Genomics and the vacuity of Intelligent Design

Posted 20 May 2006 by PvM

On Uncommon Descent, Dembski quotes a 'colleague' on the recent scientific arguments about the link between the eukaryotes and prokaryotes.

Their title refers to the "Irreducible Nature of Eukaryote Cells," which reads like an echo of Mike Behe. The logic of their argument confirms this: the structures and the genetics of eukaryotes mean that an evolutionary pathway from prokaryotes must be rejected.

Little explanation is given why this resembles the argument of Behe.

However, they do not again use the word "irreducible" in their paper. What is clear is that the "simple" pathway that the textbooks have proclaimed for years must now be abandoned. Surely there are lessons here about the way darwinism gives false leads in its appetite for a narrative about the origins of complexity.

Even if we assume for the moment that the study's results will hold and that the 'false leads' should be blamed on Darwinism, one has to realize that doing science means getting things wrong occasionally. The problem of Intelligent Design is that it has not even the luxury of being wrong since it fails to present any scientifically relevant explanation or hypothesis, other than 'Darwinian theory cannot explain 'X''. And although the latter is often argued to be evidence of design, it is clear that intelligent design is doomed to remain scientifically vacuous. On Aetiology Tara Smith explores these new research findings, and the hype. And for those who have not read the full article, the following statement may be of interest

Genomes evolve continuously through the interplay of unceasing mutation, unremitting competition, and ever-changing environments. Both sequence loss and sequence gain can result. In general, expanded genome size, along with augmented gene expression, increases the costs of cell propagation so the evolution of larger genomes and larger cells requires gains in fitness that compensate (15, 56, 57). Conversely, genome reduction is expected to lower the costs of propagation. There is an ever-present potential to improve the efficiency of cell propagation by reductive evolution.

In other words, why would ID even 'predict' a reduction in complexity in the genome? Assuming that it could even make any such prediction.

This abbreviated account of genome reduction illustrates the Darwinian view of evolution as a reversible process in the sense that "eyes can be acquired and eyes can be lost." Genome evolution is a two-way street. This bidirectional sense of reversibility is important as an alternative to the view of evolution as a rigidly monotonic progression from simple to more complex states, a view with roots in the 18th-century theory of orthogenesis (71). Unfortunately, such a model has been tacitly favored by molecular biologists who appeared to view evolution as an irreversible march from simple prokaryotes to complex eukaryotes, from unicellular to multicellular. The many well-documented instances of genome reduction provide a necessary corrective measure to the often-unstated assumption that eukaryotes must have originated from prokaryotes.

Science can be wrong, ID cannot even be science.

39 Comments

Henry J · 20 May 2006

Are eukaryotes thought to be descended from prokaryotes, or are both descended from something else?

And where do Archaea fit into it?

Henry

Anton Mates · 21 May 2006

As far as I understand it, prokaryotes are not a monophyletic group. Rather, the earliest known split would be between bacteria vs. (eukaryotes + archaea). What the Science paper (link at Aetiology) is arguing is that eukaryotes are not, as was speculated, the product of an archaea-bacteria fusion; instead, they had already diverged from the archaea before they absorbed the proteobacteria that became our mitochondria.

I think.

Bob O'H · 21 May 2006

The problem of Intelligent Design is that is has not even the ..."

I think this needs a bit of editing. More substansively, I can see the ID crowd trotting out the "evolution explains everything, and therefore explains nothing" argument. But the authors of the review at least suggest how their idea can be tested:

A unicellular raptor with a larger, more complex cell structure than that of present-day prokaryotes is envisioned as the host of the ancestral endosymbiont. This scenario, which is not contradicted by new data derived from comparative genomics and proteomics, is a suitable starting point for future work. Acquisition of genome sequences from free-living eukaryotes among basal lineages is a high priority.

and also implicitly admit that this is speculative. Bob

mark duigon · 21 May 2006

I haven't yet read the papers cited by Tara, but just happened to have seen a related item in the previous issue of Science (12 May, p. 870-872) that had a special section on viruses. This discussed notion that bacteria, archaea, and eukarya shared a common ancestor back in the old days when genetic information was stored in RNA. Some of those genes, the idea goes, evolved into viruses (RNA), and some of those viruses evolved DNA as a defense mechanism. Some of those DNA-based viruses infected cells (which were still RNA-based) and became assimilated. Host-to-virus transfer of genes allowed gene sharing (within groups having same viral DNA), and the 3 DNA-based groups we are familiar with resulted. This scenario provides an evolutionary explanation without a prokaryote-to-eukaryote progression; no ID needed.

Ron Okimoto · 21 May 2006

All we can hope for in science is to improve our understanding of nature. This line of IDiocy just shows how bankrupt the ID scam has gotten. As you point out ID isn't even wrong at this point, but the main thing is what does the new answer do for them? It isn't even a new answer, but the level of detail has improved. We have evidence that prokaryotes had split into two major branches by the time eukaryotes evolved. Eukaryotes still evolved from prokaryotes, we just have evidence that we know what type of prokaryote they evolved from. How does that help ID?

wamba · 21 May 2006

A unicellular raptor

raptor:

A bird of prey.

Frank J · 21 May 2006

Little explanation is given why this resembles the argument of Behe.
— PvM

They must be referring to Behe's "complex first cell." But they can't call too much attention to that because it offends YECs and OECs who deny common descent. The irony is that, while the media is touting it merely as "contrary to cherished notions," it could have been spinning it in even more ID-friendly language, if Behe's "first cell" were more widely known as the closest thing ID ever came to an "official" anti-evolution position (i.e. how and when the design was actuated).

mike syvanen · 21 May 2006

Eukaryotes still evolved from prokaryotes, we just have evidence that we know what type of prokaryote they evolved from.
— ron

Not necessarily. The primitive eukaryote according to the chronocyte theory evolved independently from any prokaryote. It was an RNA based life form and by definition prokaryotes are DNA based. If we also jettison the notion of a common ancestor then there no need at all to assume that the primitive eukaryote evolved "from" a prokaryote.

'Rev Dr' Lenny Flank · 21 May 2006

Where does all this "endosymbiosis" thingie come in?

Jonathan Bartlett · 21 May 2006

"In other words, why would ID even 'predict' a reduction in complexity in the genome? Assuming that it could even make any such prediction."

That's the entire point of things such as Dembski's conservation of information. That large amounts of specified complexity can only be added through intelligence, but that left to itself, it either stays roughly the same or deteriorates. Genome Decay is an active area of research in both the Creationist and ID camps, but it is something that would be difficult to even conceive of in a Darwinian setting, which has information being built up through selected mistakes.

http://baraminology.blogspot.com/2006/03/genome-decay.html

ID has information degrading or specializing from larger information sources, while Darwinism has information building up from smaller information sources.

Sir_Toejam · 21 May 2006

you act as if ID actually had any kind of theory behind it but mere supposition and incorrect evidence interpretation.

baraminology

BWAHAHAHAAH

Sir_Toejam · 21 May 2006

oh almost forgot...

"...active area of research"

again:

BWWWAAAHAHAHAHAHAHAHA

you ARE funny.

B. Spitzer · 21 May 2006

Jonathan Bartlett wrote:

That's the entire point of things such as Dembski's conservation of information. That large amounts of specified complexity can only be added through intelligence, but that left to itself, it either stays roughly the same or deteriorates. Genome Decay is an active area of research in both the Creationist and ID camps, but it is something that would be difficult to even conceive of in a Darwinian setting, which has information being built up through selected mistakes.

I disagree on both counts. Dembski's "conservation of information" may suggest a trend that IDers expect to see-- and IDers are definitely more interested in complexity increasing rather than decreasing-- but it certainly doesn't rule out the Designer pruning an existing genome if He wants to. That's the problem: ID doesn't rule out anything. As for evolutionary theory, deterioration of genetic sequences is exactly what we'd expect to see under certain conditions. The most obvious one is pseudogenes-- once the function of a gene no longer affects fitness, it should tend to decay due to mutation. See also the Y chromosome in humans, for example, or the genomes of mitochondria and chloroplasts (which, if I understand correctly, have transferred many key genes to the nuclear genome). This whole "ID predicts that things get less complex, evolution predicts that things get more complex" idea sounds a lot like the creation-science mythology. That's where evolution is a constant march up a scale of "betterness" (see some of AFDave's posts about "winning" in the game of evolution in After the Bar Closes, for example), and creationism implies that the world, having been tainted by the Fall, is slowly or not-so-slowly going to hell in a handbasket.

H. Humbert · 21 May 2006

wamba wrote:

A unicellular raptor

raptor:

A bird of prey.

metaphor: a figure of speech in which a word or phrase literally denoting one kind of object or idea is used in place of another to suggest a likeness or analogy between them.

PvM · 21 May 2006

"In other words, why would ID even 'predict' a reduction in complexity in the genome? Assuming that it could even make any such prediction." That's the entire point of things such as Dembski's conservation of information. That large amounts of specified complexity can only be added through intelligence, but that left to itself, it either stays roughly the same or deteriorates. Genome Decay is an active area of research in both the Creationist and ID camps, but it is something that would be difficult to even conceive of in a Darwinian setting, which has information being built up through selected mistakes.
— Jonathan Bartlett

Notice how ID activists are quick to confuse the concept of information as used by Dembski with the concept of information as used by science. I can understand the confusion but it only serves to undermine the ID activist's attempt to explain why ID makes any such predictions. In fact, ID is quick to claim that 'Junk DNA' would be found to have function after all. But let's look at Jonathan's claim namely that genome decay is difficult even to conceive of in a Darwinian setting. Note that Jonathan is effectively arguing the opposite of what ID and other creationist arguments claim, namely that Darwinism may explain the decay of the genome but that it cannot explain the opposite. Anyone familiar with Darwin's writings would be familiar with his comments on vestigial organs, in other words, Darwinism does in fact explain the existence of 'genome decay'. So perhaps Jonathan's argument can be saved by arguing that Darwinian theory cannot explain information in the genome? Again, Jonathan's claim would go against the scientific evidence.

ID has information degrading or specializing from larger information sources, while Darwinism has information building up from smaller information sources.
— Bartlett

Perhaps, but this does not logically follow from ID, which is in fact trying to explain the origin of information. Could Jonathan explain how this logically follows from the ID claim? In other words: Explain what the ID claim is and how it follows from first principles. Let me give an example: Claim: Darwinian theory explains the generation of information in the genome via the processes of variation and selection. Supporting Evidence: Darwinian processes can, at least in principle, explain the generation of information in the genome. See the work by Tom Schneider or Adami. First Principles: Natural selection and variation Claim: Darwinian theory explains the existence of vestigial organs or 'junk DNA' such as pseudogenes Supporting Evidence: The observed processes of gene duplication and mutation explain the existence of pseudogenes, as far as vestigial organs are concerned, see Darwin. ID is scientifically vacuous for the simple reason that it cannot make any predictions since it is based on an argument from ignorance. While ID activists have added to the confusion by calling this ignorance complexity or information, it has little relevance to the scientific concepts. In fact, scientifically speaking CSI is an expected outcome of evolutionary processes as long as information is not defined to be 'ignorance' but true 'information' for instance in the Shannon sense. Functionality, which is just another alias for specification in biology, is also an expected outcome of evolutionary processes. So in other words, Dembski's argument is merely a claim that if we do not fully understand the origins and evolution of a particular functional system we should infer design. Of course, even inferring design really does little for the ID thesis since the step to designer is an inductive step which cannot even exclude natural selection as its designer.

Sir_Toejam · 21 May 2006

sorry, Pim, but i can't see the word baraminology and take anything the writer of it said seriously.

that's the first baraminology troll I've seen here in a long while.

steve s · 21 May 2006

If ID is so down with genetic decay, they wouldn't resist the idea of vestigial organs. But they do, because ID Creationists will say anything.

steve s · 21 May 2006

dang, Pim beat me to the vestigial bit.

PvM · 21 May 2006

dang, Pim beat me to the vestigial bit.
— Stev S

Never hurts to repeat this. ID is vacuous scientifically which is why when it comes to positive claims it resorts to its creationist foundations.

steve s · 21 May 2006

an ID supporter can't open his mouth without contradicting some other ID supporter.

Frank J · 21 May 2006

an ID supporter can't open his mouth without contradicting some other ID supporter.
— steve s

Exactly. Note: Scroll up to the first post in the thread.

Adam Ierymenko · 21 May 2006

This is one of the most important reasons that ID is not science. ID is not science because it cannot be wrong.

This is the old trick of the mystics. Those who attempt to actually explain things are occasionally wrong, as the mystics point out. The mystics on the other hand are never wrong. Their pronouncements are timeless and eternal.

The mystics and religionists are never wrong because their pronouncements are content-free vague platitudes.

This is why Plato is "timeless" while Aristotle was not. Aristotle tried to actually do science, and so he was wrong about many things. Plato just said a bunch of worthless empty BS about invisible worlds of forms and stuff. That can never be tested and doesn't tell us anything useful, and so it can never be refuted.

The actual usefulness and the content-richness of one's ideas is directly proportional to their chance of being wrong. That which cannot be wrong also cannot be right. No reward without risk, even in the realm of ideas.

Adam Ierymenko · 21 May 2006

"ID has information degrading or specializing from larger information sources, while Darwinism has information building up from smaller information sources."

Not exactly.

Evolutionary theory (not "Darwinism") proposes that genomes adapt. Adaptation can involve both the gain and the loss of information. The notion that there is a long term trend of information gain in evolution has been proposed, but not proven. The jury is still quite out with regard to any long term inevitable trends in evolution.

As any human engineer knows, sometimes great improvements and innovations occur as a result of information loss.

'Rev Dr' Lenny Flank · 21 May 2006

Genome Decay is an active area of research in both the Creationist and ID camps

You act as if ID and creationists are different somehow. Let me remind you of the "five year objective" spelled out by the Discovery Institute in its Wedge Document:

* Major Christian denomination(s) defend(s) traditional doctrine of creation

Would you mind explaining to me, if IDers are not creationists, what this "traditional doctrine of creation" is that DI wants "mainstream churches" to "defend"? And when you're finished with that, would you mind citing some peer-reviewed journal articles which describe some of this, uh, "active research" being carried out by ID/creationists?

'Rev Dr' Lenny Flank · 21 May 2006

That large amounts of specified complexity can only be added through intelligence, but that left to itself, it either stays roughly the same or deteriorates.

Please show us how to measure this, please.

'Rev Dr' Lenny Flank · 21 May 2006

specified complexity

Specified when? Where? By whom?

'Rev Dr' Lenny Flank · 21 May 2006

http://baraminology.blogspot.com/2006/03/genome-...

What's a "baramin"? How do you tell whether or not two organisms are or are not the same "baramin"? What is the barrier between "baramins"? Can one baramin evolve into another baramin? Why or why not? And how can you tell? And, out of curiosity, how old do you think the earth is?

mike syvanen · 21 May 2006

Where does all this "endosymbiosis" thingie come in?
— The Hon Rev/Dr

According to the theory that the eukaryotic cell evolved independently from the prokaryotes there were three major endosymbiotic episodes. There was a very primitive eukaryote: an RNA based organism that was very large and made its living ingesting the much smaller prokaryotes. DNA based life evolved within the prokaryotes. First endosymbiosis had this eukaryote ingesting and establishing a symbiotic relationship with an Archaea. This introduced DNA metabolism and gave rise to the nucleus. This is known as the chronocyte theory after the God Kronos. After the world became aerobic it became essential for survival to learn to deal with O2. This is thought to be the selective pressure that lead the next endosymbiosis where the now nucleated eukaryote entered into a symbiosis with a more metabolically advanced alpha proteobacter that is now the mitochondria. The third endosymbiosis involved a line of O2 consuming eukaryotes absorbing a photosynthetic bacterium containing photo systems 1 and 2. These became green plants. This last endosymbiosis likely involved many different donors.

David B. Benson · 21 May 2006

I have an even simpler query: what do you mean by 'complexity'? Please define this term.

Frank J · 21 May 2006

Would you mind explaining to me, if IDers are not creationists, what this "traditional doctrine of creation" is that DI wants "mainstream churches" to "defend"?
— 'Rev Dr' Lenny Flank

You know. To a typical YEC it's "6-day creation, ~6000 years ago, global flood" etc. To a progressive OEC it's "life has a ~4 billion year history like science says, but undefined 'kinds' appeared independently over time." To an IDer it's mostly "don't ask, don't tell." Put that way, there's a big difference in strategy, if not belief (my guess is that leaders of all 3 groups privately believe that evolution, old earth and common descent are correct). What unites them is the belief that the "masses" need to be told fairy tales to behave. Even if those fairy tales are mutually contradictory, and need to be promoted indirectly.

Andrew McClure · 21 May 2006

That's the entire point of things such as Dembski's conservation of information. That large amounts of specified complexity can only be added through intelligence, but that left to itself, it either stays roughly the same or deteriorates
— Jonathan Bartlett

I'm not sure this is really a victorious prediction for ID. ID, you say, predicts that in the absence of interference, complexity will only decrease; modern evolutionary theory predicts that in the absence of interference, complexity will under some circumstances increase and under some circumstances decrease (depending on which of these two options would be more evolutionarily advantageous). We have here, with this Archea thing, what seems on the face to be an example of reduction in complexity occurring, and no interference is anywhere in sight. So both "theories" get to say they predicted this. However: ID predicts complexity will decrease in this case because complexity always decreases, just cuz. Evolution predicts complexity will decrease in this case because this is one of those special cases where a decrease in complexity is advantageous (because Archea are functionally simple enough that, like with the e.coli that Tara Smith mentions, dragging around genomic dead weight is enough to significantly impact their efficiency). It looks to me like evolutionary theory still wins here, because while it may not have made a meaningfully different prediction from ID in this case, it has greater explanatory power for the reason why it made this prediction. I incidentally want to write something here complaining about vague uses of the word "information"-- but, I'm not sure I understand the biology of this archea/prokaryote descent thing well enough to intelligently comment, so please forgive me if I make some errors: It seems like Bartlett and friends are trying to either conflate genome reduction with reduction in the amount of "information" in the genome; or conflate loss of features in the organism with reduction in the amount of "information" in the genome; or both; and I'm not sure I consider either of these assumptions fair. While intuitively genome reduction and loss of functionality would both seem to constitute reductions of information, and it seems reasonable to say that usually all these things go together, I don't think it's been shown these are automatically simultaneous events. Surely there are edge cases where you can delete part of a string without a decrease in the amount of information; the amount of information in a string is not the same as that string's length. Meanwhile surely an organism's genome can change in such a way that the amount of information in the genome increases at the same time that the organism decreases in functional complexity-- there is, after all, no requirement that information be useful. Let's say that the idea that we see toyed with here (in these papers and MSNBC articles and whatnot) is correct, that both archea and eukaryotes descend from an ancestor which was, itself, more complicated than archea; and archea simplified themselves in splitting off from this protoeukaryote line and throwing away the extra functionality that eukaryote cells continued to possess. Okay, how do we know this was a decrease in "information"? I'd imagine the "information" describing that extra functionality was tossed at some point (or we'd still be able to see the vestiges of it in archea genomes today)-- but it certainly seems possible (never mind likely) that the mutation[s] which removed those extra eukaryote-flavored cell features just disabled or otherwise broke those features, without actually removing the information that described them. The information itself could have then been tossed from the genome sometime much later on. How do we know one way or the other? Without knowing a good bit more about the organisms on either side of that pre-/post- archea line than we know right now (since we're apparently only just now starting to figure out where that line was), trying to view the transition to archea in terms of "information" seems extremely hasty. Of course, I'm trying to think of "information" here in the rigorously defined mathematical sense, not in the ID "information means whatever we want it to mean today" sense... In other news: Scientific researchers use "irreducible" in a sentence, and that is a word Michael Behe also once used in a sentence. Behe vindicated!

PvM · 21 May 2006

I have an even simpler query: what do you mean by 'complexity'? Please define this term.

An excellent question. ID activists are often surprised to find out what 'complexity' really means. I even would argue that under ID definitions, complexity should disappear once we find a natural explanation, including natural designers. In other words, complexity is merely our inability to describe in sufficient detail a natural designer.

Adam Ierymenko · 21 May 2006

"What unites them is the belief that the "masses" need to be told fairy tales to behave."

In other words, the unifying belief here is that virtue requires deception and fantasy. The root philosophical premise that lies behind this is the moral/practical dichotomy, which is a subset of the mind/body dichotomy. If the moral and the practical are at odds, then morality can only be discerned through emotion or revelation and then must be promoted through deception.

The opposite propositions are, respectively, moral/practical unity and mind/body unity. If the moral is practical, then morality can be discerned by reason and promoted by direct reference to some kind of independently verifiable and objective reality.

Those are the root philosophical issues involved. The entire evolution/ID/creation debate is a ridiculous and farcical debate-by-proxy which is engaged in to avoid facing these more challenging and difficult philosophical concepts. This obfuscation is mainly engaged in by the pro-mind-body-dichotomy crowd because they do not believe that their core philosophical premesis can withstand honest debate and yet they are emotionally attached to them. Note that by promoting fairy tales in order to teach morality, they are essentially arguing that morality is a lie and that "nothing is true and everything is permitted." We, on the other hand, are the ones who are arguing *against* this proposition and that moral principles exist and can be ascertained rationally.

To be fair though, I think that a few people on the pro-mind-body-unity side sometimes engage in debate-by-proxy via evolutionary theory. [cough] Dennett Dawkins [cough] [cough]

'Rev Dr' Lenny Flank · 21 May 2006

This isn't a "philosophical" debate. It's a political one. The fundies are open about their aims and goals. Just read the Wedge Document.

Adam Ierymenko · 21 May 2006

"This isn't a "philosophical" debate. It's a political one. The fundies are open about their aims and goals. Just read the Wedge Document."

I agree to some extent. A lot of the financiers of the Christofascism movement are connected to the corporate welfare bum class whose fortunes are a result of "wars of adventure" (e.g. Iraq) and other massive state-driven wealth transfer operations.

Along with fundamentalist religion, another lie perpetuated by the same bunch is that they represent freedom and free-market capitalism. They don't. The modern American right is feudalist, not capitalist. They promote religious fundamentalism because this is the core ideology of feudalism.

fnxtr · 22 May 2006

The mystics and religionists are never wrong because their pronouncements are content-free vague platitudes.

Is this what Dembski meant by "conservation of information"? As opposed to actually distributing any, I mean.

Morgan-LynnLamberth · 22 May 2006

Thanks Anton, I learned that it was fusion . Adam Iesynenko , you write like I have written here.I hope my buddy Lennie can undrstand you and not dismis s you as gibberish[ Linnie, you are credible otherwise.] Yes, Adam the religious come out with a two category / sphere notion when in fact they thereby , argue in a cicle [See Malcolm Diamond's and Kai Nielsen's books for a full explantion of the fallacy here used.]We just have a brute polyverse! No need for a man behind the screen ! You and I are naturalists who need no Big Daddy as Francisco Ayala alleges he and his fellow religious do in orde r to find meaning and to overcome a sense of dread of death If anyone cannot find her own meaning ,she is irresponsible . We naturalist do not embrace theism ,because we shirk responsiblity,but because we embrace respon sibility for our lives and our morality.To overcome a dread of death, seek ,counseling. We get our morality in seeing what is good or bad for humans, other animals and the enviornment as I state in other blogs. This account is on message insofar as creatonists aver that evolution makes children think they can be like the other animals,when our big brains help us discern morality.Creationists lie for morality,thus! More on the science here !

Shenda · 23 May 2006

"I have an even simpler query: what do you mean by 'complexity'? Please define this term."

If I do not understand it, it is complex. If someone else does understand it, but cannot explain it to me while I have my fingers in my ears, it is still complex.

Complex = Proof of The Designer (God)

Henry J · 23 May 2006

Re "If I do not understand it, it is complex. If someone else does understand it, but cannot explain it to me while I have my fingers in my ears, it is still complex."

LOL

Henry