Why? Because Jerry Coyne can mention this amazing conference, I can take a look at the luminaries speaking at it, and decide at the drop of a hat that I’m going. So this weekend, I’ll be spending my Halloween at a major conference on evolution. Yay!
Look forward to lots of liveblogging (I hope…if they have wi-fi in the conference halls. If not, there will be some massive data dumps in the evenings.)
Oh, look. A homeopath explains physics to us all.
I’m sorry. Did I break your brain?
Here’s a non-homeopathic cure. It takes an hour of Lawrence Krauss to counter 8 minutes of that kind of lunacy, I’m afraid.
Here’s a good science blog you can help: Biofortified, a group blog on plant genetics and genetic engineering (and, by the way, Sb’s recent addition, Pamela Ronald, is part of the team). They are in a contest to win a small cash grant and an interview with Michael Pollan, and this group is thoroughly deserving — Biofortified is kind of the Panda’s Thumb of plant genetic engineering.
Unfortunately, they’re in second place right now, trailing an anti-genetic engineering, industry sponsored site, and they need more votes to win. You can help out!
To do so, though, is a little more cumbersome than simply clicking on an online poll, I’m sorry to say. You need to register with the contest site, and then click on an entry in an online poll. It’s not too hard, though, especially since Biofortified provides step-by-step instructions. You don’t have much time, with only one day left to vote. Register, then vote for Biofortified!
David Sloan Wilson certainly got a warm and appropriate welcome here. His first post was titled Science as a Religion that Worships Truth as its God, a phrase that purées together both “religion” and “science” with “truth” as a wickedly wielded whisk, and immediately set a number of people on edge. Eric Michael Johnson jumped on it, as did Henry Gee (I know he irritated many of the regulars here last time he dropped by, but trust me, sometimes he does say smart things). Gee, in particular, succinctly corrected the title to be “Science as a Religion that Worships Doubt as its God”, which is much better. It’s still a bit confused.
Science isn’t a religion, period. It doesn’t worship anything. Science is a toolbox, and if you must stretch the metaphor even further, doubt is the crowbar we use to get at useful answers…but again, we don’t worship the crowbar. We admire it, can ooh and aaah over a particularly well-tricked-out crowbar, and we can relish opportunities to swing it, but it never, ever assumes the role of religion in our our lives.
David Sloan Wilson is going to fit right in. He’s giving everyone an excuse to swing their crowbars.
It’s yet another transitional fossil! Are you tired of them yet?
Darwinopterus modularis is a very pretty fossil of a Jurassic pterosaur, which also reveals some interesting modes of evolution; modes that I daresay are indicative of significant processes in development, although this work is not a developmental study (I wish…having some pterosaur embryos would be exciting). Here it is, one gorgeous animal.
One important general fact you need to understand to grasp the significance of this specimen: Mesozoic flying reptiles are not all alike! There are two broad groups that can be distinguished by some consistent morphological characters.
The pterosaurs are the older of the two groups, appearing in the late Triassic. They tend to have relatively short skulls with several distinct openings, long cervical (neck) ribs, a short metacarpus (like the palm or sole of the foot), a long tail (with some exceptions), and an expanded flight membrane suspended between the hind limbs, called the cruropatagium. They tend to be small to medium-sized.
The pterodactyls are a more derived group that appear in the late Jurassic. Their skulls are long and low, and have a single large opening in front of the eyes, instead of two. Those neck ribs are gone or reduced, they have a long metacarpus and short tails, and they’ve greatly reduced the cruropatagium. Some of the pterodactyls grew to a huge size.
Here’s a snapshot of their distribution in time and phylogenetic relationships. The pterosaurs are in red, and the pterodactyls are in blue.
Darwinopterus is in there, too—it’s the small purple box numbered “7”. You can see from this diagram that it is a pterosaur in a very interesting position, just off the branch that gave rise to the pterodactyls. How it got there is interesting, too: it’s basically a pterosaur body with the head of a pterodactyl. Literally. The authors of this work carried out multiple phylogenetic analyses, and if they left the head out of the data, the computer would spit out the conclusion that this was a pterosaur; if they left the body out and just analyzed the skull, the computer would declare it a pterodactyl.
What does this tell us about evolution in general? That it can be modular. The transitional form between two species isn’t necessarily a simple intermediate between the two in all characters, but may be a mosaic: the anatomy may be a mix of pieces that resemble one species more than the other. In this case, what happened in the evolution of the pterodactyls was that first a pterodactyl-like skull evolved in a pterosaur lineage, and that was successful; later, the proto-pterodactyls added the post-cranial specializations. Not everything happened all at once, but stepwise.
This should be a familiar concept. In pterodactyls, skulls evolved a specialized morphology first, and the body was shaped by evolutionary processes later. We can see a similar principle in operation in the hominid lineage, too, but switched around. We evolved bipedalism first, in species like Ardipithecus and Australopithecus, and the specializations of our skull (to contain that big brain of which we are so proud) came along later.
As I mentioned at the beginning, this is an example of development and evolution in congruence. We do find modularity in developmental process — we have genetic circuits that are expressed in tissue- and region-specific ways in development. We can talk about patterns of gene expression that follow independent programs to build regions of the body, under the control of regional patterning genes like the Hox complex. In that sense, what we see in Darwinopterus is completely unsurprising.
What is interesting, though, is that these modules, which we’re used to seeing within the finer-grained process of development, also retain enough coherence and autonomy to be visible at the level of macroevolutionary change. It caters to my biases that we shouldn’t just pretend that all the details of development are plastic enough to be averaged out, or that the underlying ontogenetic processes will be overwhelmed by the exigencies of environmental factors, like selection. Development matters — it shapes the direction evolution can take.
Lü J, Unwin DM, Jin X, Liu Y, Ji Q (2009) Evidence for modular evolution in a long-tailed pterosaur with a pterodactyloid skull. Proc. R. Soc. B published online 14 October 2009 doi: 10.1098/rspb.2009.1603
I should have mentioned that Darren Naish has a very thorough write-up on Darwinopterus!
OK, I confess: I completely lack the tools and background to evaluate this claim:
A pair of otherwise distinguished physicists have suggested that the hypothesized Higgs boson, which physicists hope to produce with the collider, might be so abhorrent to nature that its creation would ripple backward through time and stop the collider before it could make one, like a time traveler who goes back in time to kill his grandfather.
Except for one thing: the proponents of this idea are operating in the world of pure speculation, and have no evidence to support it, yet. That tells me that I’m best off provisionally rejecting it. I’ll start incorporating crazy counter-intuitive notions about the nature of the universe when the cold implacable hand of the universe starts shoving them down my throat, not before!
Perhaps you are a scientist. And perhaps you have wondered how badly the popular press could possibly mangle your research. Wonder no more: we have discovered a new maximum.
Behold this research summary in The Daily Galaxy, and be amazed!
It’s about a paper in the ACS Journal of Physical Chemistry B. It’s straightforward physical chemistry using some cool tools to image the formation of double helices of DNA: it’s simply addressing the question of how complementary strands align themselves in solution. It’s physical chemistry, OK? It’s about tiny molecular interactions…until the Daily Galaxy gets ahold of it. Now it’s about how DNA uses telepathy.
DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to. Explanation: None, at least not yet.
Scientists are reporting evidence that contrary to our current beliefs about what is possible, intact double-stranded DNA has the “amazing” ability to recognize similarities in other DNA strands from a distance. Somehow they are able to identify one another, and the tiny bits of genetic material tend to congregate with similar DNA. The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.
…
In the study, scientists observed the behavior of fluorescently tagged DNA strands placed in water that contained no proteins or other material that could interfere with the experiment. Strands with identical nucleotide sequences were about twice as likely to gather together as DNA strands with different sequences. No one knows how individual DNA strands could possibly be communicating in this way, yet somehow they do. The “telepathic” effect is a source of wonder and amazement for scientists.
Cue the theremins, everyone, and bring on the reanimated corpse of Rod Serling to narrate this sucker. Audience, say “OOOOOoooooOOOOOOOOooOOH!”
Oh, wait. Read the actual paper, first. It turns out that not only are the scientists not mystified, but they provide a reasonable explanation for the phenomenon, and go on to give some alternatives, even. None of them involve molecular telepathy. They actually are amazed at the ability of these molecules to align…at distances of one whole nanometer!
Pay especially careful to the first sentence of the following paragraph. If you are a journalist writing a summary of a paper, claiming that it says no one knows how the two molecules recognize each other, you should probably read more closely a paragraph that begins, “We hypothesize that the origin of this recognition may be as follows.” It’s a clue that an explanation will follow.
We hypothesize that the origin of this recognition may be as follows. In-register alignment of phosphate strands with grooves on opposing DNA minimizes unfavorable electrostatic interactions between the negatively charged phosphates and maximizes favorable interactions of phosphates with bound counterions. DNAs with identical sequences will have the same structure and will stay in register over any juxtaposition length. Nonhomologous DNAs will have uncorrelated sequence-dependent variations in the local pitch that will disrupt the register over large juxtaposition length. The register may be restored at the expense of torsional deformation, but the deformation cost will still make juxtaposition of nonhomologous DNAs unfavorable. The sequence recognition energy, calculated from the corresponding theory is consistent with the observed segregation within the existing uncertainties in the theoretical and experimental parameters. This energy is ˜1 kT under the conditions utilized for the present study, but it is predicted to be significantly amplified, for example, at closer separations, at lower ionic strength, and in the presence of DNA condensing counterions.
So, their preferred explanation is that there are electrostatic interactions between the molecules that favor pairs that fit together well. Not telepathy. As cautious investigators, they also suggest some alternative explanations; perhaps telepathy will appear here? Or maybe elves?
Presently, we cannot exclude other mechanisms for the observed segregation. For instance, sequence-dependent bending of double helices may also lead to homology recognition by affecting the strand-groove register of two DNA molecules in juxtaposition. The juxtaposition of bent, nonhomologous DNAs may also be less energetically favorable under osmotic stress, since it may reduce the packing density of spherulites. In addition, formation of local single-stranded bubbles and base flipping may cause transient cross-hybridization between the molecules, as proposed to explain Mg2+ induced self-assembly of DNA fragments with the same sequence and length. We consider it to be rather unlikely in this instance, since the probability of bubble formation in unstressed linear DNA of the studied length is very small in contrast to the case where topological strain is relieved by bubble formation in small circular DNA molecules. Furthermore, bubble formation would distort the cholesteric order of spherulites and we see no evidence of this in spherulites composed of a single type of DNA molecule.
I’m so disappointed. Telepathy isn’t mentioned once in the whole danged paper, and there aren’t even tiny diaphanous fairies tugging at the molecules. And no, the Intelligent Designer doesn’t appear, either.
Baldwin GS, Brooks NJ, Robson RE, Wynveen A, Goldar A, Leikin S, Seddon JM, Kornyshev AA (2008) DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment. J. Phys. Chem. B 112(4):1060-1064.
Josh Timonen has put up a video of my talk at AAI. Tear into it!
One of the things I neglected to say more clearly, but should have, is that what I’m complaining about is the creationists’ blithe conflation of complexity with order. We can build up immense amounts of complexity from nothing but noise, so just babbling about how complicated something is says nothing about the impossibility of its origin from chance events. Order, functionality, and, as Joe Felsenstein defined it, adaptedness are more relevant properties, and we have a natural mechanism for generating those, too. It’s called selection.
Someone over at the RDF also mentioned that he thought the Q&A was really good, too. I agree — I need to learn to shut up more and just get the interactivity going. Maybe my ideal talk would be 5 minutes of raillery and inflammatory incitement, followed by 55 minutes of questions and comments.
Nicholas Wade has a very peculiar review of Richard Dawkins’ book, The Greatest Show on Earth, in the NY Times Review of Books. It’s strange because it is a positive review which strongly agrees with Dawkins’ position on the central importance of the theory of evolution in biology in the first half…but the second half is a jaw-droppingly stupid attack on a small point in the book. Wade has a very absolutist and wrong view of the definitions of some terms, and he goes on and on, whining about a topic that he doesn’t understand himself.
There is one point on which I believe Dawkins gets tripped up by his zeal. To refute the creationists, who like to dismiss evolution as “just a theory,” he keeps insisting that evolution is an undeniable fact. A moment’s reflection reveals the problem: we don’t speak of Darwin’s fact of evolution. So is evolution a fact or a theory? On this question, Dawkins, to use an English expression, gets his knickers in a twist.
Oh, man. Wade has really waded into it. This is a subject that has been amply discussed and explained and expounded upon, and I’m surprised that Wade is not only unfamiliar with it, but has thrown away half of his review in a misbegotten error of his own devising. Take it away, Stephen J. Gould:
In the American vernacular, “theory” often means “imperfect fact”—part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus the power of the creationist argument: evolution is “only” a theory and intense debate now rages about many aspects of the theory. If evolution is worse than a fact, and scientists can’t even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): “Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science–that is, not believed in the scientific community to be as infallible as it once was.”
Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world’s data. Theories are structures of ideas that explain and interpret facts. Facts don’t go away when scientists debate rival theories to explain them. Einstein’s theory of gravitation replaced Newton’s in this century, but apples didn’t suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin’s proposed mechanism or by some other yet to be discovered.
Moreover, “fact” doesn’t mean “absolute certainty”; there ain’t no such animal in an exciting and complex world. The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us falsely for a style of argument that they themselves favor). In science “fact” can only mean “confirmed to such a degree that it would be perverse to withhold provisional consent.” I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
Evolutionists have been very clear about this distinction of fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred. Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory–natural selection–to explain the mechanism of evolution.
If he’d just written that one little paragraph, it would have been mildly embarrassing for him…but he just keeps stuffing his foot down his throat. It’s a good thing he keeps his pants on to hide the spectacle of his shoe poking out of his butt.
He [Dawkins] seems to have little appreciation for the cognitive structure of science. Philosophers of science, who are the arbiters of such issues, say science consists largely of facts, laws and theories. The facts are the facts, the laws summarize the regularities in the facts, and the theories explain the laws. Evolution can fall into only of of these categories, and it’s a theory.
Whoa. Scientists everywhere are doing a spit-take at those words. Philosophers, sweet as they may be, are most definitely not the “arbiters” of the cognitive structure of science. They are more like interested spectators, running alongside the locomotive of science, playing catch-up in order to figure out what it is doing, and occasionally shouting words of advice to the engineer, who might sometimes nod in interested agreement but is more likely to shrug and ignore the wacky academics with all the longwinded discourses. Personally, I think the philosophy of science is interesting stuff, and can surprise me with insights, but science is a much more pragmatic operation that doesn’t do a lot of self-reflection.
As for his definitions…sorry, but these ideas simply do not fit into the tidy pigeonholes Mr Wade wants to make for them. Evolution is both a fact and a theory. Trying to cram it into one category does violence to both evolution and his cognitive roll-top desk.
And Wade goes on with more! Here’s where we really need philosophers; they could have much more fun shredding the blithe assumptions Wade flings about.
Other systems of thought, like religion, are founded on immutable dogma, whereas science changes to accommodate new knowledge. So what part of science is it that changes during intellectual revolutions? Not the facts, one hopes, or the laws. It’s the highest level elements in the cognitive structure—the theories—that are sacrificed when fundamental change is needed. Ptolemaic theory yielded when astronomers found that Copernicus’s better explained the observations; Newton’s theory of gravitation turned out to be a special case of Einstein’s.
If a theory by nature is liable to change, it cannot be considered absolutely true. A theory, however strongly you believe in it, inherently holds a small question mark. The minute you erase the question mark, you’ve got yourself a dogma.
I don’t even like his dig at religion. There’s a funny thing about religious dogma: it evolves. It changes slowly, usually, and it’s not on the basis of reason or evidence, but more often to bend to popular expediency — I’d agree that it isn’t knowledge that changes it, but the utility of accommodating a human institution to popular perception.
I kind of agree with the general statement that facts won’t change (but as I’ll say below, the facts do shift as they are argued over), but it is possible to change the conceptual framework, the theories, we use to integrate a collection of facts into a useful model in our brains. It is entirely possible for a new model to emerge that does a better job of explaining the history of life on earth someday. After all, it’s already happened, and look, Darwin’s theory still remained a fact!
Darwin’s theory was expanded and replace roughly 70-75 years ago, with the incorporation of the science of genetics into that framework. Darwin was working with a seriously flawed idea of heredity, and all his ideas about the transmission of traits were wrong. Pangenesis was completely scrapped and replaced with Mendelian and population genetics. I can’t imagine a more radical change than that happening any time in the future — we have a solid grip on the rules of heredity now, and what we expect is refinement and the addition of details.
But notice that what happened was a reversal of Wade’s claim. A massive bolus of ‘facts’ were inserted into the theory, but the core of the theory itself, the idea that species changed over time driven by forces of selection, remained. Why? BECAUSE THAT IS ALSO A FACT. We have piled evidence high that shows the earth is old, there have been a succession of forms, that the properties of populations change from generation to generation, that all the diverse forms of life on earth are linked by molecular relationships that fit nicely into a tree of descent. A subsidiary assumption that generations changed by the transmission of acquired characters was discarded, but the big picture was unchanged…and was actually made sharper and stronger.
Any future hypothetical theory that is a better model must incorporate these facts of evolution. It’s one of the reasons creationists aren’t doing science, because they are compelled by ideology to reject the evidence. There will be no theory that denies that human beings are apes and the children of apes, no matter how objectionable creationists find that, because that is a fact. We’ll argue over the mechanisms, whether it was selection-driven or mostly chance divergence, whether group selection played a role, over which fossil fits most closely to the main path of the population that led to us, etc., etc., etc., but the fact of our ape ancestry and nature is established.
One more quibble: Wade insists that every theory must retain that little question mark of doubt, and that is true. However, it also holds true for the facts of science; we can have a fair amount of confidence in the data, but no one considers a published result to be unquestionable. It happens all the time that different labs will wrestle over the data, and the interpretation of the data. It’s one of the factors that drives science, that we work hard to confirm and disconfirm everything. What you’ll actually find when you look at the daily routine of science is that the theories are generally stable and are not strongly questioned — it takes such a massive amount of contradicting data to overthrow a theory that it’s hardly likely that your average individual or research group can demolish a major theory like evolution, or cell theory — and most of the haggling and conflict is over the day-to-day details. You know, that stuff that Wade would try to stuff in his pigeon hole labeled “facts”.
Wade concludes his little diversion into fantasy philosophy with a strange dig at Dawkins that suggests he doesn’t like his book much after all.
He [Dawkins] has become the Savonarola of science, condemning the doubters of evolution as “history-deniers” who are “worse than ignorant” and “deluded to the point of perversity. This is not the language of science, or civility. Creationists insist evolution is only a theory, Dawkins that it is only a fact. Neither claim is correct.
True, neither is crorrect…but then, I guarantee you that Dawkins does not consider evolution to be “only a fact.” Only someone who had not read his books with comprehension could come away with this freakish idea that Dawkins is unaware of the “cognitive structure of science.”
I agree that Dawkins’ words are relatively uncivil, but I’d argue that they’re too civil, and that we need more incivility. Wade does not seem to agree that creationists deny the depth of human history (I don’t understand how he could find fault with the FACT that believing the world is 6000 years old requires blindness to 13 billion years worth of time), or that by promoting false beliefs about our origins they are not merely passively unaware, but are malevolently ignorant, or that using Gould’s definition of a fact, they are in denial “to such a degree that it would be perverse to withhold provisional consent.” Those are the facts that Mr Wade claims to be able to recognize, but ignores in this case.
I also will not accept sad tut-tutting over a lack of civility when Wade so obliviously compares Richard Dawkins to Savonarola. Savonarola? Really? You compare a gentlemanly scholar who writes books to oppose the rising tide of lunacy in the world to a book-burning puritanical fanatic who opposed the Renaissance and sought the death of homosexuals??
Hypocrite.
The Digital Cuttlefish tells me in rhyme that a new ring has been discovered around Saturn, a huge (13 million km radius) but low density cloud of dust that is responsible for splattering Iapetus with dark material. Very cool.
The Cuttlefish also informed me that lazy ol’ Phil Plait hasn’t covered it yet because he’s distracted with some TAM in London, so how could I resist scooping him?
