Life on Mars

For those of you who are wondering what became of me — in 2012 I left the lab; since then, I’ve been working as a scientific language editor and developing two book proposals (including one about the biology of aging). Blogging here at Ouroboros was a joy, and I hope to get back to it someday.

At the moment, my main online activity is the new blog Life on Mars, which describes my ongoing participation in the Mars One Project, an audacious effort to send a human crew to Mars by 2025. As it matures, the blog will encompass an increasing number of topics, ranging from Mars One news to new science about Mars and planetary exploration in general. (For those of you who prefer Facebook, I have a page there too: A Biologist on Mars, and I also provide various Mars-related updates on Twitter as @DoNotGoGently.) Feel free to stop by and say hello!

 

 

 

Bay Area Aging Meeting, December 4th 2010

(For the liveblog of the meeting as it unfolds, see here.)

Earlier this year, the biogerontologists of the San Francisco Bay Area held the first of a series of biannual research meetings, the Bay Area Aging Club. More or less right on schedule, the next meeting is in a couple of weeks on Saturday, December 4th.

It’s now the slightly more official-sounding Bay Area Aging Meeting, but the format is the same: A full day of talks from labs from all around the Bay Area, with lunch, and an opportunity to network with the large and growing local community of researchers in biogerontology and allied subjects. Last time the meeting was at UCSF; this time it’s at Stanford.

Here’s the initial event announcement from Stuart Kim. Note the registration link, which contains more detailed information about time and location. Registration is free.

Eric Verdin (Gladstone), Danica Chen (Berkeley) and I are organizing the next Bay Area Aging Meeting. This is a one day meeting to hear talks from students and post-docs from the Bay Area on aging. The meeting is on Saturday Dec. 4, 2010 at Stanford University, from 900 am to 5 pm. The last meeting in April at Gladstone was very successful with about 150 attendees.

There will be talks from students/post-docs in Bay Area Aging labs, as well as a poster session. The labs and topics are:

lab/topic
Brian Kennedy (Buck) Yeast aging
Simon Melov (Buck) worm aging
Martin Brand (Buck) mitochondrial biochemistry
Melanie Ott (Gladstone)SirT1 in T cells
Bob Farese (Gladstone) mouse metabolism
Cynthia Kenyon (UCSF) worm aging
Hao Li (UCSF) systems biology of yeast aging
Kunxin Luo (Berkeley) P53 and aging
Randy Schekman (Berkeley) intracellular traficking of APP
Anne Brunet (Stanford) mouse, worm or fish aging
Tom Rando (Stanford) stem cells and aging
Mark Davis (Stanford) human immune aging

Please reserve the day for the meeting. We will send out more information including the schedule soon. To receive more information about the meeting, register for the meeting, and sign up to give a poster, please go to:

https://www.onlineregistrationcenter.com/register.asp?m=288&c=2

Sincerely,
Eric, Danica and Stuart

The April meeting was a lot of fun. I live-blogged the event, which definitely kept my fingers flying. This year I’ll be doing that again, with some degree of official blessing/support. We’ll make some kind of an announcement at the beginning of the talks directing people to Ouroboros and encouraging them to participate in comments on the posts for each session or talk. I’ll also be spreading the word Twitter and/or FriendFeed, using hashtag #baam10, and hoping that others join in that as well.

Please come! The organizers want to reach “hard core aging people,” so if your research falls under that umbrella, register now. For a sense of how the meeting went last time, here are my posts:

• Session I: Model organisms & model systems
• Session II: Sirtuins; telomeres
• Session III: Calorie restriction; protein aggregation
• Panel discussion: Free radical theory of aging

P.S.: There’s no official website for BAAM yet. I’m thinking of whipping something up for them – basically for announcements and abstracts – but if anyone with experience would like to pitch in, drop me a line in the comments.

 

Reflect: Linking protein names to rich content, as you read

Continuing with my current fascination with cool ways to enhance the experience of searching and engaging the literature online…

Deepak Singh at business|bytes|genes|molecules tells us about Reflect, a new tool for adding value to online articles:

Essentially, Reflect is an entity extraction engine with a specific purpose, recognizing molecular entities, both compounds and proteins. I have spoken at length about the value of entity extraction, and the availability of a service like Reflect just shows you how useful something like this can be. Using either the Reflect website where you can enter a URL, or the Firefox plugin, you can use extract molecular entities on a webpage quite easily. The service highlights recognized entities, and using your mouse you can get additional details as shown in the screenshot below.

Reflect identifies the names of proteins/genes or small molecules that appear in a body of text and generates a live link to a floating window containing informations (and further linkage) about that entity.

You can check it out at the Reflect website.

I had a lot of fun plugging in blog posts from Ouroboros and seeing what Reflect thought of them. It did a great job with genes and a fairly good job with small molecules, though the higher false positive rate in the latter case was a little disappointing (identifying words as small molecules that weren’t, and linking to things that aren’t small molecules at all, like the word “reset” that appears in a graph about something else).

(P.S.: By the way, Reflect was the winner of the Elsevier Grand Challenge, and its development may have been motivated by the incentive of the prize. In light of that, I just want to clarify that I still think Elsevier is the devil.)

Update: The developers of Reflect have a preprint up at Nature Precedings. Thanks to Hilary Spencer for the heads-up.

 

Science radio for scientists

There are a number of good science-related shows on Public Radio: Science Friday, Radiolab, and Tech Nation top my personal list, and there are many others. This type of programming is an important means of disseminating scientific ideas to a general audience, and as I scientist I think I enjoy the shows more than the average listener. Still, I often find myself wanting more: more detail, more description of methods and controls used to obtain results, more erudite discussion about the context of a given finding within the larger edifice of scientific inquiry. More.

So it’s been with great satisfaction that I’ve discovered several podcasts administered by scholarly journals:

• Nature Podcast
• Science Magazine Podcast
• Science Signaling Podcast (registration required)

This is “science radio” but with a twist: the intended audience is us. The producers aren’t targeting a general audience, and as a result they’re free to include highly technical content. Especially with the Science Signaling podcast, which often involves an interview with the author of a recent paper featured in STKE, the stories sound more like a lab group meeting than a radio show.

Granted, this comes at a cost: the journal podcasts have high production values but not quite as high as on general-audience NPR shows, and sometimes the phone interviews sound like they were conducted underwater, making it harder to listen in noisy environments like a car moving at 70 MPH down a California freeway.

But that’s a small price to pay. This is exciting! Podcasting is democratizing broadcasting to the extent that people are creating high-quality professional programming for a small minority of people diffusely scattered all over the world.

What are you waiting for? Check it out. All three of the podcasts I’ve mentioned are available (for free) via iTunes and the websites linked above

Two questions:

1. Does anyone else have a science-for-scientists podcasts they’d like to share?
2. When will an open-access journal step up to the mike?