Sunday, September 25, 2005

The William Paley of Young Earth Creationism

In recent years, William Dembski has risen in prominence within the intelligent design creationism movement. Dembski and his supporters have tried hard to persuade a largely oblivious scientific community that his work is nothing short of revolutionary. For example, six years ago the philosopher Robert Koons declared that "William Dembski is the Isaac Newton of information theory, [...] one of the most important thinkers of our time". So, is Dembski to information theory, what Newton was to physics and mathematics? Is he even what Newton's arch-enemy Leibniz was to algorithmic information theory? Are his ideas on the design inferrence, complex specified information, and the No Free Lunch theorems to Darwin's theory of natural selection, what Einstein's General Theory of Relativity was to Newton's theory of gravitation? Frankly, I doubt it.

One problem is that he has published almost no peer-reviewed, primary research papers, the standard way to contribute to the scientific process since... well, around Newton's time. A more serious problem is that the few substantive arguments he has advanced have been criticized repeatedly, and he has been inept in his responses (I say this as someone who is genuinely interested in some of the questions he raises) -- typically he will challenge the scientific credentials or the character of his critics, while avoiding or misrepresenting many of the serious questions they raise. (For example, see his exchange with Thomas Schneider.)

Dembski can also write some remarkably stupid (telling?) things. Pharyngula and Panda's Thumb have picked up a steady stream of these. Here's one I have just read in Philosophy of Biology on the relative merits of young earth creationism and evolutionary biology:
"[...] young earth creationism is at worst off by a few orders of magnitude in misestimating the age of the earth. On the other hand, Darwinism, in ascribing powers of intelligence to blind material forces, is off by infinite orders of magnitude."
This is particularly interesting coming from a mathematician!

Perhaps this was the aspect of Dembski's output that Koons had in mind when he drew the parallel with Newton -- he was thinking of Newton the alchemist or Biblical interpreter, not Newton the physicist or mathematician.

Read on

Friday, September 23, 2005

Waiting for Rita...

I'm in downtown Houston waiting for the storm to hit. The winds have picked up a bit, although I don't think they are quite "tropical stormish" yet. The skies are also still disquietingly clear. Of course this will change over the next few hours. Our greatest fear is that our windows will not resist the winds or some flying debri.

The city is largely deserted, although we still managed to find open business. We didn't feel like sitting at home for two days, so we decided to out for lunch. My wife's parents arrived from Sweden on Tuesday... After driving for a while through downtown, midtown, West Gray, Riveroaks and Kirby, we found that most restaurants were closed -- I remember just one open greek restaurant early on. Just as we were beginning to think about going back home, we decided to try Rice Village. It was almost completely deserted, but one restaurant was open -- Prego. Not my favorite and a bit pricey for my taste, but yesterday it felt great!

Another island of sanity in these tense days has been SciGuy's blog, written by Eric Berger, a science writer for the Houston Chronicle. His posts have been one of the best news sources around, consistently informative, clear, succint, and not overly dramatic; a wonderful antidote to the hysterical drivel from local and cable news. No wonder so many people have decided to leave town... Thank you!

Talking of science blogs, if you want to take your mind off the Rita madness you should check out Carl Zimmer's latest posts: one on whale evolution, the other on science blogging. Now I think I'm going to turn to some evolutionary biology of my own, as I prepare to resubmit my latest manuscript. The clouds are getting darker.

Update: It's over now. It lasted some 12h but, as you know by now, Houston was lucky. It was hard to sleep because one of our windows thought it was in a bad horror movie and howled and whistled all night.

Read on

Wednesday, September 21, 2005


I don't like it.

Read on

Monday, September 05, 2005

At Sea

If further evidence were needed that the federal government made a dog's breakfast of their response to Hurricane Katrina I could point to this item from yesterday's Chicago Tribune:
While federal and state emergency planners scramble to get more military relief to Gulf Coast communities stricken by Hurricane Katrina, a massive naval goodwill station has been cruising offshore, underused and waiting for a larger role in the effort.

The USS Bataan, a 844-foot ship designed to dispatch Marines in amphibious assaults, has helicopters, doctors, hospital beds, food and water. It also can make its own water, up to 100,000 gallons a day. And it just happened to be in the Gulf of Mexico when Katrina came roaring ashore.

The Bataan rode out the storm and then followed it toward shore, awaiting relief orders. Helicopter pilots flying from its deck were some of the first to begin plucking stranded New Orleans residents.

But now the Bataan's hospital facilities, including six operating rooms and beds for 600 patients, are empty. A good share of its 1,200 sailors could also go ashore to help with the relief effort, but they haven't been asked. The Bataan has been in the stricken region the longest of any military unit, but federal authorities have yet to fully utilize the ship.

Captain ready, waiting

"Could we do more?" said Capt. Nora Tyson, commander of the Bataan. "Sure. I've got sailors who could be on the beach plucking through garbage or distributing water and food and stuff. But I can't force myself on people.

"We're doing everything we can to contribute right now, and we're ready. If someone says you need to take on people, we're ready. If they say hospitals on the beach can't handle it ... if they need to send the overflow out here, we're ready. We've got lots of room."

Read on

Sunday, September 04, 2005

My Bit

Long before I became a scientist, I learned a more basic kind of skepticism from my mother. She would tell me to pay more attention to what people actually did than to what they said should be done. It's not enough to say you're a Christian, a Socialist or a Communist (common where I grew up), and to talk movingly about the suffering of the poor or the working class, if then you do little to help any actual people around you. On Friday, my wife reminded me of that lesson, when she told me that it was all very well to criticize George Bush or the federal government when we weren't actually doing anything to help the victims of Katrina.

So yesterday we took some clothes to the Salvation Army, and then spent the afternoon volunteering at the Houston Convention Center, where one of the large shelters for victims of Katrina was being set up. I spent my time in a long line of a hundred or so people passing bags of clothes from the entrance (where they were dropped off by a steady stream of locals driving by) into a huge pile inside the Center, where other volunteers sorted the clothes. I did this for over 4 hours stopping only to take a few quick gulps of water now and then. It was easy work, although I couldn't keep my eyes open by 9:30 last night (~3h early) and today I feel as if I played an unfamiliar sport for a long time. My wife spent her time playing a different kind of "sport": making beds.

The experience was humbling in many ways, and not just because there was nothing two scientists with PhDs were obviously "good for". The amount of donations was enormous. I believe that, at some point, people were told to stop dropping clothes off, because we were no longer able to process them. We were obviously an insignificant part of a huge operation that, despite much confusion, did manage to achieve something in the end.

Read on

United States of Wal-Mart

It's hard not to say something trite at times like these. From the comfort of my living room, it's easy to talk about some people's suffering or another's incompetence. However, there's a general feeling that the federal government did much to aggravate this tragedy. Here's Aaron Broussard, president of Jefferson parish, Louisiana, talking to Tim Russert this morning in Meet the Press:
Broussard: We have been abandoned by our own country. Hurricane Katrina will go down in history as one of the worst storms ever to hit an American coast, but the aftermath of Hurricane Katrina will go down as one of the worst abandonments of Americans on American soil ever in U.S. history. I am personally asking our bipartisan congressional delegation here in Louisiana to immediately begin congressional hearings to find out just what happened here. [...]

It's not just Katrina that caused all these deaths in New Orleans here. Bureaucracy has committed murder here in the greater New Orleans area, and bureaucracy has to stand trial before Congress now. It's so obvious. [...] FEMA [Federal Emergency Management Agency] needs to be empowered to do the things it was created to do. It needs to come somewhere, like New Orleans, with all of its force immediately, without red tape, without bureaucracy, act immediately with common sense and leadership, and save lives. Forget about the property. We can rebuild the property. It's got to be able to come in and save lives. [...]

Russert: Shouldn't the mayor of New Orleans and the governor of New Orleans bear some responsibility? Couldn't they have been much more forceful, much more effective and much more organized in evacuating the area?

Broussard: Sir, they were told like me, every single day, "The cavalry's coming," on a federal level [...]. The cavalry's still not here yet, but I've begun to hear the hoofs, and we're almost a week out.

Let me give you just three quick examples. We had Wal-Mart deliver three trucks of water, trailer trucks of water. FEMA turned them back. They said we didn't need them. This was a week ago. FEMA--we had 1,000 gallons of diesel fuel on a Coast Guard vessel docked in my parish. The Coast Guard said, "Come get the fuel right away." When we got there with our trucks, they got a word. "FEMA says don't give you the fuel." [...] Sheriff Harry Lee said that if America--American government would have responded like Wal-Mart has responded, we wouldn't be in this crisis. [my emphasis]

[...] And I want to give you one last story and I'll shut up and let you tell me whatever you want to tell me. The guy who runs this building I'm in, emergency management, he's responsible for everything. His mother was trapped in St. Bernard nursing home and every day she called him and said, "Are you coming, son? Is somebody coming?" And he said, "Yeah, Mama, somebody's coming to get you. Somebody's coming to get you on Tuesday. Somebody's coming to get you on Wednesday. Somebody's coming to get you on Thursday. Somebody's coming to get you on Friday." And she drowned Friday night. She drowned Friday night.

Nobody's coming to get us. Nobody's coming to get us. The secretary [Chertoff] has promised. Everybody's promised. They've had press conferences. I'm sick of the press conferences. For God sakes, shut up and send us somebody.
He then broke down crying. The last few sentences are now being shown repeatedly in MSNBC. But before the emotion got the better of him, he put forward a persuasive, non-partisan argument for "good government". Although this sounds almost intuitive to a European like me, it obviously needs to be repeated here in the US. American politicians, Republican ones in particular, have spent decades decrying the evils of "big government". I don't know whether the government needs to be bigger, but I do know that it needs to be better. When it is easy to find $231 million to build a bridge for a small, uninhabited Alaskan island, but the $105 million requested by the Army Corps of Engineers for hurricane and flood programs in New Orleans last year had to be cut, then something is seriously wrong. Denying that problems exist, be they social or environmental, be they in the Gulf Coast or the Persian Gulf, or saying that "stuff happens", is not good enough.

Read on

Thursday, September 01, 2005

A Whiff of the BS Model

I thought it would be useful to compile a summary of the problems with the Behe & Snoke (2004) paper (BS). Note, however, that despite my criticisms I commend BS for their willingness to publish in a high-profile peer-reviewed journal (albeit one that does not often publish on molecular evolution). I wish other proponents of intelligent design creationism (ID) would do the same -- I'm thinking particularly of the mathematician thought by some to be "the Isaac Newton of information theory". (Curiously, this feeling is apparently shared by at least one proponent of ID.)

Here's the beginning of the list, largely based on and Musgrave, Reuland & Cartwright's review in Panda's Thumb (MRC) and the Lynch (2005) paper (L05):
  1. "Darwinism" is tested using a non-Darwinian model.
    "The flavor of BS’ paper may be gauged by the fact that the authors are skeptical of Darwinian processes to produce complex structures, yet use a model which largely ignores Darwinian processes." (MRC)
    "Although the authors claim to be evaluating whether Darwinian processes are capable of yielding new multiresidue functions, the model that they present is non-Darwinian [...]. Contrary to the principles espoused by Darwin, that is, that evolution generally proceeds via functional intermediate states, BS consider a situation in which the intermediate steps to a new protein are neutral and involve nonfunctional products." (L05, p 2217)
  2. The base population is constructed in a bizarre way. BS (pp 2651-2) assume:
    "that newly duplicated genes encode a full-length protein with the signals necessary for its proper expression. It is further assumed that all duplicate genes are selectively neutral. [...] Any given organism in the population may be thought to have anywhere from zero to multiple extra copies of the gene; that is, duplicate copy number is considered to have no selective effect. However, the model presupposes that there are a total of N duplicate copies of the gene, equal to the number of organisms in the population".
    This problem is corrected in L05's simulation (p 2218):
    "the model presented here starts with a more realistic base population harboring a single locus in all individuals. A duplicate gene then arises in a single random member of the population [...]"
    Note that the L05 approach is actually expected to increase the time to neo-functionalization, when compared to BS' approach. (See also points 4 and 5.)

  3. Only one advantageous target sequence is considered possible. This is acknowledged in BS' discussion (p 2661, their emphasis):
    "the simulation looks for the production of a particular MR [multi-residue] feature in a particular gene, the values will be overestimates of the time necessary to produce some MR feature in some duplicated gene. In other words, the simulation takes a prospective stance, asking for a certain feature to be produced, but we look at modern proteins retrospectively."
    However, they completely ignore this caveat, despite its large potential effect on the effective population size and fixation time estimates. L05 (p 2220) corrected this problem in their simulations by introducing a new parameter: "the number of potential contributory sites to the new function (n)".

  4. The mutational advantage of duplication is ignored. L05 (p 2223) point out that BS:
    "failed to realize that a completely linked pair of duplicate genes has a mutational advantage equal to the mutation rate to null alleles (µ), owing to the fact that both members of a linked pair must be inactivated before the viability of the carrier is affected".
    This implies that, when the population size "N is moderately large (2Nµ>1), the fixation probability approaches 2µ" (L05). (See also point 2.)

  5. Intermediate alleles are excluded from the base population. L05 (p 2222) note that BS:
    "assume that the evolution of a multi-residue function requires the origin of a full set of mutations previously kept absent from the population [...]."
    Since BS assume that "the intermediate steps toward the evolution of a selectable multi-residue function are entirely neutral [...]" intermediate alleles could be present in the population before duplication. This is allowed in L05's model. (See also point 2.)

  6. The value of ρ used throughout is unrealistically high. BS define ρ as the ratio of the number of null mutations to mutations compatible with the novel function. They set the parameter to ρ=1000 in all their simulations and justify this choice by asserting that (pp 2652-3):
    "The majority of nonneutral point mutations to the gene will yield a null allele (again, by which we mean a gene coding for a nonfunctional protein) because most mutations that alter the amino acid sequence of a protein effectively eliminate function (Reidhaar-Olson and Sauer 1988, 1990; Bowie and Sauer 1989; Lim and Sauer 1989; Bowie et al. 1990; Reidhaar-Olson and Sauer 1990; Rennell et al. 1991; Axe et al. 1996; Huang et al. 1996; Sauer et al. 1996; Suckow et al. 1996)."
    This assumption is not supported by the studies cited by BS (see MRC, "Rho-Oh!" section and the L05 passage quoted in my earlier post). By their own admission, the value of ρ has a profound effect on the outcome of their model (p 2661):
  7. "The model is more sensitive to the value of ρ [...]. If ρ were less by a factor of 10 (100 instead of 1000), then the population size needed to fix the feature in the preceding example in 10^8 generations would decrease from 10^22 to 10^16."

I'll continue to add to this list over the next few days. If you let me know of other issues, I'll add them to the list as well.

Update: Two more points have been added.

Update 2: One more point has been added.

Read on