Jerry Coyne & Manyuan Long on the origin of new genes in Drosophila
Jerry Coyne reports on a new paper in Science by Manyuan Long and colleagues on the origin and history of new genes in a large group of Drosophila that have recently had their full genomes sequenced.
Having this much phylogenetic and genomic information allows researchers to estimate the phylogenetic position of the origin of a new gene (566 new genes amongst the group of 12 fully sequenced genomes, actually), and the periods of time in which directional selection, stabilizing selection, or drift were the dominant regime that the new genes were evolving under. In many cases, there is a period of high selection after the origin of the gene, which weakens later -- which is just what you would expect if the well-known, standard model for the origin of new genes is correct.
Two additional points are worth mentioning: (1) in some cases (about 30%, 59 out of the 195 they targeted for knockout studies), these new genes have become essential to viability for the species in question -- even though they are totally absent in other, basically similar, flies that do just fine without them! This is strong support for the notion that one way "irreducible" systems evolve is by evolving parts that are helpful at first, but later become essential as other parts coadapt to become dependent on them. (2) I'm sure Luskin, Ewert, and other DI people would like to dismiss this as just another case of evolutionists "illegitimately" inferring common ancestry from "mere" sequence similarity, and that "common design" could be the explanation. However, in any other context, these creationists, and virtually any creationists including the young-earthers, would easily say that all of these Drosophila are just different varieties of the Drosophila kind, and that whatever variety exists between them (minor, in the grand scheme of biology) is "merely" "microevolution within the kind!" (And in the Edge of Evolution, Behe clearly puts his estimated "edge" well above the genus level.)
What's that? Standard boring microevolutionary processes can produce new genes with modified sequences and new functions, which is clearly new information on anyone's definition, even the creationists' and even (explicitly so) Michael Behe's definition? Oh my goodness, someone better call the DI news blog to put out this fire and reassure the faithful!
References
Chen, S., E. Zhang, and M. Long. 2010. New genes in Drosophila quickly become essential. Science 330:1682-1685.
A previous bit of ranting on this topic by me (responding to Luskin's ridiculous critique of another famous paper by Manyuan Long, entered into evidence in the Kitzmiller case as exhibit P-245, actually: Long et al. (2003), Nature Reviews Genetics, "The origin of new genes" (free online in many places).
63 Comments
RBH · 21 December 2010
AS I said on Coyne's post on this research, somewhere Michael Behe should be scrooching in a corner with his hands protecting his groin region.
mrg · 21 December 2010
Pah! No, what you'll get is: "Tis but a scratch! A mere flesh wound! Come back here you cowards, I'll bite your knees off!"
Nick (Matzke) · 21 December 2010
Flint · 21 December 2010
I found Smith's article frustrating. The question presented is, how do you get through to someone who doesn't care, doesn't listen, doesn't have the slightest understanding of or respect for evidence or logic, and is simply impervious to all known mechanisms by which humans have been observed to learn?
And Smith's solution is, well, since everything we can dream of has struck out at the college level, the problem must lie in the public schools before college. THEY should fix this problem! But the public schools have found that by the time the pupil enters his very first biology class at about age 14, it's already too late. Creationism has taken root in (Smith cites) 54% of the American people and rising, even before entering the public school system at all.
Creationism really isn't an intellectual matter at all, and can't be addressed on that level. Creationism is an emotional need trained into children early on. The sorts of discussions Smith (and us here at PT) have with creationists are about juggling various justifications and rationalizations which creationists don't really need because they're basically window dressing.
As Smith has noticed, the creationist can regurgitate in full detail the utter absurdity of his belief, complete with recognition of blatant logical errors and known false statements of fact, but ends by saying "but I believe it anyway".
So Smith spends all this time pointing out that the Black Knight simply will not and cannot every admit defeat, pointing out that all attempts to get him to admit defeat have failed, and ends up suggesting that getting him to admit defeat is someone else's job. Uh huh, great. It might be worth asking WHY mainstream Christian denominations are dwindling while evangelical denominations are growing and thriving. It might be worth asking WHY Americans far moreso than anyone else in the Western World demand Absolute Truth, even if it's stupid and wrong. WHY do more and more parents FEAR that if Johnny thinks too hard about certain things, he'll jeopardize his chances of going to heaven?
I don't have these answers, but I can still see that the problem lies in the overall social and family support system starting at birth, and public school is only a small part of this. And I can see that what people know and what they believe are two different things, seated in two different parts of the brain, and that beliefs rule with an iron fist.
Mike Elzinga · 21 December 2010
Flint · 21 December 2010
Over the course of time, talk radio shows have featured commentators appealing to the audience's intelligence and knowledge, rather than to their fears and other emotions. These efforts have been roundly ignored and short-lived. The national psyche seems to have turned away from the former appeal to a sense of adventure and discovering the unknown, and toward circling the wagons in defense against imaginary enemies. We're no longer playing to win, we're playing to lose as slowly as we can.
Nick (Matzke) · 21 December 2010
It's a very tough problem. It has to be thought of as a long-term, multi-generational, multi-century effort, where the influence of any one person or even any one institution is pretty tiny. Remember that the scale we are talking about is how to persuade hundreds of millions of people in a complex, democratic society with billions of things going on besides creationism vs. evolution.
Obviously it's rock-bottom requirement that we need to make sure that higher education and the public schools are doing their jobs and teaching strong science. But beyond that? In a democratic society, evolution is going to have to compete with everything else for public attention. It's important to win the big fights when they come up, and to have scientists engaged with the public and the press, for science journalists and university press officers to do high-quality work, and (IMHO) for scientists and science popularizers to make an effort to make things better rather than worse in terms of science/public relations (and yes, this means exercising some degree of democratic civility, tolerance, and fairness towards religion and the religious -- a good model is how the Founding Fathers, even the most secular ones, treated religion and the religious).
But these are basically effects on the order of 1% of the solution, even if they were to work perfectly.
The only real solution will occur when/if the evangelical churches chill out about evolution. This includes the evangelical thought leaders, the seminaries and the pastors. This is why I think BioLogos is basically a good thing, despite various disagreements. It is evangelicals talking evolution to evangelicals.
What can one do if one is not an evangelical? I'm not sure. It would be nice, very nice, if there were a way to engage evangelicals on friendly terms over the evolution issue. Ways which didn't involve the usual catfights with creationists. But that is a tough thing to pull off, e.g. getting invites to speak to congregations. If anyone has any ideas, let me know...
Flint · 21 December 2010
I enjoyed the Doonesbury cartoon a while back, where the doctor asked the patient if he accepted the theory of evolution. The patient said no, so the doctor said "OK, we give you the straight penicillin. It won't work against your problem, but all the stuff that WILL work couldn't have been discovered without applying the theory of evolution, and using that would be against your religion."
Maybe we need a couple hundred thousand more of those doctors...
Joe Felsenstein · 21 December 2010
Flint · 21 December 2010
Ah yes, the distinction between hard-core creationists, and those whose life experience might make creationistic ideas the default, but who aren't committed to it and haven't been exposed to the alternatives.
I do wonder how many of those 54% who said people were poofed in their present form within the last 10,000 years, would change their mind if they were immediately informed that the evidence refuting this belief were vast beyond imagining, filling huge libraries and new libraries all the time. And that there is absolutely ZERO evidence for any recent creation, only evidence against it. How many would say "Oh, I never knew that. I guess evolution must be correct after all..."?
What depressed me was the poll that showed that of all creationists who entered a biology degree program and graduated, over 80% were STILL creationists. Clearly, there is an age beyond which education does not cure creationism. I think Smith is correct in implying that age is younger than college freshman. I suspect it's younger than high school biology student also.
I do applaud any attempts to train teachers to produce canned responses to canned objections drilled into school kids. I think this sort of thing has to be handled carefully, because I think the child loses the ability to reason about creationism before he reaches the age where he CAN reason at all. For a child at the critical age, it's a straight swearing contest between the teacher on the one side, and the child's parents, church, friends, daily practices, etc. on the other. For the teacher to be right, every other knowledgeable trusted authority in his life must be dead wrong. Not an easy current for the teacher to swim against.
And as Smith wrote, the students can appear to fully understand why his common creationist debating points are misleading, dishonest, or wrong, and explain this understanding in detail. But his belief in those points isn't even dented.
In the long run, I think we need to find the root of the problem, the concerns that are driving Americans toward comfortable Absolute Truths, however preposterous. What's causing all the fear and insecurity that creationism immunizes them against? I wish I knew.
Mike Elzinga · 22 December 2010
raven · 22 December 2010
It is bad, but it isn't that bad.
Copernicus published 450 years ago and still 20% of the US population are Geocentrists and can't diagram the solar system.
That fact says that no matter how good the evidence is, 20% of the population won't accept it or understand it.
And how much does this 20% matter anyway? Given that the median US IQ is 100, there are going to be a lot of 70's and 80's in there and a lot of uneducated people.
Probably not much.
Among people who matter and keep our civilization going, it is likely to be far higher.
And retention rates for kids in fundie religions is very low. The Southern Baptists consistently find it is around 30%. This is true of the Seventh Day Adventists as well. US xianity is on the skids right now and losing about 1 million members a year.
With the time frame for Heliocentrism to be accepted by the general population of 450 years, evolution is just getting started. The world moves faster these days, give it another 50 or 100 years.
Kris · 22 December 2010
Joe Felsenstein · 22 December 2010
JGB · 22 December 2010
If one is looking for a tactic to fight demographic trends, why not find a creative way to target the largest growing segments of the populace? The growth in minority populations is potentially a big area to improve understanding, and one that does not involve the dreaded knight.
OgreMkV · 22 December 2010
harold · 22 December 2010
OgreMkv -
There is a great deal of social pathology in the US. It is especially obvious in historically discriminated-against populations. Perhaps when you spend centuries telling people that they will not be permitted equal participation in society for an irrelevant and superficial reason, suspicion of mainstream society may develop. It could take time for major, long term characteristics of a society to reverse themselves, even if "official" reversal has already occurred.
Having said that, my overwhelming concern is political creationism and science denial. Most humans will have supernatural and "spiritual" beliefs for the foreseeable future. I lived in NM for two years, and nothing to do with crystals, pyramids, aliens, or anything else ever had any negative impact on me.
The vast, overwhelming majority of political efforts to jam creationism into schools, to elect or appoint science deniers to powerful positions, and to attack public education in general or on specifics, clearly come from a political party, the Republican party, that does not get much support from any definable minority population. A sole exception may be Cuban-Americans if looked at separately, and that trend is changing. Another old "ethnic" Republican block used to be, ironically, Arab-Americans. That changed in recent elections.
These are just facts. As I have stated many times, I understand that some science supporters are conservative on some other issues. I understand that a few people are left in the Republican party who don't pander full time to religious extremism. On the other hand, the recent DADT vote gives a good estimate of how many do.
That's the way it is, and the minute that a Democrat, or someone claiming to be "progressive" or "liberal", proposes specific rights-violating religious indoctrination at taxpayer expense in public schools, I will condemn that person equally. Right now that isn't that case.
raven · 22 December 2010
OgreMkV · 22 December 2010
I agree.
I had a student, who after taking notes and asking some good questions about phospors and fluorescence, then said, "The ghosts light up the TV in my room, even when it's not on."
It's a difficult circle to break.
OgreMkV · 22 December 2010
ben · 22 December 2010
JGB · 22 December 2010
I do agree that in many minority communities there is a strong undercurrent of not doing good in school for the sake of whatever. That does make it a slightly different problem than religious indoctrination. I was particularly thinking of Hispanic population with the strong history of Catholicism.
I believe at the root of it that the Black Night article identified the central problem. It's not purely anti-scientific, it's a straightforward inability to reason. They need to be taught logical reasoning across all of the disciplines, so that they are equipped to sort out the noise from the good stuff. All to often students come to adopt a weird quasi-relativistic thinking. Basically I have the right to believe whatever nonsense I wish, and since I have the right it's therefore OK to believe whatever nonsense without any notion of the idea that we can look deeper for answers, and that looking for answers across all subject matter has produced human advance. It's a very sloppy lazy attitude, which is what makes it so hard to dislodge.
raven · 22 December 2010
raven · 22 December 2010
nmgirl · 22 December 2010
I had questions about the black night article also, how to start teaching scientific fundamentals in elementary school? But I think the answer is in teaching kids to reason, how to evaluate what they read, see or hear. This would not only help in science but also in financial literacy, nutrition etc.
Kids have the inherent ability to start separating fantasy from reality, as in when they quit believing in santa claus. But many people never get past that point and they believe things like Madoff's perfect record or the risk free investment that pays 20%.
I was laughing yesterday at an ad for a "healthy" green tea drink. Green tea is the 5th listed ingredient after 3 kinds of sugar and water. Too many people can't read and understand that label. They need to learn reasoning skills.
eric · 22 December 2010
Good Science article. I think its interesting that 'essentiality' was independent of age; this would imply that the rate at which new genes are produced is much slower than the rate at which they evolve in terms of function once they are produced. (Or to put it a different way, evolution of function is relatively rapid once a new gene appears.)
There were also a couple of paragraphs in there that seem to support the 'hourglass' studies in earlier PT posts, because (my albeit layman's reading) seems to indicate that the new genes primarily impact late development. If true, that would have the effect of making the young end of the hourglass wider. However, I'm not really familiar with the names of all the stages so I could be wrong about that.
RBH · 22 December 2010
Joe Felsenstein · 22 December 2010
Joe Felsenstein · 22 December 2010
SteveF · 23 December 2010
Incidentally, the latest in the "evolution is mathematically impossible" series is out, this time from Doug Axe. It is a critique of Michael Lynch's latest work (though not his most recent paper), that eventually turns into evolution is basically useless.
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.4
mrg · 23 December 2010
harold · 23 December 2010
Joe Felsenstein -
I keep trying not to write this depressing message.
I was more or less raised going to a fairly honest, decent, non-traumatizing old fashioned Baptist church - literally a simple old wooden church with a congregation who were very tolerant and welcoming, but tended on an individual level to never drink, gamble, dance, swear, to always observe the Sabbath and say grace before every meal, and so on. Creationism had nothing to do with it; it just didn't come up one way or the other. So I know traditional old time Protestantism, and post-modern creationism is not it.
Basically, the reason no-one wants to hear about science in a Christine O'Donnell church is because they're a bunch of post-modern right wing narcissists who "shopped" for a church that told them what they already wanted to hear. If a church challenged them to develop in any way, they'd be out of their seats screaming in the minister's face.
They're not listening to evolution denial because their grandfather's grandfathers observed that ritual and it gives meaning to some community. They're listening to it because it's part of a package that they already wanted. They want Fox News reality. The creationism is just there as a means of dismissing any conventional ethical criticism. Stupid pope or professor says we should be concerned about the disadvantaged? They're going to Hell for not accepting certain very limited passages of the King James Bible, typically taken out of context, as "literally" true. They can be ignored.
Science in general is also disliked by this crowd, as I mentioned on the BW, because it doesn't tell you what you "should" do, but it does kind of remind you of what might happen if you do certain things, and that alone is unacceptable.
Joe Felsenstein · 23 December 2010
OgreMkV · 23 December 2010
Sounds like a good idea for a website: "Is Creationism True?"
I'll write an article or two, and I promise to be nice.
RBH · 24 December 2010
OgreMkV · 24 December 2010
Stuart Weinstein · 24 December 2010
fnxtr · 25 December 2010
Frank J · 26 December 2010
Apologies for continuing the tangent onto Smith's article, and apologies if this has been covered in a previous comment. But Smith wrote what I think is essential, if not sufficient, to winning over the millions who are not so invested in their fairy tales that they are beyond hope.
When someone parrots a line that implies a conspiracy, Smith recommends answering:
"So let me get this straight - for completely mysterious reasons, the entire international biological community has perpetuated a cover-up of historical proportions for the last 150 years?"
Or when they parrot a line that implies that scientists just don't understand their subject, Smith recommends answering:
"So the idea is that this flaw is so obvious that anyone who spends a few minutes
reading material online can perceive it clearly, but sincere and thoughtful people who
spend decades of their lives studying evolution all somehow miss it?"
The scam artists will Gish-gallop their way out of it, of course, and many evolution-deniers will effectively "cover their ears and say '"la la la'." But many others, especially the ones who claim to be "open-minded," will think twice before making such baseless implications again.
Frank J · 26 December 2010
Daniel J. Andrews · 26 December 2010
Daniel J. Andrews · 26 December 2010
Sorry--blockquote fail. That first paragraph is a quote from Mike's post.
mrg · 26 December 2010
Kris · 31 December 2010
Malchus · 31 December 2010
Kris · 31 December 2010
Malchus · 31 December 2010
mrg · 31 December 2010
Malchus · 31 December 2010
mrg · 31 December 2010
Malchus · 31 December 2010
DS · 31 December 2010
Malchus wrote:
"But what they “badmouth” are specific scientific conclusions, not science itself as a process."
That's like saying that you respect the law, at least the good laws. The bad ones you are free to reject and then they just don't apply to you. It just makes a mockery of the entire process. If you really do respect the law, you try to work within the system in order to make the laws asa just as possible. You can't just ignore the laws you don't like and expect that anyone will view you as anything more than a common criminal.
That's like saying that you only trust the doctor when he tells you that there is nothing wrong with you. If he tells you otherwise, you are free to ignore him because he is obviously a quack.
That's like saying that you only agree with the tax man when he says you don't owe the government any money. If he says otherwise he is obviously mistaken and should just be ignored.
Likewise with science, You can't just pick and choose which conclusions you are willing to accept and which you reject for no good reason other than you don't like them. If you think that a paper is in error, you are free to publish a rebuttal. If you think than more data is needed, you are free to collect and publish that data. Denying evidence because of religious presuppositions makes a mockery of the entire process of science. That is not a logical or tenable position for anyone to take. That is not respect for science, that is just the opposite.
Malchus · 31 December 2010
Mike Elzinga · 1 January 2011
Kris · 1 January 2011
Kris · 1 January 2011
mrg · 1 January 2011
I notice more people here are declaring that they Will Not Feed The Trolls. I would like to float an idea that it would be a good idea to get into the habit of simply commenting on troll postings:
DNFTT
-- and nothing else. Everybody has an inclination to FTT and some people insist on it, but if DNFTT were posted to every troll posting it would be a reminder to the first folks and a suggestion to the second.
Science Avenger · 1 January 2011
Malchus · 1 January 2011
Kris · 2 January 2011
mrg · 2 January 2011
Kris · 3 January 2011
Small business bloke · 9 January 2011
Very nice summary, score one evolutionists.