Molecular Genetics of Whale Evolution


Did you know that animals have extra mechanisms that plants do not have?

There is an open questions relevant here:

  1. How long before we observe the fossils for Pakicetus do they first arise? It can be substantially earlier.

  2. Was Pakicetus a direct ancestor of Ambulocetus, or just a sibling species of Ambulocetus’ precursor? I.e. most likely it is an “uncle” not a “father”.

For those two reasons, we are not as concerned about this. We think the time line could be much more drawn out. This is certainly not evidence against evolution, nor is it a solid measure of how quickly the changes happen.

However, it does demonstrate that a set of transition between whales and terrestrial animals, just as we would predict from common descent.

Not really. Seals are precisely halfway between us and hippo/whales. Far from requiring several coordinated changes, we can see an intermediate form that removes the need for coordinated changes. Moreover, it is literally exactly what you asked for when you suggested we should see examples of this process in current day. Seals are an example of the same process, though they are much more like an aquatic bear than a walking whale (Pakicetus).

That is certainly true.

That is almost always the case. We are usually looking at “granduncles” not “grandparents”. That is just how poor sampling in the fossil record gives rise to.

In the end, this does not really matter much though @Revealed_Cosmology. At best, these objections are arguments for God’s guidance or providence in evolution. Ultimately, I agree that God providentially governs all things, including evolution, even if your precise arguments (and @scd) I find wanting given what we know in biology.

Better focus focus might be where you usually do focus, on the text of Genesis and how that relates with theology of Jesus. Hopefully @scd will join us there too.


@scd what are you hoping to achieve? These observations might be helpful for you:

In my view, science is not up for public debate. Arguments on the internet between non-professionals have absolutely no bearing on how mainstream science progresses. This is just not how science works.

Science is not intuitive. It is very mathematical and technical. Science requires very careful adherence to specific logical rules and standards. There are a multitude of rhetorically strong points (that convince the crowds) that are totally false scientifically. The rules and conclusions of mainstream science, therefore are not up for debate in the public square in any meaningful sense. Therefore, I usually avoid public debates about science.

Do not mistake this as an “appeal to authority.” Science can certainly be wrong. At times it is. Even when it is right, science’s certainty and scope are sharply limited. If you feel the need, go ahead and disagree with science. You might even be right. Let’s just not fantasize that public debate affects scientific opinion at all. It does not.

Instead of debate, my goal here is to offer a clear explanation of how mainstream science understands about our world. In what way, using the rules of mainstream science, is the evidence for common descent so clear? What, exactly, is the scientific definition of evolution, and why do scientists include theistic evolutionists? What are the rules of science? What are the limits and strengths of science?

Perhaps you will disagree strongly with what you learn of mainstream science. My aim is not to change your mind. Rather, I hope that you might understand what you reject, and that, perhaps, I might understand you too.

I’m happy to explain to you why we affirm common descent in science, but I’m not sure if arguing with you about very well established science could be productive.



Here is another article that I think offers insights to how groups get separated from each other …

Galapagos finches
The Galapagos finches have been intensely studied by biologists Peter and Rosemary Grant since 1973. At that time, the Galapagos island Daphne Major was occupied by two finch species: the medium ground finch and the cactus finch. Then, in 1981, a hybrid finch arrived on Daphne Major from a neighboring island. It was part ground finch, part cactus finch, and quite large compared to the locals. It also happened to have an extra-wide beak and an unusual song — a mash-up of the songs sung by ground finches in its birthplace and on Daphne Major. The immigrant paired up with a local female ground finch (who also happened to carry some cactus finch genes), and the Grants followed these birds’ descendents for the next 28 years.


The new immigrant finch (left), a cactus finch (middle), and a ground finch (right)
After four generations, the island experienced a severe drought, which killed many of the finches. The two surviving descendents of the immigrant finch mated with each other, and this appears to have set the stage for speciation. In December of 2009, the Grants announced that, since the drought, the new lineage has been isolated from the local finches: the children and grandchildren of the survivors have only produced offspring with one another.

Several factors probably contributed to the isolation of the new lineage. Since males mainly learn their songs as juveniles in the nest, the immigrant’s male descendents also sang his strange, mixed song. This likely affected which females were willing to mate with them. In addition, female finches tend to choose mates with beak sizes similar to their own, so the extra-wide beaks of the new lineage probably also biased it towards within-group mating.

Both the blackcaps and the finches demonstrate the important role that behavioral shifts may play in the early stages of speciation, as well as the many ways these shifts can arise. For example, the blackcaps’ split was triggered by a persistent, human-caused change in the environment, while the finches’ split was kicked off by a fluke series of natural events. The behavioral shifts that result in reproductive isolation also differ between the two cases. The change in the blackcaps’ migration pattern is genetically controlled, while the finches’ unusual song, which contributed to their divergence, is a learned trait.

These two examples make it clear that the division between species is not a black-and-white issue. Rather, speciation occurs as many different sorts of traits (physical, behavioral, and genetic) diverge from one another along a continuum. Because of this, biologists sometimes disagree about where to draw the line between incipient species — about when a division has become deep enough to warrant a new species name. Whatever we choose to call them, these two cases clearly illustrate how a lineage can split and begin to make its way down two separate evolutionary paths.

Of course, there’s no way to know if these paths will converge at some point in the future or are even completely distinct now. Another chance event on Daphne Major could cause the new finch lineage to begin interbreeding with the local population again. And blackcaps may never evolve differences beyond a slight change in wing and beak shape. While we can’t know the fates of these lineages, directly observing such divergences in real time highlights the fact that we don’t always need to look into the distant past or far off future to find examples of speciation in action. Evolution is occurring all around us. We just need to learn where and how to look for it.


I did not. Nothing with that kind of power anyway.

But then how can it be evidence for what I will call “macro-evolution” (to distinguish it from the variations on a theme that I accept can and have happened)? When I point out the time seems too brief to produce the observed change in form you respond that the form may have arisen significantly earlier and we just don’t know about it- allowing more time for the changes.

OK, maybe, but that’s not evidence in the scientific sense of the word is it? The same thing if this is an “uncle” instead of a “father” species. I think you need the fathers to make the case that there were fathers “scientifically”. Uncles - similar forms that were not the ancestors of a newer form- can be explained just as easily by special creation, can it not? So can a transition between whales and terrestrial animals. Going further and further with the same theme is just what human engineers do. I think you need evidence which supports evolution while undermining special creation. “Uncles”, even in transitional forms, does not rise to that level. The explanation of special creation and evolution-we-just-haven’t-found-the-right-fossil-yet are both plausible just looking at that evidence.

Now regarding the edifying subject of seal testicle storage verses that of hippos I said words to the effect that it was different and you said…

Correct me if I am mistaken, but I believe that hippos are thought to have come from a line which never had an exterior scrotum. Whales and seals come from a line which once had them but in the case of whales pulled them back in. Besides that, they don’t have the same problems. Whales never change environment. They can keep their testicles at optimum temperature using the same system. Seals can’t. They need to cool them more when working hard on land in a way they don’t in water. IOW I don’t think this is an example of an intermediate. I don’t think seals are halfway between humans and whales- rather they have a system which works best for them given the lifestyle that they have. We have not caught anything in the midst of transition. If we have, let’s see the seal fossils or populations which have gotten less far along.

Regarding my objection to you using a whale-like creature who was not an ancestor of today’s cetaceans to argue that there was more time available for adaptation than we might think you said…

Maybe the reason is the poor sampling of the fossil record, but maybe scientists should keep their mind open to the idea that this is NOT the reason. The reason the record shows “That is almost always the case” may be because there was something else going on back then and not merely today’s known processes acting at today’s known rates.

“At best” from which side? I think they are arguments for both special creation and God’s guidance in evolution. So I would put it “at worst it is an argument for God’s guidance in evolution, at best it points to special creation.”

I think you are right about that. I do have a modest science background, but you are the scientist. Jon Garvey is a “man for all seasons” but I would say he is more philosopher than either scientist or theologian. I am not a proper theologian either, but as Providence would have it, on early Genesis I find myself in that role.



Cladograms are not “family trees”…

They are specifically designed to demonstrate the linearity of morphological or phenotypical Nested Hierarchies. This methodology does not require a precise knowledge of who are the uncles and who are the fathers.

Do we know anything about the phenotype of this arctic whale? It could very well be a dead end, yes?

I am never quite sure how to categorize your position, but the key problem of whales in general is not what the arctic whales tell us… but that all these whales and proto-whales appear to appear in the fossil stack out of nowhere …

… unless you acknowledge that no whale appears in the fossil stack before any large mammals first appear.

And that no large mammals appear before all the dinosaur age predators disappear from the fossil stacks.

Large mammals… twice larger than opossums for example … would not have thrived in a world full of carnivorous dinosaurs of equal size or larger.

So: Young Earth Creationists, for example, have the peculiar problem of explaining how giant vegetarian dinosaurs (Bronto’s and the like) all drowned before cows drowned. And why even giant marine reptiles drowned before cows did…

If you are an Old Earth Creationist, who believes in a large Regional Flood, then the sequence of the rise of dinosaurs, then the fall of dinosaurs, followed by the rise of mammals should make complete sense to you. And the question of the arctic whale becomes a mysterious footnote, yes?

And so if the six days of creation has no bearing on the reality of evolution, I’m not quite sure how to position your views within a geographically sound view of the ages of the Earth.


sure. first we need to define what evolution means. im not sure that a common descent for most creature is a part of evolution definition, since many accept any genetic variation as evolution. as we can see above with the finch speciation.



The reason so many do is because that is the sole definition of evolution: “Any change in a population gene pool.” Full Stop. Period.

There is no upward evolution vs. downward… devolution is a quack concept. There is no way to quantify what is an upward vs. downward evolution… it’s all sideways if you want a direction. But even that would create misinterpretations. Evolution cannot happen to an individual; evolution is always a population-wide issue. A single dinosaur doesn’t become a bird. But a population of small feather dinosaurs appears to have gradually become a population of creatures we would call birds.

Evolution, either randomly or driven by changing environmental factors, will frequently lead to a change in the ability of members of one sub-population’s ability to be sexually reproductive with members of another sub-population. Reproductive compatibility is a gradient; and with gradients there are Tipping Points. At some point, when sexual compatibility (as controlled by any number of possible factors) reaches the Tipping Point, the two (or more) sub-populations are no longer exchanging enough genetic information to communicate changes in one group to any other group.

Thus, by definition, changes in one group begin to dominate just that group. Once this occurs, barring any other event that would reverse the process, one population starts to look smaller, or larger, hairier or less so, more or less colorful… as well as focusing their diet on this or that food, instead of the food the other group prefers.

Over millions of years, you can end up with something that looks like a squirrel population… and another population that looks like an Otter. Both populations would be traceable to a common ancestral population.

So… as soon as the concept of speciation is included in a discussion of evolution, you automatically have “common descent”. Starting with “common descent” does not necessarily lead to speciation; but reversing the sequence does.


This is not the strongest evidence for “macro-evolution.” For that, look to the genetics. This might be a helpful summary.

In the end, it is not my goal to convince you that evolution is true. I’m just here to explain why it is such a well established and successful scientific theory (in science), and to understand exactly what it is. You can still choose to reject it, but there is still value in understanding what you reject.

At best, from your point of view.

At worst, they are just bad arguments. At best, they are arguments for God’s guidance in evolution, because they do not engage the mountain of evidence for common descent. Even if all you say is convincing (but is not), there is still very strong evidence for common descent.

To be clear, that does not mean common descent is true. God could have specially created us all in a way that looks like common descent. However, it really does look like common descent from a scientific point of view.

Have you read the 100 year old tree parable yet? It might be a helpful way to think about this.

Evolution is the process of common descent by which God providentially created all life. It is partially described by evolutionary science.

You are right that it is not merely genetic variation. Nor is even speciation (even YEC’s affirm that). Rather, a key linchpin is the common descent of man.

That might be evolution, but many people who reject evolution affirm change in the population gene pool. That is not the center of the debate. Rather, the key point for most people is the evolutionary origin (providentially governed by God) of the human race.


Hippos and whales are from the same line (look at the image in the original post, Molecular Genetics of Whale Evolution). I’m not sure we precisely know the ancestral state. For example, it is possible (I’m not sure we know) pakicetus (the whale-headed rat dog) had internal testes. In that case, going from pakicetus to a whale would not require a change in this trait.

Seals come from a different line. They are closely related to bears (their skulls look nearly identical), and likely did have scrotums in the ancestral state.

Keep in mind, even some YECs think that whales evolved from pakicetus, in just 4,000 years. That, however, too fast to believe. I think 4 to 8 million years is much more believable.

Pretty cool right?


ok. so why you choose to believe in a common descent for all life (say banana and a cat) rather then special creation? is it because the scientific consensus or because the evidence?

i also take a look at your post about evidence for evolution. for instance you said:

“humans are very different than chimpanzees, much more different than mice are from rats.”

im not sure about that. if we are talking about external morphology sure. but if we are talking about their biochemistry it may by a different story. so i see no problem here with the notion of common similarity=common designer. i dont think that there is any evidence for evolution that cant be explain by a common designer too. so why we need to prefer evolution above non evolution?


Just because a certain hypothesis is compatitable with an empirical observation doesn’t mean it isn’t evidence against that hypothesis. Common ancestry predicts the pattern of similarity (and the dissimilaraties) that we see. Design does not. So the patterns of similarity we see is more probable on common ancestry than design. Furthermore, you or any other design proponent have never provided any independent evidence that the designer shares the same psychology and design tendencies as us. You can’t just say the design could have done this. You must provide independent evidence that this is what he/she would have done. Common design provides absolutely no obstacle to common ancestry. And when I hear a design proponent resort to that I know the debate is over and evolution has come out on top.


And it’s remotely plausible that the designer could have design some traits that look like evolution occurred. But every one!? The more observations that we find that suggest common ancestry the less plausible common design becomes.


Certainly not because of the scientific consensus. That is not good enough of a reason. I’ve written about this at length before, but to summarize.

  1. I saw and understood the evidence for common descent for myself.
  2. I could no longer find any conflict between common descent and Scripture.
  3. I encountered Jesus, and found Him to be greater than anti-evolution-ism.

Did you look at the footnote?

Sure, God could have made humans and chimps 98% similar, but that is not the argument. The issue is that he also made mice and rats 80% similar, about 10x more different. What design principle explains why that is? The only design principle we know of that that explains this is common descent. A simple formula based on common descent, D = T * R, explains mathematically why humans/chimps are 10x less different than mice/rats.

That is just one example, but there are thousands of others like it, where evolutionary theory can explain mathematically and quantitatively patterns we see in the data. I’ve talked to ID advocates (all the famous ones) and creation scientists everywhere. Not one of them have presented a design principle other than common descent that explains this data.

Exactly. Until we see a design principle other than common descent that explains all this data, mathematically, most scientists will always be more convinced by common descent.

Well almost exactly =/. This is not evidence against special creation. However, it is evidence for common descent. It can be for common descent, without being against special creation.

I disagree with this. It appears common descent is God’s design principle. He did, after all create us; He did design us all.

Remember, common descent is not in opposition to design. God created us; in appears He designed us all by a process of common descent.


When I say design I’m talking special creation. See how the ID movement has taken over that word? It now creates confusion. I agree with what you say


I’ll rephrase a little. The pattern of similarity that we observe across organisms is more probable on common ancestry than on special creation. The hypothesis God created life on earth tells us nothing about what we should observe. What similarities we should see etc. We have no a priori reason to expect common design. While special creation is compatitable with what we see, it doesn’t follow that this data doesn’t favor common ancestry.


Yep. Time since likely divergence provides the best overall correlation with the amount of molecular difference. The ‘common similarity = common designer’ proposal answers nothing in terms of quantitative expectations or the time-dependence of sequence similarity. It’s too amorphous and insufficiently specific to serve as a logical argument.


great. so its all about the evidence.

the simple answer will be a similarity at the biochemical level. we can find it in a designed objects too. for instance: an electric car can be very different from a regular car. even that they are both cars and look very similar, their inside is very different. so here is an easy explanantion without using a common descent model



@swamidass brought up a very good point you are overlooking. I’m sure we can agree that mice and rats are very similar, both by visual observation and by DNA sequence observation. However, chimps and humans at the DNA level are over 10X more similar than the rats and mice. The evidence leans strongly toward common descent (and a rather recent divergence), rather than separate creation. God did not need to make humans with 97% DNA similarity to chimps, why would He intentionally make it look as though we are very close in lineage?

The analogy to automobiles that you continue to use is a poor fit for biological systems. Evolution is driven by relative fitness for selection of alleles. There are many different influences on automobile design - consumer preference (which itself varies considerably), utility, and government regulation all play a part in how cars are designed. All analogies fail at some point and this analogy happens to fail at all but the most superficial of levels.


No it is not just about evidence. It is also about Jesus. When I found Him, I was able to turn from my idolatry, and leave my scientific arguments against evolution. He was greater.

The simple answer is not sufficient.

Please give me a mathematically and experimentally grounded reason why humans/chimps are 10x more different than mice/rats. Once that is done, we will move to the next example. I’ve have yet to see some get past the first example. Maybe you can be the first.

In contrast, common descent answers the question just fine. D = T * R.

An analogy would be why is it that a particular submarine (chimp) and a particular race car (human) are 10x less different then two different bikes (mice/rat)? We just do not observe this in human designs. Which is why it is such a hard concept for us get our heads around. However, this is what we observe in biology.

I disagree. Don’t forget Duhem Quine:–Quine_thesis. To make that statement you have to insert several auxiliary hypothesis into “special creation”. Perhaps, with the right design principle, it would be more probable with special creation. However, we do not know that principle yet.

Yes we do. I affirm common design because God created us. He designed us all. The principle He used to create us is common descent.



There is no doubt about that. One can affirm that genetic mix can change in a gene pool and yet still reject evoluton. I was providing the definition of Evolution in the face of such foolishness, not as a way to change a person’s view.

And really, even Speciation is something that some YECs might accept, if they are part of the group or school of YEC-ism where a Kind is a group of species. These folks, as you know, will accept the idea that one species of bear, once released from the ark, might develop a population that splits and a new species of bear appears.

What is common among all those who oppose Evolution per se is the idea that one “kind” of animal population can change into another kind:

a fish with strong fins becoming a land-living amphibian

a large carnivore dinosaur population splitting where one sub-population eventually becomes bird-like

a hippo-like population becoming like a whale …

And so forth. With all the crazy types that have visited BioLogos, 80% of them drift into this final and most resistant of objections: evolution from involving dramatic change in size, shape and life style is not possible.
But they never explain why the DNA would know when they were supposed to stop!