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Evidences for Evolution, Part 2a: The Whales’ Tale

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June 14, 2010 Tags: Genetics, History of Life
Evidences for Evolution, Part 2a: The Whales’ Tale

Today's entry was written by Darrel Falk and David Kerk. You can read more about what we believe here.

This blog is the second piece in a series by Darrel Falk and David Kerk. The previous entry is found here.

A really fun family outing in San Diego is to visit Sea World and see the many fascinating and exciting marine exhibits. But the unquestioned main attraction is Shamu, the killer whale. If you are a real bona-fide thrill-seeker, you sit in the first few rows next to the tank, virtually guaranteeing that when the sleek but massive animal breaches the water and then falls back, you will be inundated by a huge wave and soaked to the skin! How did such marvelous creatures arise in the first place? It has taken many years of patient work by scientists operating in very different specialties, but we are now at the point where we can relate the “Whales’ Tale”. It is a story of evolution over a critical period of about ten million years, which is supported by three main types of evidence. We will consider the first two types of evidence (which are molecular in nature) in this essay, and the third type (which is fossils), in our next essay.

If evolution is true, then modern whales and other mammals should be related to previously living ancestral species, through a process of “descent with modification”. It should therefore be true that the living organisms and ancestral ones (now extinct) should form a sort of “family tree”. If you have taken an interest in your family genealogy, then you know right away what this means. You, your siblings, parents, aunts, uncles, grandparents, and so forth, can be arranged in a diagram that passes from one generation to the next. If we visualize this going deep into the past, we can use the “tree analogy” even further – the most recent generation of members of the family can be said to lie at the tips of the branches, while very early generations of the family would lie deeper in the tree, at branching points.

The metaphor of using a tree to represent ancestry comes in other varieties too—not just families. Consider, for example the growth and diversification of the historic Christian church – from its roots in ancient history to the tips of its branches—the various denominations still in existence today. As shown below, the Christian traditions which are especially closely related to each other are located near one another at the branch tips. The more distant the relationship, the further away they are in the tree of Christian traditions.

So how can one derive the family tree for organisms like whales—how can one determine the tale of the whale? Cetaceans, after all, have such a dramatically different body plan compared to all other mammals; deciphering their family tree presents a fascinating challenge. If evolution is true though, there is one group of organisms to which whales are more closely related than any other. Furthermore, if evolution is true, independent ways of deriving tree structure ought to produce very similar results.

In today’s essay we will show two methods that have enabled biologists to trace the lineage of the whale family: two somewhat independent methods that allow us to explore the structure of the whale’s family tree. In our next post, we will examine a third.

The instructions on how to build an organism are contained within the four letter DNA code: A, G, C, and T. Each gene is a short stretch of this code and the specific order of the 4 letter code is called its “sequence.” The cells of the organism read the code, gene-by-gene, working in concert with one another in constructing the body. Because it is very different than that of other living mammals, understanding the origin of the whale body presents an interesting challenge. Whales are mammals though, so if evolution is true they must have a family tree which shows how they are connected to other groups of mammals.

One useful source of information in whale family tree construction is the sequence of the DNA code-letters (bases) in a particular gene in whales compared to the sequence of that same gene in other mammals. Why would this information help us? Both whales and their related mammalian “sibling and cousin” species will each possess a version of whatever gene we look at that was inherited from their common ancestor. Random mutation will have changed each version of the gene slightly, so that the descendant organisms will generally each have a distinct sequence. More closely related species will have a more recent common ancestor, and will, therefore, have more similar sequences. This means they will tend to lie closer together in our reconstructed family tree.

We can put this DNA gene sequence information from whales and comparison mammals into a tree-building computer program. The living organisms form the tips of the branches and the interior branch points represent extinct predicted ancestral organisms. It turns out that whales sit closest in the tree to a set of hoofed mammals including cows, sheep, pigs, camels, and hippopotamuses.1 This entire group of hoofed mammals is technically called the “Artiodactyla” (Greek for “even toed”). If evolution is true, this means that whales and these even-toed hoofed mammals share a common ancestral species that existed much more recently than the ancient common ancestral species that gave rise to all mammals. Indeed, even before that there would have been a common ancestral species that gave rise to all mammals and all reptiles. All of this can be represented on the metaphorical tree of life.

There are other independent ways in which DNA analysis can be used to test whether we have correctly positioned whales on the tree of life. Scientists are always eager to obtain different sorts of data. If all independent methods lead to the same conclusion, if “all roads lead to Rome” to use the analogy introduced in an earlier essay, then we can become increasingly convinced that our model is correct. So what is another DNA feature that can be used to determine the whale family history? There are certain chunks of DNA which, on rare occasions in the history of life, move to a new location in a chromosome. These mobile chunks of DNA are sometimes called “jumping genes” although it should be emphasized that they don’t “jump” very often. The location at which a jumping gene inserts itself into a chromosome is quite random. When such an element inserts itself into a particular place in the chromosome, it will reside at that location for many generations. Indeed since “jumping” is so rare, it generally stays at the same location for millions of years.2 Since the insertion process is almost random, and the element almost never moves out once it is in a chromosome at a particular position, the chance that a “jumping gene” will be in precisely the same place in the chromosome of unrelated organisms is vanishingly small - (essentially zero). In other words, the “jumping gene” makes an ideal “marker” to trace the ancestry of living species. If you examine a set of such “jumping genes”, each inserted into a particular place in the chromosome, only related organisms will share a particular insertion, since they inherited it from their common ancestor. If one of a pair of organisms lacks this insertion at this site, it supports the conclusion that those two organisms do not share a recent common ancestor.

The figure below shows a set of chromosomes, and then enlarges one part of one chromosome to show the DNA molecule. Imagine a “jumping gene” moving in precisely between two of the millions of units of DNA in a chromosome. Since DNA replicates each generation, the chromosome with its inserted “jumping gene” gets passed on faithfully through millions of years. Once a piece of DNA has moved into a chromosome between two bases, it is a great marker to identify species that descend from a common ancestor.

One of the very nice things about this type of DNA information is that it can be tabulated, and is simple enough that you can do a little head scratching and puzzle out the relationships of the organisms involved. The data either consists of a particular “jumping gene” being present (call that a “1”), or if it is absent (call that a “0”). In practice we need a third category, and that is “we don’t know if the “jumping gene” was there or not” (call that a “?”). This third category is necessary because sometimes a random genetic event will result in the loss (deletion) of the entire region which might have contained the jumping gene insertion. Now with this background, take a look at the following figure.3 For this somewhat simplified example, we show 20 “jumping genes.” If two species share a “jumping gene” at exactly the same position, this means those species are derived from the same ancestral species. This tree confirms the prediction made based on DNA sequence data previously, that is, that whales should be closely related to the group of even-toed hoofed mammals. For example, whales share “jumping genes” 10,12, and 18 with a broad assortment these animals. This means that they all share a common ancestor with insertions in these exact same positions. No other living organisms will share this group of common insertions, or this common ancestor. In addition, these data show that whales are most closely related to hippos (note that they each share “jumping genes” 4,5,6 and 7). (In fact, DNA gene sequence studies also support such a relationship, so this is not an aspect of using “jumping gene” data alone).4

Now we come to the bottom line: so far we have two roads (DNA sequence data and “jumping gene” data), both of which lead to “Rome.” Both point to exactly the same conclusion. Whales, despite their highly specialized body form, can now be confidently predicted to lie within the group of even-toed hoofed mammals. Furthermore, of that group of living mammals, hippos are predicted to be the most closely related to whales. There is agreement between two types of DNA data, and more confidence in our result.

Editor's Note: For a correction to the data in this chart, please see David Kerk's comment below.

Therefore, if evolution is true, we would expect that living whales and living hoofed mammals should share extinct common ancestors, from which they descended with modification. Or, put another way, we should be able to find “transitional fossil forms” which we can identify by their structural features as being ancestral to both living hoofed mammals and also whales. But about how long ago would we expect such extinct forms to have been alive? It turns out that application of DNA data once again can give us a time estimate with which to start.

We mentioned above that random mutational changes to DNA in an ancestor are passed on to descendant organisms. It turns out that for a particular gene, this sort of change acts as a sort of “molecular clock”. That is, for a particular gene, the rate of change over time is approximately constant. If we can “calibrate” how fast a particular molecular clock for a particular gene is ticking, then we can use it to determine how long ago in the past two species last shared a common ancestor. For example, we know from the fossil record (which has been dated by radioactive isotope clocks, as discussed in a previous essay), that cows and pigs last shared a common ancestor about 55-60 million years ago. We can measure the total number of changes in the DNA of a particular gene in cows and pigs, divide that by the age of a fossil from an ancient species believed to be ancestral to both of them, and determine an average rate of DNA change. Our molecular clock for this gene is now calibrated. If we want to determine when whales last shared a common ancestor with cows, and then pigs, we can measure the total DNA change in our clock gene between whales and cows, and between whales and pigs. We can then divide by the rate of “ticking” of the clock, and determine when in the past these ancestors should have lived. When we do this, it turns out that such common ancestors should have lived about 45 to 50 million years ago.1 So if evolution is true, we should expect to find fossil “transitional forms” showing evidence of common ancestry of hoofed mammals and whales, dating from about this period. We will see in our next essay that this prediction is borne out.

The next blog in this series can be found here.


1. Grauer D. and Higgins D.G. 1994. Molecular Evidence for the Inclusion of Cetaceans within the Order Artiodactyla. Molecular Biology and Evolution 11(3):357-364.

2. Very often, in fact, inserted “jumping” elements are “paralyzed” and unable to jump out, but that’s another story.

3. Data from: Nikaido M., Rooney A.P., Okada N. 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements:Hippopotamuses are the closest extant relatives of whales. Proceedings of the National Academy of Sciences U.S.A. 96:10261-10266.
Figure adapted from: Freeman S. and Herron J.C. 2007. Evolutionary Analysis, 4th Ed. Pearson, Upper Saddle River, NJ, Pg. 128.

4. Gatesy J., Milinkovitch M., Waddell V., Stanhope M. 1999. Stability of Cladistic Relationships between Cetacea and Higher-Level Artiodactyl Taxa. Systematic Biology. 48(1):6-20.

Darrel Falk is former president of BioLogos and currently serves as BioLogos' Senior Advisor for Dialog. He is Professor of Biology, Emeritus at Point Loma Nazarene University and serves as Senior Fellow at The Colossian Forum. Falk is the author of Coming to Peace with Science.
David Kerk is Professor of Biology, Emeritus, at Point Loma Nazarene University. Dr. Kerk obtained his PhD in Anatomy at UCLA and is currently involved in bioinformatics research at the University of Calgary. He resides on Vancouver Island, in Parksville, B.C. Canada.

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Ryan Bebej - #17765

June 17th 2010


How do you determine that your design explanation is truer than a non-design explanation if you’re not generating any testable hypotheses? I’ll repeat the question that Larry asked in #17742: “What does it tell us to look for?” Until you answer that and collect data to test your hypothesis, your explanation will have no scientific traction.

Larry - #17767

June 17th 2010


If we are discussing science (and I think we are), in order to scientifically assess whether “an explanation is true” we need some constraints. We need to be able to say “we should definitely be able to find A, B, C, and we definitely should not find X, Y, Z.” Design still seemingly predicts anything and everything which is why it is heuristically sterile and scientifically useless. It might be true in the same way Gordon Glover’s alien hypothesis might be, but is currently too unclear and unparsimonious to consider.

“Science is a very profitable business, and design just does not fit in to the business model.”

Useful theories and models are retained and used, poor theories and models are weeded out and rejected. In this area, the ID community have had a very long time to produce something and they have produced very little (if anything at all).

pds - #17772

June 17th 2010

Ryan and Larry,

I just don’t have the time to go into ID 101 for you guys.  It is remarkable how little you know about the “inference to the best explanation” methodology and line of reasoning. 

What are they teaching the kids these days?

John VanZwieten - #17785

June 17th 2010


I think the reason it “throws people into a rage” is that they conflate your limited point with how the YECs (of various stripes) continue the argument:

1.  It’s not proven exactly how RM+NS could get us to whale
2.  So evolution can’t get us to whale
3.  So evolution is false and scientists are godless
4.  So God created everything in 6 days <6000 years ago.
5.  So there!

The more you can make clear the limited (though potentially valuable) point you are making, and especially if you make clear what does _not_ logically follow, the fewer hackles you will probably raise around here.

(Or maybe you will just raise different hackles )

Dennis Venema - #17812

June 17th 2010

Rich, why not examine two organisms for which we have complete genome sequences (say, humans and chimpanzees)? When comparing these two organisms genetically at a genome-wide level, I don’t see anything beyond the ability of RM + NS to accomplish.

Do you?

If yes, please provide examples (GenBank numbers or names of genes I can BLAST would be fine).

beaglelady - #17815

June 17th 2010

Design is also a lousy theory for getting research money.  We should probably reject it for that reason too.  Science is a very profitable business, and design just does not fit in to the business model.

Are ID proponents actually conducting research?  Are they writing up grant proposals to get money?  What are they planning to research, and how would that research be conducted? I’ve always wondered about ID research and how one would seal off the designer from an experiment as a control.

Science can be profitable (actually that would be technology,  the offspring of science) but hey, if cancer drugs work, they work.

Argon - #17819

June 17th 2010

John VanZwieten - #17732: “In my view, both are unreasonable requests given our current understanding and technology, but perhaps in the next decade or two things will change enough that such a detailed hypothesis can be offered. “

I agree with that. The problem with Rich’s request, I think, is that he doesn’t realize that for what he’s requesting, there isn’t much of difference between proposing a detailed set of hypothetical pathways and the actual one. Species and organisms are products of historical contigency. To truly understand whether a particular transition is possible largely requires that we understand the details of the precursor *within the context* of its environment, including other genes and conditions with which it may interact.

To give a feel for the scale of what is requested: We don’t have the technology to model even a single cell at that level of detail. Technically speaking, I suppose one could make the case that everyday functions of a micro-organism might be directly controlled by an active designer.

Larry - #17827

June 17th 2010


We don’t just need to be convinced that ID is the best explanation, first we need to be convinced that it is AN explanation. I still don’t see how it can ever even be a working hypothesis when nobody appears to know what we should be looking for. How can you draw any inferences about something that doesn’t predict anything? It seems to me that ‘design’ as it is currently put forward is compatible with any conceivable discovery so where does the inference come from that allows us to conclude it is the best explanation? It’s compatible with the data we have, of course, but how could it not be? When Steve Matheson said design was an “excellent and irrefutable explanation,” he was not praising it (despite what the Discovery Institute tried to claim).

unapologetic catholic - #17870

June 18th 2010

“If I ever challenged your religious sincerity, I retract my words.  I cannot judge your sincerity.”

However, that does not mean that I acknowledge the correctness of your interpretation of Catholic doctrine, on evolution or anything else.”

No problem…  We can agree to disagree.

After over five decades of being Catholic, I’ve run into Catholic heliocentrists, YECs, OECs and ID types as well as evolutionary scientists.  All are orthodox Catholics.  All are sincere in their beliefs.  Some are wrong on the science.  No big deal.

PDS:  You could perhaps advance the level of discussion by considering “The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause…”  and then identifying some of those features and the characteristics of the intelligent cause(s).

Do you have any such features in mind other than those Behe has identified in Darwin’s Black Box and Edge of Evolution? (I’m familiar with those).

in 1999, (over 11 years ago) Dembski suggested potential areas of ID research.  Here is one of them:

“Identity Problem—Who is the designer?” 

What ID research into this qurstion is currently being conducted?

Rich - #17876

June 18th 2010


Since you are (I take it) defending neo-Darwinism, the onus is on you to show us how neo-Darwinian processes could get from point A to point B.  The onus is not on others to show that they couldn’t possibly do so. 

Imagine a physicist saying:  “Elements are formed in the hearts of stars”, and someone objecting “You haven’t provided a clear account of *how* elements could be formed in that way”, and the physicist evasively replying:  “Can you give me a good reason for denying that elements could be formed in stars?”  Any good physicist would explain the process of nuclear fusion, and then proceed to set forth specific proposals for the formation of each element, complete with numbers (energy needed, energy released, etc.).  He would draw a clear picture of what happens when hydrogen fuses to from helium, etc.

So show us a sequence of specific genetic changes that did, or at least could have, turned a deer’s nostrils into a whale’s blowhole, or a sequence that did, or at least could have, given a reptile the power of winged flight.  (Use two organisms with fully sequenced genomes if you like, but make sure the change you account for is substantial, not a longer beak or a different eye color.)

Rich - #17877

June 18th 2010

Argon (17819):

I know exactly what I’m asking.  Read my reply to Dennis above.  Can you provide the account requested, or not?  And if you can’t, then how can you be *sure* that *specifically neo-Darwinian mechanisms* are the main driver of evolutionary change?

Rich - #17878

June 18th 2010

John van Zweiten (17785):

Once again, you seem to understand me better than several others here.  Thank you for reading carefully what I have written, instead of imputing all kinds of views and associations to me out of “general suspicion” (which is the normal interpretive technique around here, it seems).

You are right; #1 is *all* that I have claimed.  But my claim is slightly stronger than what you have indicated.  I would put it this way:

1a.  It’s not proven exactly *how* RM+NS could get us to a whale.
1b.  In fact, it’s not proven even *that* RM + NS (alone, anyway) could get us to a whale.

Beyond that, I agree with your post.  Several people here are evidently imputing to me at least view 2, and in some cases probably also views 3 through 5, with no authority from anything I have written.  And this is very typical of anti-ID argumentation, that it’s based on sloppy, careless reading, and the imputation of motives and agendas, and doesn’t focus on providing a reasoned argument, based wholly upon scientific and rational considerations, concerning exactly what has been proposed.

Argon - #17898

June 18th 2010

Actually, Rich, I’m not necessarily addressing you directly. I know that you are stating #1 here.

There are two arguments going on here. This is the difference between ‘does not’ and ‘can not’. and is often conflated.

The first argument is whether evolutionary theory and current technology allow us to detail at the molecular level what you would think are some of ‘major’ steps necessary in the evolution of whales. The answer is no (currently ‘does not’). However, the data we have and from what we know of the nature of mutations and biology, there is consistency and there are no obvious blocks.

The second argument relates to ID, as opposed to skepticism of any particular mechanism. Behe, for example, is at #2 when presuming that his arguments about IC systems are correct. He is of the ‘can not ’ camp which remains a core belief of most popular ID proponents. ‘Can not’ is an ID position whereas ‘does not’ is agnostic.

Another example of the ‘science does not currently explain in detail’ is the daily operation of a single cell. What’s interesting is that Behe and most biologists are not in the ‘can not’ camp here. Go figure.

Argon - #17901

June 18th 2010

Oops. Correction:
“The second argument relates to ID, as opposed to skepticism of any particular mechanism.”

Should read:

“The second argument relates to ID, as opposed to skepticism of whether any mechanism is sufficiently detailed.”

beaglelady - #17926

June 18th 2010

As you all know, I emailed Dr. Sternberg and passed along David Kerk’s suggestion that he write something up for scientists to evaluate. (See comment 17569)  I also suggested that he post something here or even ask to do a guest post.  I have not yet heard from him. Has anyone here ever contacted him and received a reply? If so, how long does he usually take to reply?


Rich - #17936

June 18th 2010

Argon (17898):

I’m not trying to catch you out on a verbal slip here, but I need to make an important point:  Behe is not at #2, because he never says “evolution can’t get us to whale”.  It’s pure neo-Darwinian mechanisms which, in his view “can’t get us to whale”.  He says that in all his writings, but extremely pointedly in *The Edge of Evolution*. 

Behe doesn’t see any reason in principle why science can’t some day explain the daily operations of the cell because Behe sees the cell as a collection of biochemical machines, and he thinks that science (in his case, biochemistry) is eminently suited to take apart such machines and analyze their operations.

There’s a difference, however, between being able to analyze how a machine works, and being able to prove that the machine could have come into being essentially by accident, without the input of intelligence.  I don’t know how a grandfather clock works, but I think it’s possible to analyze one and determine that.  I very much doubt, however, that the grandfather clock came into existence through the interaction of natural forces and bits of matter that happened along, without a designing intellect.  (continued)

Rich - #17937

June 18th 2010

Argon (continued):

I think those ID proponents who say “can not” are making a mistake.  There is always some probability, however small, that purely stochastic processes could produce an irreducibly complex system.  Even Behe and Dembski have on occasion qualified their argument for design with this admission.

However, I think ID proponents are reasonable to speak in terms of “the best explanation”.  If, for example, a well-founded calculation indicated that the probability of the emergence of a whale from a land mammal via neo-Darwinian processes alone was 1 in 10^70, one would be justified in suspecting that something more than those processes was responsible for the transformation.  And if further investigation revealed that the probability for neo-Darwinian plus all other known purely stochastic explanations was still very low, say, 1 in 10^65, then one would rightly suspect a teleological thrust to evolution.  One would then investigate both immanent teleology (e.g., self-organizational theories) and externally imposed teleology (e.g., “intervention”) as serious possibilities.

Thus, I think the language either of impossibility or of certainty is counter-productive.  I prefer the weighing of explanations.

Argon - #17946

June 18th 2010

I understand that Behe accepts common descent of some type, which is mechanistically distinct from current modes being considered by most biologists. Perhaps it’s better to distinguish Behe’s as proximate-design-supplemented evolution (Which also separates the idea from distally-organized evolution, e.g. Denton’s pre-tuned universe and VanTill’s fully gifted creation).

I have some difficulting cleanly separating evolution as a process from the mechanisms which create it. Organisms and species are the result of historical & physical processes and carry some evidence of their history with them today. There is also a fossil record. Analyzing the available data and arriving at the conclusion of common descent requires a significant background knowledge of how organisms reproduce, interact and what the conditions were in the past. Today that knowledge ranges from basic biochemistry to population genetics and ecology. At the core is reproductive descent with genetic modification. Furthermore, deducing common descent also requires some boundary conditions to the rates and patterns of change. These boundaries are mechanism-dependent.

Argon - #17954

June 18th 2010

Rich: “There’s a difference, however, between being able to analyze how a machine works, and being able to prove that the machine could have come into being essentially by accident, without the input of intelligence.  I don’t know how a grandfather clock works, but I think it’s possible to analyze one and determine that.”

I am a biochemist too. The issue is that Behe and anyone else cannot demonstate that cells work within the bounds of physics and chemistry. We can only say that we’ve seen no evidence of a limit so far and no clear hint that other ‘forces’ are at work. No unified model of a cell has ever been created or tested; only small bits have been analyzed at any one time and the complexity of interactions and biochemical details will prevent this for quite some time to come. Just because an event is commonplace or frequent tells us nothing about whether proximate design or tinkering is involved.

Argon - #17955

June 18th 2010

[continued from above…]
Personally, I agree with Behe that the cell probably is operationally reducible to chemical reactions. But to be honest, that’s because this approach has largely been successful in the past, not because we know all the details. The fact is, others have proposes things like ‘morphic resonance’ and other ideas to confront the possible shortcomings of current biochemical explanations.

I think the parallel holds: ‘There is a difference between being able to analyze how a machine works and being able to demonstrate that the natural mechanisms are sufficient for its operation.’ Perhaps doubly so because we haven’t finished analyzing how the machine (cells) work.

PS - Rich I appreciate that we can discuss this topic amicably.

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