This is a video that starts slow, but around 3 minutes in… well. It shows every nuclear bomb explosion on the Earth from 1945 — the US test before the bombs dropped on Japan — to 1998, when India and Pakistan joined the madness.

The animation is an art project by Isao Hashimoto, and is powerful indeed. I grew up when the cold war was at its coldest, and seeing this still gives me a chill. In May 1998 I was at a meeting in the Canary Islands when India and Pakistan tested their weapons, and I had a hard time finding news in English (the internet was unreliable there and then, too). Not knowing what was going on was maddening, but not nearly as maddening as what I did know.

These weapons are out of the bottle, and even though there has been no detonation in over a decade, the knowledge of how to build them will always be with us. We use nuclear power for peaceful purposes now, and in the future we may even use it for exploring the solar system and beyond — we already use fissile material to power some probes — but we should always bear in mind the first use to which this power was put.

Tip o’ the Pu-238 to AstronomyBlog, who retweeted PekingSpring.

It’s terrifying to think that we’re weeks away from the fall semester, but so it seems. I will once more be teaching an upper-level seminar at Yale called “Writing About Science and the Environment.” Last year’s class was a wonderful experience, and I’m hoping to apply some of the lessons I learned about teaching to this fall’s edition.

I’ve just uploaded my new and improved syllabus to the Yale web site. So if you are at Yale (undergraduate or graduate), check it out at the university course information page (search for EVST 215) and please consider applying.

And if you’re not interested, please pass on this information to anyone you think might be.

And finally, if anyone has any questions about the class, don’t hesitate to email me.

Thanks to genetic testing, I now know that If it were biologically possible to have a baby with Mark Henderson, Science Editor of the Times, that baby would be certain to have wet earwax. And he or she would definitely not have cystic fibrosis. Science!

This is all in aid of a session at the UK Conference of Science Journalists exploring the world of genetic testing, hosted by Mark, Daniel Macarthur from Genomes Unzipped and others. As part of the session, various journalists were offered the chance to get their genes tested for free by one of the three leading companies providing such services. I had a brief chat to Daniel about it, got his recommendations, and signed up. Four days later, a testing kit from 23andme arrived on my desk. I knew that 23andme had recently swapped some samples in a technical blunder but after reading Daniel’s blog, I was convinced that it was unlikely to happen again. If it did, I would enjoy finding out that I was secretly a black woman.

An hour later, I had delivered a dollop of my finest sputum into the tube they provided… and realised that I was only about a third of the way up to the fill-line. Doing this in the middle of the office was not a smart move. Ten further minutes later, and to a crescendo of laughter from my colleagues, the tube was full, sealed in a biohazard bag (I try not to take this as an indictment of my breath) and sealed in a Fed-ex envelope. Four weeks later, the results arrived. The whole process couldn’t have been simpler.

In fact, it was perhaps too easy. Signing up to the 23andme site, verifying the code on my testing kit and preparing the sample took little more than an hour. I had to read and agree to documents that reassured me about the privacy of my information and provide consent to analyse my samples. The same documents warn about the possible psychological consequences of finding out your data and the limtiations of the resulting information (more on these later; meanwhile, I’ve uploaded the full consent form to Posterous so you can see it for yourself). Nonetheless, I was well aware of these risks. I could have found out that I have substantially high odds of developing life-threatening diseases. I could have discovered that I’m not actually related to my parents. This is not a bottle one can re-cork.

But I grapple with issues of genetics and risk on a daily basis, both as a science writer and as part of my work at Cancer Research UK. I assumed that I would be sensible enough about my results to avoid any deterministic anxiety or any sense of false assurance. The results probably wouldn’t affect my behaviour in any material way and besides, my family history is (to my knowledge) largely free of any severe chronic illnesses. But to be honest, the biggest driver was an irrepressible curiosity. Mark Henderson said it best when he first took part in a similar test:

“Perhaps a few thousand of the 6.5 billion humans alive today have yet had the privilege of finding out so much information about the DNA that makes them unique. Here was my opportunity to become an early part of the genomic age.”

So how does it feel to be one of these pioneers? Well, as it happens, fun but a little disappointing.

23andme provides two basic services for its customers – information about health and about ancestry. I’ll leave the ancestry element aside from now (I’m genetically close to people from East Asia – who knew?) The health aspects are more interesting. They’re based on an analysis of 550,000 sites across my genome, which vary from person to person by a single DNA letter. These variations (called SNPs) are small but significant – they can affect an individual’s risk of disease, traits from eye colour to earwax texture, and response to various drugs and chemicals. By profiling the SNPs, 23andme tells its customers about everything from their risk of cancer to their ability to resist malaria.

I click on Disease Risk and I’m faced with a league table of future ills. Conditions have been arranged into three groups, depending on whether my risk is higher, lower or comparable to average. All of these risk estimates are based on research – on massive “genome-wide association studies” (GWAS) that identify SNPs behind specific traits. Each prediction has a confidence ranking, which reflects the size and number of studies that underlie the calculations. Importantly, each risk is presented in both absolute and relative terms, i.e. my actual risk of developing that condition, and my risk compared to other members of the population.

And here we hit the big snag. The “population” in this case generally refers to white Europeans or North Americans, because the vast majority of GWAS studies have been done in these regions. They are where the money to fund research and the willingness to sign up for it have been concentrated. This is a big deal because the link between SNPs and traits varies between ethnic groups.

As an example, the site tells me that I would have “slightly curlier hair on average” were I European. I’m not, so I don’t. More significantly, it also tells me that I have roughly double the average risk of prostate cancer. That’s certainly worth knowing about – it would mean that I have around a 1 in 3 chance of developing the disease within my lifetime, compared to the 1 in 6 odds that most men have. But again, this only applies to Europeans. In fact, if I set the analysis to ‘African’, I find that with exactly the same genes, I suddenly have a lower-than-average risk of prostate cancer. There’s no data for Asian populations. All in all, there are only a handful of results that I can rely on – I have an average risk of Type 2 diabetes (compared to the average Asian chap) but a slightly higher risk of rheumatoid arthritis.

I was aware of this before I signed up for the test, so my disappointment actually matches by expectations. However, things will change. Large genomic studies are underway in China and since 23andme regularly updates its information to account for new research, my reports should become a lot more interesting in time.

For the moment, there’s the odd useful nugget, veering from the useful to the humorous. I know that I am not a carrier for a variety of debilitating genetic diseases, from cystic fibrosis to Tay-Sachs disease. I’m told I have dry earwax, which I can confirm. I have “substantially higher odds of heroin addiction,” which I have no intention of confirming. Morbid fascination aside, there is a tremendous amount to play with on the site. If you had a mind to do so, you could interrogate your raw genomic data and scan your chromosomes SNP by SNP. You can even work out the odds of certain traits in a child between you and another 23andme user – hence the introductory quip to this post. The whole experience is presented through a seamless user interface and a permeating sense of fun.

This, perhaps, obscures more serious concerns. The ethnicity issue puts me in a somewhat enviable position, where results that could come as genuinely worrying can be easily brushed aside, leading to what Tom Whyntie called “the best version of Top Trumps EVER.” But not everyone would be in the same carefree position. Mark, for example, has a higher risk of glaucoma that would probably have terrified me, had it appeared in my results. Given that my entire career and virtually all of my leisure pursuits are heavily dependent on vision, I have a potent fear of eye diseases.

The same applies to neurodegenerative conditions, which led me to discover my risk for Parkinson’s disease with some trepidation (it’s average, since you ask). When you first see your report, most of your health risks are plain as day, but a few select pieces of genetic data come “locked”. To uncover them, you have to make an active choice. Your LRRK2 gene, which affects the risk of Parkinson’s is one of them. Your BRCA1/2 genes, which affect the risk of breast, ovarian and other cancers, are on the list too.

There is a good reason why these have been singled out for secrecy. Unlike the other variants that 23andme looks at, which are common in the population and have small effects on our health, mutations in LRRK2 and BRCA1 are rarer but more dramatic. Before unlocking the LRRK2 information, the site tells you “You are about to learn whether you have a relatively rare mutation in the LRRK2 gene that raises your lifetime Parkinson’s risk to more than 50% compared to the population average of between 1% and 2%.” It’s a potential game-changer.

This sort of information can also ripple out to affect people who never consented to have their genes tested in the first place, such as close family members. If I had a high-risk LRRK2 variant, chances are that some of my close relatives would too. Imagine, as an extreme situation, what would happen if I had an identical twin. The “locked” status is understandable but it is the equivalent of a big red button that says “Do not press”. How many people would resist the temptation, especially if they have been curious enough to sign up to the service? To 23andme’s credit, it uses the opportunity to make people fully aware of what they’re letting themselves in for. Amidst a lengthy statement, it tells you that not everyone with the high-risk version will develop Parkinson’s, nor does the low-risk version protect against the disease.

In fact, 23andme provides a consistently high standard of information. The original research papers that drive the risk predictions are all cited. Each trait or disease is accompanied by a lot of material – basic science, interviews with doctors, relevant posts by members of the online community, and even a timeline of relevant research. You also get practical tips for each disease, ranging from lifestyle advice to screening recommendations to contact details for relevant organisations. Judging by the cancer-related tips, these are all carefully crafted and based on decent evidence.

As mentioned, risks are presented in relative and absolute forms. This is important because a tripled risk may sound like a lot, but it’s less of a concern if it applies to a rare disease with a low background risk. You also get information in natural frequencies – an approach I like. For example, my report on rheumatoid arthritis tells me that in a group of 100 typical Asian men aged 35-79, 0.9 will get the disease. However, if all of them had my genes, 1.1 would get the disease. Nothing too much to worry about there.

But even here, there are potential problems with reliability. Mark Henderson has had his genes tested by three companies thus far – 23andme, DeCODEme and Pathway. In some cases, the three companies gave different results for the same stretch of DNA. In others, their reports gave different background risks of certain diseases. As Mark writes:

“If 23andMe is correct, then even though I have a high risk genetic variant, my overall risk of [glaucoma] remains low. If deCODEme is right, I have a one in three lifetime risk. And if Pathway is right, the population risk is low, but the peculiarities of my genome dramatically enhance my chances of getting it.”

These problems are inherent to the different companies, the tests they use and the information they provide. But further problems arise when that information enters the brains of the customers, where it often comes crashing against an inability to process information about risk. For all the careful phrases around risks and uncertainties, some folks are going to treat their report as nothing more than a sophisticated horoscope, given extra weight by the spectre of genetic determinism. For example, one brown-eyed community member was told that their genes predicted a high probability of having blue eyes with just a 1% chance of having brown eyes. They found the results “unsatisfying” and “confusing”. And this is a trivial example – the emotions that accompany a risk prediction for a severe disease must be even more potent, and especially so for people who aren’t well-versed in genetics.

Clearly, some will need more help than others at interpreting their results and that help will come at a premium. Not every jobbing health professional will have the knowledge to advise people about the implications of their genetic tests. Specialised genetic counsellors exist and 23andme will refer you to one, but you pay for the service out of your own wallet. This comes on top of the standard cost of the test, which would set the average customer back by $499.

I have mixed feelings about whether the cost is justified. The results are wonderful fodder for the curious and the confident but their limitations (especially for non-white ethnicities) prevent them from being of any obviously practical value to your health. This may change over time as more data flood in and the price starts to fall. But this doesn’t feel like a technology where there is a real benefit in being an early adopter.

Best possible result: “Mutant X-gene detected. Increased risk of superpowers, protecting world that hates/fears you”

Worst possible result: “Your ancestry is 50% Craig Venter”

Updated because I didn’t accurately reflect the contents of the consent statements, which I saved and are more informative than I remember, and on cystic fibrosis (see comment below)

Who do you think is the greatest astronaut of all time?  The good folks at Sky at Night Magazine have launched a poll to find out.  The poll is in the August issue which by the way is on sale now.

Graham Southorn, Editor of the magazine made the comment: “We are setting out to honour those brave explorers who have journeyed beyond Earth, with a poll to find the greatest astronaut. We had to make some tough choices, but in the end we’ve narrowed the selection down to 15 people. Now we need your help to select the greatest of all time.”

Notably absent from the “short list” is John Glenn which kind of surprised me, not that I’d necessarily vote for him, but I’m not sure I’d have excluded him especially after looking at the list.

Still, it’s quite a group:

1) Anousheh Ansari
2) Buzz Aldrin
3) Neil Armstrong
4) Frank Borman
5) Michael Foale
6) Yuri Gagarin
7) Sergei Krikalev
Jim Lovell
9) Alexei Leonov
10) Bruce McCandless
11) Valeri Polyakov
12) Story Musgrave
13) Harrison Schmidt
14) Alan Shepard
15) John Young

Go on over to Sky at Night Magazine to read about the choices and cast your vote!!

Click here to view the embedded video.

Source

I just want to send more love to Zach Weiner at Saturday Morning Breakfast Cereal, who is, as usual, quite correct. The guy on the right doesn’t look much like Hoagland, though. [Update: see my comment below.]

Maria, a paleontologist, writes, “Archaeopteryx, to me, represents a beautiful example of a transition fossil and of evolution in general, showing characters that both
dinosaurs and birds share.”

Click here to go to the full Science Tattoo Emporium.

I am stunned, because he seemed so alive and vibrant when I saw him in December 09 in Copenhagen, and in Feb 2010 at the AAAS meeting in San Diego. But Stephen Schneider, one of the greats of climate science–and climate policy, and public outreach–died today of an apparent heart attack.

There are tributes from the WWF blog, DotEarth, HuffPost, and many more. Let me quote Andy Revkin:

I first interviewed Schneider in the early 1980s while trying to make sense of the  percolating notion of nuclear winter, which Schneider — always following the data — ended up determining would more likely be a “nuclear autumn.” It was his caustic honesty about the complex nature of global warming, and the inherent uncertainties in the science, that kept mereturning to him for input from 1988 onward. He was a participant in the assessments of the Intergovernmental Panel on Climate Change from the beginning until the last days of his life. He encouraged scientists to get out and communicate directly with the public, maintaining a Web page, “Mediarology,” describing the challenges attending such a move.

Ralph Cicerone, president of the National Academy of Sciences, says:

His biggest goal in life was to see a rational approach to policy about climate change, where he tried to evaluate the odds and show people, just like in many other decisions in life, with climate they had to play the odds. He was trying to produce probabilistic ways to make evaluations that could work. In his lifetime, his approach on this became progressively more sophisticated.

Peter Gleick says:

His clear and comprehensive explanations of climate change, his encyclopedic knowledge of how the climate works, and his challenges to the fraudulent science that characterizes the arguments of the climate deniers, made it easier for politicians to understand the true climate threats that face us and to move the debate into the public arena. That debate continues, because the science and policy challenges are complicated, but the world is at least beginning to take key steps toward preventing a climate catastrophe because Stephen Schneider knew that the alternative was unacceptable and because he worked tirelessly to move us all in the right direction.

He will be missed….

Proposal of alternative mechanism responsible for the function of high-speed swimsuits.

“Since many top swimmers wearing Speedo LZR Racer swimsuits have broken world records, it is considered that the corset-like grip of suit supports the swimmers to maintain flexibility of movement and reducing water resistance. We propose an alternative mechanism to explain this phenomenon. The suits are so tight that the blood circulation of swimmers is suppressed.This effect accelerates the anaerobic glycolysis system but rather suppresses the aerobic mitochondrial respiration system. Because of the prompt production of ATP in the glycolysis system, the swimmers, especially in short distance competitions, obtain instantaneous force in white fibers of the skeletal muscles.”

Photo: flickr/marcopako ?

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WTF is NCBI ROFL? Read our FAQ!

It looks like Genomes Unzipped has their own Mortimer Adler, with an excellent posting, How to read a genome-wide association study. For those outside the biz I suspect that #4, replication, is going to be the easiest. In the early 2000s a biologist who’d been in the business for a while cautioned about reading too much into early association results which were sexy, as the same had occurred when linkage studies were all the vogue, but replication was not to be. Goes to show that history of science can be useful on a very pragmatic level. It can give you a sense of perspective on the evanescent impact of some techniques over the long run.

Long a standard in science fiction, wormholes are used to move the action across immense distances.  Distances that would take several generations to cross at light speed.  Several millennia, actually.  We see them as super-highways across the cosmos.  Want to get to Andromeda?  No problem, just jump into a wormhole and you’ll be there in hours.

Honestly?  That’s pretty close.  A wormhole, basically, is a hypothetical shortcut through spacetime.  If you think of “spacetime” in two dimensions, like a piece of paper, it’s easy to visualize.  Just fold your piece of paper over, and you can see how a wormhole can “bridge” two sections of spacetime to create a shortcut.  Look at this:

Spacetime in 2D - image by en:Benji641 all rights reserved

The 2D image helps you to get a fix on the concept, but it’s really more complex than that.  A wormhole is an unvisualizable structure existing in four or more dimensions.  It’s a tunnel between you and anywhere.  Imagine you want to go to Paris, France, for dinner.  Let’s say you live quite a distance from Paris… like on the other side of the Earth.  You could open a wormhole “bridge” between you and your favorite Paris restaurant and step right over to it.  This image shows that type of bridge between the Physics Building of Tubigen University in Germany and the sand dunes of Boulogne Sur Mer in North of France:

wormhole imagery - Philippe E. Hurbain all rights reserved

That’s fairly easy to imagine, right?  How about a wormhole not between two different locations in the universe, but a wormhole between two different universes?  Imagine two points of gravity (black holes) in two different universes attracting each other.  As they approach, the fabric of spacetime distorts, stretches, and then touches.  The points of contact, two white holes now, meet to form a tunnel.  Look at this:

Merging - image by University of Colorado

That sounds great, doesn’t it?  Well, it does until you get to reading more about it.  For one thing, wormholes are unstable.  Very unstable.  Also, think a moment about those two points of gravity meeting.  You enter at one point, and immediately become stuck in the center.  See, the other point, the “way out”, is drawing matter in towards the center, too.  You can’t turn around and go out the way you came in, because that’s a point of gravity drawing matter in towards the center.  Now you’re stuck in a Schwarzschild Bubble.  You cannot exit either way, because in both ways you’re moving against the force of a black hole.

Okay, how about a wormhole created by a black hole spitting matter out, as in a white hole?  If that possibility exists, you sill have the unpleasant reality of meeting the singularity before your component parts get spat out.  Notice I said “your component parts”, not “you”.  You can forget about “you” at this point.  I guess the labeling of the parts of the wormhole should provide clues to its nature; the mouth, the throat… doesn’t sound promising.

Cover art of "Portal" video game - Valve Corportation, Microsoft Studios - Game uses wormholes to traverse areas of play

Still… if only.  It would be great to pop into a wormhole and exit on the other side of the galaxy. I know there are more types of wormholes than I covered here, and some of them sound promising.  What’s your favorite?  Do you think a human could ever survive a trip down a wormhole?  Could we get back home?

There was a big step forward this week in the struggle to contain the spread of HIV and AIDS in sub-Saharan Africa. Reporting on a three-year study in the journal Science, scientists at the Centre for the Aids Programme of Research in South Africa (CAPRISA) say that a microbicidal gel reduced HIV infection rates in women who used it by 39 percent over the course of the study. It would be the first time such a gel has proven so effective.

The researchers gathered nearly 900 women for the study who were HIV-free but demographically at risk for infection. Half received the gel, half a similar-looking but inactive substance. Among those given the gel, a vaginally-administered substance that contained an antiretroviral medication called tenofovir, infection rate fell by half after a year, and were reduced by 39 percent over two and a half years.

“This is very encouraging,” said Dr. Michel Sidibe, executive director of Unaids, the United Nations AIDS-fighting agency. “It can be controlled by women, and put in 12 hours earlier, and that is empowering. They do not have to ask the man for permission to use it. And the cost of the gel is not high” [The New York Times].

Though subsequent trials will of course be needed, these first results are especially inspiring given the predicament of women in some of these nations.

Women fall victim to HIV/Aids in disproportionately large numbers – 60% of new infections in Africa are among women. Many in the poorest countries have little education and suffer from very low status, so are unable to negotiate safe sex, using a condom, with their partner [The Guardian].

Salim Abdool Karim, one of the study authors, said the product would cost women “just pennies,” which is crucial because the effectiveness goes up with the consistency of use.

“Boy, have we been doing the happy dance,” Dr Karim, from the University of KwaZulu-Natal in Durban, said [BBC News].

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Image: iStockphoto

The blue pepper-pot beetle, St. John’s jellyfish, and the queen’s executioner beetle–these distinctly British-sounding organisms share a few things in common. For one, they all have brand new names, thanks to the ingenuity of the British public.

The trio received these new names from public entries in a competition organized by The Guardian, Natural England, and the Oxford University Museum of Natural History. Other similarities include (perhaps unsurprisingly) that they all live in the UK, and that they’re all threatened with extinction.

One usually pictures an organism’s discoverer naming her find, or the organism’s common name coming from obvious characteristics (like lighting bugs or fireflies, for example), but sometimes critters just slip through the cracks; these ten were previously known only by their official scientific classifications. That made it hard, the competition’s organizers suspected, for the public to care whether or not these rare creatures disappeared. The naming competition, thought up by Guardian columnist George Monbiot, was meant to make the threatened organisms more identifiable and relatable to the public.

Comparing the cuddly appeal of the sea piglet shrimp (pictured above) vs Arrhis phyllonyx, it seems they accomplished their goal. The competition had over 3,000 entries, from which the judges picked a winner and two runners-up for each of the species based on how well the name matched the organism’s looks, habitat, and behavior. The naming competition’s overall winner was the queen’s executioner beetle, a black hooded bug from Windsor.

No matter who won, Monbiot sees the competition as a whole as a success.

“Judging the competition was very hard, as in every case there were at least half a dozen names that deserved to win…. Not only were they practical and distinctive, many of them also captured the magic and mystery of England’s wildlife.”

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Image: Moskal, Wojciech /World Register of Marine Species

David Mitchell is one half of the brilliant British comedy team that makes the show "That Mitchell and Webb Look", which commonly has skeptical themes to its humor. Mitchell has a series of short videos posted on The Guardian, and he made one about global warming that, like everything he does, is fantastic. They don’t allow embedding — hey Guardian, it’s the 21st Century now! — so I’ll just link to it and let you have a look.

Tip o’ the thermometer to Arthur Taylor.

I gave a talk at the President’s Forum at the annual meeting of the American Society for Microbiology in May about how I go about telling stories about science. The folks at ASM have done some slick video editing and posted the lecture at their site, where you can also download it in various formats. Or just watch it in the embedded player below. In my lecture, I talk about getting out of bunkers and jumping chasms, as well as the trouble parasites can get you into on a blind date.

MWV39 – Carl Zimmer: Newspapers, Blogs, and Other Vectors: Infecting Minds with Science in the Age of New Media from microbeworld on Vimeo.

30,000 years ago a Neanderthal woman died in what would become Croatia’s Vindija cave. Five years ago, 454 Life Sciences and the Max Planck Institute started working together on the tedious and time-consuming task of piecing her fossilized DNA back together. Just over a month ago, they succeeded and, in the process, revealed that most of us are between 1% and 4% Neanderthal. To crudely paraphrase the ever artful Carl Zimmer, knowing where Neanderthals fit into the evolution of Homo sapiens is essential to understanding the development of the human mind.

Knowing where Neanderthals fit, however, also creates a problem. What do we do if what makes humans “human” isn’t from a “human” at all? How do we justify “human rights” in light of evidence that our rational and moral minds are in no small part the result of prehistoric crossbreeding? In short: if human rights are based on being human, what rights would a cloned Neanderthal have?

The problem is, of course, that we don’t have a cloned Neanderthal. Which is why we need to make one.

The argument may seem absurd and offensive at first. Both Zach Zorich, writing for Archaeology, and Andrew Mossman, writing for fellow Discover blog 80beats, explore the idea and come down on the side of “it’d be nice science for science’s sake, but way too unethical to do.” Summarizing Zorich, Moseman says:

As the bioethicist Bernard Rollin points out in the Archaeology piece, there’s more to worry about than the law. While Neanderthals are our close relatives on the evolutionary tree, you’d know one if you saw one. Tulane anthropologist Trenton Holliday argues that they could talk and act like us, therefore eventually they’d fit in. But that seems like wishful thinking. With no culture, no peers, and an unknown capacity to cope with the modern world mentally or physically, a Neanderthal would be adrift—caught between a zoo animal and a human being. The main point in cloning one would be for scientists to study it, but as law professor Lori Andrews says, a Neanderthal could be granted enough legal protection to make doing extensive research on it illegal, not just unethical.

That’s not to say there would be no benefits to science. But some things are best left in the past.

Not so. We have tried, and will continue to try, to resurrect extinct species in the past, such as the Spanish ibex. Why should the Neanderthal be any different? If we assume the ability to clone safely – for a moment setting aside the current, significant flaws with the process – we can focus on the ethics of bringing a Neanderthal into the world without a familiar culture or peers. Maybe the Neanderthal would have trouble adapting, picking up language, and adjusting to a modern existence. Or maybe not. We don’t know, and there’s the rub.

Unlike examples found in science fiction, be it Mary Shelley’s Frankenstein or the more recent sci-horror flick Splice, it’s not as if our only options are to send the neo-Neanderthal into the world on its own or to trap it in a laboratory where it would be poked and prodded to death. The moral of both of those works is that when one fails to take responsibility for one’s creation, when one fails to nurture and protect that new being, that is when an ethical code is breached and damage is done. We don’t know how a Neanderthal would exist in our world, but we know we are capable of studying chimps and apes outside of their natural habitat without causing them harm or reducing their quality of life flagrantly. We also know that we are surrounded by those who are only partially mentally developed, be they children or the mentally disabled, whom we love and care for without question. The very purpose of cloning a Neanderthal would be to see where it fits in our mental development. Attentive and accurate nurture and care would be central to any scientific effort to study Neanderthal development and mental growth. Allowing the clone to be neglected would upend the very purpose of cloning her in the first place.

To assert that the Neanderthal is between human and animal and is therefore an impossible fit for our world simply not true. The line between human and animal is blurred. Dolphins, whales, chimps, great apes, and other species are already changing the way we think about intelligence and rights; perhaps a Neanderthal, fully developed but so mentally different as to be incompatible with our way of living is the very example our society needs to change our perception of intelligent non-humans. When the technology is safe and the ability to nurture and care for her in place, we owe it to humanity as a whole to clone a Neanderthal and see what wonders she might teach us about ourselves.

I did an interview with my old friend Chris Mooney for Point of Inquiry, and it’s now live. We talk about the end of the Earth, punching Buzz Aldrin, Hollywood science, and other topics astronomical and hysterical. Enjoy!

Imagine trying to rewind the clock and start your life anew, perhaps by moving to a new country or starting a new career. You would still be constrained by your past experiences and your existing biases, skills and knowledge. History is difficult to shake off, and lost potential is not easily regained. This is a lesson that applies not just to our life choices, but to stem cell research too.

Over the last four years, scientists have made great advances in reprogramming specialised adult cells into stem-like ones, giving them the potential to produce any of the various cells in the human body. It’s the equivalent of erasing a person’s past and having them start life again.

But a large group of American scientists led by Kitai Kim have found a big catch. Working in mice, they showed that these reprogrammed cells, formally known as “induced pluripotent stem cells” or iPSCs, still retain a memory of their past specialities. A blood cell, for example, can be reverted back into a stem cell, but it carries a record of its history that constrains its future. It would be easier to turn this converted stem cell back into a blood cell than, say, a brain cell.

The history of iPSCs is written in molecular marks that annotate its DNA. These ‘epigenetic’ changes can alter the way a gene behaves even though its DNA sequence is still the same. It’s the equivalent of sticking Post-It notes in a book to tell a reader which parts to read or ignore, without actually editing the underlying text. Epigenetic marks separate different types of cells from one another, influencing which genes are switched on and which are inactivated. And according to Kim, they’re not easy to remove, even when the cell has apparently been reprogrammed into a stem-like state.

But reprogramming adult cells is just one of two ways of making stem cells tailored to a person’s genetic make-up. The other is known as nuclear transfer. It involves transplanting a nucleus (and the DNA inside it) from one person’s cell into an empty egg. The egg becomes an embryo, which yields stem cells containing the donor’s genome. Kim has found that these cells (known as nuclear transfer embryonic stem cells or ntESCs) are much more like genuine embryonic stem cells than the reprogrammed iPSCs. They’re ‘stemmier’, for lack of a better word.

Kim’s research tells us that creating stem cells through nuclear transfer is not a technique that’s easily disregarded. It certainly steers into trickier ethical territory since harvesting ntESCs destroys the embryo. And it is still trailing behind technically; so far, it has only been successfully done in monkeys and other non-human mammals, and it has been mired in scientific scandal.

Meanwhile, work on iPSCs has raced ahead. The starting pistol was fired in 2006, when a group of Japanese scientists first showed that it was possible to create these cells in mice. The race intensified in 2007, when two research groups independently managed to do the same for human cells. In 2009, mouse iPSCs were used to produce live animals, passing the ultimate test of their stem-like status. Various groups have made the technique more efficient, sped it up, found ways of sorting out the most promising cells, and changed the details so that it doesn’t use viruses (or uses only viruses).

But all along, scientists have realised that there are subtle differences between iPSCs and genuine embryonic stem cells and, indeed, between iPSCs produced from different tissues. For a start, some types of cell are easier to reprogram than others – skin, stomach or liver cells, for example, are easier to convert than cells from connective tissues. And the older or more specialised the cells are, the harder the task becomes.

Kim’s team found that once the cells are converted, there are further issues. They found it easier to produce blood cells from iPSCs that themselves came from blood cells, rather than those derived from connective tissue or brain cells. By contrast, iPSCs made from connective tissue were the better choice for producing bone cells.

Kim thinks that this is because the widely used reprogramming techniques fail to strip away a cell’s epigenetic markers. He focused on one such marker – the presence of methyl groups on DNA, which typically serve to switch off genes, like Post-it notes that say “Ignore this”. Kim found that the methylation patterns of iPSCs are very different depending on the cells they came from. Those that come from brain or connective cells, for example, have methyl groups at places that are needed to produce blood cells, and vice versa. Even iPSCs that come from slightly different lineages of blood cells carry distinctive patterns of methyl marks.

In all of these tests, ntESCs (those produced by nuclear transfer) were far more similar to genuine embryonic stem cells than any of the iPSCs. Their patterns of methylation were a closer match and they were easier to convert into any type of adult cell. This certainly makes sense – when the nucleus is transferred into an empty shell, it its DNA is rapidly and actively stripped of its methyl groups. Its history is erased with far greater efficiency than the reprogrammed iPSCs.

This seems like a clear win for the nuclear transfer method, but Kim thinks there are ways of improving the reprogramming technique to get around this problem. For a start, you can efficiently convert iPSCs derived from one type of cell into another via another round of programming and reprogramming. For example, you could reprogram a brain cell into an iPSC, convert it into a blood cell, reprogram it back into an iPSC again, and get a stock that’s very good at creating blood cells. This does, however, seem like a very roundabout strategy – why not start with blood cells in the first place?

A better solution is to try and strip away the epigenetic marks more directly. Some chemicals can do that, and after treating the iPSCs with such substances for a few days, Kim improved their ability to produce tissues regardless of their origins.

Another group led by Jose Polo found the same epigenetic problem, but they discovered a simpler solution – grow the cells for a long time. When cells are grown in culture, they need to be frequently ‘passaged’. That is, they need to be split among fresh containers so that they don’t run out of room and nutrients. Polo found that continuous passaging solves the epigenetic problem, reprogramming the iPSCs into a far more stem-like state, free from the constraints of their origins. It seems that when iPSCs are created, their epigenetic marks are eventually removed even though the process is gradual and slow.

And after all, the epigenetic memory of reprogrammed cells isn’t necessarily a bad thing. If you want to produce blood in bulk, why not start with iPSCs that are very good at making blood cells but not other types? Indeed, it’s still very difficult to nudge stem cells into becoming specific tissues, and starting off with cells that naturally gravitate towards certain fates could well be a blessing in disguise.

Reference: Nature http://dx.doi.org/10.1038/nature09342 and Nature Biotechnology http://dx.doi.org/10.1038/nbt1667

More on epigenetics:

• Shutting off a single gene could improve fertility by activating dormant egg-producing cells
• Crickets forewarn their offspring about predators before they’re born
• Alcohol tastes and smells better to those who get their first sips in the womb
• Child abuse permanently modifies stress genes in brains of suicide victims
• Obesity amplifies across generations; can folate-rich diets stop it?

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

To seal more car deals, Chevrolet UK looked to arm its salesmen with the perfect weapon of confidence: an unstoppable handshake. Here’s the secret they received from Geoffrey Beattie, Head of Psychological Sciences at the University of Manchester:

PH (Perfect Handshake)= ? (e^2 + ve^2)(d^2) + (cg + dr)^2 + ?{(4<s>^2)(4<p>^2)}^2 + (vi + t + te)^2 + {(4<c>^2 )(4<du>^2)}^2

We hope (and suspect) the training posters and equation, supposedly meant for Chevrolet-sellers, are meant for publicity and are not a real attempt to improve customer relations.

The variables, as outlined in a Chevrolet press release:

(e) is eye contact (1=none; 5=direct) 5; (ve) is verbal greeting (1=totally inappropriate; 5=totally appropriate) 5; (d) is Duchenne smile – smiling in eyes and mouth, plus symmetry on both sides of face, and slower offset (1=totally non-Duchenne smile (false smile); 5=totally Duchenne) 5; (cg) completeness of grip (1=very incomplete; 5=full) 5; (dr) is dryness of hand (1=damp; 5=dry) 4; (s) is strength (1= weak; 5=strong) 3; (p) is position of hand (1=back towards own body; 5=other person’s bodily zone) 3; (vi) is vigour (1=too low/too high; 5=mid) 3; (t) is temperature of hands (1=too cold/too hot; 5=mid) 3; (te) is texture of hands (5=mid; 1=too rough/too smooth) 3; (c) is control (1=low; 5=high) 3; (du) is duration (1= brief; 5=long) 3.

The press release details some pretty common sense advice: avoid sweaty palms; don’t squeeze too hard or hold on too long; make eye contact. But putting the formula into action might be tough; if actually meant to inspire confidence (which the release says 70 percent of hand-shakers are lacking), doing the math before every hand-to-hand may instead lead to more perfect head scratching.

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Discoblog: New Study: If a Dude Sounds Strong, He Probably Is
Discoblog: Can a Brain Scan Predict Your Behavior Better Than You Can?
80beats: Want Someone to Take a Decision Seriously? Hand Them Something Heavy

Image: flickr / Aidan Jones