Just found a follow-up email from Science Debate 2008, reporting that previously planned cuts to science funding in the still-under-debate economic stimulus bill have been reduced or withdrawn. Still no obvious coverage on ScienceDebate2008.com, which is frankly weird.
Category Archives: science
Dear Senator
Sheesh. Of course science is the first thing they try to cut from the pending stimulus bill. Text free for the taking to anyone who wants to pester their congresscritters – which you should, if you care about science in the U.S.
OK, so it gets a little melodramatic at the end there, but I’m trying for impact. Edit as you see fit – individualized letters are more likely to have an impact.
Dear Senator,
I’m a graduate student in biology at the University of Idaho, and I’m writing to ask that you support President Obama’s stimulus plan, with full funding for basic scientific research.
Science and technology – the fruits of basic scientific research funded by the National Science Foundation, National Institutes of Health, and other government scientific agencies – are responsible for half of all U.S. economic growth since World War II. Yet today, after years of virtually no increases in basic research funding, laboratories across the country are at risk of shutting down, with untold consequences for our long-term competitiveness in the global economy.
Basic research makes economic sense over the short term, too – with the increase in funding proposed in the stimulus bill, granting agencies would immediately be able to fund more of the grant requests they’re considering right now. That’s money to pay lab staff, and buy reagents and equipment – most often from American companies like Thermo Fisher and Qiagen.
For these reasons, the stimulus bill before the Senate originally contained vital increases in basic scientific research funding. Now, however, a group of senators, including Susan Collins and Ben Nelson, are proposing cuts to the stimulus bill that would eliminate much – and in the case of NSF, all – funding for science. Considering what a tiny portion of the bill’s proposed spending was already devoted to science funding, and the immediate and long-term value it would have brought our economy, this is a shortsighted idea at best.
So I hope you will give full support to President Obama’s stimulus bill, and reject the Collins-Nelson cuts in science funding. The scientific and economic future of our nation depend on this.
regards,
Jeremy B. Yoder
[I should also note that the talking points above come from an email sent out by Shawn Otto over the ScienceDebate2008 e-mail list; I can’t find coverage of this issue on the SD2008 site, however.]
Draft Neanderthal genome next week
Nature News reports that the first complete genome sequence for a Neanderthal will be released, appropriately enough, on next Thursday, the 12th of February, and the 200th anniversary of Charles Darwin’s birth. It’s the same group at the Max Planck Institute that released the first million bases of Neanderthal nuclear and mitochondrial DNA sequence [$-a] back in 2006. As in the earlier work, the new data were collected with a “454” next-generation DNA sequencer.
The earlier publication, which I just read this week as part of a reading group focused on next-generation sequencing technology, was more like a stunt than a groundbreaking result in evolutionary genetics. The actual results were two new estimates of the human/Neanderthal divergence times (basically confirming earlier estimates), and a coalescent estimate of the effective population size of the common ancestor, neither of which would be worth a whole paper, let alone a letter to Nature.
But it was pretty awesome just as a stunt – at every step of the analysis, the authors did some clever error checking by comparing the Neanderthal sequence to human and chimpanzee genomes, and they came up with actual nuclear sequence data from a freaking Neanderthal. Ahem. The collection of an entire Neanderthal genome is a big deal as a stunt, but I’ll look forward to seeing what new insight into human evolution comes out of it.
Reference
R.E. Green, J.Krause, S.E. Ptak, A.W. Briggs, M.T. Ronan, J.F. Simons, L. Du, M. Egholm, J.M. Rothberg, M. Paunovic, S. Pääbo (2006). Analysis of one million base pairs of Neanderthal DNA Nature, 444 (7117), 330-6 DOI: 10.1038/nature05336
Evolution 2009: Evolution will be blogged
An advantage of being in charge of the website for Evolution 2009, the joint annual convention of the American Society of Naturalists, Society of Systematic Biologists, and Society for the Study of Evolution: when I suggest that we ought to do something to involve science bloggers in the conference, I get to set it up. Or maybe that’s actually a disadvantage.
In any event, we’re experimenting with a blogswarm for this year’s conference – if you’re attending the conference and think you’d like to ‘blog about it, or just want to help spread the word, head over to the just-posted blogging page, download a badge to put on your site (see my sidebar, and the inset on this post, for examples), and drop me an e-mail so I can add your URL to the list of participating science blogs. I’m also interested in suggestions, both conceptual and technical, for how to improve the resources at that page, which currently consist of a small selection of logo badges, and the list of participants – I’d particularly like to try aggregating relevant posts from participating blogs into a single RSS feed.
With blogging becoming more common as a way to educate the public and converse with other scientists, I hope this will improve Evolution’s profile outside academic biology and facilitate conversation among attendees before, during, and after the conference. Also, as a colleague (who shall remain nameless) pointed out, this should make it easier to organize the kegger.
Reference
S.A. Batts, N.J. Anthis, T.C. Smith (2008). Advancing science through conversations: Bridging the gap between blogs and the academy. PLoS Biology, 6 (9) DOI: 10.1371/journal.pbio.0060240
Science, blogged
Another example of how blogging can be great for science, both as public education and as communication among scientists: The Open Source Paleontologist Andrew Farke first walks his readers through his nifty new study of skull injuries in Triceratops, which suggests that their horns were used for combat (as opposed to mere display), then follows up with a post detailing the open-source technologies behind the paper.
This is better, to my mind, than whatever coverage the New York Times science section can give Farke’s result. Farke links directly to the PLoS-published paper – mainstream science coverage tells me the journal, at best, and leaves me to ferret out the paper myself. (It’s not that much work, but I’m lazy.) I can read the author’s own explanation of the result, and post comments to ask for clarification, which better approximates the experience at a conference. And, as a bonus, I learn about some ways I can improve my own, very non-paleontological, work: Zotero, for instance, looks well worth a try.
Arrested development, and reproductive incompatibility, from duplicate genes
Speciation isn’t something that evolution sets out to do – it just sort of happens. One day, a species colonizes two sides of a river, say, migration across the river drops off, and then a few million years of genetic drift later, there are two species where once there was one. The question is, what’s the final genetic change that makes the accident of speciation irrevocable?
A paper in this week’s Science pinpoints exactly that change. Bikard and coauthors report that, in the little flowering plant Arabidopsis thaliana (the plant world’s answer to white lab mice and Drosophila fruit flies), it only takes one duplicated gene to finalize speciation [$-a]. It’s a clear-cut case of a classic speciation scenario, Bateson–Dobzhansky–Muller incompatibility.
It all comes down to gene duplication, which I’ve discussed before in the context of the trouble it gives to genetic analysis. Making copies of an entire genome is an error-prone process, and sometimes a whole gene gets duplicated twice. If that extra copy is inherited, it means that the carrier has redundant coding for whatever the original gene does – so now one copy can mutate without affecting its carrier’s fitness. Often this just results in loss of function for the mutating copy – sometimes it leads to new gene functions. In Arabidopsis, it’s lead to reproductive incompatibility between two strains of the plant that took different evolutionary paths.
Bikard et al. noticed that, when they crossed two strains of Arabidopsis, the resulting seeds didn’t include every possible combination of the parental strains’ genes – and a few seeds grew short, not-quite-healthy looking roots when germinated. Some of the hybrid seeds just died in mid-development. With a lot more controlled crosses, the authors narrowed the candidate genes down to a pair that normally work together in synthesizing the essential amino acid histidine. Each of the two parental strains had working copies of the two genes – but when you crossed them, sometimes the seeds couldn’t produce histidine, and so they snuffed it.
This looked like the above-mentioned (and awkwardly named) Bateson-Dobzhansky-Muller incompatibility [$-a], which is an old idea about how populations evolve reproductive incompatibilities to become separate species. Under B-D-M incompatibility, a new gene evolves in one population that doesn’t work if it interacts with genes from the other. Imagine if Windows users didn’t have to share documents with Mac users: as the two operating systems went through multiple redesigns and their respective versions of Microsoft Office(TM) were revised to keep up, it might no longer be possible to read a Mac-written Word document on a Windows machine.
Here, as Bikard et al. showed, one of the histidine-producing genes in Arabidopsis was accidentally duplicated – and one copy mutated into non-functionality. The catch is that, in the two partially incompatible strains, different copies went nonfunctional. So now, when the two lines are crossed, a small fraction of the seeds produced get nonfunctional copies of the duplicated gene. They die. And where once there were two strains of Arabidopsis thaliana, there’s something a little more like two separate species, all because of what boils down to the flip of a coin.
References
D. Bikard, D. Patel, C. Le Mette, V. Giorgi, C. Camilleri, M.J. Bennett, O. Loudet (2009). Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana Science, 323 (5914), 623-6 DOI: 10.1126/science.1165917
K. Bomblies, D Weigel (2007). Arabidopsis — a model genus for speciation Current Op. Genet. & Dev., 17 (6), 500-4 DOI: 10.1016/j.gde.2007.09.006
Morality and empiricism
Jerry Coyne reviews two new books, Kenneth Miller’s Only a Theory and Karl Giberson’s Saving Darwin that vivisect the Intelligent Design movement, and seek to explain how Christianity (or indeed, any faith) is not only compatible with but complimentary to the scientific worldview. Coyne is effusive in praise of Miller and Giberson’s science, but he doesn’t buy their theology:
True, there are religious scientists and Darwinian churchgoers. But this does not mean that faith and science are compatible, except in the trivial sense that both attitudes can be simultaneously embraced by a single human mind. (It is like saying that marriage and adultery are compatible because some married people are adulterers.) It is also true that some of the tensions disappear when the literal reading of the Bible is renounced, as it is by all but the most primitive of JudeoChristian sensibilities. But tension remains.
Miller and Giberson make the same fundamental mistake that creationists do, says Coyne, when they look for God in the empirical world.
[To Miller], God is a Mover of Electrons, deliberately keeping his incursions into nature so subtle that they’re invisible. It is baffling that Miller, who comes up with the most technically astute arguments against irreducible complexity, can in the end wind up touting God’s micro-editing of DNA. This argument is in fact identical to that of Michael Behe, the ID advocate against whom Miller testified in the Harrisburg trial. It is another God-of-the-gaps argument, except that this time the gaps are tiny.
I haven’t read either of the books in question (I’m putting them in my queue after Dreams from My Father), but this does sound like a complaint I’ve previously had with prominent scientists who try to reconcile faith and science by direct, causal connections. It seems plain enough to me that a Christian who accepts science must also accept that God is the ultimate in untestable hypotheses, and no amount of speculation about the Anthropic Principle can change this. Furthermore, I think we need to reconcile ourselves to the idea that Homo sapiens might not be the only thing on God’s mind, as it were.
This line of thought draws mockery from fundamentalists on both sides of the religion-science schism. A six-day creationist I met with a few months ago condescended to tell me that, if I wouldn’t join him in rejecting the very laws of physics (which is what you have to do if you want to believe that Earth is six thousand years old), my faith was nothing but “warm fuzzies.” And in his own response to Coyne’s essay, the atheist PZ Myers jeers that Christianity without biblical literalism is “weak tea.” (Got the Christians coming and going on that one, don’t you, PZ?) But what all of these people are missing is that Christianity, and all religions, are not (or should not be) primarily interested in empirical claims about the physical universe. They’re about how humans can best live with each other.
The essence of Christianity, the absolute core of what it means to follow Christ, is a few revolutionary teachings, and one extraordinary act. “Love your enemies,” Jesus taught his disciples, calling them to a moral standard above and beyond the bonds of family, tribe, or nation. And when the Roman government and its local collaborators got nervous about his popularity and executed him as a common criminal, Jesus embodied that moral standard at the cost of his life. You can quibble with every factual claim in the Bible, you can cut out everything in the Gospels that smells of the supernatural as Thomas Jefferson famously did, and that’s what’s left: an innocent teacher accepting death at the hands of civil and religious authorities, and thereby revealing them for the fallible, human things that they are. Vicit agnus noster.
Science can (conceivably, at least) account for the entire history of the universe, from the Big Bang to the invention of digital watches by the ape-descended inhabitants of one small, blue-green planet. But in the end, this is just data. Data can’t tell me whether I should tip the barista at my local coffee shop, or stay late to answer a student’s questions on a lab, or give to NPR, or donate blood. But Christ crucified (Mohamed at prayer, Buddha under the Bo tree, Hume at his books) has something to say about it. The human struggle with the moral universe, the core of all religious thought, is the challenge of a lifetime – every lifetime – and the example of Christ is powerful no matter how many days it took to make the Earth.
The cost – and benefits – of hostility to strangers
Bruce Schneier points to an interesting post by Stephen Dubner, who asks why we humans are so prone to fear strangers, given that strangeness is such a poor predictor of dangerousness. Dubner proposes, and Schneier agrees, that it has something to do with our tendency to focus on rare, shocking dangers:
Why do we fear the unknown more than the known? That’s a larger question than I can answer here (not that I’m capable anyway), but it probably has to do with the heuristics — the shortcut guesses — our brains use to solve problems, and the fact that these heuristics rely on the information already stored in our memories.
And what gets stored away? Anomalies — the big, rare, “black swan” events that are so dramatic, so unpredictable, and perhaps world-changing, that they imprint themselves on our memories and con us into thinking of them as typical, or at least likely, whereas in fact they are extraordinarily rare.
That’s probably right. But when I read Dubner’s post, I immediately thought of another factor: hostility toward outsiders is instinctive because it can help communities bond.
This idea actually grew out of an attempt to understand altruism. Altruism is something of a puzzle to evolutionary biologists – the easiest thing to assume, under a “survival of the fittest” framework, is that selfishness is always the winning strategy. Yet again and again in human and nonhuman societies, we see examples of altruism, in which individuals help each other without immediate repayment. Societies in which everyone is altruistic should be able to out-compete societies in which everyone is selfish – but a single selfish person in a mostly altruistic society can out-compete her neighbors, make more selfish babies, and eventually drive altruism to extinction. So, if you can come up with a way to make altruism stable in the long term, you’ve got a good shot at publishing in Science or Nature.
One such paper was published back in 2007. Co-authors Jung-Kyoo Choi and Samuel Bowles noted that tribal human societies spend a lot of time and blood in inter-tribal wars, and wondered if what they called parochialism – hostility to outsiders – helped stabilize within-tribe altruism [$-a]. They built a mathematical model of competing tribes, in which individuals within those tribes had one of four inheritable personality types: parochial altruists, tolerant altruists, parochial nonaltruists, and tolerant nonaltruists. Parochial altruists were something like the medieval ideal of a knight, willing to fight outsiders and die for the benefit of others in their tribe. Parochial nonaltruists weren’t willing to risk their lives for others; and the two tolerant types were, well, tolerant of others.
As I described above, nonaltruists were favored by within-tribe competition: altruists all contributed toward a common resource pool, which was shared among the whole tribe. So nonaltruists got a share, but didn’t contribute, which benefits them but is ultimately bad for the tribe. Tribes that fought other tribes and won could expand their territories and take the losers’ resources. On the other hand, if tribes interact peacefully, the tolerant individuals – and only the tolerant individuals – received a resource reward. (Is this putting anyone else in mind of certain new-school German board games?)
Choi and Bowles found that their model led to two alternative stable kinds of tribe dominated by either tolerant nonaltruists or parochial altruists. This is almost too tidy, because it looks like a dichotomy between peaceful-but-selfish “moderns” and mutually-aiding, warlike “primitives.” Yet tribal societies really do seem to be more prone to a certain kind of war (more like feuding, really), as Jared Diamond discusses in a 2008 essay for the New Yorker [$-a]. And, even in our modern, globalized society, we are immediately and instinctively suspicious of – hostile to – those different from us. Commenting on Choi and Bowles’s paper in the same issue of Science, Holly Arrow called this the “sharp end of altruism,” [$-a] and wondered how to tease apart the apparent association between altruism to neighbors and hostility to outsiders.
The most obvious option may be to expand our definition of “neighbor.” In a world where an Internet user in Malaysia can see (selected portions of) my ramblings on this ‘blog, maybe I’m less of a stranger than I would be otherwise. That’s not much, really, but it’s a start. The wonderful thing about being human is that, understanding our own tendencies, we can seek to overcome them.
References
H. Arrow (2007). EVOLUTION: The sharp end of altruism Science, 318 (5850), 581-2 DOI: 10.1126/science.1150316
J.-K. Choi, S. Bowles (2007). The coevolution of parochial altruism and war Science, 318 (5850), 636-40 DOI: 10.1126/science.1144237
Blogging for Darwin, 12 February 2009
I’ll be joining a long list of science blogs in commemorating Charles Darwin’s two hundredth birthday – only 23 more shopping days left! – as part of the Blog for Darwin blogswarm. (Not sure how I feel about the word “blogswarm,” but I like the concept!) Now: what to write about. There’s a nice list of suggested topics provided, and they only scratch the surface …
Stick insects not so excited about sex, apparently
Stick insects in the genus Timema have evolved asexual reproduction on five different occasions in their evolutionary history, according to a new study in this month’s Evolution [$-a]. Why? Well, it turns out that from an evolutionary perspective, sex isn’t always a good thing.
The problem comes down to the mathematics of evolutionary fitness. Natural selection favors individuals who make more copies of their genes in the next generation – that’s the most basic definition of the “fittest” who survive. In most sexually reproducing organisms, each parent contributes half of the genes necessary to build each offspring. So for every two babies a parent makes with someone else, her genome is replicated once – half for each baby. Consider the possibilities if this parent can instead make a baby all by herself: for each baby, her entire genome is reproduced. That means that, all else being equal, an asexual critter has twice the fitness of a sexual one.
So it makes sense that asexual reproduction might pop up pretty frequently in the evolution of any group, let alone Timema – a mutant who gains the ability to reproduce asexually should be able to overrun a population of sexual competitors with ease. The question turns out to be not, why are some critters asexual? but why are any critters sexual?
One hypothesis is that sex helps in arms races against parasites, by shuffling genes to generate new combinations of defensive traits. This is called the Red Queen hypothesis because the parasite-host arms race recalls the Red Queen’s advice to Alice in Through the Looking Glass, that in looking-glass land, “It takes all the running you can do, to keep in the same place.” Population genetic studies have shown evidence of Red Queen dynamics in some species [$-a], but it’s not clear how widespread they are. Currently, more biologists favor the alternative hypothesis that sex is important in counteracting the Hill-Robertson effect, which prevents useful genes from spreading through a population if they are associated with damaging genes [$-a].
Under either hypothesis, sex is in some sense more useful in the long term than in the short term. That is, an asexual mutant can overrun a population faster than its offspring are killed by parasites or disadvantaged by the Hill-Robertson effect. This conflict should lead to a specific pattern: evolutionary lineages switch to asexuality rapidly if an asexual mutant arises, then die off when parasites or other hazards of natural selection catch up with them. This is what we see in Timema – several species have given up on sex, but all of them have recent sexual ancestors. Not only does giving up sex make life less exciting – it’s probably an evolutionary dead end.
References
M. Dybdahl, A. Storfer (2003). Parasite local adaptation: Red Queen versus Suicide King Trends in Ecology & Evolution, 18 (10), 523-30 DOI: 10.1016/S0169-5347(03)00223-4
P.D. Keightley, S.P. Otto (2006). Interference among deleterious mutations favours sex and recombination in finite populations Nature, 443 (7107), 89-92 DOI: 10.1038/nature05049
T. Schwander, B.J. Crespi (2009). Multiple direct transitions from sexual reproduction to apomictic parthenogenesis in Timema stick insects. Evolution, 63 (1), 84-103 DOI: 10.1111/j.1558-5646.2008.00524.x