Sunday, September 13, 2009

What's Right about Intelligent Design

There's an interesting set of videos over at The Science Network on the Origins Symposium that goes over issues in physics and evolution. In the panel on Origin and Evolution of Life and Phenotypic Innovations, highlights many interesting issues. At the end, Richard Dawkins steps up, and says (around 51:00):
I just want to enter a protest against the recurrence of the suggestion that there is something odd going on in the Cambrian and very early times, that we only got new phyla then and we only get new classes and orders today. That obviously has got to be true. I've compared it before to a gardener going into a garden, looking at an old oak tree and saying isn't it strange nowadays we only have little twigs sprouting from this tree, we don't see any great big boughs [trunks] anymore.
The panelists dismiss him:
It's not true with plants...Another way to see this is we can measure morphological disparity, and what we see very early maximal disparity, later on filling in this space...disparity should increase over time...that's patently the opposite of what is predicted.

In other words, Dawkins sees the Cambrian explosion as no big puzzle, while these researchers are saying it is a big puzzle. These are not creationists, they are Darwinists (ie, they are naturalists, and believe in only genetic heredity, random mutation, and selection). In Dawkins's view a phylum is defined with hindsight, and so needs time to be developed, so the fact they are all really old is necessary in the same sense that tree trunks are thicker than twigs. But the panel members state no, this is not what is predicted by standard Darwinian theory, as what was expected was more phyla to be created over time, which is what we see for the plant kindom, and can be measured molecularly and morphologically. It seems that development gets more precise over time, preventing the development of new phyla, so how did all these phyla arise? These are actual researchers published in peer-reviewed journals, something Dawkins does not do.

The lecture mentions other interesting puzzles. For example, the common ancestor for humans and fruit flies need a heart gene, a stomach gene, an eye gene, and each of these has been found in both humans and fruit flies. From a developmental standpoint, what makes a fruit fly gene express itself so differently than a human being is still a mystery given so many similar genes we share. And it's even more bizarre than that, as these eye and heart genes have also been found in jellyfish (which does not have a heart or eye). A hydra is a very simple organism, but has about the same looking DNA as a human, with 20k protein coding genes for things like hearts, eyes, etc. How does this happen?

Dawkins does not see what many cutting edge researchers see as a puzzle, because he is so focused on demonstrating that Darwinian evolution works against Creationists: there are no significant puzzles to the paradigm! However, if you want to make progress, you have to accurately identify what is preventing it, and the Creationists are basically not affecting scientific research at major universities. If you go to the popular biology section at the bookstore you see several large popular tomes arguing against creationism (discussed here). Now, the percentage of journal editors in this field preaching creationism is zero, while the majority of the great unwashed do not believe Darwinian evolution is the complete answer. So, it's strange to focus one's attack on a contigent that is large to be sure, but rather irrelevant in the day-to-day discussion of ideas with colleagues. It's a bit like going to a wine tasting and talking about how unsophisticated beer drinkers are: in some sense you have a sympathetic audience, but they are interested in wine intricacies and so should you be.

I find evolution very interesting because Stephen Jay Gould is correct to highlight that most of the big changes in life on this planet appear without any really good theory at the molecular level. In his theory of 'punctated equilibrium' species appear and remain virtually unchanged, then disappear, over say 5 million year periods. The extinctions you can explain via asteroids and large climate changes, but the origination seems to demand more than the mere extrapolation from processes we can observe in local populations (like human having different skin color based on sun exposure, or lactose tolerance based on the importance of dairy farming). The creation of new helpful functionality, via adding information to the genome, is a lot more difficult than anticipated.

For example, biologists have been tracking E. Coli for over 40k generations, and almost all of the beneficial mutations identified from the studies so far seem to have been degradative ones, where functioning genes are knocked out or rendered less active. Random mutation much more easily breaks genes than builds them, even when it helps an organism to survive. That’s a very important point. A process which breaks genes so easily is not one that is going to build up complex coherent molecular systems of many proteins, which fill the cell. You can actually do the math, and the standard Darwinian mutations do not extrapolate from simple single celled organism to human in a mere 800MM years. 10^800MM, sure, but that's not where we are.

In contrast Dawkins emphasizes that evolution of new organisms is merely the gradual evolution of little mutations in the DNA, the climb up mount improbable is merely counterintuitive because of the numbers involved (millions of years, organisms).

I've read a lot of Michael Behe, whose recent Bloggingheads TV piece was recently delinked, then reposted (with a long apology by Robert Wright about how this happened), and find his arguments very interesting. Not because I believe in God (I don't), but because they highlight how, at the molecular level, the creation of different tissues is much more improbable than Dawkins examples imply. I don't think saying 'God did it' is a better theory, but I do think Behe highlights a major flaw in the convention mechanism of evolution. We haven't identified that in my opinion, as Dawkins' handwaving about slight modifications is as deficient as Gould argued [Gould had a very different endgame, but it's the same puzzle]. That's fascinating to me, and while the ID crowd isn't on to a fruitful new path, they are highlighting key problems to the conventional wisdom, one that highlights we need a new big idea in this area, as opposed to hand-waving about how it's just an extrapolation of how dogs breeds developed.

Perhaps one reason I find this so interesting is that I feel a lot like an Intelligent Design researcher, being dismissed because I'm outside the paradigm. Not that I'm totally outside the box, arguing for some kind of Spaghetti Monster, or Taleb's vague anti-formalism. I have tried to send academic version of my SSRN paper, or arguments in my book Finding Alpha, to journals, or academics, and I don't even get a response. I get responses like: "this is not of interest to the general readers of the Journal of Finance". Now, I could be wrong, in which case of course my hypothesis is uninteresting, but if I'm right I think the idea that risk premiums generally don't exist because of relative utility functions would be of interest, so clearly, he just sees me as a kook and dismisses me. Yet, they don't even want to discuss it.

This has been going on my whole life. My 1994 PhD job-market paper emphasized the negative relation to risk and return, and it was considered so silly I got zero fly-outs, because it implied an arbitrage (see dissertation here). Now everyone agrees that my fact is indeed correct (high volatility or beta loadings is negatively correlated with returns), but supposedly the Stochastic Discount Factor is negatively correlated with these primitive metrics, if we can only find it. Around 2000, when I introduced the idea that equity returns are negatively correlated with Agency Ratings (lower for B and C rated companies), this was also considered factually wrong, I must have made a mistake. Now it is considered right, but again, merely reflects the profound subtlety of the SDF.

I see the anomalies to the standard theory as actually the rule, not the exception. One sees risk aversion in explicit hypotheticals, or fire insurance, where there is no chance for alpha, or hope, but when alpha can exist everything changes. Across and within asset classes, and over time, intuitive measures of risk are not positively correlated with actual returns. This is the consequence of a the assumption about how people evaluate their wealth, via benchmarking, as opposed to comparing themselves to zero wealth. Exploring this path is more fruitful than building branches on a framework that after 40 years, does not explain the data at 30,000 feet.


ilene said...

Hi Eric, I got lost at the end, true, but in the biological section, I was thinking that another level of complexity beyond DNA is the changes to DNA expression, "epigenetic" changes that may or may not be considered in the work you were discussing. So looking at DNA only is not good enough. I don't know if Dawkins discusses that anywhere, but it would be interesting to see more.

...I just did a google search and found this for starters:

Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life (Life and Mind: Philosophical Issues in Biology and Psychology)

Product Description
Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions" in evolution—four inheritance systems that play a role in evolution: genetic, epigenetic (or non-DNA cellular transmission of traits), behavioral, and symbolic (transmission through language and other forms of symbolic communication). These systems, they argue, can all provide variations on which natural selection can act. Evolution in Four Dimensions offers a richer, more complex view of evolution than the gene-based, one-dimensional view held by many today. The new synthesis advanced by Jablonka and Lamb makes clear that induced and acquired changes also play a role in evolution.

Erik B said...

I'm sort of with you in that I'm glad there are people like Behe challenging conventional wisdom, but Behe is a bit of an edge case and I personally despise him for defending laughably thinly-veiled religion as intelligent design in public schools. He won't admit to that, of course, but the wedge document makes it very clear. His ID theories and examples of irreducible complexity aren't really taken seriously by any countable percentage of the scientific community, and I don't think he is doing the near level of some of research presented at the conference. He's the only academic I've ever heard about whose ideas are so disparaged that his own department has a disclaimer on their homepage declaring they disagree with him:
This alone isn't a reason to dismiss him as wrong, but it is a good reason to demand extraordinary levels of evidence from him, and we certainly haven't seen that positive evidence for ID yet. I wouldn't trust his math on the rate of genetic mutations (see for an example of why).

I think the most plausible reason for decreased activity of new phyla is the reason described by Dr Peterson - excessive precision and specialization make it harder for major morphological changes to take place, except in species with systems simple enough that the interrelationships between their parts are not as complex. I think we're only scratching the surface on why certain very similar genes express themselves differently in different organisms, but it is clear the interrelationships are complex, and they can't be analyzed in a vacuum. I'd guess that there is much more to it than microRNAs, recent research into the function of "junk DNA", etc. To say different species have the same genes is a good argument for common descent, but isn't saying as much about why other genetically similar organisms don't have similar morphology without all of the details outside of rough gene equivalence, because a "gene for a heart" when found in a jellyfish isn't a heart gene anymore. Jellyfish do have (very basic) eyes.

Recent research has identified evolution real-time in microorganisms that developed the ability to digest new materials, lizards with a new stomach valve, etc. Beneficial mutations can be vanishingly rare and still add up over time, and the non-beneficial mutations can disadvantage or kill off trillions of organisms over time, but still benefit the surviving lines.

I do suspect you are right that Richard Dawkins isn't living on the cutting edge of evolutionary research anymore. For many years, his focus has been on teaching, broadly defined, and focused mainly on educating the general public. He's always been more of an evolutionary philosopher. IMO, there is something unique happening in the Cambrian, but it has nothing to do with any of Behe's research that I've seen. Intelligent design only has one tangential point to make - that there is still a lot about genetics/evolution we don't completely understand. Every reasonable biologist would agree with that statement, so I don't think there is much intelligent design specifically adds to the discussion, except for some the scientists that were motivated to disprove several of Behe's specific examples of supposed "irreducible complexity". Maybe we basically agree, but I would de-emphasize Behe's/IDs contribution to the scientific process, and openly accuse him of being sloppy with details and being very adept at cherry picking evidence. Scientists already know where the holes in neo-Darwinism are without Behe trying to shovel bad theories into them.

Michael F. Martin said...

You might like reading about Lynn Margulis's endosymbiotic theory if you haven't seen it already.

Anonymous said...

Sorry Eric, you fail to appreciate the impact of complexity & of time. This is a failing not only as an evolutionary theorist, but also as an economist. Complexity accounts for much of what traditional economics cannot explain & as an "outsider" you should embrace not only complexity economics but the developmental aspects of complex evolutionary theories as well.

Eric Falkenstein said...

anon: saying "complexity" explains it, is no better than saying "God" explains it. I think you need more color here.

eric B: the 10^20 number gets into jargon and acronyms I can't judge (CQ? Ala220?) I think 'reasonable biologists' are rather quite about the puzzles, because they are so afraid of Creationists, who are really irrelevant to the debate, which I find amusing (like me worrying about what a Marxist thinks of my equity models).

Ilene: I see there are other mechanisms, but we have to stay with genetic and epigenetic for basic evolution, and while there are transposons, and other macro mutations, these need more color to show how, say, they can turn a whale into a cow. Just saying, as Dawkins does, it just happens bit by bit over an unintuitive length of time, does not seem correct. All the little pieces have a large constellation of parts that involve a logistic support in their maintenance and creation.

Anonymous said...

Regarding the biology, clearly there are problems with evolution, but problems in the sense that "we don't understand evolution completely" not problems in the sense of "perhaps evolution is entirely invalid".

Intelligent Design is not a collection of people who say evolution is incomplete, evolution is only a partial explanation of what went on. It is people who believe in God and whose purpose is to argue that God must exist. So I appreciate your cheering for the underdog because you are the underdog, but the analogy to Intelligent Design fans is weak. The analogy to global warming denialists, which you bring up from time to time, is not much better.

J said...

You must have been having a bad day when wrote this note. You dont reject a scientific hypothesis or model because it has holes in it. When Darwin proposed evolution, no one even suspected how it operated, as genes were yet undiscovered. Slowly, the holes are being filled in. It is unworthy of you to reject DArwin's theory because some details cannot be explained, and go to Creationism, which says evolution is wrong and it was all created. Creationism has an agenda which is to make place to God in schools and so on.

BTW you can believe in God without Hebe's Creationist nonsense. I for one think that the idea of God is good for one and for one's family, and I do as if I did (and also follow the ancestral customs of my tribe.)

Eric Falkenstein said...

J: As noted, Darwin had no understanding of genetics, and so really had no idea how random variation from generation to generation occurred. He thought it was some continuously distributed blob of attributes from each parent. I think there is a giant hole in the theory, and so like an invalid step in a math proof, needs fixing if it is to explain the diversity of the all life on this planet. I don't think you can just say it caused by God/complexity/time because these all assume the listener understands and agree with a rather large, complicated mechanism, each of which I think is flawed or incomplete.

As per ID being taboo because of their endgame, I really don't care about their endgame, rather, the puzzles they highlight. Lots of very religious people, who think God instantiates regularly, are productive, fine people, and most have an understanding of religious tolerance (ie, I can still be good though not a believer). I get the sense most of this debate is political, that Creationists tend to be conservative, with all that implies, and so must be neutered. I'm not that bothered by their endgame to dismiss the flaw in the evolutionary mechanism they have identified, that these large numbers of time do not allow us to merely wave our hands and say, 'it's just like dog breeding'.

Anonymous said...

yes, after 15 years of work and billions spent we find out that the miracle called genom sequencing is not enough to create effective genetic drugs beyond 2-3 diseases. there are other things (promoters anyone?) that make it ungodly complicated. should we all grow beards and praise the lord?

yes, science is complicated. unlike economics where any fool can draw 2 lines and say "believe me supply and demand behave like this in any and all cases for ever and ever. sure i don't have any proof but trust me, i have a phd on this."

yes, falken evolution is counterintuitive but the math works. your math is wrong and i explained it to you before.

i really don't see what behe arguments you find interesting. he doesn't have any.

Anonymous said...

As a former biological sciences geek I must say that the standard account of evolution offered by darwinists like Dawkins does not move many experts in the biological sciences. While the majority are accepting of evolution in general they typically take exception to its functioning in their area of expertise. They would concur with a view the theory is under specified to account for what they see.