Category: Uncategorized

The natural history of deer, as explained by a 4-year-old

“I want a pet deer. I’ll keep it in the back yard, and when it grows up it will have antlers.

“Baby deers have antlers on the inside. And every time they cry, their antlers grow a little. Every time they grow, they make a little poke, and they have a boo-boo. But then it heals up.

“When grownup deers die, their antlers apparently fall off.

“Mom, how are baby deers born?”

(They grow inside their mama’s belly, just like you did.)

“But deers don’t have a crotch!”

(Sure they do.)

“You mean they have two crotches?”

(No, just one between their back legs. Their front legs are like arms. You don’t have a crotch in your chest, do you?)


The untold story behind the FAA electronics ban, according to a flight attendant


I wish I had caught his name. I hesitate to call him African-American, because he had an accent that was probably neither. He was very soft-spoken and sprinkled his announcements with jokes. (“There is zero chance of a water landing on this flight, but if you get bored, you can can lift up your seat cushion…”)

He got to a part in the announcements where he paused, sighed, and acknowledged that we had probably heard Delta’s fanfare about lifting the electronics ban effective immediately. He sighed again, and told a story I haven’t heard in the news.

It was a myth, he said, that electronics interfered with plane navigation. They never did. But they did interfere with pilots’ headsets, causing a hiss or whine that made it hard for them to hear ground control.

The FAA can lift the ban now, he said, because modern pilots’ headsets have noise canceling systems, same idea as the Bose headphones you sometimes see passengers using.

But, he apologized, there’s a three-stage process where the FAA has to approve each airplane individually before we can play Angry Birds on takeoff. As of that date – November 5 – Delta’s main line had been approved, but not the puddle-jumpers like the one we were on. Give it a week, he said. And enjoy your flight.

Photo by “Doug” on Flickr, CC-BY-NC

How I rooted my Nook HD+

  1. I got a microSD card. I was very careful not to breathe on it, lest it float away on the wind.
  2. I formatted the card and made it bootable with Cyanogen. There are 2 ways to do this:
    1. mkfs.vfat, fdisk to toggle bootable flag and get the right partition type (‘b’), then copy the files contained in the BOOTFILES rar here
    2. dd if=[this file, unzipped] of=/dev/sdb # Note that is /dev/sdb NOT /dev/sdb1.
  3. Mount the card if you haven’t already (still on your computer) and add a fun zipfile. Probably you want this one (explained here) which will give you a nice Android OS.
  4. Power down the nook, insert card, boot into Cyanoboot. First do a backup, then install the zip. Make sure the sd card is clicked in all the way, OK?
  5. Reboot (without the card) and enjoy

Learning something new every day

fancy_graph.pngToday: You can copy a graph from LibreOffice, paste it into Inkscape, and edit it there.

Blog has moved

Well, mostly. Science posts will now be at The Messy Machine. Bookmark that if you want to keep up on the kind of stuff you’ve seen here.

Germ DIY: Infecting yourself for fun and profit (updated)

A while back I said I had “microbiomes on the brain”. I meant that metaphorically. But now, two surgeons at UC Davis are in big trouble for deliberately putting bacteria in their patients’ brains.

Thing is, they say the patients requested it. “If I come down with a glioblastoma, I will demand that it be done on myself,” one of the surgeons told the Sacramento Bee.

Glioblastoma is a nasty, nasty brain cancer.  According to the SacBee article – I haven’t been able to track down any other information on this therapy – there are accounts of glioblastoma patients surviving years after contracting infections, leading to a hypothesis that introducing bacteria into head wounds might be an effective therapy. [UPDATE: lots and lots of info here, both on the UC Davis situation and on the idea of treating cancer with bacteria]

How did the UC Davis patients fare? One died of sepsis (infection), one died from the tumor but also had sepsis, and one lived for at least ten months after the treatment, with a reduction in the tumor but also suffering a wound infection. The surgeons then asked for permission from an ethics committee to infect five more patients.

The university said no way, launched an investigation, and ultimately told the surgeons not to do any more experimentation on humans. The surgeons say they weren’t experimenting, just applying an admittedly rare treatment.

Going rogue: DIY germ transfers

Bacterial transfers occupy a weird gray area in medicine They’re not exactly a drug, or a tissue, or a device (the categories the FDA considers for regulation). You can get bacteria from anywhere, especially if the source you’re looking for is the human microbiome: everyone you know is a potential donor.

Fecal transplants, which have a 90% success rate at curing debilitating C. diff infections, are so cheap, easy, and effective that they should be a first treatment, not a last resort; but few doctors offer them. One is working on a home enema protocol so sufferers can DIY the treatment with their donor (often a spouse or close relative).

It’s not so different from the situation with sperm donors: almost half the earth’s population possesses the little swimmers, and can churn them out on demand,  so why should the expense and red tape of a sperm bank be necessary for conception without sex? Controversially, it’s not; a lesbian couple can meet their donor for coffee and perform the transfer in a two-step process simple enough it can be done in a Starbucks bathroom.With sources of human microbiota all around us, there’s no need to limit probiotic treatments and research to species you can grow industrially and stuff into a pill, that must then make their way through the patient’s digestive tract before eventually finding their home (although, miraculously, that often works.) Why not try a more direct route?

Babies born by c-section miss out on their mothers’ vaginal microbiota, possibly leading to health problems. Probiotics and even fecal transplants have been tried, with mixed success, but the simple technique of smearing mom’s vaginal secretions onto the baby “has been proposed … but to date there are no published studies.”

Who knows what other bacterial “transplants” might be therapeutically important? For skin infections, vaginal infections, perhaps even transfer of mouth bacteria to prevent cavities? I’m not endorsing brain bacteria, but I bet there are some promising disease treatments growing in you, and on you, right now.

Highlights from #germchat

hashtagI had a fun time today on twitter #germchat discussing the human microbiome. Check out a Storify transcript here.  Here are some of my favorite things I learned:

How do oral probiotics affect health in places other than the gut? According to @DrJamesVersalov, they provide molecules that circulate through the bloodstream and “act like hormones”: vitamins, amino acids, etc.

Is it bad to be sanitizing our hands all the time? @DrJamesVersalov says handwashing avoids spreading infections, but established skin microbiota survives washing. @JATetro adds that sanitizer (as tested in his lab) actually does kill all the bacteria.

Is our idea of beneficial probiotics skewed toward certain species? @JATetro says most are fermenters (as found in kimchee, kombucha, sauerkraut) and their byproducts, like sugars and amino acids, are “buffers” between bugs and our immune system. @peterdilaura  agrees with my suspicion that there is “big potential impact from low abundant harder-to-culture bugs”. @JATetro says he found a microbe in the subway that he was asked to culture for probiotic potential.

Here’s an intriguing idea: @peterdilaura suggests we get “sub-therapeutic dosing” of antibiotics from food.

The concentration of probiotics matters, says @JATetro, and it may not be as simple as eating yogurt, as in the case of Danone’s health claims.

We are only 10% us: where did that count come from, that established bacterial cells outnumber our own cells 10-to-one? @bernat_olle says to check out Savage, 1977.

Micro links 2: what’s in grandpa’s gut and mom’s nose?

Some more quickies:

Healthy old people have healthy gut bacteria – Makes sense, right? But the logic behind it is very chicken-and-egg. The authors say that when somebody goes into a nursing home, they start eating institutional food, their diet affects their gut bacteria, and their gut bacteria affects their health. I find this theory appealing, especially if it convinces the institutions to provide better food: “Mashed potato and porridge were the only staples in this diet type that were consumed daily,” says one of the authors.

But it could be the other way around: they get sick, then enter the nursing home, where the diet changes their gut flora. Or, they get sick, which changes the gut flora, and also leads to their move to the home. The title of the actual paper sticks to the bare facts: Gut microbiota composition correlates with diet and health in the elderly – which is exactly what they found. Causation TBD.

Parents are resistant to cold and flu viruses – and the effect lasts even after their kids have long since left home. This seems only fair, since children are little disease vectors, ferrying germs to and from school (or, in my case, day care). The funny thing is, the study found that parents have the same levels of antibodies to the viruses as non-parents, but are still less likely to get sick when a researcher shoves viruses up their nose.

Their theory: parents are happier and less stressed (haha). My thought: there’s a lot more to the immune system than antibodies, so maybe one of those other aspects of immunity gets strengthened by frequent exposure.

Twitter chat about germs today (Thurs) at 1:00pm EST. Follow #germchat. It’ll be like sitting at the cool kids’ lunch table, except the table is, um, full of germs.

Micro links: dirt is alive, light is a killer, and you’re breathing plant viruses

Ultraviolet light kills microbes – specifically UVC rays. Not surprising if you’ve ever laid a stinky blanket outside (or, you know, your roller derby kneepads). A new study tested UVC light on skin wounds in mice, and found that it kills germs without damaging skin cells or slowing healing. (Unanswered question: what about the good skin microbiota?) The researchers are excited about this as an alternative to antibiotics, since it’s hard to evolve resistance to radiation.

D. radiodurans - pic from Wikipedia(Well, D. radiodurans has done it, but they say they can kill that off too, if they just crank up the voltage enough. That’s D. radiodurans in the picture – it lives in a tetrad so it has four copies of DNA segmented from each other. Its DNA is packed into toroids to limit damage, and it can use the four copies to fix each other. Pretty awesome bug, famously nicknamed “Conan the Bacterium.”)

Lab tests on pesticides have been missing something big: soil microbes. A recent study on RoundUp ready weeds (that is, they are resistant to the pesticide glyphosate, which is supposed to kill weeds but leave transgenic soybeans alone) found that the plants survive better in sterile lab soil than in “field soil” with its microbes intact. One possibility: the plants are weakened by glyphosate, and pathogenic microbes take advantage.

Quote of the day, from one of that study’s authors: “Dirt is a living organism”

You’ve heard of airborne infections. Try not to think about how many germs are a single breath of air – too late, I guess. It’s like when you see sunlight streaming through a window, illuminating all the dust in its path, and realize you’re breathing that stuff in all the time. Well, scientists in Korea have done the first metagenomic analysis of the “air virome” – all the viruses that are floating around. (It turns out the most common type is plant viruses.) Maybe the air is a living organism too?

Swabbing your nooks and crannies for science

navel gazingI learned about this one through a tweet announcing that “[well-respected science writer] Carl Zimmer has weird belly button fluff.”

Don’t we all? I thought. But the story was a good one: the belly button microbiome is now being studied, and Zimmer has some unusual species in his. The project comes from the lab of Rob Dunn; you may recall that Dunn and Zimmer were two of the three authors whose books I mini-reviewed last week.1

Dunn’s area is the ecology of species surrounding people, including but not limited to microbes, and the idea behind the belly button project was to find an area of skin that should be roughly comparable between people, and not washed too often. Preliminary results, reported by Jason “Germ Guy” Tetro, suggest that we accumulate belly-button bacteria from all the places we have lived, making it “a museum of lifetime experiences.”

My belly button pops inside-out when I’m pregnant. Have I just washed off all my lifetime experiences?

This is where you come in

Cotton SwabsSixty volunteers had their navels swabbed and cultured for the project, which is now listed as “sampling complete,” but if you missed out, don’t worry – the next phase of research is about to begin: Armpit-pa-looza.

Dunn has plenty to say about armpit stink and why it’s valuable to humans, but perhaps the most astounding is that our bodies seem to deliberately cultivate stinky bacteria there (and in our crotches, sorry, genitoanal region) – feeding the critters with secretions from our apocrine sweat glands, and providing a hairy trellis for the resulting bacterial garden.

If armpits aren’t enough, you can also donate your poop to science – I mean, the website doesn’t mention poop, but what else could it be? – through the American Gut project. They are looking for diversity in their subjects, especially dietary diversity, which I think is an excellent question:

The government’s Human Microbiome Project effort sampled only healthy adults, mostly medical students! While it was an amazing project, did it really capture the American Gut? We are not sure, so we decided to find out. We are calling on athletes, couch potatoes, vegans, diabetics, Paleo dieters, centenarians etc – we need your help. If you have IBD, diabetes, autism or some other ailment – we need you too.

You know what to do. Go forth and swab thyself.

1 Obviously I foresaw this, rather than just choosing my library’s three least boring books on microbiology that weren’t checked out already. Expect Idan Ben-Barak to join the story in some further, bizarre way.

WordPress Themes