Dances with robots

December 13, 2010 • 2:55 pm

I’m putting this up for no reason other than I find it remarkable—and also a tad creepy (click to enlarge):

The lead singer isn’t human, but a robot—the HRP-4C Gynoid. I swear that when I first saw this video, I thought “she” was a human dressed up and acting like a robot. (The oversized hands were, however, a giveaway.)

According to Technovoigy.com,

HRP-4C is a robotic woman just unveiled to reporters in Tsukuba City (northeast of Tokyo) Japan. This cybernetic human sells for about $200,000.

Developed at the National Institute of Advanced Industrial Science and Technology, the HRP-4C female robot is able walk and follow some basic commands. The robotic woman is about the same size as an average Japanese young woman, at a height of 158 centimeters; it weighs just 43 kilograms (including battery).

Thirty motors in the body help it to walk and move about; eight motors power facial expressions.

and

The dance routine for HRP-4Cwas produced by dancer/choreographer SAM-san, who is a member of the music group TRF, and has worked with numerous well-known artists like SMAP and BoA. The song is a Vocaloid version of “Deatta Koro no Yō ni” (Every Little Thing) by Kaori Mochida.

Here’s a demo video showing her true robotitude:

h/t: Yokohamamama

Meteor shower tonight

December 13, 2010 • 10:26 am

If you’re up for staying up late tonight, National Geographic reports that you can see one of the most spectactular meteor showers of the year: the Geminid shower. It’s best seen in the Northern Hemisphere.

“The quarter moon will obscure the first part of the show, but once it sets after midnight [your local time], the conditions should be ideal,” said Geza Gyuk, an astronomer at the Adler Planetarium in Chicago, Illinois.

“If you can’t stay up that late, then after 10 p.m. is okay too, but the later the better.”

The missed sleep may be worth it: The Geminids have been rising in intensity and brightness, and the upcoming show may outshine the more famous August Persieds as the best meteor shower of 2010.

“The Geminids have been slowly getting better over the past years, making it one of the best showers,” Gyuk said. “And it has become very reliable, so we can expect a fairly nice show.” . .

The Inquisitr reports:

Skygazers can expect as many as 140 shooting stars during the Geminid shower, starting around 9pm EST. Peak hours are from 10pm until 5am Eastern time, and Geminids are expected to be most frequent in the two hours around 1:10 am EST. Viewers can expect “beautiful, long arcs” of light across the night sky lasting a few seconds. Those in areas without significant amounts of light pollution can expect a peak of 60 meteors an hour.

Part of last year’s Geminid shower

IDers already distorting Behe’s new paper

December 13, 2010 • 8:42 am

Over at the intelligent-design site Uncommon Descent, the ever befuddled Denyse O’Leary has already glommed onto the review I wrote yesterday of Michael Behe’s new paper. And, exactly as I predicted, she distorts Behe’s conclusions:

So, not only must the long, slow process of Darwinian evolution create every exotic form of life in the blink of a geological eye, but it must do so by losing or modifying what a life form already has.

In other words, she’s extended Behe’s conclusions, based on viral and bacterial evolution in the lab, to evolution of “every exotic form of life” on the planet.  This is exactly what one cannot do with Behe’s conclusions.

If you read Behe’s paper, or my take on it, you’ll see that Behe restricted his conclusions to the types of mutations that create adaptations in certain short-term laboratory experiments on viruses and bacteria.  He concluded that adaptive mutations in these experiments usually involved either inactivation of genes or genetic elements, or point mutations that modified, but did not qualitatitively change, gene function.  In these studies one doesn’t often observe the evolution of entire new genetic elements—Behe calls them “functional coded elements” or “FCTs”—in the lab.

Importantly, there were two critical caveats about his conclusions that restrict their relevance to evolution as it’s happened in nature. Indulge me while I repeat these:

1) The experiments Behe reviewed deliberately excluded important sources of mutations that create new genes and gene elements of evolution in naturally-occurring bacteria and viruses.  Those studies are not, then, a good model for what actually happens during microbial evolution in nature, which is known to involve uptake of new genes and genetic elements from other species via horizontal DNA transfer.  And this type of evolution involves the appropriation and creation of new FCTs.

2) Behe’s conclusions also can’t extend to eukaryotic species (those with “true” complex cells), because we know that in those groups the creation of new FCTs via gene duplication and other processes has been hugely important in evolution in nature.

See yesterday’s post for a more detailed explanation.

O’Leary either didn’t read what I wrote or, more probably, chose to ignore it.

She further distorts what I said:

This, apparently, got evolutionary biologist Jerry Coyne’s recent attention:

“Anyway, Behe reviews the last four decades of work on experimental evolution in bacteria and viruses (phage), and finds that nearly all the adaptive mutations in these studies fall into classes 1 and 3. We see very few “gain of FCT” mutations. Although this is not my field, the review seems pretty thorough to me, and the conclusions, as far as they apply to lab studies of adaptation in viruses and bacteria, seem sound.”

It looks as though Coyne must now actually take Behe’s argument seriously.

Bad of her to leave out these parts that I wrote:

Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes (note that at least one of these—Rich Lenski’s study— extends over several decades).  But his conclusions may be misleading when you extend them to bacterial or viral evolution in nature, and are certainly misleading if you extend them to eukaryotes (organisms with complex cells), for several reasons . . .

While Behe’s study is useful in summarizing how adaptive evolution has operated over the short term in bacteria and viruses in the lab, it’s far less useful in summarizing how evolution has happened over the longer term in bacteria or viruses in nature—or in eukaryotes in nature.  In this sense it says nothing about whether new genes and gene functions have been important in the evolution of life.  Granted, Behe doesn’t make such a sweeping statement—his paper wouldn’t have been published if he had—but there’s no doubt that his intelligent-design acolytes will use the paper in this way.

Thanks, Ms.O’Leary, for confirming my prediction.

_____

UPDATE:  I’ve changed the title from “Discovery Institute” to “IDers” to reflect the fact that O’Leary was commenting on Uncommon Descent which, as far as I know, is not a formal arm of the DI.  But the the DI’s approbation will surely come in time.

Hitchens on Beck and the Tea Party

December 12, 2010 • 4:10 pm

In his latest Vanity Fair column, “Tea’d off,” Christopher Hitchens goes after the Tea Party, its guiding light Glenn Beck, and all the more “moderate” Republicans who excuse Beck’s palpable racism and lunacy in the interest of political power.  It’s a hard-hitting and truthful column, and brings up an elephant in the room that I’ve long perceived:  much of the opposition to Obama is based, pure and simple, on the fact that he’s partially black.  I’ve never been able to fathom the vehemence of the opposition without this hypothesis.

Hitchens:

Most epochs are defined by one or another anxiety. More important, though, is the form which that anxiety takes. Millions of Americans are currently worried about two things that are, in their minds, emotionally related. The first of these is the prospect that white people will no longer be the majority in this country, and the second is that the United States will be just one among many world powers. This is by no means purely a “racial” matter. (In my experience, black Americans are quite concerned that “Hispanic” immigration will relegate them, too.) Having an honest and open discussion about all this is not just a high priority. It’s more like a matter of social and political survival. But the Beck-Skousen faction want to make such a debate impossible. They need and want to sublimate the anxiety into hysteria and paranoia. The president is a Kenyan. The president is a secret Muslim. The president (why not?—after all, every little bit helps) is the unacknowledged love child of Malcolm X. And this is their response to the election of an extremely moderate half-African American candidate, who speaks better English than most and who has a model family. Revolted by this development, huge numbers of white people choose to demonstrate their independence and superiority by putting themselves eagerly at the disposal of a tear-stained semi-literate shock jock, and by repeating his list of lies and defamations. But, of course, there’s nothing racial in their attitude …

Behe’s new paper

December 12, 2010 • 12:37 pm

The latest issue of The Quarterly Review of Biology has a paper by intelligent-design advocate Michael Behe, “Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution.” It’s a review of several decades’ worth of experimental evolution in microbes (viruses and bacteria), with an eye toward revealing exactly what kinds of mutations have occurred in these studies.  He concludes that microbial evolution in the lab has been based largely on mutations that either 1) degrade or destroy functional elements like genes and promoter sequences, or 2) “modify” the function of pre-existing genetic elements so they do something slightly but not qualitatively different. What Behe does not observe is the evolution of “new functional elements” (see below): new genes, new coding sequences, new promoter regions, and the like.

When Behe produces a paper like this, it’s hard to resist imputing a motivation for the work.  After all, the man has a long history of promoting ID, and has written two books (which I’ve reviewed—negatively—here and here [click “God in the details” at the bottom of the page]) purporting to show that a celestial hand was necessary in evolution.  I’ve also caught Behe deliberately misquoting me in the service of his creationist views.  I believe—and think that time will prove me right —that his intention is to show that evolution cannot provide new structures or new “information” (e.g., genes), but can only either tinker with ones already present or degrade them.   Thus, to explain the evolution of truly new genetic information, one must invoke the intervention of an intelligent designer.

I think that while Behe’s summary of the results of these short-term lab experiments is generally accurate, one would be completely off the mark to extend his conclusions to evolution in general—that is, evolution as it has occurred in nature, be it in microbes or eukaryotes.

To make a long paper short, let me give the definitions Behe uses to reach his conclusion.

These are the things Behe doesn’t see arising in lab experiments:

Functional Coded elemenTs (FCTs): “An FCT is a discrete but not necessarily contiguous region of a gene that, by means of its nucleotide sequence, influences the production, processing, or biological activity of a particular nucleic acid or protein, or its specific binding to another molecule. Examples of FCTs are: promoters; enhancers; insulators; Shine-Dalgarno sequences; tRNA genes; miRNA genes; protein coding sequences; organellar targeting- or localization-signals; intron/extron splice sites; codons specifying the binding site of a protein for another molecule (such as its substrate, another protein, or a small allosteric regulator); codons specifying a processing site of a protein (such as a cleavage, myristoylation, or phosphorylation site); polyadenylation signals; and transcription and translation termination signals.”

In other other words, FCTs are new genes or new parts of genes, including those genetic changes that produce proteins with qualitatively new functions, not just a change in protein amount (e.g., changes in splicing or phosphorylation sites).

According to Behe, there are three types of adaptive genetic mutations that can be seen as differing in their effects on FCTs:

1.  “Loss-of-FCT” mutations. Those are the changes that have adaptive effects by destroying or degrading an FCT.  These include frame-shift mutations that render a protein inactive, or mutations that destroy a gene’s ability to bind to a transcription factor.

2.  “Gain-of-FCT” mutations.  These are the ones that Behe doesn’t see.  He defines them as mutations “that produce a specific, new, functional coded element while adapting an organism to its environment. The construction by mutation of a new promoter, intron/exon splice site, or protein processing site are gain-of-FCT mutations. Also included in this category is the divergence by mutation of the activity of a previously duplicated coded element.” In other words, mutations in this category produce new genes, parts of genes, or confer drastic new capabilities on genes by adding new splicing sites.  Also note that because almost no bacteria or viruses have introns in their cellular genes, it’s impossible to even see one class of this mutation in lab experiments on these groups.

3.  “Modification-of-function” mutations. These include every adaptive mutation that doesn’t fall in the above two categories, including point mutations that affect protein structure or quantitatively affect protein quantity, gene duplications that occur without sequence divergence,  rearrangements of gene order, etc.  He calls these “modification of function” rather than “modification of FCT” because the functional change doesn’t have to occur by changing an FCT itself.

Now these categories are not cut and dried.  For example, the “sickle-cell” mutation that, when present in one copy, protects carriers against malaria, is a point mutation in the beta hemoglobin molecule, changing a glutamic acid residue to a valine. You’d think that this would fall under class 3 (“point mutations”), but Behe considers it an adaptive gain of an FCT because the mutation causes the mutant hemoglobins to stick to each other in blood cells, somehow inhibiting the growth of the malaria parasite.  And because the point mutation is thereby said to specify a “new protein binding site”, Behe puts it into class 2 (gain of FCT).  Unfortunately, a lot of the single-gene mutations that Behe reviews from the experimental microbial-evolution literature work in unknown ways, so he could be missing similar cases that really fall into class 2.

Anyway, Behe reviews the last four decades of work on experimental evolution in bacteria and viruses (phage), and finds that nearly all the adaptive mutations in these studies fall into classes 1 and 3.  We see very few “gain of FCT” mutations.  Although this is not my field, the review seems pretty thorough to me, and the conclusions, as far as they apply to lab studies of adaptation in viruses and bacteria, seem sound.  From this Behe formulates what he calls “The First Rule of Adaptive Evolution:

Break or blunt any functional coded element whose loss would yield a net fitness gain.

What this means is that if adaptation can be gained by losing gene or enzyme activity, it’s more likely to occur by a loss-of-FCT mutation than the appearance of a new FCT itself with altered and reduced function.  That’s not really a “law” but a generalization from these lab experiments.

My overall conclusion: Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes (note that at least one of these—Rich Lenski’s study— extends over several decades).  But his conclusions may be misleading when you extend them to bacterial or viral evolution in nature, and are certainly misleading if you extend them to eukaryotes (organisms with complex cells), for several reasons:

1.  In virtually none of the experiments summarized by Behe was there the possibility of adapting the way that many bacteria and viruses actually adapt in nature: by the uptake of DNA from other microbes.  Lenski’s studies of E. coli, for instance, and Bull’s work on phage evolution, deliberately preclude the presence of other species that could serve as vectors of DNA, and thus of new FCTs.   This is not an idle objection, since we know that adaptation in natural populations of microbes often arises by incorporating new FCTs from other species.  Pathogenicity and antibiotic resistance in bacteria, for example, arise in this way.  Howard Ochman at Yale has done many studies on the acquisition of new bacterial functions by uptake of DNA from other species (and the source of the new DNA is often mysterious).

2.  In relatively short-term lab experiments there has simply not been enough time to observe the accumulation of complex FCTs, which take time to build or acquire from a rare horizontal transmission event.  Finding adaptation via point mutations or loss of function is much more likely.  Behe admits this much, but downplays it by saying this:

After all, one certainly would not expect new genes with complex new properties to arise on such short time-scales. Although it is true that new complex gain-of-FCT mutations are not expected to occur on short time-scales, the importance of experimental studies to our understanding of adaptation lies elsewhere. Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory—by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. This is a significant addition to our understanding of adaptation.

and this:

A third objection could be that the time and population scales of even the most ambitious laboratory evolution experiments are dwarfed when compared to those of nature. It is certainly true that, over the long course of history, many critical gain-of-FCT events occurred. However, that does not lessen our understanding, based upon work by many laboratories over the course of decades, of how evolution works in the short term, or of how the incessant background of loss-of-FCT mutations may influence adaptation.

What he’s saying is this:  “Yes, gain of FCTs could, and likely is, more important in nature than seen in these short-term experiments.  But my conclusions are limited to these types of short-term lab studies.”  Well, good, but then let us not hear Behe’s ID colleagues tout these results as giving strong conclusions about microbial or eukyaryotic evolution in nature, particularly because the lab studies deliberately exclude sources of gain-of-FCT mutations that we know are important in nature.

3.  Finally, Behe does not mention—and I think he should have—the extensive and very strong evidence for adaptation via gain-of-FCT mutations in eukaryotes.  While that group may occasionally acquire genes or genetic elements by horizontal transfer, we know that they acquire new genes by the mechanism of gene duplication and divergence:  new genes arise by duplication of old ones, and then the functions of these once-identical genes diverge as they acquire new mutations.   Or, new genes can arise by unequal crossing-over between different genes, so that new genes arise by mixing bits of old ones.  Behe would count both of these as type 2 mutations (“gain of FCT”).  Think of all the genes that have arisen in eukaryotes in this way and gained novel function:  classic examples include genes of the immune system, Hox gene families, olfactory genes, and the globin genes.  And in many cases the origin of new genes via duplication or swapping of bits is untraceable because the genes originated so long ago and have diverged so greatly in sequence that their origin is obscure.

Vertebrates are thought to be the product of two whole-genome duplication events, giving rise to many genes with novel functions.  This has probably happened in yeast at least once, and many plants are the results of ancient “polyploidy” events in which entire genomes were duplicated at least once.  More than 40% of the genes in the human genome arose via gene duplications; this rises to more than 75% if we count those ancient rounds of whole-genome duplication. And over a third of the genes in the invertebrate  Drosophila genome arose via duplication, with most of these having new functions. There are many, many papers describing and discussing the importance of duplicated genes (and regulatory elements) as a source of evolutionary novelty; see, for example, Long et al. (2003), Wray et al. (2003), and Kaessmann et al. (2009).

While Behe’s study is useful in summarizing how adaptive evolution has operated over the short term in bacteria and viruses in the lab, it’s far less useful in summarizing how evolution has happened over the longer term in bacteria or viruses in nature—or in eukaryotes in nature.  In this sense it says nothing about whether new genes and gene functions have been important in the evolution of life.  Granted, Behe doesn’t make such a sweeping statement—his paper wouldn’t have been published if he had—but there’s no doubt that his intelligent-design acolytes will use the paper in this way.

Finally, this paper gives ID advocates no reason to crow that a peer-reviewed paper supporting intelligent design has finally appeared in the scientific literature.  The paper says absolutely nothing—zilch—that supports any contention of ID “theory.”

_______

Behe, M. 2010. Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution. Quart. Rev. Biol. 85:419-445.Kaessmann, H., N. Vinckenbosch, and M. Y. Long. 2009. RNA-based gene duplication: mechanistic and evolutionary insights. Nature Reviews Genetics 10:19-31.

Kaessmann, H., N. Vinckenbosch, and M. Y. Long. 2009. RNA-based gene duplication: mechanistic and evolutionary insights. Nature Reviews Genetics 10:19-31.

Long, M., E. Betran, K. Thornton, and W. Wang. 2003. The origin of new genes: Glimpses from the young and old. Nature Reviews Genetics 4:865-875.

Wray, G. A., M. W. Hahn, E. Abouheif, J. P. Balhoff, M. Pizer, M. V. Rockman, and L. A. Romano. 2003. The evolution of transcriptional regulation in eukaryotes. Molecular Biology and Evolution 20:1377-1419.

Kitteh contest: grand prize winner!

December 11, 2010 • 2:34 pm

In the final stage of the competition, the judges were unanimous on this one, entered by Oriana Varas (who has her own blog, Ori’s Glob).  It had a winning combination of an awesome photo and an endearing, first-kitteh tale, and so nabs the autographed hardback of WEIT.  Here’s Oriana’s (And Lucy’s) entry:

My Siamese Blue Point is interested in participating in your “Bring out your kittehs” contest. As one of her humans, I believe she is more than worthy of being entered, at the very least. Her name is Lucy Varas and she is a desperate housecat.

This is her story:

My Queendom

by Lucy Varas

My name is Lucy (Lucifer) Varas and I am the ruler of my queendom. I enjoy long walks on the roof, sitting on laps watching movies, the fanciest of Fancy Feasts – we’re talking Florentines – but tuna straight from a can is also an acceptable meal, as is raw fish of any kind. I have three humans: comfiest, warmest, least-likely-to-carry-me-too-long Mama; understanding, best-when-in-bed-and-immobile, most-likely-to-receive-food-from Sister; male who I have a soft spot for (I always purr for him), most-likely-to-carry-me-for-too-long Brother. My duty is to protect my humans. Any stranger who comes into my queendom will be put under surveillance and subject to many tests, one of which includes the “I will rub against your leg and make you think I have accepted you but IN FACT I HAVE NOT; you are the equivalent of a chair leg to me, imbecile!” And if the stranger fails this test, the punishment is a scratch-and-hiss. Scratch-and-hisses are the most common form of punishment in my queendom and only when I try to leave my queendom (temporarily) might I inflict this upon one of my humans. I am pleased with my humans’ understanding of my stranger-intolerance, as they tell guests, upon arrival, not to touch me, for they are not worthy. They should be grateful for being in my presence at all. However, many strangers have ignored these warnings and accuse me of being the guilty one, but this is, of course, nonsense. After all, this is my queendom and I meow the rules.

Dawkins writes his father’s obituary

December 11, 2010 • 12:53 pm

I haven’t often seen someone write the official newspaper obituary for a relative, but Richard Dawkins has just produced one in The Independent for his father, Clinton John Dawkins, who died December 8.  (Richard’s own official first name is also “Clinton”).  Dead at 95, father John had a varied life that took him from Mandalay to Kenya (where his son was born) and finally to a family farm, Over Norton, in the UK:

They turned the big house into flats, specialising in colonial servants sent “home” on leave. Tractors didn’t have compulsory cabs in those days, and Farmer John, wearing his old KAR hat (think Australian bushwhacker) could be heard across two fields bellowing psalms at the top of his voice (“Moab was my washpot”) on his diminutive Ferguson tractor (diminutive was just as well, since he once contrived to run himself over with it).

There’s a shorter but more heartfelt piece on Dawkins’s website, as well as a reprint of the The Independent piece with two photographs.

Condolonces to Richard on the loss of his father.

Clinton Richard (l.) and Clinton John (r.), from the Dawkins website

Kitteh contest winners: runner-up #2

December 11, 2010 • 12:12 pm

The second runner up, and winner of an autographed paperback of WEIT, is Eamon, who entered his two cats Zeno and Russell. Here are their stories:

Some friends of ours foster kittehs for the Ottawa Humane Society. So about three years ago when the passing of one of our older Siamese deprived Kizhe of his favorite playmate (and me of my favorite lap-cat), we asked our friends if they had any kittens who might make a suitable replacement.

Thus we came to adopt Russell (on the right; full name Bertrand Alfred Russell Wallace North Whitehead). He’s now a great furry easy-going beanbag of a cat who greets me with loud purrs and petting-demands every day when I get home from work, and tries to shove my laptop computer out of the coveted spot. Once they got past the obligatory dominance negotiations, Kizhe became excellent kitteh-friends with him.

Two years later, Kizhe grew sick and died; thus Russell now needed a new playmate. Back we went to our friends, this time to adopt the fluffy ball of tabby grey on the left. Zeno is now a year larger than in the picture, a sort mottled grey animated dustmop with a magnificent tail. At 13 lb. Zeno is the largest cat we’ve yet had, and he’s still growing. His favorite treat is oatmeal — every morning he begs for a spoonful of our porridge, which he devours. Every good kitteh needs to have at least one endearingly bizarre preference, and this is his.

So consider this a PSA: Support your local animal shelter, and consider adopting a kitteh from them (or if you really must, a doggeh).