Sunday, September 30, 2012

Ben Goldacre

Ben Goldacre,
This week I've read a couple of pieces by Ben Goldacre, a doctor who writes a regular column called "Bad Science" in The Guardian and has written columns for The British Medical Journal, among other rags. The excerpt from his book Bad Pharma, called "The drugs don't work: a modern medical scandal" is good. Even more approachable, and somewhat broader in its target, is his TED video from this summer, "What doctors don't know about the drugs they prescribe".

In both the excerpt and the TED talk, he uses a case where he, a doctor probably more careful than most, was misled into prescribing a drug later shown to be not only ineffective, but harmful.

Two of my favorite science writers, Ed Yong and Carl Zimmer, got me reading Goldacre.

The Short List (29 Sept 2012)

Ed Yong's "Missing Links" list this week was short (nearer 60 than 100+), because he was traveling. My favorites from his list are all photos or short videos.

Ed Yong at Not Exactly Rocket Science

Some videos and photos (with and without text)
WOW! Watch from INSIDE a mussel’s shell, as a starfish shoves its stomach in and starts digesting [Rusten: fascinating in spite of the hyperdramatic Peter Coyote voice-over]
Hummingbirds are just as efficient when flying backwards or hovering forward. [Rusten: not exciting video, but amazing how utterly stable their flying is in different wind conditions]
A hummingbird skeleton  next to an elephant bird femur [Rusten: Wikipedia for elephant bird]
Drones. Crap. [Rusten: I liked the third video on tiny bot swarms. Hadn't seen the toy, armed drone helicopter.]

Friday, September 28, 2012

Friday Bits

Here are a couple of stories that appeared today, one semi-technical, the other not technical at all.

Ed Yong, "Thanks to one gene, this fly needs a cactus to escape Neverland"
Without feeding on the Senita cactus, a Sonoran desert fly can't transform from larva to adult.
Story teaser:
In North America’s Sonoran desert, there’s a fly that depends on a cactus. Thanks to a handful of changes in a gene called Neverland, Drosophila pachea can no longer make chemicals that it needs to grow and reproduce. These genetic changes represent the evolution of subservience – they inextricably bound the fly to the senita cactus, the only species with the substances the fly needs.

Robert Krulwich, "The Best College Prank Of The 1790s (With Bats, Poop & Grass)"
A simple story of a bit of eco-terrorism (ok, my anachronism, not his) over 200 years ago carefully designed to help introduce British gardeners to the wonders of guano. (With illustrations by Benjamin Arthur.)
Story teaser:
When William Buckland was a kid, an undergraduate at Oxford in the late 1790s — around the time George Washington had just finished being President — he pulled a prank that was so rude, so smart, and so biologically sophisticated for his day, I think he deserves a second crown, this one for Best Use of Grass Ever.

Tuesday, September 25, 2012

Why's this so good?: Banaszynski

[from Nieman Storyboard]
The whole "Why's this so good?" series at the Nieman Storyboard is a great resource for writers. But Jacqui Banaszynski's contribution, "No. 36: Alice Steinbach and one boy's vision", on Steinbach's Pulitzer Prize-winning 1985 piece, "A Boy of Unusual Vision" in the Baltimore Sun (PDF) is magnificent.

In fact, Banaszynski's whole reading list for her Intermediate Writing class, which you can find on the Nieman Storyboard's What's on your syllabus? page, would, with her annotations, be a great way to remind oneself of what writing can be.

Banaszynski won her own Pulitzer for Feature Writing in 1988 "for her moving series about the life and death of an AIDS victim in a rural farm community" in the St Paul Pioneer Press and Dispatch, titled "AIDS in the Heartland" (PDF).

The Pursuit of Balance

A nice little post at The Last Word on Nothing reminded me of the ever-changing cairn garden near one of the old lime kilns in the Pogonip near UCSC. The photo at left, taken in the fall, doesn't have enough contrast to do the cairn-builders justice. The cairns are always changing, sometimes incorporated into mazes, sometimes riding the limbs of surrounding trees as well as inhabiting the ground.

Follow the links in Nijhuis's post to more wonderful balanced stone sculptures. The beautiful, fanciful, and sometimes astounding ones by Adrian Gray were new to me.
I recommend going to his site and watching the two BBC videos of Gray working with stones on the beach. Goldsworthy, less a rock-balancing specialist, is always amazing.

Michelle Nijhuis, "The Pursuit of Balance"
Top of the story:

My neighborhood, as I've mentioned, is an interesting place: At our weekly potlucks, we speculate on everything from the number and sex of the next batch of goat kids (money's on two girls) to the efficacy of bourbon as mouthwash (not promising, sadly). Last week, a guest announced that he was on his way to a stone-balancing celebration in Flagstaff, Arizona. Was this a competition, we asked? No. Just a bunch of people stacking stones? Well, yes, but it's more fun than it sounds. Do you leave the stacks for other people to find? Yup.

"Just Google it," he finally said, giving us a beatific smile.

So I did, and found that yes, a bunch of people gathered in Flagstaff this past Sunday to stack stones. It seems to be habit-forming: this was the third international gathering of stone balancers, and balancers have even written an "Art Manifesto of Stone Balance" with ethical guidelines. (No glue, no bolts, no wires. Just gravity.) For some, such as artists Adrian Gray and Andy Goldsworthy, stone balancing is high art. For others, it's a meditative practice or just a prankish pastime ...

[Photo in Nijhuis's post from Flickr user jayul.]

Monday, September 24, 2012

Plants Are Cool, Too!

Botanist and biodiversity scientist Chris Martine at Bucknell University has begun an online project called "Plants Are Cool, Too!" to spur interest in plants as part of understanding biodiversity. The first two in a series of roughly 15-minute videos are out on YouTube (PlantsAreCoolToo) and highlighted in a little promo piece from Bucknell, "The dawn of adventure biology". In each video, Martine goes into the field with folks who are exploring the world of plants and their histories. They're well done and worth watching.

The first episode, on "The Pale Pitcher Plant", explores its ecological setting in the Southeastern US and dissects its "stomach" to show both how it collects the insect food it needs in a soil-nutrient-poor habitat and how other critters collaborate in breaking down those unfortunates the plant has trapped.

The second episode, on "Fossilized Forests", heads to Clarkia, Idaho, and a set of sediments where leaves were trapped 15 million years ago at the bottom of an inland lake created when lava flows blocked a river. The leaves aren't just fossils. They're the actual leaves that can still be lifted from the sediments. Their structure and color have been preserved, and folks are trying to recover their DNA.

Saturday, September 22, 2012

Mystery in the Fields

An intriguing three-part series "Mystery in the Fields" by Sasha Chavkin and Anna Barry-Jester reports that a mysterious and deadly form of chronic kidney disease is killing tens of thousands of young farm workers from Sri Lanka and India to Central America. There are clues that may link all of the cases, but researchers remain uncertain.

The impressive investigative project, part of it done in collaboration with PRI's The World, includes the three stories, helpful infographics, a photo slideshow, and two short videos by Anna Barry-Jester.

The stories as listed on the project website:

Ed Yong pointed out the first of these stories in his weekly "Missing Links" post at Not Exactly Rocket Science: "A mysterious kidney disease is killing young farm hands continents apart. Is there a connection?"

Corruption & Manipulation in a GM Story

Handling of a recent story about GM crops and health raised questions about science writing, integrity, and skepticism. Science journalists called out some of their colleagues and those who tried (and, in some cases, managed) to manipulate them. Lots of discussion of this case among science writers. Other folks may find the tale interesting as well.

First a link to Deborah Blum's post at Knight Science Journalism Tracker:

"A rancid, corrupt way to report about science"
Top of the story:
The quote in the headline on this post comes from Carl Zimmer's blog, The Loom, in a commentary on coverage of recent European study on possible health effects of eating GM crops. To give you the short version, the study authors appear to have practiced some very questionable science and some - and cynical - manipulation of the science media.

And then the story as outlined very briefly by Ed Yong in this week's "Missing Links" post at Not Exactly Rocket Science:

Lots of panicked headlines this week about GM-corn that supposedly led to tumours in lab rodents. The study’s incredibly weak – here’s an incisive analysis by SciCurious and another good one by Deborah Mackenzie at New Scientist. And here’s the real headline: reporters were prevented from even seeking outside opinions about the paper. Not only weak science but an absurd use of the embargo system.

Dew-Covered Insects (photos)

Thanks to Ed Yong for including a link to this wonderful set of photographs in his weekly "Missing Links" post at Not Exactly Rocket Science:

Macro Photographs of Dew-Covered Dragonflies and Other Insects by David Chambon

Here are just three images (reduced in size) to give you a taste of what you'll find on the site itself. And follow the links on the site to many more by Chambon and other photographers.



Thursday, September 20, 2012

The Birth of the New, The Rewiring of the Old

This is a nice update from Carl Zimmer at The Loom on a (now) 24-year-old experiment, explaining something "weird" that happened in one of the serial cultures 4 years ago: the appearance and then improvement of citrate-eating E. coli in one of the flasks. "World domination soon follows."

Carl Zimmer, "The Birth of the New, The Rewiring of the Old"

Top of the story:
The Birth of the New, The Rewiring of the Old
  In 1988, Richard Lenski, an evolutionary biologist now at Michigan State University, launched the longest running experiment on natural selection. It started with a single microbe–E. coli–which Lenski used to seed twelve genetically identical lines of bacteria. He placed each line in a separate flask, which he provisioned with a scant supply of glucose. The bacteria ate up the sugar in a few hours. The next day, he took a droplet of microbial broth from each flask and let it tumble into a new one, complete with a fresh supply of food. The bacteria boomed again, then starved again, and then were transferred again to a new home. Lenski and his colleagues have repeated this procedure every day for the past 24 years, rearing over 55,000 generations of bacteria.

I first reported on Lenski's experiment 12 years ago, and since then I've revisited it every few years. The bacteria have been evolving in all sorts of interesting ways, and Lenski has been able to reconstruct the history of that evolution in great detail, thanks to a frozen fossil record. Every 500 generations Lenski and his students sock away some bacteria from each flask ...

One way to skin a cat

Nice story from Ed Yong on gene interactions in coat patterning. Beautiful photo, a good explanation of coat pattern genetics and protein diffusions, and even a Java applet of Turing reaction-diffusions to play with. In the story, Ed links to a previous story of his (which I think I sent) on pattern mixing in fish that included this classic image:

But back to today's story:

Ed Yong, "One way to skin a cat – same genes behind blotches of tabbies and king cheetahs"

Top of the story:
The cheetah's spots look like the work of a skilled artist, who has delicately dabbed dots of ink upon the animal's coat. By contrast, the king cheetah – a rare breed from southern Africa – looks like the same artist had a bad day and knocked the whole ink pot over. With thick stripes running down its back, and disorderly blotches over the rest of its body, the king cheetah looks so unusual that it was originally considered a separate species. Its true nature as a mutant breed was finally confirmed in 1981 when two captive spotted females each gave birth to a king.

Two teams of scientists, led by Greg Barsh from the HudsonAlpha Institute for Biotechnology and Stephen O'Brien from the Frederick National Laboratory for Cancer Research have discovered the gene behind the king cheetah's ink-stains. And it's the same gene that turns a mackerel-striped tabby cat into a blotched "classic" one.

Back in 2010, Eduardo Eizirik, one of O'Brien's team, found a small region of DNA that seemed to control the different markings in mackerel and blotched tabbies. But, we only have a rough draft ...

A couple of images ...

... and brief explanations from a Facebook page I follow: I f**king love Science. I've followed each image with a link to a site with more images and more explanation.

For the inhabitants of Singapore this bizarre yet spectacular sight took a while to get used to. Architects have designed 18 synthetic 'supertrees' which, for the last few months have been acting as thermal storage systems and providing sha
de and nutrients - just like natural trees. Their shape allows them to collect rainwater and they're equipped with solar panels to store energy from the sun. A sophisticated system of channels, similar to the roots of a tree, ensures that all 200 plant species cultivated inside the supertrees are regularly watered.

[Rusten: Here's a CNN story with a nice photo gallery of the park: "Solar-powered 'supertrees' breathe life into Singapore's urban oasis"]
When underwater photographer Yoji Ookata discovered these bizarre geometric sand circles off the coast of Japan, he was understandably pretty confused. 
After returning to the site with colleagues and a television crew, they worked out that they're being made by male puffer fish. It's thought to be a 'display' to attract females and/or a shield to neutralize ocean currents that could pose a threat to their young.

[Rusten: Here's a site with a bit more detail: "The Deep Sea Mytery Circle - a love story"]

The Sweetness of Human Evolution

"The Sweetness of Human Evolution" is a lovely piece by Heather Pringle at The Last Word on Nothing on the honey-passionate Hadza in Tanzania ... though I want to know more about the interactions of the Hadza, the honeyguide bird, and the honey badger. So, below the "Top of the Story" bit, I've put a couple of links to YouTube videos that show some of the interactions.

Top of the story:
Quite by accident last week, I came across something, an ethnographic detail really, that captured my imagination, and that has clearly delighted and puzzled anthropologists and even contributed to a new theory of human evolution. The detail concerned the Hadza, 1000 or so modern hunter-gatherers who speak an ancient click language and who live in the woodlands around Lake Eyasi, Tanzania, not far from Olduvai Gorge.

The Hadza, as I discovered, prize honey above all else in their diet. Hadza mothers wean their young on liquid honey, and during the wet season, particularly the months of February and April, Hadza families gorge for weeks on its sticky sweetness.  The men possess an expert knowledge of bees and bee behavior, giving the honeys produced by different species different names. Those who forage for honey figure prominently in Hadza mythology.

And there is indeed something almost magical about the way that Hadza collect honey.

While out hunting, the men listen for the call of a small, robin-size bird known as the greater honeyguide (Indicator indicator). The bird dines almost entirely on beeswax and bee larvae, but it needs help to crack open hives. So the honey guide calls to both honey badgers and Hadza hunters ...

[Rusten: as promised, some video links to follow up on that last suggestion of interaction.]

Attenborough did a bit on the human-honeyguide interaction in Kenya:

BBC Talking to Strangers: honey birds
Believe it or not, also called honeyguides, these birds communicate with humans....

And here's a bit bringing in the honey badger:

Tuesday, September 18, 2012

Will we ever… photosynthesise like plants?

An excellent piece by Ed Yong on just how complex photosynthetic symbiosis is: Will we ever… photosynthesise like plants?

Top of the story:

Will we ever… photosynthesise like plants?

Here's the tenth piece from my BBC column

Humans have to grow, hunt, and gather food, but many living things aren't so constrained. Plants, algae and many species of bacteria can make their own sustenance through the process of photosynthesis. They harness sunlight to drive the chemical reactions in their bodies that produce sugars. Could humans ever do something similar? Could our bodies ever be altered to feed off the Sun's energy in the same way as a plant?

As a rule, animals cannot photosynthesise, but all rules have exceptions. The latest potential deviant is the pea aphid, a foe to farmers and a friend to geneticists. Last month, Alain Robichon at the Sophia Agrobiotech Institute in France reported that the aphids use pigments called carotenoids to harvest the sun's energy and make ATP, a molecule that acts as a store of chemical energy. The aphids are among the very few animals that can make these pigments for themselves, using genes that they stole from fungi. Green aphids (with lots of carotenoids) produced more ATP ...

Saturday, September 15, 2012

Favorites from Ed Yong's Picks (15 Sept 2012)

Fewer meaty stories this week caught my attention among Ed's picks. Some good photos and shorter pieces, though. I especially love the Google Earth fractals.

Ed Yong at Not Exactly Rocket Science

Stories, Mostly Short This Week

On the trail of a weird and wonderful mammal, the Pyrenean desman
Eagle regains ability to preen & drink w/ 3D-printed prosthesis. [Rusten: The sequelae to the prosthesis are interesting. Not a simple story.]
Awesomeness: How to boil water without bubbles
This Ewen Callaway piece on the genetics of tasting coriander features anti-coriander haikus and a recipe.
Deaf Mexican police officers tasked w/ monitoring security cameras; not recruiting disabled ppl, but “super-able”. Great Vaughan Bell piece.
Tiger tiger burning bright, avoiding humans in the night. Very cool study, covered by Bora Zivkovic.
This is a really sensible way of looking at whether electronics on flights are dangerous. Kudos to Dan Simons and Chris Chabris

Some photos (with and without text)

Winners of the 2012 British Wildlife Photography Award. Those GANNETS!
Mmmm… natural fractals as seen through Google Earth [Rusten: Go to the Google Earth Fractals site for more.]
 Jumping spider turns assassin bug into assassinated bug

Rob Dunn on Leaves

Rob Dunn has a lovely new piece in The National Geographic on leaves. Rob manages to pack rich detail into a short piece in language filled with grace and vitality.

Rob Dunn, The Glory of Leaves

[Rusten: Here's the top of Rob's story.]

We have all held leaves, driven miles to see their fall colors, eaten them, raked them, sought their shade. Since they are everywhere, it’s easy to take them for granted.

But even when we do, they continue in their one occupation: turning light into life. When rays of sunlight strike green leaves, wavelengths in the green spectrum bounce back toward our eyes. The rest—the reds, blues, indigos, and violets—are trapped. A leaf is filled with chambers illuminated by gathered light. In these glowing rooms photons bump around, and the leaf captures their energy, turning it into the sugar from which plants, animals, and civilizations are built.

Chloroplasts, fed by sun, water, carbon dioxide, and nutrients, do the leaf’s work. They evolved about 1.6 billion years ago when one cell, incapable of using the sun’s energy, engulfed another cell—a cyanobacterium—that could.         ...

Two by Ed Yong

Ed Yong always brings even simple stories alive with an interesting twist, an analogy, or just good writing. Here are links to two of his stories from late this week ... with a taste of each.

Ed Yong, Why type 2 diabetes is a bit like The Bourne Identity
Why type 2 diabetes is a bit like The Bourne Identity
In The Bourne Identity, the eponymous hero is presumed dead by his former employers, but turns out to have merely lost his memory. Thus unburdened, he attempts to change his fate.

Which reminds me of diabetes.

People with type 2 diabetes face two problems, both related to insulin – the hormone that regulates the levels of sugar in our blood. They don't respond properly to it (they become insulin resistant), and they don't make enough of it. As a result, the levels of sugar in their blood become too high. Insulin resistance is fairly steady throughout a person's lifetime, but the failure to make insulin gets progressively worse. The typical explanation is that the beta-cells – a type of insulin-making cells within the pancreas – die off.

But Domenico Accili from Columbia University has a different idea. By studying diabetic mice, he has found beta-cells do indeed disappear over time, but not because they die. Instead, they revert back to a more basic type of cell that doesn't produce insulin. Like Jason Bourne, they lose their former specialised identities and become more of a tabula rasa. In the film, it's simple memory ...


Ed Yong, Why do killer whales go through menopause?

Here's yet another reason why humans are weird: menopause. During our 40s, women permanently lose the ability to have children, but continue to live for decades. In doing this, we are virtually alone in the animal kingdom. From a cold evolutionary point of view, why would an animal continue to live past the point when it could pass on its genes to the next generation? Or put it another way: why don't we keep on making babies till we die? Why does our reproductive lifespan cut out early?

One of the most popular explanations, first proposed in the 1966, involves helpful grandmothers. Even if older women are infertile, they can still ensure that their genes cascade through future generations by caring for their children, and helping to raise their grandchildren.* There's evidence to support this "grandmother hypothesis" in humans: It seems that mothers can indeed boost their number of grandchildren by stepping out of the reproductive rat-race as soon as their daughters join it, becoming helpers rather than competitors.

Now, Emma Foster from the University of Exeter has found similar evidence among one of the only other animals that ...

Three by Krulwich

There's something so gentle and generous about Robert Krulwich's pieces. Not always packed with information, but provocative little hints about different ways of looking at the world. Here are three of his pieces from this week ... with just a taste of each. Follow the links to the full stories.

Robert Krulwich, The Miracle Of The Levitating Slinky

[Rusten: Top of the story follows. Several embedded videos in the piece.]

I should say right off, this is no miracle. The Slinky I'm going to show you does what all Slinkys do, even if it seems so astonishing, you figure, "Oh, come on. Somebody doctored this footage. This can't be."
It can be. It is. Nobody manipulated anything.
Here's what's going to happen. Derek Muller from the Australian science video website Veritasium is going to take a slinky and hold it from the top with his hand. He will then release the lower part. It will slink down to its full extension, elongating, and come to a dangling rest.
Then Derek is going to let the Slinky go. Now comes the miracle. If you keep your eye on the bottom of the slinky, on the last curl at the very end, you will notice that as the top of the slinky starts to fall, the bottom doesn't drop. It just hangs in the air, levitating, as if it had its own magic carpet. It will stay there, hovering quietly, until a wave, or signal, passing through the slinky finally reaches it. Apparently, the bottom doesn't know it's supposed to fall, so it sits there, seeming to defy gravity, until the very end ...


Robert Krulwich, That Old Rice-Grains-On-The-Chessboard Con, With a New Twist

[Rusten: Top of the story follows. This piece has several Krulwich drawings.]

Once upon a time, says the science writer David Blatner, there was this con man who made chessboards for high-end clients — in this case, a king.
The craftsman was good; his chessboards were better than beautiful. The king, he knew, loved chess. So he hatched a plan to trick the king into handing over an enormous fortune. His plan? He figured, "This king is not too good at math."
So when the craftsman presented his chessboard at court, he told the king,
"Your Highness, I don't want money for this. Or jewels. All I want is a little rice."
"Hmm," thought the king, who was a con man himself. "I've got rice. How much rice?" ...

Robert Krulwich, Odd Things Happen When You Chop Up Cities and Stack Them Sideway

[Rusten: Instead of giving you the top of this story, I'll just give you two images of Berlin: an overhead depiction of the size and shapes of building plots, and those same plots arranged "after an autopsy. The city has been dismembered, dissected block by block, the blocks then categorized, sorted and stacked by shape". Krulwich compares these with similar images of other major cities, like Paris, New York, and Istanbul ... with his usual, interesting take on the project that produced these. All of the images in the piece are larger, of course.]

Berlin from above.                           Berlin in parts.