Language evolution

I once met a French guy who not-pologized for his pitiful English by saying that he loved his language and didn't want to lose it (implying that he would if he improved his English). Hogwash. I commented later that that would not happen, French having over 110 million native speakers, but rather that by becoming a universal language, English would be the mangled tongue.

Under the headline This Is English, Rules Are Optional a book about the evolving English language is reviewed in the New York Times, ending with this quote:

“All the signs point to a fundamentally reconfigured world, in which what we now think of as the English-speaking world will eventually lose its effective control of the English language.”

Exactly.

The Lexicographer’s Dilemma: The Evolution of ‘Proper’ English, From Shakespeare to ‘South Park

Adaptation is fast and effective in a fungus

The introduction
Watching adaptation - the process of organisms and populations increasing their fit to the environment - is not easily observed in nature, and when it is, it is often hard to tell what the details of the process are. Crucially, the mutations (and by "mutation" I mean any change to the genome) are mostly unknown, leaving us to guess what kind of genomic changes are responsible for shaping life through evolution.

Fortunately, some organisms are amenable to manipulation and fast evolutionary change: unicellular organisms and viruses have been extensively used with great success to investigate many questions of evolutionary import (though I hurry to caution that such organisms cannot say much about evo-devo and morphological change, as these are areas pertaining to multicellular organisms).

Bacteria (e.g. E. coli), viruses (e.g. φ6), fungi (e.g. yeast), algae (e.g. Chlorella) enlighten us on the mutational basis for evolution, as many experiments have recently shown.

This time a study using the fungus Aspergillus nidulans is manipulated in the lab to attempt to answer an important question in evolutionary theory: During adaptation, how many mutations are needed, and what are their size, i.e. how much do they affect the fitness of the organism?

The short answer is that adaptation is short and fast, requiring only a few mutations. Among those mutations, the first is of greater effect on fitness than the following, which is expected from theory when the organisms are climbing a peak in the fitness landscape, but contrary to the "gradualist view of adaptation dominant since the 1930s."

The experiment
One strain of Aspergillus nidulans is resistant to a fungicide, but resistance is known to be a costly trait, meaning that compared to a fungicide sensitive strain, it grows slower (has lower fitness) when there is no fungicide present. The crazy scientists then let populations of this resistant strain evolve without fungicide, and watch them adapt to the new fungicide-free environment.


Click to go to original figure.

Schoustra et al. placed a few spores (more than 10,000) on a medium (food), and let it grow for five days (about 80 generations) during which the population grew by mitosis (cellular duplication, similar to cell-division of somatic cells in the human body, but not of the gametes (sperm/egg), which is meiosis). After five days either 50,000 or 500 cells were transferred to a fresh medium (designated large and small bottlenecks, respectively). This process was repeated until the populations had gone through 800 generations. Fitness was estimated by measuring the diameter of the colony at generation 0, 80, 160, 240, 320, 480, 640, and 800. These experiments were done 120 times each.

Click to go to original figure.

The results
A fitness of 1 was given to the ancestral strain, and fitness of evolved strains was measured relative to that. In figure 2 the fitness trajectories are plotted as a function of the number of generations into the experiment for large bottlenecks (A) and small bottlenecks (B). Notice how most of the lineages quickly increase their fitness for both large and small bottlenecks.


                      Figure 4. Properties of adaptive walks.
Click to go to original figure.

Without going into the rather complicated details of how the number and effect size of mutations were estimated (it involves a Maximum Likelihood model and comparisons with simulations), we can see from figure 4 that the effect of the first three mutations are not different in the large (triangles) and small (squares) bottleneck lineages, and that the slopes (which are significantly different from zero) are negative, indicating that the first mutations are of the largest effect, followed by the second, and - for the large bottlenecks only - then by the third. (The selection coefficient is a measure of the effect of a mutation, and is given by the fitness of the mutated genotype minus the fitness of the unmutated parent divided by the fitness of the unmutated parent.)

Additionally, the number of mutational steps taken within the 800 generations is very small: for the 50,000 spores bottlenecks the average is 2.39±0.53 standard deviations, and for the 500 spores bottlenecks the average is 2.00±0.74 steps.

The discussion
These results indicate, according to Schoustra et al., that we need to change our expectation of how evolution proceeds:

Taken together, these results imply that the gradualist view of evolution is incorrect; rather, the bulk of adaptation in mutation-limited populations is likely to be achieved by the first few mutational steps.

The authors also found significant differences in genetic variation of the 800 generations evolved lineages, and from this they conclude that

although we do not know in detail the identity of the molecular changes responsible for fitness increases, we can be confident that they were achieved through a variety of genetic routes.

One pleasant surprise is that the different lineages clearly did not evolve the same way. We could have expected that they would all re-evolve sensitivity to the fungicide, thereby increasing their fitness. Rather, from figure 2 we can see that fitness was increased in many different ways, and with differing results. What this indicates is that the fitness landscape in the neighborhood of the ancestral genotype is very rugged (also called epistatic), because many different fitness peaks were climbed. If they hadn't climbed different peaks, we would expect the fitness measurements to be very similar. Instead, there are many different ways to increase fitness, and further, only some include re-evolving fungicide sensitivity (only five lineages re-evolved sensitivity).

I say this is a pleasant surprise because my own work with simulations suggest that fitness landscapes - which is a property of both genotype and environment - are likely to evolve to become epistatic. However, it is bad news for fighting resistant strains in general, because if the strains occupy a rugged area of the fitness landscape, they can increase their growth rate without losing their immunity to the fungicide/antibiotic/other drug.

The reference
Schoustra SE, Bataillon T, Gifford DR, & Kassen R (2009). The properties of adaptive walks in evolving populations of fungus. PLoS biology, 7 (11) PMID:19956798

Philosopher nonsense

Usually I shy away from blogging about news items that I can only find in Danish, but today I'll make an exception, because a Danish philosopher, Vincent Hendricks, has said something so stupid that I simply must comment.

Hendricks says that the reason the COP15 negotiations failed so spectacularly is that we are too clever. How so?

»Vi kan se, at når andre højerestående dyr bliver truet på livet, løber de enten skrigende bort, forvirrer fjenden eller går til modangreb. Men menneskets høje intelligens gør det muligt for os at abstrahere. Det er der mange fordele ved, men det betyder også, at vi overser det nødvendige, fundamentale overlevelsestræk. Vi intellektualiserer os ud af det og ender med komplicerede forklaringer og bortforklaringer i stedet for at handle her og nu«.

That translates into:

»We can see that when other higher animals are threatened on their lives, either they flee, confuse the enemy, or attack. But the high human intelligence makes it possible for us to think theoretically. That has many advatanges, but it also means that we overlook the necessary, fundamental way to survive. We intellectualize the situation and end giving complicated explanations instead of acting on the spot.«

No it doesn't. We are not overlooking anything essential to survive, which is eating, staying healthy, and fighting off the enemy. Dealing with global climate change is something that's only possible with this high human intelligence.

»Det forekommer os i hvert fald ikke længere naturligt, at arten skal overleve. Det ligger af en eller anden grund ikke lige for. Hvis det gjorde, ville vi have gjort hvad som helst i Bella Center for at komme ud af de problemer, vi står over for«.

»It doesn't seem natural to us any more, that the species must survive. It is, for some reason, not aparent. If it was, we would have done anything at Bella Center [i.e. COP15] to get rid of the problems we face«.

It has never before occurred to any living organisms that any species should survive. It is not how natural selection works, and it is only recently that any living organisms have cared for other species, including their own. Animals care for other individuals, but does not have a concept of species at all to care for. This philosopher has a profound lack of understanding of evolution given that he is a professor talking about it.

Ville en flok aber have kunnet lave en mere ambitiøs klimaaftale?

»Det ville i hvert fald have været nemmere, hvis mennesket havde haft abernes flokintelligens, hvor alle er intelligente på samme måde. Alle andre arter plejer at gøre noget, når de er på vej ud over en afgrund, men menneskets intelligens styrer os direkte mod den«.

Would a flock of apes have been able to make a more ambitious climate agreement?

»At least it would have been easier if humans had the flock-intelligence of apes, who are all intelligent in the same way. All other species usually do something when they are headed over the cliff, but human intelligence are steering us directly towards it«.

Come on! What utter nonsense. I simply cannot believe anyone educated would say anything as daft as this. If we thought more like apes we would have seen the global climate trends and been able to do something about it? Jeesh, this is dumb. No, other species would never know they were headed towards a cliff, and would still only care about the very next move. Humans, on the other hand, have the capacity to foresee these events and do something about it. It is our very urge to care only for ourselves in the present that makes it hard to do something collectively, not our ability to think theoretically - to think ahead.

Normalt betragter vi det som upassende at rette os efter vores dyriske instinkter. Slår du her til lyd for det modsatte?



»Nej, men det kan ikke nytte noget at have et højintellekt, hvis man er på vej ud over kanten med det. Min pointe er, at vi må kombinere urinstinktet med vores høje begavelse og begynde at bekymre os om vores egen overlevelse«.

Usually we consider it unsuitable to do as our animalistic instincts suggest. Are you here suggesting the opposite?

»No, but it is no use to have a high-intellect, if you are headed over the cliff with it. My point is that we much combine our instincts with our higher intelligence, and begin to concern ourselves with our own survival«.

Eh? Presently we aren't worried about our own survival? But many people and statesmen are worried right now, and this worry is the reason why we had COP15 in the first place.

Here is a philosopher with appointments at Copenhagen University and Columbia University, and he gets away with displaying such systematic ignorance. I find that embarrassing in the extreme. A disgrace rarely equalled among learned people.

A New Year's resolution: hate me

My New Year's resolution: Get on Fred Phelps' list of people God hates. It wasn't under the Christmas tree, so now I'm aiming for achieving this goal some time in 2010. The sooner the better, because Fred Phelps is 80, and I have a feeling that God loves him so that he's going to call him home soon.

If God, Phelps, and the whole Westboro Baptist Church hate lady Gaga because she loves homosexuals, then I demand that Phelps' God hate me too. I advocate same-sex marriage, and I'm an atheist. I realize the former is worse in Phelps' God's eyes, because God Phelps is a closet homosexual, but probably not a closet atheist, though that would be another great conspiracy theory.

Thou hadst a whore's forehead, thou refusedst to be ashamed... Will he reserve his anger forever?

(...)

Does the simple slut truly think she can change God's standards by seducing a generation of rebels into joining her in fist-raised, stiff-necked, hard-hearted rebellion against Him? Get real!

Major chuckle. A call to get real? I gather Phelps isn't trying to be sarcastic, but I feel certain that Gaga couldn't have come up with a better advertisement for her concerts herself.

China doing in the climate

Interesting, interesting article about why COP15 went so wrong, and where the real blame lies, as reported by a delegate who was in the room when China trashed the talks.

Copenhagen was a disaster. That much is agreed. But the truth about what actually happened is in danger of being lost amid the spin and inevitable mutual recriminations. The truth is this: China wrecked the talks, intentionally humiliated Barack Obama, and insisted on an awful "deal" so western leaders would walk away carrying the blame. How do I know this? Because I was in the room and saw it happen.

(...)

What I saw was profoundly shocking. The Chinese premier, Wen Jinbao, did not deign to attend the meetings personally, instead sending a second-tier official in the country's foreign ministry to sit opposite Obama himself. The diplomatic snub was obvious and brutal, as was the practical implication: several times during the session, the world's most powerful heads of state were forced to wait around as the Chinese delegate went off to make telephone calls to his "superiors".

You can just see how the Chinese delegation planned this... "Imagine the frustration everybody else will feel when we sit at the hotel watching Baywatch while on the intercom. Hahaha!"

To those who would blame Obama and rich countries in general, know this: it was China's representative who insisted that industrialised country targets, previously agreed as an 80% cut by 2050, be taken out of the deal. "Why can't we even mention our own targets?" demanded a furious Angela Merkel. Australia's prime minister, Kevin Rudd, was annoyed enough to bang his microphone. Brazil's representative too pointed out the illogicality of China's position. Why should rich countries not announce even this unilateral cut? The Chinese delegate said no, and I watched, aghast, as Merkel threw up her hands in despair and conceded the point. Now we know why – because China bet, correctly, that Obama would get the blame for the Copenhagen accord's lack of ambition.

China, backed at times by India, then proceeded to take out all the numbers that mattered. A 2020 peaking year in global emissions, essential to restrain temperatures to 2C, was removed and replaced by woolly language suggesting that emissions should peak "as soon as possible". The long-term target, of global 50% cuts by 2050, was also excised. No one else, perhaps with the exceptions of India and Saudi Arabia, wanted this to happen. I am certain that had the Chinese not been in the room, we would have left Copenhagen with a deal that had environmentalists popping champagne corks popping in every corner of the world.

Perhaps someone could tell me why China had to be in the room at all? If the other countries knew China would bust their balls over the numbers to this extent, then why not just make a deal around China? So China wouldn't sign, but at least everyone else would (save for Sudan, and maybe India). Are the US and EU really so dependent on Chinese plastic toys? (Okay, I am fully aware that I am opening a can of worms that I know next to nothing about already, but I would also advocate more than a couple of steps backwards away from all the consumerist considerations that I do know the whole show is so deeply entrenched in.)

All this raises the question: what is China's game? Why did China, in the words of a UK-based analyst who also spent hours in heads of state meetings, "not only reject targets for itself, but also refuse to allow any other country to take on binding targets?" The analyst, who has attended climate conferences for more than 15 years, concludes that China wants to weaken the climate regulation regime now "in order to avoid the risk that it might be called on to be more ambitious in a few years' time".

The thing is, surely someone among the EU and US delegations knew about China's agenda, no? I mean, I could have cooked up such a theory over two Tsingtao no problem, and yet Merkel was (apparently) truly frustrated? But maybe that's just how the game is played when in the room - everyone know the agenda of everyone else, but you have to keep playing your part.

So, does China not care about the climate at all? May it does, but quite understandably (but wrong, I say), they care much more about the short-term economic rise to power and prosperity.

This does not mean China is not serious about global warming. It is strong in both the wind and solar industries. But China's growth, and growing global political and economic dominance, is based largely on cheap coal. China knows it is becoming an uncontested superpower; indeed its newfound muscular confidence was on striking display in Copenhagen. Its coal-based economy doubles every decade, and its power increases commensurately. Its leadership will not alter this magic formula unless they absolutely have to.

But that doesn't mean the rest of us can't.

Shit, no ball lightning

Sigh sigh sigh. When I was a teenager I read about ball lightning, and ever since I have dreamed of seeing one. It's supposed to be a spherical ball of electricity, but an article in eSkeptic argues somewhat convincingly that the phenomenon does not exist at all. I'm disappointed!

One argument against its existence is that description of balls of lightning (BL) are very varied/contradictory:

According to reports, BL occurs in any type of weather, not just storms; it can be any color; it can be motionless or moving at any speed, often against the wind; it can disappear violently or silently; it may follow wires or edges or travel independently; it may be outside or inside; its life time varies from a fraction of a second to several minutes; its shape can be spherical or pear-shaped; it is either silent or noisy; etc.

Besides, apparently there are many other explanations for this supposed phenomenon, such as

• bright astronomical objects at low altitude, sometimes seen in mirage
• normal lightning igniting hydrocarbon gases in the atmosphere, and (of course)
• misinterpretations of photographs:

Until the early 1970s, a photograph taken in 1961 at Castleford (Yorkshire, England) had been interpreted as showing the path of BL. Even New Scientist magazine described it as the ‘Path of a Thunderbolt’. But a decade later it was claimed that it showed the pulsed trace from a street lamp (Davies and Standler) and a decade after that it was demonstrated that this was correct (Campbell 1981b): the photographer incautiously moved the camera while the shutter was still open. A Russian photograph taken in 1957 had the same explanation, but not before a member of the Soviet Academy of Sciences endorsed the picture on the basis of similar pictures he had seen in a 1939 US journal (Campbell 1987). He did not know that the pictures were all produced by lamps, presumably as hoaxes.

This is all very disappointing to me. Yet another childhood dream gone the way of Santa*, vampires, and ether.

* I actually never believed in Santa, because I knew no white dude would dare enter my neighborhood after dark.**

** Okay, the actual reason was that no one in my neighborhood had chimneys. I recently read somewhere that I cannot find now that children aren't at all as disappointed when they realize that Santa is a hoax as some adults think. Rather, they play along with the adults for the benefit of the younger children, and in this way feel a subtle connection with adults. Neat, no?

Garrison Keillor in grumpy old bigot mode

I usually like to listen to Garrison Keillor on A Prairie Home Companion. He's got a great voice the perfect looks for radio. And I have noticed his frequent references to "good, decent lutherans" in the show, but I thought that was entirely in jest, and only today did I become aware that he is really a religious nut.

Keillor espouses the not uncommon view in the US that if you aren't a Christian, then you have no business celebrating Christmas:

Christmas is a Christian holiday -- if you're not in the club, then buzz off. Celebrate Yule instead or dance around in druid robes for the solstice. Go light a big log, go wassailing and falalaing until you fall down, eat figgy pudding until you puke, but don't mess with the Messiah.

Well, I do celebrate Yule, as he says, but it's the same thing! The direct translation of Christmas (indeed, the only one) - with all the Christian components - is 'jul' in Danish (weihnachten in German, jól in Icelandic). It is a celebration with roots that aren't Christian in origin, which the Christians then hijacked as a celebration of the birth of the son of himself. If Garrison wants non-Christians to stay clear of celebrating it, then could I ask that he in return stays clear of the parts that are pagan, like the tree? Seems fair to me. His club messed with our celebration first, goddammit, so fuck off Garrison.

Christmas does not need any improvements. It is a common ordinary experience that resists brilliant innovation. Just make some gingerbread persons and light three candles and sing softly in dim light about the poor man gathering winter fu-u-el and the radiant beams and the holly and the ivy, and you've got it. Too many people work too hard to make Christmas perfect, find the perfect gifts, get a turkey that reaches 100 percent of potential. Perfection is a goal of brilliant people and it is unnecessary where Christmas is concerned.

Yeah well, IMO Scandinavia didn't need any improvement a thousand years ago, and, while most of the pre-Christianity traditions have been lost (because they became Christian), I am quite certain that people didn't go around thinking that their Winter Solstice celebration needed divine improvement.

What prompted this tirade from Garrison?

Unitarians listen to the Inner Voice and so they have no creed that they all stand up and recite in unison, and that's their perfect right, but it is wrong, wrong, wrong to rewrite "Silent Night." If you don't believe Jesus was God, OK, go write your own damn "Silent Night" and leave ours alone. This is spiritual piracy and cultural elitism and we Christians have stood for it long enough.

Does anyone feel the burn of the irony? (Here I stop to note that Garrison is an English-major, and very fond of the English language. It is therefore with exquisite delight that I mangle the English language, and I can only hope that he ever stops by and sputters his eggnog all over his keyboard.) On top of that I wonder if this is about a five-year old hoax that Bill O'Reilly fell for, fighting the war against the war on Christmas?

I'm a loser

and I'm not what I appear to be.

I applied for a postdoc position in Copenhagen (where I'm from), but was notified yesterday that I didn'get it (320 applicants).

I submitted a blog post for the competition to win a award to go to ScienceOnline 2010, but got an email five days ago telling me I didn't win (2 winners, 10 submissions).

I posted a reply to the question Can natural processes produce an increase in complexity?, but was beaten by someone called Calilasseia in the competition on Pharyngula. (Ironically, the winning reply references my advisor to make his/her case.)

I was just in Okinawa, and it rained most of the time.

I can take a lot more.

Do insurgents read Nature?

An interesting new paper in Nature explains how timing and casualties of insurgent attacks follow a power-law. [Synopsis.] This basically means that such wars are predictable to a certain extent.

But what would be the underlying factors that cause these patterns?

Johnson and his colleagues argue that the pattern arises because insurgent wars lack a coherent command network and operate more as a "soup of groups", in which cells form and disband when they sense danger, then reform in different sizes and composition. The timing of attacks, the authors say, is driven by competition between insurgent groups for media attention.

So the fact that they are media-whores makes them predictable? The study is not free from criticisms, but still it makes you wonder if insurgents read Nature. If they want to remain elusive, perhaps they should.

Evolution highlights X

Here's a longish list of new papers I ought to read. I'm really posting it as a reference for my own benefit, but of course I think these are papers that everyone with even a cursory interest in evolution should read in detail. Most are behind pay-walls, so if you aren't sitting at an institution that has a subscription (like me at the moment), then you can only read the abstracts.

A Complete Skeleton of a Late Triassic Saurischian and the Early Evolution of Dinosaurs
I have kids, so I really need to keep up with dinosaur research. I will totally lose their respect if I don't. Here's a press-release on Tawa.

Two papers on group selection - a contentious topic concerning the evolution of altruism:

Demography and the tragedy of the commons

The group selection controversy

Evidence for abrupt speciation in a classic case of gradual evolution
This is in unicellular plankton with hard shell, so they're preserved in the fossil record.

The Genetic Basis of Phenotypic Adaptation II: The Distribution of Adaptive Substitutions in the Moving Optimum Model
Theoretical study with agent-based simulations.

Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain
I have before hypothesized (somewhat provocatively) that the only differences between humans and chimps are in the gene expression patterns.

Competition between recombination and epistasis can cause a transition from allele to genotype selection
A paper by a friend of mine about a topic that I am working on myself (i.e. epistasis in the NK model).

Acting Like a Prion Isn't Always Bad
Prions, of course, misfold and cause disease in humans and animals, but not always (we do have genes to make them ourselves).

The Evolutionary Dynamics of a Rapidly Mutating Virus within and between Hosts: The Case of Hepatitis C Virus
Rapidly mutating anything is interesting, since evolution happens much faster. (PLoS is free, so you can read the whole paper.)

Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. IV. Genetic Constraints Guide Evolutionary Trajectories in a Parallel Adaptive Radiation
I totally love experiments with bacteria? Why? Basically because they have so short generation times. Like with viruses, evolution can be directly observed (yeah yeah yeah, they are still bacteria).

The evolutionary consequence of the individualistic response to climate change
Pertinent topic.

Detecting positive selection in the budding yeast genome
See, again unicellular organisms rock.

Octopus tool use

Octopuses carry coconut halves around and use them for shelter.

---

Update 12/15:
I totally predicted that everyone would be all over this right away: PZ, Jerry, Ed, Zen. Videos on those sites.

Clear science from scripture

All of these are theories posed by evolutionists. What I see in Qur'an is concrete proof. We in time are trying to understand what God already has created. Sometimes we prove our theories. Sometimes we disprove our theories.

As a Muslim, the Qur'an gives me clear science. I read it with 100 percent belief in it. I don't look at it critically. It is God's scripture.

Would you believe the above is a statement by someone with a Ph.D. in biochemistry working as a scientist?

The Qur'an is concrete proof exactly how, do I wonder. A scientist should not read anything with 100% belief in it. Skepticism is the foundation for scientific thinking. He should look at everything critically. What a shame.

Roy Moore is still running for governor

A friendly commenter on an older post of mine reminded me that Roy Moore is running for governor in Alabama. Thanks.

Here's Moore's view on education.

Moore thinks that what's wrong with the American education system is that there isn't enough freedom:

By freedom, I mean the freedom within our education system to allow other schools to compete with public schools, freedom of parents to control the education of their children, freedom of teachers to do their job without burdensome restrictions, and freedom of both students and teachers to express their belief in God and moral standards.

As governor, I will fight to allow parents greater freedom to choose the proper education for their child, whether public school, private school, Christian school, or home school.

Muslim school, Jewish school, Scientology school, FSM school.

Finally, we must remember that God is the true source of wisdom and understanding. As governor, I will protect the freedom of teachers and students to recognize God in prayer and our Pledge of Allegiance.

I wonder if he'll protect the freedom of teachers and students to recite Muslim, Jewish, Hindu, and Buddhist prayers in school.

In other news:
Roy Moore disrespects the non-religious.

Quantitative evolution school in Okinawa, 2010

At the winter school I'm at in Japan, I've just learned of an interesting summer school they will be having here next year in May:

Quantitative Evolutionary and Comparative Genomics.

It will be at OIST in Okinawa May 24 to June 4, 2010.

The theme is ultra-conserved sequences:

The theme of the 2010 Summer School is the phenomenon of strong (or extreme) sequence conservation, which will be explored from a quantitative and multidisciplinary perspective, and connections forged with parts of biology outside of genomics.

Students can apply to have all travel and accommodation costs covered. Application deadline is February 15.

Speakers:

• Nadav Ahituv, UCSF
• Peter Arndt, MPI Berlin
• Gill Bejerano, Stanford
• Emmanouil Dermitzakis, Geneva
• Takashi Gojobori, National Institute of Genetics, Japan
• Ueli Grossniklaus, Zurich
• Jotun Hein, Oxford
• Jonathan Miller, OIST
• Erik van Nimwegen, Basel
• Howard Ochman, Arizona
• Anirvan Sengupta, Rutgers
• Gasper Tkacik, U. Penn
• Byrappa Venkatesh, IMCB Singapore
• Ting Wu, Harvard Medical School

Sex is too weird for this blog

Sexual selection. Mmmm. No field matches biology, with lab meetings full of discussions about the benefit of sex, details of reproduction, and anatomical wonders of private parts.


From PartiallyClips.com.

Sexual selection is - apparently, and to my amazement - contentious. Not really, but someone think's it doesn't fit the bill. I find that... [just, no comment].

1 fucked-up weird trick, indeed

Has anyone else seen this advertisement?



I watched the whole video (almost), and the basic idea - though wrapped in escapades and ennuendos* - is very interesting.

It is this.

Back in time when we (they, really) were all cavemen and up for group photos, we were all slim and beautiful not despite but exactly because we ate whatever we wanted whenever we wanted to. Steak for breakfast and brie at tea-time. It was all a big mess, and that's precisely why it worked. Not because food was scarce (come on, it was the days of the giant sloths), but because one day you'd eat breakfast at IHOP and Denny's at the same time, and then nothing until the afternoon two days later, when you stumbled upon a truck-load of zebras who had fourtuitously died right in your back-yard, and the only thing you ate were the fat dripping off their zebra ears. Point is, that food came irregularly, and somehow eating irregularly then made us stay slim and beautiful. It had nothing at all to do with our genes, the fact that food was scarce (because zebra live in flocks, don't you know), or that estrogen-like compunds were in all sources of food, or even that you lived in America, which is God's chosen people for the obese-experiment.

Cavemen stayed slim because they followed this 1 wierd old trick: eat irregularly (but do, FOR GOD'S SAKE, buy my book priced at $39.99 for your benefit) and follow this detailed plan of what to eat when (because that's what the cavemen would do).

* Look, you fucker, number one I am typing on a Japanese keyboard that's got all these funky characters from outer space and number two I've had a truck-load of pseudobeer and number three fuck commas and number four I am watching Eddie Izzard on youtube, so you can bloody well substitute my attemps at being the proper grammarian (yes, that's a word) with the proper britshit.

Computational modeling in Okinawa

I have just arrived at Okinawa Institute of Science and Technology to participate in Winter School on Computational Modeling in Biology - Data and model sharing by SBML and insilicoML. I expect it will be a hugely advantageous learning experience, and that attending the program will increase my bargaining power enormously. I've never been to Okinawa before, but I must say it's really nice here. I have a room with a ocean view, but absolutely no time to go outside at all for the four days I am here.

The school will present and train participants in these technologies:
SMBL - a markup language for describing systems biology models
SBGN - visualizing biological and models
insilicoML - XML based language for describing hierarchy and modularity of physiological functions in multiple levels
insilicoIDE - model editor working in conjunction with insilicoML
CellDesigner - biochemical networks modeling

What does this all mean? I'm not quite sure, but I just might tell you when I find out.

Carnival of Evolution 18

Carnival of Evolution number 18 is up at Biochemical Soul. Irradiatus, founder of CoE, has been managing the carnival really well for a long time, but now he has decided that the time has come to let it go, so he can get some serious research done. He has asked me to take over CoE, which I have happily accepted.

More news to follow on carnivalofevolution.blogspot.com.

Dog speciation

Great post on skepticblog by Daniel Loxton revealing (I think that's the right word) that AiG-type creationists actually think Darwin was right.

creationist leaders share Darwin’s belief that species routinely change (and even originate) through mutation and natural selection.
Indeed, according to Answers In Genesis’ (AiG) current web feature “Top 10 Myths About Creation,” it’s a straw-man to suppose creationists think otherwise:

A popular caricature of creationists is that we teach the fixity of species (i.e., species don’t change). And since species obviously do change, evolutionists enjoy setting up this straw-man argument to win a debate that was never really there in the first place.

Weird, right? But wonderful, that they believe in evolution after all. Or not?

Creationists have long been amazed by the diversity within each created kind (or baramin, roughly on the family level). We know that species do change—but only within the original kinds God created roughly 6,000 years ago.

Species changing via natural selection and mutations is perfectly in accord with what the Bible teaches. Such changes are not evolution—they remind us that God put enough information in the genome of each original kind to live and flourish in a cursed world.

Oh, what scientists call evolution they do not. But they do allow (again, I think that's the right word) changes within families - which would then allow for speciation. But not change at taxonomic levels higher than that.

My reply to John Heininger in the comments of skepticblog:

John, at what hierarchical level of taxonomy do you require observed bifurcation before you will accept macroevolution? Bacteria are a domain, amphibians (tadpoles) are a class, finches are a family, pigeons are a family, monkeys are two pavorders, humans are a species, fruit flies are two families, and viruses are completely off the charts.

The point is that what you are asking for as the only evidence you'll accept for macroevolution is something that we know takes many times the life-span of humans. Speciation, which has arguably been directly observed (e.g. in E. coli, Podarcis lizards, certain plants, finches), is macroevolution by everyone else's definition, and yet the examples you apparently crave have raised the bar intolerably.


Same species, really?

Suppose you were an alien visitor to Earth, and you have to classify species by the same criteria that biologists today use. Surely you would say that ruby throated tigers and lions are different species, right? Sure, they can actually interbreed, and yet it is common sense that they are different, based on their morphology, behavior, etc. Next look at dogs. If at first you only see a great dane and a chihuahua, SURELY you would say they are at least as different from each other as lion and tiger are from each other. My point is that the two dogs, though both characterized as dogs (which is normally considered a species), are different enough to be labeled as two different species (in fact, I challenge the common notion that they can interbreed, which if true would rule them different species), and we know that those two dogs share a common ancestor.


More chihuahua.

Harvey Mudd Conference on mathematics of environmental sustainability

Harvey Mudd College, located minutes away from Keck Graduate Institute where I work, is holding a conference in the end of January. If you're interested in the topic, the Mathematics of Environmental Sustainability and Green Technology, then there is the option for students to apply for travel funding (see below).

The conference will begin on Friday evening January 29th with a panel discussion featuring representatives from the colleges and the Claremont community working on issues of sustainability.

On Saturday there will be four speakers from a variety of disciplines posing problems of interest to mathematicians and scientists:

Harry Atwater (California Institute of Technology) Light-Matter Interactions for Solar Energy Conversion

Ken Golden (University of Utah) Climate Change and the Mathematics of Transport in Sea Ice

Julie Lundquist (University of Colorado at Boulder) Harnessing the Power of the Wind

Ron Lloyd (Fat Spaniel Technologies) Modeling Problems in the Green Economy.

We invite students and faculty to submit posters. There is travel funding available for students. Please see website for more details.

http://www.math.hmc.edu/conferences/2010

I'll probably drop by on Saturday 30th.

Darwin wasn't really a gradualist

John Taylor, dept., og biology, University of Victoria, sent this email today to the EvolDir mailing list:

The title of Richard Bateman's upcoming lecture is "Gradualism: Darwin's big mistake?".

I may be jumping the gun, the question mark hints at a lecture debunking this myth (though the abstract suggests something else), but I can't help but express some frustration over the habit of evolutionary biologists of enhancing their research programs (or presidential lectures) by claiming to address mistakes or solve difficulties in the Origin of Species.

Darwin had no problem with rapid evolution.

Page 148: ".... a new and improved variety might be quickly formed on any one spot, ...."

Page 310: "I may here recall a remark formerly made, namely that it might require a long succession of ages to adapt an organism to some new and peculiar line of life, for instance to fly through the air; but when this had been effected, and a few species had thus acquired a great advantage over other organisms, a comparatively short time would be necessary to produce many divergent forms, which would be able to spread rapidly and widely throughout the world."

Page 318: "There is some reason to believe that organisms, considered high in the scale of nature, change more quickly than those that are low: ...."

And then there's the first chapter, Variation under domestication. It sets up the whole argument and it is a discussion about variation between different sheep herds and about dog breeds. Darwin remarks (page 93) that "King Charles's spaniel has been unconsciously modified to a large extent since the time of that monarch".

Let's give the man a little rope. The common view in 1859, according to Darwin, was the immutability of species. That gradualism was emphasized shouldn't be surprising in this context.

Kevin Padian has pounded this myth before, too.

9 December 2009 - 6.00pm
The President's Talk
Professor Richard Bateman, RBG Kew
Gradualism: Darwin's greatest mistake?
The Linnean Society, Burlington House, London, UK

December 8 1980

Died 29 years ago today.

My favorite atheist singer. Had lots of faults. Had lots of insight.

Arseholegate

More evidence that those climate science people use foul language! If they can cuss on TV, what won't they do with the raw data?



But seriously, one Peter Kelemen has written very nicely on the hacked CRU emails and the implications, as well as making it clear on what grounds it is thought that 1) human activity has caused a steep increase in CO2 emissions, and that 2) increased CO2 emissions leads to a warmer atmosphere (on page 4).

For these reasons, and based on carbon isotope data, it is all but certain that the present, unprecedented rise in CO2 is due mainly to human output. But one cannot rule out with complete certainty other factors, for example, global warming itself, that could also be significantly contributing to the atmospheric CO2 increase.

CO2 (and methane) in the atmosphere are nearly transparent to UV and visible radiation, but absorb in the infrared, creating a "greenhouse." If it were not for this, the surface of the Earth would be much colder. This leads to the inference that increasing CO2 will lead to increasing warmth. Also, high CO2 concentration in the air leads to ocean acidification, which is probably bad for coral and perhaps also for plankton that make their shells from calcium carbonate (soluble in acid) and form the base of the ocean food chain.

Get a B.S. in biology without taking evolution

At Southwestern Adventist University in Texas, Biology majors don't have to take a single class of evolutionary biology. In fact, as far as I can see there are no evolution classes offered at all. They do require the students to take religion classes ("religion elective").


[Click for larger image - also to enjoy the Lorem ipsum dolor sit placeholder still going strong.]

This shouldn't come as a surprise, given the recent push from the Seventh-Day Adventists to force the Adventist universities to teach creationism.

Iranian government threatens Swiss

The government in Iran, of all countries, think it reasonable to threaten Switzerland with consequences because of a ban to build minarets. In Switzerland, that is.

An East-West clash over a Swiss referendum last week banning the construction of mosque minarets heated up today as Iran's foreign minister warned of unspecified "consequences" if the ban were enforced.

I was going to write that they are hypocrites, but apparently Iran actually allows Christians to build churches.

Iran's population is 90% Shiite Muslim. But it permits construction of Christian churches and Jewish synagogues, though some Sunni Muslims have complained they have a tough time building houses of worship in some parts of the country.

And yet, they are bloody hypocrites, because they dare talk lecture the Swiss government on human rights:

But Mottaki had harsh words for Switzerland, saying enforcement of the ban on new minarets was “against the prestige of a country which claims to be an advocate of democracy and human rights" and would "damage Switzerland’s image as a pioneer of respecting human rights among Muslims' public opinion," according to a report by the official Islamic Republic News Agency, or IRNA.

All true, perhaps, that the choice made the the Swiss voters will damage Switzerland's image among Muslims. But seriously, clean up your own house because you threaten other with unspecified consequences and urge them to care about human rights. This was easy to find:

An Afghan citizen was executed in a prison in northern Iran
One man was flogged 80 times and then hanged in a prison west of Tehran
30 people have been executed in the southwestern Iranian province of Khuzestan

Shermer/Prothero vs. Meyer/Sternberg continues

The debate between Shermer/Prothero and Meyer/Sternberg still has everyone in flames.

Now there's an audio of the debate available (I still have to find the time to hear it all).

Prothero rebuts the criticisms listed on the Discovery Institute's site.

And Michael Shermer has written his review of the debate, too, in which he points out the IDists convoluted debate tactics:

The problem, of course, is that evolutionary theory primarily deals with how life changes, not how it originated in the first place. No matter, because in the entire 25 minutes allotted for Meyer and Sternberg, they never once even mentioned the origin of life, and instead attacked “neo-Darwinism,” population genetics, rates of mutation, etc., none of which has anything whatsoever to do with the origins of life. By contrast, Don devoted his 15 minutes to instructing the audience on where the science of life’s origins is today, basically covering his 15-week college course in one minute per week’s worth of material.

(...)

Unbelievably, Meyer opened by accusing us of dodging the debate question!

Robert Crowther has a reply to Shermer, which contains this jewel:

In our uniform and repeated experience, information only comes from minds (read: intelligence). So why should we attribute the information in DNA to a mindless process like natural selection? Meyer doesnt' think we should. Obviously, ID is an inference from the evidence, not from religious scriptures or practices.

Bad, bad, bad inference.

Second, it is clear that Darwinists are unable to demonstrate that the mechanism they champion, natural selection acting on random mutation (the subject of the debate), is capable of accounting for the complexity and diversity of life. On the contrary, it is clear that it is incapable, a point made repeatedly during the debate by Sternberg and Meyer.

How is it clear? By what evidence? That Meyer et al. repeat that it is so does not make it so.

Still no word about the debate from Meyer/Sternberg to be seen anywhere. They are probably just busy doing science...

Evolution highlights IX

Yet another study of the evolution of bird beak size. This time in England, where a smaller fraction of some warbler population don't migrate to southern Spain every winter anymore (fools!), but stay in England eating an abundance of food provided by humans. Incipient speciation, I'd say. And also, yet another possible example of domestication. All in only 30 generations.

Under the headline of Evolutionary Bullshit, we get yet another rant against evolutionary psychology based on the assumption that all human behavior and preferences are learned, and on the tired tenet that if the science can be used to justify immoral behavior, then it is wrong. Good grief!

Comment moderation

The time has come when I am too annoyed with the spam. I get links to dating-sites and bots posting Viagra advertisements.

Comment moderation is on for posts older than seven days, and I've added a captcha image for commenting.

Supremely incompatible accounts of an ID/evolution debate

This is really strange.

It's not that I don't know that when two opposing sides debate, they will often walk away with different observations of what went down. We are human, and we are biased. We will naturally focus on the wins we get in, and automatically downplay our losses. So when Shermer/Prothero debates Meyer/Sternberg on Nevember 30th, it is not unsurprising that they will each report that the debate went well on December 1st.

But this is just waaaay over the top in that category. The accounts are parsecs apart.

Jonathan Wells and Robert Crowther each posted victory cries on the discotute's website, Evolution New & Views.

Crowther:

It was all shaping up to be a serious heavyweight bout. And then Meyer and Sternberg simply KO'd the competition in the opening round. If I were being generous I might say that Prothero tripped over his own arrogance and impaled himself on his condescension, but let's be honest; he was completely knocked out by Sternberg. I think Sternberg earned a third degree tonight, one in evolutionary bulldozing.

I read this first, and though to myself that surely he is exaggerating, but perhaps Prothero did somehow trip and make a fool of himself, perhaps misspeaking on some factual issue.

More Crowther:

To call the debate a massacre would be a discredit to Sitting Bull. The only thing I can say is that Shermer needs to add a point to his booklet on how to debate "creationists" — namely, leave Donald Prothero at home in his van by the river.

This guy is to be taken seriously? I had to remind myself not to laugh every so often during his presentation — it was so pathetic and ill-informed. Basically, Shermer and Prothero blathered on about supernaturalism, and Meyer ceded his time to Sternberg, who made an interesting presentation about whale evolution

(...)

Some of the best points came later in the debate, when Sternberg slammed Prothero with factual put down after factual put down, citing the current literature time and again. His command of the subject matter — from population genetics to junk DNA — was so far and above beyond Shermer and Prothero's knowledge, so far above their pay grade, that it was almost painful to watch him school them point after point.

Wow, right? Even if we expect the "winners" to exaggerate somewhat more than slightly, this is as far as I can tell an account of rare kind of resounding victory in a creationism/ID vs. evolution battle.

So, I looked around after an account from Shermer or Prothero, and found Prothero's on Panda's Thumb.

My subjective summary of it is that our side did very well: I caught them off-guard with new arguments they had no answer for;

Wait, what? I had to double-check that there weren't two different debates, but no.

More Prothero:

we both pushed them hard on the fact that neither of them ever addressed the topic of the debate, “Origins of Life.” I could tell that they were rattled a number of times, and I definitely shook up Meyer and got under his skin with my answers.

(...)

We both chastised them on ignoring the debate topic entirely, but to their minds, the debate was about Neo-Darwinian gradual selection.

(...)

At another point, I tried to get in a complete rebuttal to Sternberg’s weird whale argument, highlighting his invalid assumptions about population size, reproductive rates, and the constancy of point mutations, and arguing that a lot of people are looking at evo/devo to explain the suite of soft-tissue modifications that whales show. Somewhere in there, Meyer used the “condescending” sympathy line but their rebuttal to evo/devo was so garbled that they ended up arguing with each other about those hypothetical reconstructions of 12-winged dragonflies and completely missed the point of evo/devo. (I never got a chance to set that one straight). I knew they were desperate when they suddenly pulled out their “junk DNA” kit of lies, and I slammed them with endogenous retroviruses, pseudogenes, and the onion argument — and then Sternberg got all tangled up admitting these were real but trying to dismiss their importance. Even though the moderator let them get away with more time and interruptions, I feel like we held our own, and most of their garbage got a least a partial challenge and rebuttal from our side.

We then each took a few questions from the audience and moderator, and most were a piece of cake to answer.

(...)

We must have done something right to rattle Meyer as we did, getting under his skin so that he tried to question my qualifications to talk about molecular biology (and then I cut in with “I have a degree in biology”), pull out his “condescension” sympathy line, and now the DI flacks are now busy trying to spin and lie their way out of the debacle.

(...)

Several of the fence-sitters in the audience said I’d convinced them and beat the creationists soundly.

I mean, can these two accounts, supposedly of the same event, really be more at odds? I don't know who the heck Crowther is, but I do know Prothero. I read his book, I heard him talk, we've emailed, and he commented here. This gives me some feeling that he knows what he is talking about, that he isn't some kind of lunatic paleontologist, and that his words carry some weight. (I also know Shermer quite well, and can say the same things about him and his area of expertise.) But Crowther? I have no clue. I hesitate to Google him before I have written this... may I'll do it later. Stephen Meyer is a philosopher. Perhaps you see what I am getting at...?

But, do read both accounts and compare them yourself. And if we're real lucky, a video of the whole debate will go up in the near future, and we can all see for ourselves (that is the plan). I'll for sure see it and write about the experience.

Lecture on why it doesn't matter that Nidal Malik Hasan is Muslim

Here's a little lecture I would very much like to go to. It is, incidentally, right in my hood, but I am afraid I most likely won't be able to go.

Responding to the Fort Hood Tragedy

Imam Zaid Shakir will be presenting a talk to the Claremont College community to address the Fort Hood tragedy: the events asssociated with it as well as those ensuing from it. He will also explain how and why the crime perpetrated by Major Nidal Malik Hasan can not and should not be attributed to Islam.

Date: Wednesday, December 9, 2009
Time: 7:00pm - 8:00pm

"Should not" - sure, I can see why a Muslim would say so.
"Can not" - why not? I'd go to find out what his reason is.

Funny ad

I'm looking intensively for a postdic job for when (if) I graduate in the end of Spring 2010, and today I came across one of the funnies at the Broad Institute:

Job Title: Associate Computational Biologist - Infectious Disease Initiative

General abilities required: multi-task, work independently, collaborative skills, adapt to changing priorities, work in face paced environment, analytical skills, verbal communications skills, written communication skills, presentation skills

[Emphasis added.]

I'd love to work in a face paced environment. I'd also love to try a fast paste environment.

But, I am not going to apply. While EVERYTHING is evolution, this position requires only a Master's degree. What the hell would have been the point of the last four years, then? If my next job doesn't require a Ph.D., I'd much rather write a creationist handbook, slap "Ph.D" after my name on the cover, and go for the Templeton Prize.

Skeptic to save money and lives

Bruce M Hood is a writer and blogger from England, and he has come across information about a bomb-detection device used in Iraq. Bruce raises a lot of doubt about whether this device, the ADE651, works at all.

How To Make A Killing With the Woo Bomb Detector

The “ADE651 device” costs around £35,000 ($60k). It appears to be a telescopic car aerial attached to a black box. Inside there is a plastic card that is supposed to be ready programmed with an electromagnetic ‘resonance’ of what needs to be detected. It is claimed to be based on the principles of nuclear quadrupole resonance but from what I understand that would require generating a magnetic field and sending out a strong pulse – something that seems to be absent in the ADE651 – its powered by body energy! Even if it does use NQR then it seems highly implausible that it can work from an airplane 3 miles up as claimed in the product details. Still, they have already sold an unbelievable £51 million’s worth to Iraq.

The really interesting news here is that Bruce lives close by the company that manufactures the ADE651, and he is in the process of arranging a visit to see the device for himself, together with a physicists friend.

That would be highly interesting however it turns out. If the device doesn't function, then this is a major scandal. If Bruce and his friend goes away unconvinced, then one wonders how the company could get away selling for £51 million of them. If, on the other hand, the device works, then I can't wait to hear how that is. If so, then how could it be that

when a guard and a driver for The New York Times investigating this story, both licensed to carry firearms, drove through nine police checkpoints that were using the device, none of the checkpoint guards detected the two AK-47 rifles and ammunition inside the vehicle. Later, it even failed to detect a grenade and pistol in plain view on the table of the General in charge of the checkpoint, who replied that the operators needed more training.

Do check back with Bruce later on. I'll keep you posted here as well.