My old sparring partner Salvador Cordova recently posted this essay over at Uncommon Descent. Salvador describes his intent as follows:
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?
Pretty brazen, but hardly new. ID folks have been telling us precisely this for over a decade. I'm still waiting for them to open just one door, even if just a crack.
So how does Cordova back up his statement? He begins with a lengthy anecdote about airplanes:
Let me illustrate my point with some anecdotes. I was piloting a small airplane in the spring of 2002. My airplane suffered a potentially serious systems failure during the flight. In piston powered aircraft, the electrical ignition system (called a magneto system) is life-critical. Aircraft engineers consider the magneto system so crucial that they design each engine with two redundant, independent magnetos. If one magneto fails, the other seamlessly takes over. In fact, these dually redundant systems are so effective that a pilot will not even know if one of the magnetos failed in mid-flight until he's back on the ground doing a routine inspection of his airplane!
Cordova next recounts how during a standard pre-flight check on his plane he discovered that one of the magnetos had failed, but that he had not been aware of it when he was flying because of the back-up system.
The point?
What does this have to do with biology and Darwinism? One way Darwinists conclude something is evolutionary junk, a vestigial feature, or an otherwise useless biological artifact is to apply “knock-out” experiments on an organism. If a piece of the organism is knocked out, and the organism still functions well and is otherwise “fit”, then the knocked-out piece is deemed useless, an evolutionary leftover, junk, or even bad design.
The really silly part of Cordova's essay is still to come, but first we must comment on this remarkable paragraph. First off, “knock-out experiments” are carried out in genetics to determine the function of particular genes. The idea is to remove a particular gene from the organism's genome and attempt to determine the effect this has on the resulting organism. They have nothing do with determining whether a structure is vestigial. The point is that the thing being knocked out is a gene, not a “piece of the organism”.
Furthermore, vestigial is not synonymous with non-functional. In fact, the term vestigial can be defined without any reference to evolutionary theory at all. Thus, the sightless eyes of cave-dwelling rodents or the pelvic bones of snakes are deemed vestigial not because we are making some assumption about evolutionary history, nor because they are non-functional. It is because they are reduced or rudimentary versions of more complex structures that exist in other organisms. They are evidence for evolution because they can be viewed as a logical consequence of organisms adapting to new ways of life. Organisms that live in perpetual darkness do better by diverting resources away from the preservation of eyes that are no longer useful for vision, for example. They are hard to explain as the products of ID. Which is why most ID folks hide behind the inscrutable motives of the designer in trying to eexplain such structures.
For much more information on this subject, click here.
Furthermore, knock-out experiments have little to do with the determination that a given stretch of DNA is junk. Rather, “junk DNA” is a term used to refer to DNA that does not code for protein. The determination that a piece of DNA is “junk” is normally based on the fact that we can determine where the DNA came from. Such DNA frequently arises from endogenous retroviruses, or from tandem repeats of other genes, among other sources. Determining that such DNA can be knocked-out or mutated without discernible effect on the organism is certainly a helpful piece of supporting evidence, but it is not the main evidence used to determine that something is junk.
We should also point out that the conclusion that much of an organism's genome is junk is also suggested by the fact that closely related organisms frequently have wildly different quantities of DNA in their genomes. More information on this can be found here. ID folks, of course, have no explanation for why these genome sizes differ as much as they do.
Let us continue. Cordova now links to this article about new research into the size of the minimal genome required for a living bacterium. He presents the following quote from the article:
“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,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath.
“This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product.
When you knock out one gene, the genome can compensate by using an alternative gene.
But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead.
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.” (Cordova's Emphasis)
From here Cordova continues:
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.
The strategy of using several different means to achieve a particular goal where each of the individual means is sufficient by itself to achieve the goal is used in many engineered systems to ensure that the goal will be achieved, even if one or more of the means fail. For example, the space shuttle's on-board inertial guidance system, consists of five redundant computers!
And after a lengthy quote from Michael Denton Cordova seals the deal as follows:
Denton describes what I call contingency designs. It should be hopefully obvious that contingency designs are exactly the kinds of designs that are hard pressed to be created via natural selection. How does one evolve a contingency design when the primary design functions just as well? If a creature mutates a failure into a life-critical primary system, it will more likely be selectively eliminated before it can evolve a fully functioning backup system!
ID's explanatory filter is therefore a potentially more effective tool at identifying designs which elude Darwinian style tests (such as knockout experiments) for functionality. ID's explanatory filter looks for possible functionality by identifying specified complexity in biological artifacts which may not evidence any immediate effect on the organism if the biological artifact is knocked out.
In an attempt to keep this blog entry to a reasonable length, let me focus on Cordova's two main claims. He argues that (1) Evolutionary thinking leads scientists to the erroneous conclusion that knock-out experiments are a sound means for detecting non-functional parts of the genome, and (2) ID avoids this pitfall.
I'm sure everyone will be shocked to learn that both of these claims are false.
We start with point number one. Knock-out experiments have nothing to do with evolutionary thinking. They are of obvious utility in genetics, because they frequently identify crucial functions performed by individual genes. The information they provide is certainly useful to evolutionary biologists, but they are neither motivated by nor central to evolutionary theory. The idea that evolutionists are so eager to view various bits of anatomy as useless junk that they cling to whatever feeble evidence they can find to make that detemrination is nothing but an ID fantasy. As should be obvious, it is essential to proper evolutionary reasoning that we have a solid understanding of the functions performed by various genes.
The error made in concluding from a single knock-out experiment that a particular gene should not be considered a member of the “minimal genome” likewise has nothing to do with evolutionary thinking. It is, instead, an error made by being unaware of certain aspects of organismal genetics. Knock-out experiments are certainly valuable for detecting genes that are essential to proper function. It is the exstrapolation from “inessential” to “should not be included in the minimal genome” that is unwarranted.
(Incidentally, let me add that I am simply accepting the characterization provided in this news brief, that geneticists really have been systematically guilty of this oversight. News briefs are frequently sensationalized in an attempt to exaggerate the importance of the work being described. But since it has no real impact on my arguent, I will accept the claims made in the brief.)
So such errors as were made were not the result of misapplied evolutoinary thinking. But how were these errors uncovered? Was it the result of ID thinking? Happily, the news brief tells us:
The researchers made this discovery after developing a new approach to genome modelling which, given the organism's evolutionary history and knowledge of its surrounding environment, allows them to predict which genes a bacterium's genome should contain. (Emphasis Added)
Gosh. I wonder why Salvador didn't quote that part?
So the error that was made had nothing to with misapplied evolutionary thinking. Quite the contrary. The error was uncovered by applying evolutionary thinking to certain problems in genetics.
Taking Cordova seriously for a moment, we are led to the following question: The unwise extrpaolation described in the news brief has been going on for quite some time now. It was just recently exposed by scientists applying evolutionary thinking to the problem. But if ID provides a better framework for addressing these qustions than evolution, then why didn't some clever ID person jump into the breach? Where were Jonathan Wells and Michael Behe and the other biology mavens on the ID side to point out this error?
Salvador can blather all he wants about how ID is a more useful framework than evolution, but the fact remains that it was evolutionists, not ID folks, who exposed this error. Scientists are still waiting, as they have been for over a decade, for ID folks to justify their assertions that ID provides a useful framework for scientific research. Instead of making good on that promise, ID folks prefer instead to waste everyone's time with ever more bloated claims about the future time when ID will triumph. Less talk, Salvador. More action.
Which leads us to point number two. Hard as it is to believe, Salvador is actually arguing that redundancy in complex systems is what signals design. Which is amusing, since the main weapon in the ID arsenal, irreducible complexity, is based entirely on the idea that it is lack of redundnacy that signals design. A structure is said to be irreducibly complex if it has several well-matched parts, such that the removal of any one part causes the system to cease functioning. Here's William Dembski explaining the logic:
Far from being a weakness of irreducible complexity as Miller suggests, it is a strength of the concept that one can determine whether a system is irreducibly complex without knowing the precise role that each part in the system plays (one need only knock out individual parts and see if function is preserved; knowing what exactly the individual parts do is not necessary).
But in arguing in this way, ID folks entirely ignore the possibility that a part that is essential to proper function today might have been redundant in some ancestral organism. Indeed, this is one of the primary fallacies of irreducible complexity.
In other words, a lack of awareness of the possibility of systemic redundancy is an essential part of ID's main scientific assertion.
We might also point out that if Salvador is serious that redundancy in complex biological systems is the hallmark of design, than an awful lot of complex systems were not designed. It is a commonplace in biology to find that systems that are absolutely vital to an organism's survival show no redundancy at the genetic level.
So I'm afraid Salvador's argument is, as usual, ridiculous.
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Inelegance and redundancy are in fact hallmarks of systems derived from mutation and selection. Andreas Wagner wrote a whole book on this topic: Robustness and Evolvability in Natural Systems.
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.
I can't picture Salvador and Behe actually disagreeing in person. For them, design is real, it happened. If a system is redundant, this proves it was designed. If it has no redundency, this is also proof it was designed. Why? Because all life forms were designed. This is simply not to be questioned. And so we examine every life form, determine its characteristics, and declare whatever characteristics we find to be in support of design. They must be, right?
In his usual and roundable way, Salvador illustrates the Prime Directive of creationism: evidence doesn't matter.
Wait! What about Sal's examples? And his explanation in, uh, which journal was it?
By-the-bye, there was an article in Science within the past few weeks 312(5776):1044-1046, about reducing the genome of E. coli, and discovering bugs with the reduced genome had evolutionary advantages. Maybe Sal quoted that article.
Great post. I guess we'll forever be waiting for some real research from the DI instead of constant press releases on how cool their little psuedo-theory is.
You knew that MonkeyBoy DaveScot couldn't resist jumping in to let everyone know what a great pilot his instructor seemed to thikn he was. I am still trying to figure out how his story added anything to that conversation other than some self ego bloatation.
If Cordova really believes what he wrote, then no wonder he thinks scientists are studpid. It's amazing how we biologists get anything done with our limited reasoning powers.
Yeast biologists (myself included) are among the most frequent users of knock-out organisms. Yeast have about 5,800 real genes; of these 5,800, about 1,100 are lethal when knocked out individually (under standard growth conditions). If biologists actually reasoned the way Cordova described, you would see papers discussing the astounding fact that 80% of the yeast genome is absolutely useless junk.
I can't believe these ID guys actually take themselves seriously.
Sal is wrong in another aspect as well. Biological systems contain degeneracy as opposed to redundancy. In redundancy you have identical systems leading to a similar response. In degeneracy you have dissimilar systems perform similar functions.
Giulio Tononidagger , Olaf Sporns, and Gerald M. Edelman
Measures of degeneracy and redundancy in biological networks Neurobiology, Vol. 96, Issue 6, 3257-3262, March 16, 1999
Lots of work on degeneracy and evolution exist, so I am amazed to hear that somehow ID should be relevant here since as far as I know ID has produced nothing in this area of science showing once again how scientifically void of content ID really is.
And for that I thank my pal Sal.
Cordova understands (as opposed to parroting primers) pitifully little about aircraft too. Magnetos operate in parallel. Both work continuously and both contribute to optimised engine running. Pre-flight tests include checking engine revs with left-only, right-only and both. The increments between these are usually consistent within a maintenance cycle and logged. Changes are easily observable and are grounds for at least another pre-flight inspection. Changes in-flight are similarly noticeable, and perceptible by ear.
To continue the simile and correct the other half of Cordova's comparison, genes *all* work in parallel. Not just alleles, but partially functional pseudogenes. Knockouts (or new additions) are easily subtle but rarely imperceptible to observers (arguably never so to the cell) and are easily regarded as a basis for selection.
Cordova's understanding of basic aircraft function and of biology is hardly subtle or probing at undergrad levels. He will benefit from obtaining a good grade 11 chemistry primer and reading the section on catalysts.
Rustopher.
The essay of Cordova is a complete mess up of biological concepts and inappropriate comparisons of machines and organisms.
Being involved in several knock out mouse projects during the last decade I would like to emphasize that this approach does not aim to knock out junk DNA. Indeed any gene targeting project is driven by assumptions based on knowledge of the gene of interest. Gene trapping and tranposon mutagenesis (sleeping beauty or frog prince) apply constructs that will only function when interfering with functional DNA. In the case of random chemical mutagenesis (ENU) junk DNA may be mutated. However, the identification of ENU induced mutations relies on phenotyping. Thus, again only mutations interfering with functional DNA will be identified. Functional DNA does not necessarily mean coding sequences but may involve regulatory sequences as well.
Since random approaches are phenotype driven there is nothing like lack of phenotypes per definition. In the case of targeted mutations lack of a phenotype does not imply a lack of function. One has to keep in mind that KO animals are kept under certain experimental conditions that may make certain gene functions dispensable. In addition one can only observe phenotypes for which the equipment necessary for the observation is available. Finally, since gene targeting is a hypothesis driven approach one may oversee non-obvious phenotypes that are not in the scope of the working hypothesis. Thus, lack of phenotype does not mean redundancy.
In contrast to man build airplanes redundancy in animals is not achieved by the presence of two copies of exactly the same gene (in the haploid genome). Rather one will find converging pathways. E.g. if one knocks out a receptor for certain bacterial cell wall components receptors for other bacterial components may still elicit an immune response. In the long run duplication of polymerase II transcribed genes will lead to either the partitioning of functions between the two copies, to the acquisition of new functions by one of the copies or one of the copies is turned into a pseudogene. The main source of redundancy in animals is diploidity. As a matter of fact the vast majority of targeted mutations will not display any phenotype in the heterozygous state.
In contrast to designed space crafts or planes living organisms can even cope with complete system failure (i.e. death). They just have to reproduce before.
Sal is correct to point out that evolution should not favor an organism that has a wasteful extra gene that provides no fitness advantage to the organism. His logical error though appears to be at least three-part:
1. He doesn't explain why a designer should put a gene in an organism that doesn't aid in fitness under any circumstances. But of course, we can let him worry about that.
2. He doesn't acknowledge the widely known known examples of how genes with overlapping function come to be, that fit within our knowledge of genetics and natural selection. These include (but are not limited to):
a. Recent gene duplication events. These can be "errors" in replication that weren't significantly deleterious to fitness to have been selected out in the relevant time period.
b. Activity of viruses, transposon or other mobile genetic elements that copy themselves, as mentioned previously.
3. Importantly, he neglects to admit that of course having multiple identical or nearly identical copies of genes, or multiple dissimilar genes or loci with "redundant" functional activity, often does actually aid in fitness. Sometimes the different genes/loci have different expression profiles, or they just have only partially overlapping function. If having multiple "redundant" genes can help the organism survive and/or reproduce in any way, then it fits neatly into evolutionary theory. Also, it's important to remember that if we don't yet know how this "redundancy" might aid in fitness for any given example, we can't positively conclude that it has no independent function just because we knocked it out and didn't observe a phenotype. That would be an irresponsible jump to an unsupported conclusion.
I'm sure there are more examples, but those are just a few of Sal's notable omissions.
Sal Cordova has doody for brains and ethics. You are lowering yourself immensely by considering him a "sparring partner".
Sparring partner? Punching bag is more like it, I think.
In designed "artifacts," don't we see redundacy in functionally critical systems? So for Sal's "redundancy" argument to be relevant for ID, wouldn't we need to see backups in the neurological and cardiovascular systems?
Salvador has been harping on about this stuff for a while now. Here is where he got the wrong end of the stick on the connection between knock-outs and "junk" DNA -- Dan Graur mentioned the results of deletion experiments as supporting the hypothesis that "gene deserts" are "junk" DNA (which is true). Salvador then showed how little he understands about gene regulation with his comments on the development of the C. elegans vulva (discussed here).
I enjoyed your dismantling of Sal, and should you be called upon to do it again in the future, I will surely enjoy those beatings, too. You do good work. I would like to contribute a nitpick here, though. Your typos frustrate me greatly. Please run the spellcheck on your post.
I do not pretend to have credentials or authority in the fields of evolution, mathematics, or "Intelligent Design", but I am a reader, and I like your posts better when there are no spelling errors.
Thanks!
I like and agree with what "haliaeetus" said; if redundancy is so important and such a sign of intelligent design, why *don't* any of our critical systems have redundancy?
A post and comments to learn from.
But that wasn't why I posted. I seemed to recognise an author in PvM's comment since I have read about his definition of complexity. (Which BTW, while maybe contingent on the subject area of neuroscience, differs from information so is a problem for ID.) It is Giulio Tononi. The "dagger" is a dagger tag from his name to his email in that paper, that translates to "Tononi dagger" in Google.
Since I'm here:
sanjait says:
"Sal is correct to point out that evolution should not favor an organism that has a wasteful extra gene that provides no fitness advantage to the organism."
I'm not sure he compares with wasteful extra genes, but neutral ones. And I thought those were beneficial as material that could be activated later.
dre,
Maybe you could look at Jason's typos as demonstrating the worth of redundancies, or perhaps degeneracies, instead. He is still eminently readable.
Flint:
This is a great observation. Cordova is so wrong on so many levels in his essay that it's easy to miss what's most hilarious about it.
Shorter Cordova: when a biological system lacks what Behe calls "irreducible complexity", this is a sure proof of intelligent design.
I have one question for creationists etc. How often have you seen watches mating?
I've tried to post a comment here, without success. In any event, here's my take on Salvador's post.
Jason,
Thank you for your comments on my essay. I'm pleased to see Ricardo Azevedo here.
It is not productive for me to counter all of your points, but let me raise this question, I said,
"Knockout experiments have also been used to argue ?junk DNA? is junk."
That does not mean that's the only way the junk DNA argument has been arrived at. Your comments almost insinuate that I was claiming knockout experiments have been the only avenue to make the deduction of junk DNA, and that is not my position. Knock out is a way that some individuals argue DNA is junk.
For example, one of Dan Grauer's colleagues mentioned knockout as proof of non-functionality at on of our IDEA meetings:
http://mason.gmu.edu/%7Ekfryxell/ID_short.htm
I remember him talking knock out experiments, transposons, retro-elements, etc.
The rest of you essay I could offer similar criticisms...
In any case, I don't think any malice was intended on your part, you were simply offering where you felt I erred, and that is fine...I will simply leave it that we disagree as to who is closer to the truth on these issues...
Ricardo Azevedo's offerings I think I will pursue more as I think he has interesting ideas...
Ricardo,
In one of his weblogs he mischaracterized my position on the Generalization of Andreas Wagner's work. My meaning for generalization to other systems implies it is generally applicable, not restricted to a few isolated cases. I can understand how he may have misinterpreted my remarks, however, and so I hope this post sets the issue straight. So if you find a few isolated cases rather than a general overarching principle, I would not consider that a counter example to my hypothesis, but rather a strawman knockdown.
Shapiro and Sternberg have published good papers on "junk DNA" with the help of Salthe, Jonathan Wells, Todd Wood, and Paul Nelson.
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:
http://www.uncommondescent.com/index.php/archives/1173
The problems Sanford higlights are worsened for natural selection because of redundant and degenerate systems.
regards,
Salvador
Salvador-
Let me remind you that you wrote the following:
This statement is false. The knocked out gene would be deemed nonessential in that case, and that is all. If there are other reasons for thinking the gene in question is junk DNA, the fact that it is nonessential might then be used as supporting evidence for that conclusion. But the fact remains that your plainly stated words are not correct.
I'll accept your clarification, but it badly undercuts the point you are trying to make. You are arguing that evolutionary thinking leads scientists to draw incorrect conclusions about the relevance of knockout experiments. If you are agreeing that scientists do not use knockout experiments as the sole piece of evidence in determining that something is junk, then I don't see how you have any point left at all.
I too am pleased to see Salvador here, although I find it a little strange that he has chosen this forum to reply to an old blog post of mine (as opposed to replying there directly). I'm a little less happy with the points that Salvador makes. Since my reply was turning a bit long, I've decided to move it to my blog.
Ricardo commented on how little I know about C. Elegans Vulva. I never pretended to know, I simply related Michael Denton's quotation which reference Cynthia Kenyon's article:
Perfect Vulva Every Time
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.
I'm glad to see Salvador engaging with us here. At least now we know what piece of redundancy he (and Denton) were referring to in their comments about the vulval development. However, I stand by my comments -- Cynthia Kenyon's speculation in the paper you cite (written over 10 years ago) does not warrant your conclusions. The two mechanisms are only partially redundant. I'll elaborate in my blog later today. I hope to continue our conversation there...
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Written a long time before Venter knocked out so much DNA in Mycoplasma Laboratorium that you'd need to call in the road sweepers to clean the mess off the cutting room floor...
My next move... to go off and find out how creationists handled that bit of news...
Unless you'd like to bring me up to date on where their nonsense went to after finding out a ton load of junk DNA really was junk and surplus to requirements...
Mick