They are mum’s first gift to her newborn baby on the day of its zeroeth birthday – bacteria, fresh from her vagina. Vaginal bacteria are among the trillions of microscopic hitchhikers that share our bodies with us. Collectively known as the ‘microbiota’, these passengers outnumber our own cells by ten to one. Children partly inherit their microbiota from their mothers. During birth, they pass from the largely bacteria-free conditions of the womb through the microbe-laden vagina into the equally bacterial outside world.

Being slathered in vaginal microbes might not seem like much of a treat from our adult perspective, but to a newborn, it’s a key event. The microbiota are important partners, influencing our physiology and our risk of disease. Now, Maria Dominguez-Bello from the University of Puerto Rico found that the way we enter the world determines the identities of our first bacterial colonisers. Babies delivered by Caesarean section end up with a very different portfolio to those who are born naturally.

To characterise baby’s first bacteria, Dominguez-Bello compared the microbiota of 10 mothers and their newborn babies, four of who had been delivered naturally and six of who were born through C-sections. She sampled the mothers’ skins, mouths and vaginas an hour before delivery, and the babies’ skins, mouths and noses less than five minutes afterwards.

She found that all the infants had the same bacteria all over their bodies. That’s very different to the situation in the mothers (and indeed, other adults), where different parts of the body are as varied in their resident species as deserts are to rainforests. In adult bodies, certain species of bacteria dominate certain habitats, so that your butt microbes have more in common with mine that they do with your elbow bacteria. Again, this wasn’t the case in babies.

Dominguez-Bello also found that the membership of the babies’ bacterial clubs was mainly influenced by their route of delivery. Those who were delivered naturally harboured bacteria all over their bodies that resembled those in their mother’s vagina – mainly Lactobacillus, which help us to digest milk.

But babies who were delivered by C-section were colonised by bacteria that are more commonly found on the skin, including Staphylococcus. These colonists didn’t necessarily come from mum either. The skin bacteria of C-section mothers were no more similar to those of their own babies than to those of other infants delivered in the same way. Instead, it seems that C-section babies pick their first bacteria from the hospital environment.

These early differences could directly affect a baby’s health. Staphylococcus is mostly benign but they can also go rogue, causing a wide variety of infections from spots to pneumonia. Antibiotic-resistant strains such as MRSA are particularly problematic and it’s perhaps unsurprising that in a Californian study, between 64-82% of newborns with MRSA infections were delivered through C-sections.

Other scientists have found similar trends for the bacteria in a baby’s gut, which also differ depending on how the child is delivered. Dominguez-Bello’s new study extends this knowledge to other parts of the body, but it’s more of a starting point for further research (and perhaps a narrow one at that, given that it only considered ten babies) rather than a conclusion in itself. We still need to understand the shifts that take place as children grow and the members of their microbiota rise, fall and take up residence in different body parts.

Dominguez-Bello suspects that all of these events hinge on the moment of birth. She thinks that the bacterial heirlooms that babies inherit from their mothers might act as a shield, preventing more dangerous microbes like MRSA from setting up shop. In this way, early colonisers can influence the direction of late successions. By changing baby’s first bacteria, C-sections could alter the make-up of their later communities, leading to long-term effects on health and nutrition.

There is some evidence to support this idea, but to date, it’s pretty circumstantial. Some studies have suggested that babies delivered through C-section might be more susceptible to allergies, although the increase in risk is pretty small. Nonetheless, in one study, probiotic drinks containing Lactobacillus could help to counteract this increased risk, at least for some types of allergies.

Results like these are easy to politicise, especially since a quarter of babies in the UK are delivered by Caesarean section. But this study is no condemnation of C-section deliveries, which are often necessary. Opinion pieces often decry women who opt for elective C-sections because they are allegedly “too posh to push”, but the reality is very different to the ones these straw (wo)men caricatures present. Official records show that such births only account for 1.5% of the total. And last year, a UK study showed that just 3% of women would opt for a C-section if they didn’t have a medical need for one.

It’s also important to note that this new study merely documents how the method of delivery affects the bacteria that babies inherit. The effect that this has on our health is still largely speculative (contrary to what some papers would have you believe). And whether those effects have any significant importance in the grand scheme of things also remains to be seen. Dominguez-Bello’s paper ends with a call for more research and that’s exactly what is now needed.

Reference: PNAS http://dx.doi.org/10.1073/pnas.1002601107

More on the microbiota:

• Gut bacteria in Japanese people borrowed sushi-digesting genes from ocean bacteria
• The bacterial zoo in your bowel
• The bacterial zoo living on your skin
• Gut bacteria – fat or thin, family or friends, shared or unique
• Human gut bacteria linked to obesity

Some good news from Texas! Yeehaw!

The Institute for Creation Research — one of the biggest nonsense-peddlers in the 6000 year history of the world — was handed a nice defeat this week. That link to the National Center for Science Education (the good guys) has all the info you need, but to summarize: the ICR moved from California to Texas. In the previous state, for reasons beyond understanding, they were able to grant Master’s degrees in their graduate school. But Texas didn’t recognize their accreditation, so they filed to get it approved.

Not so surprisingly, scientists and educators rose in protest, and in 2008 the Texas Higher Education Coordination Board — the organization that grants accreditation — denied the ICR. The creationists appealed. In the meantime, they also tried to extend their ability to grant degrees temporarily while the lawsuit continued. What happened this week is that the extension as denied.

And I mean denied. Check out what the court said:

It appears that although the Court has twice required Plaintiff [the ICR] to re-plead and set forth a short and plain statement of the relief requested, Plaintiff is entirely unable to file a complaint which is not overly verbose, disjointed, incoherent, maundering, and full of irrelevant information.

That’s not surprising, as that’s the only kind of information the ICR is capable of producing. Not to mention wrong. See the Related Posts links below for lots more on the ICR’s recent follies.

As far as I can tell, this defeat means that the ICR is still seeking accreditation, but until and unless it does, it cannot grant degrees in Texas.

So what can be said about this? Oh, let me quote one of the pithiest and to-the-point minds of our day:

<Nelson Muntz>Haha!</Nelson Muntz>

Just kidding with the title. I don't have anything particularly insightful to say about the physics of the game. Rather, this post is just to say, I'm off to watch the USA (and England). I won't be blogging this am at least until that is over and done with. But I'm sure people have opinions about the team, so this is a place to leave them, and discuss the game....

Larry Witham’s Marketplace of the Gods: How Economics Explains Religion is a manifestly ill-timed book. He states that “…around 2006 I began to notice a good deal of hoopla in the book market about economic explanations for just about everything-books that were best sellers.” Marketplace of the Gods was obviously written to capitalize on the prestige of economic explanations, but unfortunately it has come out after the bubble had burst on that market, so to speak. Within the past few years even many economists have come to admit that the power of their discipline’s logic can explain far less than they’d once thought. In fact, it seems a bit much for economics to explain everything when the core competency in financial domains are themselves being challenged. Even in 2008 in The Logic of Life Tim Harford was engaging in a rearguard attempt to prevent behavioral economists such as Dan Ariely from knocking the legs out from under the central thesis of his book. A more accurate subtitle for Marketplace of the Gods would have been “economic explanations of religion.” Not punchy or imperialistic, but true to the content of the text.

These explanations are rooted in a few assumptions derived from conventional economic methodology and applied to religion. Humans are rational, they settle upon strategies which can fulfill their preferences, and their world is characterized by scarcity and opportunity costs. Phenomena are best explained in a reductionist framework which takes a methodologically individualist stance. In other words, what’s in it for the individual, not society. Larry Witham documents the intellectual journeys of two giants in the field, Rodney Stark and Laurence Iannaccone. I have read Iannaccone’s papers, as well as most of Stark’s academically oriented books. There’s a lot of clear and crisp thinking there. Marketplace of the Gods reviews the long history of woolly theorizing about religion which explained everything and so nothing, and served as the ideal seedbed for the invasion of the subject by those wielding sharper tools.

But the supply side model of individuals consuming goods and services from competing religious firms, to translate religious phenomena into economic language, can not explain everything. The author acknowledges this in the text, but falls into traps whereby the theory which he has encountered allows for superficial inferences which are plainly false if one was aware of a richer set of data. Consider this passage:

In traditions that invest more intensely in human religious capital the rentention rate is highest. For example, Hindu, Catholic, and Jewish groups lose the least number of adherents over their lifetimes. In America today, 90 percent of Hindus were reared in that tradition, and the same goes for 89 percent of today’s Catholics and 85 percent of today’s Jews….

This sounds plausible enough, but the explanation that Hindus and Catholics have high retention because they “invest more intensely in human religious capital” is probably wrong. Hindus and Catholics have huge immigrant communities, and come from societies where religious switching is rare or taboo. The majority of American Hindus are immigrants, so they are not integrated into the American marketplace of gods. The Religious Landscape Survey which Witham references makes it obvious that American Hindus are not even particularly religious. Witham assumes they invest more intensely in human religious capital probably because of the 90 percent figure, but theory is misleading him because of the incompleteness of his data base. Similarly, Catholics have been the biggest contributors in the past decade to the irreligious segment of Americans. The last finding is relatively recent, and so may not have been available when Marketplace of the Gods was being written, but it shows the lack of robusticity of the set of inferences which one can generate from these models. New data easily overturns novel inferences on a regular basis.

Obviously there’s some real insight that can come out of the intersection of economics and religion. And Marketplace of the Gods serves as a decent precis of the literature, and its bibliography is well worth perusing. But if you know anything about religion it will be rather clear that the current theoretical contributions of economics in explaining most of the variation in the phenomenon is limited. Religion is a big topic, and a true “explanation” necessarily has to encompass evolution, psychology, history, and, economics.

“OBJECTIVE: The 21st birthday celebration is often associated with excessive alcohol consumption. The current study examined whether individuals consume more alcohol than anticipated during their celebration and whether situational factors contribute to prediction errors. METHOD: College students (N = 150; 50% female) who planned to drink during their 21st birthday celebration were contacted by telephone 1 week before their celebrations and asked about their birthday plans, including anticipated alcohol consumption. The week after the celebration, in-person semi-structured interviews and self-report measures were administered to obtain information about the 21st birthday celebration, including type and amount of alcohol consumed, pace of drinking, influential peer involvement, and engagement in 21st birthday traditions. RESULTS: The majority of 21st birthday celebrants consumed more alcohol than they anticipated, with men showing greater prediction error than women. Situational factors were positively associated with the discrepancy between anticipated and actual alcohol consumption. CONCLUSIONS: Drinking shots, drinking at a fast pace, celebrating with influential peers, and engaging in 21st birthday traditions were associated with drinking more alcohol than anticipated during 21st birthday celebrations. Findings suggest future interventions that target situational factors could reduce excessive 21st birthday drinking.”

Image: flickr/tifsims

Related content:
Discoblog: NCBI ROFL: Binge drinking in Jewish and non-Jewish white college students.
Discoblog: NCBI ROFL: Girls Gone Wild: science edition!
Discoblog: NCBI ROFL: Beer consumption and the ‘beer belly’: scientific basis or common belief?

WTF is NCBI ROFL? Read our FAQ!

Here we go again... From the AFP:
BEIJING — A floating expanse of green algae floating off China's eastern seaboard is growing and spreading further along the coast, state-run media has reported. * * * * * Algae blooms are typically caused by pollution in China and suck up huge amounts of oxygen needed by marine wildlife to survive and leave a foul stench when they wash up on beaches. * * * * * According to a 2008 State Oceanic Administration report, raw sewage and pollution from agricultural run-off has polluted 83 percent of China's coastal waters, leading to algae and other problems.

When a person’s cornea is burned it’s not necessarily the splashed chemicals or hot liquids that causes blindness, but the eye’s recovery. Scar tissue, formed from cells in the white part of the eye, can cover the cornea in a cloudy haze. But researchers have found that cells drawn from another part of the body can correct the problem.

A paper published yesterday in the New England Journal of Medicine brings news of a regenerative stem cell treatment that has had striking success: It restored sight to 82 of 117 eyes with burnt corneas, and worked partially on 14 others. The treatment also seems to have a long-lasting impact; in one patient, the beneficial effect has lasted for ten years and counting.

The treatment offers hope to those who received little benefit from existing therapies–such as artificial cornea replacements, which can also be overpowered and clouded by white-colored cells, or stem cell or cornea transplants from cadavers, which patients can reject.

“[The patients] were incredibly happy. Some said it was a miracle,” said one of the study leaders, Graziella Pellegrini of the University of Modena’s Center for Regenerative Medicine in Italy. “It was not a miracle. It was simply a technique.” [AP]

That technique, first performed in 1995, requires harvesting healthy “limbal stem cells” from the cornea’s border. Stefano Ferrari in Italy then grew these cells into a sheet and grafted them onto the cornea. Since the cells come from the patient and not from a donor, the procedure does not have the risk of rejection present with transplants.

The treatment “is like putting on a biological contact lens,” said Dr. Stephen Pflugfelder, a practicing corneal specialist and professor of ophthalmology at Baylor College of Medicine in Houston, who says the technique works well. A clear cornea–essential to good vision–”is the clear window on the eye,” like a watchglass on a watch, added Pflugfelder, who was not involved with the Italian study but is familiar with its findings. [HealthDay]

For successfully treated patients, vision improved within months, and of those that did not fully regain their sight the treatment still often helped.

Even when not completely effective, the treatment usually alleviated a patient’s sensitivity to light and eye pain, Pellegrini said in a telephone interview. “In any case, the patient has improvement in symptoms,” she said. The researchers were also able to pinpoint which types of cells were more likely to work well. [ABC]

Unfortunately, the technique requires a healthy population of “donor” stem cells from the patient, so it will not work for those who have severely burnt both their corneas (leaving few healthy limbal stem cells). A benefit of the technique is that it requires fewer total stem cells than previous procedures (as ABC reports, about .002 square inches of tissue) since researchers cultivate these sample cells in the lab to make the graft.

Related content:
80beats: Gene Therapy Cures Color Blindness in Monkeys
80beats: The Part of the Brain That Lets the Blind See Without Seeing
80beats: Can Sight Be Restored With Stem Cells Grown on Contact Lenses?
80beats: Brain Reconstruction: Stem-Cell Scaffolding Can Repair Stroke Damage
80beats: Stem Cells Could Regenerate Inner Ear Hairs—and Hearing

Image: New England Journal of Medicine

An image from Opportunity's NavCam taken on May 8, 2010 showing the tracks from a recent drive just before the Winter Solstice. Click for larger. Image Credit: NASA/JPL-Caltech

A comment in yesterday’s post asked what was going on with the Mars Exploration Rovers — good question.  The rover site isn’t updated very often due to it being the Martian winter.  The winter Solstice was on May 12 so spring is approaching Mars even if very slowly.

On May 20th the rover Opportunity surpassed the Viking Lander’s longevity record of 6 years 116 days.  As the daylight increases Opportunity will beginning to drive more.  At the moment drives are worked out so the solar panels are in a favorable position to catch sunlight.  The eventual destination for Oppy is the  Endeavour crater.

The situation with Spirit isn’t quite so good.  You probably know Spirit got stuck on what looks to be a rock, kind of hung up, well, it’s stuck and is now immobile.  Being immobile placing the rover in a position to best collect the feeble Martian sunlight was impossible.  Spirit is in a hibernation mode.  Will it awaken?  A question everybody involved is waiting to be answered.  If it does and resumes communication, it will get the longevity record since it arrived three weeks before Oppy.  Keep your fingers crossed!

The newest rover named Curiosity is well on its way to a late 2011 launch, the robotic arm and associated tools are being tested, two cameras built by Malin Space Science Systems Inc has been delivered.  The cameras will be used on the Mast Camera Instrument which will be a workhorse.  Finally, the radar system to be used in landing is undergoing rigorous testing.  The actual launch date is driven by geometry and communications it’s quite a balancing act between the shortest route and optimal communications.  The launch date will be between November 25 and December 18, 2011 for a August 2012 Landing.  To learn more about Curiosity, click here.

I’ve mentioned before on this blog that I’m not one for arbitrary milestones. I’m OK with birthdays and such, but when it comes to celebrating attaining some certain number of things just because it’s a round number, it seems a bit silly.

Of course, that’s just my rational mind. My emotional mind still squees a little when that nice, round number is achieved.

And here I am, at my 5000^th post. This very post, in fact, if you excuse me getting a little meta.

I know that if we evolved to have 8 fingers, or 12, this post wouldn’t be quite the same milestone. But contingent, stochastic processes are what they are, and so here I am, 4999 posts from the first one. That one, published on March 13, 2005, was just a "Welcome to the blog!" kind of thing. But it was the start of a long series of posts about science, astronomy, Doctor Who, skepticism, religion, LOL cats, politics, and just about everything else that’s caught my attention.

Along the way the blog moved to its new home at Discover Magazine (that anniversary is pretty soon, too). And what news has unfolded over this period! Direct pictures of planets orbiting other stars were first taken. Methane was found cycling on Mars. Water on the Moon. Two moons of Pluto discovered. The first private company launched a rocket. MESSENGER headed for Mercury. Two impacts on Jupiter. Lakes on Titan. An asteroid seen before it impacted the Earth. Just to randomly pick out a very few.

And, of course, the fight against antireality, pseudoscience, nonsense: that continues as well. The title of this blog is Bad Astronomy, but that doesn’t limit the content. The forces of darkness will always be with us, and you can count on me to always fight them.

And as for the future, I will always write about what interests me, what makes me happy, and what angers me. But I can’t do it without you. Well, OK, sure, I can, but it’s not as much fun. Since that first post in 2005, nearly a quarter of a million comments have been left here, too. People praising me, insulting me, leaving non sequiturs, links to related material, corrections, stories, discussions, and so much more. It may be my name on the blog, but it’s the community here that keeps it alive.

So, after 5000 posts, consider this one a simple thanks.

Thanks.

[Update (a few hours after posting): I've read all the comments, and, and... I think I have something in my eye. Thanks again everyone.]

The Washington Post’s blogger-journalist Dave Weigel has a post up where he preemptively apologizes for stuff he posted on an “off-the-record” e-list,. Extracts are going to be published by a gossip site. Journalists are the tip of the iceberg; privacy is fast becoming a total fiction, remember that. We’re slowly drifting toward David Brin’s model of a “transparent society”, but it’s happening so fluidly that people aren’t even noticing. And yet as I have noted before, people are resisting the push to merge all their personas into one. Interesting times.

It would be an advertiser’s dream: knowing the exact location in your brain that indicates whether an ad has worked, and whether you intend to buy that cat food or wear that suntan lotion. Now, some researchers claim they’ve found a region which might predict whether viewers will act on what a commercial tells them.

For a study published yesterday in The Journal of Neuroscience, researchers asked 20 participants to listen to a series of “persuasive messages.” While the test subjects listened, researchers used an fMRI to record the activity in various regions in their brains. The study was small–but researchers say that, with these 20 participants, they could determine many of these listeners’ intentions by looking at a region associated with self-consciousness, called the medial prefrontal cortex.

The subjects listened to messages covering a range of subjects, but the team, lead by Matthew Lieberman at UCLA, was really interested in a public service message about the importance of using sunscreen. Before the brain scans, researchers surveyed the participants about a variety of their behaviors, including their expected sunscreen use for the next week.

After the brain scans were complete, researchers asked about their intentions again and gave participants “goodie bags” that included sunscreen towelettes. But a surprise follow-up phone call a week later revealed that only about half of the participants had lotioned up as often as they said they would.

The researchers then went back to the scans to hunt for hints that might have predicted this “complex real world behavior,” and that’s when they teased out possible predictions in the medial prefrontal cortex. By examining the activity in that area when the listeners heard the sunscreen messages, the researchers say they could predict the real sunblock use of three-quarters of the subjects. Thus, they claim, the brain scans were better predictors of behavior than the subjects’ own projections.

Emily Falk, a coauthor of the paper, told Reuters:

“We are trying to figure out whether there is hidden wisdom that the brain contains.”

Even if their lackluster sunblock use might leave these sunny Californians at risk for skin cancer, they don’t have to worry about brainwashing quite yet. Given the variability of people, the researchers will need probably need to test their tech on more than 20 people before they can use this information to craft the perfect public service announcement, or advertisement.

Related content:
Discoblog: AD4HERE: Digital License Plate Ads May Come to California
Discoblog: Lather Up: New Sunscreen Could Be Inspired By Hippo Sweat
80beats: Neuroscientists Take One Step Closer to Reading Your Mind
80beats: Brain Scans Can Predict When You’re Going to Screw Up
80beats: Mind-Reading Infrared Device Knows If You Want a Milkshake

Image: flickr / candescent

In a lab at Yale University, a rat inhales. Every breath this rodent takes is a sign of important medical advances looming on the horizon, for only one of its lungs comes from the pair it was born with. The other was built in a laboratory.

This transplanted lung is the work of Thomas Petersen and a large team of US scientists. Their technique isn’t a way of growing a lung from scratch. Instead it takes an existing lung, strips away all the cells and blood vessels to leave behind a scaffold of connective tissues, and re-grows the missing cells in a vat. It’s the medical equivalent of stripping a house down to a frame of beams and struts and rebuilding the rest from scratch. The whole process only took a few days and when the reconstituted lung was transplanted into a rat, it worked.

This is important because the lungs are notoriously bad at regenerating and repairing themselves. If a person’s lungs are severely damaged, the only real solution is a lung transplant. But that’s easier said than done. The procedure is expensive, only 20% of patients at most are still alive ten years later, and the demand for donor lungs far exceeds their supply.

Peterson’s ultimate vision is to solve these problems by fitting patients with a transplanted lung grown using their own stem cells. The scaffold would come from a dead donor, or possibly even a primate or pig. Its own cells would be stripped away and the patient’s stem cells would give the scaffold a personalised makeover, seeding it with the various types of cells in the lungs. The whole process should only take around 1-2 weeks. Laura Niklason, who led the study, says, “The value here is that the resultant lung would not reject, which is the key that limits survival of lung transplant patients right now.”

The team’s latest success in rats is a proof-of-concept – it shows that the technique should eventually be possible. But as Petersen notes, there are many technical hurdles to overcome before it could ever used in humans. That achievement is still years of hard work away. “I think that 20 to 25 years is not a bad time frame,” says Niklason. “I previously developed an engineered artery that will be ready for patients next year. It was first published in 1999. If an artery takes 12 years from first report to patients, then a lung will take 20-25.”

First, the team used detergents to strip away all the cells and blood vessels from freshly harvested lungs, leaving behind the ‘extracellular matrix’. This scaffold of connective tissues keeps the lung’s physical properties, as well as its three-dimensional structure. Right down to the microscopic level, every branch was preserved. So were the structures of the alveoli, the little spheres through which our lungs exchange gas with our blood.

The complicated nature of the scaffold explains why the team ruled out the possibility of simply growing a lung from scratch. “We grow arteries from scratch all the time in my group,” says Niklason, “but lungs are harder because of the enormous surface area that is required for adequate gas exchange.” You’d need to provide a template for that surface area and a man-made material is unlikely to do the trick. “That is, technologically, a very tall order.”Other groups have tried this approach and failed to produce anything that can actually exchange gases as a real lung can. For this reason, the team decided to use nature’s template – the lung’s own matrix.

Having exposed the matrix, they marinated it in a cocktail of lung cells taken from newborn rats. The added cells stuck to the matrix in the right places and started reproducing quickly, in a way that they normally struggle to do on standard plastic surfaces. The conditions certainly helped – the team incubated the lung matrix in a ‘bioreactor’ designed to mimic the conditions inside a growing foetus. Different tubes imitated the flow of blood and air into the developing organ, with everything was maintained at just the right pressure. All of these conditions proved to be essential for getting the lungs to re-grow in the right way.

Within just four days, the lungs were once again full of alveoli, blood vessels and small airways, all containing the right types of cells. Then, the big test: Petersen transplanted four of these brand-new lungs (just the left ones) into living rats. Within seconds, the lungs became suffused with blood, which rapidly turned from dark to bright red as it started taking up oxygen. When the team took samples of blood from the major vessels, they confirmed that the new lungs were indeed exchanging gas as they were meant to.

Their biggest challenge now is to find a good source of cells to seed the empty frames they expose. The re-fitted lungs will be immediately rejected by the immune system unless Petersen can grow them using lung stem cells derived from the patients themselves. These aren’t available yet, although techniques that reprogram adult cells into stem-like ones may help to solve this problem in the future. “The stem cell biology will be the biggest hurdle,” says Niklason. “Making the cells and growing them is not so bad, but controlling their fate within the lung matrix will be a substantial issue.”

The team have already shown that the technique works on human lung samples taken from a tissue bank. But even in rats, the results are far from perfect. Chest X-rays revealed that the fresh left lungs were indeed inflating with air but to a lesser extent than the native right ones. There were also signs of minor bleeding into the airways and some clots after a few hours. The matrix had probably become slightly damaged during the process of removing its cells. These leaks will have to be addressed before the procedure can be used in the clinic, but other scientists regard them as a sign that Petersen’s group have rushed ahead too quickly.

Joaquin Cortiella, who works on lung tissue engineering at the University of Texas Medical Branch, says, “I believe that they did not wait long enough with their cultured lung before they implanted it in the animal.” His colleague Joan Nichols agrees. “The big problem with tissue engineering is that because of the clinical need very often researchers have rushed to implant tissues before they had really produced materials worthy of transplantation,” she says.

Nichols’s own own group is working with engineered tissues that are two months old, and they only plan on implanting them into animals in 4-6 months, after careful evaluation. In particular, they want to see if the lung’s blood vessels form a proper junction with the alveoli and the matrix, something that Petersen’s group haven’t established. These junctions are the places where gas exchange takes place. If they aren’t formed properly, gas will probably still diffuse through the blood vessels because the whole organ is sitting in an oxygen-rich environment, but you get blood leaks.

Nonetheless, both researchers say that the technique used to actually produce the lung was “careful, well planned and beautifully presented”. Cortiella says that it “shows the importance of using the organ’s own extracellular matrix”, while Nichols notes that it “advances our view of what a bioreactor needs to look like in order to both grow and mature lung tissue”.

And Nichols is particularly excited about the fact that other researchers are making significant headway in engineering a lung. “It is hard to make headway in a field when so few people have tried to engineer a lung,” she says. “Good science does not take place in a vacuum. You need a critical mass to move the field along.”

Lung engineering may not be a competitive field, but it’s clear that similar approaches are being tested for other organs. Just last week, another team from Massachussetts General Hospital achieved the same trick for livers, stripping them down to a scaffold, re-growing them, and transplanting them back into rats. Again, we’re a long way off from the clinic but the fact that progress is being made at all makes this a very exciting time to be alive.

Reference: Science http://dx.doi.org/10.1126/science.1189345

More on tissue engineering: Making new heart cells

Here’s the best paleontology routine I’ve heard in the last…well, I’m not sure I’ve ever heard a paleontology routine before. This guy knows his dinosaurs, cold! Just look at his contempt when an audience member shouts out “Pterosaur.” Warning: f-bombs away!

Thanks to Boing Boing

Oh, this is nice, someone is auctioning off a nice replica TARDIS from Doctor Who and it looks pretty good, and in fact OMG IT’S AN ACTUAL TARDIS FROM THE FIRST SERIES OF DOCTOR WHO SQUUUEEEEEE!

Seriously. An actual TARDIS from the show is being auctioned. It’s from 2005, and was used during the first series by Christopher Eccleston and Billie Piper. How awesome is this?

Incredibly, the expected price is less than $20,000! Who out there in BA land wants to send me a check? I’ll let you play in the TARDIS if you do^*.

Wow. If someone out there reading this does somehow manage to score this, let me know so I can come over and play. Wow.

Tip o’ the sonic screwdriver to Crunchgear and BABloggee Doug Troy.

Perhaps it’s a disservice to continue calling the oil pouring into the Gulf a spill. “Spill” makes it hard to conceptualize the estimated 60,000 barrels of oil per day blasting up from a well more than 5,000 feet below sea level. It also makes it difficult to picture how, as BP estimates, as much as 40 percent of the material “spilling” is methane gas. That methane has been largely overshadowed by the horror of oil-soaked pelicans and tar balls washing ashore, but now a survey, completed on Monday, has measured how the methane has spread.

What’s the problem with methane? The microbes that feed off it. It can create “methane seep ecosystems”–shallow food chains that eat crude oil and dissolved methane and in the process consume all available oxygen, leaving nothing for other marine life forms. Bacteria eat the methane and “ice worms” (so-called because they live around ice-like methane hydrate) eat bacteria, but nothing else eats these worms. This creates a “dead zone.”

So in short [an abundance of creatures that use] methane for food and oxygen to “breathe” will create areas where only bacteria and a few other non-life sustaining organisms can live. All others die. [San Francisco Chronicle]

John Kessler, a Texas A&M University oceanography professor, finished a ten-day exploration of the spill earlier this week, measuring levels of dissolved methane around 4,500 feet under the water’s surface from 35 different sites, the furthest seven miles from the spill.

Levels of methane in deep-ocean waters near the Deepwater Horizon oil spill are 10,000 to 100,000 times higher than normal, and in some very hot spots “we saw them approaching 1 million times above” what would be normal, says ocean chemist John Kessler. [USA Today]

Kessler’s team also measured the levels of oxygen depletion–the sign that microbes are feeding on the methane. These numbers varied.

“At some locations, we saw depletions of up to 30 percent of oxygen based on its natural concentration in the waters. At other places, we saw no depletion of oxygen in the waters. We need to determine why that is,” he told the briefing. [Reuters]

We’ll have to wait for further results to see if the dissolved methane is indeed fueling a new dead zone in the Gulf. As Science Insider reports, Kessler and David Valentine, an oceanographer at the University of California, Santa Barbara, also hope that measuring the dissolved methane may be a way to quantify the extent of the spreading oil.

Recent posts on the Gulf Oil Spill:
80beats: From Marsh Grass to Manatees: The Next Wave of Life Endangered by BP’s Oil
80beats: Obama’s Speech on the Oil Spill: What Do You Think of His “Battle Plan”?
80beats: BP to Kevin Costner: We’ll Take 32 of Your Oil Clean-up Machines
80beats: Should We Just Euthanize the Gulf’s Oil-Soaked Birds?

Image: NASA and the MODIS Rapid Response Team

36,000,000,000,000,000,000,000,000,000,000 is a big number. But that’s actually the number of microbes in the ocean. How on Earth do you comprehend that monstrous menagerie? In my new Meet the Scientist podcast, I talk to pioneering microbiologist Mitch Sogin about a major new project to census the sea’s microbial diversity. Check it out.

The weird phenomenon of blindsight—in which people take in visual information about objects without actually “seeing” them—has long intrigued scientists, and with good reason. They’ve watched people navigate obstacle courses and identify colors while being technically blind. This week, in a study in Nature, neuroscientists point to a part of the brain called the lateral geniculate nucleus (LGN) as the neural key that might make blindsight possible.

They used macaques in which the primary visual cortex had been destroyed. The monkeys’ eye-focusing movements revealed that they were “seeing” images shown at the periphery of their visual field, but only if their LGN was intact [New Scientist].

The authors refer to the LGN as the “main relay” between the retina and main visual cortex.

Other work had shown that the LGN also has projections to a number of secondary visual areas, suggesting that it may serve as a major hub in the visual system. To test this suggestion, the authors injected the LGN with a chemical that activates the receptor for a major inhibitory signaling molecule…. When the chemical is present, nerve cells receive a signal telling them to stop signaling, so this this injection has the effect of shutting the LGN down entirely [Ars Technica].

When the scientists shut down the LGN, the primates in the study didn’t experience any blindsight, as it appears no information was reaching any of their brains’ visual centers.

Related Content:
DISCOVER: What You See Is What You Don’t
80beats: Blind Man Navigates an Obstacle Course Using Only “Blindsight”
80beats: By Developing “Blindsight,” Stroke Patients Can See—And Drive—Again

Image: iStockphoto

I begin with a full disclosure: As many readers know, Vanessa Woods is one of my very best friends. I love spending time with her because she's insightful, outrageous, brilliant, and funny. And I can sincerely say I love her new memoir, Bonobo Handshake for the very same reasons. But most of all, I'm recommending this book because it's so important. At the start of Bonobo Handshake, we're introduced to Vanessa as she sets off rather haphazardly on an adventure to Africa with her new husband, Duke anthropologist Brian Hare. By the end, she--and we--are not the same. Woven in between is a beautiful and complex narrative about people and other primates that slowly unravels what's really at stake. There were times I laughed out loud reading about the challenges of working with a species that--yes--famously approaches sex as easily as humans would a handshake. But there is a lot more to bonobos than their sexual behavior. Just as Jane Goodall documented the unforgettable antics of chimpanzees like Flossie and David Greybeard, Vanessa brings us into the world of 'Empress' Mimi, mischievous and lovable Malou, and my favorite bonobo of all, sweet little Lodja. It's easy to fall in love with all ...

Tonight’s the night: Futurama returns with fresh episodes on Comedy Central, starting at 10 PM Eastern Time. Two weeks ago we featured our conversation with Billy West, the voice actor behind Fry, Professor Farnsworth, and other characters. Today, it’s executive producer David X. Cohen, who worked on The Simpsons before creating Futurama with Matt Groening more than a decade ago.

Cohen discusses how he went from scientist to comedy writer, the logic (or illogic) behind heads in jars, why things still don’t work in the 31st century, and how he sneaks math jokes into the show.

*Plus, read through to the end for some spoilers about the plots of some new episodes coming this season.

DISCOVER Magazine: I feel compelled to ask: Does the X stand for anything? Or is it like the Harry Truman S, and it stands for nothing?

David X Cohen: I’ll get that off my chest right off the bat: It’s a fraudulent middle initial, but there is a logic behind it. The reason for that is the writer’s guild, which has a regulation that no two writers can have the same name for on-screen credits. So, when you join the union, if your name is already taken, you have to change your name. Being named David Cohen—as you can imagine, there were several other David Cohens already in the guild, [and] one with my actual middle initial, S, for Samuel.

So, I decided to go for the craziest most sci-fi letter available, X.

DM: Both of your parents were scientists, correct?

DXC: Yes. Both PhDs in biology. I grew up in a house that was very science-oriented. The family activities we did were usually science-related—trips to the zoo or the museum of natural history in New York. So it was just taken for granted—by me at least—that I would be a scientist sooner or later. I tended to gravitate, though, more toward the physical sciences and math and computer science and physics, and I actually majored in physics in college. So, my undergraduate degree is in physics, and then I got a master’s degree in theoretical computer science as well. Before I derailed.

DM: How did you “derail?”

DXC: When I was growing up I just wasn’t really aware that there were careers such as writing cartoons. It wasn’t something that anybody I knew did and never popped into my mind. But then, when I went off to college, I worked on the Harvard Lampoon humor magazine, and suddenly I did know some people who had the career goal of becoming writers, or specifically, comedy writers.

And after that, I was somewhat torn. Should I continue down my path to be a scientist, or should I pursue this thing which (I thought) I did for fun? Ultimately, [I decided] I would like to go to graduate school before forgetting everything I did as an undergraduate. I went to UC Berkeley and had a good time there, but got to the point where I had reached the end of the line of what I was working on, and I had to reevaluate. I decided I might rather try the other option after all.

It worked out. So, my leave of absence from graduate school is still in progress.

Next: Fermat’s Last Theorem, Star Trek, and suicide booths

Gifted astrophotographer Stéphane Guisard — whose Easter Island picture garnered him the #3 spot in my Top Ten Astronomy Pictures of 2009 — has done it again. He just published this amazing picture of star trails, but it’s not like one you’ve ever seen:

[Click to see a bigger, cleaner pic, and yes, you really want to!]

This astonishing picture shows the entire sky from horizon to horizon with the help of a wide angle lens (to help orient you, south is to the left, north to the right, west at the bottom, and east is at the top). It was taken on a volcano called Chimborazo, which is in Ecuador. The volcano has a latitude of 1.5° south, so it sits almost exactly on the Equator [Update: Stéphane sent me a note that he has been to this volcano before, and has an amazing Milky Way picture taken from it.] Guisard started the exposure about an hour after sunset, once the sky got dark, and ended 10 hours later, about an hour before sunrise. Because of this, it shows roughly 90% of the entire visible sky!

How can this be?

If you’ve ever been to this blog before, you know I’ll be happy to explain. But it takes a minute, so I’ve split the rest of this post up into two sections: you can read about the guts of how this picture works just below, or you can skip to the part where I describe what’s in it (stars and so on). Enjoy.

1) How this can be:

[First, a note: when I say "entire sky", I mean the whole thing, like you were floating out in deep space and could see in every direction with nothing blocking your way. It would feel like you were in the center of a sphere with the stars surrounding you no matter which way you look. On Earth at any one moment, the most you can see is 1/2 the sky, because the Earth itself blocks your view.]

OK, we need a a little geometry lesson. Imagine you are standing on the north pole. As the Earth spins under you, the stars appear to make circles centered directly over your head. Polaris would make a tiny little circle in 24 hours (it’s not exactly on the north celestial pole, the point in the sky directly over the Earth’s north pole, but it’s close), and stars farther from the pole would make bigger circles. At the horizon, the circles would be biggest.

But that’s all you could see. The Earth itself blocks your view of the southern sky, so you can only see half the entire sky. The stars all make circles that are parallel with the horizon, so they never rise nor set. It doesn’t matter what time of night you go out; you see the same stars, just in different positions in the sky. You’ll never see Alpha Centauri or the Southern Cross.

The same is true if you were to stand on the south pole, except this time you can only see the southern sky. The Earth would forever block your view of the Big Dipper, Polaris, and other exclusively northern sights.

Things change if you’re on the Equator. Facing north, you would just see Polaris on the horizon — and actually it would be a bit above the horizon, due to, of all things, our atmosphere. The air of the Earth acts like a lens, bending the path of the light from stars near the horizon. Because of this, Polaris would actually be about two degrees (about 4 times the size of the full Moon) above the horizon. If the Earth had no atmosphere, Polaris would be exactly on the horizon as seen from the Equator.

Turning round and facing south, you’d see the south pole of the sky (marked by the much fainter star Sigma Octans), which would likewise be on the horizon. Facing east, you’d see stars just now rising, and facing west those that are just now setting. If we had no Sun, over the course of 12 hours you’d see every single star in the sky as the Earth rotates beneath you. That’s because any star just setting in the west as you start your observation will be just rising in the east 12 hours later.

However, we do have the Sun (yay!) and so you can’t observe for 12 straight hours, only realistically about 10. So you don’t see the whole sky over the course of the night, you can only see about 10/12 = 5/6 = 80%. If you can push the observing for another half hour you can get up to about 87% of the sky. [Update: Stéphane corrected my math here, and he's right. My apologies for any confusion!] Astronomers divide the sky up into 24 hours — in this case, each "hour" is the distance a star on the Equator of the sky will travel in that time. It’s equivalent to 15 degrees (360 degrees / 24 hours = 15 degrees per hour). The part of the sky not seen in a picture like the one above is shaped like a watermelon slice, with the narrow points at each pole and the widest part at the Equator, near the Sun’s position. It’s one hour wide on each side of the Sun, so altogether that slice is two hours wide. That means the picture has the entire sky (24 hours) minus those two hours, for a total of 22 hours. The amount of sky seen is therefore 22/24 = 11/12 = 92%.

Plus, the Earth’s air give you a bonus: because it bends the light of stars low to the horizon, you can actually see stars that are below your physical horizon! In a sense, the air is acting like a periscope, allowing you see around a corner.

So all this together means that Guisard’s remarkable all-night photo from the Earth’s Equator shows over 90% of the entire sky that is possible to see from the ground.

Amazing.

2) So what’s the deal with this picture, anyway?

He used a fish-eye, a wide angle lens, to capture the entire 360° view of the sky. That’s why star trails near the poles are distorted. The bright trails near the southern pole are from Crux, the Southern Cross. You can also see a bright meteor that blazed its way near the pole, too.

Other stars are identifiable if you know your way around — though without labels they’re hard to find and even harder to describe. Let me try a few (though no promises on my accuracy!):

The reddish-orange streak to the right of center and extending almost the whole picture vertically is from Arcturus. I suspect the red streak just to its left that only extends a third of the way up from the photo’s bottom is Mars. I think the whitish streak to the upper right is Capella, and the bright blue one just to the right of that is Vega.

Interestingly, Orion straddles the Equator, so the three stars marking the belt would all blur together in a picture like this. Plus, this picture was taken when Orion was near the Sun, so it’s only seen briefly in this picture, making a short trail: orange-hued Betelgeuse is the very short streak at the bottom of the image, just to the right of center. I suspect the bright streak at the very top is Sirius, the brightest star in the night sky, and the bright streak near the bottom just to the left of center is Fomalhaut. The famous star Alpha Centauri is the long yellow streak to the left of center starting at the top of the image. Where that streak ends, at about the center of the picture, you can see an orange streak continuing just to its left; that’s Beta Centauri.

I’ll leave the rest to you to discover. And I’ll note that I spent some time a couple of years ago in the Galapagos, at pretty much the exact same latitude this picture was taken. The southern skies are breathtaking, and seeing Alpha Centauri for the first time was incredible. I hope sometime to repeat the experience. And if I do, I may just try to get some star trail pictures for myself.

Picture courtesy Stéphane Guisard, who actually alerted me to it.