I was pleasantly surprised to discover a new flash game that was released today at Kongregate Games. CellCraft is a truly great flash game about building, controlling, and surviving as a human cell, viewed at the microscopic scale. I was even more surprised to find how accurate the game was, depicting organelles correctly and even conversion ratios of glucose to ATP. The game is a great primer for those who wish to learn some cell biology, or even for those of us who know plenty about the cell but want a refresher without cracking open a textbook.

Check out CellCraft at Kongregate and see for yourself!

Edit: Accurate… with the exception of human cells with chloroplasts. Maybe they’re looking to a future evolutionary step?

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What if there really was a wolf..(*ahem*) panspermia?!

Just last month, 2010. 5th floor of a gray building so nondescript that half the people showed up late. Richard B. Hoover, Astrobiology Group Leader at NASA’s Marshall Space Flight Center in Huntsville, Alabama has something he wants us all to see. I look across the table to see all eyes patiently waiting for his powerpoint images. I look back at Richard.  Like a scene out of a 2001 Space Odyssey, Dr. Floyd delivering the bureaucratic spin to top scientists. Only here, their isn’t any cover story, their isn’t any giant black monolith. Here we have but one passionate, smiling and very knowledgeable Hoover trying to convince an exceptionally tough crowd.   The other scientists… only the most respected leaders in the fields of meteorites, prebiotic chemistry, solar system formation and the origins of life, and none of them believe that we have ever found clear evidence of life in space, at least not life we didn’t send up there on purpose.

So let me get straight to the point. In that one moment, in that nondescript room, I went from being 99% sure that evidence of ancient life in space was explained away by contamination (or wishful thinking) to less than 50% sure it didn’t already exist and exactly 0% sure of how to explain the evidence we did have.

It really comes down to a sense of time and a respect for past conclusions about Earth based fossil life. Dr. Hoover is keenly aware of the pitfalls of his observations and yet can’t deny the apparent truth of fossil evidence that life was in space as early as we have detected it on Earth. Here are what I consider some of the strong arguments: They look like bacteria fossils to the same degree that scientists unarguably identify and categorize Earth bacteria, Amino acids in the fossil regions of these meteorites do not match modern contamination profiles (only 12 Amino acids not 20), the nuclear abundances of these meteorites indicate off Earth histories and specifically early solar system formation.

The real question for me now (and maybe should be for all of us) is “why are we so against it?”. Would your God be offended? Would your parents? Would your Priest, Rabbi, Imam, or Manbo Asogwe? I mean come on people, what’s so wrong with Panspermia? The earlier evidence of Martian fossils has been disputed to the point of scaring away reasonable observations now made on MICROFOSSILS IN CARBONACEOUS CHONDRITES. Read on and decide for yourself!

http://www.daviddarling.info/encyclopedia/O/Orgueil.html

http://www.lpi.usra.edu/meetings/lpsc2010/pdf/1949.pdf

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Allergies are a broad category of disorders that all have one common trait, immune reactions to normally non-harmful substances. They are chronic diseases (ranked 5^th on the list among chronic diseases in the US) that can dramatically degrade the lifestyle of those affected depending on the degree of severity. About 55% of the population has an allergic response to one or more allergens. However, some of the most dangerous forms of allergies are food allergies. Just imagine your body reacting negatively to the fruit, meat, nuts, or dairy products that are normally needed for survival. Just imagine not being able to eat at the restaurant you love because you are scared of what ingredients they use. These disorders can be more than physically harmful, but psychologically detrimental to the carrier as he or she becomes afraid of that which is need to sustain life.

However, advances in allergy research are being released almost daily. In an article published in Nature Genetics, scientists have discovered a candidate gene associated with the condition known as eosiniophilic esophagitis (EoE) – an inflammatory response to food allergens that leads to rapid buildup of eosinophils in the tissue of the esophagus eventually leading to dysphagia (difficultly swallowing). The candidate gene known as thymic stromal lymphopoietin (TSLP) gene, is found on chromosome 5q22.1 and is produced by epithelial cells that line the surfaces of the body. TSLP gene over expression has been shown to contribute to other allergy related diseases such as asthma and eczema in prior studies.

There is much more researched needed in this area of study to determine if treatment to reduce TSLP expression will be beneficial. However, identification is a very crucial step and this article provides potential groundwork for future developments of treatments and better understanding of the genetic basis of allergies.

Rothenberg, ME et al. Common variants at 5q22 associate with pediatric eosinophilic esophagitis. Nature Genetics (2010).

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Scientists from Harvard Teaching Medical Hospital have discovered that Mitochondria respond to trauma by creating patient inflammation and a response not unlike bacterial infection. Best known as the energy producing powerhouses of the cell (being home of the Citric Acid Cycle and oxidative phosphorylation), Mitochondria have long been recognized as ancient symbiots – not originally part of the eukaryotic cell line, but were once prokaryotes that have, through a selectively advantageous symbiotic relationship, become incorporated into the eukaryotic cell line. These organelles have their own genetic code, their own DNA, their own plasma membrane, and are able to reproduce independently of the cell. Now, this newly understood behavior may shed light onto their ancient bacterial origin.

Beth Israel scientists have shown that during respiration, molecules from spent or disrupted mitochondria escape the cell and enter the bloodstream causing an immune response with  an evolutionarily conserved similarity to bacterial infection. The study suggests that during times of severe injury when the body is undergoing rapid metabolism in response to the damage, this process is elevated and thus allows larger concentrations of the spent mitochondrial DNA to induce a cascading response in the patient. These circulating mitochondrial protein signatures ultimately cause the body to respond as though a bacterial infection were running rampant. This immune response leads to a syndrome known as Systemic Inflammatory Response Syndrome (SIRS) that can be very dangerous leading to a racing heart, fever, breathing difficulties, and eventual organ failure.

It’s interesting to think that the body contains self-destructive mechanisms like this. However problematic these by-products may be, they are definite parts of mitochondrial energy production and therefore a requirement for life as we know.

Zhang et al. Circulating mitochondrial DAMPs cause inflammatory responses to injury. Nature (2010) vol. 464 (7285) pp. 104-107.

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The patterns of social behavior are predicated upon biological patterns which are themselves driven by environmental and physical patterns. Sometimes though, Nature throws us for a loop and things are discovered which seem to defy our perceptions of evolution.  Examples of ideas, organisms and phenomena that stand out as temporal oddities are all around us.

Many technologies and skilled arts have been invented numerous times. Lost and forgotten… and then remembered again! The evidence of such cycles in thinking are not uncommon. And also not uncommon to be debated. Behold, three examples of undisputed forgotten art, risen again from the depth of human creativity: the pottery of Maria Martinez of San Illdefonso recalled in fire, the cast Roman glass windows once again transparent, the Antikythera mechanism spins around again.

The feeling of looking into the face of ancient wisdom is romantic and the further back it goes and the more technologically advanced it is, the better. Perhaps that’s why last week’s New York Times article on a 130,000 year old seafaring people on Crete inspired me to search for forgotten knowledge. Looking further into that time period we discover that such sailors, if they existed, may have been part of the fresh batch of people to rise again from a time when our population dwindled to a mere 10,000 or so men, women, and children. Artifacts from this chronozone are particularly interesting because they come from a time when the people to which all humans are related spread from Africa after ‘oxygen isotope stage 06‘. To think that all human knowledge was held precariously by such few people.

But all you temporal oddity seekers beware! Ruinous sentiments lay to both sides of these discoveries: first, the underestimation of pre-ancient wisdom (e.g. “Nazca lines are only understood from above so ancient people must have been able to fly.”) and second, the underestimation of modern progress (e.g. “People can fly now so smart people could have flown 1000 years ago.”). I believe that most apparent oddities fall under the sword of evidence. To quote Carl Sagan, “very few require more than passing mention“.

So after much reading I now believe that 130,000 ago is simply too long ago for sea faring capability and the idea will turn out to be wishful thinking. For example could not the tools found on Crete have been found many tens of thousands of years after their construction and brought to Crete in more recent (say 70,000 years ago) times? Rocks seem to work for a very long time after all!

I leave you with perhaps the oldest temporal oddity… 2 billion years ago there were nuclear reactors. Ok, so it’s not cognitive but it is still very odd.

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Our recent post on the shadow biosphere attracted a lot of attention, including from Dr. Paul Davies himself.  We’ve been talking to Dr. Davies now and were happy to learn that he has just published a new book on the implications of shadow life for the search for extra-terrestrial beings. Here’s what Dr. Davies had to say about his new book:

Fifty years ago, a young astronomer named Frank Drake pointed a radio telescope at nearby stars in the hope of picking up a signal from an alien civilization. Thus began one of the boldest scientific projects in history — the Search for Extraterrestrial Intelligence (SETI). But after a half-century of scanning the skies, astronomers have little to report but an eerie silence — eerie, because many scientists are convinced that the universe is teeming with life. The problem could be that we’ve been looking in the wrong place, at the wrong time, and in the wrong way. In this book I offer a new and exciting roadmap for SETI’s future, arguing that we need to be far more expansive in our efforts, by questioning existing ideas of what form an alien intelligence might take, how it might try to communicate with us, and how we should respond if we ever do make contact. It will appeal to fans of science and science fiction alike.

If this book is half as interesting as his previous books, “The Fifth Miracle” and “The Goldilocks Enigma” then it should be a mind expanding read.

One more interesting follow up point. We are proud to have coined a new word in the shadow biosphere post. Did you catch it? Bio-hadronistry and by default hadronistry. The concept was described by Robert Forward in his book, “Dragon’s Egg“.  On the surface of a neutron star, the gravitational force would be so great that most complex molecules (DNA for example)  are dissociated into their constituent nuclei. However, precisely because of this gravitational force, the nuclei themselves could interact and even take on complex shapes. Indeed, scientists are already observing non-spherical nucleons at normal gravity with high mass elements. Forward suggested that these complex nucleon mixtures could combine in their own analogous way to molecules. These “molecules” could potentially form structures that would allow life to form. One major difference would be their reaction times which would be many, many orders of magnitude faster than normal chemistry. A hadron is a particle made of quarks held together by the strong force (similarly to how molecules are held together by the electromagnetic force), thus protons and neutrons are hadrons. So looking for a word to describe Forward’s concept succinctly, we proposed hadronsitry and now (for completeness) hadronecule. We hope it sticks!

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The possibility of strange forms of alien life seems to have just got a whole lot closer to home.  Astrobiologists from Arizona State University, Florida, UC Boulder, NASA, Harvard and Australia have recently theorized about a “shadow biosphere” – a biosphere within a biosphere where alternative biochemistry may be thriving in a way that we haven’t yet thought to examine. Such “weird life” may have had, for hundreds of millions of years, their own ecologies right here in our own backyard.  Indeed, like Dark Energy and neutrinos, “weird life” may be all around us even now, only in a non-obvious way. Some astrobiologists are now suggesting that “weird life” is just as likely to be found here on Earth as it is in the Martian regolith, the seas of Europa , or certainly the complex bio-hadronistry on the surface of a neutron star.

I have included a link to their full article here: Davies_etal_Astrobio2009.pdf

Now, while I think that shadow organisms and shadow biospheres are certainly cool enough to blog about, please allow me to take the logical next step by citing yet another intriguing astrobiology paper that came out of the Santa Fe Institute. Published nearly a decade ago in an astrobiology related Nature commentary article titled, “Where are the dolphins?” scientists Jack Cohen and Ian Stewart realized (and showed mathematically that it’s already happening here on Earth) that as a civilization advances they begin to use the available electromagnetic spectrum for communication more fully and efficiently until ultimately their radiative emissions are indistinguishable from blackbody radiation.  In other words, when we look out into space with telescopes to search for signs of alien life  (SETI for example) we will likely mistake it for being just a regular old hot rock! So either three things must be true to find life through a telescope: 1. The civilization is at a very precise moment in its development,2. The civilization wants to be found and so sets aside some broadcast space for a message, 3. We know their decompression algorithm and what frequency band to apply it to.

It’s this last possibility that relates to the shadow biosphere in a philosophical sense. Unless we know how to interpret the signs of such life, we may not be able to distinguish it from the natural background.

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1. What a long strange trip it’s been: Paul Davies’ New Book and Hadronistry Coined

The Lancet, one of the world’s leading medical journals, retracted a study on February 2nd that linked autism to vaccinations. The study by Andrew Wakefield and his colleagues, originally published in 1998, is titled “Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children.” The study was one of the first scientific publications that spurned the dramatic rallying against childhood vaccinations and was one of the direct influences causing many parents to not give their children MMR vaccinations (Dr. Wakefield himself called out for parents to stop giving their children vaccinations for MMR).

Fortunately for parents, children, doctors, researchers, and anyone else who doesn’t buy in to the unsubstantiated, illogical, and downright dangerous surge against vaccinations, the editors of The Lancet and the UK General Medical Council’s Fitness to Practise Panel have announced that elements of the paper

are incorrect, contrary to the findings of an earlier investigation. In particular, the claims in the original paper that children were “consecutively referred” and that investigations were “approved” by the local ethics committee have been proven to be false.

As a result, the paper has been officially retracted.

This, undoubtedly, is a benefit for everyone. Everywhere.

Read the official retraction statement at The Lancet.

Read the original article at The Lancet. If you can’t get to the PDF, read it at Braindeer.

Read a full analysis at the New York Times, JREF, Times, or CNN.

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An extremely rare brown and white panda was recently spotted in the Qinling region of China. Only 7 such examples of this pigmentation have been seen in the past 25 years, suggesting that the low numbers of giant pandas have lead to inbreeding. This suggestion stems from the nature of this particular sort of pigmentation, which has been hypothesized to only be inherited when both parents carry the gene; in other words, the pigmentation is a recessive trait.

While this may contradict the apparently maintained genetic diversity revealed in the giant panda genome published last month in Nature, it is still an important question to consider and investigate. If inbreeding is indeed occurring, and genetic diversity being reduced due to that, it may leave the giant panda species susceptible to widespread disease in the future (like the captive tiger and lion species).

I’ll be sure to post updates on this topic when the current research into the inheritance of brown and white pigmented pandas is published.

Read an in-depth article at Nature: Mystery of the brown giant panda deepens

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I’m sure by now that we’re all aware of the actress and “activist” Jenny McCarthy and her crusade against the medical and biomedical research community. Her unfounded and dangerous belief that vaccines increase the frequency of autism has been making a splash in the easily convinced minds of many parents who are desperate to help or protect their children. However, when parents do not listen to scientists and doctors (the ones with the education to understand the situation, and not just go off what google searches suggest) and choose to not get their children vaccinated or treated properly, death and sickness ensues.

Recently McCarthy went on the front line again and went on public television to say that a recently published scientific study was wrong. Why do you say? Does she have another study to cite or some sort of evidence or empirical/quantitative support for her claim? Nope, she has “anecdotal evidence.” The study, which was published in Pediatrics (click to view the original article), concludes that “No significant associations were found between autism case status and overall incidence of gastrointestinal symptoms or any other gastrointestinal symptom category.” However, McCarthy and others would argue that this is, to their non-scientifically trained opinions, false and that special diets aid with autism symptoms (she has personally removed wheat and dairy from her child’s diet). Instead of blaming medicine, maybe they should consider pollution caused by ourselves as a cause.

The video pictured above from ABC news (click to view) contains one of the more ridiculous quotes I’ve ever heard come directly out of her mouth:

“We’re the ones seeing the real results, and until doctors start listening to our anecdotal evidence, which is ‘this is working’ it’s going to take so many more years for these kids to get better.”

Oh. Really? Your “anecdotal evidence” which has no controls, miniscule sample sizes, and no true methods of analysis has more weight than a refereed scientific study?

How do we stop the madness?

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