes of chimps. You're just saying it can't. Back that up with rigorous science.ReferenceInference of Human Population History From Whole Genome Sequence of A Single Individual, 2011.

The paper I cited above gives a neat "when" to your question. How did the bottleneck happen? There are plenty of mechanisms for bottlenecks. Bottlenecks aren't implausible at all; we know they happen.

This doesn't make much sense. Because our genome differs roughly 5% from the chimp genome, that means there couldn't have been enough beneficial mutations? Do you have something to back that line of thought up? And: Selection pressures can lead to a higher-than-average U value. That's nothing new. Edited by Genomicus, : No reason given.

Ah, one of my favorite varieties of creationist nonsense ... the non-quantitative quantitative argument. Hooray, you can prove that you're right with numbers. But without any actual math, 'cos that's hard.

We didn't evolve from the chimp.We evolved from a common ancestor with the chimp.How much of that divergence from chimps is due to our evolution from the common ancestor, and how much of that divergence is due to the chimps evolution from the common ancestor?Neither of us species hold all of the evolution from the common ancestor. Some of it is ours and some of it is their's.

What do you mean "instead of"? Both of those figures are from the same paper, and they are measurements of different things. The 1.33% is a measurement of the number of changes in the DNA we still share with chimps. The 5% includes the divergence caused by DNA we no longer share, the DNA that has either been removed or added to each lineage. These are answers to different questions, not an "instead of". Based on what evidence? The 1.33% involves 35 milllion mutation events. The 5% involves the addition of just 5 million more mutation events. Why do you think the addition of just 5 million more mutations pushes it over the edge? Yes, just as most atmospheric molecules are either nitrogen or radon. Neutral mutations are not added to those genetic loading numbers. You would have to show that the U would be too high, first.

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The Toba catastrophe theory suggests that a bottleneck of the human population occurred c. 70,000 years ago, proposing that the human population was reduced to perhaps 10,000 individuals[3]

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All these bottleneck scenarios involve some kind of low population over extended time frames. That is not really tenable when you take into account the needed mutation rates for divergence between the human and chimp genome. A heavy mutation load in a small population tends to cause that population to be susceptible to sudden collapse (or a sustained downward spiral in population).

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You would have to show that the U would be too high, first.

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The following is the calculation for a "U" given a needed mutation rate for a divergence of 5% (95% similarity) and a 5.6 million year divergence from human to chimp.5.6 million years is 244 thousand generations (given 23 years per generation).t= number of generations since divergence (244 thousand)
k= percentage of sequence divergence Estimated at 5%
Ne= effective size of population ~10^3
(u)= mutation rate needed.u= k/(2t+4Ne) or 9.5x10^-8 or ~ 600 mutations per generation (mutation rate times the diploid genome in humans).Now calculating deleterious mutation rate (U) from the following suggesting that 1.7% of the genome is subject to constraint (normal estimate, citation on demand).This gives: (600x.017)= U = 10.7 (completely untenable) A acceptable amount by evolutionists would be around U=1.3.Calculating the statistical birth rate to avoid passing on deleterious mutations to the next generation by the poisson distribution.B = 2e^U (U=10.7)=
88 thousand offspring needed per mating pair per generation.This is clearly impossible.I am sure most of you professionals can follow that calculation... If I need to, I will go over it step by step for you (maybe tomorrow).You can make up all the stories you like about how and when bottlenecks happen in a population but you must temper that story to real world conditions. Edited by zaius137, : No reason given.

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We didn't evolve from the chimp.

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Please read what I said carefully.. I said diverged.

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How much of that divergence from chimps is due to our evolution from the common ancestor, and how much of that divergence is due to the chimps evolution from the common ancestor?

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All things made equal, most scientists will assume half in their calculations Citation on demand.

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Neither of us species hold all of the evolution from the common ancestor. Some of it is ours and some of it is their’s.

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True, but also true is that we are more closely related to the common ancestor than to the chimp. So did the common ancestor look more like us or like the chimp? I would say neither.