Common Descent: Humans and Chimps / Mice and Rats


#1

Which is it, please? We are 10X more different from chimps than rats/mice, or we are 10X more similar?


Molecular Genetics of Whale Evolution
#2

They are more similar


#3

Also the genome sizes of the mouse, rat and us are pretty similar. Close to the same amount of genes as well. I think we share like 99% percent of our genes with mice . If I’m not mistaken


#4

Very good point @agauger. If you notice, I never wrote “10X more similar,” which is not true. I only wrote “10x more different”. There is a difference, and the difference is consequential. 98% similar is 2% different and 80% similar is 20% different. 2% is one tenth of 20%. Human/chimps are about 10x less different than mice/rats.

I also point out that I have simplified and rounded numbers here to aid understanding. You, @Agauger, will have a more detailed understanding of this that I also share. Do not interpret the rounding of numbers as a lack of precision in my understanding.


#5

I believe I’ve seen some people make similar arguments to justify putting Pan in Homo


#6

@swamidass
Just a few more points of clarification–

  1. chimp/human difference 4% difference (my number from the literature-I know different people cite different differences
  2. rat/mouse difference is 20%??
    3 Time from divergence to now for each?

I have always wondered what you meant by this. Maybe now I will see.


#7

#8


I’m seeing anywhere from 12-30mya for mouse/rat divergence


#9

Thanks for engaging @agauger, but I have to disclose that I am traveling internationally now. I will give you a full response, but it may take as long as week. I’m not ignoring you, and will get back to this as soon as I can.

The one point I would emphasize before I leave is that it is critical that measure of divergence is the same for human/chimp and mice/rat. Your 96% divergence is using is a different number, which is okay, but by that measure, mice/rate divergence is closer to 70%.


#10

Safe travels!


#11

Also, in the meantime, this article by @vjtorley covers most of the key points. Perhaps @T.j_Runyon could summarize with the key references he points to. Of course, I will add my assessment when I can.

This discussion has the key points scattered about, but there is more to discuss and details to refine. @vjtorley quotes me:

A common lawyerly objection to this evidence is that these similarities are “equally” explained by common “design.” As scientists, our response to this objection is data. Many modern creationists think that the genetic evidence shows that mice and rats share a common ancestor, even though they are 10 times less similar than humans are to chimpanzees. Starting from the genetic evidence, why is it hard to believe chimpanzees and humans are related (less than 1.5% codons different), when we readily accept mice and rats are related (more than 15% different)? Of course, on the outside, not looking at our genomes, humans are very different than chimpanzees, much more different than mice are from rats. Common ancestry predicts this discrepancy between function and genetics by recognizing that genomes are better explained by evolutionary history than readily observable differences between species; mice and rats are more different because they changed more quickly (because of their shorter generation time) for a longer period of time than humans and chimpanzees. What design principle can explain why humans are 10 times more similar to chimpanzees than mice are to rats? No one knows.


#12

@swamidass

Have a good trip, Joshua, and thanks for citing my article.


#13

i have at least 3 points:

  1. we dont have evidence for evolution.
  2. we have problems like the ic systems.
  3. evolution cant be test.

#14

This depends on what you are calling “evolution”. Young Earth Creationists accept some aspects of evolution. Could you be more specific about what part you do not accept evidence for?

What “we” are you referring to? How do you explain Michael Behe’s acceptance of human/chimp common ancestry if ic systems are such a big problem?

This is rather closely related to your #1. Again, there are absolutely things that can be tested. You are likely familiar with Lenski’s LTEE. There are certainly some aspects that cannot be directly tested, but you might consider exactly what parts of the theory you are referring to.


#15

i referring to a change at the family level in most cases. dogs and cats for instance.

indeed some id scientists accept common descent. but they still reject natural cause for some biological systems like flagellum or a complex protein.

see above. we cant test for instance the claim that dog and banana share a common descent.


#16

I fail to see why a “design principle” is needed to explain that. The difference that stat is measuring is overwhelmingly not functional evolution, but “noise” evolution. The rat/mice genome picked up a lot of differences over time just due to random chance which had negligible fitness impact, not functional differences.

Even if God looked at a chimp ancestor six million years ago and said “I am going to use that genome as a template but modify it into a homo erectus” and then 5.8 million years later said “I am going to modify that genome and make Man” then we would still expect our genome to have far less differences in them than the genome of rats and mice who have been going their own way for 12 million years.

I am having trouble seeing what it is creationists would have to explain since it is also what would be expected from that model. The changes you are measuring are almost all noise, not evolution of new function. I am not even sure most of that happens at the protein-making gene level. A lot of it is regulatory, using the same parts in different ways.

Your argument works against YEC, not against OEC. Am I missing something?


#17

Finally back. I’ll be responding soon. Looking forward to continuing the conversation.


#18

Okay, now to return to this thread finally. Thanks for everyone’s patience. First off, I need to emphasize that when I’ve made this argument in public, I am always pointing out that I am (1) simplifying the math to make it easy to understand, and (2) rounding numbers to make it easy to remember.

However, @Agauger deserves a more careful answer to her questions.

Into the Weeds

I’m going to, now, enumerate several of the details that I’ve usually left out. In my view, none of these details undermine my point, or misrepresent the data.

  1. The formula D = T * R is only approximately correct, because it does not take into account mutations that (1) revert a lineage to its ancestral state (decreasing D), (2) are convergent with the other lineage (increasing D), or (3) mutate an already mutated position to a non-ancestral state (leaving D the same). It turns out that as TR increases, these effects cannot be ignored. So a more complicated formula is required when the observed D deviates far from 0%, which we will just represent as D = f(T * R) which is less than TR, where f() is a non-linear function that we are not going to specify here.

  2. Moreover, I often leave out the fact that it is actually closer to D = 2TR (because chimps are mutation away from ancestral sequence too). I can see why that might be confusing to people, but it is because I’m imagining the phylogenetic tree in my head, and computing lengths along both legs. I’ll still use the convention that leaves out the 2 here, but keep that in mind if you try and do your own work on this.

  3. The T in the formula is to the time of coalescence of the DNA lineage, which also depends on the Ne before divergence. The larger the Ne, the larger T will be compared to the time the two species separate. For this reason, we expect D to be larger than a naive calculation based on separation (6 to 9 million years ago, in the case of humans/chimps) would indicate.

  4. Mutation R (per year) is dependent on generation time. This introduces some real uncertainty as we extend these values millions of years into the past. The shorter the generation time, the higher the mutation rate per year. https://www.ncbi.nlm.nih.gov/pubmed/8673286/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4711947/ So, if generation times for our ancestors were shorter, say, 6 mya to 2 mya, than we would expect D to be higher than we expect using a R measured using measured rates from today.

  5. The often quoted 2% and 20% (alternatively 1.5% and 15%) are rounded numbers from the original chimpanzee genome paper. https://www.nature.com/articles/nature04072 This measures the percentage of synonymous codons that are different between Humans and Chimps. Here is below. Note that the Ka/ Ks ratio is exactly as predicted by neutral theory (<1), as is the Ki / Ka ratio (in the paper). From the table below, you can see the actual percentages are about 1.2% for human/chimp and 18.7% for mice/rat.

  1. It is true that taking the whole genome into account, the difference between human/chimp is about 4%, but the difference between mice/rats by that measure is about 30%. Keeping in mind #1 above, that fits the pattern of being about 10x more than T*R, keeping in mind that D = f(TR) not TR itself. The two key points here is that the exact same measure of distance/similarity has to be used between mice/rat and human/chimp to be comparable, and the farther D is from 0%, the less the precise ratio of 10x will hold up. Nonetheless, we will always see humans/chimps much less different than mice/rats. If you do not like the measure I’ve used #4, use another measure, but you have to be consistent or the comparison is invalid.

  2. This information alone is enough to qualitatively (and semi-quantitatively) explain the human/chimp vs. mice/rate observation. As has already been noted, mice/rats have lower generation times and therefore higher mutation rates, and they diverged from each other very farther back in the past. In contrast, humans/chimps diverged more recently and mutate slower. That is why mice/rat is more different than human/chimp. No other design principle (other than common descent) has been able to even qualitatively explain this fact.

What About Quantitation?

One might legitimately ask for a quantitative test of all of this. I would expect as much from @agauger, and can give some published answers here. however, we have to keep all the uncertainties in perspective as we do this. There are several unknowns, so anything within a multiple of the true rate is a real success.

  1. Careful analysis (taking into account #1, #2, #3, and #4) was done of human and chimpanzee sequences in 2000 to compute R from D and T in humans. The rate ® computed from this analysis was 1e-9 bp / year (http://www.genetics.org/content/156/1/297), about 2x the mutation rate we’ve directly measured in humans since 2010, which is about 0.5e-9 bp / year (and faster in chimps, https://doi.org/10.1016/j.gde.2016.07.008). Given all the uncertainty here, that is a pretty good estimate, however it did not include the whole genome and our best analytical approaches. Nonetheless, given all possible reasons for the math to be a bit off, this is a remarkably good prediction.

  2. Subsequently, we have developed better methods (see https://doi.org/10.1093/molbev/mst019) that can more accurately estimate mutation rate across the genome. Of not, this what was used by the ArgWeaver paper, http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004342#pgen.1004342-Gronau2. These common descent estimates put the mutation rate closer to 0.7e-9/year.

  3. Keep in mind, once again, this all assumes that that mutation rates are constant. We know this is not the case. For example, chimpanzees certainly have higher mutation rates than us, at 0.6e-9/year. https://www.nature.com/articles/s41598-017-13919-7. All the discrepancies we see are easily explained by lower generation times in the past, for example, or a high Ne before divergence.

  4. A very important point is that the Y-Chromosomes mutate quicker and are also more divergent between chimp/human. That is an indepedent verification of common descent. This is a much better controlled experiment than looking at chimp/human vs. mice/rat. I’m going to leave out the details here, but they are fairly easy to find. Y-Chromosome divergence is often explained as problem for common descent, but it is actually a very strong validation of the D = TR formula.

All together, mutation rates are stunning validation of evolutionary theory. It was a quantitative test of common descent, showing that evolutionary theory could predict decades before genomes were known, what the generation to generation mutation rate would be when we could finally measure it.

Common Descent is a Design Principle

Perhaps there is another principle can explain these patterns, but no one has produced one. It is not enough to say that “God could have created things this way.” I agree. I think He created us too, just this way. However, He chose to create us in a manner perfectly explained by common descent. In science, we need a better mathematical and quantitative explanation of all this data before we leave common descent.

Notice also why all the ID and anti-evolution arguments we have heard leave these facts untouched. This is a positive case for common descent. At absolute best, if they were not in mathematical error, ID and anti-evolution arguments are evidence that God inspired some proteins here and there. However, even if Doug Axe is correct (he is not), we cannot show new enzymes are needed in human evolution, so his argument has no bearing on human evolution.

Not Against God’s Action

To be 100% clear, maybe God did act in our origins, science has not ruled it out. I affirm alongside you all that God providentially governs all things, including evolution, but I know this from Scripture, not any ID argument. From a Scriptural point of view, we might even find it warranted to affirm the de novo creation of Adam. I’ve been making that argument, so my opposition to ID is not because I oppose affirming God’s action. I just see no need for a bad argument to support something we already know.

Seeing no conflict between common descent and theology, I see no problem with this finding. Common descent is just how God created us.


@Agauger thanks for the honest engagement here. I hope that this makes sense to you. Happy to answer any more questions. I appreciate you’ve heard me out, and welcome attempt to engage this data.


#19

Yup. I’ll explain.

The reason is that this is all data that common descent explains. To plausibly reject common descent, you have to provide a better answer. By better, here, I mean mathematically fits the data better with fewer parameters and similar rigor. Science does not discard theories that work, even if they are working on “noise” evolution. Common descent explains the “noise” in our genomes, so that is why we we affirm it.

The reason it is important is because common descent explains what most of our differences are made up of, “noise.” The greater the ratio of noise to functional mutations, also, the easier it is to find functional mutations. It is like we are allowed more “misses” before having to hit one of the many “target” mutations.

Pull on this thread, and you’ll see how all the quantitative arguments against human evolution just fall apart. They do not withstand scrutiny as soon as we realize that evolutionary theory (common descent) explains that vast majority of differences between humans and chimps.

What you are describe here is, exactly, a type of God-guided evolution or creation-by-modification that looks exactly like evolution. This is common descent. Think through the implications of what you are saying carefully. If what you are saying is how God did things:

  1. Disproving evolution was not one of his design goals, because this method of creation is legitimately mistaken as common descent.
  2. Only a tiny number of mutations (just as predicted by evolution) are required to turn a chimp into a human. This is a major concession that ends up undermining every anti-evolution argument we’ve seen.
  3. I’ve already pointed creation-by-modification out as a viable option many times. See for example:

There are some creationists that argue God periodically create new species by special creation in a particular way: by copying their genomes, tinkering a bit, and instantiating a new species. This possibility is raised by Reasons to Believe (RTB).

Depending on the exact manner in which God does this type of special creation, it is possible that this could explain the data. God would have to be creating us from lower species, using transformations of our genomes that are readily understandable by known biochemical mechanisms (like point mutations, chromosome fusions, neutral drift, and transposons). Is this possible? Absolutely. Perhaps it is even true. But why would God do this? Why would He choose a creative mechanism that is so easily understood through the lens of common ancestry? Why was evidence against evolution not part of His design goals? Maybe the theologians can help us here.
http://peacefulscience.org/evidence-and-evolution/

I think this is a viable position, but because of the entailments above, it calls into serious question all the opposition to evolution. If God did not care to disprove evolution in our genomes, why should we?


#20
  1. Just gave you evidence for evolution in T=MR, that has yet to be countered.
  2. IC systems are a falsified argument against evolution, but even if they argument was correct this would only be an argument for God’s guidance. Even Micheal Behe himself, the one who put forward IC, affirms common descent, because the evidence is so overwhelmingly strong.
  3. Just showed you a test of evolution in T=MR and mutation rates.