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Signature in the Pseudogenes, Part 1

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May 10, 2010 Tags: Genetics

Today's entry was written by Dennis Venema and Darrel Falk. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

Signature in the Pseudogenes, Part 1

In our previous post, we likened comparing genomes of related organisms to reading alternative history novels. We noted that before two species diverge, they share the same “backstory” but then go on to accumulate changes after separation.

One interesting feature of looking at genomes is that often we can find the mutated remains of once-functional genes. These are called pseudogenes, or “false genes.” Pseudogenes might be part of a shared backstory for two species, or they might crop up independently after two species go their separate ways. Either way, they are easy to spot at the molecular level because they retain a lot of similarity. For example, here are the DNA sequences for the start of one particular gene1 in several species (for our purposes, its function is not important).

As you examine the sequence of letters above, note that DNA contains a four letter code. This string of “letters” is made up of the molecules adenine, guanine, cytosine, and thymine strung together within the large super-molecule, DNA. Our cells read the encoded instructions and, interpreting the code, build each of the different proteins required for the maintenance of life.

Note that the instructions have changed a little since these five species had a common “backstory” (ancestor). Despite the changes, for the dog, mouse and chicken, the protein is fully functional. This is not so, however, for the chimp and human. The “dot” (highlighted by the red arrow) means that one single letter of the instructions has been deleted. This change would be like finding this sentence in the first edition of a book:

THE BIG RAT HIT THE RED MAT.

But, in the second edition of the same book, we find this instead:

THE BIG RAT HTT HER EDM AT

The sentence has no meaning anymore, but, as we compared the first and second versions of the book, we would be able to tell exactly what had happened: the letter “I” had been deleted from the sentence, and everything following would be messed up. A single deletion throws off the whole code from that point on. Thus, for chimps and humans, the instructions become gibberish, and the protein molecules produced according to that gene’s instructions are now badly mangled and unable to function.

As you go back and examine sequence in the human/chimp pseudogene, notice how both species carry the exact same deletion. This suggests that the occurrence of this single deletion occurred in one individual, a common ancestor with whom both species have a shared backstory.

Let’s return to our book analogy. Presumably all copies of the second edition had the exact same non-functional sentence about the BIG RAT. If someone was to examine two second edition copies of the book, each of which were missing that same letter, “I,” it would be unthinkable to propose that the exact same mistake occurred independently in the printing of each of the two books. Similarly, it would be incorrect to propose that the new incoherent sentence had some important meaning which literary scholars will discover some day. We would know, plain and simple, that a mistake had occurred. Anything other than that would be highly contrived.

Today both chimps and humans carry the exact same mutation because they both have the same backstory. However, it is even more poignant than that. There are 20,000 pseudogenes in the human genome. Each has its own unique backstory. Each can be traced out in the same manner we have just done for this one.

The hypothesis of common ancestry makes precise predictions about how pseudogenes will be distributed in related species. Once a gene has been mutated into a pseudogene in a certain species, that pseudogene with its specific inactivating mutation will be passed on to all descendents of that species.

The figure below demonstrates this for a specific pseudogene, which we will term pseudogene “y.” Note that in a very specific individual at a very specific time, gene “y” underwent a change in its code—it mutated. That altered code was passed on to the subsequent generations and ended up in two daughter species, Species A and Species B.

Now consider a second gene, which we call “x.” It also underwent a mutation, but did so earlier in the lineage. Let’s call the new mutated form of this gene pseudogene “x.” This is shown in the next figure. Since this mutation occurred earlier in the lineage in an organism that was a common ancestor to Species A, B, and C, all three of these species carry the abnormal, non-functional version of “x.” The lineage to species D, however, had already broken away. It does not carry the mutated version of “x.”

Finally, consider another gene, which we’ll call “z.” This gene is perfectly functional in Species A, B, and D. However, when you examine its code in Species C, guess what? It carries a non-functional pseudogene. What do you think has happened here? This is a recent change, so recent that it occurred in an individual whose ancestors only went on to become Species C. Here is a summary figure which illustrates the time at which each of the three mutations occurred and the ramifications of each change.

In this example, since gene “x” is mutated to a pseudogene in the common ancestor of species A, B and C, we would expect to find this pseudogene, with the same exact inactivating mutation, in these three species. Similarly, the pseudogene version of gene “y” with exactly the same code-change should be found only in species A and B. Finally, there are many cases in which a pseudogene is found only within one species, or, at most, a couple of closely related sister species. Pseudogene “z” is our example of that.

If life really does have a backstory of this sort, then you can see the power of this technique for tracing the lineage. It allows us to trace the history of life, species by species. Interestingly though, there have long been other—non-genetic—ways of tracing life’s history. Biologists have been using these alternative methods for many decades. For example, by examining fossils (paleontology) and tracing changes in body structure (comparative anatomy), the history of life had already been pretty much worked out before DNA sequencing data ever came into the picture.

For the most part, the data which are emerging from DNA sequencing projects simply verify that which biologists have known for years through these other methods of exploring life’s history. Still, the results are extremely gratifying in their consistency. In science, one looks for corroborating evidence. If the DNA data had suggested totally different lineages, then there would have been good reason to doubt the common descent hypothesis. Such is not the case though. The supporting data keep piling up; there is no longer any doubt.

Remember how science works. If there are multiple lines of evidence—each internally consistent with the central overarching principle—a consensus is reached. The theory is judged to be correct and the scientists move on to further explore its ramifications.

If the theory of common descent is true, then it also makes predictions about what we would not expect to find at the genetic level. We go on to explore this topic in our next post.


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.
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.

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MAS - #13255

May 11th 2010

Glen I pointed out that in the three most recent ID/Intelligent Design debates; that are publically verifiable and easy to find (Falk/Meyer, Craig/Ayala, Meyer-Sternberg/Shermer-Prothero) demonstrate that the ID proponents are scientifically literate, perhaps more so, than the Darwinists. It is only the Darwinists that insist ID is ‘theistic apologia’ and hence try to dismiss it on theological and broadly philosophical grounds. The ID community sticks to the science and then use it to beat their opponents into the ground. The claim that ID is ‘theistic apologia’ also fails on the simple fact that some proponents/sympathizers of ID are atheists (like Bradley Morton). By the way even if ID is ‘theistic apologia’ this does not negate its truth claims (if you think so then you are committing a generic fallacy).


MAS - #13256

May 11th 2010

cont…
I noticed that my posts have been removed hence demonstrating another tactic – censorship- usually on the grounds of not being significantly respectful of the Darwinist community, your post #13210 demonstrates this point perfectly (that I ‘[H]ave done nothing attempt to defame your betters, which is about all that ID ever does’). Falk said something similar when Meyer responded to Ayala’s review of SoTC, Falk was reluctant to post it as
‘ [F]elt his tone was insufficiently respectful of one of Biology’s living legends’


MAS - #13258

May 11th 2010

coun..
and only did so because
‘Steve made it clear that he would post it elsewhere unless BioLogos posted it “as submitted.” I did not want it to go up anywhere unless I could make it clear that Dr. Ayala had not been asked to do a book review’.


MAS - #13259

May 11th 2010

Of course we all know what happened after that, Falk was intellectually overwhelmed by Meyer and was forced to concede that ‘ID movement ought to be considered a scientific movement’ and ‘I appreciate that they are doing science’.
Unfortunately I cannot reply adequately to your reply as my post was taken down, but I did not make out any ‘naked and false assertions’. The claim that my
‘[L]ack of regard for evidence and standards of truth, your “witness” to such absurdities counts for very little indeed’
Is very strange as my I showed in my post where the forum users can verify what I said themselves. You obviously, and biologos, want to keep the issues I raised hidden.

I will log back on in a few hours but I bet these posts will be removed.


MAS - #13260

May 11th 2010

For what it’s worth I am not an ID advocate.


Glen Davidson - #13262

May 11th 2010

Sorry, MAS, finding a few examples of educated apologists proves nothing at all, except that you don’t understand how to use evidence properly—assuming that you’re not deliberately using the fallacy of generalizing from the exception (which is what I assume, but could not demonstrate). 

Also, I wouldn’t care if Sternberg were more intelligent than a particular opponent, his “arguments” against evolution simply don’t hold water.  Moreover his understanding is an exception to the frequent lack of knowledge evinced by IDists in general.

And you haven’t back up all of your other false charges and attempted ad hominem fallacy.  While I cannot generalize to all IDists from your substanceless “arguments,” I can clearly point to them as an example of, say, the general attempts to win by name-calling sans demonstrable fact that one sees at UD.

Glen Davidson


Chris Massey - #13269

May 11th 2010

MAS,

Do you have a link to the Meyer-Sternberg/Shermer-Prothero debate that you mentioned? I just finished reading Prothero’s “Evolution: What the Fossils Say and Why it Matters”. It was a very thorough review of the fossil record. I’d be interesting in seeing him debate Meyer.

Also, if you’re not advocating ID, what position would you espouse?


MAS - #13272

May 12th 2010

—-Sorry, MAS, finding a few examples of educated apologists proves nothing at all, except that you don’t understand how to use evidence properly—assuming that you’re not deliberately using the fallacy of generalizing from the exception (which is what I assume, but could not demonstrate).—-

My posts refer to only to the Falk/Meyer, , Craig/Ayala Meyer-Sternberg/Shermer-Prothero debates and the general trend for Darwinists to label ID theology (or in your words ‘theistic apologia’) . At no points did I say, indicate, or suggest that the considerable intellectual prowess and education of these individuals are the norm for ID proponents (or Darwinist proponents for that matter).  Hence your assumption that I argue from the exception to the general is without merit


MAS - #13273

May 12th 2010

——Also, I wouldn’t care if Sternberg were more intelligent than a particular opponent, his “arguments” against evolution simply don’t hold water. —-
Yes I agree Sternberg certainly got the better of Prothero in Beverly Hills. But please remember Prothero also claimed that Sternberg’s arguments about junk DNA, hox genes and so on did not hold water and look what happened. Claiming that Sternberg’s arguments don’t hold is merely an assertion (like Prothero’s 12 wing dragonfly).

——Moreover his understanding is an exception to the frequent lack of knowledge evinced by IDists in general.——
Again I only mentioned the above six individuals. By the way Sternberg is, strictly speaking, a structuralist, who is very sceptical of Neo-Darwinism.  Just to clarify things in my deleted post I was very careful about making these distinctions (i.e. Meyer is an ID supporter, William Lane Craig is sympathetic of ID but not convinced) but in this and my previous post I mean ID as an umbrella term to as scientific scepticism of Neo-Darwinism. I made this point in my deleted mail and forgot about it until I saw this reply.


MAS - #13274

May 12th 2010

——And you haven’t back up all of your other false charges and attempted ad hominem fallacy.  While I cannot generalize to all IDists from your substanceless “arguments,” I can clearly point to them as an example of, say, the general attempts to win by name-calling sans demonstrable fact that one sees at UD.—-

I made these claims in my first post;
In the three mentioned debates the ID proponents argue science; their opponents argue theology, (poor) philosophy and argue from consensus.
The ID proponents win the debates. I mention that the two of the debates Craig/Ayala and Meyer-Sternberg/Shermer-Prothero are on youtube with Falk/Meyer on biologos. Hence fully justifying my claims that these debates happened. Of course others may think the Darwinists managed a draw or even won but the point is still the same – the ID people argued science. I also wished to make people aware of these excellent and insightful debates so no matter what side you are on you may get an idea of where your opponent is coming from.


MAS - #13275

May 12th 2010

In my second post I added;
The problems of censorship of ID ideas in the public arena. I point out that my first post is deleted and mention Falk’s reluctance to publish Meyer’s response to Ayala’s review of SiTC. Again justifying my claims
The written debate between Falk and Meyer result in Falk conceding that ID is science (and not just theology). This is on biologos and again this is easily verified.


MAS - #13276

May 12th 2010

I have not engaged in name calling or resorted to ad hominem attacks. However you have
described Neo-Darwinists as my ‘betters’,
claim that I have made ‘naked and false assertions’ but give no examples,
claim that I have a ‘lack of regard for evidence and standards of truth’, despite the fact I have backed up everything I have claimed
Say that I have made ‘false charges against actual scientists and scholars’ but give no names
and that I have resorted to ‘name calling’ but give no details of such behavior.

MAS
(and still not deleted)


MAS - #13279

May 12th 2010

Dear Chris Massey - #13269 I just checked and the first part is at

http://www.youtube.com/watch?v=m3ThFiBLxtU

Unfortunately the individual who posted the audio does call it -Stephen Meyer & Richard Sternberg impressively defeat Michael Shermer & Don Prothero- But please make up your own mind. There is also commentry on Panda’s Trumb and at the Discovery Institute.

I was a happy to describe my position as TE, but the debates I have mentioned as well as Meyer SiTC have really called into question my assumptions. My educational background is in mathematics and to a lesser extent Physics and so I cannot call myself a biologist. A friend of mine is a research biologist at Oxford University and when I discussed these issues with him he did acknowledge that much of the raw data in his field supports multiple interpretations including ID – especially since the Encode project. I feel this is not enough to teach ID in science class or to place ID as an interpretation equal to Darwinism.


MAS - #13280

May 12th 2010

coun…
However I do know that ID has not been given a fair hearing and it is this which gives me the most worry (in that I feel the science community and biologos are trying to sell me something rather than providing evidence so I can come to the conclusion that Darwinism is the only theoretical underpinning of biological phenomena) . Meyer, Sternberg etc all seem both sincere and intelligent and may very well be on to something. I don’t know

All the best
MAS


Bilbo - #13281

May 12th 2010

Oops, that’s “Darrel” not “Darryl”.  Sorry about that.


Malcolm - #13295

May 12th 2010

MAS,

The subject of this post is common descent, a subject on which you have not made clear your position. Have you for example seen Dr. Venema’s presentation he gave at the American Scientific Affililation meeting at Baylor?

Human Genomics: Vestiges of Eden or Skeletons in the Closet?

Or this one?

Can an Evangelical Christian Accept Evolution?


Malcolm - #13311

May 12th 2010

Could the moderator remove my comment #13294 and this one?


MAS - #13321

May 12th 2010

Malcolm - #13295

I know that the blog post ‘Signature in the Pseudogenes, Part 1’ is about common descent. My posts were largely directed at Glen’s jibe about ID being ‘theistic apologia’ despite the claims of the ID movement to the contrary. ID has no problem with common descent (But may have with the above presentation of Pseudogenes as they argue that a majority of genes which do not code for protein are still vital to the organism and to dismiss them on the grounds that they are the waste product of natural selection is plain wrong. I felt Biologos should have asked Meyer or another fellow of the discovery to comment, or write their own article as they have responded very successfully to claims by Falk in the past). 
I do think it is a shame there is not more communication between ID and biologos. This could be improved by, perhaps, inviting those skeptical of Neo-Darwinism to contribute once every two or three months (without endorsing those views of course). 
Thanks for the web links I will definitely look at them later

MAS


Malcolm - #13324

May 12th 2010

MAS,

I’m rather confused by your post, even if we grant the extremely dubious claim that “a majority of genes which do not code for protein are still vital to the organism,” how does this do anything to undermine the understanding that these genes have lost their original function and the same inactivating mutations have caused it? Moreover, why do we have the precise pattern described above, identical inactivating mutations shared by humans and orangutans are also shared by gorillas and chimps, those shared by gorillas and humans are also shared by chimps? What is your alternative explanation for this data other than that humans and chimps share a more recent common ancestor than either does with gorillas, and that humans, chimps and gorillas share a more recent common ancestor with each other than any does with orangutans.

I’d suggest you see Venema’s presentation on other pieces of genomic evidence and especially his discussion of olfactory and vitellogenin pseudogenes.


Unapologetic Catholic - #13339

May 12th 2010

“ID has no problem with common descent”


Absolutely incorrect.

A single sample Discovery Institute post will illustrate that statement is jsut flatly incorrect.:

http://www.evolutionnews.org/2010/03/does_darrel_falks_junk_dna_arg.html

Ther are many many more like that one.  Nobody who is familiar with the Intelligent design literature can make such an incorrect statement.  Just visit either the Discovery Institute website or Willaim Dembski’s blog, meanignfully entitled “UNCommon Descent.” 

So do DI Fellows Paul Nelson, Nancy Pearcy, William Dembski, Phillip Johnson, Jonathan Witt, Casey Luskin, Stephen Meyer, Dean Kenyon, or Ray Bohlin accept common descent?  No, not a single one.

Has any DI Fellow stated that common descent is well established?  Yes—-one person.  That person then qualified his answer so as to contradict himself entirely.


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