Weekly Weird News Roundup: Feeding Coyote Skulls, Cow-Dung Toothpaste, and More | Discoblog

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roundup-pic-web• Coyotes are what they eat: Feeding pups soft food changes their bones and muscle structures, making it more difficult for them to chomp on harder stuff later in life. That bites.

• About one-quarter of the food in the U.S. is wasted each year–and 16 percent of our energy goes toward food production. The result? We waste more energy in the food we throw out than is available via offshore drilling.

• If you get bored this weekend (and have $8,000 to spare), fret not. You can always build and launch your very own satellite.

• Run DMC: Listening to music in which the tempo matches a runner’s stride increases athletes’ endurance by about 15 percent.

• Cow-dung toothpaste, a deer penis, and guinea pigs: just a few of the bizarre items travelers have been caught attempting to smuggle through JFK International Airport. No wonder it takes so long to go through customs.


Koreans, not quite the purest race? | Gene Expression

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ResearchBlogging.orgPLoS One has a paper out on Korean (South) population genetics and phylogeography, Gene Flow between the Korean Peninsula and Its Neighboring Countries:

SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry using 320 subjects covering 24 regional groups including Northern ( = 16) and Southern ( = 3) Asians, Amerindians ( = 1), and four HapMap populations (YRI, CEU, JPT, and CHB). Additionally, we evaluated the effectiveness and robustness of 50K autosomal SNPs with various clustering methods, along with their dependencies on recombination hotspots (RH), linkage disequilibrium (LD), missing calls and regional specific markers. The RH- and LD-free multi-dimensional scaling (MDS) method showed a broad picture of human migration from Africa to North-East Asia on our genome map, supporting results from previous haploid DNA studies. Of the Asian groups, the East Asian group showed greater differentiation than the Northern and Southern Asian groups with respect to Fst statistics. By extension, the analysis of monomorphic markers implied that nine out of ten historical regions in South Korea, and Tokyo in Japan, showed signs of genetic drift caused by the later settlement of East Asia (South Korea, Japan and China), while Gyeongju in South East Korea showed signs of the earliest settlement in East Asia. In the genome map, the gene flow to the Korean Peninsula from its neighboring countries indicated that some genetic signals from Northern populations such as the Siberians and Mongolians still remain in the South East and West regions, while few signals remain from the early Southern lineages.

I can’t comment too much on the inferences they make from the results because I’m not familiar with the geography of South Korea, or particular historical details. But more generally the genetics of Korea are of particular interest for social reasons:

South Korea is one of the most ethnically homogeneous societies in the world with more than 99 per cent of inhabitants having Korean ethnicity…The Koreans call their ethnic homogeneousity of their society using the word, ?????? (Dan-il minjok gook ga, literally means the single race society.)

Korean racialism has recently gotten the spotlight in works such as The Cleanest Race: How North Koreans See Themselves and Why It Matters, articles in The New York Times about South Korean prejudice against dark-skinned people, and the rise of mixed-origin Koreans nationals due to the large number of Vietnamese brides in rural areas. Here’s an interesting comment on South Korean race consciousness, Western Mixed-Race Men Can Join Military:

Western mixed-race men can join the military beginning next year.

Currently, Asian mixed-race men, dubbed “Kosians,” are subject to the country’s conscription system, but “Amerasians” or “Eurasians” are exempted from the mandatory service.

The parliamentary approval of a bill proposed by Rep. Yoo Seung-min of the governing Grand National Party has paved the way for them to join the military.

Western mixed-race men, who have distinctive skin colors, had been exempted because they could have experienced difficulty mixing with Korean colleagues in barracks, the defense ministry had said previously.

The article was published in January of 2010. And that’s not the weirdest idea to come out of the Korean peninsula. With all that in mind, the distinctiveness, or lack thereof, of the Korean nation as adduced from scientific genetics is of particular curiosity, as it is a clear example of the intersection of science and culture. First, here’s the figure which shows where in Asia & South Korea they got their samples from:

journal.pone.0011855.g001

And here’s a detailed breakdown of samples:

journal.pone.0011855.t001

One point to note is that there seem to be some mixed-nationality individuals in the sample; Korean-Japanese, and Korean-Vietnamese. Here’s a MDS plot showing the relationship between the various East Asian groups:

journal.pone.0011855.g002

And Structure (remember K = putative ancestral populations which contribute quanta to the genome of individuals):

journal.pone.0011855.g003

I think it is important to note that their Chinese samples were all north Chinese; Beijing and Manchurian. Fujianese and Cantonese would span the Vietnamese and Chinese cluster. The outliers are probably due to the moderately cosmopolitan nature of the Beijing HapMap sample. The Han Chinese are less diverse than Europeans as a whole, but not inordinately so (using pairwise Fst’s a measure). There is an asymmetry when talking about China and any other East Asian nation because it is feasible that Han groups from various regions of China are more genetically similar to non-Han groups which are geographical neighbors. This is what L. L. Cavalli-Sforza found in History and Geography of Human Genes. The northern Chinese clustered with northern Asians, while the southern Chinese clustered with Southeast Asian groups. There have been conflicting results since that initial finding, but I think that points to the sensitivity of some of the inferences to the geographical and linguistic biases of sampling (different dialect groups in Guangdong may be very genetically distinct).

With all that said it’s pretty clear from the above figure that the Japanese and Korean samples are close enough that you need to zoom in on them specifically. So here you go:

journal.pone.0011855.g004

KB_Japanese = Kobe Japanese. In the paper itself they’re testing a few historical hypotheses. So I’ll leave it to them for the interpretation:

The gene flow events of the three selected models for SW, MW and SE Korea can be assessed using the genome map. The populations in Model I (SW Korea) are closer to Mongolians than are the other two regions in the genome map (Fig. 2B). Historically, some of the loyal families and their subjects in the Goguryeo Empire moved to this region and formed the BaekJae Empire in BC18-22. This region also showed connections with populations in Tokyo (JPT), as illustrated in Fig. 4. Certain outliers in Model II (SE Korea) display some similarity to the people of Kobe, a port city near Osaka, indicating that there may have been links between the two regions. In addition, considering that the SE Korea region has some connections with Siberian lineages, with respect to grave patterns and culture, it is possible that the outliers in the GU and Kobe (KB) populations could be of Siberian lineage. On the other hand, the GR and US populations showed average signals in the Korean Peninsula. Historically, the Kaya Empire, with its southern lineages, was formed in the GR region and then the Shilla and Kaya Empires became united around AD532. Very recently, the US region became one of the rapidly developing regions, and people from other provinces moved to this region. This might explain why it shows an average signal in South Korea. Model III (MW Korea): the Middle West area formed a melting pot in the Korean Peninsula because populations moving from South to North, North to South, and from Eastern China, including the SanDung peninsula, to the Middle West in Korea all came together in this region. In the genome map, the signals for MW Korea are also close to those for Peking (CHB) in China. The overall result for the Korea-Japan-China genome map indicates that some signals for Mongolia and Siberia remain in SW Korea and SE Korea, respectively, while MW Korea displays an average signal for South Korea.

The connections between coastal southern Korea and the western islands of Japan are well known. It seems like that the Yayoi people, who probably contributed the preponderance of the ancestry of modern Japanese, arrived in Kyushu approximate ~2,500 years ago. And were originally a group within the Korean peninsula. Over the past 2,000 years Korea has gone through a process of ethnic-linguistic homogenization during the ethnogenesis of the modern Korean nation, but it seems possible that the original group(s) which gave rise to the Yayoi existed in southern Korea to facilitate contact between the islands and the peninsula into the historical era.

Citation: Jung J0, Kang H, Cho YS, Oh JH, & Ryu MH (2010). Gene Flow between the Korean Peninsula and Its Neighboring Countries PLoS ONE : 10.1371/journal.pone.0011855

The end of Sex Week and the start of SciFoo | The Loom

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I hope you enjoyed Sex Week (in a purely intellectual way, of course). I’m now off to a confab called SciFoo, which I’ve heard a lot about over the years and am now finally able to attend. Each year, Google and O’Reilly Media bring together a motley crew of scientists, writers, and others, and basically tell them to make up a conference on the spot. There are a whole bunch of people on the attendee list that I’ve waited years to meet in person, so it will definitely be worth the trip to California. But if there are any SciFoo vets out there with advice for making the most of the experience, I’d love to hear it.

I will try to report on my experience, either in a measured reflection next week, or in a torrent of half-baked tweets.


Genetically Identical E. Coli Cells Show a Lot of Individuality | 80beats

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250px-EscherichiaColi_NIAIDOne might think that identical-twin bacteria—clones of each other—would grow up and live very similarly. But a study published today in Science that examined individual bacterial cells in detail found that genetically identical E. Coli cells actually seem to express their genes quite differently, simply because of the random accidents of how their molecular machinery happens to operate.

“The paper is quite rich,” said Sanjay Tyagi, a molecular biologist at New Jersey Medical School who was not involved in the research [but published a perspectives piece on it]. “People think that if an organism has a particular genotype, it determines its phenotype [observable characteristics]–that there’s a one-to-one relationship,” said Tyagi. “But as it turns out, [differences in gene expression] can arise just from chance.” [The Scientist]

Specifically, a team at Harvard University sorted through E. Coli bacteria, analyzing them one at a time. They looked at the amount of mRNA (messenger molecules that carry protein blueprints) and the amount of protein built from those blueprints. They noticed a lot of variation–or “noise”–from one cell to the next.

At any given moment, a fraction of cells didn’t have a single molecule of mRNA or protein from a given gene, and a surprising subset of genes–more than 20 percent of those analyzed–expressed one or fewer copies of protein per cell. The ability to measure with this kind of single-molecule sensitivity is valuable for single-cell studies, said [senior researcher on the study, Sunney] Xie. [The Scientist]

Besides each genome varying in how it expressed itself, the researchers also found a discrepancy with, what Science News reports as a “central dogma” of molecular biology: the amount of mRNA for a specific protein and the amount of that protein should correspond. The researchers counted mRNA molecules and proteins associated with 1,018 genes in each microbe. More mRNA did not necessarily mean more of the associated protein: Instead, they discovered that each cell varied in the exact number of proteins present and the amount of mRNA it employed. As The Scientist reports, Tyagi suspects that short life of mRNA (only minutes) and of E. Coli (which divides about every 30 minutes) could, in part, cause these random variations. The mRNA might disappear during counting while the longer-lived protein made from it remains, and that dividing E. Coli might throw off the count by passing proteins from parent to offspring.

The researchers think the study may help research practice and perhaps to understand one cause of antibiotic resistance.

The results provide a “cautionary note” to researchers when they measure mRNA levels in single cells, Xie says: They need to take into account that the mRNA level in a cell does not reflect the level of its associated protein. Xie and his team next will study how this “noise” might contribute to antibiotic resistance in bacteria. [Science News]

Related content:
80beats: Engineered E. Coli Bacteria Produces Road-Ready Diesel
80beats: GM Corn Leads to Organ Failure!? Not So Fast
80beats: Red Meat Acts as Trojan Horse for Toxic Attack by E. Coli
DISCOVER: Reviews: The Wonderful World of E. Coli
DISCOVER: E. Coli Collision

Image: E. Coli / NIH


Compasskirt | Bad Astronomy

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I love geeks. I love clever people. I love sciencey stuff.

So this fills my heart with squishiness: a skirt with rows of lights that illuminate when facing north:

Make those LEDs red and every astronomer could use it. Not to mention campers, hikers, and let’s face it, nerds like all of us. I would dance all night with someone wearing this.

Want one? She’s selling kits so you can make one yourself!

Of course, in 2012* when the poles flip the skirt will light up when facing south. Oh! I know! You could wear it backwards. Problem solved.

Tip o’ the compass needle to that bon vivant, Josh A. Cagan.

* This is a joke, OK? A joke. If you actually think I am being serious about 2012, then I suggest you check your tin foil beanie for breaches.


Found: Jupiter-sized Brown Dwarf, Hiding in a Tight Orbit Around a Young Sun | 80beats

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comparisonsizeImagine an infantile version of our 4.6 billion-year-old sun. Now picture a “failed star,” a brown dwarf, about the size of Jupiter, tightly orbiting that 12 million year old stellar baby–at the distance Uranus orbits our sun. Astronomers have just found such a duo: a star about the mass of our sun with an unusually close brown dwarf companion.

Of the similarly situated brown dwarfs that astronomers have imaged, most keep their distance, orbiting at about 50 AU (or 50 times the average distance from the Earth to the sun). A team of astronomers believe the distance between this young sun, called PZ Tel A, and its dwarf companion, PZ Tel B, is less than half that, a mere 18 AU.

A paper to appear in Astrophysical Journal Letters details the find, which was made using images from the Near-Infrared Coronagraphic Imager, on the Gemini-South telescope in Chile. The researchers predicted the orbit by using two observations, one in April of 2009 and another in May of 2010 and then calculated the brown dwarf’s motion using a computer model.

Because PZ Tel A is young and sun-like, researchers say, that it might present a good history lesson on our own solar system.

In fact, PZ Tel is young enough to still possess significant amounts of cold circumstellar dust, which may have been sculpted by the gravitational interaction with the young brown dwarf companion. This is the material that can form planets so the PZ Tel system is an important laboratory for studying the early stages of planetary system formation. [Gemini Observatory]

Astronomers say that the brown dwarf is about Jupiter’s size, but is around 36 times its mass. Though they have imaged PZ Tel A before, they couldn’t pick out its dim companion because of its proximity.

An older image, taken seven years ago and reanalyzed by Laird Close, a professor at UA’s Steward Observatory and the department of astronomy, showed PZ Tel B was obscured by the glare from its parent star as recently as 2003, indicating its orbit is more elliptical than circular.”Because PZ Tel A is a rare star being both close and very young, it had been imaged several times in the past,” said Close. “So we were quite surprised to see a new companion around what was thought to be a single star.” [University of Arizona]

orbitThe Near-Infrared Coronagraphic Imager gave them more power than previously possible, as its a high-contrast instrument designed for finding dim bodies circling bring stars, like exoplanets or brown dwarfs, and can pick out a companion up to one million times fainter than the host star.

The research team was able to take pictures so close to the star by using an adaptive optics system and coronagraph [a device to block out light from the brighter star] to block our excess starlight. They then applied specialized analysis techniques to the images to detect PZ Tel B and measure its orbital motion. . . “We are just beginning to glean the many configurations of solar systems around stars like the sun,” said Michael Liu, NICI campaign leader. “The unique capabilities of NICI provide us with a powerful tool for studying their constituents using direct imaging.” [Space.com]

An international team is now using the telescope to complete a 300-star survey, the largest such survey to date, so hopefully more brown dwarfs will come out of hiding soon.

Related content:
80beats: A Hidden Cosmic Neighbor: Cool Brown Dwarf Found Lurking Near Our Solar System
DISCOVER: Hi Ho, Hi Ho—Brown dwarfs are the missing links between stars and planets
DISCOVER: Works in Progress—When it’s a planet that’s not a planet
Bad Astronomy: Brown Dwarf T Party
Bad Astronomy: The Upper Limit to a Planet

Images: Jon Lomberg, provided by Gemini Observatory, and Beth Biller and the Gemini NICI Planet-Finding Campaign


New Point of Inquiry — Science Under Obama with Francesca Grifo | The Intersection

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My latest hosted installment of Point of Inquiry just went up. The show is with Francesca Grifo of the Union of Concerned Scientists. Here’s the description:

When President Obama was inaugurated in January of 2009, he pledged to “restore science to its rightful place” in the U.S. government. And true to his word, the president promptly staffed his cabinet with distinguished scientific leaders, liberated embryonic stem cell research from the Bush era restrictions, and released a memorandum on “scientific integrity” intended to reverse the kinds of problems seen in the Bush years.

Since those days, however, the “scientific integrity” agenda does not seem to have filtered through the federal government as hoped. And according to a recent report in the Los Angeles Times, some scientists are having problems in this administration when it comes to speaking with the media, or having their research results properly handled by their superiors.

To put these developments in context, Point of Inquiry called upon Francesca Grifo, director of the Scientific Integrity Project at the Union of Concerned Scientists. As Grifo explains, claims that the Obama administration is behaving like the Bush administration did on science are absurd. However, the administration must do more to deliver on President Obama’s pledge to restore science to its “rightful place”—and move swiftly to address reports of scientific discontentment.

Francesca Grifo is a senior scientist at the Union of Concerned Scientists and an expert in biodiversity conservation, and heads up UCS’s Scientific Integrity Project. She has testified before Congress about scientific integrity and is widely quoted in the press on the topic. Prior to joining UCS, she was at Columbia University where she ran the Science Teachers Environmental Education Program.

Once again, you can find the show here, and you can stream it here.


The Enemy Within: Deadly Viruses Show Up in Genomes of Humans & Other Animals | 80beats

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EbolavirusIn a medical sense, you’d be wise to steer clear of filoviruses, a group that includes the deadly Ebola, and bornaviruses, which cause neurological diseases. But in a genetic sense, it may not be possible to avoid them. A new study in PLoS pathogens shows that bits and pieces of these viruses have been floating around in the human genome, as well as those of other mammals and vertebrates, for millions of years.

It’s not that having genetic material left behind by viruses is odd—previous research had shown that viruses account for 8 percent of the human genome. But scientists thought most of that material came from retroviruses, which use their host’s DNA to replicate and leave some of their genetic material behind. What’s weird about this is that filoviruses and bornaviruses are not retroviruses—they’re RNA viruses, which don’t use the host to reproduce in the same way.

When researcher Anna Skalka heard the peculiar news of RNA viruses leaving material in plant genomes, she and her colleagues rushed to see if the same thing is true for vertebrates.

Unlike the previous studies that focused on certain species or a particular RNA virus, Skalka went broad: She and her colleagues surveyed every vertebrate genome available, 48 in all, and looked for hints of 5666 RNA viral sequences from 38 known families and nine genera that were unclassified. It was “everything available that could be looked at,” Skalka says [ScienceNOW].

While previous research had spotted bornaviruses genes in the human genome, Skalka’s study found that squirrels, guinea pigs, zebrafish, and many other species besides us showed remnants of RNA viruses in their genomes. And Skalka’s team found that just those two groups—Ebola’s filoviruses group and the bornaviruses—dominated. So how did those RNA viruses get their material into our genomes, why has it lasted for so long, and why do we only see these two groups?

First, the how:

How these gene fragments jumped from viruses to vertebrates is a matter of speculation. Skalka suspects that malfunctioning machinery in sperm or egg cells could have copied RNA virus genes, then slipped them into chromosomes later duplicated during reproduction. Also speculative is what these viral fragments did — or still do, given their conspicuous lack of random mutations that gather in unused genes — for their unwitting recipients [Wired.com].

As for the why:

Because these pieces have been present in vertebrate genomes for some 40 million years, “there might be some selective advantage to having them,” Skalka says. For bornaviruses and filoviruses in particular, she notes, “there must be something special about these viruses,” to have kept them around for so long [Scientific American].

It’ll take a lot more research to figure out what that “something special” might be. But there’s perhaps another reason why Skalka’s team saw so much material from these two viruses groups and so little from all the others. While most viruses seem to evolve quite rapidly, perhaps some—like these two groups and others like hemorrhagic fever viruses—haven’t changed too much over millions of years, which would explain their over-representation in this study.

Studies like this can’t help but miss genetic sequences from viruses that have changed significantly over time, and the viruses may now look very different from how they did when they inserted themselves into a genome. “There may be some ancient ghosts in there,” Skalka agrees, “but the surviving viruses have evolved so far that we can’t recognize them anymore” [ScienceNOW].

Check out DISCOVER on Facebook.

Related Content:
DISCOVER: Too Close to Ebola, an American doctor’s tale from Uganda
80beats: My Excrement, Myself: The Unique Genetics of a Person’s Gut Viruses
80beats: The Swine Flu Virus Is Evolving. Are We Paying Enough Attention?
80beats: Number of Humans with Pig Ebola in the Philippines Rises to Five

Image: Wikimedia Commons


Tom Johnson: A Final Word | The Intersection

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As I’ve said, I was impressed by Jerry Coyne’s debunking of the story originally posted as a comment on this blog–and then regrettably elevated to greater prominence–by “Tom Johnson.” Let me just add a few last points:

1) I am confident Coyne knows, as I do, “Johnson’s” real identity. And I, like Coyne, have been in dialogue with his adviser, whom I originally alerted to this situation back on July 7. So I too know that “Johnson’s” behavior is being investigated, and will be dealt with, through proper university channels. I think his adviser has handled things very well and am confident in this person’s judgment about how to deal with the situation.

2) I don’t think Johnson’s original story is true as described. More on this below.

3) As I’ve previously said, I should never have elevated Johnson’s original comment or called it an “exhibit.” I regret that I gave this story undue prominence, and I want to apologize to all who were affected by that action.

4) At the same time, it now looks like I was deceived by “Tom” in October when I contacted him to check things out. If I had been told the truth about his story at that time, the original comment would not have stood, and any issues would have been dealt with then, rather than now.

5) I think something probably did happen to “Johnson” to make him a fervent “accommodationist.” But whatever the nature of that experience or experiences, it is no justification for the trumped-up original story or for his other actions—which, as we now know, included creating multiple sock puppets over a long period of time and using them to nastily trash his “New Atheist” opponents.

6) We are left with no reliable evidence of loud, boorish, confrontational public behavior by atheists at events with religious believers. Those who have problems with the “New Atheism” should not use this line of argument in their critiques, unless or until such evidence is produced.

There is a bit more to say. To quote Jean Kazez (who has been sorely and unjustly abused online over this affair): “There’s one more thing that hasn’t been cleared up. What did the student put in an email to Chris Mooney in October 2009 to make him believe his story? Obviously it will be up to Chris to explain or not explain.”

The answer is that I believe I was deceived about the story back in October 2009, and led to believe a falsehood.

You will recall that “Johnson” originally claimed to have witnessed atheists at conservation events “mock the religious to their face, shout forced laughter at them, and call them ‘stupid,’ ‘ignorant’ and the like.” This is the story that caused such an uproar. And it was, crucially, the image of loud, public, and confrontational behavior that drew such attention. If Johnson had said something more minor—for instance, that a colleague at a conservation event had said something critical about religion to him privately, in a one-on-one fashion–it wouldn’t have been a big deal.

When I emailed him back in October about his story, “Johnson” identified himself as a graduate student at a major university, and described his academic publishing record as well as his in-depth involvement in science education, outreach, and conservation activities. He included his website, and told me where to find his CV. He included his phone number. He also provided the website of the conservation group he was involved with, and the names of the religious organizations involved in the events where supposed transgressions had occurred.

All the details about his identity were accurate. Despite a lie told later on about not being a graduate student—presumably because people were getting too close to his true identity–”Johnson” really was who he said he was. He could have seen precisely what he claimed to have seen.

But in my view, his story has now fallen apart. Let’s examine:

1) “Johnson” told me he’d witnessed this loud public atheist misbehavior at specific events, which he had attended, involving a Baptist group and an Episcopalian organization;

2) He said that the harshest comments he’d heard had been at outreach events with the Baptist group.

There’s no longer any reason to believe this. First, “Johnson” is now known to be a completely unreliable witness. On top of that, he has backed down from the original story, which claimed loud public confrontations—and we have one witness that refutes it regarding the Baptist group.

More specifically:

1) In answers submitted to his adviser and shared with myself and Jerry Coyne, “Johnson” backed away from the original story, admitting there were no harsh statements about religion made “with a raised voice to a group.” He called the original story an “exaggeration.”

2) Regarding the Episcopalian organization, “Johnson” said he had mistakenly mentioned it to me as a place where atheist misbehavior had occurred. Nothing of the sort described happened in connection with this group.

3) Regarding the Baptist group, “Johnson” also backed away from the claim that some sort of loud public confrontation had happened in connection with this organization. He did suggest that a “colleague” who had been with him at a 2008 event had made more minor critical remarks, but nothing on the scale originally described. Even if we were inclined believe this—and I really don’t believe anything at this point—it would not justify the much more dramatic claims of the original story.

4) Coyne has been in touch with this colleague, who says that nothing like what Johnson originally described occurred at the Baptist event; and I’ve also contacted this colleague to confirm the accuracy of Coyne’s assessment. In sum, it looks like there’s no there there regarding the Baptist group either—at least regarding loud, public confrontations.

In conclusion, I want to thank everyone who has tried to establish and to explain the truth here: “Johnson’s” adviser and Jerry Coyne; and also TB and Jean Kazez.

I still have my philosophical and tactical problems with the “New Atheism.” But I’m disturbed that someone on my “side” of this debate would do the things “Johnson” has done, painting a group as uncivil based on what is at best a serious exaggeration, while simultaneously spewing reams of incivility towards that group online, under multiple identities. There is no excuse for such behavior–and moreover, there has been a very big cost in this case to a lot of people, both in time and in grief.

If there is any silver lining at all here, perhaps after working to find out the truth together about “Tom Johnson,” so-called “New Atheists” and “accommodationists” might feel the inclination to be just a little bit more civil and trusting towards one another. We do have a shared commitment to the truth, and a means of discerning it—and those have won out in this case. Let’s not forget that as we carry on the argument for science and reason in the future.


We Can Rebuild You: 8 Ways Science Can Fix Your (or Your Cat’s) Broken Body | Science Not Fiction

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Star Wars, A.I., The Six Million Dollar Man, Star Trek and a host of other science-fiction films all share a particular futurist’s dream: a broken body is repaired with an artificial replacements. Reality is finally catching up with our imaginations. Stem cells, mind-controlled arms, osso-integrated prostheses, exoskeletons, and xenotransplants are here. It’s important to note that most of these innovations are right on the cutting edge, either experimental, prohibitively expensive, or both. Individually they each may seem like small or too esoteric to matter, but as a whole, it looks like we’re on our way to a very cyborg future.

1) Rex

rex-robotic-exoskeleton-0

Rex Bionics has created what will be a commercially available set of robotic exoskeleton legs. The only currently existing set, custom built for Hayden Allen, allow him to walk up and down stairs and take awesome, super-mecha pictures like the one above. In an interview, he talks about basic quality of life issues (blood circulation, knowing when you have to go to the bathroom) that come from being ambulatory. Take that, paralysis!

2) Tooth Regeneration

Have you ever had a cavity? How would you like it if you could just undo the cavity instead of getting a filling? Instead of drilling and filling, a gel containing the peptide melanocyte-stimulating hormone (MSH) could let teeth grow back from within! According to Discovery News “Previous experiments, reported in the Proceedings of the National Academy of Sciences, showed that MSH encourages bone regeneration.” What good news! Now where is my barrel of Mountain Dew?

3) Organs to Order

Right now two major universities, Wake Forest and Yale, are trying to grow organs in a lab to put in you. At Yale, Thomas Peterson’s team is trying to master regrowing rat lungs. At Wake Forest, Dr. Anthony Atala’s team is attempting to master growing, um, everything else. Peterson, and Atala, who has spoken at TED, are rightfully skeptical of speed but hopeful for the eventual success of their experiments. Before you take up smoking, Laura Niklason, the member of Peterson’s team who lead the rat lung study, has a sobering statistic:

“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.”

4) Mind-Controlled Prostheses:

DARPA armDean Kamen isn’t the only fella trying to replicate Luke Skywalker’s amazing prosthetic arm. The good folks at Johns Hopkins University, working with DARPA–military funder of all things futuristic–have just received over 30 million bucks to continue developing and testing their own robot arm. The creatively named Modular Prosthetic Limb has 22 points of actuation, weighs as much as a human arm, and is uses mind control.

For an idea of how mind-controlled prostheses work, check out the Dean Kamen DEKA “Luke” arm video and this surreal monkey robot-arm clip from the New York Times.

5) Osso/dermal Integrated Prostheses:

Oscar the cat had a run in with a combine harvester that lopped off his back two feet. A British veterinary surgeon, Noel Fitzpatrick, decided to get the little black cat back to being a quadruped, and, in doing so, revolutionized prosthetics. One of the holy grails of artificial limbs is osso and dermal integration: that is, fuzing metal and plastic to the bone and having the skin grow naturally over it. Just look at the joy on Fitzpatrick’s face when the bandages are removed from Oscar’s stumps and, then again, when the cat has to be reined in because he’s exploring a bit too heartily with his new kicks.

6) Replace Your Face:face-transplant-278x225

Another unlucky Oscar, in this case a frightful shooting victim, has had the first full-face transplant. Muscle, bone, nerves, blood vessels–the whole kit-and-kaboodle–has been replaced. The overwhelming complexity of the operation is a testament to the progress medicine has made. Oscar, as it would happen, lives in the organ donation capital of the world: Spain. ¡Olé!

7) HULC and SARCOS

Lockheed Martin and Raytheon are racing to complete the first untethered, full-body exoskeleton. Both are working on military applications, as well as competing to see who can have the goofiest nu-metal music accompanying their dry, engineer-narrated videos of their exoskeletons (Lockheed’s HULC and Raytheon’s SARCOS) doing things like helping a soldier carry a bomb and shadow box. While still very, very early in the development phases, it’s not hard to see where exoskeletons have a real potential to change the modern battlefield.

8.) All Together Now:

Every one of these innovations is worthy of our awe independently, but considered together we have a rough picture of where medical, biological, and robotic science are flowing together. Even non-human breakthroughs, like Oscar the cat, herald great things: Noel Fitzpatrick, Oscar’s surgeon, has a facility dedicated to animal prosthetics that is serving not only to help amputated animals but as a test bed for techniques which might one day be used to help people. Robotic exoskeletons like the REX, HULC, and XOS, combined with mind-synched technology, complex articulation, and osso-dermal integration pave the way for complete rehabilitation and mobility of those with traumatic amputating and paralyzing injuries and diseases. Coupled with lab-grown, transplantable organs and the necessary techniques to successfully complete even the most complex transplants, not to mention the ability to coax certain parts to heal themselves, and we have one amazing looking future.

No one technology or breakthrough is going to change how we heal ourselves, but every year cyborg science-fiction gets a bit closer to cyborg science fact.


WHAM! Bulls-eye! | Bad Astronomy

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I have a Martian mystery for you today, and one that is writ quite large and dramatically. It seems weird at first, then simple next, but when you dig deeper — literally — things get very weird indeed.

It all starts with an out-of-control awesome picture that honestly made me reel back and say "Wow!"

I present to you out-of-control awesome:

hirise_bullseyecrater

Wow!

Click the pic to embiggen. This unnamed crater is about 700 meters (roughly half a mile) across, and sits in the northern mid-latitudes region of Mars. It’s interesting, isn’t it? The multiple concentric bowls of the crater are trying to tell us something, but what?

My first thought, also mentioned on the HiRISE blog, is that this is a coincidental double impact: the big terraced crater was the original impact, then a later, second object impacted almost exactly in the center of the older one, hitting the bulls-eye like William Tell splitting an arrow.

The topography seems to support that; the inner crater has a raised rim, as you might expect from a second impact, and that would be hard to explain in a single impact. The terracing — shelf-like structures sortof like an upside-down wedding cake layering — is seen sometimes when an impactor smacks into layered ground. Imagine a layer of dirt on top of ice on top of rocks: each layer reacts differently to the impact, leaving the circular, concentric shelves in the crater bowl.

Note too that the central crater doesn’t look exactly centered, supporting a second impact.

Case closed… but wait, Your Honor! We have a surprise witness!

This picture is actually part of a much larger region which provides some context:

hirise_bullseye_context

You can see the extensive ejecta blanket (excavated material laid down from the impact ) around the crater now, which is nifty. But note the smaller crater to the lower right (indicated by the arrow): it looks a lot like the bigger crater! There’s a shallow bowl with a deeper crater almost but not quite in the center. There’s no terracing, but it’s a smaller impact and wouldn’t have dug so deeply into the surface.

hirise_bullseye2So what gives? If all we had here was the big crater, I might believe the coincidence of a nearly perfect second impact bullseye inside it. But two of them? Right next to each other?

It seems unlikely, to say the least. And I thought I had an explanation for it… which I’ll give you. But note: I chatted for a few minutes with Alfred McEwen, the Principle Investigator of the HiRISE camera (which took the image), and he told me things still aren’t quite as they seem. Keep that in mind while I describe my thought…

My idea is/was this: both of those craters were single impact events. The terrain itself must explain the weird structures; there must be several layers of material with different solidity. In the lower right crater, the softer surface material deformed and splashed back, forming a shallow bowl. Underneath it is a stronger material, forming the raised rim central crater that’s slightly off-center. The fact that’s it’s not centered may be due to sloping in the surface, or that the surface layer isn’t constant in thickness across the surface. Perhaps there is stronger material to the left which resisted the impact pressure, leaving the inner crater off-center once the event was over.

This explains the big crater too. The outer bowl is shallow. Inside that is a raised rim, as you’d expect from a stronger material. The impactor was big enough to dig below even that layer to a third, deeper and even more resilient layer, leaving a beautiful raised rim. It’s not centered either, again perhaps due to the layers being irregular in thickness or to different material strengths in the layers themselves.

Finally, in the context image, you can see lots of shallow smaller craters. Again, I think this shows the top layer is something soft like ice, which leaves those barely visible bowls behind after smaller impacts.

Tadaa! Done.

But wait! Not so done. As Alfred pointed out to me, note that the second crater is actually sitting on the ejecta blanket from the first one (which is how we know that the smaller crater impact occurred after the bigger one). Since it’s on top of that material, the ground underneath the impact would’ve been different than the ground into which the original impactor hit. The other shallow craters are all sitting in that material as well. So we can’t simply state that the terrain was similar to the original event because the original impact changed the surface structure.

Also, the detail of the structure is difficult to interpret. Turns out that at this latitude glaciation is common, and that tends to screw up details, changing the way things look. Interestingly, the rim of the innermost crater in the big crater looks pretty fresh, too, like it happened after the original event, supporting the William Tell idea that a second asteroid impact hit right in the middle of the previously excavated crater.

Finally, in the top image, look at the floor just outside that innermost crater. See the two crescent-shaped lobes at 1 and 2 o’clock? Those may be slumped material from the walls of the crater. If a second impact happened in the center of a pre-existing crater, you’d get some disturbance of the material, including debris flowing down from the walls.

So what do we conclude?

This place is a mess. That’s what I conclude. Alfred said my idea that layered terrain explains most everything has some merit, but so does the idea that a second impactor did the deed. We simply can’t tell.

If you think I’m having fun figuring this out, then dingdingding! I am. Because it is fun. This is good old-fashioned sleuthing, detective work on the scale of a city block. When we look at pictures like these we get evidence of a crime scene, perhaps millions of years old — talk about a cold case! — but still fresh enough that we can puzzle out what happened. The big crater is the main clue, drawing our attention, but the second, smaller crater may be a smoking gun, the surprise evidence that just might make everything else make sense.

It’s CSI Mars. But in this case it’s not some procedural drama on TV. It’s real, it’s huge, and it’s sitting there on another world for everyone to see. All you need to do is go there and look.


Pocket Science: plague-running mice, and how to watch mutations in real time | Not Exactly Rocket Science

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Not Exactly Pocket Science is a set of shorter write-ups on new stories with links to more detailed takes, where available. It is meant to complement the usual fare of detailed pieces that are typical for this blog.

Prairie_dog

Plague-running mice create epidemics

The bacterium behind bubonic plague – Yersinia pestis – has a notorious track record for massacring humans, creating at least three major pandemics including the Black Death of the 14th century. But it’s mainly a disease of rodents and it regularly infects the black-tailed prairie dogs of North America. It’s an enigmatic killer. It will remain relatively silent for years before suddenly exploding into an epidemic that kills nearly all the prairie dogs in infected colonies within a few weeks. Now Daniel Sakeld from Stanford University has found the culprit behind these lurk-and-kill cycles – the tiny grasshopper mouse.

Prairie dog colonies, and their diseases, are generally isolated from one another. Even though Yersinia is very persistent, it eventually fades away unless it finds a new group of hosts. The grasshopper mouse provides it with just such an opportunity by acting as an alternative and highly mobile host for Yersinia. It’s a plague-runner. By scampering across the grasslands, it inadvertently creates a network between otherwise unconnected colonies, opening up corridors for Yersinia to spread.

By creating a mathematical model, and observing both rodents in the wild, Sakeld found that when the mouse is absent, only a small proportion of prairie dogs are plagued by plague. In these conditions, infections spread very slowly during fights and hostile takeovers between neighbours. When mouse numbers pass a threshold, fatal plague epidemics are virtually guaranteed.

The numbers of grasshopper mice in the grasslands rises and falls over time, a cycle that could spell life or death for the prairie dog. These patterns of lengthy lurking and sudden death are also shared by many other deadly diseases like anthrax and hantaviruses. In these cases, alternate hosts like the grasshopper mouse might also be involved in the sudden rise of deadly epidemics.

Reference: PNAS http://dx.doi.org/10.1073/pnas.1002826107

Mutation

Events occur in real time – watching the birth of mutations

Life is a massive game of Chinese whispers – information is constantly being passed on and as this happens, errors build up. Every time a cell divides in two, its genetic information is copied and there’s a small chance that mistakes (or ‘mutations’) will creep in. Some of these mutations will be beneficial, others will be fatal. Either way, they provide fuel for evolution, producing the variation that natural selection acts upon.

Now, Marina Elez from University Paris Descartes Medical School has found a way to spot mutations in real time. She can look at dividing cells and literally watch the moment when mutations show up across the entire genome. The technique works in bacteria, and it could be expanded to study the birth of mutations in more complex cells or even cancers.

Studying mutations isn’t easy. They’re very rare and most don’t produce any noticeable effects that would give away their presence. More often not, they’re repaired by proofreading proteins, which watch for errors in copied DNA and edit them back into shape. Elez realised that these proofreaders could lead her to the location of mutations – all she needed to do was follow. She focused on one bacterial proofreader called MutL, which forms large clusters around mutations that it can’t repair. Elez tagged MutL with a molecule that glows in the dark. The result: bacteria that give off tiny pinpricks of light at every point of their genome with an irreparable mutation.

By counting these bright dots, Elez could estimate the mutation rate in her bacteria. And fortunately, her estimate was a good match for the predictions of earlier studies. Elez also thinks that the approach should work in other living things because proofreading proteins like MutL are very similar from species to species. The technical challenges might be greater in more complicated cells, but the principle of watching mutations in real time is sound. And that opens up all sorts of possibilities. You could, for example, look at tumours, to see when and where the genetic changes that create a cancer will emerge.

Reference: Current Biology http://dx.doi.org/10.1016/j.cub.2010.06.071

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


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The End of Sex Week: Darwin, Sex, and Dada | The Loom

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[This is the last post for Sex Week]

The animal kingdom is filled with wild extravagances, and a lot of them have something to do with sex. Hermit crabs wave their claws, swordtail fish flash their swordtails, manakins leap and buzz their wings. Darwin considered these displays so important and so puzzling (”the sight of a feather in a peacock’s tail, whenever I gaze at it, makes me feel sick!” he wrote to a colleague), that he dedicated half of a book to the subject.

Darwin argued that many extravagant displays in male animals were the result of a special kind of evolution he called sexual selection. Females preferred males with certain traits over other males, and so those males had more offspring, which inherited their traits. In recent decades, scientists have documented many cases in which females do indeed prefer males with certain traits over others. As I mentioned in my post on electric fish, for example, female bulldog fishes are more attracted to long electric pulses than short ones.

But why should females have any particular desire? For many scientists, the most compelling explanation is that there’s some meaning in the displays that attract them. One possible meaning is that the male who sports a particularly extreme version of a trait has good genes. As I wrote in my post on the love songs of yeast (sic), the amount of pheromones a yeast cell produces is a reliable clue to the quality of its genes. Other scientists have found similar links between the length of tail feathers and the quality of male birds.

There are other possible meanings, though. Some scientists have argued, for example, that female of some birds species prefer bright feathers on males simply because they’re easy to spot. A female with such a preference will be able to mate more efficiently than a female attract to drab, harder-to-find males. She’ll be less likely to get killed by a predator and can spend her time and energy on more useful things than hunting for a mate. Wham, bam, thank you, sir.

All of these explanations share something in common: sexual signals evolve because they signify something. Many scientists see little evidence to think that sexual displays evolved for no good reason.

And yet in other realms of evolution, biologists have come to accept that some patterns can emerge without the help of selection. Each of us is born with around 70 new mutations in our DNA. In a few cases, a mutation will cause a lethal disease and will not be able to be passed down to the next generation. In a few cases, a mutation will boost a person’s reproductive success and will gradually spread. In both these cases, natural selection is at work. It’s the reason why the harmful mutation is rare, and the beneficial one is widespread. But the spread of mutations is also governed by chance. A mutation that has no benefit or risk at all can spread throughout an entire species thanks to a fortunate roll of the genetic dice.

There was a time when most biologists did not believe that neutral genetic variation even existed. It all had to be the product of selection. Now, however, biologists generally agree that neutral genetic variation is rampant. In fact, netural evolution has taken on an important role in the study of natural selection. Scientists who want to know if a particular stretch of DNA has experienced natural selection must reject the null hypothesis that it is simply the result of neutral evolution. If you can show that neutral evolution couldn’t have produced a particular sequence of DNA, then you can be fairly confident that selection was responsible. Once you do that, you can start to investigate what sort of selection was at work. (For more on the underappreciated role of neutral evolution, check out Larry Moran’s periodic posts on the subject on his blog, Sandwalk.)

The phrase null hypothesis was first coined in the early 1900s by a British mathematician named Ronald Fisher. Fisher did some of the most important work to put Darwin’s theory of evolution on a sound mathematical footing–figuring out how to represent things like natural selection as equations and graphs, rather than just verbal arguments. Fisher showed, for example, how natural selection could proceed through the spread of lots of mutations with tiny effects. But Fisher also developed an idea that’s not so well remembered these days. Like Darwin, he pondered how sexual displays could evolve through female preferences. One idea he came up with is that a display–and a female’s preference for it–could both be completely arbitrary.

It’s fair to say that most evolutionary biologists today don’t find Fisher’s idea very useful. Nevertheless, some important thinkers have embraced and updated it. And in a new review in the journal Evolution, the Yale evolutionary biologist Richard Prum makes a bold case for taking Fisher seriously. Prum argues that it’s quite reasonable to expect sexual signals to be totally arbitrary, signifying nothing deeper about the animals who show them off. In fact, he argues, it should be the null hypothesis for scientists studying sexual displays.

I’ve known Prum for a few years now, having written some articles on his work and having had him talk to my writing class. Many of our conversations have gravitated to this big idea, which he’s been mulling for some time. So it’s good to finally see this argument in print at last.

The idea that something like a courtship dance or a song can evolve with no help from selection is a tricky one to grok. Here’s a simple version of the model. Imagine a population of birds. The males have genetic variation in the size of a red spot on their breast. Some have a bright red spot, and others have a dull one. The females, on the other hand, have genetic variation in their preference for the trait. Some only mate with males with bright red spots, and some will mate with any males. The extravagant males will have more offspring than the plain ones, because they can mate with all the choosy females and some of the non-choosy ones. The plain males only mate with the non-choosy ones. What’s more, the males with the bright red spot and the choosy females combine their genes in their offspring. The population increasingly is made up of males with an extravagant trait and females with a preference for it. And so the extravagant display spreads quickly through the population–even though the trait doesn’t signify anything.

Mark Kirkpatrick of the University of Texas, Russell Lande of Imperial College London, and their colleagues have developed much more sophisticated mathematical models of Fisher’s idea. They have found that even if the variations in male traits and female preferences are subtle, they can still get swept up into all sorts of complex evolutionary changes. Yet many others have been skeptical. One scientist declared that excepting this runaway process as an explanation for sexual selection without a lot of proof was “methodologically wicked.”

One objection was that sexual displays often impose such a big cost that they have to have some major benefit. Yet Kirkpatrick and Lande have shown that female preference and male displays can drive each other’s evolution so hard that males may end up with traits that are a major burden. They’re just so sexy that the males still continue to spread their genes. In fact, Prum argues, this runaway process is much more powerful and flexible than sexual selection based on an honest signal. If sexual displays are just relaying honest information about males, then why are closely related species so different in what they find attractive?

In his review, Prum looks at a series of studies in which scientists tried to figure out the reason that birds have extravagant traits, such as complex songs. He notes how the scientists always go into the studies assuming that there must be some meaning to the trait, so that its evolution can be driven by selection. Sometimes they fail to find that meaning, and when they do, they conclude that there must be another meaning they haven’t found yet. All they’re doing is trying to confirm a foregone conclusion, Prum argues, when they out to be trying to reject the null hypothesis.

If they can’t reject the null hypothesis, they should conclude that the best explanation for a bird song or a dance or some other display is that it’s just arbitrary. Prum doesn’t think that every sexual display will turn out to be arbitrary, but he expect that a lot of them will.

“I do not claim that the ‘Emperor has no clothes,’” he writes in his conclusion. “I would predict that the ‘Emperor wears a loincloth.’”

I’d be curious to know what evolutionary biologists who work on sexual selection think of Prum’s manifesto (paging Marlene Zuk). It’s certainly provocative, evoking not just Stephen Jay Gould’s attacks on Dawkins and other adaptationists, but even the Dadaists, who toyed with the arbitrariness of beauty in pieces such as Marcel Duchamp’s Fountain, shown here. And it’s also a good way to end Sex Week, as we leave biologists continuing to argue and marvel over the mysteries of sex.

[Image: Wikipedia]


NASA Ames Makes Payloads Out of Phones and Toys

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Cheaper, Better Satellites Made From Cellphones and Toys, Wired

"Instead of investing in their own computer research and development, engineers at the NASA Ames Research Center are looking to cellphones and off-the-shelf toys to power the future of low-cost satellite technology. The smartphone in your pocket has about 120 times more computing power than the average satellite, which has the equivalent of a 1984-era computer inside. "You can go to Walmart and buy toys that work better than satellites did 20 years ago," said NASA physicist Chris Boshuizen. "And your cellphone is really a $500 robot in your pocket that can't get around. A lot of the real innovation now happens in entertainment and cellphone technology, and NASA should be going forward with their stuff."

Bolden Is Operating In Cloaked Mode These Days

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Keith's note: In case you haven't noticed Charlie Bolden has been invisible for several weeks after the Muslim outrech media storm. No one in the media has interviewed him. He hasn't been quoted. He's just been, well, invisible. He surfaced yesterday at a stealth visit to GSFC. NASA only admitted this via Twitter a few minutes ago. No doubt he will disappear again. You can tell if he is arriving (or departing) stealthily if you hear this noise. This way he can avoid the media more easily.

Gordon’s Attempt To Shove HR 5781 Through Flops

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Vote on NASA Bill Appears Unlikely Before September, Space News

"With little time remaining in the fiscal year that ends Sept. 30, House Science and Technology Committee Chairman Rep. Bart Gordon (D-Tenn.) sought to bring the measure to the House floor under suspension of the rules -- a move that prevents amendments to a bill and requires a two-thirds majority vote to pass. But Gordon encountered resistance from House members hoping to weigh in on the measure during floor debate. Rep. Adam Schiff (D-Calif.) and other House Democrats met with Gordon early July 29 to address concerns with key elements of the legislation."

NASA bill stays grounded, Politico

"Despite the best attempts of Rep. Bart Gordon (D-Tenn.), chairman of the House Science and Technology Committee, to bring the three-year funding plan to a vote this week, a coalition of members frustrated by his haste protested to the majority leader, ultimately forcing the chamber to punt until September."

NASA Unions Split On HR 5781

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IFPTE/AFGE Letter on NASA Authorization Act

"The International Federation of Professional and Technical Engineers (IFPTE), and the American Federation of Government Employees (AFGE) are writing to inform you that this bill is far from non-controversial. In this regard, IFPTE and AFGE urge you to oppose HR 5781 if it comes before you in its current form."

Vote on NASA Bill Appears Unlikely Before September, Space News

"The International Association of Machinists and Aerospace Workers said in a July 29 statement that the organization supports the House version of the NASA authorization."

NASA and PeTA on CNN Tonight

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This isn't rocket science, Houston Chronicle

"Since leaving her position at NASA, [April Jean] Evans has devoted much of her time to building support for an international treaty that would ban primate experiments for the purpose of space exploration. Already the European Space Agency has adopted such a position, with Director Jean-Jacques Dordain stating in an April 1 letter that ESA's formal position is: "there is absolutely no research interest or planning for experiments with primates." Such is Evans' aspiration that all space agencies would adopt a similar position. But there's also the real-world issue of no longer having a regular income. Since leaving NASA, Evans has moved into her brother's spare room. She's also falling into debt."

Keith's note: PeTA tells me that April Jean Evans is supposed to be on CNN Headline News Channel on "Issues With Jane Velez-Mitchell" at 7 pm EDT tonight to talk about this. If you are going to comment on NASAWatch, then stay on topic and don't try and post stupid stuff anonymously - it won't appear online.

Ex-NASA Engineer on HLN Tonight, PeTA