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The layers and fault-lines of genes | Gene Expression
At Genomes Unzipped Luke Jostins elaborates on how the genetic facts he now has about his paternal lineage change how he views his own personal history:
… my father’s father is Latvian, and the N1 haplogroup is not rare in the Baltic regions. In fact, the subgroup, N1c1, is more common in parts of Eastern Europe than it is in Asia.
Initially, this seemed to play nicely into a part of our ancient family history. There is a folk history, relayed to me be my Dad and my uncle Johnny, that Jostins blood may contain traces of Mongolian. The justification for this is that in around 1260, just before the civil war caused the Mongol Empire to die back in Europe, the Empire extended all the way to the Baltic States. It was at this point, my fellow N1c1-bearers hypothesise, that Mongolian DNA entered the Jostins line.
Unfortunately on closer inspection this tale is not really supported by the DNA evidence. The famous Mongol Expansion haplogroup is actually C3, which is the modal haplogroup of Mongolians. In contrast, N1c1 has existed in Europe for thousands of years, and is far to old and too wide-spread to represent a recent expansion.
To the left is a frequency map of the concentration of N1c1. Based on the current distribution, and the diversity being modal in the East Baltic, one has to be skeptical of a simple east-west model. Interestingly the frequency difference of this haplogroup between Finland and Sweden is very high. Also, branch of N1c1 seems to be found among the Rurikids of Russia. This was the ruling dynasty of the Rus, a people who originally seem to have been ethnic Scandinavians from Sweden. Eventually they ruled over a polyglot state of Finns, Slavs and Scandinavians, and submerged their own identity with that of the Slavic peasants. In this they followed the example of the Bulgars, who were ethnically distinctive from their Slavic subjects, but were totally absorbed excepting that their ethnonym persisted. There is some evidence that the Serbs are a similar case, an Iranian group which was eventually absorbed into the South Slav substrate.
Going back to northern Europe, let’s try to get some more perspective. Luke Jostins’ personal history is after all a slice of population history, and what we know about the background of the population impacts how Luke views his own personal history. To do that I thought I’d quickly poke around a few older papers on Baltic genetics which I had stashed away. It didn’t turn out to be so quick. But here are some figures. First, from Genome-Wide Analysis of Single Nucleotide Polymorphisms Uncovers Population Structure in Northern Europe:
From Genetic Structure of Europeans: A View from the North–East:
Finally, from Migration Waves to the Baltic Sea Region (N3 = N1c1):
Also see my recent posts on Northern European genetics, as well as the argument about agriculturalists vs. farmers. Ten years ago we have a few simple models, but now it gets more confusing and complicated. Confounders:
- Different reproductive skew parameters for males and females. In short, high fertility of “super-males” as well as dominance of patrilocality can produce different patterns in Y and mtDNA
- Selection on mtDNA. The “neutral” markers which we think of as neutral may not be neutral
- Poor correspondence between inferences of the past based on contemporary patterns of variation and what ancient DNA has discovered. Our assumptions are faulty, or we’re just too stupid to extract the real patterns
- Persistent problems with dating and typing some uniparental lineages. Consider the debate over the pan-Eurasian haplogroup R1a1a* (Dan MacArthur and I both carry this Y lineage, but what’s in a few letters?)
- Reality is complicated. This may be the most intractable issue over the long term
I have used the analogy of a palimpsest to describe the flow of genetic variation over time and space. I think that perhaps that that is misleading in some fundamental ways. Demographic patterns are characterized by different dynamics, persistent and long standing “flows,” as well as punctuated “explosions.” Rather than a palimpsest, a better analogy might be the layering of geological strata. Although there are long periods of gentle wearing and layering, volcanism and earthquakes periodically erupt to disrupt the smooth accumulations. Sequences of catastrophic events can produce inversions.
Consider three dynamics:
- Isolation-by-distance. This is the conventional band/village-to-band/village process of gene flow. This may be analogized to sedimentary accumulation (mutations) and erosion (drift)
- Demic diffusion. The rapid demographic expansion into virgin territory by a culture which introduces a more efficient mode of production. One of the most recent occurrences of this was the rapid multiplication of New England Puritans from ~30,000 circa 1640 to over 700,000 150 years later. Not only did these New Englanders “fill up” their home territory, in the early years of the republic they burst out of the northeast and populated many regions of the Great Lakes. Demic diffusion is like an earthquake, a rapid and ordered shift of the local geology
- The leap frog. The settlement of Europeans in the southern cone of Latin America, Australia, or Mongols in eastern Iran, are instances of leap frogs. We have clear textual of these leap frogs, but without that we wouldn’t know what to make of them. Leap frogs are like volcanic eruptions, reordering the layers beneath and also deposition from above
At least with Luke’s hypothesis about descent from Rurik he can test his own N1c1 profile against other Rurikids. Presumably the modal haplotype and its near relations are those of the original Rurik.
NCBI ROFL: And you thought walking while chewing gum was hard. | Discoblog
Effect of masticating chewing gum on postural stability during upright standing.
“The purpose of this study was to investigate the effect of masticating chewing gum on postural stability during upright standing. To address this issue, 12 healthy subjects performed quiet standing on a force platform for the posturography study. The subjects were instructed to stand as stable as possible on the force platform in order to record the trajectory of the center-of-pressure (COP). After measuring the postural sway in the initial condition (pre-condition), the subjects were asked to stand while masticating chewing gum (gum-condition). Following the gum-condition, quiet standing without mastication was evaluated (post-condition) to ensure the effect of masticating chewing gum on postural stability. The trajectory and velocity of the COP were analyzed for each condition. We found that the postural stability tended to enhance during mastication of chewing gum. The rectangle area of the COP trajectory significantly diminished in the gum-condition and significantly enlarged in the post-condition. A similar effect was observed in the maximum velocity and standard deviation (SD) of the fore-aft amplitude of the COP trajectory. The values were significantly smaller in the gum-condition compared to those in the post-condition. These findings suggest that mastication of chewing gum affects the postural control by enhancing the postural stability during upright standing.”
Photo: flickr/sjon
Thanks to Lee for today’s ROFL!
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WTF is NCBI ROFL? Read our FAQ!
iPhone Users Report That Daydreams Make Them Sad | 80beats
In many high-tech parts of the world, iPhones are what people turn to when their minds wander from what they were supposed to be doing. For a study in this week’s Science, however, researchers turned the tables on these people, using the iPhone as a tool to study the wandering mind. Matthew Killingsworth and Daniel Gilbert found that the minds wanders a lot (no surprise there), but also that daydreaming could make people unhappier.
Their app, called Track Your Happiness, takes advantage of the iPhone’s unparalleled ability to butt into its owner’s life.
iPhone users, aged 18 to 88, signed up for a Web application that contacted study them at random times during their days to ask a simple set of questions: How happy were they at the moment? What were they doing? Were they thinking about something other than what the task at hand, and if so, were they thinking of something pleasant, neutral, or negative? [Boston Globe]
The stats: “We analyzed samples from 2250 adults (58.8% male, 73.9% residing in the United States, mean age of 34 years),” the scientists write. Altogether, 46.9 percent of the time the responders said their minds were wandering when the iPhone rang to query their thoughts. The only activity during which people reported daydreaming less than 30 percent of the time was having sex. (Though, this means respondents either stopped having sex long enough to answer the survey—in which case DISCOVER applauds their dedication to science, but questions their judgment—or they heard the phone buzz and thought, “That must be the survey, I should answer it afterward”—in which case they perhaps were lying about not being distracted.)
But Killingsworth and Gilbert’s main finding is that all this mind wandering does generally make people unhappier, at least according to the self-reported survey. Respondents who reported that their thoughts had drifted from the task at hand were more likely to declare themselves unhappy.
The link may be due to an asymmetry in how daydreams affect mood. Killingsworth and Gilbert found that daydreams about pleasant things were linked to improvements in mood, but only slight improvements. Thinking about neutral topics while mind-wandering was linked to a similarly modest drop in happiness, but daydreams about unpleasant topics coincided with a 20-point drop on the 100-point scale that app users used to rate their mood. [New Scientist]
Eric Klinger, a daydream researcher at the University of Minnesota, Morris, told the Boston Globe that this study’s data backs up what scientists have found about the frequency of mind-wandering in the past. However, he says, isn’t it possible that getting interrupted by your iPhone asking you how you’re feeling could change how you’re feeling?
He noted that it would be interesting to know whether the interrupted activity, itself, was experienced as pleasant or not, to better understand whether the nature of the activity influenced a person’s happiness. “Daydreaming and mind-wandering serve a number of crucial roles,” Klinger said. “They are nature’s way of keeping us organized.” [Boston Globe]
On behalf of lifelong daydreamers everywhere, I appreciate this defense of letting one’s mind drift away, even if it doesn’t always lead to happiness.
Innovative ideas and insights often arise through free association. And being able to plan and strategize effectively require a focus on the future, not the now. “There’s no doubt that this capacity is beneficial in a variety of ways and it’s certainly very possible that a lot of creative thinking involves mind wandering,” says Killingsworth. [TIME]
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Image: flickr / William Hook
Each Time Your Cat Takes a Sip, It’s a Marvel of Physics | 80beats
Cats have been our companions for almost 10,000 years. They have been worshipped by Egyptians, killed (or not) by physicists, and captioned by geeks. And in all that time, no one has quite appreciated how impressively they drink. Using high-speed videos, Pedro Reis and Roman Stocker from the Massachusetts Institute of Technology has shown that lapping cats are masters of physics. Every flick of their tongues finely balances a pair of forces, at high speed, to draw a column of water into their thirsty jaws.
Read the rest of the post at Not Exactly Rocket Science, where Yong explains that each sip is a tug-of-war between inertia and gravity. Here’s a little of that high-speed video:
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Prescription for an Aggressive Man: Look at More Meat | Discoblog
Even the sight of the reddest, rawest steak won’t get your blood boiling. Surprising new research has found that staring at pictures of meat actually makes people less aggressive.
The insight comes from McGill University undergraduate Frank Kachanoff. He wondered if the sight of food would incite men’s defensive desires, much like a dog aggressively protecting its food bowl, he explained in a press release:
“I was inspired by research on priming and aggression, that has shown that just looking at an object which is learned to be associated with aggression, such as a gun, can make someone more likely to behave aggressively. I wanted to know if we might respond aggressively to certain stimuli in our environment not because of learned associations, but because of an innate predisposition. I wanted to know if just looking at the meat would suffice to provoke an aggressive behavior.”
To determine aggression, the experimenters put a man in a room and give him the ability to punish a person who was sorting photograghs. In one iteration of the test the pictures showed neutral objects, and in the other they showed cooked meat dishes. The amount of painful sound the participant decided to inflict on a bad picture sorter for his mistakes was used as a guide to the level of aggression the participant was feeling.
Kachanoff presented his work at an undergraduate research symposium at McGill. He found that the men who watched the sorter work with pictures of meat inflicted less painful punishment than the men watching the neutral pictures, which makes some sense in hindsight, Kachanoff explained in a press release:
“We used imagery of meat that was ready to eat. In terms of behaviour, with the benefit of hindsight, it would make sense that our ancestors would be calm, as they would be surrounded by friends and family at meal time,” Kachanoff explained. “I would like to run this experiment again, using hunting images. Perhaps Thanksgiving next year will be a great opportunity for a do-over!”
With all such evolutionary explanations for modern behavior, this should probably be taken with a few grains of salt (just like a tasty steak should be). But it would be interesting to see if this phenomenon would carry over into any other food images, and if meat had the same effect on females.
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Image: Flickr/soyculto
How the cat that got the cream then drank it | Not Exactly Rocket Science
Cats have been our companions for almost 10,000 years. They have been worshipped by Egyptians, killed (or not) by physicists, and captioned by geeks. And in all that time, no one has quite appreciated how impressively they drink. Using high-speed videos, Pedro Reis and Roman Stocker from the Massachusetts Institute of Technology has shown that lapping cats are masters of physics. Every flick of their tongues finely balances a pair of forces, at high speed, to draw a column of water into their thirsty jaws.
Drinking is more of a challenge for cats than for us. They have to drink from flat, horizontal bodies of water. Even with our hands tied, we could do that just by putting out mouth at the surface and sucking, but then we have large cheeks that can form a proper seal. Pigs, sheep and horses have the same ability, but cats and dogs do not. Their cheeks don’t extend far enough forward so they have to use a different technique: lapping.
Cat owners have watched their pets lap at water for thousands of years but when Stocker did so, his curiosity was piqued. “Three years ago, when I was watching my cat Cutta Cutta lap during breakfast, I realized there was an interesting biomechanics problem behind this simple action,” he says. The lapping motion is so fast that to fully appreciate it, you need a high-speed camera. Slow-motion films of Cutta Cutta revealed that a cat doesn’t actually scoop up its drink with its tongue in the way that a dog does. Its technique is more subtle.
For a start, it drinks only using the very tip of its tongue. As it extends its tongue, it curls the tip upwards so that the bottom side rests on the surface of the liquid, without actually breaking it. The cat lifts its tongue, drawing a column of liquid with it. Just before the column collapses, the cat closes its mouth, captures the elevated liquid, and takes a refreshing drink.
This sequence depends on a battle between two forces. The first is inertia, the tendency for the water column to keep moving in the same way until another force acts upon it. That force is gravity, which constantly threatens to pull the water column back into the bowl. With its rising tongue, a cat uses inertia to “defeat gravity” long enough to close its mouth on the almost-collapsing tower of liquid.
Amazingly, Reis and Stocker found that this sequence was first filmed way back in 1940, in an Oscar-winning documentary film called Quicker ‘n a Wink (the cat’s at 4:42). “MIT has a center for high-speed photography started by and named after Doc Edgerton,” says Stocker. “After we had borrowed high-speed cameras several times to get shots of Cutta Cutta, conversation casually turned to the topic of our investigation. When Jim [Bales, who runs the center] heard it was the lapping of a cat, he got very excited and immediately pointed us to a 10 second video clip by Doc Edgerton, who had captured high-speed videos of a cat lapping 70 years ago! Edgerton did not attempt to explain the mechanism of lapping, but his clip remains timeless (the commentary even more so!).”
Skip forward 70 years, and Stocker and Reis’s modern (and colour) videos reveal the action in even greater detail. Reis used these to work out Froude’s number, a value that measures the trade-off between inertia and gravity. For domestic cats, the number is 0.4, close enough to 1 to indicate a good balance between the two forces.
The duo also analysed the lapping action using a glass disc to mimic the tongue-tip of a cat, and robotic stage to lift the disc at pre-programmed speeds and heights. These revealed that the cat pulls its tongue back at just the right speed and to just the right height to draw the largest volume of water into its mouth.
Stocker and Reis even found that all types of cats, from the humble house tabby to the mighty tiger, lap in the same way. He grabbed some films from a local zoo and in an astonishing case of the Internet providing useful cat videos, he scoured YouTube for videos of big cats lapping. The videos showed that just like domestic cats, the Froude’s numbers for lapping tigers, lions and leopards are all close to one. Again, inertia and gravity are play off against each other to produce the greatest possible sip, although the bigger cats compensate for their bigger tongues by lapping more slowly.
All of this started with something as simple as a cat owner watching his pet drink from a bowl and wondering how it does it. From there, the team pursued their project without any funding, or help from graduate students. They just really wanted to know the answer. If you look at the world through the eye of a scientist, even an unassuming sight like a cat drinking from a bowl can be a cool discovery just waiting to happen. Rather than killing cats, curiosity can thrive on them.
Reference: Science http://dx.doi.org/10.1126/science.1195421
More on cats:
- Cats manipulate their owners with a cry embedded in a purr
- Sabre-toothed cats had weak bites
- How many people did the man-eating lions of Tsavo actually eat?
- Pocket Science – 2.1 billion year old fossils, and arm-wrestling a sabre-tooth cat
If the citation link isn’t working, read why here
Stem Cell Injections Give Mice Mighty Muscles | 80beats
Injecting stem cells into injured mouse muscle not only helped the muscle heal, but gave the mice enhanced muscle mass for years to come.
The study, published in Science Translational Medicine, used skeletal muscle stem cells from young donor mice and injected them into injured muscles of mature mice. Researchers figured that the stem cells would be able to create new muscle cells in the recipient mouse, but the question was: could these new cells be incorporated into the existing muscle on an adult mouse?
After injuring the recipient mouse’s muscle and injecting the cells, the researchers noticed that the injury healed quickly and the mice had larger muscles (about twice the volume, and a 50 percent increase in mass) than before the injury, which they expected. But were surprised to see that the muscle enhancement was sustained throughout the recipient mouse’s lifetime, up to two years.
“This was a very exciting and unexpected result,” [Bradley] Olwin, who worked on the study, said in a statement. “We found that the transplanted stem cells are permanently altered and reduce the aging of the transplanted muscle, maintaining strength and mass.” [Reuters]
The recipient muscle had to be injured, though, to accept the stem cells. When the researchers injected the cells into uninjured muscle they weren’t incorporated into the muscle and they didn’t see changes in muscle mass or volume.
“The environment that the stem cells are injected into is very important, because when it tells the cells there is an injury, they respond in a unique way,” [Olwin] said. The team hopes eventually to find drugs or combinations of drugs that mimic the behavior of transplanted cells. [Reuters]
The researchers say a similar procedure could possibly help aging muscles regain their vigor, or could help people suffering from muscular diseases, such as muscular dystrophy. But human trials are still a long way off. Hans Degens, an expert on muscle atrophy who wasn’t involved in the current study, explains:
“One of the worrying things for humans is the need for an injury to be simulated prior to treatment. In muscle wasting you would have to decide which muscles to treat, as the treatment would only affect a single muscle. It should also be noted that mouse muscles are considerably smaller than human muscles – you may have to make multiple injections.” [BBC News]
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Bad Astronomy audio book now available | Bad Astronomy
My first book, Bad Astronomy, came out in 2002. It’s enjoyed a few printings since then, and still sells nicely.
I get a lot of requests for an audio version, and I’m happy to announce that Audible.com has made one! It’s narrated by Kevin Scullin, a nice guy who contacted me a while back about it. We had some interesting email exchanges, mostly involving pronunciations. That’s something that hadn’t occurred to me! When you write a book, mispronouncing a word in your head is no big deal, but I imagine will generate a lot of mail in an audio book.
The book sells for $19.95, but they have a deal there where you can get it $7.49. Go to the link above for details.
Not to forget you UK folks, there’s a version for you guys as well. It’s pretty much the same, but in your version color is spelled with a u.
There’s a sample on the Audible site, and it’s a little odd to hear my words spoken by someone else. I guess I’ll never make it as a screenwriter.
Anyway, if you get a copy, please leave a comment and let me know what you think! And also rate it on the Audible site. I’m sure they dig that kind of thing. Thanks!
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NASA Woes: Hubble’s Replacement Behind Schedule; Shuttle Cracks Found | 80beats
Hubble’s successor will be late, and over-budget. So concluded a NASA panel this week that investigate the James Webb Space Telescope, NASA’s next big thing, intended to survey the skies in infrared light with its 18-segment mirror. The word all along has been that James Webb would launch in 2014 at a cost of $5 billion, but the independent review (pdf) concluded that the earliest possible launch would be September 2015, and at a cost of more like $6.5 billion.
The report raised fear that other projects would be hurt. “This is NASA’s Hurricane Katrina,” said Alan P. Boss, who leads the subcommittee that advises NASA’s astrophysics program. The telescope, he said, “will leave nothing but devastation in the astrophysics division budget.” [The New York Times]
John R. Casani, who managed missions like Cassini and Voyager that are the picture of NASA success, led the panel. The technical side of the Webb telescope isn’t the problem, the report found–the management side is. The report faulted the management team for failing to make realistic estimates of the project’s costs and timetable, and further criticized NASA headquarters for not calling the managers on their impractical assessments.
Even to meet the delayed launch date of 2015, Casani says, NASA would need to scrounge up an additional $200 million next year and in 2012. Christopher J. Scolese, NASA associate administrator, said that feat of financial juggle was unlikely. But Charles Bolden, the head of NASA, said he would act on the recommendation to shake up the project’s management.
“No one is more concerned about the situation we find ourselves in than I am, and that is why I am reorganizing the JWST Project at Headquarters and the Goddard Space Flight Center, and assigning a new senior manager at Headquarters to lead this important effort,” Bolden said in the statement. [MSNBC]
All this comes just weeks after Nature called JWST “the telescope that ate astronomy” and wondered whether the telescope’s huge scale and budget would squeeze out other projects, leaving science too dependent on the big machine.
It hasn’t been the best month for NASA, anyway. A planned space shuttle Discovery launch was delayed last week after inspectors found a fuel leak. Subsequent looks at Discovery have now turned up cracks in the external fuel tank that could indefinitely delay the mission.
The two cracks – each 9 inches long – were found on the exterior of the aluminum tank, beneath a larger crack in the insulating foam that covers the 15-story tank. The cracks are in an area that holds instruments, not fuel. NASA spokesman Allard Beutel said engineers believe the tank can be repaired at the launch pad, although it’s never been tried before. It’s unclear, though, whether the work can be done in time to meet a Nov. 30 launch attempt. [AP]
Lastly, a bit of good news: The ever-productive Cassini probe, which surprised its operators by going into safe mode on November 2 in the midst of its grand tour of the Saturn system, should be fully operational again before Thanksgiving.
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Image: NASA/MSFC/Emmett Givens
Trouble. | The Intersection
Over at The Star:
U.S. Representative John Shimkus, possible future chairman of the Congressional committee that deals with energy and its attendant environmental concerns, believes that climate change should not concern us since God has already promised not to destroy the Earth.
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Shimkus already serves on the committee. During a hearing in 2009, he dismissed the dangers of climate change and the warnings of the scientific community by quoting the Bible.
First, he noted God’s post-Flood promise to Noah in Genesis 8:21-22.
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“The Earth will end only when God declares it’s time to be over. Man will not destroy this Earth. This Earth will not be destroyed by a Flood,” Shimkus asserted. “I do believe that God’s word is infallible, unchanging, perfect.”
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On Tuesday, Shimkus sent a letter to his colleagues burnishing his credentials by saying he is “uniquely qualified among a group of talented contenders to lead the Energy and Commerce Committee.”
Representative Shimkus may be unique, but he’s certainly not uniquely qualified to lead the nation’s Energy and Commerce Committee. Climate change isn’t simply about balmier temperatures, but a changing environment. The nation–and world–need to prepare for the myriad of ways it will impact food production, water, health, national security, immigration, and so much more. Shimkus clearly fails to understand what’s at stake.
Your Next Sponge Bath May Come From a Robot Named Cody | Discoblog
A team at Georgia Tech is looking to replace your sponge bath nurse with this sexy beast to the right. No, not the girl. The sponge bath robot next to her, named Cody. He’s the one that wants to wipe you down with his delicate towel hands.
The robot was developed by researcher Charles Kemp’s team at the Healthcare Robotics Lab, and was described in a presentation and accompanying paper (pdf) at the International Conference on Intelligent Robots and Systems.
The robot uses cameras and lasers to evaluate the human’s body, identifying dirty spots, then gently wipes with its towel hands, making sure not to apply too much or too little pressure. It has flexible arm joints with low levels of stiffness to make sure that it doesn’t push too hard.
Study coauthor Chih-Hung (Aaron) King put himself in the tester’s spot for the robot’s first rubs. He relived the experience for Hizook:
“As the sole subject in this initial experiment, I’d like to share my impressions of the interaction. In the beginning I felt a bit tense, but never scared. As the experiment progressed, my trust in the robot grew and my tension waned. Throughout the experiment, I suffered little-to-no discomfort.”
Hit the jump for a video of the bot rubbing on King:
An interesting note about robots performing this kind of task: They are the ones that initiate human-robot contact. It may not seem like a big deal, but being in the receiving position of a robot-induced sponge bath might be a little unnerving, King explained to Hizook:
“The tasks performed in this experiment involved the robot initiating and actively making contact with a human. This differs from most (current) research on human-robot contact, which is initiated by humans rather than robots. It would be interesting to study how the general population, specifically patients, would react to such robot-initiated contact. Indeed, the psychological impact of robot-initiated contact may become important for future human-robot interaction (HRI) research.”
Meanwhile, we can’t make up our minds: Would it be more unnerving having Cody wipe you down than it would be embarrassing to have a human nurse or loved one do it?
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Image: Travis Deyle/Hizook Video: Georgia Tech Health Robotics Lab
Ancient Rocks Show Oxygen Was Abundant Long Before Complex Life Arose | 80beats
A huge spike in the Earth’s atmospheric oxygen about 800 million years ago, the story goes, paved the way for the Cambrian explosion a couple hundred million years later, and with it the rise of complex life. But a new study out in Nature says that picture is incomplete. Researchers found evidence of substantial oxygen 1.2 billion years ago, meaning that the conditions needed for complex life appeared much earlier than scientists knew, and that perhaps something else was required to set off the explosion of biodiversity.
The geologists led by John Parnell hunted in the Scottish Highlands for clues in ancient rocks, where evidence of ancient bacteria could reveal how much oxygen was around 1.2 billion years ago.
Before there was a useful amount of free oxygen around, these bacteria used to get energy by converting sulfate, a molecule with one sulfur atom and four oxygens, to sulfide, a sulfur atom that is missing two electrons. Geologists can get a glimpse of how efficient the bacteria were by looking at two different sulfur isotopes, versions of the same element that have different atomic masses. Converting sulfate to sulfide leaves the rock with a lot more of the isotope sulfur-32 than would be there without the bacteria’s help. [Wired.com]
Those isotopic levels showed Parnell how efficiently the bacteria used oxygen in the cyclical chemical reactions, with one group of bacteria turning sulfate into sulfide and another doing the opposite conversion. This allowed the geologists to gauge how high the atmospheric oxygen level may have been, Parnell says.
“Evidence of this chemical reaction tells us that the levels of oxygen in the atmosphere were at this key point for evolution, at this much earlier stage in Earth’s history. Our findings, which shift this key point in the evolution of life on Earth to a much earlier date than previously proven, will give impetus to further investigations into the timescale of the development of complex life, which followed this event,” he said. [The Independent]
Suppose Parnell’s team is correct, and these chemical reactions mean that the level of oxygen 1.2 billion years was roughly the same as the during the Cambrian explosion—that is, high enough to give rise to more complex forms of life than simple microbes. Then why did complex life wait so long to get going? It’s an open question, but one possible trigger was the end of an ice age:
The earliest indisputable evidence for complex animal life – slug-like organisms called Kimberalla – are not seen until the Ediacaran Period, which came at the end of the last great global glaciation These fossil remains are found today in 555-million-year-old rocks in Australia and Russia. “What we are now showing is that the conditions in the atmosphere were in place [1.2 billion years ago], so it probably needed some other factor to trigger the early evolution of complex life and the fact that the Ediacaran fauna occurs after the ’snowball Earth’ episode suggests those two are linked somehow,” said Professor Parnell. [BBC News]
Related Content:
DISCOVER: Just One Bite And Life Took Off
80beats: How “Snowball Earth” Could Have Triggered the Rise of Life
80beats: Why Didn’t the Young Earth Freeze Into an Ice Ball?
80beats: One of the Earth’s Earliest Animals Left Behind “Chemical Fossils”
80beats: Study: 650-Million-Year-Old Sponges May Be World’s Oldest Animals
Image: Parnell et. al / Nature (The cave where the rocks were found)
More bad news about the Congressional Energy Committee | Bad Astronomy
Remember yesterday when I pointed out the Republican Congressman Joe Barton who wants to be head of the Energy and Commerce Committee? Well, there are other Republicans vying for it. One of them is John Shimkus from Illinois. You need to understand that this Committee has a lot of overlap with the issue of global warming, as oil, gas, and coal are major contributors to the buildup of CO2 in the atmosphere.
Having said that, gird your loins to hear what Representative Shimkus had to say last year:
Did you catch the important bit there? God will decide when to end the Earth, not man. The obvious inference is that Congressman Shimkus thinks humans cannot destroy the Earth, or hurt its habitability. Terrific.
This is the same guy who tried to argue that producing less CO2 would starve plants.
The last thing this country — this world — needs, quite literally, is someone running the Energy and Commerce Committee who is this egregiously and willfully ignorant about global warming and the effects of carbon dioxide. Of course, tied for last place is Joe Barton. A third Republican, Fred Upton of Michigan, is also eying the top spot on the Committee, and I’m not sure he’s a whole lot better.
No matter what happens here, the news is either awful or worse. My only hope is that the Senate will stonewall any regressive measures made by the House… but that would mean the Democrats would have to stand up to the Republicans. We’ll just have to wait and see how that turns out.
Tariffs, not trade? | Gene Expression
In the the 19th century the Democratic party, rooted in large part among Southern planters who were dependent on exports of commodities and imports of finished goods, was the party of free trade. The northern Whigs, and later the Republicans, were the party of tariffs. They were the faction which drew support from the industry of the North which benefited from protection against European competitors. The Republican support for tariffs and Democratic opposition persisted into the early 20th century. Only after World War II did this long standing division between the two parties diminish, so that by 1993 a much larger proportion of Republicans than Democrats supported the ratification of NAFTA.
Because of NAFTA’s prominence in my mind, as well as the tinge of economic nationalism on the labor Left and the maturing anti-globalization sentiment on the cultural Left, I had assumed that the Republicans tilted toward free trade more than Democrats. Not so. Pew came out with a survey a few days ago, and the results indicate that my preconception was wrong.
I don’t really want to litigate the issue of trade. Whatever your nuanced view, and I’m sure you have a nuanced view since you’re reading this weblog, I think we can agree that most Americans are not economically enlightened. These are gut emotional responses, drawn out during a time of economic stress and anxiety. The fact that ~1/3 of Americans think that trade makes prices higher seems crazy. You don’t need to know about comparative advantage, or track the CPI. Just consider how Walmart has flooded the US with cheap Chinese goods.
So we’re not talking about people who have a good grasp of international economics. What’s going on here? I think this has some element of xenophobia. Those with high school educations or less have rational reason to worry. But what’s going on with senior citizens? Many of these are retired and drawing fixed Social Security income, don’t have to worry about losing health insurance because of job loss, and might be deriving income from pension funds invested in the global pool of capital. The deflationary pressure of cheap foreign goods and services should be welcome to those on constant but modest incomes. Again, it isn’t a matter of reason, but reflexive aversion to the foreign. It is the young who are having to hustle in the globalized labor market, but the young are most pro-trade.
The Republican party has long had a tension between populists who oppose free flow of labor (immigration) and are suspicious of international capital, and the economic elites. If the populists turn against the free flow of goods & service then the problem will be compounded. As for the Democrats, it looks like the economic nationalists and anti-globalists are fading. I’m updating my stereotypes as of now.
Addendum: The outlines of this are kind of evident in the GSS. I think I ignored/didn’t see the patterns because of my preconceptions. Shame on me!
The Pi-on | Cosmic Variance
I am in love with this comment and want to have its babies:
pi appears as a constant in many formula of physics. General relativity says that it isn’t constant. Is it the origin of the pi particle, aka pion?
A curmudgeonly literalist might, when faced with a question such as this, harrumph a simple “No.” A more loquacious sort might explain that general relativity does not say that π is not a contstant. Pi is not a parameter of physics like the fine-structure constant, which could conceivably be different or even variable from place to place. It’s a universal answer to a fixed question, to wit: what is the ratio of the circumference of a circle to its diameter, as measured in Euclidean geometry? The answer is of course 3.141592653589793…, or any number of representations in terms of infinite series.
But the point of the question is that GR says we don’t live in Euclidean space; we move through a curved spacetime manifold. That’s okay. In a curved space, we could imagine defining the “diameter” of a circle as the maximum geodesic distance connecting two of its points, and taking the ratio of the circumference with that diameter, and indeed it would typically not give us 3.14159… But that doesn’t mean π is changing from place to place; it just means that the ratio of circumference to diameter (defined this way) in a curved space doesn’t equal π. If the circumference/diameter ratio is less than π, you are in a positively curved space, such as a sphere; if it is greater than π, you are in a negatively curved space, such as a saddle. Geometry can also be much more complicated than that, with different ratios depending on how the circle is oriented in space, which is why curvature is properly measured by tensors rather than by a simple number.
Taken from Mathematics Illuminated, which says that pi really does depend on the geometry of space, which is crazy.
(Parenthetically, one of the dumbest mathematical arguments ever given was put forward by the world’s smartest person, Marilyn Vos Savant. The columnist wrote an entire book criticizing Andrew Wiles’s proof of Fermat’s Last Theorem. Her argument: Wyles made use of non-Euclidean geometry, but what if geometry is really Euclidean? Touche!)
However … despite the fact that π doesn’t really change from place to place in general relativity, the geometry does change from place to place, and there is a particle associated with those dynamics — the graviton. Although the formulation of the original question isn’t accurate, the spirit is very much in the right place. And I, for one, will henceforth be perpetually sad that the physics community missed a chance by attaching the word pion to the lightest quark-antiquark bound state, rather than to the particle associated with deviations from Euclidean geometry. That would have been awesome.
Aziz Ansari is not a Muslim, he is an atheist | Gene Expression
A few days ago a friend was asking me about Aziz Ansari, the brown American comedian who grew up in South Carolina, and is of Tamil Muslim heritage. Since I don’t watch Parks and Recreation, I knew about him mostly through the Sepia Mutiny weblog. Some of the comments there indicated that Ansari was a practicing Muslim. That did not surprise me, South Asians are very religious. In particular, group religious identity matters a great deal to people whose origins are in Indian and Islamic civilization (and their intersection).
This is in contrast to East Asians, for whom group religious identity matters far less. It is notable that the most Sinic Southeast Asian nation, Vietnam, is closest to the East Asian model, with no single organized supernatural tradition being identified with the national consciousness. In contrast the more Indic mainland Southeast Asians, and those of maritime Southeast Asia, do fuse religion and national identity. To be Thai is to a great extent to be a Theravada Buddhist, and to be a Malay is to be a Muslim.*
The USA, unlike Canada, Singapore, or the UK, does not have breakdowns of religious affiliation by ethnic group down to the level of sub-Asian ethnicities, so I don’t know how religious or irreligious South Asians are. I assume that they’re less religious than Canadian or British South Asians, in large part because they’re a more advanced community in terms of education and economics vis-a-vis the mainstream in the USA (though to be fair it seems that the Punjabis of British Columbia and the Pakistanis of Britain are responsible for most of the social dysfunction of South Asians in those countries). But it still seems that a substantial number of American South Asians retain nominal religious identity even if their personal beliefs and practices are relatively secular. Fareed Zakaria was for example drafted as a “moderate Muslim” in the wake of 9/11 despite the fact that he used to be Slate’s wine columnist. Here’s Zakaria on the role of religion in his life:
Growing up in a country like India, riven by sectarian violence, Zakaria says, “you’re absolutely aware of the power religion has, in a positive and negative sense—in its ability to inspire people and its ability to inspire people to kill.” On the other hand, his own upbringing was open-minded and secular; he sang Christian hymns at school and celebrated Hindu as well as his own Muslim holidays. “I do know a lot about the world of Islam in an instinctive way that you can’t get through book learning,” he says thoughtfully, but admits he finds the role of token Muslim explainer in the American media slightly uncomfortable. “I occasionally find myself reluctant to be pulled into a world that’s not mine, in the sense that I’m not a religious guy.”
He was born and raised in India, so no matter how assimilated he is Zakaria retains the stamp of the nation of his birth. The Zakarias are a powerful Indian Muslim family, and in India his identity was that of a Muslim, albeit one who was comfortable with South Asian supernatural pluralism.** Zakaria also believes that he has an implicit cultural understanding of Islam because that was the milieu in which he was raised. But he admits candidly what is pretty obvious, he’s not particularly religious in any conventional understanding for a Muslim. Nevertheless he does not disavow Islam, or assert he’s an atheist or agnostic.
I’m obviously not in Fareed Zakaria’s camp. I’m not a Muslim, I’m an atheist. Just like my paternal grandmother was not a Hindu even though she was born into a Hindu family. This sort of plain and naked assertion of atheism is not something that many Americans are comfortable with, since theism is normative. But in a South Asian context the bigger issue is the rupture with historical communal memory. I have met Americans who were born into a Hindu family who were atheists and ate beef who nevertheless winced when I admitted that there were Hindus in my family tree only a few generations back who obviously converted for reasons of rational self-interest. The power of “team Hindu” and “team Islam” still remains within Diasporic South Asian communities. Of course this sort of phenomenon is cross-cultural, an atheist friend who was from a Calvinist part of the Netherlands felt confident in mocking the special superstition of Roman Catholicism in a manner which would have made the Reformers of yore smile.
For myself, close readers will be aware that my explicitly asserted denial of the existence of God and rejection of identification with Islamic civilization is something of an affront to the memory of my recent ancestors. My mother’s paternal grandfather was a wandering Muslim mystic. In his lifetime he came to be revered for his piety, and the site of his grave has become a object of pilgrimage in the local region. The superstitious local folk naturally believe that we who descend from this man carry his holiness in our blood, and my mother remembers as a small child people approaching her as if she was a special talisman. On my father’s side I come from a line of Ulama.
But if religiosity is heritable it is highly amusing to me that I probably come very close to lacking the “God gene.” My understanding that I was an atheist as a small child was less of a rejection of the existence of God than an acknowledgment of the lack of belief which had always implicitly been part of of my model of how the world worked. I simply was never “Wired for Creationism.” But by lack of belief in and of itself does not entail that I reject “team Islam.” I was always struck by the fact that Edward Said, a Christian Arab by birth, an atheist as an adult, defined himself as a product of Islamic civilization. The connection between an individual and a religious ethos runs deeper than belief alone. It even runs deeper than explicit identification. I have argued repeatedly that most American Jews and Roman Catholics adhere to a view of what religion is, and what their religion is, that is clearly in keeping with the confessional sectarian Protestantism which has shaped the history of the United States of America. For me my personal disaffection with Indian and Islamic civilization was completed by my reading of Chinese philosophers, in particular Xun Zi, as well as the pre-Socratics of the Greeks. The fact that my ancestors wasted their lives on metaphysics, mysticism, and the Madhhab is a shame. Their Eudaimonia would have been deeply alien to me, in a way that Marcus Aurelius never was.
So what about the point of the article? Here’s an addendum to an article from last spring in The New York Times:
In an earlier version of this article, Michael Schur, the co-creator of “Parks and Recreation,” partly described Mr. Ansari as a Muslim. Mr. Ansari describes himself as an atheist.
Whoever claimed Ansari was a practicing Muslim was lying, deluded, or mistaken. Because of my general knowledge that South Asians do not usually disavow any religious identity I simply accepted this as a given and repeated the falsehood. And that is why I am putting up this post, and hoping that Google picks up this for the appropriate search queries.
* I am aware that there are small communities of Thai-speaking Christians, as well as larger communities Thai-speaking Muslims.
** I once talked to a man who was of Indian Christian background whose personal beliefs were closer to Hinduism, but in India everyone defined him as a Christian because of his birth, despite his rejection of Christian beliefs and acceptance of Hindu ones.
Image Credit: Mb3741, Wikimedia Commons
We Need Gattaca to Prevent Skynet and Global Warming | Science Not Fiction
Independence Day has one of my most favorite hero duos of all time: Will Smith and Jeff Goldblum. Brawn and brains, flyboy and nerd, working together to take out the baddies. It all comes down to one flash of insight on behalf of a drunk Goldblum after being chastised by his father. Cliché eureka! moments like Goldblum’s realization that he can give the mothership a “cold” are great until you realize one thing: if Goldblum hadn’t been as smart as he was, the movie would have ended much differently. No one in the film was even close to figuring out how to defeat the aliens. Will Smith was in a distant second place and he had only discovered that they are vulnerable to face punches. The hillbilly who flew his jet fighter into the alien destruct-o-beam doesn’t count, because he needed a force-field-free spaceship for his trick to work. If Jeff Goldblum hadn’t been a super-genius, humanity would have been annihilated.
Every apocalyptic film seems to trade on the idea that there will be some lone super-genius to figure out the problem. In The Day The Earth Stood Still (both versions) Professor Barnhardt manages to convince Klaatu to give humanity a second look. Cleese’s version of the character had a particularly moving “this is our moment” speech. Though it’s eventually the love between a mother and child that triggers Klaatu’s mercy, Barnhardt is the one who opens Klaatu to the possibility. Over and over we see the lone super-genius helping to save the world.
Shouldn’t we want, oh, I don’t know, at least more than one super-genius per global catastrophe? I’d like to think so. And where might we get some more geniuses? you may ask. We make them.
In his essay, “The Singularity: A Philosophical Analysis”, philosopher David Chalmers notes that there is a very real chance that if machines become self-aware and start improving themselves, we’re going to have a problem (*cough* Skynet *cough* Liquid T-1000 *cough, cough*). One of his potential solutions is to enhance ourselves to keep up:
This might be done genetically, pharmacologically, surgically, or even educationally. It might be done through implantation of new computational mechanisms in the brain, either replacing or extending existing brain mechanisms. Or it might be done simply by embedding the brain in an ever more sophisticated environment, producing an “extended mind” whose capacities far exceed that of an unextended brain.
Does any of that sound familiar? Perhaps a little film called Gattaca may ring some bells? Chalmers is arguing enhancement may be necessary to prevent extinction. Why not extrapolate that logic to other existential risks. Alien invasion? Superhumans would probably put up a better fight. Skynet goes live? An army of hackers with a collective IQ of 200+ and neuro-integrated interfaces would clean that up in a jiffy. But what about our current problems? Although heavy-handed, the message in both versions of The Day the Earth Stood Still is that humanity’s greatest existential threat is itself. War, suffering, poverty, and environmental destruction all seem like problems that would merit allowing our best and brightest to become even better and brighter for the sake of everyone.
A common fear is that the super-intelligent would just step on us normals, creating second-class citizens. Enhancement doesn’t just mean the ability to do complex equations and create new molecular compounds; raw intellectual horsepower is just one among many possibilities. We know that some people have moral problems caused by damage to specific parts of their brain. As neuroscience progresses, there is a very real possibility we’ll be able to improve those specific parts of the moral brain. I don’t mean we’d have a society of lock-step rule followers, but instead people who were genuinely better at being moral than most of us. Can you imagine a world where politicians had improved ethical scruples? Or, to put it simply, where the most brilliant minds were also the most caring?
Which brings me back to Jeff Goldblum in Independence Day. Not only does he come up with the solution, but he selflessly gets in the nuke-strapped UFO with Will Smith to fly into the middle of the enemy mothership. Same for professor Barnhardt, who is as good at moral philosophy as it seems he is math, attempting to show Klaatu the best of our species.
In science fiction, when humanity is faced with existential crises, we turn to great minds attached to great hearts. While we aren’t under alien attack or facing sentient machines, our world has its own share of problems. Human cognitive enhancement might just be the solution from which all other solutions are born; or maybe it brings too many risks of its own.
ID4 Promotional Image via Wikipedia under fair use
WilWheaton… WilWheaton… WilWheaton… WilWheaton… WilWheaton… aaarrrggg! | Bad Astronomy
[Update: It occurs to me after posting this entry that it might make more sense if you watch this first. My apologies for any confusion.]
This is for your own good, folks.
The future Indian Yao Ming | Gene Expression
In a nation of ~1 billion, even one where a large minority are positively malnourished, you’d expect some really tall people. So not that surprising: NBA Awaits Satnam From India, So Big and Athletic at 14:
In a country of 1.3 billion people, 7-foot, 250-pound Satnam Singh Bhamar has become a beacon for basketball hope.
At age 14.
…
That potential starts with his size, which is incredible itself. At age 14, he is expected to grow for another couple of years. For now, he wears a size-22 basketball shoe. His hands swallow the ball. His father, Balbir Singh Bhamara, is 7-2. His grandmother on his father’s side is 6-9.
Punjab is one of India’s more prosperous states. Interestingly this kid’s paternal grandmother is as tall in standard deviation units as her son or grandson. In Western developed societies height is 80-90% heritable. That means that there’s very little expected regression back to the population mean for any given child. The article doesn’t mention the mother’s height though. If she is of more normal size then Satnam is either a fluke, or, there are dominant large effect rare alleles being passed down by the father, perhaps from the paternal grandmother.
