Evolution highlights XI

Speciation happens in coral reefs
This makes is all the more troubling that climate change are destroying the reefs, which may all be gone by 2050.

Oldest Land-Walker Tracks Found--Pushes Back Evolution
This does not make Tiktaalik uninteresting as a transitional fossil, but merely tells us that tetrapods evolved earlier than previously thought.

Evolutionary Surprise: Eight Percent Of Human Genetic Material Comes From A Virus
Not the only study that suggests that incorporating virus genetic material into our DNA has been important in our evolution.

Lately several items in the news about the evolution of resistance to herbicides and other drugs to control pests:

US-German team measures how quickly genomes change

On the other hand, the new findings easily explain why weeds become quickly resistant to herbicides. In a large weed population, a few individuals might have a mutation in just the right place in their genome to help them withstand the herbicide. "This is in particular a problem because herbicides often affect only the function of individual genes or gene products," says Weigel. A solution would be provided by herbicides that simultaneously interfere with the activity of several genes.

(...)

"Everything that is genetically possible is being tested in a very short period," adds Lynch, emphasizing a very different view than perhaps the one we are all most familiar with: that evolution reveals itself only after thousands, if not millions of years.

Disinfectants Cause Some Bacteria to Adapt, Thrive

The research team focused on Pseudomonas aeruginosa, a bacterium responsible for a range of infections in people with weakened immune systems. When the scientists added increasing amounts of disinfectant to P. aeruginosa cultures, the bacteria adapted to survive not only the disinfectant but also the antibiotic called ciprofloxacin.

(...)

"What is more worrying is that bacteria seem to be able to adapt to resist antibiotics without even being exposed to them."

What??? I just saw this, and I really must find out what the heck this is supposed to mean. How it is possible to adapt something that the organism has never been exposed yet is a mystery.

Dimwits rewriting history in Texas

The Texas State Board of Education decides the textbooks standards for Texas and influences the rest of the country, and it is simply scary what those ideologues are trying to do.

“I don’t care what the educational political lobby and their allies on the left say,” he declared at one point. “Evolution is hooey.” This bled into a rant about American history. “The secular humanists may argue that we are a secular nation,” McLeroy said, jabbing his finger in the air for emphasis. “But we are a Christian nation founded on Christian principals. The way I evaluate history textbooks is first I see how they cover Christianity and Israel. Then I see how they treat Ronald Reagan—he needs to get credit for saving the world from communism and for the good economy over the last twenty years because he lowered taxes.”

Holy sh....! These are the words of Don McLeroy (he's a dentist), and that's just awful. Talk about religion influencing science and education - and he isn't shy about breaking down the separation of church and state either.

The ultraconservatives argued that they were too light on basics like grammar and too heavy on reading comprehension and critical thinking. “This critical-thinking stuff is gobbledygook,” grumbled David Bradley, an insurance salesman with no college degree, who often acts as the faction’s enforcer.

I can just see the guy fighting to keep in the drool: "I just don't get this thinking part at all. Keep them children learning spelling and proper writin' instead."

Next they'll be demanding universities to relinquish the grip on professorships by the godless: "Qualified applicants are considered for employment without regard to age, race, color, religion, sex, national origin, sexual orientation, disability, veteran status, or belief in evolution."

A tempting offer indeed

Here's one of those Nigerian emails that puts the rest to shame:

please good day my name is shilsells from nigeria and i most be frank with you as a matter of your help please i am in need of a sum of $2,500 us$ to enable me move a sum of $17,million us$ to you within the next few days from now please kindly get back to me along with your cell phone number and your real name if you want to help me out, please if you are not interested to help me kindly dont reply this email i waiting to hear from you along with your cell phone number.

If you ever wondered how the scams promising you millions of dollars left by dead bankers work, here is the explanation. "We have all this money that we need to shift, but we need to buy a truck to haul it. We promise we will give you millions of dollars in return after you wire us 2,500 dollars first. Cross my heart and hope to die."

Also, I think I figured out why these letters often have so bad grammar and punctuation: It is done on purpose to better align themselves with the victims they are seeking - people who can't spell or construct a proper sentence.

Skeptics save money on audio-equipment

Great little article in eSkeptic this week on Audiophoolery: pseudoscience in consumer audio

Some audio scams are so blatant you wonder how anyone could fall for them, like a replacement volume control knob that sells for $485. The ad copy proclaims, “The new knobs are custom made with beech wood and bronze … How can this make a difference??? Well, hearing is believing as we always say. The sound becomes much more open and free flowing with a nice improvement in resolution. Dynamics are better and overall naturalness is improved.” Yes, I bet that’s just what they always say. Wood is a common theme among audiophile scams, falsely implying a relation to a fine old violin where the wood’s vibration really is a part of the sound. But a volume control knob?

Hahahahahahahahaha!

Indeed, a volume control knob made of wood improves the sound of your stereo? For nearly 500 dollars? Pulease. No one falls for that. Really? Who?

The article list loads of other scams that people need to be aware of if they are out to spend money trying to improve the quality of their audio-equipment.

Incidentally, when I was waay younger I played a gig with a band at a private party. Unfortunately, the wine was free, and I had too much before we played, and the drummer was pissed. As we finished, the sound of my amplifier suddenly disappeared. It was, apparently, quite dead, without even a hiss left over. The band broke up after this, and no one ever really told me why.

Fuckers.

I took my amp to repairs (at a place on Åboulevarden in Copenhagen, in case that means anything to you), and they told me the pap was broken (the thing that makes up the vibrating part of the speaker), and I paid approximately $500 for the repairs. Too bad, because I had next to no money at that time (now I have somewhat less).

Then much later I was playing in a new band sharing a room for practice with another band. One day my amp was again completely dead in exactly the same way as before. But this time I noticed that the electrical fuse was gone and had been used elsewhere by someone from the other band. Once reinserted, the amp was fine.

The rest is theory: The drummer in the first band removed the fuse to shut me up, and never deigned to tell me [and, if this guy should be reading this: Fuck you, asshole!]. Then, at the repair shop, I was totally scammed. What they told me was a complete lie. If the pap had been broken, there would still have been an electrical hiss audible - it would not have totally silenced the amp. All they did was replace the fuse and make up a story to earn free money from an unsuspecting twenty-year-old.

I think that place went out of business. Good. I never heard from that drummer again. Good.

In between those two bands I played for a while with three guys who eventually threw me out because I wasn't grown up enough for them, or something. It was a really ambitious band with our own material, and we had been practicing forever to get out and play live when they offed me. The singer called me first and told me not to panic, but not why I should or shouldn't. Then they came to my home and told me the news.

Years later I met the drummer of that band in a bar, and when I asked he told me that the band broke up some time after I left, because they were unable to find a replacement bass player.

What would be an appropriate comment to end with?

Pursue your scientific failures

It is no exaggeration I think to say that I have had my share of failures, but I have also had a bit of luck. The path of trial and error epitomized by "" [I am still trying to remember this one] and "chance favors the prepared mind", while perhaps trivial or, in some situations, unavoidable, is the way to succeed.

Now, as detailed in a Wired article, Accept Defeat: The Neuroscience of Screwing Up, research on research suggest that scientific researchers should embrace their failures a lot more than they apparently do. Rather than taking failures in experiments at face value, research shows that researchers explain them away because they don't conform to theory. Here's how to correct that:

There are advantages to thinking on the margin. When we look at a problem from the outside, we’re more likely to notice what doesn’t work. Instead of suppressing the unexpected, shunting it aside with our “Oh shit!” circuit and Delete key, we can take the mistake seriously. A new theory emerges from the ashes of our surprise.

(...)

While the scientific process is typically seen as a lonely pursuit — researchers solve problems by themselves — Dunbar found that most new scientific ideas emerged from lab meetings, those weekly sessions in which people publicly present their data. Interestingly, the most important element of the lab meeting wasn’t the presentation — it was the debate that followed. Dunbar observed that the skeptical (and sometimes heated) questions asked during a group session frequently triggered breakthroughs, as the scientists were forced to reconsider data they’d previously ignored. The new theory was a product of spontaneous conversation, not solitude; a single bracing query was enough to turn scientists into temporary outsiders, able to look anew at their own work.

Our weekly lab meeting is in ten minutes. Expect a breakthrough.

This is why other people are so helpful: They shock us out of our cognitive box. “I saw this happen all the time,” Dunbar says. “A scientist would be trying to describe their approach, and they’d be getting a little defensive, and then they’d get this quizzical look on their face. It was like they’d finally understood what was important.”

Yeah! I concur.

Incidentally, the example used in the article is Penzias' and Wilson's experimental discovery of the cosmic microwave background radiation left over from the Big Bang. They got the Nobel prize for that, but I think it should have been given to Gamow for predicting it.

---

Update 1/25:
I finally remembered (the brain is a curious thing):
"Success comes from experience, and experience comes from failure."
I also had a gigantic déja vu this afternoon. I wonder if these two events are connected?

Lethal mutagenesis

Drugs fight bacteria and viruses by killing them fast, but the problem is that this eventually leads to the microbes evolving resistance to the drug. However, if another drug was given that increases the mutation rate of the microbe, perhaps this would lead them to die out, since most mutations are harmful?

Carl Zimmer interviews several scientists in The New York Times on the matter of lethal mutagenesis, and the question of whether the microbes could evolve resistance to the mutagenic drug is raised.

Irish blasphemers

Atheist Ireland has put up a list with quotes by famous people who would have fallen under the new blasphemy law in Ireland. It includes Mr Christ, Muhammad, Mark Twain, Tom Lehrer, Frank Zappa, Salman Rushdie, Bjørk, George Carlin (duh!), Tim Minchin, Richard Dawkins, the current Pope, Christopher Hitchens, PZ Myers, and some Irish clergy and politicians to round it off.

Clearly this blasphemy law, making material "that is grossly abusive or insulting in relation to matters held sacred by any religion, thereby causing outrage among a substantial number of the adherents of that religion; and he or she intends, by the publication of the matter concerned, to cause such outrage" a crime, will not work, unless they plan to seriously fine their own politicians and clergy €25,000 (though I wonder if they get a pass because what they said was not intended to cause an outrage).

I am not scheduled to go to Ireland any time soon, but foreseeing that I will at some point (and that I have loads of Irish readers - 208 to be exact in 2009), I will here post something that I trust someone will find grossly abusive or insulting to their religion, intending and hoping to cause an outrage among a substantial number Christians:

"The Christian doctrine that a good person is expected to go to Heaven enjoying the rest of eternity while some of his or her loved ones will be tortured in Hell for the same amount of time, because they didn't live up to the same standard, is so emphatically evil, that should God really exist, I hope to get the chance to say to his damned racist, misogynist, vain, unjust, unloving, and selfish face just how much I despise him."

Additionally, since the Irish law doesn't define "any religion", I think before I go to Ireland I better give people a fair warning that according to my personal religion, under which it is blasphemy to refer to The Religion as anything but "The Religion", it is highly blasphemous to talk about the notion of life after death, because in The Religion we aren't given any information about the afterlife, and therefore it may not be discussed in any form or shape, including it's very existence, except by the high clergy of The Religion, which currently includes only me, and doing so will tangibly insult and abuse all followers of The Religion, which currently also only includes me.

---

Interestingly, PZ will be going to Ireland soon. Hopefully he will get arrested on arrival.

---

Update 1/4/2010:
George Carlin is just too precious not to quote:

15. George Carlin, 1999: “Religion easily has the greatest bullshit story ever told. Think about it. Religion has actually convinced people that there’s an invisible man living in the sky who watches everything you do, every minute of every day. And the invisible man has a special list of ten things he does not want you to do. And if you do any of these ten things, he has a special place, full of fire and smoke and burning and torture and anguish, where he will send you to live and suffer and burn and choke and scream and cry forever and ever ’til the end of time! But He loves you. He loves you, and He needs money! He always needs money! He’s all-powerful, all-perfect, all-knowing, and all-wise, somehow just can’t handle money! Religion takes in billions of dollars, they pay no taxes, and they always need a little more. Now, talk about a good bullshit story. Holy Shit!”

Carnival of Evolution #19

A new edition is up on Christie Wilcox's blog, Observations of a Nerd.

Notice that this is a very important edition: It is the first after the celebration of Darwin 200th birthday (year) has ended, and there is some speculation that nothing much will happen in evolution research and blogging in 2010. Fourteen submissions for January 2nd isn't bad at all in that light. However, those posts and that research was of course done last year, so maybe the February edition is going to really slim?

It is still to be decided what the hosting schedule for this spring will be - just a few have volunteered so far, and I'd like to hear from more before I write a list. But, rest assured there will be a new CoE #20 up somewhere in the beginning of February, so don't forget to submit one (good) or two (better) posts about evolution before then. Please use this online form to submit.

Image from Lab Rat's post on bacterial cell wall evolution.

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.

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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.