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

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 in which organisms can carry seemingly deleterious genes around with them.

The concept of interest is called "developmental buffering," and it's just another fascinating biological phenomenon that creationists and ID propagandists are wise to ignore.

Read the article at the Panda's Thumb.

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

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 creationist characterizations of the human genome.)

Here are the basic data that lead me to conclude that intron sequences are mostly dispensable for biological function. I've provided links to key references, and we can go into more detail in further posts or in the comments.

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

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 functions that are associated with introns then some comments on my specific dispute with Richard Sternberg.

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

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. That's 768 million base pairs. And biologists have identified "important functional roles" for a handful of them. How many? Oh, probably a dozen, but let's be really generous. Let's say that a hundred introns in the human genome are known to have "important functional roles." Oh fine, let's make it a thousand. Well, guys, that leaves at least 189,000 introns without function, and gosh, they're snipped out of the transcripts and discarded before the darn things even leave the nucleus.

One critic has interpreted me as claiming that I know that 189,000 introns have no function. That's not my point, and I think most people know that.

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

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 other creationists purposefully generate around the issue. You can learn all you need to know by reading the previous series, and by reading the extensive work of Ryan Gregory. But here's a brief re-introduction.

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

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.

I love that dirty water...

...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 libation. If you're a friend of the Discovery Institute, I'll buy.

An open letter to Stephen Meyer

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 would be great to follow up on our brief meeting onstage, and to find ourselves in situations in which topics of mutual interest are discussed by knowledgeable and intelligent people (at conferences, for example, or in multidisciplinary working groups). For my part, I'm eager to be involved in such activities, and in the coming years I intend to seek and create opportunities for scholars to consider concepts of biological design in the context of Christian belief.

Right now, I don't see how you could be a thoughtful contributor to such an effort. It's not because you're stupid, or because you have "bad relationship skills," and it's not because you prefer ID-based explanations for biological phenomena. It's because you seem to have abandoned scholarship and the intellectual community, and instead embraced apologetics and political persuasion. As near as I can tell, you've almost completely isolated yourself from science and from scholarship, and this means you have no future as a contributor to the consideration of design in biology. That strikes me as a sad waste; hence my letter to you.

Here are my observations, along with some unsolicited advice.

1. Although you claim to be interested in the origins of biological information and genetic control systems, you seem not to have any serious contact with scientists and scholars who study such things. Do you attend conferences on these subjects, or initiate contact with experts in these fields? Your ideas are potentially very significant – you seek to rule out naturalistic explanation for the origin of life and of DNA – but even if they were merely interesting, it would be foolish for you to think that you could contribute to the development of new theories or viewpoints outside of regular and rigorous interaction with colleagues who know this stuff the best. I have the impression that you don't do this. That's a crazy mistake.

2. A very serious and related problem is the nature of the scientific community that you do interact with. Jonathan Wells just isn't an accomplished or respected scientist, and his ideas are considered laughable by those (including me) who know and understand the relevant fields. Richard Sternberg's platonic views of biology are interesting, but he's on the fringe (to put it mildly) and, worse, he seems not to understand molecular biology. Doug Axe is a smart guy, it seems to me, but the two of you desperately need to get out of your freakish little gated community and talk to people who know that the initiation of cancer is indeed fueled to a large extent by driver mutations, and that genome sizes are indeed a hard problem for design theorists to tackle. When you have Wells whispering to you in one ear, and the bizarre perspectives of Richard Sternberg echoing in your mind, you have a huge problem: you're out of touch with real science, with real biology, with the ideas that you have to engage in order to really put design on the map.

Steve, seriously: you have no chance of having any influence outside of the church school circuit as long as you are isolating yourself and, worse, listening to some pretty confused people who seem not to even understand the ever-changing fields they claim to represent. Get out more. And find some new friends. It is without sarcasm or guile that I say that you are welcome to contact me anytime to ask questions or discuss ideas.

3. Your Discovery Institute is a horrific mistake, an epic intellectual tragedy that is degrading the minds of those who consume its products and bringing dishonor to you and to the church. It is for good reason that Casey Luskin is held in such extreme contempt by your movement's critics, and there's something truly sick about the pattern of attacks that your operatives launched in the weeks after the Biola event. It's clear that you have a cadre of attack dogs that do this work for you, and some of them seem unconstrained by standards of integrity. I can't state this strongly enough: the Discovery Institute is a dangerous cancer on the Christian intellect, both because of its unyielding commitment to dishonesty and because of its creepy mission to undermine science itself. I'd like to see you do better, but I have no such hope for your institute. It needs to be destroyed, and I will do what I can to bring that about.

4. If you want to save your legacy, to make your movement into something other than repackaged creationism, you should do both of the following. First, you should acknowledge the excellence of natural explanation in general and the steadily growing prowess of origin-of-life theories in particular. I don't mean that you should embrace these explanations, I mean that you should stop misleading your credulous audiences (in print and on stage) into concluding that such ideas are silly. Everyone who knows these fields knows that you are engaging in profoundly misleading tactics, and we have a right to question your integrity when we see that kind of stuff. There's a difference between pointing to the weaknesses in a theory and deliberately portraying it, inaccurately, as obvious nonsense. Stop it. Second, you should pay more attention to the ideas of Simon Conway Morris and (to a lesser extent) Michael Denton. If there's any hope for your movement at all, any hope that it can make intellectual headway and offer rational and useful explanation, it is to be found in the deliberate focus on design that Conway Morris and like-minded thinkers offer.

Steve, I just don't see how the Discovery Institute can be saved; from here it looks to be wholly corrupt. But you can still become a part of the scholarly examination of the phenomenon of biological design, and as a Christian you can offer insight into how these questions impinge on issues of faith. It would be a shame if your only contribution was as a political propagandist who served as an impediment to the honest consideration of design and intelligence in biological origins and who was remembered as an enemy of science.

Best regards,

Steve Matheson

In rage deaf as the sea, hasty as fire.

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 hear
The 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 Shakespeare

So Richard Sternberg, that aggrieved martyr of the Smithsonian Institution, butchered at the hands of Evil Darwinists and now among his people in Seattle, has posted a nasty rebuttal to a three-month-old post of mine on Signature in the Cell. I had resolved to ignore the minions of that awful place, but I'll grace Richard with a response since he's found a mistake that I do need to correct.

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

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 Meyer's hired guns. I hope that this will be crystal clear when I'm done here.