Common Descent: Humans and Chimps / Mice and Rats


#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.

(Curtis Henderson) #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.


(Mark M Moore) #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?


(S. Joshua Swamidass) #17

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


(S. Joshua Swamidass) #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.


Uncommon or Common Descent?
(S. Joshua Swamidass) #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?


Jumping genes: Cross species transfer of genes has driven evolution
(S. Joshua Swamidass) #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.

(S. Joshua Swamidass) #21

2 posts were split to a new topic: The Mathematical View of Origins


(Mark M Moore) #22

I will say what I said on Jon’s blog…

Getting our definitions straight is essential to sorting this out and preventing us from talking past one another. We can’t tell to what extent we agree or disagree without it.

For example “Descent with modification” is one definition of evolution, I guess a preferred one around here. To me it could also be a form of creationism or at least intelligent design, depending on how the modifications occur. For example, farmers breed animals for certain traits and get them through descent with modification. They select far more powerfully for desired traits than nature does. So that fits this definition of evolution, but surely it is intelligent design as well.

Let’s have a thought experiment: Now suppose instead of farmers who went around selecting for traits, God Himself did so. If a certain group got a rate mutation that would produce a benefit if paired with another mutation which existed only in a second isolated group He would know it and be able to put those two populations together so that they would have the suite of mutations that, when combined with yet another rare mutation four generations from now, would result in a new function. So He is using Divine knowledge to leverage natural processes to produce something new. I would say that is evolution (descent through modification), intelligent design (intent drives the changes not natural selection) and “soft-touch” creationism (He intervened in the natural world to produce outcomes even if He never touched the genomes directly, He merely guided natural events in a way that nature would not in herself at anything like the same rate).

Now suppose that instead of taking the role of a selective breeder (with perfect knowledge) only, He also assumed the role of Genetic Engineer. That is, instead of strictly waiting for Nature to come up with mutations which could be combined to create new function, He did just what our engineers do. He made cuts and inserts in genetic code. Maybe nature would never get a particular protein to fold just right waiting for chance or mutation so He inserted a gene which would. So when our scientists make mice which glow because jellyfish genes have been inserted in them, and this population breeds, is this “descent with modification”? Well maybe, but the modification did not come wholly by NATURAL descent. It is doubtless intelligent design and specialcreation, and questionably evolution as well.

That said, such a situation could still involve natural descent, but that would not be where the modification would come from. Take the gap between a fish and an amphibian. What if over the course of thirty or forty generations He put just enough changes in each generation that they would still be able to be birthed and bred by natural means but each generation would also be further toward the amphibian end of things. This so that even though no amphibian was created out of thin air, or clay, one still had a very different creature through only forty generations removed from the fish, thanks to genetic engineering moving things a bit further along each generation. That is “descent with modification” but the modification is via genetic engineering. So is that evolution, special creation and intelligent design all rolled up into one?

Like Jon, I don’t think “natural selection” or any of the natural means we have discovered could have on its own produced the vast diversity we see today or in the fossil record. I think nature had help. And I think some of this arguing we are doing over it is because we are talking past one another on terms.

I can help here. Genesis chapter one is describing creation in two realms in parallel. High heaven where His will is done quickly, perfectly, and without His having to do it Himself. Then there is where we live. It is a creation suitable for beings like us. We can’t execute His will without His help either, just like the natural universe.

So the reason it looks like evolution is that it was supposed to be like TE. The natural universe just couldn’t pull it off without His subsequent (in some way) intervention. The first four and a half minutes of this video gives more detail even though its main focus is on a difference in time…

https://youtu.be/tijmm1hFLRs


(Mark M Moore) #23

But as you mentioned earlier, humans and chimps are much more different in phenotype than rats and mice, even though the latter have much more “noise”. Isn’t our much greater phenotype differences a sign that we have more significant functional differences with chimps than rats have with mice? I understand why in general what you are saying would be true if evolution by natural means were the full explanation, but in this case the opposite appears to be true.


(S. Joshua Swamidass) #24

No, I’m using “common descent”. @jongarvey misunderstood my position when he wrote about it.

Of course. I affirm God created us all by common descent. I presume God is intelligent. And creation is a partial synonym of design. Evolution is and common descent are neither anti-design nor anti-creation.

Sure, that is all reasonable. This is just common descent.

That is fine too. This is just evolution where God inspires some mutations. I’ve already said this is consistent with the evidence.

Fine. That also is consistent with science.

However, we do not have a good scientific argument to prove this. That is where the conflict lies, with people putting forward bad arguments to prove God’s action in scientific terms. Maybe evolution did require God’s help at times, but certainly not because 1 + 1 = 3, as many arguments against evolution presume. Why not just take the “win” (guided evolution is consistent with the evidence) and move on?

@Revealed_Cosmology you are just putting forward different models of common descent. This is a long way of just agreeing with the argument that the evidence shows common descent.


(S. Joshua Swamidass) #25

Not at all a problem. Remember, there are only a small number of mutations that explain the difference between humans and chimpanzees, perhaps just a few thousand and we do not know what many of them are. For “noise” mutations (as you put them) we have our formula, D = TR, but for functional mutations there is no equivalent theory.

We expect to have much greater differences in the rate that functional mutations are acquired. It is not possible to estimate the number of functional mutations in such an easy way, let alone identify which ones are functional. We know, for example, that the rate of acquisition will be very dependent on changes in the environment and selective pressure, and population size. These things will increase the rate of functional mutation acquisition.

Nonetheless, because evolution does not make any solid, quantitative predictions about the rate functional mutations are acquired, and we cannot measure this rate any ways, this just not a problem.


#26

ok. lets test this argument. its basically base on the molecular clock. to test the molecular clock we need to check the clock against the fossils, so we need to take a group of species and check if there is any correlation betweem their phylogeny and their fossils. here is one paper that try to deal with that:

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.13114

as we can see: there is no real correlation between the genomic data and the fossil one. as the author admit: “Here, we looked at many new plant fossils from the extremely productive region of Patagonia, and we found the opposite, that the fossils are much older than the clock dates. In this case, we can definitely say that the clocks are wrong. The fossils prove it”

so evolution doesnt realy predict what should be the difference among human\chip or rat\mouse, since we have no real correlation between fossils and the molecular clock.

its also important to note that even if we were found such correlation it will not prove a common descent, as i explained before.


(S. Joshua Swamidass) #27

Sorry @scd. You are missing the point entirely.

That paper is doing something different. It is looking at naive estimates (e.g. assuming constant mutation rate) over a much larger timeline (e.g. 50 mya), where we have much less information in the fossil record, and we have no direct measure of actual mutation rate, neither do we have full genomes on most these plants. All these things work together to make the molecular clock really bad in these cases. We are not troubled, because there are just to many unknowns to make a confident calculation.

In contrast, human/chimp evolution is about 6 million years, we have a much stronger fossil record, and we can and have directly measured mutation rates, and we have full genomes now too.

We found out a long time ago from studies like this that mutation rate varies a great deal. However, we did not know how to directly measure mutation rate till the last decade. That is what provides the independent verification.

@scd, you do not have to agree, but you have an opportunity to understand the thing you reject. Give that a shot.


(S. Joshua Swamidass) #28

Earlier, we looked at different parts of the genome (Y-chromosome vs. the rest), and compare their rates and divergences to test of common ancestry. That comparative work removes a great deal of uncertainty and the unknowns, and makes the results much more accurate. It is a very well controlled experiment.

Very closely related to this conversation is some work that Stephen Shaffner did. His angle uses the same formula (T = MR), but focuses on different types of mutations, and the relative differences in rates. He looks at the very tight correlation between the variation among humans, and the differences between chimps/humans, and other species too.

The key point about this analysis is that it does a much better job controlling for uncertainties in T and R. We know T is hard to tell from the fossil record. We know that R varies by type of mutation (we can measure this in the lab). So instead of trying to infer T, we can just see if the relative rates ® match up with the relative differences (D) for different classes of mutations. That is why the fit is so tight on these graphs. It is a much better controlled experiment.

From here, we can see that there are several lines of converging evidence, that are all correlated with each other.

  1. Mutation rate (the rate of change)
  2. Variation (difference between genomes of the same species)
  3. Divergence (difference between genomes of different species)

All these things are tightly correlated. Without common ancestry, there is no reason divergence should be correlated with these things.

Human variation, which is the cumulation of a lot of mutations, looks just like divergence (human with other species) as if it is the cumulation of a lot of mutations too. That is the key point. It just looks like the differences are the result of the cumulation of a lot of mutations by the same process.

See the data below…

This carries over to other species divergences too.


Behind the Shadow of Oz
Uncommon or Common Descent?
What about Noah and Population Genetics?
(Mark M Moore) #30

This statement sounds like there is a relationship between the amount of mutations as a whole and the functional mutations. That is, where there is a lot of “noise” there are more functional or “target” mutations.

Then when I pointed out that a comparison of rat/mice to human/chimp genomes shows that though the former has more “noise” the later seems to have more functional genetic differences you write…

So that statement seems to say (correctly I think) that there is no strong positive correlation between the amount of “noise” (mutations that are not important functionally) and the number/magnitude of functional differences. Chimps and humans don’t have as much noise as rats/mice, but clearly are much more different than rats/mice. Not sure that fits with your first statement. There are more differences in function than expected given the low amount of “noise” given your first statement.

To me, that is the fingerprint of God. There are more functional changes in less amount of time than is typical with what we typically see in other parts of nature. To you, the environment just drove the changes faster. No problem. Me, I wonder if the fast changes really happened by the same process as the slow changes. Sort of like @Jongarvey 's latest post at the Hump of the Camel. Or as I was pointing out on the whale evolution thread between the very slow changes in roquoral whales compared to what we know about Pakecitus to Rodhocetus.

I see it as a problem, if common descent with special creation at least of specific genes and proteins is automatically excluded from consideration, as it is by others not you. If they can’t make verifiable predictions yet about how fast nature can create observed change in function then its not even a theory yet, maybe not even a hypothesis unless it can be tested without numbers. They can’t rule out the finger of God until they are able to quantify what can be expected from the “natural” universe alone, quotes around that in a tip of the hat to JG.

Not just quantity, but quality too. That is, how big a jump in say…protein fold changes can “nature” make by processes we know about. If those changes can’t accomplish the changes they think happened, then they are missing something.

I know you have a broader view of “common descent” than your more secular colleagues. Maybe I should focus more on the theology. I am not sure there is any real resolution to this issue with our present level of knowledge. I just don’t want naturalists in the name of science attempting to impose a resolution before we truly have one by sweeping these sorts of incongruities under the rug.


(T J Runyon) #31

I hate all this what do you mean by evolution stuff. Then people will list off 5 definitions for evolution. Just stop. Everyone knows what is meant. When talking biology you can understand evolution in two ways. 1. The thesis of common ancestry. Or the process by which new species emerge as the modified descendants of pre-existing ones. 2. It can be understood as evolutionary theory. Or the tgeory that explains how evolution has taken and still takes place on earth, with reference to particular, old and current, aspects of life on Earth and to particular episodes of its history. Simple as that.


(S. Joshua Swamidass) #32

We will never be able to rule in or rule out the finger of God.

It is not a problem to exclude God’s action from the outset because the purpose of science is not to determine God’s action. Rather it is to understand creation, the way nature works. To understand God’s action, we look to Scripture.

Science, at absolute best, only gives us partial accounts of the world. Never complete descriptions or entirely sufficient explanations. This is transparently obvious to most people who actually work as scientists.


(S. Joshua Swamidass) #33

I see your frustration, but it is helpful to focus it in on common descent, of which the common descent of man is the most important example. All the conflict has, historically, centered on the evolution of man. That, also, is where the evidence for evolution is the strongest. When we see the evidence for the evolution of man, and theologically come to terms with that, there is no reason to hold out on all the rest.