Monday, June 26, 2006

Redundantia ad absurdum

[Update: I've fixed and added some links. An argument has been added, in red.]

You might have thought that this discussion was over (see also here and here). However, Salvador has now decided to reply (also here) to parts of my last piece. My immediate responses can be found under the comments cited, but I thought I should bring some of the more interesting points over here for detailed consideration.

Full or partial redundancy?

Salvador has finally clarified what he and Denton were talking about in their repeated claims that the C. elegans vulva "is generated by means of two quite different developmental mechanisms, either of which is sufficient by itself to generate a perfect vulva". It turns out that they meant the graded, action at a distance by the EGF-like ligand LIN-3 vs the sequential, non-graded lateral signal mediated by LIN-12. (Note: The earlier ambiguity was a serious failure of communication on their part. When you make a scientific assertion you must be very precise on the details. Mentioning "two mechanisms" in the context of vulval development will be interpreted as referring to "vulval induction and lateral signaling" by any C. elegans biologist. My second guess was the synMuv genes, because Salvador was discussing knockout experiments at the time. How was I supposed to know what Salvador meant?)

They based their arguments on a mini review by Cynthia Kenyon. Here's a crucial passage:
"[...] A simple and attractive model is that the two pathways both operate and are partially or fully redundant. This set-up would enable the vulva to form perfectly in every animal, which it does."
Salvador then decided to go on the offensive:
"I will be interested to see if he affirms or retracts his comments based on Cynthia Kenyon's article which way pits Sternberg (not richard) against others in the debate over nematode vulva development. Ricardo cited sternberg, but not the competing opinion it seems. However, I am willing to stand corrected."
First of all, let me introduce the figures involved. Cynthia Kenyon and Paul Sternberg are both giants of C. elegans developmental biology. Apart from doing classic work on several systems, such as vulval and embryonic development, and Hox genes, Kenyon turned to the genetics of aging and completely revolutionized the field (for example, with her work on the insulin receptor daf-2 and the transcription factor daf-16, or the signal from the germline that inhibits life-span). While I occasionally disagree with some of her evolutionary thinking, I have enormous respect for her work. Paul Sternberg began by resolving the gonadal and nongonadal post-embryonic cell lineages of the nematode Panagrellus redivivus, a classic evo-devo study from before the time it was called that. He then became famous for discovering the EGF receptor / RAS / RAF / MAPK vulval induction signaling pathway. He has also spearheaded the development and evolution of WormBase in recent years (that's the tool that allows me to gene-name-drop so effectively). Sternberg (definitely not Richard) is perhaps the most knowledgeable scientist in the world when it comes to vulval development.

I hate to disappoint Salvador, but it isn't helpful to talk about "competing" opinions here, for three reasons. First, the mechanisms raised by Kenyon are explicitly discussed in Sternberg's review. Second, Kenyon's piece is a small review written over 10 years ago, and it's hardly appropriate to compare it to the latest comprehensive survey of the field. Third, Kenyon was clear about the speculative nature of her proposal. She admitted that the papers she was reviewing did "not indicate which of the two signaling mechanisms plays the predominant role during normal development" (p. 172). Her proposal was described as "a simple and attractive model", not the final answer to the problem.

So what's the answer? My answer is that the two mechanisms are only partially redundant, not fully redundant (you'll notice that Kenyon was open to either possibility), for two reasons. First, the signal from the anchor cell (encoded by lin-3) is necessary and sufficient for vulval development. If the signal from the anchor cell, graded or not, is abolished (for example, by killing the anchor cell), all
vulval precursor cells (VPCs) acquire tertiary fates and no vulva is formed at all. Second, lin-12 (lateral signaling) is necessary and sufficient for specification of the secondary fate VPCs. Mutant individuals with null alleles of lin-12 do not generate secondary fate VPCs and, thus, cannot form a vulva. However, lateral signaling cannot form a vulva on its own, in the absence of a signal from the anchor cell. All this means that Denton's contention that the vulva "is generated by means of two quite different developmental mechanisms, either of which is sufficient by itself to generate a perfect vulva" is incorrect. And so is Salvador's original contention that got this discussion started:
"One can do a knockout experiment on one of the develomental pathways of a nematode vulva and then an alternative develomental pathway kicks in to create the vulva. There are two independently successful redundant developmental pathways in the vulva."
No. The graded signal is not sufficient to generate a vulva (it cannot generate secondary fate VPCs in the absence of lin-12 activity). I hope Salvador remains "willing to stand corrected".

So does it matter whether any particular biological system shows partial as opposed to complete redundancy? I believe it does. Most biological systems show some redundancy, but full redundancy is relatively rare. Partial redundancy is exactly what you'd expect to appear under natural selection. In contrast, I suspect that if perfect, full redundancy were all around us in biological systems, Salvador would be claiming it as evidence for design (more about this later).

Here's a point by Sternberg which Salvador might appreciate:
"C. elegans VPC patterning involves multiple sources of information each of which would be capable, in principle, of generating a normal pattern. [...] These pathways might act in combination to generate an exquisitely precise pattern. In C. elegans the graded anchor cell LIN-3 signal and LIN-12-mediated lateral signaling are the major players. In other species, the other pathways might predominate."
Surprise, surprise, this Sternberg is talking about evolution.

[Note: Pharyngula has some nice introductions to vulval development and evolution.]

The Platonic vulva

So why are vulval development mechanisms redundant? Apparently, we are all in agreement about that. In Kenyon's memorable phrase "this set-up would enable the vulva to form perfectly in every animal, which it does". Sternberg makes essentially the same argument. Redundancy is for robustness. Where we differ is over whether this redundancy and robustness have evolved (Kenyon, Sternberg, myself, and just about every practicing biologist in the planet) or designed (Salvador, Denton, and a few others). Before getting to that question, let me just make another point.

I suspect that another reason why Kenyon's piece appeals to Denton and Salvador, is the Platonic undercurrent of the concept of a "perfect vulva". As I've argued in the past, this is an old foible of C. elegans biologists; taking the whole "959 somatic cells" thing far too seriously. Christian thinkers have long been attracted to Platonism, of course. Darwin showed that this was the wrong way to look at biology. A better way is to embrace variation -- what Ernst Mayr called "population thinking". So are worm vulvae as Platonic as Kenyon suggests? No, worms do not challenge population thinking in any way. In one of my favorite C. elegans evolution papers of the last decade (i.e., one I wish I had written), Marie Delattre and Marie-Anne Felix showed that the vulva doesn't actually "form perfectly in every animal": they found a few errors here and there when they looked at thousands of individuals. Incidentally, Felix and her co-workers are doing some of the most exciting work on developmental robustness I know of, much of it on the vulva. It's largely unpublished at the moment, but I'll summarize it here when it comes out.

An argument from redundancy?

So why does Salvador believe redundancy supports ID creationism? This is actually a difficult question to answer because the argument hasn't been laid out in sufficient detail (compared to, say, Behe's "irreducible complexity" argument). Indeed, redundancy is the opposite of "irreducible complexity" (see comments here), so it isn't at all clear what Salvador is talking about. However, going back to the original discussion, Salvador did sketch an argument:
"Regarding the issue of redundant functionality, it does pose a problem for natural selection as a mechanism for it's evolution. Since there are frequently circumstances under which the functions may not visible to selection over several generations, this poses a problem for natural selection. I would not say insurmountable, yet, but substantial."
Substantial? Why? You agree that redundancy is for robustness, right? Now, we know that robustness evolves. For example, C. H. Waddington selected in the laboratory on several different kinds of developmental robustness in Drosophila melanogaster and readily observed selection responses. In the 1950s! Since then, robustness has been characterized in different kinds of organisms (e.g., viruses, bacteria) and systems (e.g., genetic code, development, circadian clocks). We know that robustness responds to selection imposed by high rates of mutation, recombination or environmental perturbation. We know it responds to different kinds of selection, such as, stabilizing, directional or fluctuating. We have simulation models and mathematical theory (also here, here, here, ...). The field has been reviewed, re-reviewed and re-re-reviewed. So what is the problem, exactly? Redundancy can be selected for if it promotes robustness, which it obviously does -- no problem!

Salvador then returns to the vulva:

"In the case of the nematode vulva, without some co-option, the independent path way can not be selectively advantaged unless the other develpmental pathway is knocked out. The independent pathway, would have to be pretty much functional when it appears as it is critical to perpetuation."

No. Partial redundancy does not require such an explanation. An initial sloppy pattern can evolve, and then partial redundancy can be added piecemeal to stabilize it. Even complete redundancy could, in principle, have evolved from partial redundancy, making highly suspect any "arguments from redundancy" for ID. In order for you to claim that redundancy implies design, you must show that there is no way the redundancy could have evolved by natural selection. Good luck establishing that for any system.

I'm afraid that against this background Salvador and Denton and Sanford have to be a lot more specific. It isn't good enough to assert that "problems" exist, especially when you give the impression that you haven't done your homework. If anyone is going to pay any attention you also have to explain where exactly the hundreds of earlier studies went wrong.

Read on

Thursday, June 22, 2006

Salvador's Redundancy II

[Update: The saga continues.]

Salvador has chosen an strange venue to reply to my recent posts about him. I tried adding another comment there, but it was becoming too long, so I moved it here. I'll focus on three points.

"Junk" DNA

After his comments it's no longer clear (if it ever was) what Salvador is actually arguing on "junk" DNA. The point is that deleting a piece of DNA that we suspect to be "junk" (e.g., because it is a pseudogene) is a scientific test of whether the DNA is "junk". If the deletion doesn't have any detectable effect, then the "junk" hypothesis is supported. That does not mean that we have proven that the DNA is "junk" (we cannot accept a null hypothesis); any number of alternative hypotheses may, conceivably, turn out to be correct in the end. However, it does mean that one cannot simply assert an alternative hypothesis (e.g., unknown interacting regions) and expect everyone to just accept them without further scientific test. Incidentally, many researchers (only a handful of which are connected to ID creationism) have proposed hypothetical functions for "junk" DNA, so Salvador isn't even right in his claim that ID is particularly well suited for thinking outside the 'evolutionary box'. I for one find the ideas of John Mattick on "junk" DNA much more interesting than anything ID supporters have ever said. However, his ideas will have to be tested in the laboratory or the computer -- something he is actively engaged in. I would love to hear about the research efforts of the ID scientists. In other words, we are still waiting for a good example of the supposed superiority of ID as a "framework for scientific investigation".


Salvador writes:
The premise that systems with survival value are sufficiently visible to natural selection for them to be maintained and evolved is a false one. Those issues are theoretically pursued in Cornell Geneticist, John Sanford's book [...]
Salvador is simply hallucinating here. Is this the same John Sanford who declared in the Kansas Evolution Hearings that the earth was probably between 5,000 and 100,000 years old? Is this the Courtesy Associate Professor at the Department of Horticultural Sciences who has never published a peer-reviewed article on evolutionary biology? You'll forgive me if I continue to walk down the corridor (toward Dan Graur's office and lab) for my genome evolution.

C. elegans vulva

Salvador: when will you retract that nonsense about the "independently successful redundant developmental pathways" for making a vulva? Knocking out either the EGF receptor / RAS / RAF / MAPK inductive signaling pathway or the LIN-12 / Notch lateral signalling pathway results in the development of an abnormal vulva (often, no vulva at all). It would appear that your ID colleagues' "never apologize, never explain" attitude is contagious.

Read on

Concealed, denied or confused

The national academies of science of 67 countries have issued a joint statement on the teaching of evolution. It opens with:
We, the undersigned Academies of Sciences, have learned that in various parts of the world, within science courses taught in certain public systems of education, scientific evidence, data, and testable theories about the origins and evolution of life on Earth are being concealed, denied, or confused with theories not testable by science. We urge decision makers, teachers, and parents to educate all children about the methods and discoveries of science and to foster an understanding of the science of nature. Knowledge of the natural world in which they live empowers people to meet human needs and protect the planet.
It goes on to list some basic "evidence-based facts" on cosmology, geology and evolution which we can all agree on. It concludes with a statement on the nature of science. It's not beautiful, but it's pretty good. Hopefully it will have some impact.

There was one disappointing element, though. Going down the list we find:
Albania, Argentina, Australia, Austria, Bangladesh, ..., Nigeria, Pakistan, Palestine, Peru, Philippines, Poland, Senegal, ...
Wait a minute! Where on earth is the Portuguese Academy of Sciences? One wonders what the hell they do all day over there. They should be ashamed of themselves! I'm off to write them an email. I wonder what the excuse will be: concealment, denial or confusion?

[Via Afarensis]

Read on

Monday, June 19, 2006

Salvador's Redundancy

[Update: This discussion is continued here and here.]

When we last met Salvador Cordova, the energetic proponent of intelligent design (ID) creationism, he was saying spectacularly silly things about the robustness of biological systems over at evolgen. Now he's at it again:
"Intelligent design will open doors to scientific exploration which Darwinism is too blind to perceive. The ID perspective allows us to find designed architectures within biology which are almost invisible to natural selection. Thus, the ID perspective is a far better framework for scientific investigation than the Darwinian perspective. What do I mean, and how will I justify my claim?"
Give the man credit: this opening paragraph has flair. But does the rest of the post deliver? Sadly, it's just the same argument that redundancy and robustness are somehow a problem for evolutionary biology. Bizarrely, he chooses to illustrate his point with a press release from Laurence Hurst about his latest paper in Nature. He quotes the following passage with approval:
"Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life [...] This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product [...] Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments."
The point being made is uncontroversial to any biologist who knows her genetics. So what does Salvador conclude from this? Incredibly this is what he writes:
"Knockout experiments have also been used to argue 'junk DNA' is junk. This is out rightly bad science, but it persists because of Darwinist’s eagerness to close their eyes to design and paint various artifacts in biology a the product of a clumsy blind watchmaker rather than an intelligent designer."
This is wrong on so many levels that it's hard to know where to begin. Jason Rosenhouse did a good job debunking this, but I'll make a couple more points. First, where did this connection to "junk" DNA come from? I suspect it arose from the discussion on evolgen. My colleague Dan Graur made the point that experiments where large portions of "gene deserts" (long stretches of nongenic DNA without apparent function) were deleted support the hypothesis that they truly are "junk" DNA. The "Darwinist's eagerness" is entirely in Salvador's imagination. Second, Salvador seems to be suggesting that Darwinists have been getting the wrong end of the stick about knockout experiments. So who is this Hurst fellow? Surely, he must be a rising star at the Discovery Institute. Actually, you'll be shocked to find that that is not the case: Laurence Hurst is one of the brightest young British evolutionary biologists, a disciple of Darwin if ever I've met one. Indeed, the abstract of the paper the press release was about leaves us in no doubt as to what Hurst and his colleagues were doing (I've highlighted a few key concepts in bold):
It is possible to infer aspects of an organism's lifestyle from its gene content. Can the reverse also be done? Here we consider this issue by modelling evolution of the reduced genomes of endosymbiotic bacteria. The diversity of gene content in these bacteria may reflect both variation in selective forces and contingency-dependent loss of alternative pathways. Using an in silico representation of the metabolic network of Escherichia coli, we examine the role of contingency by repeatedly simulating the successive loss of genes while controlling for the environment. The minimal networks that result are variable in both gene content and number. Partially different metabolisms can thus evolve owing to contingency alone. The simulation outcomes do preserve a core metabolism, however, which is over-represented in strict intracellular bacteria. Moreover, differences between minimal networks based on lifestyle are predictable: by simulating their respective environmental conditions, we can model evolution of the gene content in Buchnera aphidicola and Wigglesworthia glossinidia with over 80% accuracy. We conclude that, at least for the particular cases considered here, gene content of an organism can be predicted with knowledge of its distant ancestors and its current lifestyle.
Isn't it strange how ID, with its "far better framework" keeps opening "doors" in blog posts, while the Darwinists keep publishing papers in Nature, despite having their eyes closed.

What about the rest of the post? Interestingly, we learn where Salvador got his misconceptions on nematode vulval development. He quotes the following passage from Michael Denton:
"The development of the female sexual organ, the vulva, in the nematode provides perhaps the most dramatic example to date of redundancy exploited as a fail-safe device at the very highest level. A detailed description of the mechanism of formation of the nematode vulva is beyond the scope of this chapter, suffice it to say that the organ is generated by means of two quite different developmental mechanism, either of which is sufficient by itself to generate a perfect vulva."
Since Salvador seems to have missed my earlier discussions of this example (here and here), I'll repeat it. Here's a good review of vulval development in the nematode Caenorhabditis elegans, by the leader of the field. The abstract gives an overview:
A single cell of the somatic gonad, the anchor cell, organizes the development of the vulva from epidermal precursors as well as the physical connection of the epidermis with the uterus. WNT signaling acting via the HOX gene lin-39 renders six epidermal precursor cells competent to respond to other developmental signals. The anchor cell induces nearby epidermal precursor cells to generate vulval cells via an epidermal growth factor (EGF) signaling pathway. The precise pattern of vulval precursor cell fates involves the graded action of the EGF signaling and LIN-12 (Notch) mediated lateral signaling. EGF promotes the primary fate while LIN-12 promotes the secondary fate. Both EGF and LIN-12 prevent precursor cells from adopting the tertiary fate, which generates non-specialized epidermis.
So what about those "two quite different developmental mechanisms, either of which is sufficient by itself to generate a perfect vulva"? Well, the thing is, the two signaling pathways are not redundant. Of course there is redundancy in the network (I've discussed one kind here), as there is in almost all biological networks known -- it's just that there are no "independently successful redundant developmental pathways" for making a vulva, to use Salvador's earlier description. This shows a recurrent pattern in ID literature, and other pseudoscience -- grandiose claims based on sloppy scholarship, selective quotation and ignoring reality.

So what of the more general claim that redundancy and robustness pose difficulties for evolutionary biologists? As I've argued before, this is a delusion. Redundancy arises readily from a common evolutionary mechanism: gene duplication. And robustness is an exciting active area of research in evolutionary biology. As regular readers of this blog will know, even I work on it.

I should end by quoting a comment made by Mark Perakh to Jason's post:
It would be entertaining to watch a debate between Salvador Cordova and Michael Behe, wherein Salvador would defend his thesis that biological entites possess redundancy which points to design, while Behe would defend his thesis that biological system are irreducibly complex, hence possess no redundancy, which points to design. A moderator (say, Dembski) would dance between them reconciling these two mutually incompatible arguments by means of writing lengthy equations and inventing new terms, say of "irreducibly complex redundancy," as a corollary to a newly discovered Fifth law of thermodynamics: the law of conservation of redundant irreducible complexity. A lot of fun watching Cordovas and his ilk pretending to have (redundant) brains.
In other words, anything is considered evidence for an intelligent designer by these people, no matter how inconsistent. Now, that is what I call a framework!

Read on

Saturday, June 17, 2006


Yes, it's happened for the first time since 1966 -- Portugal has moved on to the next stage in the Football World Cup. Figo and Deco showed how it's done (although Deco was lucky not to be sent off early in the second half), and the rest of the team had a great match as well. Now, the question is whether we play Argentina or the Netherlands in the Round of 16. No offense, but I'd prefer the latter right now. I suspect that the way to achieve that will be to win or draw against Mexico...

Read on

One for the Team

Judge John E. Jones III has been speaking out about his experiences after the Kitzmiller decision:
"Because I was a Republican judge appointed by a Republican president, I was supposed to throw one for the home team. What was lost was the role of precedent and the rule of law. My job was to find the facts and apply the law - nothing more, nothing less [...] If the majority thinks we should teach creationism in schools, does that mean judges are supposed to go with the flow?"
For his courage and integrity, Judge Jones got death threats, and was called a "fascist" by none other than Bill O'Reilly!

[Via Red State Rabble]

Read on

Thursday, June 15, 2006

Counter Coulter

PZ Myers (here, here) and other evolutionary bloggers (here, here), have been fuming at Coulter's latest pronouncements on evolution. Apparently, the Sir Isaac Newton of information theory helped her along, so we know what to expect.

I'm always amused when creationists accuse natural selection of being simultaneously illogical and tautological (sometimes they make this claim about evolution, for a trifecta of nonsense). Of course, natural selection is not illogical. It's so logical that when you get it it's hard not to share Huxley's sentiment: "how extremely stupid for me not to have thought of that!" The tautology charge is harder to dismiss out of hand. It is easy to see that natural selection is not trivially tautological in the way that the statement "either Dembski is the Isaac Newton of information theory or he isn't" is. Some have argued that fitness does not have to be defined tautologically, but I'm not that bothered. Natural selection may be tautological, but only in the same way (that of being internally consistent) as the whole of mathematics and logic. The point is not whether a theory, such as Newton's laws of motion, is tautological, but whether it is useful scientifically, in the sense of helping us understand how the world works. Only someone who knows nothing about the last 150 years of evolutionary thinking could delude themselves into thinking that natural selection has been a fruitless idea.

Read on

Sunday, June 11, 2006

The World Cup is Better than the Olympics

The Economist has a couple of interesting articles about football this week (I refuse to call it soccer, of course). This is unusual because they do not cover sports news, which is one of the reasons why I read it. In a leader ("Let the Games Begin"), they point out that "the World Cup, unlike the Olympics, is wonderfully difficult to manipulate for political purposes":
"Over its long history, success at the Olympics has usually been a fairly accurate measure of global political power. [...] During the cold war, the United States and the Soviet Union repeatedly struggled to gain a symbolic victory, by winning the most medals at the Olympics. Already a similar, politically charged battle for supremacy between America and China looks likely in the 2008 Beijing Olympics.

By contrast, the World Cup has its own hierarchy, which is pleasingly divorced from the global pecking order. There is a sole superpower—Brazil. The Italians and French, apparently doomed to gentle decline in the real world, remain formidable competitors on the football field. And then there are the rising powers—which are more likely to hail from Africa than Asia. America will field a serious team at the World Cup, but nobody expects it to win. The Chinese, who have discovered a passion for football, failed to qualify for the tournament."

Another good excuse to watch some games...

Read on