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

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June 14, 2010 Tags: Genetics, History of Life

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

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

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.

Notes

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 The BioLogos Foundation. He transitioned into Christian higher education 25 years ago and has given numerous talks about the relationship between science and faith at many universities and seminaries. He 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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Rich - #18189

June 21st 2010

beaglelady:

The folks over at the Ayala thread have recently acknowledged your latest contribution there.


Argon - #18192

June 21st 2010

Rich: “If the basic theory of the atom—our basic notions such as nucleus, proton, neutron, electron, etc.—were to collapse, almost all of theoretical science would collapse.”

Doubtful. Everything would still work but we’d have to find an alternate idea why subatomic world behaves as though there were particles like the proton. Organic chemistry would easily go on because it mostly relies on gross, empirical characterization of atomic properties. In fact it had already progressed a long way before quantum mechanics came on the scene.

I think what Alan is referring to is that a lot of the physics on which all these characterized, higher level (emergent?) phenomena rest are not well understood. And yet without all these supporting details filled in, atomic theory still works quite well.


beaglelady - #18194

June 21st 2010

The folks over at the Ayala thread have recently acknowledged your latest contribution there.

 

A professional, Dennis Venema, would be happy to discuss genetic mechanisms with you right here and now.


Dennis Venema - #18197

June 21st 2010

Re: 18194

Actually, if you have a look at the end of the whale evolution thread, that’s what we’re doing. The ball’s in Rich’s court right now.


Dennis Venema - #18198

June 21st 2010

Whoops - I thought this was a different thread.


Rich - #18222

June 21st 2010

Argon:

Doubtful!!!???

I thought you were a scientist!

If atomic theory had to be completely junked, every science textbook I ever had, from elementary school through to undergraduate, would have to be almost completely re-written.  They must study science differently in your parts than in mine.


Rich - #18228

June 21st 2010

Dennis:

Let me get this conversation straight.  I originally asked, on a thread about whale evolution, for a list of the morphological changes that would be necessary to turn a land mammal into a whale, and for the genetic changes that could bring about those morphological changes.

If I understand your reply so far, you are tacitly admitting that you cannot do this, and that no biologist known to you has done it, or has come anywhere close to doing it.

If I understand the next step in your argument, it is that you don’t need to show the actual steps in whale evolution; you only have to compare human and chimp genomes, and can infer the viablity of whale evolution (and by extension all the rest of macroevolution) from the differences in those genomes.

In your comparison of human and chimp genomes you have not discussed (a) even *one* specific morphological feature whereby the human differs from the chimp; (b) even *one* hypothetical evolutionary route which could convert the chimp genome (or a putative commone ancestor’s genome) into the human one, producing the specific morphological difference.

(continued)


Rich - #18231

June 21st 2010

Dennis (continued):

Again, if I understand your argument correctly, you believe that you don’t need to do either (a) or (b) to prove that the differences could have arisen via neo-Darwinian mechanisms.  So let me get this straight:

Even if (hypothetically) you didn’t have a clue what *any* gene in either the human or chimp genome produced (morphologically speaking), you could tell, *just from the genome map* (a) that chimps and humans have a common ancestor; (b) that both evolved from the common ancestor via neo-Darwinian means.  Is that what you are saying?  That neo-Darwinians shouldn’t waste their time trying to demonstrate the capacity of neo-Darwinian mechanisms—they can just infer them?  That you don’t even need a mechanical theory of how evolution works, to be sure that it works neo-Darwinistically—you just have to be a geneticist and be able to read genomic data? 

So is the science of evolutionary biology not a science of mechanisms at all?  If so, it’s much, much different from other historical sciences, like geology and cosmology.

If this is what you are arguing, I find it staggering, but I want to be sure that it is indeed what you are arguing before I reply further.


Dennis Venema - #18246

June 21st 2010

Rich,

Of course biologists should look into the details: what genes are involved? did selection play a role? how important was drift in this case? etc. Biologists love details - we’ll go as deep into the details as the funding agencies will allow.

What I’m doing is testing your specific hypothesis: can Darwinian mechanisms effect a major evolutionary change?

To address this, we’ve moved to a pair of species where there is relevant data. (Surely ID cannot only seem plausible where there is absence of data?)

We agreed that humans and chimps have major phenotypic differences. So, we look at their genomes - any genetic changes responsible for the phenotype will be there to see. We can’t be sure which genes are the important ones for this trait, so we err on the side of caution and look at everything.

When we do, we see only changes easily accessible to Darwinian mechanisms.

Therefore, your hypothesis is not supported.

To deny this logic, you need to (a) find non-darwinian changes (try Ensembl, link above), or deny common ancestry for humans and chimps.


Rich - #18252

June 21st 2010

Dennis:

Why do you keep speaking of “my hypothesis”?  I have no hypothesis.  The only hypothesis on the table, which was not mine, is that “A primitive artiodactyl was transformed into a whale within about 9 million years entirely or mainly via neo-Darwinian mechanisms, i.e., mutations random with respect to the outcome, plus natural selection.”

I questioned whether there was enough evidence to support the hypothesis.  I suggested that the best way to support such a hypothesis would be to identify all the morphological changes that would need to me made, identify the genetic causes of those morphological features, and suggest some hypothetical evolutionary events which could turn one set of genes into the other.

You are apparently denying that this is the rational or sensible or scientific way to go about validating the hypothesis.

Why do *I* have to find *non-Darwinian* changes?  The onus is on *you* to specify the *Darwinian* changes.  But you can’t do that unless you can connect the morphological differences with genetic causes.  And I’m beginning to get the impression that you can’t do this.  Otherwise you would be naming genes which cause feature X in both humans and chimps.  Why would you hold back?


Dennis Venema - #18256

June 21st 2010

Rich, I’m saying they are all Darwinian changes. All of them. That’s the whole point.

Of course I can connect “genetic causes” and “morphological changes” - unless you are claiming that the changes we see are the result of non-genetic causes?


Rich - #18259

June 21st 2010

Dennis:

I am claiming nothing.  I don’t know the causes of morphological change.  I’m interested in hearing them from a biologist.  I’m interest in hearing something like: 

“A shrewlike animal could add sonar to its sensory apparatus by the following chain of mutations:  Gene X7453 is deleted, Gene 43687 is transposed three genes over, Gene 4B20 is rotated in its present position; meanwhile, over on the fourth chromosome, Gene ZX251N, which controls (along with three other genes) the skull shape, is altered as follows…”

But I’ve never heard anything like that from you here, or any biologist anywhere.  And I take it that I am never likely to.


Dennis Venema - #18281

June 21st 2010

Rich,

The detail you are asking for takes a long time to reach. We have that level of detail for certain structures in some model organisms, but not for anything else (nor will we for anything without, at bare minimum, a completed genome, and even then not for quite some time).

We can, however, be quite confident that the changes we see are due to Darwinian mechanisms. We can compare whole genomes of related organisms (such as humans and chimps). If there were non-Darwinian mechanisms in play, we would observe their effects when doing the comparison. We don’t.

You’ve often made a careful distinction between “evolution” and “darwinian evolution” - accepting the former (as common ancestry) in limited measure but questioning the latter (darwinian changes as the mechanism). Well, the genomics evidence does not support the hypothesis of non-darwinian processes in common ancestry, and strongly supports the hypothesis that darwinian mechanisms are a sufficient mechanism to effect large-scale phenotypic changes.

As evidence I proffer the comparison of the genome sequences of humans and chimpanzees.

If you accept the conclusion that darwinian mechanisms can effect major changes, then fine - my point is made.


Rich - #18288

June 21st 2010

Dennis:

“Well, the genomics evidence does not support the hypothesis of non-darwinian processes in common ancestry, and strongly supports the hypothesis that darwinian mechanisms are a sufficient mechanism to effect large-scale phenotypic changes.”

On this, we’ll have to agree to disagree.  Sternberg does not agree with you.  Denton does not agree with you.  Some of the “Altenberg 16” don’t agree with you.  I think you know your genetics very well, but it does not seem to me that you read very much about what is going on at the theoretical frontiers of evolutionary biology.  I think your interpretation of the genetic evidence is dated, and is going rapidly out of fashion.  Let’s check back in here in 10 years and see who’s right.  Thanks for the conversation.


Dennis Venema - #18299

June 21st 2010

Rich,

Some of the Alt 16 deny that darwinian mechanisms can effect major changes? Sorry, Rich, you’re misreading them. Don’t take this personally, but I don’t think you have the chops to read them and understand what they’re saying at a deep level. Margulis *might* be construed to appear to agree with you, but even that’s a (pretty big) stretch.

Have you read their work in its original form, or filtered through ID channels?


Rich - #18308

June 21st 2010

Dennis Venema wrote:

Denton I know well, and I’ve read a fair bit of Sternberg recently; the Altenberg 16 I know of only through indirect reports. I was given to understand that the whole premise of their discussions was that neo-Darwinian notions, while still of some value, were no longer nearly adequate for a 21st-century evolutionary theory, and would have to be *seriously* supplemented by (not just dressed up a little with) non-Darwinian insights.  Perhaps you can give me some links so that I can study their writings more closely?

I “have the chops” to read a lot of things, if the specialists will take the time to put their arguments into plain, natural English prose, such that a highly educated non-specialist can understand the structure of the argument.  But too often specialists hide behind jargon and graphs with labels comprehensible only to the specialist, because they know this will intimidate others into silence. 
Darwin did not write in that way; his goal was to make as many people understand as possible, not to lose the non-specialist in the dust.  Darwin said,  “Come and refute me if you can”, whereas Biologos says “You aren’t qualified to refute us—but of course you are qualified to praise us.”


Rich - #18314

June 22nd 2010

Ooops!  #18308 fixed:

Denton I know well, and I’ve read a fair bit of Sternberg recently; the Altenberg 16 I know of only through indirect reports. I was given to understand that the whole premise of their discussions was that neo-Darwinian notions, while still of some value, were no longer nearly adequate for a 21st-century evolutionary theory, and would have to be *seriously* supplemented by (not just dressed up a little with) non-Darwinian insights.  Perhaps you can give me some links so that I can study their writings more closely?

I “have the chops” to read a lot of things, if the specialists will take the time to put their arguments into plain, natural English prose, such that a highly educated non-specialist can understand the structure of the argument.  But too often specialists hide behind jargon and graphs with labels comprehensible only to the specialist, because they know this will intimidate others into silence. 
Darwin did not write in that way; his goal was to make as many people understand as possible, not to lose the non-specialist in the dust.  Darwin said,  “Come and refute me if you can”, whereas Biologos says “You aren’t qualified to refute us—but of course you are qualified to praise us.”


Dennis Venema - #18348

June 22nd 2010

Rich, the point I am making is simple - if you’re going to make blanket statements about experts outside your field, you should at least have read them for yourself (and understood them and their arguments).

I’m not aware if any of them have written on their material for a non-specialist audiences. I know Pigliucci writes some popular stuff, but I don’t think it’s on his technical material.


Gingoro - #18365

June 22nd 2010

Dennis Venema @18348

if you’re going to make blanket statements about experts outside your field, you should at least have read them for yourself (and understood them and their arguments

Fine Dennis If I were interested in stellar evolution I can easily pick up a 500 page college undergrad level text that provides all kinds of details on the mechanism and stages of a star’s life.  For example I went to Amazon and trivially found ” Principles of Stellar Evolution and Nucleosynthesis” by Donald D. Clayton.  As best I see, biological evolution it is considerably more complex than stellar evolution so choosing just one example of a complex transition I’d like to find the equivalent for biological evolution that provides a putative sequence of genetic changes, the associated morphology (when there is any), the survival advantages of each morphological change, fossil records demonstrating the external changes in the species along the way and an estimate of the number of generations required to effect the transition.  My understanding is that one is most likely to be able to find fossils is in a water environment.  Thus land mammal to whale, sea animal to land dweller etc seems most likely to provide the appropriate data.


Gingoro - #18367

June 22nd 2010

Dennis Venema @18348

When I look in Amazon I find 4 pages of books listed under stellar evolution but when I try finding the same kind of book for biological evolution giving the kind of details that I am looking for then I find essentially nothing. 

The only book I have ever found that even begins to go down the path I am looking for is “Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body” by Neil Shubin but it does not go to the level that interests me.  Yes if I found such a book I might not have the chops to understand it.  Just finding it in itself would be a significant indication that the field is becoming mature.  Someone like my daughter who has a phd in biochemistry could also give me a good feel whether or not the descriptions of the mechanism are adequate or not.  She is skeptical like I am but even more so.  Even though my degrees are in engineering and applied math I can follow the storey of stellar evolution why not in evolution?

Dennis it is not that I deny that the neo Darwinian synthesis is capable of producing complex transitions but that it does not seem adequately demonstrated at this point in time.  Maybe you can point me to the kind of book I am looking for. 
Dave W


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