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MicroRNAs Can Activate Translation!

Wow! One of the biggest findings of the year! I'll have to read the article more carefully before I comment on it - previously, I wrote a post on the paper that led to this new discovery that was just published online in Science. Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation. Vasudevan S, Tong Y, Steitz JA. AU-rich elements (AREs) and microRNA target sites are conserved sequences in mRNA 3'-untranslated regions (3'UTRs) that post-transcriptionally control gene expression. Upon cell-cycle arrest, the ARE in tumor necrosis factor-alpha (TNFalpha) mRNA is…

Proks have dynamin like molecules!

When I was a grad student, eukaryotes had all the neatest toys ... actin, microtubules, kinesins, dynein, myosin, dynamin, SNAREs ... OK that's not totally true - bacteria had their version of tubulin (the constituent of microtubules), and it's called FtsZ. Then others found that bacteria had a version of actin, the most known is called MreB. The latest is that prokaryotes have dynamin. (Click here for previous dynamin entries.) From the paper: Given the presence of large GTPases with predicted dynamin-like domain organization in many members of the Eubacteria such as E. coli and Bacillus…

Lost years for sea turtles revealed

Researchers used stable isotopes of carbon and nitrogen on old and new parts of the shells of 44 Bahaman green turtles (Chelonia mydas) to examine changes in sea turtle diets between their juvenile and elder stages. The results indicate green sea turtles spent their "lost years' in the deep ocean as carnivores feeding on jellyfish, before moving closer to shore and switching to a vegetarian diet of seagrasses. The new research was published in the online journal Biology Letters. Karen Bjorndal led the study. She is a zoologist and director of the University of Florida's Archie Carr Center…

#scio10 preparation: A very brief proto-thought about civility.

Sometimes I think the whole question of civility and incivility (online or offline) boils down to the question of am I welcome in this space? Do you think I belong here just as much as you do? Do you think I don't really belong here? Are you going to exert the effort to run me off, or are you just going to wait until I give up and go away on my own? Do you welcome me enough that you'll tell me when I've messed up -- not because you were waiting for me to slip up, but because you respect me enough that you think I'd want to know that I'd messed up so I could fix it? Do you trust me enough to…

La Presse on the eco-sceptics' web war

Montreal's La Presse has published an article on the global warming skeptics' on-line war on science. (Google translation here.) I get mentioned: Certains vont jusqu'à accuser les éco-sceptiques d'utiliser de fausses identités dans les blogues afin de donner des voix multiples à leur opinion, en s'approuvant eux-mêmes. Le blogueur australien Tim Lambert dit ainsi avoir découvert sur son site deux commentateurs qui n'étaient qu'une seule et même personne, le blogueur torontois Stephen McIntyre, cadre de l'industrie minière à la retraite. Les responsables du site environnementaliste…

What is next-generation sequencing?

Most of the posts I've written recently have involved next-generation DNA sequencing in one way or another, which may have left some readers scratching their heads - keeping track of the different technologies, how they work, and their strengths and weaknesses is a challenge even for those immersed in this fast-moving field. Fortunately, help is at hand for readers who don't know their SOLiD from their 454. Luke Jostins (who wrote a guest post here on Genetic Future a while back) has a great new post up on his blog Genetic Inference providing some background on second-generation sequencing.…

Fake Videos Presentation

I put together this short presentation on fake videos for a class. What the heck, I will also put it online so that maybe some other people can use it. So, here it is. I have it in many forms. First, a video of me going through the talk. Then I have the keynote and PowerPoint files with the movies. Feel free to use it as you see fit. You might want to modify some of the files, I have no problem with that. How to spot a fake video from Rhett Allain on Vimeo. And the other versions: Keynote (fakevideos.key - 46.1 MB) - this has the movies embedded PowerPoint (fakevideos.ppt - 2.6 MB) -…

Powers on the Genome

Richard Powers, one of my favorite novelists, just got his entire genome sequenced and wrote about the results for GQ: I come from a long line of folks, on my mother's side, with congenital difficulty making choices. My father's family, on the other hand, are born snap deciders. This time the paternal genes won out, and half an hour after reading the invitation, I was on board. So I went shopping. A day online gave me my first taste of the bewildering range of consumer genetic products. There was Family Tree DNA, specializing in tracing genetic genealogies. There was DNA Direct, whose Web…

Diagnosing TB in developing countries

SciDev.Net's TV Padma reports that tuberculosis experts are looking to India to develop affordable TB-testing kits. An estimated four million cases of the disease go undetected, and two million TB patients die every year. India has increased its efforts at finding and treating cases of the disease, but diagnostics still present a challenge, Padma explains: TB tests come in a range. Latent infections can show up as a reaction when the protein, tuberculin, is injected under the skin. Blood tests may reveal immune molecules (gamma interferon) produced by the body to protect against the bacterium…

Holiday microscope shopping

Since Phil has suggestions for holiday telescope shopping, I have to offer some suggestions for microscope shopping. If you really want to get a kid interested in biology, a microscope is a great gift, but I'll give you the price tag right up front: $150 is probably the minimum to get a decent, low-end student scope. First, a few don'ts. Don't buy a microscope at a toy store, unless you want cheesy, cheap plastic junk. And probably the most important advice: don't judge a microscope by the highest magnification. You'll see lots of ads that shout "1500x!!!", but trust me: you can't get a good…

New FireFox plugin for 23andMe customers [Genetic Future]

Software company 5AM Solutions has just launched a neat little FireFox plug-in for customers of consumer genomics company 23andMe.  The idea is very simple: Download your raw data from 23andMe (or use one of the files from me or my colleagues at Genomes Unzipped); Install the plug-in from here and point it to your 23andMe data; Browse to a website discussing one of the genetic variants included on the 23andMe chip, and you'll see highlights around the rsID of any variant on the page (rsIDs are unique codes assigned by dbSNP to most of the common variants targeted by personal genomics…

New FireFox plugin for 23andMe customers

Software company 5AM Solutions has just launched a neat little FireFox plug-in for customers of consumer genomics company 23andMe.  The idea is very simple: Download your raw data from 23andMe (or use one of the files from me or my colleagues at Genomes Unzipped); Install the plug-in from here and point it to your 23andMe data; Browse to a website discussing one of the genetic variants included on the 23andMe chip, and you'll see highlights around the rsID of any variant on the page (rsIDs are unique codes assigned by dbSNP to most of the common variants targeted by personal genomics…

Billy Bragg podcast #3 is up

Yay! Fabulous Friday. The third Billy Bragg podcast is online now Includes the tale of the Famous Curry Incident. Hm... I wonder if that'd work on Nature Editors?

Whew...some content arrives!

Hey, you want some science? My latest Seed column on battling beetle balls is online. (And I've just arrived in Ann Arbor after a long travel day!)

Anthro Blog Carnival

The seventeenth Four Stone Hearth blog carnival is on-line at Hominin Dental Anthropology. I love that blog's name. Check it out! Archaeology anna anthropology anna boom shakalaka.

OMG! ROBERT HOOKE!

Squeeeee! I like totally love Robert Hooke, and now you can read Hooke's notebooks online. The broadband version is phenomenal — it's like leafing through the 17th century.

Links

JoVE: Journal of Visualized Experiments, an online video-publication for biological research. schlolarZ.blog, a new blog by a group of young scientists at the University of Wuerzburg, Germany.

The new Palaeontologia Electronica is here!

After a long wait, the new Palaeontologia Electronica is now online! It even includes a review of Jane Davidson's A History of Paleontology Illustration by yours truly. Check it out!

Nature Network, Tonight in Central Square

I just read in Corie's blog that Nature's new online local community (NatureNetwork Boston) is having a pub night. I'll try to be there. Click here for details.

Around ScienceBlogs

Poor, poor Ida, Or: "Overselling an Adapid" Physics in Star Trek Online social networking isn't for everyone Decoding the brain's response to vocal emotions Philosophy and evolution

Even the food is dangerous in Iraq

Not even dinner is safe in Iraq. Reports seem to agree on is that there was a mass food poisoning of Iraqi policemen on Sunday, although whether 11 died and hundreds fell ill or 7 died and hundreds fell ill or no one died but over a thousand became ill is still unclear. Authorities are saying it could have been from "spoiled food," but this is highly unlikely. The victims reportedly became ill immediately upon finishing their meals: Some collapsed as soon as they stood up from the meal, others fell "one after the other" as they headed out to the yard in the base to line up in formation, Mr al…

Nature Biotech: The Good, the Bad, & the Ugy of Blogs

I am back from an excellent science journalism conference in Denmark and will have more to say on the meeting which highlighted several issues that speak directly to challenges faced here in the US. But for now, I wanted to return to our Commentary article "Science Communication Re-Considered" published last week at Nature Biotechnology. Of particular interest to readers, we discuss the rise of science blogging as just one small part of the complex puzzle which is public engagement. There is a lot to like about blogs but there is also a lot to be cautious about. Importantly, despite great…

Greetings From the People of Earth

Greetings from the People of Earth from World Science Festival on Vimeo. I made the above video, Greetings from the People of Earth, to open the World Science Festival 2010 panel "The Search for Life in the Universe," which featured personal hero Jill Tarter, David Charbonneau, and Steven Squyres. In 1977, taking advantage of a fortuitous alignment of planets, NASA dispatched two spacecraft named Voyager into space. These probes, now the farthest human-made objects from Earth, carry with them a unique recording, the Voyager Golden Record. Compiled by a team under Dr. Carl Sagan, the Golden…

ScienceOnline'09: Interview with Peter Lipson

The series of interviews with some of the participants of the 2008 Science Blogging Conference was quite popular, so I decided to do the same thing again this year, posting interviews with some of the people who attended ScienceOnline'09 back in January. Today, I asked one of my SciBlings and friends, Peter Lipson, aka Pal MD of the White Coat Underground, to answer a few questions. Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your (scientific/medical) background? I'm a husband, dad, and internist. An…

Congratulations to danah boyd!

danah boyd was hired by Microsoft, where she will have freedom to continue her research on online social networks at Microsoft Research New England in Boston. Congrats, danah!

My car is worth more than I am!

$5175.00The Cadaver Calculator - Find out how much your body is worth Mingle2 - Online Dating Do you think I might appreciate in value as I get older? (via brokenhut)

Encephalon Haiku edition

The 51st edition of Encephalon is online now at The Mouse Trap. This time, host Sandeep has interspersed the entries with haikus about the mind and brain.

Silly Rabbit, Commodities Tricks Are For Kids

This is a little off the beaten path, but it's a silly little diversion with some classic "the press lacks numeracy skills" complaints as a bonus. Thomas Frank writing in the Wall Street Journal has written a rather wild piece - One Cross of Gold, Coming Up: How the government could get even with right-wing cranks. It's mainly in a Modest Proposal sort of vein; I don't expect he's even a little serious. Still, fun to take a look at. His proposal runs more or less as follows: 1. All those right wing cranks are hoarding stashes of gold. 2. The federal government has lots of gold in Fort…

Stock Versus Water

Michael Ruhlman says to not waste money on store bought stock: I cannot say this strongly or loudly enough: DO NOT use canned stock/broth. Use WATER instead. I repeat. You DO NOT NEED to buy that crappy can of Swanson's low sodium chicken broth! It will HURT your food. Use water instead. When that recipe says 1 cup of fresh chicken stock (or good quality canned broth), please know that your food, 90 percent of the time, will taste better if you use tap water instead of that "good quality" canned broth. Water is a miracle. Last time I was doing a recipe for a book with one of the most…

Fast from Fast Food: ‘Values of justice are faith values — they’re one in the same’

In Boston, you’re never too far away from a Dunkin’ Donuts. In fact, the Massachusetts-based company inspires a fiery sense of loyalty in many Bostonians. It’s kind of hard to give up the city's ubiquitous fast food staple, but Paul Drake is committed. “As somebody who’s pretty poor at fasting, it’s been hard,” said Drake, executive director and lead organizer at Massachusetts Interfaith Worker Justice. “Here in Boston, there’s a Dunkin’ Donuts on every corner…it’s easy to see the convenience that is fast food. But it’s actually been a really good teaching moment for me — I do this work every…

Extra, Extra

Another week, another new blog network. Go say hello to the bloggers at Wired Science. Five of the six should look familiar, if you've been around Scienceblogs for a while: Brian Switek, David Dobbs, Daniel Macarthur, Maryn McKenna, Rhett Allain and Brian Romans, joined Jonah Lehrer, who had already been there a few weeks. Science Melody Dye and I discussed psychology on the Bloggingheads Science Saturday program yesterday. The second edition of the Carnal Carnival is up at Carin Bondar's place, and the theme is vomit! Christie Wilcox tells us that, apparently, the most highly cited academic…

NC Blogging plans for the year

Foodblogging, Storyblogging, Healthblogging, Bowlging...this is turning into one busy year in North Carolina online. But Anton can't do it alone. Please participate and make the local blogosphere matter!

Online Science Discussion

Curtis, one of the founders of JeffsBench wrote a very interesting article comparing JeffsBench to PLoS ONE in their roles in fostering online scientific discussions. Register, look around and comment....

Anthro Blog Carnival

The twentieth Four Stone Hearth blog carnival is on-line at Afarensis. Check it out! Archaeology and anthropology to put a spring in your step and a glint in your eye.

Encephalon 52 online now

Encephalon 52 is online now at Ouroboros, and includes entries about grandmother cells, the neurobiology of sleep and the use of transcranial direct current stimulation to improve bad driving.

Etna Images

If you're interested in the latest eruption at Mt. Etna (Italy), here are some great images posted at Stromboli Online. Nothing like some good spatter amongst friends.

There's many a slip 'twixt spit and SNP: errors in personal genomics data

Peter Aldhous has a great piece of detective work in New Scientist, which has revealed a bizarre and sporadic glitch in the online software provided by personal genomics company deCODEme to allow customers to view their genetic data. The glitch appears to be restricted to the display of data from the mitochondrial genome (a piece of DNA with a special fascination for genetic genealogists, since it is inherited almost exclusively along the maternal line). On several separate occasions the deCODEme browser presented Aldhous with a mitochondrial profile that was spectacularly wrong, differing…

Financial Shenanigans: the Repo 105

I'm glad to report that electricity has been restored to the Chu-Carroll household. So now I'm trying to catch up. During the outage, I got a bunch of questions about the latest news coming out of the big financial disasters. A major report came out about the failure of Lehman Brothers, and one thing that's been mentioned frequently is something called repo105. The whole repo105 thing is interesting to me, not so much because of what it actually means, but because of how it's been reported. The term has been mentioned everywhere - but trying to find any information about just what the…

Another Book Meme!

June 07, 2005 and another one of those....had to change all my answers so they differ from the previous one! I got tagged by Revere to do the Book Meme. I did the Other Book Meme recently, which is similar, so this time around I have to make it different - all different titles to double your pleasure. Number Of Books I Own: Last time I was able to estimate the number of books was almost four years ago. They were neatly arranged: fiction by alphabetic order of the author in one room, non-fiction by topic in another room, sci-fi in alphabetical order in our bedroom, kids books in their rooms,…

End of whaling in Iceland

On tuesday Hvalur HF announced that the whaling ship Hvalur 9 was back in harbour and that the fin whaling season is over for the year. Seven fin whales were struck and landed, out of a quota of nine total. I want to provide my perspective on the whaling issue in Iceland and a possible political resolution: to cut a long story short, the whaling quota should be open for bids, and the whale watching companies should buy it and not use it. Whaling in Iceland has an extensive history. In Konungsskuggsj&aacute (Speculum Regale), a 13th century "advice to kings", the expected yield of whale…

A primer on federal gun law

As ScienceBlogs' resident firearms enthusiast (I might own more guns than the rest of the SB writers combined - and I don't own very many), I've occasionally written about gun rights and related issues. One of the things I've noticed is that a lot of people aren't very familiar with what gun laws actually are in the US. Here I'm going to take you on a tour of what's legal and what isn't in the US. I'll try to do so in a mostly neutral way, but for full disclosure I'd generally want to change the law in two directions - fewer restrictions on use, greater penalties for misuse. When my…

ScienceOnline2010 - introducing the participants

As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what. John Hogenesch is an Associate Professor at the University of Pennsylvania in the Department of Pharmacology where he studies a topic dear to my heart - biological clocks. I interviewed John a few months ago. At the conference, John will moderate the session on Science in the cloud and do a Demo of Social Networking and performance evaluation in scientific centers.…

Balko on Political Fallout from Gambling Bill

Radley Balko has a suggestion for Democrats on how to exploit the passage of the anti-gambling bill and I think it's sound advice: Over the last week, some 10-15 million Americans who play online poker logged on to their favorite poker sites, only to get a message telling them that, thanks to the U.S. Congress, they're no longer allowed to play. The GOP just politicized a rather large group of people who heretofore were rather apolitical. And they skew rather wealthy. Of course, we run into the same old problem: Are the Democrats any better? They ought to be. If they were smart, they'd carry…

The stupidity of ISP filtering no barrier to its implementation

The Labor government has a policy to force ISPs to filter web requests to prevent child pornography. Sounds nice in theory, but I've been using a filtered ISP at my university (they're running a trial) and what I can do online at home in one minutes takes the better part of fifteen at work. I am doing all work online at home in the mornings before I go to work, because just trying to find images for my slides is grindingly slow. Now a consultant's report gives it a tick (what else? They're being paid to), and no matter what the results, minister for communications Stephen Conroy says it will…

The Rise of Slime

Overfishing, eutrophication, acidification, and climate change are leading to what Dr. Jeremy Jackson describes as the rise of slime in the oceans. For some recent evidence, check out this invasive algae in Crystal RIver or this recent story about increase in jellyfish on the Jersey shores. According to the research published last Friday in Science, there are now more than 400 dead zones worldwide, double the number reported by the United Nations just two years ago. Ugh. A new article by Dr. Jeremy Jackson, Ecological extinction and evolution in a brave new ocean, was published early…

XKCD: the Map

One of three best XKCD ever No, you must click through to enlarge A finite fraction of my online communication now consists of "XKCD:###" where ### gives the appropriate xkcd number.

In the name of balance

I really want Dara O'Briain's sack. P.S. I think we're back online now. P.P.S. Ooops. Comments aren't working. The tech people are trying to turn those back on right now.

Where are we?

I pored over this map of online communities, and couldn't find scienceblogs! I was so disappointed. There's an obvious place for us, though: somewhere down in the bottom left corner, around Sulawesi.

Killer Virus Sequence Published

Within a few days of the completion of the on-line draft of Sungudogo: A Novel, scientists have published the key data describing a killer H5N1 virus. Coincidence? I would assume so. But still....

MORE CONTEXT ON THE INHOFE HYPE: CJR Daily References Framing Science as Source in Reaction to Senator's Attack on the Messenger

Last week, the online news section of the Columbia Journalism Review ran this very useful reaction to Senator Inhofe's attack on journalists covering global warming, referencing the analysis posted here.