18 April 2008

Weekly sampler 15

Last quiz on genome size, with animals chosen at random. The first quiz post explains what this is all about, the second one has additional commentary, and the answers to both previous quizzes are in previous Weekly samplers.

Which organism has the larger genome?

This one? Or this one?
1
2
3
4

Here's some help for you. These are the C-values (amount of DNA per cell) for those animals, in ascending order:

0.23 -- 1.50 -- 2.24 -- 2.72 -- 2.91 -- 3.00 -- 3.29 -- 5.87

And here's a hint: the biggest number does not go with the biggest animal. Good luck!

1. We're living in the postgenomic era, and comparative genomics has already made it impossible to be an intellectually fulfilled anti-evolutionist. I've written before about genome sequencing and the imminence of large-scale and inexpensive sequencing. Well, the first super-fast (4 months vs. more than a decade for the Human Genome Project), super-cheap ($1.5 million vs. billions for the HGP) human genome sequence is now official. It's Jim Watson's genome. Blecch. Someone should use BLAST to search his coding sequences for this amino acid sequence:
Alanine - Serine - Serine - Histidine - Glutamine - Leucine - Glutamic acid
Don't get it? Think about this guy's conduct, then check out the amino acid code.

2. If you think I'm never nice to Reasons To Believe, check out the discussion this week at the ASA listserv. The topic: RTB's statement in which they distance themselves from Expelled.

3. Speaking of Expelled, which I will do infrequently, here's a good reason to avoid the movie and its cynical attempt to enlist and co-opt evangelical Christendom: its indefensible linkage of "Darwinism" with Nazism. If that's not bad enough, check out John Lynch's examination of the diabolical credentials of one "expert" interviewed in the film.

If you're a Christian who thinks that the Nazis are a useful polemical tool against evolution, then maybe you should read about some of Hitler's best-known influences. In my view, if you can read Luther's words and still think there's any moral high ground surrounding the Holocaust that can be claimed by Christendom, then you're crazy. The Holocaust is an unspeakably abhorrent stain on the Church, if you ask me, and it's not Darwinists (whoever they are) who have hard questions to answer. I, for one, believe that Christians should be overwhelmingly humbled by the occurrence of the Holocaust, and not because of the Problem of Evil.

Christopher Heard has several recent posts on Expelled that are worth checking out. Just promise me you won't give any money to these chowderheads.

I say: skip Expelled. Send the money to Compassion International. Or give it to a library or school. Say no to the minions of the Discovery Institute who have given up the pretense of "scientific" explorations of "design" and have lustily embraced full frontal culture war. [spits]

3. [Deep breath] So, were you alive in the 1980's? Remember Bloom County? It's my favorite comic strip of all time (apologies to Calvin & Hobbes). The strip often tracked current events; during the 1981 Arkansas creationism trial, Bloom County presented the famous "penguin evolution" trial in which "scientific penguinism" was being advocated by certain characters. Some classic excerpts from that brilliant series are illicitly available in the blogosphere; don't miss the one (second from the bottom) in which the scientific expert states, "Penguin evolution is a fib." You can find some similarly scintillating examples on Berkeley Breathed's site. My favorites: the first and the next to last.

4. Kevin Corcoran writes this about a recent piece by Stanley Fish on deconstruction:
John Searle said it first, but it applies here: it’s stuff like this that gives bullshit a bad name.
Now that's funny.

5. The online repository of Darwin's works at the University of Cambridge announced this week that they were making available a gigantic collection of Darwin's private papers, including "the first draft of his theory of evolution" and notes from the Beagle voyage. One little tidbit: apparently they sold tickets to lectures at the University of Edinburgh. Hmmmm. [rubs chin]
Via my brilliant brother, who works at HP and helps his wife run her cool small business.

6. There was a lot of cyberspace snickering when Answers Research Journal started up, and some of the articles there are pretty lame (the metaphysical piece would, I think, do poorly in a 200-level philosophy course at Calvin). But have a look at the new article on peer review; the authors are worth listening to, and their discussion of peer review from a Christian perspective is worth considering. I'm not crazy about the occasional proof-texting, and the authors frequently address the YEC community specifically. But here's the type of clear-headed wisdom you'll find in their paper:
By striving for excellence, we also love our neighbors. In our modern, western culture, many people view scientific pronouncements as authoritative. Christians who are also scientists therefore have an even higher duty to speak with excellence than the average Christian, simply because of the perceived authority that they possess. Errors made by Christians speaking in the name of science, no matter how well intentioned, can become “common wisdom” and thereby very difficult to correct. Even greater responsibility lies upon the scholar who professes ideas to the general public rather than just scholarly colleagues. In doing so, the scholar becomes a teacher, with all the attendant responsibilities (e.g., Matthew 5:19, 18:6; James 3:1). We therefore love our neighbors by striving to present the excellence of God in our written work and avoid the dangerous alternative of leading them into error.
I probably don't need to explain why that passage rang true. You might notice, by the way, the links take you to the New King James Version. What is it with the conservative/fundamentalist fondness for 400-year-old prose bearing the name of an English monarch?

11 April 2008

Weekly sampler 14

Answers to Quiz 2. (Poor John Farrell.) Row 1: the deer tick on the right has a genome almost 8 times the size of the ladybird beetle's (C value of 2.48 vs. 0.33). I take it that the scholars of RTB would postulate that a deer tick is many times more "advanced" than is a ladybird beetle. Similarly, Hugh Ross would have to surmise that a grasshopper is 4 times as "advanced" as a bengal tiger (row 2; C value 2.71 vs. 12.66). Indeed, it would seem that this wonderful insect is far more "advanced" than every mammal ever examined. Row 3: let's see...which is more "advanced", a snail or a giraffe? Well, the snail, of course, though perhaps just by a hair (heh): 2.69 vs. 3.58.

We'll have one more of these quizzes, but next time the species will be chosen randomly. At least then the success rate of Hugh Ross' proposals has a chance of reaching 50%.

1. Back in the day, I learned about the cool Monty Hall puzzle on a Usenet newsgroup. I found the puzzle to be very interesting, in that those who understand probability fairly well are most prone to being tricked by the puzzle. Here's the problem.

You're playing Let's Make a Deal with Monty Hall, and you are offered a choice among three doors. Behind one of the doors is a new Toyota Prius, yours to keep if you reveal it, and behind each of the other two doors is a goat (which, presumably, you don't want to take home). The game always proceeds as follows. You announce your choice of a door. Then Monty says, "Hmmm. Are you sure about that? Here, let me show you something that might change your mind." He then opens one of the two doors you did not choose, revealing a goat. Then he asks you: do you want to stay with your first choice, or would you like to change your mind? And the question is: do your odds of winning change (i.e., improve) if you change your mind, and choose the remaining door?

Now, if you've never encountered this famous puzzle, stop and think about it. I've put the rest of this section at the end of the post. Note, though, that there is no trickery here; Monty will always show you a goat (that's important) and the solution has nothing to do with semantics or other uninteresting chicanery. It's all about probability.

2. The evolution (and prevalence) of sex has long been considered one of the most perplexing phenomena in biology. Some of the most creatively-named hypotheses in all of science are hypotheses addressing the adaptive nature of sexual reproduction.

Image from PLOS Biology, photo by William F. Duffy.

Enter the bdelloid rotifers, animals whose "scandalous" claim to fame is that they don't have sex. For centuries, it seems that the evidence that these microscopic animals are asexual amounted to the fact that no one had ever seen a male. A very nice recent review in Nature News explains how biologists have established that the bdelloids are actually asexual, and how these animals – alone among all others – pull it off. If you want more, PLOS Biology has an interesting review of how one famous theory of sexual evolution recently held up under duress.

3. Brain doping?! So, how many scientists are taking cognitive enhancers in order to outperform their competitors? And should federal granting agencies ban this practice, perhaps to motivate Major League Baseball to follow suit? (Beware of leftover April Fools jokes.) Some of my colleagues apparently do indulge in this practice. Some, I daresay, really should start.

4. I don't have much to say about Expelled, and I don't intend to spend any of my childrens' inheritance on it. (In fact, if you are contemplating such a foolish move, consider redirecting your expenditure in some more constructive direction.) But Chris Heard at Higgaion has posted a very important piece on Why Ken Miller isn't in Expelled. Check it out, and if you decide to waste synaptic activity on this issue, tune in to the NCSE's Expelled Exposed site.

5. According to Siris, philosophy is enduring a zombie invasion. David Chalmers must be pleased. I know I am.

6. Okay, back to Let's Make a Deal. The answer is: yes, you should change your guess to the other door. Your probability of winning is 2/3 if you do that.

When I first encountered the puzzle, I had a response that is typical among people who know a little about probability. I figured that Monty's little stunt with the goat is irrelevant; it couldn't change my chance of winning any more than any other silly behavior on his part. My chance of winning is 1/3, period. And of course I was partially correct. My chance of winning is indeed still 1/3 if I make my choice and just stick with it. But I was wrong in assuming that Monty's action is irrelevant. On the contrary, his goat-revealing gesture is determined by my choice. And it changes the situation entirely.

There are many ways to explain this, but here's my favorite. On average, 1/3 of the time I choose the car at the outset. In those situations, Monty gets to choose between the 2 goats, and I lose if I change my choice to the remaining goat. But 2/3 of the time I choose one of the goats at the outset. Monty is forced to reveal the sole remaining goat to me, and that means the car is behind the remaining door. So, I have a 2/3 chance of winning by randomly picking a door and then watching Monty show me the location of the car.

Why mention this on the blog? Well, for one, it's interesting. But also, this week the Monty Hall puzzle surfaced in a scientific context. Psychologists are debating the extent to which the Monty Hall phenomenon has affected the outcomes of numerous experiments examining so-called cognitive dissonance. Read about it at John Tierney's blog at the New York Times, and don't miss your chance to play the Monty Hall game yourself, especially if (like many others) you are unconvinced by my explanation.

09 April 2008

Mutations, selection, and bacteria

Several weeks ago, a commenter (Donald) asked an interesting question about natural selection and genetic variation, and I promised to address it because I want the issue to be a theme on QoD in the coming months. Here's Donald:

The link below is to a NYT blog where it says that E coli studies have found that there are 100,000 harmful mutations for each single beneficial one. I'm no population geneticist, but this kind of thing does make you wonder how selection could work with that much noise to overcome.

That aside, I have read a little of Ronald Fisher and I recall his mathematical argument that for mutations of very small effect, there was a 50 percent chance that the net effect would be beneficial. This is in "The Genetical Theory of Natural Selection". The mutations with large effects, on the other hand, are almost certainly going to be deleterious.

So are these studies only detecting mutations with large effects, or was Fisher wrong?
The blog article that Donald is citing is at The Wild Side by Olivia Judson, and the figure of 100,000 deleterious mutants for every helpful one is widely referenced.

Donald raises two questions, which I'll rephrase somewhat.

1. How can natural selection lead to adaptation when there is so much interference from harmful mutations?

I think there are at least three misconceptions that are acting together to create this common misunderstanding. First, that widely-cited ratio of harmful to helpful mutations is apparently an overestimate, off by three orders of magnitude, or a factor of 1000. The study that reported this dramatic correction in our understanding of bacterial mutations was published in Science last August, and represents a wonderful case study of the difference between real scientific thinking and the thinking of most design advocates. (Subject of an upcoming post.)

Second, the existence of harmful mutations doesn't necessarily "interfere" with adaptation. Many deleterious mutations will just kill the organism, and that's that. Natural selection does that all the time, and it doesn't get in the way of life in general, so there's no special reason to worry that it will get in the way of adaptation.

But most importantly, I think Donald is a little confused about the material on which natural selection acts, and understandably so. (This error is the centerpiece of Michael Behe's ludicrous recent book The Edge of Evolution.) The mistake seems subtle, but it's gigantic, and I think it arises in part from a semantic shortcut that is often used when explaining selection and adaptation. To see the problem, consider these two alternative descriptions of the process of adaptation.
  • Adaptive evolution occurs when natural selection favors certain mutations which are beneficial as opposed to harmful. When new challenges arise, new adaptations arise as new beneficial mutations are generated and selection favors these mutations.
  • Adaptive evolution occurs when natural selection favors previously-existing genetic combinations that are more fit than others. When new challenges arise, new adaptations arise as selection favors individuals whose genetic endowments are best suited to the new challenges.
The first description probably sounds more familiar to you than the second one does, but they're quite different, and the second description is far more accurate than the first. The distinction between these two scenarios lies in the implication of the first scenario that new mutations must arise "on demand" or "just in time." Michael Behe's whole silly book is based on calculations that assume that new mutations must be generated, simultaneously, after the introduction of the new challenge. (His main example is the adaptation of the malaria parasite in the face of drugs intended for its destruction.) Those who promulgate this error (intentionally or not) tend to emphasize natural selection acting on mutations, and consequently it's easy to picture a species "mutating around" a challenge or obstacle. (Behe, for example, uses such language repeatedly.)

But that's a mistaken view of the process, and the way to avoid the trap is to picture selection acting on variation, specifically on variation that is always present in any population of organisms. (Populations without significant genetic variation, when confronted with serious challenges, are more likely to illustrate extinction than evolution.) Such variation is continuously generated and therefore continuously present. This is the lesson from studies of the effects of human selection on domesticated species of all kinds: when selection is applied, such populations typically reveal a remarkable propensity for rapid and dramatic change, because they harbor vast resources in the form of genetic diversity. If you carefully attend to this distinction, you will understand Darwinian evolution far better than any ID advocate.

2. Are most large-effect mutations harmful, and many small-effect mutations beneficial, as predicted by Fisher?

Well, first of all, kudos to Donald for reading Fisher. I've been browsing The Genetical Theory of Natural Selection, and it's demanding (but comprehensible). Michael Behe either hasn't read it, or didn't understand it, and in either case is therefore unqualified to write on evolutionary genetics.

Fisher was certainly right that large-effect mutations are almost never beneficial, but it is largely unknown whether very small-effect mutations are frequently beneficial, as he postulated. Theoretical and experimental work in this field has recently accelerated, and the current model is that effects of beneficial mutations are exponentially distributed, such that beneficial mutations are far more likely to be of very small effect than of large effect. This was Allen Orr's proposal, and it has been borne out in some very recent experimental analyses. The most recent, and significant, was the Science paper I mentioned above, in which the authors found that beneficial mutations in bacteria are far more common than previously estimated, but have relatively small effects (individually). Here's an excerpt from their last paragraph:
...our estimate of [the beneficial mutation rate] implies that 1 in 150 newly arising mutations is beneficial and that 1 in 10 fitness-affecting mutations increases the fitness of the individual carrying it. Hence, an enterobacterium has an enormous potential for adaptation and may help explain how antibiotic resistance and virulence evolve so quickly.
That's enough for now. Start with papers by Allen Orr when reading on the genetics of adaption; his historical overview in Nature Reviews Genetics in 2005 is particularly helpful.

08 April 2008

Diagnosed...at last.

I thought it was the coffee, or maybe the Scottish buttheadedness. But no: it's a real live syndrome. Note that this newly-described malady, SIWOTI syndrome, sounds a bit like 'snotty' or 'so what-ee', so please be careful not to offend sufferers by mispronouncing the name, or by oversimplifying the affliction with crude cartoons. Via Pharyngula, a silly little blog written by one of the syndrome's most severely-affected victims.

05 April 2008

Quiz 2 on genome size. How's it going so far?

Quiz 2. (Directions, and rationale, can be found in a previous post.) Ready?

Which organism has the larger genome?

This one? Or this one?
1
2
3

Which of these organisms displays the greatest "degree of advancement"? Which would require the most "information" to build and maintain? What predictions would design theorists such as William Dembski and Hugh Ross offer us in this exercise?

Think, people. If the proposals of these thinkers made any sense at all (at least with respect to non-coding DNA), it would be pretty straightforward to determine which of these organisms would have the largest genome, and which would have the smallest. But if you want to do well on this quiz, you don't want to peek at Hugh Ross' paper. You're better off throwing darts. Blindfolded.

03 April 2008

Weekly sampler 13

First, answers to the quiz in last week's sampler. Row 1: the genome of the funnel-web spider on the left is more than 3 times as big as that of the bald eagle (C value of 5.36 vs. 1.43). Row 2: The monarch butterfly's genome is less than 1/8 the size of the alligator's (0.29 vs. 2.49). Row 3: The duck-billed platypus has a significantly smaller genome than that of the octopus (3.06 vs. 5.15). So how'd the "degree of advancement" criterion work out? You do the math. More quizzes to come.

1. As a Reformed Christian (and former Catholic), I typically feel that Catholics are kindred spirits when it comes to science and the arts, and those of us who embrace the Creeds and common descent are prone to pointing to various papal endorsements of evolutionary science. This makes it all the more alarming to see Catholics falling for the ID line. Enter John Farrell with a sharp piece this week, following up on a nice analysis by DarwinCatholic.

2. David Sloan Wilson is the big name (that I know) behind an interesting site at Binghamton University on the topic of "Evolutionary Religious Studies." The program is Templeton-funded, and as near as I can tell is focused on outreach and dissemination but is not a degree program. I'll poke around some more, and will be interested to hear from anyone who knows more about it.

3. Thursday on Pharyngula, PZ Myers posted an article with a sadly typical description of some evangelical idiocy, then voiced a challenge I've heard from him before:

But I would think the concerted and largely successful effort in our culture to equate Christianity with the idiocy of belief in a 6000 year old world or a god who meddles in trivialities or denying the facts of a natural world would piss you off. Unless it's true, that is, that you don't mind having your religious beliefs associated with flaming anti-scientific lunacy.

Maybe you should try squawking a little louder.
I responded in the comments and would be interested in feedback here.

4. Olivia Judson has a superb piece on mutations and randomness at The Wild Side.


5. This week sees a nice edition (#102) of Tangled Bank at Further Thoughts.

6. Like I need another reason to cook up an insane road trip to NYC? As reported in the NY Times.

7. And speaking of the newspaper of record, check out this interesting piece by a couple of neuroscientists, attempting to explain why I can eat salad and ride my bike, but can't resist playing Text Twist when I have three (or is it four) papers to write. The comments are enlightening too; it's like sitting in on a contentious platform session at the Society for Neuroscience annual meeting.