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 - #18369

June 22nd 2010

Dennis:

Sure, I’ll withdraw my claim about the Altenberg 16 for now, until I’ve read the primary sources.  I agree with you that one should read the primary sources, and not rely on hearsay.

I agree with gingoro’s point above:  It’s less important that I can understand all the details of a particular science than that I can see in broad terms what the science has accomplished.  I can’t understand the physics of stellar evolution any more than I can read a detailed genome map, but I *can* tell, from good popular works on astrophysics (written by Ph.D.s who supposedly know the field), that the physicists are in fact giving step-by-step accounts of the formation of heavier and heavier elements, and describing the fusion mechanism in detail.  If I see the physicist doing that, I take his word for the math and so on.  I haven’t yet seen the equivalent sort of feat in evolutionary biology.  Therefore, I draw the wholly logical inference that evolutionary biologists are less entitled to supreme confidence (regarding the mechanisms, at least) than the astrophysicists are.  Yet when I point this out, the vaunted “scientific humility” goes out the window, and the invective starts.


Argon - #18397

June 22nd 2010

Rich:
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.

Seriously. Newtonian mechanics is ‘wrong’ but it’s still used. The Bohr model of the atom is wrong but we more often draw atoms with little circles of electrons instead of fuzzy clouds of probability. Basically, whatever came afterward would still look an awful lot like what we have today. For example, hadrons like protons & neutrons aren’t the elementary particles once thought. That discovery changed chemistry very, very little. Actually, we know that the underpinnings of the Standard Model for particle physics is woefully incomplete and that alternate models may supercede it. Whatever emerges is still going to align with what we’ve already observed. An electron may or may not actually be vibrating string in 11-dimensions but a resistor banded with red-red-brown stripes will still be 220 ohms, regardless.


Rich - #18404

June 22nd 2010

Argon:

You’re not understanding me.  I’m not talking about interpreting electrons slightly differently, while still regarding them as part of the atom.  I’m not talking about different subdivisions of particles below the level of the neutron.

What I meant by a rejection of atomic theory was:  There is no such thing as an atom.  There are no such particles.  There is no nucleus.  There are no protons, neutrons or electrons.  There is no correspondence between the notion of a basic particle and what we call an “element”.  Salt is not a lattice of sodium and chlorine atoms.  The particles out of which DNA is supposedly made, and which we supposedly detect via x-ray methods, do not in fact exist.  Nothing splits in a nuclear reaction.  Electromagnetic radiation has nothing to do with excitation level of electrons.  Etc.  That’s what I meant by removing “atomic theory” from science.  So now there would be a yawning theoretical hole at the very heart of modern science.  The reality out of which we constructed everything would no longer be available.  (continued)


Rich - #18406

June 22nd 2010

Argon (continued):

Now take away “evolution” from biology.  We would no longer be able to speculate about biological origins in the same way.  But we would still be able to sequence genomes, study genetic diseases, develop drugs, study embryology and physiology and ecology and so on.  Most biologists would not notice any change in their day-to-day operations.  Their lab methods would remain the same.  They would lose a historical narrative, but they would still be able to continue as an operational science.  And most of the other sciences (astronomy, chemistry, etc.) would be utterly unaffected. 

Regarding textbooks, except for textbooks specifically on evolution or related subjects (paleontology, parts of anthropology), most biology textbooks could easily stand, with perhaps a few interpretive glosses omitted, without evolution.  The diagrams for cell structure, meiosis, mitosis, photosynthesis, osmosis, food chains, Mendel’s peas, etc. would remain exactly the same.  The physiology of the cardiovascular system would remain the same.  The parts of the brain that control speech, reading, hormones, etc. would remain the same.  But take atoms out of a chemistry or physics textbook, and you’re in trouble.


Dennis Venema - #18413

June 22nd 2010

Rich / Dave W,

I think what is important here is that you actually look at some comparisons of gene sequences across various species - i.e. you need to see what geneticists see.

Now, these things are all over the primary literature, but you don’t read the primary literature. I’ve pointed you (Rich) to a summary paper (link above) but I see no evidence that you’ve attempted to read it. A few weeks ago I gave you a paper on whale genetics/development/evolution - did you ever read that one?

Well, here’s an attempt to make things simpler for you. Here is a figure that compares the sequences of insulin in several different mammals, from humans to mice. Cut & paste the link and pull up the PDF before continuing.

http://www.twu.ca/academics/science/biology/faculty/venema/venema-asa-figure1.pdf

Part A shows the DNA sequences; B the amino acid translation (in single letter code) and C shows the phylogeny for these species.

Have a look at the nucleotide sequences (say, for humans, chimps and gorillas, the upper three sequences). What do you think? Can you explain these differences as single nucleotide changes of an ancestral sequence?


Argon - #18436

June 22nd 2010

Rich,
I originally responded with a clarification to Alan’s note (#18157), which was that there are fundamental gaps in our understanding of Standard Model on which a large portion of particle theory is based, yet no one is claiming atomic theory is a theory in crisis. (This is similar to my earlier comments about Behe being convinced that the operations of the cell are fully natural when we in fact have never modelled a cell in sufficient detail).

Discussions about the relative centrality of various theories debates a point that was never raised.


Rich - #18490

June 22nd 2010

Argon:

I see that we have been talking at cross-purposes.  It looks like each of us bears part of the blame for not reading the other’s statement in its local context, and reading the wrong claim into it.

As to whether or not evolution is a “theory in crisis”, it depends on what one means.  Even Denton, when he wrote a book of that title, was not arguing, “Gee, maybe evolution never happened at all.”  What he meant by the title was that the main engine which had long been assigned to evolution—Darwinian mechanisms—no longer looked capable of the starring role assigned to it.  And there are plenty of life scientists, before and after Denton’s book, who have had serious doubts along those lines.

Behe is so careful to put “neo-Darwinian” or “Darwinian” as a qualifier before “evolution” that his position cannot be mistaken as an attack on “evolution” as such.  For him, the “crisis” is in neo-Darwinian explanation, which he thinks can explain some things adequately but other things very improbably.  And there is nothing wrong with criticizing a mechanism.  It’s done all the time in science.  Only the team at Biologos thinks that no one should be allowed to criticize the currently reigning mechanism.


Rich - #18492

June 22nd 2010

Dennis:

If you are referring to another thread where you gave me a reference to an article on whale evolution, yes, I did look up that article, and in fact replied to you about it.

In that context, you were making a different argument than the one your are making here.  There, you were saying that there *were* attempts in the literature to link specific genes to specific morphological features (limbs, fins, etc.) and to explain whale evolution in that way.  I replied that yes, this is an example of the sort of literature I am looking for.  I acknowledged that, in principle, that sort of article could constitute a scientific reply (albeit a very partial and limited one) to Sternberg’s challenge.

Your current argument, however, eschews detailed accounts and claims we can infer the success of the mechanism *merely from knowing how to read genome charts*.  I disagree, but, as you’ve been trying to intimate, I’m not a geneticist and therefore not “qualified” to refute you.  So by Biologos rules, you win.  But some will notice that your charts and your theory entirely avoid the “how” question.  You population geneticists can only stall for so long before the world notices this.  I’m done with this thread.  Best wishes.


Dennis Venema - #18495

June 22nd 2010

Likewise, Rich. It’s not so much that you’re not “qualified to refute me” - it’s that your lack of understanding of biology makes this conversation challenging. I don’t say that in a pejorative way - it would be the same issue if I tried to engage at depth on something far outside my expertise. (Now, I’m not likely to do that, but that is a personality difference between us, I guess). 

A few more comments (in case anyone is still following this or interested in it.)

I’m not trying to “pull rank” on you by shoving a “genome chart” in your face. I am trying to get you to see the scale of what needs to be explained when comparing humans and chimps at the genetic level. The point is, very, very little. Even if you don’t know an A from a G in DNA, just look at the sequences and tell me what you think. It should be obvious to anyone that these sequences are nearly identical. Well, that’s how every gene looks when comparing humans and chimps (well, some are a little more different, and some are less different, but I chose this example because it represents the average difference).

(cont)


Dennis Venema - #18496

June 22nd 2010

(cont)

The point is, we don’t need to invoke wildly non-darwinian mechanisms to explain the changes that we see. Small mutations will do just fine. You’ve already agreed that humans and chimps have major differences - well, it would appear they arose through darwinian mechanisms.


Argon - #18549

June 23rd 2010

Dennis, are there *any* truly ‘new’ biological structures that appear in humans vs. other great apes?


Gingoro - #18551

June 23rd 2010

Argon @18549

Dennis, are there *any* truly ‘new’ biological structures that appear in humans vs. other great apes?

I have wondered the same thing and rather doubt that there is much change except possibly in the brain but even that could be bigger memory and a faster (more parallel) processor with more connections.  Presumably God did something to make mankind more in his image. 

Think about a pc in the late 90s.  In terms of the hardware, today the processor is faster and the memory is much larger but otherwise there is not much essential change.  Try running today’s software on a pc from that era and it is a complete fiasco.  I have a couple in the basement and sometime if we have a blizzard all day it might be fun to try.  IMO sometimes bigger and faster seems to result in a qualitative change.  As the human interface folks used to say faster provides better human factors and interaction just in itself.  Dave W


Argon - #18553

June 23rd 2010

Personally, I find the loss of toe dexterity a bit aggravating sometimes… There are many instances where having a third or fourth hand would have made soldering small parts and repairing instruments a whole lot easier.


Dennis Venema - #18554

June 23rd 2010

I would say brain development qualifies, yes.

The point was that Rich agreed they were major differences. So, it was an opportunity to explore the genetic basis of such a change.


Argon - #18560

June 23rd 2010

Ah, mostly regulatory variations then…


Dennis Venema - #18564

June 23rd 2010

Yes, the evidence seems to point mostly to regulatory changes.

The general point is that small changes to an already complex system can have large effects - especially if the changes affect regulatory genes that act early in development.


Argon - #18568

June 23rd 2010

HAR-dee, HAR HAR?*

* A cryptic reference to human/chimp variation.


Rich - #20381

July 3rd 2010

Information re Altenberg 16:

There was some debate above (18288 ff.) as to how some members of the Altenberg 16 stood regarding neo-Darwinian mechanisms.  I had relayed the information that some of the Altenberg 16 were seriously raising the question whether traditional ND mechanisms should still be regarded as sufficient causes of macroevolution, or whether they might require major supplementation by other mechanisms.  One of the 16 was interviewed by Suzan Mazur, and about an hour of it is available on You Tube.  I presume that even Dennis Venema would admit that Stuart Newman “has the chops” to correctly interpret the drift of the conference discussions.  He and others might find Newman’s comments educative.

I found parts 4 and 5 of the interview quite revealing, but as I’m no longer here, I won’t debate them.  This is a public service announcement only.  Here are some links:

Part 1:  http://www.youtube.com/watch?v=a3O2Founays

Part 4:  http://www.youtube.com/watch?v=jmpH18J-6HI&feature=related

Part 5:  http://www.youtube.com/watch?v=BJR6ActyheM&feature=related

Main list:  http://www.youtube.com/results?search_query=altenberg+16&aq=f


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