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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 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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Dennis Venema - #17977

June 18th 2010

Rich, would you accept the cognitive differences between humans and chimpanzees as a “substantial change” for the purposes of this discussion?


Rich - #17988

June 18th 2010

Dennis:

“Cognitive differences” are intangible.  How about some major structural difference in the organization of the brain, one that would clearly, even in neo-Darwinian terms, require hundreds of mutations affecting the nervous system and other parts of the body (sensory apparatus, cranium, related parts of the circulatory system, etc.)?  If there is such a major difference between human and chimpanzee, or rather, between human and chimp-human common ancestor, then by all means, use that.  But do we know enough about which parts of the genome organize the human brain, the sensory organs, the shape and size of the skull, etc., to offer a hypothetical evolutionary pathway?

Again, I’m not saying that if you *can’t* come up with an answer, that neo-Darwinism is “wrong”, still less that “evolution” is wrong.  I’m merely saying that if evolutionary biologists can’t give these kinds of detailed explanations, at least for *some* major morphological changes, they should hold off on grand statements like “Darwinian evolution is as firm a part of scientific knowledge as the theory of gravitation or the germ theory of disease” —statements which Miller, Ayala, Coyne, Dawkins, Collins, etc. make constantly.


Rich - #17992

June 18th 2010

Argon:

I, too, have appreciated the tone of our dialogue.  It was evident to me from the beginning that you had substantial knowledge, and that you were willing to listen to my points without making wild charges of theocracy etc.  I’ve been grateful for that.

A historical point, if I may.  You say that you find it hard to separate the evidence for the mechanisms from the evidence for the process.  However, when you read Darwin, you see that he was convinced of the truth of the process of macroevolution while lacking the overwhelming majority of the evidence for the mechanisms we have today for even microevolution.  He didn’t really understand what a cell was.  He didn’t know even Mendelian genetics, let alone post-DNA genetics.  He accepted the process without anywhere near a scientifically adequate mechanism.  Neo-Darwinism has been largely the activity of finding the mechanisms which justify the conclusions Darwin adopted on very thin and circumstantial evidence.

Also, Lamarck postulated the process before Darwin, but had a different mechanism.  So the process can be separated from the mechanism.  But I agree that a detailed account of the mechanism is the best argument for the reality of the process.


Dennis Venema - #18005

June 19th 2010

Rich,

I don’t think the differences are intangible: humans use technology, languages, write Shakespeare, receive Divine revelation (I assume we both accept that), etc etc.

Chimps? Not so much. Hints of some things, maybe.

You don’t think the differences are significant enough to qualify as a major change?


Rich - #18006

June 19th 2010

Dennis:

Oh, I agree that they are major differences; it’s just that I don’t understand how you are going to find a gene for smartness, a gene for toolmaking, a gene for compassion, a gene for the desire to tell stories, etc.  I would think it would be easier to find genes for brain size or neural complexity or eye-brain connections or the like.  But you’re the expert on genes; if you can find genetic causes for the less tangible things, then that would be fine with me.

I must say, however, that I’m not sure where this is going.  Is this going to end up answering my question?  I’m looking for the equivalent of:  How do you convert a radio into a television set?  What parts do you have to add?  What parts do you have to subtract?  What tools and techniques do you use?  So how do you convert a swimming bladder into lungs?  What has to be added?  What connections to the heart and arteries have to be made?  What new regulatory system has to be set up in the brain for the new organ?  And what genetic changes are needed to effect all of that?  And are these genetic changes just going to happen to emerge in a convenient order to create the viable intermediate forms that make the progression possible?


Dennis Venema - #18008

June 19th 2010

Hi Rich,

I’m trying to test your hypothesis by finding a case where there is relevant data. Asking for a basal artiodactyl-to-whale transition all in one go is tricky for a few reasons, especially since we don’t have the genomes of either organism available. Eventually we’ll have a modern cetacean genome, but the basal artiodactyl is lost to us. The other difficulty is that there are MANY intermediates between those two types of critter.

So, I’m trying to answer a slightly more abstract question (which in fact I think is the relevant question here): can relatively small changes, of the sort known to be in reach of “Darwinian” mechanisms, effect major changes in a (geologically) short period of time?

To answer that question, we need the following: closely related organisms, recently diverged, with full genome sequences available for both, yet displaying at least some major differences. I think humans and chimps qualify on all counts.

Now, you ask, how can I identify the relevant genes? Here’s the thing - I don’t need to. I know that they are a subset of the sum total changes between the genomes. If I examine EVERY change I can be sure I have looked at the changes underlying the traits I am interested in. (continued)


Dennis Venema - #18010

June 19th 2010

(continued from 18008)

Here’s the thing: in looking over the entire genomes of humans and chimpanzees, I see no differences (i.e. changes) that are beyond the easy reach of “Darwinian” mechanisms. If you do, please point them out (GenBank numbers or gene names would help).

So, I conclude that the changes relevant to the trait under discussion (cognition) or any other difference between the two species, are easily explained by “Darwinian” random mutation and natural selection (or perhaps neutral variation, drift, etc).

So, it seems to me that the hypothesis that Darwinian mechanisms can easily effect a major change through minor adjustments to a genome has significant empirical support.

Extrapolating to other organisms, I would expect that changes of this sort underly the transitions we see in other groups. Of course, I would expect to see a nested hierarchy where synteny,  homology and shared pseudogenes support any given model (for extant organisms, of course).

(For folks who may not have seen them, you can click on my name to see posts explaining what synteny and pseudogenes are all about. 

Best,

Dennis


Rich - #18042

June 19th 2010

Dennis:

I’ll get back to you.


Dennis Venema - #18066

June 19th 2010

Great, I’ll look forward to your thoughts.


Gingoro - #18082

June 20th 2010

pds @17624

If one is plotting parent child relationships then the diagram is a tree.  However, if you are plotting genetic flow then the name of the diagram is a network.  This is simple graph theory.
Dave W


Gingoro - #18097

June 20th 2010

Argon @17819

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. 

I think that Rich realizes quite well what he is asking for in terms of the detailed pathways between species.  I ask for the same thing.  The lack of the detailed pathways does NOT dis-prove neo Darwinian theory but should render it more tentative and less assertive until the appropriate scientific work is in hand. Our opinion is that until such pathways are available much of the neo-Darwinian theory is simply a good reasonable hypothesis.

Dave W


Rich - #18131

June 20th 2010

gingoro:

Yes, that’s all I’m asking for:  more scientific tentativeness, more intellectual humility, more statements acknowledging the difficulty of explaining new body plans, more statements acknowledging data that seem to pose difficulties for Darwinian explanation, and less cranked-up volume about how Darwinian evolution is as certain at gravity or atomic theory.  I don’t think this is an unreasonable request to make from purportedly sober and serious scientists, who are supposed to be more interested in a steady, cautious advance toward the truth about nature than in defending an entrenched position.

Just provide more and more detailed mechanical descriptions of how new organs, systems, and body plans are formed.  That’s all that it will take to silence public skepticism about evolution.  On the other hand, every attempt at evasion of detailed description will only heighten public skepticism.  Really, the fate of neo-Darwinian theory is in the hands of its defenders.  Evidence will win everyone over; over-claiming about what has been proved, especially when coupled with scorn, ridicule, and appeals to consensus and authority, will turn the public against the theory.


Dennis Venema - #18136

June 20th 2010

Rich, are you planning on responding to what I’ve written? You’re asking for evidence; I’m attempting to discuss it with you.

We’ve agreed that humans and chimpanzees have major differences.

It’s basic logic that the genetic differences that form the basis for these differences must be a subset of the total genetic differences we see between the genomes.

Of the changes, all appear to be within reach of Darwinian processes.

Ergo, Darwinian processes can effect major changes.

Do you disagree?


Rich - #18138

June 20th 2010

Dennis:

Yes, I am planning to respond.  But I want to think about my answer, rather than to give you a knee-jerk response.

I do have at least one question of clarification.  How did you determine that *all* the changes appear to be within reach of Darwinian processes, without determining what *any* of the changes were?  If I were to say that *all* the changes between a log cabin and the White House were within the capabilty of a ninth-grade woodworking student, but could not specify even a *single* external change that would need to be made to turn a log cabin into the White House, coupled with a specification of the tools, materials and knowledge that the ninth-grade student would need to make that single change, would you not be suspicious of my claim?


Dennis Venema - #18149

June 21st 2010

Rich:

We’re talking genetic changes here. You can compare the entire genomes of humans and chimpanzees - meaning, you can determine what the changes are for every gene (actually, for every gene and everything else, whether one knows if it is a gene or not).

The changes, at a genome-wide level, are within reach of Darwinian processes.  The two genomes are incredibly similar - same genes, same order, only very minor differences. The differences are easily understood as small mutations of the type Darwinian processes can accomplish.

Yet, the human genome gives human traits; the chimp genome, chimp traits. If you agree these traits have “major differences” you agree that major differences can be brought about through very small changes at the genetic level.

If you want to “see” the data yourself, it’s available online - for example, via a genome browser like Ensembl:

http://uswest.ensembl.org/index.html

or you could read the primary literature on the subject, for example:

http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html


Alan - #18157

June 21st 2010

“more statements acknowledging data that seem to pose difficulties for Darwinian explanation, and less cranked-up volume about how Darwinian evolution is as certain at gravity or atomic theory.”

Have you ever considered our modern understanding of atomic theory? It has huge, gaping holes in much of it and is clearly contradicted by various pieces of empirical data. Yet it is still the best model we have and that atoms actually exist is beyond question. Oddly we do not hear that it is a “theory in crisis” and people are not constantly pointing out its flaws while attempting to proffer ad hoc supernatural alternatives. Strange that, isn’t it? As far as evolution goes, of course not everything is known - far from it, but certain things are very well known and understood. The ‘Project Steve’ statement phrases it well;
“Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence.”


Argon - #18174

June 21st 2010

Dennis Ventenna: “To answer that question, we need the following: closely related organisms, recently diverged, with full genome sequences available for both, yet displaying at least some major differences. I think humans and chimps qualify on all counts.”

Bingo! Older events have worse records—The signals tend to decay with time. This is why obsessing over things like routes to the bacterial flagellum are pointless. Go for the most recent events with the most amount of surviving data. Work with the lest complicated system that is most likely to yield results. That’s the approach good experimental scientists take. Personally, I’d work with bacteria (to study interactions between macromolecules in real time) and plants (to study morphological plasticity). A worm like C. elegans isn’t a bad model system either,  and there are even behavioral studies available. For humans, I’d look for genes related to neoteny—In connection with studies in dogs.


Argon - #18175

June 21st 2010

Sorry Dennis, I botched your last name in my post. I mutated it with the name for a company that makes automated histochemistry and slide staining equipment…


beaglelady - #18176

June 21st 2010

And all the while we have to accept the Richard Sternberg whale video, without getting to sneak a peek at his data.


Rich - #18188

June 21st 2010

Alan:

Re your parallel with atomic theory:

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.  The notion of the atom ties together everything from nuclear power plants to the generation of electromagnetic radiation to the chemistry of everyday substances and the processes of life.

If neo-Darwinism were falsifed tomorrow, most of natural science would be completely untouched.  Physics, chemistry and astronomy would go their merry way, unaware that anything had happened.  All of geology except paleontology would remain intact.  Biochemistry would be untouched.  Huge tracts of biology itself would be untouched.  You can measure the toxins in the flesh of a sea gull, sequence a genome, understand meiosis, study food chains, etc. without knowing the putative ancestor of the sea urchin.

There’s no comparison. 

(Oh, btw, like several others here, you’ve blurred together “evolution” and “Darwinian evolution”, despite the fact that I’ve made the distinction about fifty times.  I hear olive oil is good for ear wax.)


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