Here’s part of an explanation I’ve liked for a long time: they’re a product of developing cognitive processes that bias the brain to model the world with supernatural shortcuts.
(Moved below the fold because the silly video defaults to autoplay.)
I’m liking these CreatureCast videos from Casey Dunn — I showed the first in this series, now here’s the second. It uses very simple animation to illustrate basic concepts…like the evolution of multicellularity in this one.
CreatureCast Episode 2 from Casey Dunn on Vimeo.
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.
