Research news

A new set of fossils from Gabon may be the earliest evidence of multicellular creatures. Or, not. I wrote about them briefly, but Nature News has a great piece with thoughts from various scientists, and Chris at Highly Allochthonous explains why, at the very least, we can confidently say that the fossils at 2.1-billion years old.

Scientists have created a remote controlled “robofish” that sticklebacks accept as one of their own, says BBC News. Now, for Phase Two…

XMRV – the virus that has or has not been linked to cause chronic fatigue syndrome – is stirring up headlines again. Heidi Ledford at Nature reports on the CDC’s decision to delay the publication of a new study, following the emergence of conflicting results elsewhere. And Grant Jacobs at Code for Life uses this as a case study for context in science journalism.

You’ve probably heard about the new super-whale called Leviathan, which I and everyone else wrote about. What you may not have heard about is that the name may not be valid, given that Leviathan had previously been assigned to a mammoth. SV-POW has the story and some great debates in the comments. The authors are checking out the problem but if they are forced to change the name, what will they choose? Megaleviathan? Ultraleviathan? Mechaleviathan? Brian? Failocetus?

The human body makes rare antibodies effective against all flu viruses and these might be boosted to design a better universal flu treatment, says Maggie Fox at Reuters

A new technique for deciphering the calls of sperm whales allows the magnificent, mysterious creatures to be studied in unprecedented detail, says Brandon Keim in Wired. Researchers identified subtle variations caused by differences in the shape of individual whales’ heads. It’s the first time that sperm whale vocalizations have been linked to specific individuals.

A new scent is enough to spark the evolution of a new moth species — and it can start with just a single genetic mutation. More from Wired.

Other goings-on

The early buzz on Brian Switek’s first book Written in Stone is tremendous. I read three chapters when they were in a very early draft stage and they were superb. We can only guess what he’s managed to do with them since then, but the book is available for pre-order on Amazon. Go and buy it.

Simon Jenkins has launched another half-arsed attack on science in the Guardian. Scientists decided that mockery was the only good response to such tripe, and launched #SpoofJenks Monday. I particularly loved the efforts from Matt Parker, Jon Butterworth, and Stephen Curry. Meanwhile, Imran Khan spoils the fun with a substantive response to Jenkins with, you know, points and stuff.

Peter Aldhous at New Scientist reports on a zoo with plans to save endangered species by reprogramming cells from dead animals into stem cells. First step: a drill (it’s a monkey, not a tool).

You know that things are bad with the oil spill when the fact that thousands of turtles not burning to death is a cause for celebration. You know, earlier this year, thousands of turtles weren’t burning to death on a fairly regular basis.

Ben Goldacre has a somewhat depressing take on a paper about people’s reactions to scientific evidence. “When presented with unwelcome scientific evidence, it seems, in a desperate bid to retain some consistency in their world view, people would rather conclude that science in general is broken. This is an interesting finding. But I’m not sure it makes me very happy.”

Is a parasite influencing people’s World Cup skills? Is a parasite influencing people’s tendency to ascribe everything to parasites? Mind Hacks has more, but Vaughan’s probably been taken over by a parasite that reproduces by searching Pubmed.

Neurodojo talks about what happens to neurons when you’re as small as a shrew or as large as an elephant.

What do astronauts want to be when they grow up? A lovely piece by Tom Whyntie in the Guardian.

Despite an election pledge to take an evidence-based approach to health, the Conservatives have appointed MPs Nadine Dorries and David Tredinnick to the health select committee. Martin Robbins laments.

Heh/Wow

The Large Hadron Collider FAQ. “What would happen if I went inside it?” “Just. Don’t.”

What, if anything, is Big Bird? The Loom brings us a talk on the evolutionary affinities of a strange bird species

A gallery of close-ups of bug eyes, from Wired

Susan Orlean can apparently write about anything. Including hashtags.

Journalism and communication

The big news this week is that the Times has finally disappeared behind a full paywall. It’s a sad day for science journalism, for the Times provides some of the best science reporting out there thanks to folks like Mark Henderson, Hannah Devlin, Sam Lister et al. Through Eureka, they’ve shown that a science supplement can work in a national newspaper. They set up one of the only science blogs from a mainstream source that actually works. And they’ve always shown a great understanding of the value that the Internet and social media can bring to science journalism. To see all of that be less accessible to people is a big shame, but to be honest, I would be happy to pay a little less than the current asking price of £2/week for access to the science sections alone… (Also, the Sunday Times has disappeared behind a paywall too, so you win some, you lose some.) In the meantime, it’s interesting that the Guardian is going to the opposite extreme, by offering a plug-in that ports their content directly onto blogs. There’s also a good discussion on the future of paywalls at the Strange Attractor blog. Hint: people pay for the platform not the content,

More kerfuffle on embargoes this week around a study on menopause and the increasingly appropriately named Jonathan Leake. Ivan Oransky, as per usual, has a great take on the whole affair and Leake’s own thoughts. Fiona Fox is discusses Leake’s priors, Natasha Loder praises him and thinks he should be offered an apology, and Gimpyblog disagrees, having read the ESHRE’s media policy.

An interesting thought-provoking thread from Jack of Kent on the image of skepticism, with some great comments building up.

A truly inspiring interview with Eric Roston on science journalism, writing, new media and more, brought to you by Bora Zivkovic.

Scott Rosenberg at Wordyard is knocking them out of the park at the moment, with two great posts on journalists and public criticism, and the recent journo/blogger war (Episode #38302) at the Washington Post. Meanwhile, Brian Cubbison has another excellent piece on journos/bloggers (Episode #38303). I loved this: “Anyone who speaks of bloggers vs. journalists should be made to show their work. Strengthen the argument with links to actual bloggers and journalists. Anyone who uses the saggy, worn-out cliche of bloggers in pajamas should name one, just one, or be made to take down that sign above the desk, “When your mother says she loves you, check it out.”

“Do arrogant, condescending, and dismissive attitudes contribute to the journalism crisis?” asks Abel Pharmboy. This isn’t one of those question headlines where the answer is no…

Andrew Maynard publishes a wonderful satire on this topic. An excerpt:
But I am a reasonable man Mr. Mooney. And so I thought I would at least give your naive and misguided ideas a go. So after cleaning up the Cheerios and milk spattered across my Washington Post, I grabbed myself a member of the public and tried listening to them.
As I suspected, it was a disaster.
Accosting the first person I came across, I asked them a few simple questions:
Me: What’s the second law of thermodynamics?
Member of the public: Err, um…
Me: Okay, forget that. How do airplanes fly?
Member of the public: Err, excuse me, could you just loosen your grip a little…
Me: Come on come on, I’m trying to listen to you – say something intelligent. Please! Why don’t you accept evolution? Why do you believe vaccines cause autism in children? Why don’t you understand simple statistics? Why are you so stupid?
Member of the public: Get your hands off me now, or see me in court!
You see what I mean Mr. Mooney? There’s no reasoning with these people! Listen to them? I’d rather listen to a lamp post. Read more: http://2020science.org/2010/07/04/scientist-listen-to-the-public-surely-youre-joking-mr-mooney/#ixzz0sj2YgXuE

Every year on this date, I take a few minutes and read The Declaration of Independence^*. For my money, it’s one of the greatest documents ever written in the English language.

I know not all of my readers are Americans. Even if you’re not, the Declaration is a fantastic work and you should read it. And if you have the time — and you should make the time — read The Bill of Rights, too. You may not be from a country with the same laws we do, the same values we do, or the same attitudes we do, but the Founders of the United States of America had some pretty good ideas about what the citizens have the right to do, and what the government does not.

Living up to those ideas, those ideals, is what America is about. These freedoms are not given, they are earned, and must always be protected. Remember:

Happy 234^th, America.

I’ve been hearing about structural adjustment due to technology and gains to productivity from people since the early 1990s. The sort of dynamic which motivated the original Luddites. But this chart from Calculated Risk makes me lean toward the proposition that the time is nigh. In relation to previous post-World War II recessions the big difference in unemployment seems to be in the area of the long term; these are those whose skills will degrade, and are probably least likely to reenter the labor force at an equivalent position.

I absolutely adore this parody of Katy Perry's I Kissed A Girl by the Damsels of Dorkington, and agree--Big brains are hot! I hope this makes readers smile and wish everyone a very happy holiday weekend!

The latest episode of Point of Inquiry is something a little different--and I hope in a good way. Here's the write-up:
Recently in Amherst, New York, two of Point of Inquiry’s hosts sat down for a special in-studio episode of the show. One was a conservative (Robert Price), one a liberal (Chris Mooney)—and both were atheists.
The topic they tackled: Is there any necessary correlation between one’s disbelief in God and one’s place on the political spectrum?
The result was a fascinating—and notably civil, and frequently entertaining—conversation ranging across foreign policy, abortion, stem cell research, animal rights, and many other topics. In the end, the discussants actually found not only much disagreement, but also some common ground. You can stream the episode here, and subscribe to Point of Inquiry here. And if you want to join a discussion at the Point of Inquiry forums, visit here...

Daryl Cunningham — the man who did this devastating comic strip about antivaxxers — has turned his sights on homeopathy. In just a few dozen panels he describes this alt-med nonsense, shows why it’s nonsense, shows why it’s dangerous, and then provides a dramatic and emotional example of just how and why belief in homeopathy can kill.

His terse description of the Penelope Dingle case hits like a punch in the throat. Homeopathy is dangerous, mostly because it lures people away from real medicine. But it’s also dangerous because it promotes magical thinking, which eats away at all of reality.

Testosterone changes during vicarious experiences of winning and losing among fans at sporting events.

“Basking in reflected glory, in which individuals increase their self-esteem by identifying with successful others, is usually regarded as a cognitive process that can affect behavior. It may also involve physiological processes, including changes in the production of endocrine hormones. The present research involved two studies of changes in testosterone levels among fans watching their favorite sports teams win or lose. In the first study, participants were eight male fans attending a basketball game between traditional college rivals. In the second study, participants were 21 male fans watching a televised World Cup soccer match between traditional international rivals. Participants provided saliva samples for testosterone assay before and after the contest. In both studies, mean testosterone level increased in the fans of winning teams and decreased in the fans of losing teams. These findings suggest that watching one’s heroes win or lose has physiological consequences that extend beyond changes in mood and self-esteem.”

Note from the ladies of NCBI ROFL: We will be on hiatus next week (July 5-9) because we are both traveling to conferences. If you’re going to be at the SMBE meeting in Lyon or the FASEB Biology of Cilia and Flagella meeting in Vermont and want to hang out/buy us a beer/hear about the research we do when we’re not blogging, drop us a line at ncbirofl[at]gmail.com!

Related content:
Discoblog: NCBI ROFL: World Cup Week: Celebrate FTW!
Discoblog: NCBI ROFL: World Cup Week: Can watching World Cup football kill you?
Discoblog: NCBI ROFL: World Cup Week: Vuvuzela – Good for your team, bad for your ears.
Discoblog: NCBI ROFL: World Cup Week: World cup soccer players tend to be born with sun and moon in adjacent zodiacal signs.

WTF is NCBI ROFL? Read our FAQ!

I said yesterday I would say a bit more about the new paper on rapid recent high altitude adaptation among the Tibetans when I’d read the paper. Well, I’ve read it now. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude:

Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP’s association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.

The exome is just the protein-coding part of the genome; so they’re focusing ostensibly on functionally relevant single nucleotide polymorphisms (SNPs). About a month and a half ago a similar paper on Tibetan high altitude adaptations was published in Science (I posted on that too), but their methodology was somewhat different. That group was looking at a set of genes, candidates, which they’d assume might have been under selection and so have functional significance in explaining Tibetan vs. non-Tibetan phenotypes at high altitudes. This second paper takes a more bottom up approach, scanning the genome of Tibetans and Han Chinese, and trying to spotlight regions which exhibit a great deal of between population variance, far greater than one might presume from the total genome genetic distances.

As to that last point…the timing of this has been causing a major problem with archaeologists. The supplements lays out the details a bit more than the press reports, so below is figure 2:

It looks like to get a better sense of the model you’ll have to read the cited paper, and I’m not sure that that will satisfy the archaeologists. They did use a large number of neutral markers though, so I’m not too worried about biases in their data set. Some have been confused about the population numbers, but this value in a population genetic context can be counterintuitive, especially over the long term (low values are given much more weight than high values). The small Han value can be easily made less confusing when you consider a massive demographic expansion from a small founder group, as well as persist long term biases in reproductive value within the population (e.g., some males in a given generation are way more fecund than others through polygyny). A higher N for Tibetans may be explained by a more stable population where diverse subsets and across individuals the reproductive value may be more equitable. In other words, an effective population size is a statistic which is bundling together a lot of evolutionary history, and is not a simple measure of perceived census sizes (the Tibetans may also be something of a melange of a diverse set of ancient groups which took refuge in the highlands, while the Han are the descendants of early adopters of agriculture which expanded demographically; so they’re opposite ends of the demographic tunnel).

The time of divergence of a little under 3,000 years is important for the rest of the paper, so I suppose other workers had better replicate their findings in the future. Figure 1 is rather striking, so let’s jump to it:

This chart is simply showing frequencies of SNPs in Tibetans and Han. The two are obviously correlated, as evident by the diagonal. Shading indicates the density of the number of SNPs at a given position. Look to the bottom right, and you see the gene around which much of the paper hinges, EPAS1. It’s an enormous outlier, with SNPs where Tibetans and Han differ a great deal. This is important in regards to looking for genes which may drive adaptation to higher altitudes; if you don’t have different genes then you don’t have different traits. If the Tibetans and Han diverged ~3,000 years ago, then those adaptations may be recent and would have emerged through rapid allele frequency changes (though they observe that it may be drawn from standing variation). The researchers didn’t go looking for EPAS1 as such, rather, it came looking for them. What does it do? From the text:

EPAS1 is also known as hypoxia-inducible factor 2{alpha} (HIF-2{alpha}). The HIF family of transcription factors consist of two subunits, with three alternate {alpha} subunits (HIF-1{alpha}, HIF-2{alpha}/EPAS1, HIF-3{alpha}) that dimerize with a ? subunit encoded by ARNT or ARNT2. HIF-1{alpha} and EPAS1 each act on a unique set of regulatory targets…and the narrower expression profile of EPAS1 includes adult and fetal lung, placenta, and vascular endothelial cells…A protein-stabilizing mutation in EPAS1 is associated with erythrocytosis…suggesting a link between EPAS1 and the regulation of red blood cell production.

Next, they dig into the functional significant of EPAS1 variants, in the literature, and in their current sample:

Associations between SNPs at EPAS1 and athletic performance have been demonstrated…Our data set contains a different set of SNPs, and we conducted association testing on the SNP with the most extreme frequency difference, located just upstream of the sixth exon. Alleles at this SNP tested for association with blood-related phenotypes showed no relationship with oxygen saturation. However, significant associations were discovered for erythrocyte count (F test P = 0.00141) and for hemoglobin concentration (F test P = 0.00131), with significant or marginally significant P values for both traits when each village was tested separately (table S5). Comparison of the EPAS1 SNP to genotype data from 48 unlinked SNPs confirmed that its P value is a strong outlier (5) (fig. S4).

The allele at high frequency in the Tibetan sample was associated with lower erythrocyte quantities and correspondingly lower hemoglobin levels…Because elevated erythrocyte production is a common response to hypoxic stress, it may be that carriers of the “Tibetan” allele of EPAS1 are able to maintain sufficient oxygenation of tissues at high altitude without the need for increased erythrocyte levels. Thus, the hematological differences observed here may not represent the phenotypic target of selection and could instead reflect a side effect of EPAS1-mediated adaptation to hypoxic conditions. Although the precise physiological mechanism remains to be discovered, our results suggest that the allele targeted by selection is likely to confer a functionally relevant adaptation to the hypoxic environment of high altitude.

There are random anomalies in nature, but it seems too perfect that this is the outlier in allele frequencies across two populations which differ in adaptations which relate to many of the traits above.

OK, so they found an outlier SNP. The gene seems to have a reasonable probability of being involved in functional pathways relevant to altitude adaptation. But so far we’ve been focusing on the Tibetan-Han difference. If the two populations separated about 3,000 years ago one assumes that genes with SNPs with huge F_sts, where most of the variation can be partitioned between the groups, not within them, are good candidates for having been driven by selection. But it would be nice to compare with an outgroup. So they compared the Tibetans and Hans with the Danes, who are an outgroup who separated from the East Asian cluster about one order of magnitude further back in time (~30,000 years). Next they generated a “population branch statistic,” (PBS), from the the F_st data (see the supplements). Basically you’re getting a value which describes allele frequency differences normalized to the expected genetic distance as known from population history. I’ve extracted out Panel B from figure 2. T = Tibetans, H = Han, and D = Danes. The smaller tree represents genome average PBS values. It’s what you’d expect, the Danes are the outgroup. Over time genetic difference builds up because of separation between the groups. The Han and Tibetans are very close, as you’d expect from genetically similar populations. But look at the larger tree, the Tibetans are the outgroup by a mile! The Danes and Han differ far less from each other on EPAS1 than they do from the Tibetans. This seems like a clear deviation from the level of allele frequency difference one might be able to generate by neutral random walk processes.

EPAS1 isn’t the only gene which they found, but it was the most significant, and illustrates the nature of the methodological orientation of this group. Sift through the genome and look for something which is totally unexpected, and put a focus on the peculiar diamond in the rough and see what it can tell you. They conclude with the big picture:

Of the genes identified here, only EGLN1 was mentioned in a recent SNP variation study in Andean highlanders (24). This result is consistent with the physiological differences observed between Tibetan and Andean populations…suggesting that these populations have taken largely distinct evolutionary paths in altitude adaptation.

Several loci previously studied in Himalayan populations showed no signs of selection in our data set…whereas EPAS1 has not been a focus of previous altitude research. Although EPAS1 may play an important role in the oxygen regulation pathway, this gene was identified on the basis of a noncandidate population genomic survey for natural selection, illustrating the utility of evolutionary inference in revealing functionally important loci.

Given our estimate that Han and Tibetans diverged 2750 years ago and experienced subsequent migration, it appears that our focal SNP at EPAS1 may have experienced a faster rate of frequency change than even the lactase persistence allele in northern Europe, which rose in frequency over the course of about 7500 years…EPAS1 may therefore represent the strongest instance of natural selection documented in a human population, and variation at this gene appears to have had important consequences for human survival and/or reproduction in the Tibetan region.

Natural selection is somewhat stochastic; it can take different tacks to the same process because it doesn’t have infinite power in its search algorithm. Given enough time and gene flow no doubt adaptations would homogenize and converge upon a perfect optimum, but given enough time the universe will devolve into heat death. Evolution has to operate extemporaneously for eternity because the conditions are ever changing. Second, the big headline grabbing assertion about EPAS1 being the strongest instance of natural selection needs to be moduled by the fact that the conclusion was generated assuming the validity of the inferences of a particular model, and models can be wrong. It does seem like the evolutionary change is likely to be recent, I doubt they’d be off by an order of magnitude. But for lactase persistence we’ve extracted genetic material from ancient remains. The conclusion then is much more concrete in this case. Until we get remains from ancient Tibetans and can infer their allele frequencies, there will be some asymmetry in the confidence with which we can make a claim as to when the selection event began.

Citation: Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z., Pool, J., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T., Zheng, H., Liu, T., He, W., Li, K., Luo, R., Nie, X., Wu, H., Zhao, M., Cao, H., Zou, J., Shan, Y., Li, S., Yang, Q., Asan, ., Ni, P., Tian, G., Xu, J., Liu, X., Jiang, T., Wu, R., Zhou, G., Tang, M., Qin, J., Wang, T., Feng, S., Li, G., Huasang, ., Luosang, J., Wang, W., Chen, F., Wang, Y., Zheng, X., Li, Z., Bianba, Z., Yang, G., Wang, X., Tang, S., Gao, G., Chen, Y., Luo, Z., Gusang, L., Cao, Z., Zhang, Q., Ouyang, W., Ren, X., Liang, H., Zheng, H., Huang, Y., Li, J., Bolund, L., Kristiansen, K., Li, Y., Zhang, Y., Zhang, X., Li, R., Li, S., Yang, H., Nielsen, R., Wang, J., & Wang, J. (2010). Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude Science, 329 (5987), 75-78 DOI: 10.1126/science.1190371

Apparently, in the animal kingdom, it’s better to be a girl. We have seen that women macaques are superior conversationalists. We learned that lady humpbacks enjoy long-lasting friendships. Now research published in Current Biology shows that baboon ladies with good friends around them may live longer.

At Botswana’s Moremi Game Reserve, Joan Silk of the University of California, Los Angeles and her team spied on 44 female chacma baboons over the course of six years. Among other things, Silk looked at which girls had the most visitors and how often the women picked junk out of each other’s hair. In other words, true friendship. She also tracked each baboon’s circle of friends, seeing how each lady’s top three buddies changed over time.

Silk saw a correlation between sociability and longevity. She divided the baboons into three groups, and found that the least friendly lived 7 to 18 years, while the friendliest group lived from 10 years on (they were still kicking when the study ended). They also found that those baboons who formed stable, enduring bonds were more likely to have long lives than those with flightier friendship habits.

It’s tempting to look for parallels between baboons and humans, and indeed, the researchers engage in a little speculation.

Such findings in a nonhuman primate, the authors write, “suggest that the human motivation to form close and enduring bonds has a long evolutionary history.” … They note that previous research in humans has shown that socially isolated people suffer more from high blood pressure and sleep disorders and have longer wound-healing times. [ScienceNOW]

But back in the animal world, it’s still not clear how these stable friendships could make baboons live longer. It’s possible, they say, that more friendly grooming could mean fewer parasites, or more social interactions could mean more eyes to watch for predators.

“It all depends on what causes the death of female baboons, which is hard to determine because there’s seldom a single cause,” comments New York University anthropologist Clifford Jolly. [Science News]

In this baboon species, males miss out on friendship and its possible benefits. It seems that chacma males never groom each other, and only groom women before sex.

Follow Discover on Twitter.

Related content:
80beats: Female Monkeys Chat More Than Males to Maintain Social Ties
80beats: Lady Humpback Whales Make Friends & Meet up for Summer Reunions
80beats: Maternal Monkey Love: Macaque Moms Coo Over Their Babies
80beats: Monkey See, Monkey Do: How to Make Monkey Friends
Discoblog: How to Win Friends and Influence Monkeys

Image: flickr / Graham Racher

Gabon fossils are earliest traces of multicellular life… or are they?

These unassuming fossils may be some of the earliest known examples of complex life on Earth, composed of many cells (like animals and plants) rather than just one (like bacteria). They were uncovered in Gabon by a Abderrazak El Albani from the University of Poitiers, and they’re around 2.1 billion years old. They have been preserved in remarkable detail for their age. They are centimetres in length, and El Albani thinks that they’re probably some of the oldest multi-cellular organisms so far discovered. If he’s right, they’re half a billion years older than the previous record-holders.

Leading a team of 21 scientists, El Albani has painstakingly analysed the fossils. Their three-dimensional structure came with radial slits, scalloped margins and a complicated folded centre. To the team, these complex patterns tell us that the fossils were not simply rock formations. Instead, they were the remnants of once-living things that grew through coordinated signalling between different cells. The fossils are also rich in the mineral pyrite, which is the work of decomposing bacteria; again, this suggests that they were once living.

Back when they were still alive, the Earth was a radically different place. Oxygen made up a small fraction of the atmosphere and a toxic mix of greenhouse gases choked the air instead. Still, things were on the up. The “Great Oxidation Event” was underway, kick-started about 300,000 years previously by tiny bacteria. These microbes pumped oxygen into the air around them as a waste product of photosynthesis, enriching the atmosphere with the gas that would change the planet’s fate. These rising oxygen levels could have been the trigger that allowed multicellular organisms to survive. Without the oxygen, they couldn’t have achieved a large size.

Of course, it’s possible that the fossils could simply be complex colonies of bacteria, rather than true multicellular organisms. El Albani doesn’t rule out that possibility but again, the fossils’ complex three-dimensional shapes don’t quite fit with the idea of a simple bacterial mat. They also contain chemicals called steranes, which often give away the presence of complex eukaryotic cells. But Philip Donoghue from Bristol University, while impressed with the fossils, thinks that we can’t rule out the bacteria idea yet. The steranes, for example, could have moved into the fossils from surrounding rocks. And some scientists aren’t even convinced that the Gabon fossils were once alive.

Bruce Runnegar, who studies the origins of multicellular life, says, “It is difficult to know if this is some unusually complex [non-living] structure, a feature made by a consortium of individual microbes, or evidence for primitive multicellular life.” Some of the fossils’ shapes – such as the wavy surfaces and radial slits – are sometimes seen when different kinds of fluids mix. “The wavy surfaces are unusual, but not unusual enough to convince me to put my money on these structures being “ancient representatives of multicellular life,” he says.

Reference: Nature http://dx.doi.org/10.1038/nature09166

Read more about these fossils, including opinions from several other scientists, at Nature News and an excellent explanation of why we can confidently say that the fossils at 2.1-billion years old at Highly Allochthonous

Sabre-tooth cats wrestled prey with powerful front legs

From looking at the skeleton of a sabre-tooth cat, it would seem obvious what its main weapons are. But impressive though the huge canines are, they’re only part of its arsenal. Its stocky frame and sturdy front legs are equally important. Julie Meachen-Samuels and Blaire van Valkenburgh from the University of California, Los Angeles, have studied the skeleton of Smilodon fatalis, the most famous of the sabre-tooth cats (they’re not tigers). Using a digital X-ray machine at the Smithsonian Institution, the duo showed that its humerus (the bone between shoulder and elbow) was reinforced by extra-thick bone.

Its outer shell, or cortex, was thickened to a greater degree than any other living cat. In terms of sturdiness, it even outclassed the equally extinct but considerably larger American lion. The extra reinforcement made Smilodon’s front legs very difficult to break, bend or compress. These sturdy limbs also had expanded attachment points for the cat’s relatively large muscles. The hind legs, while still thickened, was still within the range of normal variation for other cats.

This new research fits nicely with the modern image of Smilodon as a subtle killer that hunted in a very different way than modern cats. It combined elements of a wrestler and an assassin, grapping large prey to the ground with its powerful front legs, and killing them quickly with a lethal stab of its famous teeth.

Modern cats inflict death more slowly, with a suffocating bite to the throat. But there is no way that Smilodon could have done the same. Its skull and teeth are surprisingly weak, and might have broken during a protracted struggle. Instead, they were probably used to deliver an incisive and fatal bite to the blood vessels of the neck, after the prey had already been pinned. This specialisation allowed it to tackle very large prey, but it might also have been its downfall. As the largest mammals went extinct during the last ice age, Smilodon’s overpowering tactics would have done little good against smaller, more agile targets.

Reference: PLoS ONE to be confirmed; Image by Dantheman

If the citation link isn’t working, read why here

Things may be looking up, ever so slightly, for the Gulf of Mexico’s endangered sea turtles. A few days ago, environmental groups announced that they were suing BP and the Coast Guard over the “controlled burns” that were intended to burn off oil slicks in the water; the environmentalists said that sea turtles were getting caught in the infernos and burned alive. This morning a judge was prepared to hear arguments on a proposed injunction, but at the last minute the parties declared that they’ve reached a settlement.

The agreement comes in advance of an emergency court hearing set today in New Orleans federal court, where environmentalists sought to force BP to either stop controlled burns or place rescuers on the boats to scoop federally protected sea turtles out of floating sludge patches before the corralled oil is ignited [Bloomberg].

According to Sea Turtles Restoration Project, one of the plaintiffs in the case, BP and the Coast Guard have agreed to station a qualified biologist on every vessel involved in the burns, and to remove turtles from the burn area before setting the blaze. This is good news for the leatherbacks, loggerheads, and Kemps Ridley turtles that make their home in the Gulf. Of course, it would be better news if their home wasn’t saturated with oil and periodically set on fire, but we’ll take what we can get.

Elsewhere in turtle news, conservationists are preparing to collect 70,000 turtle eggs from Alabama and Florida beaches. The ambitious scheme, coordinated by the U.S. Fish and Wildlife Service, is seen as the best chance of preventing a massive die-off of the threatened creatures.

“This is an extraordinary effort under extraordinary conditions, but if we can save some of the hatchlings, it will be worth it as opposed to losing all of them,” said Chuck Underwood of the U.S. Fish and Wildlife Service. “We have a much higher degree of certainty that if we do nothing and we allow these turtles to emerge and go into the Gulf and into the oil … that we could in fact lose most of them, if not all of them,” he added. “There’s a chance of losing a whole generation.” [AP]

In the next couple of weeks, turtle experts will start the painstaking process of excavating up to 800 nests; each egg must be carefully lifted from its nest without rolling or repositioning it, to avoid disrupting the growing embryo inside. Then the eggs will be transported to a climate-controlled hanger at Kennedy Space Center on Florida’s east coast where they’ll stay until hatching. Finally, if all goes well, the next generation of loggerheads and other sea turtles will be set loose in the oil-free Atlantic.

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Image: Sea Turtle Restoration Project / Blair Witherington

A group of new drivers may never watch where they’re going. They won’t need to: Instead, they’ll listen and feel. The National Federation of the Blind and Virginia Tech are developing a car for the blind, and hope to demonstrate a prototype in January of 2011.

Don’t be fooled: Unlike like the do-it-themselves cars that compete as part of the DARPA Urban Challenge, this car will actually let the blind driver take control and drive, and will require the same quick judgments needed by sighted drivers. The only difference will be how these drivers sense what’s around them.

Instead of looking at the car cutting them off or the pedestrian about to step into traffic, the blind drivers must feel them or hear them. Though the final design is still in the works, the car may communicate an obstacle’s presence by audio instructions, vibrating gloves (called DriveGrip), and puffs of compressed air (called AirPix). AirPix is sort of like a map of the road, a flat board with different air jets corresponding to different obstacles.

This vehicle is the next step in an ongoing project at Virginia Tech. Last summer, mechanical engineering professor Dennis Hong and his team unveiled a buggy that used laser tracking systems, audio commands via headphones, and a vibrating vest to tell blind drivers where to go. Several blind volunteers successfully steered the buggy through an unfamiliar obstacle course (see video below).

Mark Maurer, the president of the National Federation of the Blind, came up with this challenge about a decade ago. Even after this new car’s unveiling next January at the Daytona International Speedway, it may still be a long while before blind drivers take to the road. But, Maurer says, that’s not the point. Instead he wants to show that blindness is a difference rather than an insurmountable impairment. He told The Telegraph:

“We’re exploring areas that have previously been regarded as unexplorable. . . We’re moving away from the theory that blindness ends the capacity of human beings to make contributions to society.”

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Image: iStockphoto

The New York Times is reporting that the Japanese space probe Hayabusa — sent to physically land on the asteroid Itokawa, get a sample of the rock, and return to Earth — may have come back without such samples. While it’s not confirmed yet, it will be disappointing news if true.

Hayabusa was plagued with problems, from faulty engines to a misfiring mechanism designed to force pieces of the asteroid into a collection container. Despite these issues, engineers were able to coax the probe back into an Earth-return orbit and retrieve the sample container after a dramatic re-entry. Apparently there are traces of gas which may be vaporized rock from Itokawa, but no solid chunks. I’m sure they’ll be scouring the container to look for microscopic pieces as well.

I hope they find some. Itokawa is a rubble pile, an asteroid that has been shattered by collisions and held together by its own gravity. We know very little about such asteroids, and we need to find out more if we should ever see one on a collision course with Earth and want to push it out of the way. And we do want to do that!

But even if Hayabusa didn’t get any samples, Japan learned a lot of valuable information on how to run (and save!) a space mission of this depth and complexity, and scientists got a lot of info about Itokawa itself. Hayabusa voyaged for seven years in space, and despite these problems I think that the scientists and engineers at the Japanese space agency JAXA should be proud.

Here’s a letter to The American Journal of Human Genetics worth reading, Genetic Landscape of Eurasia and “Admixture” in Uyghurs:

…In the papers…by Xu and Jin, the genetic structure of Uyghurs was described by 8150 ancestry-informative markers (AIMs). These markers estimated the admixture rate of the Uyghur population to be around 50% East Asian ancestry by comparing Uyghurs to East Asians and Europeans. However, we suspect that the estimate of Xu and Jin may be considerably biased by insufficient reference population coverage….

The difference between the estimate of Xu and Jin (52%) and our estimate (31%) may stem from either the different population coverage or the sample size. We analyzed a different and larger sample of Uyghur individuals (n = 48) than that analyzed by Xu and Jin….Their small sample size may have contributed to their overestimation of the European component to admixture (i.e., to cluster assignment). However, the insufficient population coverage may be more responsible for the difference than the sample size or the number of markers. Concerning the number of markers, it is known that a relatively small but specifically selected number of AIMs can accurately predict ethnicity proportion…As the two papers of Xu and Jin have demonstrated, the estimated admixture rates reported did not change much regardless of whether they were using chromosome 21 data only or the whole genome, and thus a large number of markers may not be necessary to estimate the “admixture” rate of Uyghurs. When we analyzed only the 12 markers with the highest F_ST values in our samples…the Uyghurs had a 30.2% assignment at K = 2 to the Europe and Western Asia cluster. This estimate was not significantly different from the above 31.2% when using all 68 markers. We consider it unlikely that a different set of appropriately chosen SNPs would give a markedly different answer based on unpublished data on some of these same populations….

Basically the authors are arguing that you’d rather have a more diverse range of populations (to get more between population genetic variance) than just keep increasing the number of markers within individuals to really capture geographic diversity. Reference population matters. I know that 23andMe tells South Asians to expect to get back that they’re 70-90% “European,” with the balance “East Asian.” People with only Native American ancestry are going to be 75% “East Asian” and 25% “European.” These sorts of results from the reference populations are pretty misleading in my opinion. If you model the variation of all the world’s populations as the combination of variation of a few reference populations you’re getting a stylized fact which is confusing if you don’t know to interpret it correctly.

Below is figure one, where they show the difference between K = 2 and K = 6 (assume two or six ancestral populations for your data set). The map illustrates the distribution of K = 6, as the intensity of each color represents the current contribution in that region of a K ancestral group.

With the perpetual flow of filthy crude from BP’s oil leak in the Gulf of Mexico, just about anything seems like a better energy solution than deep sea offshore drilling. One new proposal, though, has the potential for similarly disastrous environmental harm.

The Keystone XL is a huge proposed pipeline that could carry oil from Canada’s oil sands on a snaking path through the American Midwest and all the way down to Texas, where it will be refined. The idea has been up for public comment for months, and that period comes to a close soon. So, should we build this thing?

YES

There is one good thing about the project: It would be a source of energy that’s not the Middle East, Iran, Venezuela, or another region or country hostile to the United States.

From an energy perspective, Keystone XL delivers one thing the United States needs: plentiful oil from a friendly neighbor. Most oil companies have invested heavily in Canadian oil sands and are firmly behind it [The New York Times].

The project would bring in another million barrels of oil per day from Canada, which is already our biggest foreign oil supplier.

A study released this month by the Perryman Group, an economic analysis firm based in Waco, concluded that the project could generate as much as $2.3 billion in new spending for Texas during construction and $1.1 billion in property taxes to local and county governments over the pipeline’s operating lifetime [Houston Chronicle].

NO

The oil sands are one of the dirtiest energy projects in the world. The oil is dirty to extract and dirty to refine, plus there are the transportation dangers.

The energy-intensive process emits three times more greenhouse gases per barrel than production of conventional oil, environmental groups say. Friends of the Earth, which opposes the project, estimates that the pipeline would increase greenhouse gas emissions by 38 million tons, equivalent to 6 million new cars on the road [Houston Chronicle].

Oil refining is no clean business anyway, and this oil could be even worse: watchdog groups like Air Alliance Houston say that it causes more emissions of sulfur dioxide and particulate matter. Unsurprisingly, the company behind the project disputes this and also promises that pipelines are the safest way to transport oil. Forgive us, though, if we’re still a little wary of assurances that everything will fine.

At the hearing on Tuesday, Tom Rudolph, a farmer from Circle, Mont., expressed his reservations “as a landowner directly on the route.” He called the draft environmental impact statement “insufficient,” noting in particular the lack of a “complete spill response plan” in the event of a leak. “The disaster in the gulf serves as a warning,” he said [The New York Times].

We should also consider that the Canada-to-Texas route passes through some of the most valuable agricultural land in the United States. In addition, the area is home to the giant Ogallala Aquifer, which provides drinking and irrigation water for the High Plains.

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Image: NASA

Just because I am no longer at Duke, doesn't mean I don't keep tabs on Stuart Pimm and the rest of the family. Recently Stuart spoke to the Endangered Species Coalition about the oil spill in the Gulf of Mexico describing how it's been so devastating to wildlife, why scientists cannot predict the long-term ecological damage, and the scale of restoration that will be required. This is a sad, but very important podcast and I encourage readers to listen here. You can also read more from Stuart on biodiversity at his terrific National Geographic blog.

Caitlin, a graduate student, writes:

About four years ago, a close friend from college got her first tattoo – something meaningful and marking a particular point in her life – and she asked me if I would ever get one. I said sure, but that at that point in my life there was nothing I could come up with that was meaningful enough to have permanently etched in my skin. That was my first year of graduate school and I was still very unsure of myself and my future.

Four years of graduate school later finds me in the final stages of earning a Ph.D. in evolutionary biology – a place I was not convinced I was cut out to reach at the start of graduate school. After 2009’s year of Darwin celebrations, including my own involvement organizing a conference celebrating 150 years of evolutionary biology, the perfect tattoo came to me in class one day in March, and I found myself at the tattoo parlor by the end of that week.

My tattoo is Darwin’s very first phylogeny, from his Notebook B on Transmutation of Species and it is on my right shoulder. These notebooks contained much of his brainstorming on evolution after returning from the Beagle, and I was able to see this one in person at the American Museum of Natural History’s Darwin exhibit in 2006. I also added his signature and the date which can be found on the inside cover of the notebook.

I chose this particular piece of Darwinia for several reasons. As a perpetual student of science and of nature in particular, I love the slight hesitation and perhaps excitement in the “I think.” I am amazed that Darwin was thinking about phylogenies in 1837, 22 years before the Origin was published – that you can see the seed of his great work (and the preface to the only figure in the Origin) so early in his writings. The phylogeny itself as an image is meaningful because I study speciation, and spend a great deal of time studying, thinking about, and building my own phylogenies. I had also selected it to be part of the cover of the program for the conference I was involved in, and many attendees asked me about it. In short – it carries a lot of meaning to me.

So, my tattoo honors Darwin, the father of my field; it represents my own personal research; and it exemplifies the slight hesitation and excitement of scientific discovery that I hope will stay with me always as I launch my academic career. It is a mark of confidence, in myself, and my chosen profession. I have no doubt that I will never regret permanently etching this image on my skin, and I know that it will serve as a reminder to me that even though the pursuit of scientific knowledge is a long, sometimes daunting journey, I love what I do and I can’t imagine doing anything else.

Click here to go to the full Science Tattoo Emporium.

Believe me, there are many inconveniences that come with being left-handed: Your childhood art projects look like they were accomplished by jittery beavers on account of those damn right-handed safety scissors, and simple kitchen tools like can-openers and soup ladles can become the enemy. But now we lefties can add in a high-tech complaint: The iPhone 4’s antenna problems are particularly troublesome to the likes of us.

The iPhone 4’s sales have been spectacular since it debuted last week, but consumers immediately noticed a glaring problem with the metal band that wraps around the phone’s perimeter and acts as an antenna; holding the phone in certain ways interfered with the antenna and could lead to dropped calls. In response, Apple advised customers to “avoid gripping it in the lower left corner” when making or receiving a call. That’s when a U.K. group called the Left-Handers Club got irate.

According to The Telegraph, spokeswoman Lauren Milsom issued a blistering statement:

“It seems ludicrous to suggest that 10 per cent of potential users should be told they have to adopt a less natural hand hold to use this latest technology. I would strongly suggest that Steve Jobs employs left-handers in his design and testing team in future, and urgently address this issue to ensure the phone is fit for purpose.”

Lefties are reportedly not the only ones upset about the apparent design flaw. One couple that’s suing Apple says their phone’s faulty antenna has caused them “emotional distress,” and class-action lawsuits are starting to spring up.

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Image: flickr / Jorge Quinteros