Updates: Comet landing, #shirtstorm, virus moratorium, Jonah Lehrer

For today, bringing you up to date on a few past posts.

Adieu, Philae. Or is it au ‘voir?

In our last episode, the plucky little lander Philae was finally on the surface of  Comet 67P/Churyumov–Gerasimenko. But Philae wasn’t getting enough sun, so its solar battery was running out. European Space Agency scientists to the rescue! Could they move Philae into the sunlight in time for its several-week mission to continue?

No.

Philae died.

The End.

Or, long shot, maybe not. There’s a literal ray of hope. It’s possible that the comet’s position as it nears the sun (its closest approach is next August) will move Philae out of the shade and its battery will recharge. Stay tuned.

Philae lander photographed from mother ship Rosetta as it falls toward the comet. Credit: ESA/Rosetta/MPS for OSIRIS Team MPS/UPD/LAM/IAA/SSO/INTA/UPM/DASP/IDA. From the Science slide show.

Philae lander photographed from mother ship Rosetta as it falls toward the comet. Credit: ESA/Rosetta/MPS for OSIRIS Team MPS/UPD/LAM/IAA/SSO/INTA/UPM/DASP/IDA. From the Science slide show.

Clara Moskowitz’s SciAm post is a nice summary of our necessary mixed feelings about Philae’s traumatic landing on Comet 67P/Churyumov–Gerasimenko: sorrow that the little lander ended up in a shady place where its solar battery gave out and put an end to its mission, joy that the Rosetta mission did, in fact, put a lander on a comet. Pretty unlikely, really. A triumph, even.

Bad astronomer Phil Plait rhapsodizes a bit–justifiably–about human successes in space, pretty damn marvelous when you remember that we’ve only been flying for a century or so. “We’ve sent our spacecraft to every major body in the solar system, and quite a few minor ones besides. We’ve continuously occupied space for years, and we’ve launched observatories into orbit that examine the Universe in every wavelength regime of the electromagnetic spectrum. And we’ve done even more: We’ve set down on other worlds.” All this in a few decades, less than a human lifetime.

 

Doing science on a comet

During its brief lifetime, Philae did manage some science. It detected organic molecules. That might be a big deal because one of the theories about the origin of life on Earth is that it was triggered by organics delivered here by comets. But George Dvorsky at io9 says organics are not a big deal, or at least not yet, because the European Space Agency hasn’t released information on just which organics.

Amino acids could be a very big deal. Methane, not so much, even though it can be produced by living creatures. Organics, as it happens, are abundant in the universe.

Scientists gathered lots of other data too, in the couple of days when Philae’s battery was still functioning. Those data will take months to analyze, according to Eric Hand at ScienceInsider, and Rosetta will continue to orbit the comet for another year.  Science also has an open-access slide show of its favorite photos of the landing process.

 

Final Frontier Miscellany

It’s nice that Rhett Allain at Dot Physics has enough time on his hands to figure out how big Comet 67P/Churyumov–Gerasimenko is in relation to other big things. For example, if you laid the six 725 meter-long concourses at the Atlanta airport end to end, they would be about the length of the comet. Looks like quite a bumpy surface too, so a long uncomfortable walk, even with a spinner bag.

A Brit consortium wants to go back to the moon and has launched a Kickstarter campaign to pay for the project.

 

Conspiracy Theory about the comet mission

The conspiracy theorists at the Breitbart site are alleging that Philae could have survived to do its work except for those !@#$%^&*! environmentalists. “[G]reen lobbyists were behind moves to bar rocket scientists from using nuclear energy to power the device forcing scientists to rely on solar power instead.”

It seems possible that this is not just right-wing nutcase babble but that nuclear power for a spacecraft is a question for reasonable debate. See, for example, the brief post by Ethan Siegel at Starts with a Bang and his longer argument at Medium about why the ESA scientists should have used Plutonium-238 to power Philae.

I await some journalist(s) to explain the arguments pro and con.

 

The #shirtstorm

I can’t leave this topic without a brief mention of the #shirtstorm over the garment that ESA project scientist Matt Taylor was wearing, and the comment he made, when he appeared at a press conference to talk about the Philae landing. His inevitable later apology seemed sincere, and I have no reason to think that the episode wasn’t misogyny but rather largely a manifestation of clumsy, clueless geekery. I wish deeply that one of his colleagues had had the wit to say, “Hey, Matt, I’d wear a different shirt if I were you,” and I expect he does too, now. Maybe they are all clueless geeks.

The shirt. Credit: Phil Price

The shirt. Credit: Phil Price

I won’t recap because several others have done so. A selection: Phil Price at Statistical Modeling, Causal Inference, and Social Science, an odd-sounding repository for this screed; Janet Stemwedel at Doing Good Science; the anonymous physicist at Skulls in the Stars.

What these critiques argue is that the shirt and comment are just another small expression of the idea that the point of women is their orfices, and that science is a boys’ club, No Girls Allowed. Isis the Scientist sums it up: “So, the issue isn’t that it’s one shirt. It’s that as a woman scientist, I see the equivalent of that shirt numerous times a day.”

I know that’s true, but it seems to me unnecessarily parochial. Women in other professions–indeed, women of every age and occupation–can tell similar stories. If you’re in science, of course you want to fix the problem in science. But I don’t want us to forget that this is not a problem just for women in science. It is a problem for women (and, worse, for girls.)

The Skulls post recounts the usual particularly appalling eruptions on Twitter, directed at a (female) friend of the blogger who tweeted an objection to the shirt. “Since being targeted, my Female Friend has received thousands of insulting tweets and emails.  Her personal information was released online — a process known as doxxing — and the messages included death threats.  Don’t believe me?  As of today — nearly a week after the landing — people are still attacking her.” If you want proof, he provides it, quoting tweet after noxious tweet. “Trigger warning: lots of nastiness here, a true snapshot of depravity.”

 

Update on the virus research moratorium

Late last month, I posted here at On Science Blogs about the White House’s moratorium on disease virus research involving making the virus more virulent or infective.

On Monday Jocelyn Kaiser reported at ScienceInsider that the moratorium is affecting virus research at 14 institutions. Lots of detail.  At Shots, Nell Greenfieldboyce has a post recounting the particular problems of a MERS researcher.

Screenshot of NIAID stop work order, via Science.

Screenshot of NIAID stop work order, via Science.

The re-Return of Jonah Lehrer

Are you surprised? I’m not. Disgraced science writer Jonah Lehrer has yet another book deal, this one a collaboration with UCLA behavioral economist Shlomo Benartzi. At New York Magazine, Katie Zavadski tells us that it is to be “a Lehrer-esque pop science self-help book focusing on increasing productivity online — at least according to its product description on Amazon.”

Lehrer’s doings and undoings have been recounted in several posts here at On Science Blogs. Most of them appeared when the blog was still on the site of the National Association of Science Writers, before PLOS invited me to become part of the PLOS Blog Network. You can find a list here. It’s a long, juicy story. To science writers, at least. Possibly inside baseball for the rest of you.

When last heard from, Lehrer was supposed to be writing a book about, gasp, Love. Zavadski reports that Simon & Schuster says it has a draft of the love book but no pub date yet.

There’s been next to no blogging about this more recent book development, and that is a bit of a surprise. Razib Khan has a rambling post at Gene Expression urging Lehrer to take up a different line of work and let some other science writer have a chance. Dream on.

 

Thank-you note

Next week I will be taking Friday off to continue giving thanks, and among the things I’m thankful for is readers of On Science Blogs. Much obliged to you all. Next post, Friday December 4. Good grief, December already.

 

Category: Uncategorized | Tagged , , , , , , , , | 1 Comment

The good news, maybe: Landing on a comet. The bad news, maybe: Supremes vs. Obamacare

 

START HERE for the quite wonderful story of landing on a comet..  And when you get there, click PREV to continue (in reverse chronological order) seeing xkcd’s live comicking of the Philae lander’s arrival on Comet 67P/Churyumov-Gerasimenko (67P/C-P for short).

The first image of the lander on the comet's surface, a  two-image panorama taken by the Philae lander. Credit: European Space Agency

The first image of the lander on the comet’s surface, a two-image panorama taken by the Philae lander. Credit: European Space Agency

For background on the European Space Agency’s 20-year Rosetta mission to land on a comet, see previous posts at On Science Blogs here and also here. Several bloggers have been regularly updating this week’s actual landing, although as I write things have gotten a bit sticky. First, the horse’s mouth: ESA’s Rosetta blog.

John Timmer at Ars Technica on Philae’s post-landing state–exact locale uncertain, and in shadow, with perhaps not enough solar power to keep its battery going beyond 60 hours. Here’s the Ars Technica home page, which will have the latest.

At io9, George Dvorsky has details about how the uncertain landing spot will complicate Philae’s mission. It’s still sending good data to Rosetta from its onboard instruments, but it’s not clear if it will be able to do chemical analyses of the surface as planned.

At ScienceInsider, Eric Hand is updating and live blogging from Rosetta mission control in Germany. Jacob Aron has been doing that too, and Creativist is carrying his New Scientist posts and stories, open access. Of course Phil Plait is writing updates at Bad Astronomy.

VOX is selecting photos for magnificent display, nothing like the tiny snippets posted here. Here’s Day 1. And here’s Day 2.  Caleb Scharf at Life, Unbounded explains why the Rosetta mission is time travel back 4.57 billion years.

Dan Satterfield, who blogs at the American Geophysical Union, loved Rachel Maddow’s MSNBC explanation of why Philae’s landing was so scary.  EarthSky is one of the places where you can hear Comet 67P/Churyumov-Gerasimenko’s “song.”

The snafus are a bit of a downer, to be sure. Still, what with the Middle East, and Ukraine, and the economic picture, and the election, and glaciers melting, and the future of health insurance (see below) etc., etc., etc., it’s cheering to be reminded, as Josh Witten observed at The Finch and the Pea, “No matter what else we might be, we are a species that landed a robot on a comet about 500 million kilometers away for the purpose of scientific exploration. Not too shabby.”

 

The fate of Obamacare

Also at Vox, Joseph Sternberg notes that the Rosetta mission has cost 1.4 billion euros ($1.74 billion). He finds that cost, spread over a couple of decades, compares favorably with a number of other expensive recent projects. For example, it’s about 47 percent of what was spent on the 2014 US midterm elections ($3.67 billion).

Which brings us to the terrifyingly uncertain topic of Obamacare (aka ACA).

First, the guesses about what the new Republican majorities in both houses of Congress will do, or try to do.  At Covering Health, the blog at the Association of Health Care Journalists, Joanne Kenen says there will be attempts at repeal, but they will fail. The House will vote overwhelmingly for repeal, but even with the new Republican majority in the Senate, there won’t be enough votes there–60 are needed–to overcome a filibuster. And in any case, Obama would veto a repeal.

But certain features of Obamacare might be voted away.  For example, the medical device tax, which helps fund patient subsidies. The Republicans might also try to repeal the employer mandate requiring that businesses with more than 50 full-time employees offer affordable health insurance coverage. Kenen mentions other possibilities too, and includes links explaining the possible consequences.

She points out that at this stage no one knows whether the Republicans will be merely confrontational or whether some changes to the law that Obama might accept could be negotiated.

 

Enter the Supreme Court

Another possibility is that Congress will wait to see what the Supreme Court does, a ruling that is expected in June.

And the Supreme Court is where the real terror lies. A week ago, at least four of the Justices unexpectedly agreed to hear a weird challenge to the ACA. If they rule in favor of the challengers, the decision would possibly, or maybe probably, destroy  Obamacare. That’s because it would kill off most of the federal subsidies that make it possible for poorer people to buy health insurance.

A Rosetta mission poster showing the deployment of the Philae lander to comet 67P/Churyumov–Gerasimenko. The image of the comet was taken with the navigation camera on Rosetta. Credit: ESA/Rosetta/NavCam

A Rosetta mission poster showing the deployment of the Philae lander to comet 67P/Churyumov–Gerasimenko. The image of the comet was taken with the navigation camera on Rosetta. Credit: ESA/Rosetta/NavCam

The argument in the case, usually called King v. Burwell but sometimes referred to as Halbig, is a bit technical and intricate. It’s based on sloppy wording in the ACA law that makes it possible to say–although not with an entirely straight face–that only people who buy insurance through the few state insurance exchanges, not the numerous federal insurance exchanges, are entitled to apply for those subsidies.

That would mean only people who bought insurance in the 15 states that established their own exchanges could qualify for subsidies. Such a ruling would immediately snatch away the subsidies that have made it possible for 5 million previously uninsured people to buy health insurance.

Even though it’s completely clear that Congress always intended subsidies to be available to everybody everywhere.

Even though the Internal Revenue Service has issued a regulation declaring that anyone who bought insurance through either state or federal exchanges is eligible.

 

The politics of destroying Obamacare

In a series of tweets amounting to a Twitter Essay, Grist’s David Roberts observes: “The Halbig argument, in my mind, marks the point at which the right finally & completely embraced postmodernism. . . It’s like pointing to an apple and saying, “this is an orange.” It takes practice to train your mind to be able to do it. . . Halbig is endpoint of that process: arguing that a law says something that literally everyone involved knows it doesn’t.. . . In this way every dispute, even over matters of fact, becomes a contest of power — loudest, best funded, most persistent voices win.”

Grist has reprinted the entire essay. A stunning political analysis, highly recommended.

Under the headline Obamacare Is Doomed! Everybody Panic!, at Slate Barry Friedman and Dahlia Lithwick consider the Court’s decision to take case and conclude that it is not inevitable that the justices will rule against the ACA. At a Stanford Law School blog, Hank Greely agrees that panic is not the correct response. He recommends “concern and righteous anger.” But he’s not hopeful about the outcome for the ACA.

I gotta say that it’s hard to cling to any shred of hope that Obamacare will survive after Linda Greenhouse’s demoralizing take at the New York Times. I’ve been reading Greenhouse on the Supremes for decades, and I’ve never known her to say things like this:

“This is a naked power grab by conservative justices who two years ago just missed killing the Affordable Care Act in its cradle, before it fully took effect.”

And this, “There is simply no way to describe what the court did last Friday as a neutral act.”

And this, “It bears repeating that what’s at stake is whether the Affordable Care Act can continue on its successful trajectory or whether it will collapse into the “death spiral” it was structured to avoid.”

And, finally, “[The case's] arrival on the Supreme Court’s docket is also profoundly depressing. In decades of court-watching, I have struggled — sometimes it has seemed against all odds — to maintain the belief that the Supreme Court really is a court and not just a collection of politicians in robes. This past week, I’ve found myself struggling against the impulse to say two words: I surrender.”

Oy.

Category: Uncategorized | Tagged , , , , , , , , | Comments Off

Election: marijuana, climate change, abortion, Obamacare, soda tax, GMOs

 

Still going to pot

The Republicans won big last Tuesday. But so did marijuana.  Here’s a summary, from Conor Friedersdorf at The Atlantic:

“Oregon and Alaska just became the third and fourth states to legalize the drug. Washington, D.C., voted for legalization, as did the city of South Portland, Maine. The island territory of Guam chose to allow medicinal marijuana. And while Florida voters defeated a constitutional amendment legalizing medicinal weed, it required 60 percent support to pass and received roughly 58 percent of the vote. A healthy majority in the state want medical cannabis to be legal.”

Credit: MarkBuckawicki

Credit: MarkBuckawicki

I have said here before that the push to legalize is one of the most consequential social developments around–especially in light of how little is known about marijuana’s effects, therapeutic and otherwise. This should be a very big research priority, but I’ve seen few signs of that happening.

The National Institutes of Health is in a tough position here. It can’t easily launch a lot more pot research when federal laws are agin it. As a result of new state laws around the country, the pot industry will get richer and mount even more serious lobbying efforts. The federal government will grow even less enthusiastic about enforcing the laws against marijuana, as a practical matter ceding decisions about law enforcement (if any) to the states. And if the federal laws are not enforced, there won’t be much pressure to get rid of them.

It looks to me as if it will be many years before we have a handle on what marijuana is good for and where its bodily dangers lie. Meanwhile, a vast experiment has been launched by the citizenry on the citizenry. Life being what it is, some bad things are going to happen that might have been prevented if we knew more.

 

The environment, climate change, and money

Environmental issues figured big in this election and enormous amounts of money were invested in attempts to influence the outcomes. Advocates of doing something about climate change spent, at a minimum, an estimated $85 million, according to John Light at Grist. Most of that ($50 million plus) came from Tom Steyer. Light doesn’t think green groups got much for their money. That’s partly because, although voters in general care about the environment, it’s not at the top of their priorities as a pocketbook issue. Yet.

Dot Earth’s Andy Revkin argues that to compare the efforts of one side against the other is to set up a false equivalence. “The Koch brothers and their allies want to maintain the status quo, while Steyer and others seeking a political path to a post-carbon economy have an epic challenge in trying to prod Americans out of a fossil-fueled comfort zone that took a century to form.”

More bad news for the environment is likely to come from Congress. The Keystone Pipeline has lots of friends there. At Observations, the SciAm editors’ blog, Joshua A. Krisch notes that the new chairman of the Senate Environment and Public Works Committee, which oversees the Environmental Protection Agency’s budget, will be the notable climate-change denier James Inhofe.

Because the Republicans gained a majority in the US Senate in the election, come January they will occupy the chairs of each Senate committee. ScienceInsider has a complete list of likely incoming chairs of committees that affect science.

Also at ScienceInsider, David Shultz summarized the results from other science-related initiatives on state ballots. In Michigan, for example, they voted down permission to hunt wolves.

 

Health matters in the 2014 mid-term elections

At Kaiser Health News, Phil Galewitz says that wins for Republican governors in Florida, Georgia, Wisconsin, Maine and Kansas is bad news for Medicaid expansion in those states.

Here’s the Kaiser summary (with links to other pieces) of what might possibly perhaps maybe happen to Obamacare (aka ACA). The calls for repeal have grown fainter, but changes (so far not firmly delineated) seem likely. And here’s the Kaiser summary (with links to other pieces) on other health-related election results.

Also at Kaiser, Julie Rovner summarized results on an assortment of health matters in various states. Voters in North Dakota and Colorado “rejected so-called ‘personhood’ amendments that would have recognized rights for unborn fetuses.” In Tennessee, however, voters essentially overturned a state court decision loosening restrictions on abortion.

 

Department of somewhat fuzzy extended election metaphors

At Out There, Corey Powell takes off from Stephen Hawking’s ideas about the eventual collapse of the universe to conclude that the biggest challenge of American politics is not, as so many would have it, entrenched ideology. Instead, he says, the problem is the opposite of ideology. It is “excessive volatility, as voters change their minds too quickly in response to shifting circumstances, and in response to inputs that are too small or inconclusive. Great insights do not emerge that way.”

Greg Laden has a long, peculiar post-election analysis using one of the Harry Potter books as an extended metaphor for describing US political parties. It wasn’t worth my time to figure out what he was getting at, but if you have nothing else on today, you may want to pursue it.

 

Food matters in the 2014 mid-term elections

Some of those election results were about food, and optimist Marion Nestle tells us at Food Politics that there was plenty of good news for the food movement. (Food movement? Given what happens to food after it’s eaten, that’s a curious and somewhat off-putting name choice for diverse political aims. But never mind.)

Credit: pic_p_ter

Credit: pic_p_ter

In Berkeley, 75% of voters agreed to tax soda. In San Francisco a soda tax was not passed even though a majority of voters approved it; passage required two-thirds of them. Initiatives to require foods containing genetically modified ingredients to be labeled as such were voted down in Oregon and Colorado. Nestle says industry spent $60 million in these campaigns.

Grist’s Nathanael Johnson also analyzed election results related to food and farming and promises more detailed analyses in the weeks to come. He has followed up with a meditation on why the GMO labeling efforts keep failing. There are a number of reasons, definitely including the amount of money industry spent fighting labeling. But “The main problem with the anti-GMO crusade is that it picks one very limited issue out of the whole constellation of agricultural practices. And when clear-eyed people see the big picture, they often conclude that there are much more important issues to address.”

Johnson says a big change could come with mandatory labeling, which he thinks may happen in Vermont. People will see the labeling so much that they’ll just ignore it. I agree, and wrote a SciAm blog post last year urging the industry to embrace labeling voluntarily for exactly that reason.

Here’s my plan: Get people used to the idea of GM ingredients by first labeling a beloved and ubiquitous food. A perfect choice is corn chips, which is pretty much 100% GM. And don’t be shy. Make a virtue of necessity. We’re turning a lemon into lemonade here. Slap a great big proud label on the chips. Make the label convey something like this message, maybe in red letters: GM [BRAND NAME HERE] CORN CHIPS—MADE WITH DELICIOUS NUTRITIOUS GENETICALLY MODIFIED CORN!!!

A prospective boutique corn chip maker who sees this as an opportunity to get rich selling non-GM corn chips will likely be frustrated. First, finding corn that hasn’t been genetically modified is going to be really really hard. Nearly all of today’s corn is a GMO. Also, non-GM chips will inevitably cost more.

Meantime, millions of corn chip devotees are not going to deprive themselves, and they’re not going to want to pay a lot more either. Before long, I foresee, they will sink happily back into their couches with their family-size bags of crunchy, salty, tasty, less expensive GM-labeled corn chips. Yum.
Credit: Glane23

Credit: Glane23
Category: Uncategorized | Tagged , , , , , , , , , , , , , , , , , , , , , , , | 1 Comment

Population Explosion 2.0, perfect writing software, model organism sex, tardiness

 

Son of The Population Explosion?

It matters hardly at all what is done to control population growth. If Homo sap‘s birth and death rates remain more or less as they are, we will grow from 7 billion plus today to number 12 billion people by the end of this century, according to a semi-terrifying new model of population growth just published in the Proceedings of the National Academy of Sciences.

Writing at Science Insider, Jennie Dusheck reports that the Australian researchers who developed the model ran 10 different population-growth scenarios–fiddling with changes in mortality, life span, family size, and a mother’s age at first birth, and the results were much the same. Even collision with an asteroid or other catastrophes that kill as many as half a billion people would reduce 2100 population size only to about 10 billion instead of 12, Dusheck says.

At io9, George Dvorsky says that even two billion deaths in mid-century would leave the planet with 1.5 billion more people in 2100 than we have now. Another way of keeping the population at 7 or 8 billion, Dusheck notes, would be to eliminate all unwanted pregnancies, accounting today for about 16% of live births, or instituting the drastic one-child policy. Good luck with that.

I know, I know, it’s only a model. But still.

 

For writing readers

When I encounter them, I usually read (and am illuminated by) pieces by Edward Mendelson, an authority–indeed, the authority–on W.H. Auden. Mendelson writes not only for the New York Review of Books but also PC Magazine, and is an acquaintance from the early days of personal computers. We were part of  a User Group in New York City that met to provide mutual tech support (or in my case to receive same) for the much-beloved long-gone writing software XyWrite.

Mendelson has a recent post on NYRBlog about another piece of cult writing software, the DOS version of WordPerfect, which dates to before the turn of the century. Mendelson contrasts WP with the program we all love to hate but must use because our editors do, Microsoft Word.

Word, he says, is “almost always wrong as an instrument for writing prose.” This we all know, but he also calls it a work of genius, the embodiment of the Platonic idea of writing form. I won’t spoil the delightful analogy for you by paraphrase; go read it. The point for writers, though, is that DOS WordPerfect, not a work of genius, is far more accommodating to how writing is done.

It’s possible to run DOS WordPerfect in Windows, even the 64-bit kind. As essentially a public service, Mendelson maintains a site telling you, among other things, how to do it. I toyed with this temptation briefly but soon abandoned the fantasy that I might–at last–connect with the perfect writing program. I lost heart and got more realistic about software perfection after two days spent wrestling (to no purpose) with two Windows programs.

You may be made of sterner stuff.

 

Sex in model organisms

Last May the National Institutes of Health announced a new policy requiring researchers to even up the sex ratio in experiments with model animals, nearly always done on males only. I wrote about the new rules here at On Science Blogs at the time. Now Scicurious has explored the problems in more detail.

She emphasizes a pretty crucial clarification of the rules. They do not mean, as some have apparently thought, that researchers must investigate sex differences they turn up the the course of the research. “Instead, they just have to establish whether the sexes respond differently to a particular experiment,” she says. Some researchers, though, say that’s not good science.

minnie mouse n mickey

A big concern is the additional costs the new policy will impose. NIH has said it will provide a $10 million supplement to cover the new expenses, but some believe that’s nowhere near enough.

One commenter to GenomeWeb’s summary of the Scicurious post argued that the new rules would give results much greater clinical utility. “Reminds me of the whining people did when Title IX passed. Embrace the complexity!

 

I’m late, I’m late.

Apologies for this tardy brief post. Exigency. I believe that–except for the occasional holiday–this is the first Friday morning I’ve missed since I began On Science Blogs in 2009. I’ll have to look up the exact date, but I think the 5 year anniversary is near upon us.

Category: Uncategorized | Tagged , , , , , , , , | Comments Off

Moratorium on virus research, epigenetics and fear, open access to journals

 

A moratorium shuts down research on flu, MERS, and SARS viruses

The debate began quickly over the moratorium that the White House has  declared on certain sorts of virus research, the sort where researchers are deliberately trying to make a disease virus more virulent or infective. These are often called gain-of-function experiments, but that does not mean all gain-of-function work is potentially dangerous.

Deliberately making a disease organism more scary sounds loony at first glance, and lots of people think it’s loony no matter how many glances you give it. See, for example, Steven Salzberg’s post at Genomics, Medicine, and Pseudoscience. Salzberg is one of the scientists involved in the Cambridge Working Group, which has been pressuring the administration to restrict the experiments–pressure that was one factor leading to the moratorium.

Credit: Star5112 via Flickr

Credit: Star5112 via Flickr

The moratorium applies to the viruses that cause flu, SARS, and MERS–influenza, severe acute respiratory syndrome, and Middle East respiratory syndrome. Here’s what the White House blog had to say about the decision, with links to commentary from other US government agencies.  At ScienceInsider, Jocelyn Kaiser reports that about two dozen NIH-funded studies will be affected, plus some at the Department of Agriculture.

There are, arguably, reasons for doing this sort of gain-of-function research. One example is the need to develop small animal models to better study a disease. One researcher is claiming the moratorium will halt her surveillance of circulating flu viruses. Another points out that potential flu drugs must be tested on wild strains, which could produce resistant viruses.

The risk assessment began immediately on Wednesday when the previously moribund National Science Advisory Board for Biosecurity met for the first time since 2012. There’s a story there that hasn’t been told yet. Anyway, the NSABB heard from scientists who believe a moratorium is more of a threat to public health than the research is.

But the dismaying truth is that historically, bioterrorism has been much less of a risk than accidents emanating from well-meant research efforts to protect ourselves, a topic I wrote about here at On Science Blogs in June. Thus the White House has decided to err–and lot of scientists do think it’s an error–on the side of safety.

The moratorium is supposed to be voluntary and temporary, until the risks can be better assessed. But Nell Greenfieldboyce reports at Shots that some researchers who study these viruses say the National Institutes of Health, which holds the purse strings, has already sent them “cease-and-desist” letters.

The White House says the decision was prompted largely by the recent revelations about sloppy and potentially worrisome conditions at several government labs–where, for example, cleanup crews happened upon forgotten stores of the smallpox virus, supposedly banished from the face of the Earth to the safety of repositories in Russia and at the US Centers for Disease Control and Prevention decades ago. (You can read about this revelation at an On Science Blogs post from July.)

I can’t help wondering, though, how much the irrational panic over US cases of Ebola–and the vituperation President Obama’s opponents have loosed upon him as a result–doesn’t have something to do with the moratorium. Details of the Ebola panic, collected by Maryn McKenna at Superbug, will astound you. (HT also to McKenna for bringing us the marvelous “panic button” photo, which I have appropriated herewith. And hearty thanks to Star5112, who shot it. Brilliant.)

 

Inheritance of fear unto the third generation

A paper showing that unconditioned mice could inherit memories of the conditioned fears of their grandfathers , which appeared late last year, made quite a media splash. The work was done by Brian Dias and Kerry Ressler of Emory University, and the paper ran in Nature Neuroscience.

The embrace of its findings–which made the case for transgenerational epigenetics,  transfer of a memory of behavior for three generations–was more than usually rapturous. In the two items I wrote about the paper, here at On Science Blogs and in my weekly column at the Genetic Literacy Project, I noted that other scientists would be racing to replicate the study. Since mouse generation time is short, I hoped we might have confirmation of the startling findings (or failure to replicate) pretty soon.

Attempts at replication of the work haven’t been reported yet, but something else  has. Gregory Francis, a psychologist at Purdue, argues in the journal Genetics that the paper’s statistics are too good to be true. He notes that the researchers reported uniformly positive results for the epigenetic memory experiments. The probability of such a result is only 2.3%, Francis says. And if you add in the other positive neuroanatomical results the paper reports, the probability of the reported numbers drops to 0.4%.

Neuroskeptic doesn’t know what to make of this critique, noting that if the reported probability was one in a million, there would be cause for serious concern. But, using Francis’s analysis, Neuroskeptic says the probability is about one in 300. A one-in-300 event may be unlikely, but it’s by no means impossible.

In a comment on the Neuroskeptic post, Francis says “these odds are estimates of replication success, and it seems that most scientists want odds better than 1 in 2. . . The 1 in 300 odds might be high enough to imply that Dias & Ressler were simply (un)lucky with their experimental findings, but their data still does not provide good support for their theoretical ideas.”

Francis’s critique in Genetics is accompanied by a reply from Dias and Ressler, who say they have been able to replicate the work themselves “multiple times.” Francis told me in an email, “I find the Dias and Ressler reply to be disappointing. In particular, one can hardly dodge a critique of being too successful by reporting more replication success.”

The critique is preceded by comments from Genetics‘s editor Gary Churchill. He seems to be presenting an Argument from Authority in favor of Dias and Ressler’s findings, declaring that an important journal like Nature Neuroscience wouldn’t have published the paper without thorough vetting.

For further discussion (and critiques) of Francis’s critique, see Kate Yandell’s piece at The Scientist. I would be delighted refer you to the paper itself–and the reply by Dias and Ressler, and  Churchill’s comments. But I can’t. The papers are not open access.

I was startled by the fact that the papers and commentary were not easily available, having grown accustomed to even closed-access journals often granting free access to papers of unusual interest. It seemed particularly odd in this case since Genetics is published by a professional association, the Genetics Society of America, among whose members are K-12 teachers and community college instructors.

 

Against the tide of open-access

It seems particularly odd since this week I encountered a delightful statistic: At the Nature News Blog, Richard Van Noorden tells us that more than half the peer-reviewed papers published between 2007 and 2012 are now available free for downloading. Many other interesting details in this post. Which you can read for free because, although Nature is paywalled, Van Noorden’s post about open access–is open-access.

The recent papers, the ones we want to see most, are of course an entirely different story. Compared to olden times, however, even recent papers are often pretty easy to get.

  • Search the paper through PubMed and you’ll be linked to full text or author manuscript if available. An encouraging number are.
  • If not, email the corresponding author. Your copy will quite often arrive within a few hours; that’s how quickly Francis sent me his paper, plus the comments from Churchill and Dias and Ressler.
  • Or email the senior author’s PIO or the journal’s PR department.
  • Sometimes an even quicker solution is to find it on somebody’s site. Google the paper’s exact title in quotes (leaving off the period, if any.)

 

 

Category: Uncategorized | Tagged , , , , , , , , , , , , , , , , | 2 Comments

Out in the cold: Freezing feces and human eggs. Also, scientific easter eggs

 

More germ warfare, this time about fecal microbiota transplants

Despite their mind-boggling track record, fecal transplants as  effective treatments for intestinal disorders (and possibly those elsewhere in the body) have encountered PR problems–what Loom blogger Carl Zimmer calls the yuck factor.

That’s doubtless chiefly because of what they are, literal shit. After a century and a half of sanitation inculcation, it’s hard to get the mind around the idea that the microbes they contain are life-giving. At Pacific Standard, Bryn Nelson recounts a tidy theory that once upon a time, in agricultural societies, feces were looked upon with favor as fertilizer. But when we moved to cities, close quarters, the appalling state of the streets, and and disease transmission (cholera in particular) turned friendly fertilizer feces into something dangerous and disgusting.

The implication is that the yuck factor is not an inborn and inevitable human reaction to our own excrement, but a historical development born of demographic changes. Be that as it may, the yuck factor is surely the reason that the adoption of therapeutic fecal transplants–which, Nelson tells us, originated in China more than 1500 years ago and were experimented with successfully in the US in the 1950s but then vanished–has been so slow.

Now comes a development that could help change that: frozen feces in pill form. A smallish experimental study at Massachusetts General Hospital has shown that the frozen feces pills are as effective as the predominant forms of feces administration: enemas and nasogastric feeding tubes. Both are embarrassing and–especially the tube method–painful.

Credit: Hohmann Lab

Credit: Hohmann Lab

Also, as Nancy Shute points out at Shots, with the tube method there’s the possibility of inhaling feces. That’s not just yuck or even gross, it’s potentially dangerous. Excrement makes good fertilizer and is full of microbes that are essential for good health and even life. But there are bad bugs in there too.

The researchers have now tried frozen feces on some 40 patients with infections from Clostridium difficile, the antibiotic-resistant, debilitating, potentially fatal cause of massive diarrhea. It often follows antibiotic treatment for some other infection that kills the target bug but also the normal resident microbes that usually keep C. diff from getting the upper hand.

The cure rate in this treatment was 90%, similar to other C. diff fecal transplant tales. These terrific results were reported at a meeting only last Saturday, but the Journal of the American Medical Association had snapped  up the paper and published it (open access) the same day, to the researchers’ delight. “I’ve been a microbiology researcher for 25 years, and this is the biggest thing we’ve done,” lab head and senior author Elizabeth Hohman told Shute.

The researchers are making the frozen pills available “to qualified patients” without formal clinical trials, according to the New York Times. I don’t know who they regard as a qualified patient, but I’m betting there’s a stampede of desperate people toward Mass General.

Regulatory agencies will doubtless have something to say about that. But they’re going to have to move fast. The approaches to fecal transplants are changing all the time, and the demand for this near-miraculous cure is unstoppable. Alexander Gaffney points out at Regulatory Focus that the Food and Drug Administration is already in a quandary over how to deal with fecal transplants. FDA issued something close to a cease-and-desist order in the spring of 2013 and ended up in deep shit.

 

From freezing feces to freezing eggs

Apple and Facebook probably thought they’d be seen as deserving a lot of, um, brownie points when they offered women employees an unlooked-for reproductive benefit: up to $20,000 to freeze their eggs.

Some women probably do like the idea of a company assist with postponing childbearing. They might change their minds if they read up on the risks of egg recovery and the disappointments of in vitro fertilization and other forms of assisted reproduction.

egg n sperm

There are several reasons why offering women a chunk of money as enticement to delay childbearing in order to continue working (because that is what this “benefit” is) is a rotten idea.  Canadian bioethicist Françoise Baylis lists 7 of them at the Impact Ethics blog.

The most potent argument against putting off children is that pregnancy and childbirth become increasingly iffy with time. For one thing, a woman’s eggs are present at her birth, and they age right along with her.  As Ricki Lewis, my colleague here at the PLOS Blog Network, points out at her blog DNA Science, the eggs of a female fetus start developing when a pregnancy is about 5 months along. So a pregnant woman is carrying not only her own potential children, but her grandchildren too.

The most common abnormality among the children of older women is an extra chromosome, as is the case in Down syndrome. Lewis says that the specific reason older women are more likely to generate eggs with extra or missing chromosomes is not known. But the statistical fact is that for a woman in her 20s, the risk of a fetus with an extra chromosome is about 3%. For a woman in her 40s, though, the risk increases tenfold, to more than 30%.

I suppose the companies might argue that’s exactly the reason to undergo egg freezing when you’re younger, and here’s $20,000 to help you do it. But, Lewis argues,”Facebook and Apple are attempting to pay female employees to undergo a very risky procedure with not-well-understood consequences, when we don’t even know the mechanism behind the maternal age effect.”

 

Speaking of eggs, easter eggs in scientific papers.

HT to science writer and sleep expert Lynne Lamberg, who sent along this amusing tale of risqué acronyms in scientific papers. I suspect distribution may be a bit limited, however, since to get the the jokes you not only have to be pretty good at French, you have to be pretty good at idiomatic French expressions of the naughty kind.

But that item triggered my hunting instinct. Recalling that software engineers have named the jokey items they bury in their programs “easter eggs,” and that the term has now migrated to jokes hidden in computer games, on YouTube, and divers elsewhere, I searched “easter eggs in scientific papers”.

Lo and behold. A treasure trove devoted to bringing  public attention to little inside science jokes, and named exactly my search string. I wasn’t really surprised. You can find anything on the Internet. Be warned, though, that many are (like the French one) examples of inside baseball.

Easter Eggs in Scientific Papers is up-to-date with an example from the new chemistry Nobel winner, Stanford’s William Moerner, who has worked on microscopy of single molecules. He writes of a guacamole, which he says is the inverse of a mole.

To get that chemical joke, you have to know that a mole is a quantity of something that contains  6.02×1023  particles, and 6.02×1023  is known as Avogadro’s Number. (A mole, About Education explains, is simply shorthand for A Very Large Number.) According to Moerner, guacamole is, of course, one single molecule [that is, 1/(Avocado's Number) of moles.]

As I said, inside baseball.

But the author of Easter Eggs in Scientific Papers, an anonymous self-described computational biologist, is nothing if not thorough. He has traced the origin of Avocado’s Number back to 1988, to another Nobel Laureate, the beloved molecular biologist Sydney Brenner. Brenner defines it differently. A guacamole does indeed depend on Avocado’s Number, but Avocado’s Number can be anything you want it to be, Brenner says. “So a guacamole is I don’t know how many numbers.”

Here’s another science easter egg, from the same archivist on a different blog. Still inside baseball of a kind, but intelligible at least to anyone familiar with the academic world. From a scientific paper: “Order of authorship was determined by proximity to tenure decisions.”

Credit: Tony Esopi from el

Credit: Tony Esopi from el

Category: Uncategorized | Tagged , , , , , , , , , , , , , , | 5 Comments

RIP ScienceOnline, cave art in Indonesia is as old as European cave art, how human were Neandertals?

This just in: RIP ScienceOnline (#scioX)

ScienceOnline, which for the past few years has run the small annual meeting in North Carolina that brought together a disparate bunch of scientists and science groupies, most of them bloggers, is no more. Knight Science Journalism Tracker Paul Raeburn has details.

The sexual harassment disgrace of the ScienceOnline co-founder Bora Zivkovic last fall, which I covered (more than once) here at On Science Blogs, was doubtless a big part of the reason the project couldn’t find funding and has been abandoned. But I suspect there were other reasons too, not least that the science blogging world, and science online, has gotten huge and incoherent.

scienceonline logo

The last session I attended, in 2011 I think, seemed to me to take place in separate enclaves: journalists, scientists, educators, multimedia types, etc. There was little talk across those borders. The borders hadn’t mattered, hadn’t even existed, in the early meetings, when science blogging was a small and pioneering world. The fact that they did it, and did it with great seriousness, was enough to give people lots to talk about.

The Bora Affair was a terrible blow, and no doubt made potential funders run away screaming. But #scio’s end may have been in part a natural death too.

Thank you all, especially Karyn, for your midwifery. You played an enormous part in bringing science blogging into the world.

 

Take that, Chauvet

One reason the revelations about Indonesian cave art being 40,000 years old has gotten so much attention is the snarking it encourages. See, for example, Razib Khan at Gene Expression. It’s yet another blow to the idea that Europeans are more advanced culturally than other H. saps.

The cave art long known from the Indonesian island of Sulawesi has been redated and shown to be nearly 40,000 years old, just as old as the oldest cave art in Europe. John Timmer explains at Ars Technica.  A post at Vox by Joseph Stromberg contains especially nice photos and a video. Good photos comparing the Sulawesi and European paintings and a video on cave art at the BBC.

The discovery poses an interesting question about human evolution. Here’s one view, expressed by Annalee Newitz at io9: “Something happened to humans roughly 40 thousand years ago, some evolutionary and cultural development, that allowed us to start expressing ourselves symbolically. It’s extraordinary to imagine it arising in disconnected human communities throughout the world.”

Is the artistic impulse a trait that arose simultaneously in human brains on the opposite ends of the Earth, as Newitz says? Or–much more plausible to me than the orphic pulse of cultural synchronicity that she suggests–does it date from before that?

Did we start getting arty sometime after we evolved in Africa but before we set out for parts unknown some 60,000 years ago? Did people arrive in France and Sulawesi already experienced at putting pigment to stone? There’s a bit of evidence that might be so, early evidence of use of pigment in Africa (although no cave art. Yet. Absence of evidence is not evidence of absence.)

“I think these exciting discoveries allow us to move away from Eurocentric ideas on the development of figurative art to consider the alternative possibility that such artistic expression was a fundamental part of human nature 60,000 years ago, when modern humans not only occupied most of Africa but were beginning to disperse out towards Europe and the Far East,” said Chris Stringer, of London’s Natural History Museum. He was quoted in a post by Hayley Dunning at the Museum’s blog, Nature Plus.

Stringer predicts even older art finds on Sulawesi and mainland Asia and in Africa too. Kate Wong, at the SciAm Editor’s blog Observations, agrees. “I’m betting that archaeologists will eventually find much older examples of such art in humanity’s motherland,” she says.

The oldest hand stencil, Sulawesi. Credit: Kinez Riza

The oldest hand stencil, Sulawesi. Credit: Kinez Riza

On the other hand, ahem, I wonder whether cave art, originally, was an artistic impulse at all. The very earliest artwork on Sulawesi, laid down just under 40,000 years ago, is a stencil of an individual hand, and hands are far more common than animal portraits. The oldest hand there is also a little older than the oldest hand stencil in Europe, where there are also plenty of hands on cave walls.

That hand stencils seem to have happened before the animal cave paintings suggests to me that the aesthetic urge may not have originated as the desire to capture the world our distant forebears found themselves in so much as it was the desire to leave one’s mark. Not unlike what the New York subway system looked like years ago, or what the class of 2014 painted on water towers across the country last spring. Pay attention, I was here. The earliest graffiti.

 

Speaking of cave art, what about the Neandertals?

So glad the Indonesian find came up this week because it gives me a chance to segue to that possible perhaps maybe Neandertal rock art in Gibraltar that surfaced last month and that I didn’t have space to write about then.

It’s not a hand stencil, let alone an animal. And it’s not painted, it’s etched into the rock with a stone. As many have noted, it calls to mind tic-tac-toe or a hashtag. (Which one springs to mind immediately may depend on how old you are.)

The Gibraltar etching. Credit: Stewart Finlayson

The Gibraltar etching. Credit: Stewart Finlayson

The abstract crosshatching was definitely deliberate, not accidental or produced by natural forces. African engravings dated at 60,000 and 77,000 years ago are abstract patterns too.

The carving was lying under a layer of Neandertal stone tools and has been dated at before 39,000 years ago. Anatomically modern humans–that’s us, the last Homo standing–had not yet come to Gibraltar by then.

Kate Wong discusses the find at Observations and provides links to other posts about Neandertal cognition. Iain Davidson offers some caveats at The Conversation.

Among them, his reservations about the dating: “[T]he radiocarbon dates obtained from the layer above the marks are rather mixed, with younger dates found below older dates, even in an area claimed to have been a hearth. This means that it would be possible to argue that the sediments were redeposited some time after the latest date (about 29,000 years ago).”

 

Are we and Neandertals the same species?

The arguments about this find are, at bottom, about Neandertal cognition. How smart were our vanished close relatives? Did they have language? Are these crosshatch incisions evidence of symbolic behavior that would make them more like us than like the cavemen of the comics?

Davidson, I sense, would like to believe this, but thinks the evidence is just not there yet. He speculates that perhaps the crosshatching could be related to the emerging ability to count.

Anthropologist Rosemary Joyce, who blogs at What Makes Us Human at Psychology Today, says the hashtags provide “a Rorschach Test for our comfort level with the complexity of our human heritage.” She thinks we may be suffering from guilt about our possible (plausible) role in why Neandertals disappeared about 40,000 years ago.

She points out that people don’t seem to be able to get the caveman prototype out of their heads. That’s probably true, but I doubt you need the formal tools of psychology to explain it. As science writers know to their despair, the fact that the caveman image lingers may have more to do with widespread ignorance of science, in this case recent scientific discoveries about Neandertals. For example, the fact that most of today’s humans are, genetically speaking, part Neandertal.

I concede that some may be horrified at the news that most of us are part Neandertal. Not to mention that some of us are also part Denisovan. I am reminded of the apocryphal 19th Century tale about Darwin’s work, which appears to have really originated with Ashley Montagu about 1940: “It is said that when the theory of evolution was first announced it was received by the wife of the Canon of Worcester Cathedral with the remark, ‘Descended from the apes! My dear, we will hope it is not true. But if it is, let us pray that it may not become generally known.’” HT to Laelaps for unearthing the Montagu quote.

Alas, despite the best efforts of some of us, the fact that we possess Neandertal and Denisovan genes has still not become generally known.

 

Language as the defining trait of our species

Joyce writes that “Spoken language and symbolic thought become the central battlefield for maintaining that we are not them.” I wouldn’t characterize it as a battlefield. Whether Neandertals could speak and think as we do seem to me perfectly legitimate questions about how similar we are.  To ask those reasonable questions is not at all the same thing as embracing the caveman caricature.

I won’t tackle “symbolic thought” here because I’m never sure what people mean when they use that term. But spoken language does mark a real dividing line. It is not too much to say that we owe our stunning success–7 billion of us and counting–to our ability to speak to others and to understand what they say to us.

The invention of writing some 5000 years ago, plus widespread literacy (and numeracy) in the last few hundred years, were essential to bringing us where we are today, of course. But they are built on our fluent speech, and on brains that handle language universally and easily almost from birth.

How long ago did spoken language originate? Long enough ago that it was present, at least in nascent form, in the ancestor of us and the Neandertals? There are opinions, but no one knows.

The genetic evidence on whether Neandertals had the capacity for speech is murky. I took up that topic in a piece I wrote a few months ago about whether we and the Neandertals are the same species. I’m happy to call many of our archaic relatives human, and I very much hope they died out of natural causes rather than us. But the ability to speak is, to my mind, the very definition of our species. If Neandertals (or any other archaic humans we interbred with) could do it, then they r us.

Category: Uncategorized | Tagged , , , , , , , , , , , , , , | Comments Off

Very old new species, hospice v. hospital, & once more: how many microbes in the human body?

New animal, perhaps from before the Cambrian Explosion

They look sort of like mushrooms, but they are animals. All hail discovery of not just a new species, but possibly a new phylum. Possibly even an animal remnant, thought to be extinct, from before the Cambrian Explosion that began about 542 million years ago and gave rise to most of today’s animal life.

Becky Oskin provides an intro to the PLOS One paper describing the new genus, Dendrogramma, at LiveScience. Get more detail on the circumstances of the find and where it might or might not fit on the Tree of Life from Jennifer Frazer at The Artful Amoeba.

Dendrogramma discoides (starred, at left.) The others are D. enigmatica. Credit: Just et al. 2014

Dendrogramma discoides (starred, at left.) The others are D. enigmatica. Credit: Just et al. 2014

Frazer points out that the Dendrogramma, recovered from the ocean off the coast of Southeastern Australia in 1986, were preserved in formalin and alcohol. So there’s no hope of recovering DNA that might settle the question of when and where they came from and who they’re related to. The paper classifies them as Animalia, Metazoa incertae sedis. That’s Latin for “of uncertain placement,” and according to Wikipedia, a couple dozen lifeforms are in this category.

At Why Evolution is True, Jerry Coyne explains that the question of where the major groups of multicellular animals fit in evolutionary terms is still unsettled, a further complication. He also brings us a guest post by Latha Menon, who studies pre-Cambrian life in a rich assemblage in Newfoundland. She points out something I didn’t realize, which is that none of these early lifeforms is known by its fossils. Everything scientists have learned about pre-Cambrian life comes indirectly, from impressions they left in rocks.

 

End-of-life care: Hospice or hospital?

Congress did something wildly uncharacteristic a few weeks ago: both houses passed a health care bill. The bill provided for somewhat increased oversight of hospice care. Paul Raeburn, the sole remaining Knight Science Journalism Tracker, wondered why this important legislation had been so poorly covered. “Are all the healthcare reporters covering ISIS? Or the National Football League?” he asked.

One of the concerns, Raeburn notes, is that hospices have been taken over by the for-profit health care industry. There’s a suspicion that these for-profit hospices are recruiting patients who don’t really need hospice care yet.

In a comment on Raeburn’s post, Laura Newman, who blogs at Patient POV, says the legislation doesn’t provide much to cheer about, which was perhaps why it was supported by the hospice industry.

The once-every-three-years inspection that the legislation provides (pre-scheduled, not a surprise visit) is not going to achieve much reform, she says. She also argues that long lengths of stay do not necessarily mean that the for-profit hospice industry is gaming the system. Palliative care experts are urging the dying to enroll earlier because they can’t get the kind of care they really need elsewhere.

At Covering Health, the blog of the Association of Health Care Journalists, Paul Kleyman complains that the bigger problem with end-of-life care is “the relegation of dying patients to painful and unwanted high-tech medical interventions.” He cites a significant jump in the number of U.S. patients treated by 10 or more physicians in their last six months of life.

In 2012, the median length of service in US hospices declined to 18.7 days. He agrees with Laura Newman: Rather than overusing hospice services they don’t yet need, Kleyman says, nearly 2 out of 3 hospice patients aren’t getting there soon enough. Almost one-third of Medicare’s budget is spent not on hospice care, but on in-and-out hospital stays in the last two years of life.

 

Once more, germ warfare: How many microbes in the human body?

I’ve written several times here at On Science Blogs on my favorite statistic, which is that only 1 in 10 cells in your body is you; the other 90% is microbes.

It’s just such a dazzling idea, the notion that we lumbering apes, in addition to being DNA’s way of making more DNA, are also microbes’ way of making more microbes. And it gets even more dazzling in light of the increasing evidence that our microbiomes have profound effects on our health and even our brain and behavior. That they are, in fact, essential to our lives.

microbiome

Last time, late last year, I described bioinformatician Neil Saunders’ noble attempt to trace the original source of this statistic, which even major figures in microbiology quote. In “We’re only 10% human. According to…who?”, Saunders ascribed it to an obscure scientist named T.D. Luckey, who calculated this number in a 1972 article in the American Journal of Clinical Nutrition.

Judah Rosner, who heads a lab that studies antibiotic resistance at the National Institute of Diabetes and Digestive and Kidney Diseases, was one of the commenters on the Saunders post, noting that the Luckey paper has to be a low estimate because it counted only bugs that could be grown in the lab, and now we know that many can’t be.  The number, he speculated, could be 10-fold greater.

Rosner attacked the data more systematically in a letter-to-the-editor in Microbe, a magazine from the American Society for Microbiology. He quoted a great range in  the number of human body cells from a recent estimate: as few (!) as 10.5 trillion to as many (!!) as 724 trillion. In 1999, Rosner says, the number of gut microbes was estimated at between 30 and 400 trillion. Which doesn’t count our other microbe communities, on our skin and in our noses and reproductive passages, for example.

In his letter, Rosner also pointed out that microbe numbers are likely to vary in each of us depending on many factors: diet, body size, age, ethnicity, culture, stage of life, state of health, and the environment around us. He says, “there is no a priori reason for thinking that the ratio of microbial to human cells is constant among humans or even for one individual in the course of a lifetime.”

See also the post by Meredith Knight at the Genetic Literacy Project, who called my attention to a piece by journalist by Peter Andrey Smith at the Boston Globe, writing about Rosner’s letter in Microbe. Smith managed to unearth some facts about the eccentric T.D. Luckey, who produced his immortal 1972 estimate of a 10-to-1 ratio by counting microbes in one gram of feces.

The irrepressible microbiologist Jonathan Eisen says at his Tree of Life blog that he meant to write about this specious datum in 2007 but got distracted. He confesses that he even found himself quoting it in a TED talk, although he had sworn he wouldn’t.

Here’s the upshot: Despite the fact that this zombie Microbiology Legend of 10 to 1 has even top scientists in its thrall, neither they nor we have a clue what the true ratio of microbes to human cells is.

It’s not known even how many cells we have, let alone the number of single-cell organisms we’re host to. The ten-to-one figure may be arbitrary, but not much more so than 3-to-1 or 40-to-1 or even the remote possibility that human cells outnumber microbes nearly 2-to-1.

I don’t know where that leaves science writers, but I’m hoping that last one, that we have twice as many human as microbe cells, doesn’t turn out to be true. Call me a romantic.

Category: Uncategorized | Tagged , , , , , , , , , | 1 Comment

Jack the Ripper, more poison at NIH, Rosetta & the comet

 

Ripped from the headlines

Scientists have greeted with hoots and catcalls the claim that Jack the Ripper, the near-mythical late-19th Century London serial killer, has been identified from DNA as an immigrant Polish baker named Aaron Kosminski.

The DNA evidence is from a bloodstained shawl that maybe perhaps belonged to one of the victims. Besides the maybe perhaps victim’s blood, the shawl is said to also bear semen stains and an epithelial cell containing mitochondrial DNA that purportedly matches the mtDNA of one of Kosminski’s relatives.

"Nemesis of Neglect": Jack the Ripper as a phantom embodiment of social neglect. Punch cartoon, 1888.

“Nemesis of Neglect”: Jack the Ripper as a phantom embodiment of social neglect. Punch cartoon, 1888.

It might be true that he did the Ripper murders. Kosminski was one of the top suspects at the time, was confined to an asylum three years after the last Ripper murder, and spent the rest of his life in assorted similar institutions. But Naming Jack the Ripper, the book recounting this hypothetical by self-described armchair detective and Ripper tour operator Russell Edwards, is not persuasive.

Any decent TV defense attorney would rip the shawl to shreds. It must  contain dozens of DNA deposits from the many people who have handled it in the past century and a quarter. Svante Pääbo, who believes that as far as DNA analysis is concerned, cleanliness is lots better than godliness, would faint dead away. At Neurologica, Steven Novello is quite dubious about the meaning of the shawl and its contents and calls for independent replication of the results.

The evidence has not been published, and certainly not peer-reviewed.  At the BioMed Central Blog, James Balm calls that omission a pretty important hurdle to ignore. The samples were not blinded. There appear to have been no controls. Etc.

In a Pacific Standard post, Ted Scheinman dryly notes that the provenance of the maybe perhaps victim’s shawl “remains semi-conjectural.” He quotes British geneticist Sir Alec Jeffreys as pointing out that “no actual evidence has yet been provided.”

Novello also notes that there will be a lot of resistance to this idea, if only because the whole reason the Jack the Ripper tale–at least five brutal murders and maybe as many as 11–is so fascinating is that it’s a mystery. If it is truly solved, and solved in such a conventional way–a series of prostitute murders committed by a misogynist madman who was eventually locked up for good, instead of (as I believe one theory holds) the syphilitic Prince of Wales who became, briefly, King of England–well, that’s no fun.

At Comment is Free, historian Julia Laite wonders why Jack in particular commands so much public attention more than a century after the grisly murders. She thinks it has to do partly with how gruesomely savage they were, with parts of sexual organs–a uterus, a vagina–cut out and carried away. Trophies?

And the victims were whores, lost women from another world. It was possible to feel fascination without feeling empathy. She tells us that at least one of them, the lady of the maybe perhaps shawl in fact, was not a sex worker, and calls for more attention to the victims, not Jack.

More toxins galore

I can’t decide whether this makes me feel better about my slapdash housekeeping or not. It’s yet another Ooops! moment for the National Institutes of Health. More bad stuff has been found hither and yon in its labs, some of it said to date back to 1914. Plague, tularemia, botulinum–that’s Botox to you–and, oh yes, the deadly poison ricin.

Castor beans, the source of ricin.  Credit:  HediBougghanmi2014

Castor beans, the source of ricin. Credit: HediBougghanmi2014

These were found in a thorough search undertaken after the various finds of toxics stored higgledy-piggledy–some in Ziploc bags–in labs at the Centers for Disease Control and Prevention and the Food and Drug Administration. I wrote about that here at On Science Blogs in July.

Jocelyn Kaiser’s account of the recent discoveries at Science Insider includes the text of a memo from NIH director Francis Collins. He conceded that the new finds highlighted the need for constant vigilance, but also said that the samples, while not stored properly, were sealed and never endangered anyone. To my mind, NIH gets at least a few points for going in for some serious housecleaning. Probably terrified of what it would find. Maybe relieved that it wasn’t as bad as feared.

At C&EN’s Safety Zone, Jyllian Kemsley predicts that more unsettling toxic finds may lie ahead. A White House memo dated August 18 recommends that government labs and nongovernment labs that get federal money do “an immediate sweep of their facilities that possess, use, or transfer human, animal, or plant infectious agent or toxin holdings to identify Biological Select Agents and Toxins (BSA) and ensure their proper registration, safe stewardship, and secure storage or disposal.”

Kemsley has a theory about how this bad stuff accumulates. “Someone left without clearing their bench or their lab. Someone else took over. Instead of cleaning out, they pushed the samples to the back of the fridge or storage area. Repeat.”

Rosetta and 67P/Churyumov-Gerasimenko

On Monday (September 15), the European Space Agency will announce  the site where the Rosetta spacecraft will land on the comet 67P/Churyumov-Gerasimenko in November.

Josh Witten at The Finch & Pea republished tweets explaining why that’s a big deal: the Rosetta team has identified four potential landing sites, but all are riskier than had been hoped. Pamela L. Gay (@starstryder) explained: Landing site needs Sun 7-8hr/day for power, but want day-night cycle, also onsite gas&dust activity, organics, & not too sloped.

Credit: ESA/Rosetta/MPS for OSIRIS Team MPS/UPD/LAM/IAA/SSO/INTA/UPM/DASP/IDA

Credit: ESA/Rosetta/MPS for OSIRIS Team MPS/UPD/LAM/IAA/SSO/INTA/UPM/DASP/IDA

The multicolor pic came from Deborah Byrd at EarthSky, who explains,
“A preliminary map of morphologically different regions on the surface of Comet 67P/Churyumov-Gerasimenko – as revealed by the Rosetta spacecraft – shows the comet to be a unique, multifaceted world. We now know that comets can have cliffs, depressions, craters, boulders or even parallel grooves.”

I just thought it was cool. Also, that’s the longest (and yet unintelligible) photo credit ever, heading for the territory occupied by authors on a physics paper or organismal genome sequence.

Hiatus, probably

I’m off to family events, including a wedding, and will be on the road until the end of this month. Meaning it’s very likely I will not be posting here at On Science Blogs again until Friday, October 3. Unless I get inspired. Or bored. At a family wedding, though, bored is not likely to happen.

Category: Uncategorized | Tagged , , , , , , , , , , , , , , , , | 1 Comment

Low carb v. low fat for losing weight plus Knight Science Journalism Tracker again

 

Those dueling diets

This week we have a replay of the dueling diets thing, low carb vs. low fat. Low carb continues to appear to have a very slight edge, with many caveats.  The sane advice continues to be that the best diet for weight control is the one you’re most likely to stick to.

The paper that made the bigger splash came from the Annals of Internal Medicine (paywall) on Monday.  The splash happened partly because it appeared to be the most careful comparative study yet. And it seemed to show that low carb was better, and that’s what the media said.

That’s also what some bloggers I’d expect to be more careful with the data said. Shocking example: Incidental Economist Aaron Carroll.  His hed read: “Low carb crushes low fat. Screw you guys! I’m going home.”

Bottom line: After a year, the partly-Paleos lost 11.7 pounds on average and the low-fat folks a measly 4. Low carb was also better for cardio risk factors.

But not so fast. The study may have been the most careful yet, but that’s not much of a compliment. Obesity doc Yoni Freedhoff actually read the paper and pointed out at the blog Weighty Matters:

 

  •     Food consumption tallies were based on self-reports. i.e., not reliable.
  •     The low carb group lost 88% of their weight in the first 3 months. They were supposed to be eating no more than 40 grams of carbs/da but self-reported 80g during that time–and by the end said they were eating 112g.
  •     Their self-reported calorie intake was lowest in the first 3 months too. It increased during the year, but by the end they were still taking in 100 cal/da fewer than the low-fat folks.
  •     They did eat somewhat more protein than the low-fatties, and Freedhoff is one who thinks higher protein consumption may have more to do with low-carb diet success than reducing carbohydrates.
  •     Both groups received diet counseling and a replacement meal bar or shake every day. Freedman thinks that controlled meal may have had a significant impact on the weight loss in both groups–which was in any case pretty modest.
  •     He also concludes that the low carb diet was not truly that, nor was the low-fat diet (which specified 30% of calories from fat) truly low.

Kamal Patel makes some of these points and has some additional cautions at Examine.com.  First, and maybe most important, 90% of the subjects were women. I’m not going to complain about including women in medical research. It took too many decades to get to NIH’s current policy of insisting on a more rational sex ratio in clinical studies. But it does introduce the question of whether these results, unscintillating as they may be, apply to both sexes. There were 75 people in the low-carb group, and only 9 were men.

Patel concludes, “it would be disingenuous to state that ‘low carb is superior to low fat for long term weight loss’. . . A more accurate headline would have been: ‘If you are obese, decreasing carbs and upping protein may lead to greater weight loss, but sticking to any diet that has you eat less will lead to weight loss.’”

The meta analysis

The week’s second diet study appeared in JAMA on Wednesday behind a paywall. It was a meta analysis of several named diets, for example the canonical low-carb Atkins and the equally canonical low-fat Ornish. The results showed low carb slightly ahead at 6 months but the two approaches were pretty much a wash at 12 months. Low fat and low carb, the paper said, turn out to be equally good.

Or, actually, bad. Average weight loss on either was between about 12 and 20 pounds. After a year.

These equivocal findings could explain why the JAMA paper hasn’t yet gotten anything like the reception of the earlier study, which was interpreted as proclaiming that low carb was superior.

Doc Howard LeWine examines both studies at the Harvard Health Blog and concludes that the Mediterranean Diet combines the virtues of both approaches, although it doesn’t seem low carb to me. He’s part of the any-diet-that-you-can-stay-on-is-a-good-diet school.

It’s easy to understand the craving for a conclusive answer. This rigamarole has gone on too long. There is certainly enough information now to at least make it clear that insisting on low fat as the only way to go is just plain wrong. Not only inaccurate, but maybe verging on morally wrong too. That includes various professional associations. Also the government.

Speaking of which, the Centers for Disease Control and Prevention has seized the moment and just published its depressing 2013 map of self-reported obesity state by state.

obesity map cdc

 

Fin del Tracker?

The sole remaining Knight Science Journalism Tracker, Paul Raeburn, said goodbye to his (former) Tracker colleagues Wednesday, thanking Charlie Petit, Faye Flam, and Pere Estupinya, who finished their tours of duty last week. Raeburn traced the Tracker history briefly from its founding by Charlie Petit and Boyce Rensberger in 2006 to now, its last few months.

Or are they the last few months? I suspect we have just been given a taste of the kind of thing the new Tracker, assuming there is one, could contain.

Yesterday (Thursday) a most intriguing guest post went up on the old Tracker. It’s a fine piece by freelance science journalist Nadia Drake, a polite, almost decorous, well-researched savaging of the cover story in the September-October issue of the Columbia Journalism Review.

Columbia J Rev cover

The CJR story is a profile (apparently a fawning profile; I haven’t read it) of Elise Andrew, proprietor of the Facebook page I Fucking Love Science, which has acquired more than 18 million Likes and is turning into a mini-media empire featuring a news site, a YouTube channel, live events, and a TV show in the pipeline.

Among the problems with IFLS that the CJR profile skates over, Drake says, is a past history of copyright violations/plagiarism on images and a consistent inability to get the science right. Fucking loving science appears not to always require understanding it or being capable of explaining it.

The profile was written by Alexis Sobel Fitts, now editor of CJR’s sciency column The Observatory, formerly run by Curtis Brainard, now blog editor at SciAm. The response to the profile, Drake says, has not been friendly, partly because it “appeared in a journalistic publication, written in an unjournalistic way, about a person whose work is not journalism.” She concludes, “Having a large, loyal audience does not make you immune to the rules – if anything, it makes you even more beholden to them. And I don’t think either IFLS or CJR should get a pass on this one.”

This unusual post got into the Tracker via Deb Blum, who is not officially in charge of the Knight Science Journalism Program until next summer but who is clearly a big part of its current affairs. Blum told me in an email that Drake proposed the piece to her. “I think she did a great job of analyzing both the CJR story and about issues at IFLS and of backing up her points. I’m really glad we could host it and I hope it reminds people that we’re very open to these kind of posts at KSJ.”

If that’s not an invitation, guys, I don’t know what is.

A somewhat broader audience?

Among the dozen mostly mournful comments on the Raeburn post was one by Wade Roush, who is temporarily heading the Knight Science Journalism Program until Blum arrives. Roush said:

     I wanted to explain once again, however, that we are *not at all* discontinuing our support for the idea of publishing a regular, expertly curated collection of reviews and commentaries on science and technology reporting.
The real situation is that the Tracker is going on hiatus while we rework the concept. We have some big plans for introducing a renewed daily publishing operation that will serve a somewhat broader audience and, we hope, have an even deeper impact. For a number of practical reasons, we need to stop publishing the existing Tracker (effective January 2015) while we do that.

That’s a slight clarification of future plans that have seemed murky to many. But it’s also a bit confusing. Big plans for a daily publishing operation of reviews and commentaries on science and technology reporting sounds just the ticket. Hurray! But what is this “somewhat broader audience?”

Re: the broader audience, Deb Blum told me, “[W]e’d like to make it higher profile and draw an even larger audience. At least that’s definitely what I would like.”

In an email Roush told me they want to widen the subject matter to include technology. (Hmmm. The Knight Program is based at MIT, also the home of Technology Review.)

Also, they want to include more types of media. (Hmmm. I hope this doesn’t include the completely useless and mischief-making television news, a field HealthNewsReview’s Gary Schwitzer abandoned in despair a while back. But wouldn’t it be intriguing if they took on, say, YouTube and other video? Hands off blogs, please!)

In addition to the core science writing audience, Roush said, they plan on “serving up material that’s useful to the larger circle of people involved in engaging the public around technology and science.” (Hmmm. Policy-makers? PIOs? The producers at NOVA?)

The Tracker as practicum

The Tracker has been a valuable resource for science writers because its judgements about science journalism have set professional standards for a broad science-writing audience when nobody else was doing that. You can catch up on background about this decision to cease publication, cause of universal science writer kvetching, in my On Science Blogs post of a few weeks ago here.

Just an example of the Tracker’s practical value to science writers, something that happened to me this very week. In my column for the Genetic Literacy Project Tuesday I wrote about the two arresting studies on modification of memory published last week. Both were technically complex, the one on changing an unpleasant mouse memory to a good one in particular.

My real subject was the long-term impacts–policy, ethical, and whatnot–of being able to modify memory, not the science itself, which I didn’t have space to explain in detail. Fortunately, Faye Flam had evaluated several news stories about the mouse study. It was her final Tracker post in fact. She had found most of them lacking, but I was able to refer readers interested in technical details to her post and her recommendation, which was to Emily Underwood’s open-access piece at Science.

Charlie Petit’s last post was about the fastest-moving science story of the moment, Ebola. First, genetic sequencing of strains of the virus, replete with the throbbing detail that five of the paper’s authors had died of Ebola. Also, details on a hurried test of an experimental vaccine. Many links, which is what we’ve always gotten from Tracker posts. If you’re writing about Ebola, and who isn’t, save this URL.

Pere Estupinya, who Tracked Spanish-language media in the Spanish language, said farewell with a collection of his favorite posts–and a reminder of what a big world this is. He hopes, he said, that Tracker v.2 “considers the science, health, environment and innovation journalism published in Spanish. Latin America is a vibrant region full of challenges and opportunities for science journalism. Honestly, it really is.”

I believe him.

Pere Estupinya waves goodbye

Pere Estupinya waves goodbye

Category: Uncategorized | Tagged , , , , , , , , , , , , , , , , | 5 Comments