Quintessence of Dust

How bad genes can escape the Grim Reaper (and why this is good)

Published on 2010-08-11 09:48:00

Last month, PZ Myers wrote an interesting piece at the Panda's Thumb in which he discussed some problems with very simple models of evolutionary genetics. One of his main themes was the idea that many genetic changes are neutral with regard to fitness; instead of immediately triggering selection (positive or negative), they're just "tossed into the stewpot." I recently joined the crew at PT, so for my first post I picked up on PZ's point and discussed a very recent article that describes one way

Introns. Let's think about this, people. Part IV.

Published on 2010-07-11 15:29:00

So why is it that I and many other biologists hypothesize that introns are mostly non-functional?(I'll assume that you've read the previous posts, and that you understand what it is that I mean when I challenge claims that introns are functional elements in an information-rich genome. And to avoid confusion, I'll speak only for myself, although I surmise that a tiny minority of biologists would agree with Steve Meyer's characterization of the human genome.)Here are the basic data that lead me to

Introns. Let's think about this, people. Part III.

Published on 2010-07-07 21:25:00

What does it mean to claim that an intron has a function?The question is obviously important, at least as long as there are disputes about whether introns have "functions" and whether science ignored them for decades.Now, I can't help the ID people with their propensity for repeating falsehoods about the history of "junk DNA" and the role of "Darwinism" in its characterization. But I do think we can move a little closer together on this intron thing. So, first a discussion of the types of functi

Introns. Let's think about this, people. Part II.

Published on 2010-06-29 18:32:00

Before we explore what introns are and how they work, let me correct the misuse of my words by one of the ID attack kittens. Months ago, referring to Steve Meyer's claim that introns "are now known to play many important functional roles in the cell," I sought to put intron "function" into context as follows:The human genome contains at least 190,000 introns (though it's been recently estimated to contain almost 210,000). Together those introns comprise almost 1/4 of the human genome. One fourth

Introns. Let's think about this, people. Part I.

Published on 2010-06-24 22:30:00

It's time to talk about introns and function, so at least the ID people and I can agree on what we're disagreeing about. First, though, a little housecleaning.When confronting the avalanche of misinformation on so-called "junk DNA" from intelligent design creationists, it can be hard to know where to start. In a previous series, I addressed many of the falsehoods that are employed by these folks, but the basic outline of the problem is easy to lose in the fog of confusion that ID advocates and o

It's okay, Bono. I'm on it.

Published on 2010-06-23 22:13:00

U2 can't make it to Michigan this year, due to Bono's back injury. (Me: "Ouch. He'll be fine." My girlfriend Susan: "What do you expect? He's old. He should pack it in.") So here are my attempts to fill the void.1. I was a guest on the Skeptics Guide to the Universe podcast about a week and a half ago. The subject was "junk DNA" and boy was it fun to talk to people who actually understand. Check it out; the whole show is really entertaining, and I've decided to subscribe. You know me and skeptic

I love that dirty water...

Published on 2010-06-08 13:10:00

...oh, Boston you're my home.Well, it was for five years, if Woburn counts as "Boston." And the lab was at least half my life, so sure, Boston was my home. But anyway, Wednesday through Saturday I'll be at Gordon College, on the North Shore, about 40 minutes from where we used to live, at this Biologos conference. And the point of all this? Well, if you're in the neighborhood, and especially if you're bored on Saturday afternoon, contact me and I'll let you buy me a geographically-appropriate li

An open letter to Stephen Meyer

Published on 2010-06-05 23:47:00

Dear Steve:It was good to meet you last month at Biola. The Q&A period after your presentation was a little too short, but I thought that we identified a couple of areas in which we could "continue to converse." These might include concepts of explanation, ideas surrounding supernatural action, notions of randomness and divine oversight, or more importantly the ways in which people (especially Christians) go about assessing the explanatory power and success of what we call science.Yes, it wo

In rage deaf as the sea, hasty as fire.

Published on 2010-06-05 01:54:00

No one should take advice from this character, I'll grant you. But even King Richard II could see the obvious:Then call them to our presence: face to face,And frowning brow to brow, ourselves will hearThe accuser and the accused freely speak:High-stomach’d are they both, and full of ire,In rage deaf as the sea, hasty as fire.--The Tragedy of King Richard the Second, Act I, Scene I, The Oxford ShakespeareSo Richard Sternberg, that aggrieved martyr of the Smithsonian Institution, butchered at th

Bread and circus: Signature in the Cell at Biola (Part III)

Published on 2010-05-31 13:25:00

Here I'm continuing my discussion of the Signature in the Cell book-signing event at Biola University on 14 May. You'll want to read Parts I and II before reading on.My second question to Steve Meyer was the one question I most wanted to ask him, both out of personal curiosity and because I thought the answer would help demystify many of his claims. The exchange that resulted was memorable – on that, everyone seems to agree. But the nature of my comments has been profoundly misrepresented by M

Bread and circus: Signature in the Cell at Biola (Part II)

Published on 2010-05-27 23:42:00

Here are some further observations on the Stephen Meyer book-signing appearance. Part I dealt with Meyer's talk and the other festivities. Here I'll describe the last third of the event, in which Art Hunt and I (the "powerful group of credentialed critics") spent a short time questioning Meyer.1. Our time was short. The original proposal, some months back, simply mentioned a three-hour event which I pictured as Meyer facing a panel of experts for at least two hours. But the schedule for the even

Bread and circus: Signature in the Cell at Biola (Part I)

Published on 2010-05-22 00:53:00

So last week was the big book-signing shindig and Discovery Institute Annual Convention at Biola University. I knew the DI spin machine would move quickly, and sure enough I've already been quotemined and utterly misconstrued. But my real weakness is research, lab meetings and new papers to present in lab meeting, so some of you had to wait. I'm okay with that.1. Meeting students and faculty at Biola UniversitySo the hyperbolic description of the event claims that the organizers "assembled a pow

Signature in the Cell: Chapters 9 and 10

Published on 2010-04-24 22:51:00

"He..strikes at randome at a man of straw."– Richard Saunders, A Balm to heal Religious Wounds, 1652. Quoted in the Oxford English Dictionary, 2nd Edition"An imaginary adversary, or an invented adverse argument, adduced in order to be triumphantly confuted."– Second definition entered for "man of straw" in the Oxford English Dictionary, 2nd EditionChapter 9 is called "Ends and Odds." Chapter 10 is "Beyond the Reach of Chance." Between them, they advance a straw man so idiotic that I won

Signature in the Cell: Chapter 8

Published on 2010-04-18 00:53:00

It's been a month and a half since my last post in this series, and recently a friend asked me why I stopped. I can think of two reasons: first, I spent the month of March teaching a graduate course for the first time; second, I'm worried about how this is going to go. I'm worried because I can see that the book is poor scholarship – Meyer is either underinformed or overcommitted to his cause – and I can see that my critique will be considered within a religious milieu that hinders straightf

Behe and probability: one more try

Published on 2010-04-04 16:48:00

Almost two years ago, I reviewed Michael Behe's latest book, The Edge of Evolution, here on the blog. I was unimpressed, to say the least, and remain of the opinion that Behe should not be considered a serious scientific thinker given his failure in that ludicrous book.Since then, my posts have been referenced occasionally in the blogosphere, typically by people trying to explain Behe's surprisingly crude mishandling of probability in the context of genetics. One particular p

Introns and design

Published on 2010-03-28 20:40:00

Mike Gene has posted an interesting series on introns that's worthy of a few comments. His thesis is that "introns facilitated the evolution of multicellular life."A. The idea is interesting and rational but not novel. Research on introns and evolution is active and lively, and one prominent scientist in the field, Eugene Koonin, has proposed that introns drove many aspects of the evolution of eukaryotes (i.e., non-bacteria).B. The more general proposal that mobile genetic elements have facilita

Love. Peace. Unity. Or?

Published on 2010-03-23 20:42:00

Last month, I read that Biologos (a Christian "think tank" that advances evolutionary creation) and Reasons To Believe (a Christian "think tank" that advances old-earth creationism) were reporting on a dialogue between their two organizations that was intended "to discuss areas of agreement and disagreement" with a particular focus on "the biological record of the past 700 million years."This is very interesting to me. My position is very closely aligned with that of Biologos, so natur

Signature in the Cell: Chapter 7

Published on 2010-02-27 22:30:00

The chapter is called "Of Clues to Causes" and it's about scientific explanation. That's an interesting and important topic, one that opponents of evolutionary theory rarely understand. Meyer's summary is predictably fluffy but not inaccurate. Those seeking an introduction to philosophical questions pertaining to scientific explanation should look elsewhere, since Meyer says little in the 22-page chapter. His main points:There are indeed legitimately scientific means of understanding and seeking

Signature in the Cell: Chapter 6

Published on 2010-02-21 20:44:00

The chapter is called "The Origin of Science and the Possibility of Design." It's short, unimportant and uninteresting. Its purposes, along with Chapter 7, are twofold: 1) to counter the claim that ID theory is "not science" and 2) to establish that "historical science" (that which deals with the past) is not all that different from "operations science" (as defined by Charles Thaxton and others), specifically because the theorizing of "historical science" can be considered testable.Comments in n

Signature in the Cell: Chapters 4 and 5 - errors and problems

Published on 2010-02-14 22:11:00

Meyer's basic idea in chapters 4 and 5 is reasonably coherent. But I find further evidence in both chapters that Meyer is careless and underinformed on the subjects he addresses.(I explained before why I think this matters. If you think I'm not being nice enough to Meyer, consider providing me with the Rules of Engagement that apply when criticizing culture warriors who are proposing world-shifting new ideas.)1. A bizarre paragraph in chapter 4 makes me wonder if Steve Meyer is terribly confused

Signature in the Cell: Chapters 4 and 5 - major themes

Published on 2010-02-13 12:26:00

Chapter 4 is called "Signature in the Cell." It's an important chapter for two reasons. First, along with chapter 5 ("The Molecular Labyrinth") it lays out Meyer's central question by pointing to the specific features of cellular information systems in need of explanation. Second, it exemplifies an aspect of ID thought that I want to highlight. I'll discuss these two themes here, then add some further critiques in a second post.1. Meyer's central questionEach chapter can be summarized in a short

Signature in the Cell: Chapter 3

Published on 2010-02-06 21:20:00

The chapter is called "The Double Helix," and there's not much to say about it. Meyer provides a fairly standard narrative of the discoveries that led to Watson and Crick and molecular biology. Anyone who's read The Eighth Day of Creation, along with a decent genetics textbook and/or a memoir by one of the principals (What Mad Pursuit by Francis Crick is a personal favorite) will already know everything here.Two observations.1. Meyer makes a basic error on page 66 while describing the early evid

Signature in the Cell: Chapter 2

Published on 2010-02-03 22:27:00

The chapter is called "The Evolution of a Mystery and Why It Matters." It's interesting and engaging, and I enjoyed reading it.The "mystery" in question is first described on page 35:...most philosophers and scientists have long thought that Darwin's theory of evolution by natural selection destroyed the design argument. Yet I also discovered that Darwin himself admitted that his theory did not explain the origin of life itself. [...] His theory assumed rather than explained the origin of the fi

Signature in the Cell: Chapter 1

Published on 2010-01-26 16:11:00

The chapter is called "DNA, Darwin, and the Appearance of Design." It's a poor start.Meyer sketches some key themes of the rest of the book in this sloppy chapter. Here are those themes (in my words) and some comments.1. DNA stores information, using a code that is similar to that of a computer. We know a lot about how that works.2. Life gives the appearance of design. No one disputes that. But the source of the design is, of course, controversial.Our commonsense reasoning might lead us to concl

A quick note about a hero

Published on 2010-01-14 14:12:00

My chapter-by-chapter commentary on Signature in the Cell will resume shortly. But I can't resist writing a little about someone I know who did something extraordinary. Here's the short version.This friend of mine, we'll call her "Susan," became inspired several months ago while reading accounts of people resisting Nazi occupation during World War II, and especially those who risked their lives (and often lost their lives) working to assist Jews and others targeted by the occupiers. She wondered