Common Descent: Humans and Chimps / Mice and Rats


@vjtorley I’d appreciate some comment from you on this too. I was very impressed that you, as a philosopher, was able to pick up on this immediately when I first made the argument several years ago. How were you able to do that? Why do you think it has it been difficult for others?


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…


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.


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.


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.


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:

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.


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.


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.


Hi Joshua,

I should say by way of explanation that I’ve been interested in the creation-evolution controversy since 1973, when I was in junior high school. My opinions have see-sawed back and forth over the years. I was raised in a creationist household, but not rigidly so: I was brought up Catholic, but my grandfather (who died when I was six) was a Presbyterian, and I often perused his Scofield Reference Bible, which espoused the gap theory. H. G. Wells’ 1926 Outline of History (which also belonged to my grandfather) was on our family bookshelves, too, so I imbibed his outlook as well. Over the next few years, I devoured everything I could get hold of on the creation-evolution controversy, ranging from Did Man Get Here By Creation Or By Evolution (published by the Jehovah’s Witnesses in 1967) to The Emergence of Man. As a result, I came to accept not only the evolution of living things, but also human evolution - a subject in which I was avidly interested.

When I went to university, I came across the work of young-earth creationist Melvin A. Cook, as well as Douglas Dewar’s book-length debate with H. B. Shelton, titled, Is Evolution True? (1947, edited by Arnold Lunn). That reawakened my interest in the creation-evolution controversy. At the time, I was studying for a science degree, but biology was not one of my subjects. However, geology was, and I asked the head of the geology department at the Australian National University, Dr. Campbell, what he thought of Cook’s arguments. Dr. Campbell was kind enough to read a summary of the arguments and comment on them. What he said persuaded me that my anxieties regarding the reliability of radiometric dating were groundless.

A few years after completing my science degree, I moved down to Melbourne. By now I was finishing off a couple of other degrees. In the meantime, I came across Science and Earth History (Prometheus Books, 1987), and I was highly impressed by its cogent and detailed refutation of creationist arguments. I came to regard scientific creationism as a pseudo-science.

My views changed about a decade later, when I came across Mike Behe’s book, Darwin’s Black Box (Free Press, 1996). That convinced me that a solid scientific case could be made for intelligent design. However, Behe accepted common descent, and on this point, I saw no reason to change my opinions. I showed Behe’s book to a few friends of mine. Not all were equally impressed, and over the next few years, I came across criticisms of his arguments on the Internet, which made me question his views.

Around 2006, however, I came across botanist Alex Williams’ article, Astonishing DNA complexity demolishes neo-Darwinism, which had a huge impact on my views. The following passage struck me, since I had previously spent ten years working as a computer programmer, from 1989-1999:

“DNA information is overlapping-multi-layered and multi-dimensional; it reads both backwards and forwards; and the ‘junk’ is far more functional than the protein code, so there is no fossilized history of evolution. No human engineer has ever even imagined, let alone designed an information storage device anything like it. Moreover, the vast majority of its content is metainformation—information about how to use information. Meta-information cannot arise by chance because it only makes sense in context of the information it relates to.”

That article persuaded me anew that the genetic code was intelligently designed. Later on, when I came across the work of Douglas Axe, my certainty was reinforced.

Even at the time when I read Alex Williams’ article, I demurred from his young-earth creationism (based on Haldane’s dilemma), but I mentally divorced it from his case for Intelligent Design. Many years later, I found that he was wrong about junk DNA, and I gradually came to realize that Dr. Axe’s mathematical arguments for proteins having been designed were flawed.

Another finding that influenced my views on origins for a while was the discovery of de novo genes - in particular, a 2011 paper by the Croatian biochemist Dr. Branko Kozulic, titled, Proteins and Genes, Singletons and Species, which argues that the presence of not one but literally hundreds of chemically unique proteins in each species was an event beyond the reach of chance, and that each species therefore had to have been intelligently designed. I was much taken with these arguments, until it gradually dawned on me that the math underlying them was faulty.

So in answer to your question, Joshua, although I’m a non-scientist, I am broadly familiar with the arguments put forward on both sides from many decades of reading, and I am used to changing my views as new information comes to light. That makes me intellectually flexible, you might say. If there’s one thing I have learned, it’s this: always pay attention to the mathematics which is used to support an argument, whether for or against evolution.

I might add that my long-standing interest in human evolution and my background reading on the subject helps me to sort the wheat from the chaff, so to speak.

I hope that answers your question. Cheers.


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.


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.


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.


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.


hi prof swamidass.

but this is a problem for several reasons:

  1. it means that evolution cant predict what will be the difference among species. and therefore evolution cant be test at this point.
  2. we can claim such a thing to any such contradiction we will find.
  3. this evidence fit naturally with special creation but not with a common descent. so the best (and simplest) explanation will be creation in this case.

how we can know it for sure? for instance: if we have T in human, how do we know that the original base was A?


This is a complete non-starter for me, @Revealed_Cosmology.

If the natural universe couldn’t pull it off, there would be no need for God to hide this fact.



Common descent is a default logic. If the earth is 5 billion years, common descent is unavoidable… because nothing can stop DNA and RNA from changing and evolving.

Rejecting common descent is like rejecting the age of the earth.

Now, if you insist the Earth is 10,000 years old or less, then you are not just making a religious avowal, you are also opposing the eye witness of nature . . . and to no avail! Why? Because if think most of the fossils are from the flood, you still end up with the inexplicable:

  1. where are all the human fossils that should be in the same layers as the dinosaur fossils?

  2. to end up with the 1.5+ million species of terrestrial creatures that we see in the modern world, you still have to conclude there was hyper-evolution in the animals released from the Ark.

None of these conclusions can be sustained!


I am sorry you feel that way. I don’t see that He is “hiding” anything. We just don’t have the ability to see everything, along with extreme personal bias when examining the evidence.



I do not accept the position that God was “compelled” to do things in a way to that fools humanity into concluding what would otherwise be a common-sense conclusion.

The default position satisfies Occam’s Razor better than any other position.


Nor do I. He is not “compelled” to do anything but tell the truth since His Word is Truth. Your basis for the assumption that He is “fooling” us is based on the idea that we should be able to detect His intervention at our current level of knowledge. That is, that He forced big dramatic instantaneous changes that made a lot of “noise”. But if He has perfect knowledge why does He need tremendous force of intervention? Think of the “butterfly effect”. If He knows that a butterfly flapping its wings and time and place “X” will cause a hurricane 1,000 miles away next week, why does He need to get a big spoon and stir up a hurricane?

That’s not Him “hiding” anything. Maybe inside a certain window of knowledge we can’t see it but when we press on it is even more sublime than His getting a big spoon and intervening with a lot of force later rather than use a maximum amount of wisdom and foreknowledge to do the same things with minimal force.

In your view the conclusion is “common sense”, but I and others on this board have pointed out situations where some things happened that are not “common sense”. Again, you have to be able to see things from outside your own skin. Pakicetus to Rohocetus in 200K years coming from the same processes which took blue whales and finbacks 3 million to split up is not “common sense”. It is something a reasonable person should be able to question.


So much of the “noise” being generated by the debate of “creation versus evolution” comes from a fundamental misunderstanding of the Hebrew term translated by the English word “create.” The Hebrew verb “bara” carries with it no connotation of how, or even how quickly, something was done.
Let me illustrate, because not even the word “create” in English does so.
Starting from a huge slab of marble, Michelangelo masterfully and painstakingly, over a long period of time, carved out a sculpture called “The Pieta,” a masterpiece of art. Were we to have asked him at the time whether he was the one who made the carving, he might have said (in Italian) “yes; I created it.”
He would not thereby have communicated any information whatsoever about HOW he did it, nor of HOW LONG it took.
Similarly, when confronted the biblical statements regarding God having “created” something, we have to look deeper into the context for any such information, since the phrase itself is not specific.
So, please, please, please stop hearing “all of a sudden, out of thin air” when you come across this word in the Bible. Instead, you can focus on the de novo nature of what was accomplished, when this phrase is used.
'Nuff said. Cheers!