The Decision Tree: Thomas Goetz’s upcoming book on predictive/personalized medicine

In the past months Thomas Goetz begun writing a book on the radical changes already ongoing but mostly upcoming in healthcare due to affordable new technologies and quantitative approaches in personalized genomics and medicine.

The book is to be called The Decision Tree (explanation below) accompanied by a new website. Thomas is the perfect man for this job, he is the deputy editor of Wired magazine (=he is well informed and connected), a good journalist who took his job (writing on science, health and medicine) so seriously that he went back to school to get a degree in Public Health. Back in the days his very early coverage on 23andMe (actually published before the official launch of the service) was actually the only serious insight on 23andMe.

With this book Thomas will have a chance to become the Chris Anderson or Malcolm Gladwell of personalized medicine and public health.

“The premise is that we are at a new phase of health and medical care, where more decisions are being made by individuals on their own behalf, rather than by physicians, and that, furthermore, these decisions are being informed by new tools based on statistics, data, and predictions. This is a good thing – it will let us, the general public, live better, happier, and even longer lives. But it will require us to be stewards of our health in ways we may not be prepared for. We will act on the basis of risk factors and predictive scores, rather than on conventional wisdom and doctors recommendations. We will act in collaboration with others, drawing on collective experience with health and disease, rather than in the isolation and ignorance that can come with “privacy” concerns. And we will act early, well before symptoms appear, opting to tap the science of genomics and proteomics in order to mitigate our risks down the road.

Together, these tools will create a new opportunity and a new responsibility for people to act – to make health decisions well before they become patients. This can be characterized as a decision tree, a series of informed choices we will make to minimize uncertainty and optimize our outcomes. Indeed, we will use decision trees to navigate most of our health decisions, sometimes in overt ways – new decision support tools will both inform us and guide us, and they’ll be steeped in statistics, prediction, and the power of collective experience.”

Nature Personal Genomics Very Special

The newest Nature issue concentrates on personal genomics and its consequences via many types of articles some of them with free access.

I only read 1 piece so far by Erika Check Hayden, who has the exclusive freedom at Nature to always pick the best stories and write on any of them, but being a heavy 23andMe user I was instantly reminded again on the program Promethease with which I can extend the interpretation of my data with an approximately 2 hour run.

According to two commercial gene-testing services — 23andMe and deCODEme — US Army medic Timothy Richard Gall of Fort Belvoir, Virginia, has a higher-than-average risk of basal cell carcinoma, type 2 diabetes and psoriasis. But much more enlightening than these results, which cost Gall more than $1,400, was a free online program called Promethease that he used to further analyse the data. By offering more in-depth information and interpreting of more of his genetic variants, Promethease “gives a much more realistic view of the usefulness of the information”, Gall says. Start-ups and services such as Promethease are now developing ways to improve the limited value of information provided by personal genomics companies for consumers and scientists alike.

Petabyte Age Wiredesque lesson on what science can learn from Google

I argued many times here that biology based biotechnology is the next information technology but in order to do so, biotech should harness good IT patterns and mimic its massive computing practices to handle the enormous amount of constantly accumulating data. Often this trend could be summarized in a simple way: keep your eye on Google and conduct thought experiments in advance in which science is done in a Googleplex like environment in terms of the computing & financial resources and algorithm heavy engineering culture. Use Python and learn cluster computing and MapReduce. With the expected launch of the massive scientific dataset hosting Google service – nicknamed Palimpsest – this year finally a direct interface between scientists and Googlers emerges and hopefully opens up possibilities for scientists to cooperate with Google. (Remember my joke on Google BioLabs back in 2006)? I get emails from biologists, bioinformaticians asking me how to be hired by Google ever since then. As I tweeted yesterday: I growingly have the impression that “being ambitious” today = ‘worked, is currently working, is going to work at/for Google’ Taking Google’s inter-industrial power into consideration I see a real chance that some day the “Google of Biotechnology” title goes not to a startup yet to be emerged, not to Genentech or to 23andMe but……to Google itself. No kidding here. Fortunately Google’s model is “to build a killer app then monetize it later” says Andy Rubin, the man behind Google’s Android mobile software in the July issue of Wired so scientists working for the big G probably won’t have to worry about turning their scientific killer app into an instant cash machine.

And now in the very issue of Wired magazine (not online yet ) there is an exciting cover story on the same pattern I talked about concerning the life sciences but in the broader context of every kind of science with the provocative, Fukuyama-like title The End of Science. There is a witty and short essay from editor-in-chief Chris Anderson entitled The End of Theory followed by examples of the ‘new science’ like the The Large Hadron Collider expected to generate 10 petabytes if data/second, The Sloan Digital Sky Survey heaven catalog maker accumulating 25 terrabytes of data so far, the skeleton scanning project of Sharmila Majumdar and the Many Eyes project “where users can share their own dynamic, interactive representations of big data”.

For many people around the globe, Chris Anderson is a freeconomist & the author of a popular airport book but fewer people are aware that he was actually trained as a (quantum) physicist and even worked at Los Alamos

80 is the new 50 so Carl Icahn has a blog without content.

Billionaire investor Carl Icahn (72) recently made the bloglines with his energetic position on the Microsoft – Yahoo deal. He has a blog too or at least it is coming soon since 01/31. /Having a blog for more than 3 months without any content is kinda equivalent with planning to sign up for Twitter but actually not doing it./

Daniel Gross, Newsweek: Eighty Is the New Fifty

“Carl Icahn has a blog (though it doesn’t contain any content)”….

“In time, it’s likely that prejudices toward older workers will be eroded less by the exploits of eternally youthful financiers, and more from a longstanding demographic trend. As they’ve moved through life, the baby boomers have altered societal attitudes on everything from smoking marijuana to Botox. As boomers coast into their golden years, it’s likely the acceptance of older workers at every rung of the corporate ladder will grow. In the 1960s, the boomers’ mantra was: don’t trust anyone over 30. In the 2010s, it’ll probably be: don’t trust anyone under 70.”

SciBX trial edition for May 22, 2008

from my mailbox:

Science-Business eXchange aka SciBX is a new publication from the makers of Nature and BioCentury that aims to improve the translation of today’s science into tomorrow’s products for the diagnosis, treatment and prevention of disease.

Puzzle: Which Wired article is cited in Nature Biotechnology?

Nature Biotechnology is the (peer review) journal for me: it’s geeky, fresh and it takes into account more than just one point-of-view, that of the scientist-academist’s: technology & business are hand in hands also. (Recommending Nat Biotech makes a niche sense here while recommending Nature, which is actually the only science journal I’m reading issue by issue is hm… too obvious)

But Nature Biotech goes as far as citing even a non peer review journal – I am also pretty familiar with – called Wired.
So my puzzle is /please use your contextual knowledge first & just then your typing skills while thinking of an answer/: which Wired article is cited in a March Nature Biotech News and Views article (very good, by the way) named Synthetic genomes brought closer to life by Robert A Holt amongst strict science articles. Don’t think too high, it’s rather a reflection.

Here is a little help:

What you get when you multiply the same ideas by different inventors!

Malcolm Gladwell has a nice, but a bit Microsoft heavy essay on scientific/technological multiples, ie. the phenomenon of simultaneous discovery in New Yorker: In the Air

Gladwell argues that it is always misleading to apply the paradigm of artistic invention to scientific/technological invention and he is probably right.

Two sections just for your appetite:

“This phenomenon of simultaneous discovery—what science historians call “multiples”—turns out to be extremely common. One of the first comprehensive lists of multiples was put together by William Ogburn and Dorothy Thomas, in 1922, and they found a hundred and forty-eight major scientific discoveries that fit the multiple pattern. Newton and Leibniz both discovered calculus. Charles Darwin and Alfred Russel Wallace both discovered evolution. Three mathematicians “invented” decimal fractions. Oxygen was discovered by Joseph Priestley, in Wiltshire, in 1774, and by Carl Wilhelm Scheele, in Uppsala, a year earlier. Color photography was invented at the same time by Charles Cros and by Louis Ducos du Hauron, in France. Logarithms were invented by John Napier and Henry Briggs in Britain, and by Joost Bürgi in Switzerland.”

Let’s meet Stiegler’s law:

Social or semantic connections? Tell me, infofriend!

Clive Thompson – undoubtedly a good journalist – has a piece, entitled Information Overlord in May Wired issue (not online yet, but already problematic) on his experience with semantic Web app Twine. Clive also formulates a provocative though about the value of information modulated social connections.

“But the truth is, sometimes social connections are less useful than semantic ones.
I’ve experienced this myself. My Facebook page attracts my friends, with whom I share social bonds. Meanwhile, my science blog attracts complete strangers, with whom I share a common interest in a topic – like a scientific study I’ve blogged about. It’s a semantic relationship, based on shared meaning. So those strangers tend to tell me things – and point me to links – that are more useful than the social stuff on my Facebook page. Information trumps friendship”

I am not sure whether the distinction behind: emotional, social friends vs rational, information only semantic cooperators

Michael Kingsley on competitive, bitter, boomer longevity

Michael Kingsley – diagnosed with Parkinson disease at the age 42 – wrote an utterly fatalist, sad&straight and death conscious essay entitled Mine Is Longer than Yours on the last boomer game he calls competitive longevity published in the New Yorker. This piece is the dark counterpart of the recent Wired Kurzweil coverage on Mr. K.’s enormous efforts of being prospectively healthy as long as to reach next generation life extension technologies.

In contrast to that, Mr Kingsley, who underwent deep brain stimulation and lives with wires in the brain and batteries in the chest, seems to be somewhat restricted in the age of web to “switching your subscription from Newsweek to Time”. Still, “longevity is not a zero-sum game” – he admits.

Mr. Kingsley is pretty ignorant about any non-selfish motivation behind life extension (he is a political journalist by profession):

Kurzweil follow-up in life extension exhausted Wired

Last year I approached a powerful Wired editor with the following story pitch: “A full and deep but cool report on the current (scientific) life extension technologies, persons, battles, camps, grants, problems, perspectives.”
His reply was a diplomatic and definite naysaying:

“Thanks for the idea. Alas, we’ve done *way* too many stories on life-extension over the years, from profiles of the singularity guys and Aubrey De Gray (sic) to shorter takes on various startups and stuff. There may be cool stuff out there, but I’m afraid we’ve exhausted our appetite on the subject.”

However the life extension appetite is not something that could be exhausted until the problem is solved systematically and the Wired guys’ appetite seems to be restored and healthy again as in the April Wired issue (not online yet) there is a full story (or rather follow up) on the No.1 singularity guy and baby boomer escapist artist Ray Kurzweil called Stayin’ Alive by senior Wired contributing editor Gary Wolf (whose book Wired – A Romance is a good reading).

What is interesting in Kurzweil for experimental scientists/robust life extension supporters is not his meditations on singularity, accelerating change and mind uploading (see the counterarguments by Mark Anderson in the same Wired issue), but his experimental, futuristic, life extensionist lifyestyle:

Kurzweil takes 180 to 210 vitamin and mineral supplements a day, so many that doesn’t have time to organize them all himself. So he’s hired a pill wrangler, who takes them out of their bottles and sorts them into daily doses. K. also spends one day a week at a medical clinic, receiving intravenous longevity treatments. The reason for his focus on optimal health should be obvious: If the singularity is going to render humans immortal by the middle of this century, it would be a shame to die in the interim.

Kurzweil’s physician and coauthor is Terry Grossman (also a SENS3 conference attendee) with an interesting clientele.

The New York Times advertises itself with stem cell research

I’ve just noticed a New York Times paid “stem cell research” Google Adwords ad in my gmail inbox besides the automated “Rejuvenation Research Vol. 11, No. 1, Feb 2008 is now available online” mail. That said, The New York Times is ranking the “stem cell” buzzword high and fishes for layman readers interested in the whole regmed topic for its own stem cell site both in the search results and next to articles (in the content network – explains Anna, my online marketer wife, next to me). I wonder for how long they have been paying for these ads? Other mainstream journals have similar ads, like The Washington Post. C’mon folks, let’s spend a part of those ad dollars to real stem cell research too!!!

Working without a personal assistant on the top of the big G…is fun!

I’m on my way to a Friday comprehensive exam from stem cell and mitochondrial biology which gives me no time to immerse into blogging this week. I mostly think of big holes in my knowledge like mitochondria and Ca²⁺ signalling. That’s why I can only offer soft things like the following quote from a fresh New Yorker article by Ken Auletta called The Search Party on Google:

Gabe Rivera of Techmeme: A Self-Meme Man

This would better fit to be a Twitter update, but I cannot resist to cite this sentence from Gabe Rivera Techmeme inventor in an older Wired conversation:

Partial immortalisation goes mainstream with an ‘s’ – thanks to the Economist!

The Economist print edition (Jan 3rd) has a summary article on the current healthy and scientific life extension scene starting with Aubrey De Grey’s engineering, umbrella SENS approach and talking about anti-oxidants, mitochondria, sirtuin activators and stem cell based regenerative medicine amongst others.

To my positive surprise the unknown writer of the article (do you know who wrote it?) is using the term partial immortalisation when talking about regmed’s chance to extend healthy lifespan with a link to Pimm saying “Pimm is a blog focussing partial immortalistaion” in the web version:

Stemming time’s tide

One way that might let people outlive the limit imposed by disposable somas is to accept the machine analogy literally. When you take your car to be serviced or repaired, you expect the mechanic to replace any worn or damaged parts with new ones. That, roughly, is what those proposing an idea called partial immortalisation are suggesting. And they will make the new parts with stem cells….

Some partial immortalisers seek to abolish the Hayflick limit altogether in the hope that tissue that has become senescent will start to renew itself once more. (The clock that controls it is understood, so this is possible in principle.) Most, though, fear that this would simply open the door to cancer. Instead, they propose what is known as regenerative medicine—using stem cells to grow replacements for tissues and organs that have worn out. The most visionary of them contemplate the routine renewal of the body’s organs in a Lincoln’s axish sort of way.

The term Pimm – Partial immortalization was introduced by me in this blog referring the idea, gradual and continuous replacement process and future technology of systemic regenerative medicine aiming indefinite life extension. There is a compelling logic behind I explained it many times here. The difference is in the letters, the sense is the same: ‘immortalisation’ is a British English ‘s’ version while ‘immortalization’ with a ‘z’ is rather American English (see the Google Fight graph on the right). Enough said, it is an ad hoc translation from the Hungarian “részleges immortalizáció” by me.

The source and short history of the term: For my MA thesis in philosophy (in Hungarian) I chose the term “weak immortalization” to address the philosophical problems of a though experiment of an unlimited healthy life extension technology through regenerative medicine which would eliminate problems concerning ageing (ageing related physiological problems), while strong and (technologically impossible) immortalization would eliminate death related problems. Later I replaced the weak – strong opposition to the more proper partial – whole opposition and the credit here goes to János Kis philosopher who suggested the term “partial immortalization” for me instead of the more metaphorical ‘weak’ and the modified version of my thesis was published in a book using ‘partial’. You can download the pdf here.

Since then I totally switched back to science and today I am more inclined to use the term systemic regenerative medicine (I adopted this ‘term’ used first by Maximum Life CEO David Kekich in a life extension blogterview for Pimm) which denotes the future branch of regenerative medicine focusing on otherwise ‘healthy’, aged, ‘normal’, ‘physiologic’ people instead of the characteristically and FDA approved diesased and catches the technology that is needed to reach reversible unlimited healthy lifespan, that is partial immortalization. Systemic regmed is a rather immature from a scientific point of view without an established experimental basis, I admit and more of a theoretical frame of my thoughts on the science I am practicing right now. Nevertheless it gives a fruitful, heuristic and holistic angle on regmed.

Here is the whole text referring to Pimm in the Economist piece:

Biogeekipedia: collecting raw materials

Wired’s Geekipedia is marketed as “People, places, ideas and trends you need to know now“. As such you can find biology and biotech related terms in it (part of the current hip and tech-savvy culture) like ‘stem cells‘, ‘RNAi‘ or ‘brain implants‘, explained. But you won’t find the terms ‘Natureplex’, ‘executable cell biology’, ‘Open Notebook Science’, ‘SciFoo Camp’, ’23andMe’ or ‘Pharyngula’ in it. The idea of building a Geekipedia (call it Biogeekipedia) specialized to the life sciences (biology, biotech, biomedical sciences, bioengineering, biobloggers…) seems pretty straightforward. (Or you can expand it to all natural sciences, but that is not my concern here.) So here I’d like to ask my readers to suggest entries for this Biogeekipedia, exotic, rare, but cool niche terms, buzzwords, good phrases, sentences, ideas and people within the biotech realm (web included) we all need to know. Use your imagination instead of your tag cloud. I start with my own embyronic list right now on the top of my head without links and explanations (Intensive work hours are inversely correlated to the number of quality blog posts). Needless to say it is more of a joke than a serious adventure. (List updated with the suggestions of Mr. Gunn, Jon Rowley and Matthew Oki O’ Connor.)

23andMe

Adie, Euan

aging

ATP/ADP

biobase

biogerontology

biomaterials

biotech DIY (DIY biology, bioDIY, home biology , garage biology, Homebrew Molecular Biology Club)

cancer immunoediting

cell fusion

Chemical Blogspace

CIRM

Connotea

convergent medical technologies

Craig Venter

deCODE

Easton, Alf

embryome

executable cell biology

FACS

Geekipedia

Genentech

genetic reprogramming

Google First Ladies

Google Palimpsest Project

What is your (science) blogging writing style, Chris Patil?

I have to interrupt my 23andMe streaming cause there are more interesting things are goin’ on. Chris Patil of Ouroboros has already been a blogterviewee (Part 1, 2, 3) on Pimm. He then shared his detailed views on aging and life extension technologies, but I always wanted to ask Chris about his approach on blogging as it was obvious from the launch of Ouroboros that he has a style and angle on the aging literature that goes far beyond the usual and sometimes dead boring “this journal published this and that journal published that” science blogging subgenre. We all need to find new and experimental ways in science blogging to make it more than just simply echoing the peer review literature and a sharp focus, good arguments and neat English definitely helps, so below you can read the secrets of Chris in blue. I also encourage you to try to mimic him to the amount of one blog post as a blogging homework. (The picture was made by Bora of the Clock fame at Berkeley, California this August when there was a science blogger party one day before the SciFoo Camp. Chris is on the left. The other guy is an unidentified science blogger.)

It’s a challenging question. Like speech mannerisms or your own personal walk, style is something that emerges from a lot of little decisions that happen below the level of explicit consciousness. As I’m writing this, I’m wondering, ‘Is this in my style?’ It’s like listening to my own voice on tape. Nonetheless, I shall try:

My own history in science writing goes back to college, when I wrote a weekly Q&A column for the Stanford Daily (‘The Science Bug’; I had inherited it from an earlier staffer and passed it along to someone else when I left; years later, my younger brother took up the job). The audience was mostly other students, i.e. bright and educated but not necessarily scientists, so the main challenge was providing necessary factual and conceptual background without sounding like a lecturer — the readers were getting enough lectures in their coursework, and I knew that an overly didactic style would turn them off.

Unlike a reporter, I had a great deal of freedom to explore different styles, and eventually I found one that really felt like me which is not to say I didn’t have influences. I worshipped Cecil Adams (of the famous syndicated Q&A column The Straight Dope) at times perhaps veering across the line into outright imitation. From him I learned that questions don’t really want “answers”; they want “stories“, with a beginning, middle and end. You have to take the reader somewhere, from familiar ground to unfamiliar ground (and, sometimes, safely back again).

Today’s top story on Blogrunner Science from 2 days ago

Why? Oh, it’s the TierneyLab.

Blogrunner Science vs. Scienceblogs vs. Postgenomic?

Alien vs. Predator like stupid question for the weekend: Which do you think is the best source when it is about interesting and quality science content: the Techmeme clone Blogrunner (here it’s the science channel of Blogrunner), that is the newly launched automated online news service and blogs aggregator by the New York Times or Scienceblogs or Postgenomic? Which model is the best?

And what do you think about the tons of Eurekalert Press Releases on Blogrunner? Do you like to read press releases?

Robust life extension reaches the Washington Post on Halloween day

Let’s meet the informal version of the ‘pro-aging trance’ in a portrait on Aubrey de Grey in the Washington Post (thanks for the tip, Jim):
Why is it, when you bring up the idea of living forever — even if robust and healthy, not drooling on your shoes — some people just recoil viscerally?

“It’s probably the majority that recoils viscerally,” de Grey says. “It’s what I call the pro-aging trance.

“Since the beginning of civilization, we have been aware that aging is ghastly and that aging is utterly inevitable. . . . So we have two choices. Either we spend our lives being preoccupied by this ghastly future or we find some way to get on with our miserably short lives and make the best of it.

“If we do that second thing, which is obviously the right thing to do, then it doesn’t matter how irrational that rationalization might be. . . . It could be, well, we’re all going to go to heaven. Or it could be, we’re going to have overpopulation. Or it could be, it will be boring. Or, dictators will live forever.

“It doesn’t matter what the answers are. It’s so important for them to maintain their belief that aging is actually not such a bad thing, that they completely suspend any normal rational sense of proportion.”

But if people don’t die, won’t we indeed fill the planet shoulder to shoulder?

“The birthrate is going to have to go down by an order of magnitude,” de Grey acknowledges. “But even if that is going to be a severe problem, the question is not, do problems exist? The question is, are they serious enough to outweigh the benefits of saving 100,000 lives a day? That’s the fundamental question. If you haven’t got an argument that says that it’s that serious that we shouldn’t save 30 [bleeping] World Trade Centers every [bleeping] day, don’t waste my time. It’s a sense of proportion thing.”

Picture made by me with the iPhone on Aubrey and Adelaide on the SENS3 conference in the dining hall of Queens’ College.

Feed reading trends: I am a Valleywag addict, help me!

Show me your feed reading habits and I’ll tell you who you are! I hope this statement is not true as according the item reading trends on Google Reader I have been a serious Valleywag addict in the last 30 days and more, I suspect. Although extensively reading a funny, well-informed but malicious tech gossip site like Valleywag of the Gawker Empire admits no excuse my explanation is this: after 10-12 hours of experimental lab work I do need something light and ridiculous for mental regeneration at home before switching to more serious content. I want to laugh and for some reason Valleywag is tuned to the frequency I need for entertainment (and also gives me the option to instantaneously present the posts to my wife disturbing her web time). If my click path is a body with different physiological functions, then Valleywag is my

Nature’s history site: how to keep the tradition and identity alive

Disciplinary science has a rather short-term memory (see the reference section of peer review articles) while science publishing is relying on the long-term version, especially if it is the journal Nature, published first in 1869.

Now they launched an innovative new site dedicated solely to the history of the journal, full with multimedia snippets and short stories. Source: Nascent

As Reb Tevye says: How do we keep our balance? That I can tell you in one word: Tradition.

Wired style SENS3 conference intro or be aware of your audience

As this very site here is embedded in the blog medium, we could and should be experimental and eclectic in our style as we cannot control (just target) our audience, thank the web. Now a report on a science conference could be addressed to very different audiences, and yesterday I showed an example on how to present an unconventional science conference to the mainstream science establishment. But if I’d like to target, say, the geeky-layman Wired audience, than I should find another angle on the SENS3 conference which is not restricted to the science content but highlights the inconvenience around it. (Just take a look on how journalists at the Wired Science blog are considering to cover their subject.) Say the story would look like this:

Summary (Lead): A recent unconventional strategic conference on translational science in ageing related damages and diseases shows the benefits of mixing the traditionally homogeneous audience of science conferences with visitors from outside science in order to gain new insights, and put ageing and lifespan extension in a broader cultural context.

First paragraph: Question: Which science conference has such a variety of participants that includes hardcore life scientists from top-notch universities, entrepreneurially inclined benefactors, former IT professional turned bioinformaticians, practicing life extensionists, high school talents, fitness fanatics, lawyers, and even a Hollywood scriptwriter, or an investment banker turned biology student due to a recent cancer survival? Answer: The SENS3 conference in Cambridge.

Compare this to that:

Unpublished SENS3 conference report for mainstream scientists!

Recently I wrote a meeting report on the SENS3 conference for a very prestigious science journal, but finally it did not go through the filters. I knew that the chance for publication is small as the journal rarely publish such meeting reports and as it was in many respects an unconventional science conference. The standards were really high and the genre itself is strictly restricted: no more than 900 words and only 1-2 conference topic could be covered focusing on new data. On the whole it was a really good science writing experience for me. I finally realized how challenging it is to introduce the concept of robust scientific life extension for the mainstream science audience although it is not impossible at all.

But if a man has an interactive blog with a quality readership even an officially unpublished text could be useful, so please read my draft in its final form and think about it. Links of the video versions of the referred presentations and references are included, a perpetual advantage of the web comparing to offline publication. I’d like to say thanks for the folks who helped me with the draft: Aubrey de Grey, Michael Rae, Mark Hamalainen from within the SENS camp, Matthew Oki O’ Connor and Chris Patil, fellow scientists-bloggers and first of all, Anna.

Subject scrapline: Biotechnology

Title: Translating ageing

Summary: A recent unconventional strategic conference on translational science in ageing related damages helps to put some puzzle pieces together.

Changes in the adult tissue stem cells or in the mitochondria are two main processes under constant investigation amongst researchers curious about the ins and outs of the ageing process. At the SENS3 conference in Cambridge scientists and laymen shared their results and ideas, respectively.＊

Despite its mixed population with a scientist majority, the conference resembled a mainstream life science conference due to its topic sessions focusing on the different types of lifelong, ageing accumulated damages. SENS decodes as Strategies for Engineered Negligible Senescence, which aims to suggest a panel of interventions on how to robustly extend the mean and maximum human life span and claims to identify the adequately exhaustive list of main age-related pathologies ranging from cell depletion to mitochondrial mutations. SENS is by definition a flexible enough umbrella term to include other coming life extension technologies and concepts under its brand. Also, it is an engineering project compiled by main organizer Aubrey de Grey, a computer scientist turned theoretical biologist with a grand mission and hypotheses yet to be experimentally tested. The presentations were mainly reviewing the progress in the related branches, with enough new data to keep the experts interested.

Stem cells exhausted

Blogs invade The Scientist: vote for your favorite life science blog!

At The Scientist, the editors are awaiting your suggestions on your favorite life science blogs to gather the list of blogs that are especially hot for life science researchers. They asked 7 science bloggers, 5 from ScienceBlogs by SEED (Abel Pharmboy, Bora Zivkovic, Carl Zimmer, Newamul Khan, PZ Myers) and 2 independent bloggers (Ed Silverman and me) to nominate some of their favorite blogs for a start. Below you can find my answer:

Instead of picking three individual blogs, I’d like to mention three topic-related branches of blogs or blog aggregators, referring this way to many individual bloggers and a larger amount of information and information filters. This approach follows from my blog reading habit as my starting point for blogs and all web related science and technology things, are the web sites that could be reached through RSS feeds using a feed reader, which is Google Reader, in my case.
The groups are: a) science blogs written by scientists, b) science related blogs written by journalists and editors, and c) technology and web related blogs written by “alpha geeks and early adopters.”

The Gonzo Scientist on IdeaCity in Science and on the web

If you compare the Nature and the Science front pages (which is not the topic of the current post) you can notice a big difference: there are a lot of “web 2.0″ish fresh features on the Nature site while significantly fewer on the Science counterpart. Now Science came up with a new, less academic and more popculture driven (the name is telling) column, The Gonzo Scientist written and edited by John Bohannon, regular Science contributor. Bohannon writes and even audioslides (illustrations by Katrien Kolenberg) about his experience in IdeaCity.
IdeaCity is Canada’s premier geek summer camp in Toronto, and was modeled after the TED conferences. Now my synonym for the geek camp is SciFoo, but there is a big difference here: IdeaCity is free only for the 50 invited celeb speakers, while it is $3000 for the 3 days for every other visiting Idealists.

Trivia: Joshua Davis, the journalist is not Joshua Davis, the designer

So far I’ve had the wrong belief that my favourite Wired Journalist, Joshua Davis is the same person as Joshua Davis, the designer, who once has been featured in Wired (not by Joshua Davis, the journalist). The root of my misconception was the common source of my knowledge on these 2 guys, namely Wired magazine. After all, it was good to think that there is this man, who could not only be the subject of a Wired article due to his terrific design work but he is also capable of writing really good stories as a journalist. But then doubts have arisen as I saw that the Joshua Davis I had in mind, is writing at least one major article in almost every Wired issue reporting from different locations all over the world, so how on earth could he find time to do his everyday designer job? Instead of figuring out the “Joshua Davis situation” with 1 simple Google search, cognitive dissonance led me to ignore this emerging doubt and I still maintained my belief that the journalist and the designer is the very same creative person.

But at the SciFoo Camp, Thomas Goetz, another camper, deputy editor of Wired magazine (good job: hunting for good stories and suggesting them for journalists) and blogger behind Epidemix taught me that this one double-faced Joshua Davis is in fact 2 people, although other people used to believe in their unity too. Conclusion: Do not trust in your non-Googlised beliefs.

Puzzle: Which Joshua Davis made this?

Granpda is 150 years old: Artifacts from the (Wired) future

Unfortunately replicative senescence in dividing somatic cell populations through telomere shortening and organismal level aging is not as strictly related as the September Wired (not online yet) issue’s Artifacts From the Future section suggests:

Biotech Geek Blogger goes Nature Stem Cell Blogger at the Niche

In my opinion the Google of science publishing is the umbrella brand Nature Publishing Group. The best indicator of it is the growing number of freshly released beta products making NPG web initiatives a heaven for scientific early adopters. As Timo Hannay, web editor of Nature said in an interview in Spiegel: The core business of Nature is not to produce a magazine,” he says, “but to facilitate the exchange of ideas among scientists.” Indeed, Nature is technologically a step ahead of other publishers in many respects. Let’s take a look at other giant science journals’ websites. (OK, marketing blablah is over, I am not paid for this, I am just simply enthusiastic about the progress.)

I positioned myself here as the Biotech Geek Blogger with an ideal target audience of researchers and IT guys curious about BT things. A clever and fast scientist turned entrepreneur once called me a Google Biotechnologist. Now I realized a bit lately that the niche Google of my profession is called Nature.

I always wanted to participate in a professional group-blog and I had some opportunities in the past. Now I was offered to contribute freely to the Nature Stem Cell Reports‘s new blog The Niche. What could I say?

Yes. (And I won’t be the only one.) It is a huge opportunity for a rookie stem cell researcher like me and an ideal way to get in touch with the recent literature and regmed happenings, continuously process it and make it digestible to other people. The agreement is: concerning articles prepared specifically for The Niche, full blog posts will be published there, while excerpts will be published here.

The Niche: The Stem Cell Blog hosted by Nature Stem Cell Reports

How many fine niche stem cell blogs do you know? 4-3-2-1? How many with an attractive, easy to remember name? 0? Good, short, actual and proper blog names are rare. Let me introduce you The Niche which intends to become THE Stem Cell Blog in the niche of the niches. It is the newest Nature blog hosted by the also newly launched Nature Reports Stem Cells “to provide an informal forum for debate and commentary on stem cell research and its wider implications for ethics, policy, business, and medicine.”

Here is the RSS feed for the posts: http://blogs.nature.com/reports/theniche/atom.xml

also don’t forget to subscribe to the comments: http://blogs.nature.com/reports/theniche/index.rdf

Who will be the new blogger behind Business 2.0′s BioTech(nically)?

Earlier: BioTech(nically), Business 2.0’s new biotech blog

Cell’s Superhero Cover: the role of comics in science popularization

I’ve just realized how cool is Cell magazine May 4 issue’s cover (the one with the Scientist Enter the Blogosphere report by Laura Bonetta) with the S-nitrosothiol superhero T-shirt. This substance may have some therapeutic utility in diseases such as heart failure and asthma.

Illustration: Cell and me this morning.

Cartoons are terrific education tools, let’s consider howtoons for instance. Howtoons are cartoons showing kids of all ages “How To” build things. What about cartoons for scientists?

Looking for user friendly, attractive peer review article titles….

These two titles are freshly out of my feed readers: B-type natriuretic peptide inhibited angiotensin II-stimulated cholesterol biosynthesis, cholesterol transfer and steroidogenesis in primary human adrenocortical cells. and

In vivo expression of human ATP:cob(I)alamin adenosyltransferase (ATR) using recombinant adeno-associated virus (rAAV) serotypes 2 and 8.

How user friendly these titles are? Let’s examine me: Theoretically I have some (limited) background knowledge on these topics as they are covered by my Google Reader with some properly chosen search terms. For the first trial I see only familiar characters in a weird arrangement without any intelligence flash in my mind, for the second some mental forms are beginning to take shape, for the third a little more context enter, but instead of a fourth title trial I skip to the abstract in case I’m interested in what follows based on the previous title impressions. But I’d truly appreciate if I could capture at least half of the title at first. And the titles above are not the worst at all. After reading the steroidogenesis-one many times, it became my friend. But people would like to put less energy into conceiving a simple title and more to understand and apply the new results. A good title is about the proper filtering of the proper reader and vice versa.

Yes, there must be some good policies on titles of peer review articles. In case of the steroid paper, the Instructions to Authors for Endocrinology says on title requirements: Full title (a concise statement of the article’s major contents)

PNAS has a longer title guide for instance, this paragraph is from an older version of PNAS Information for Authors: Title: Titles should be simple, informative, and comprehensible for a broad scientific audience. Authors should avoid nonstandard abbreviations and colonic phrases. Titles may not be phrased as questions. Titles are limited to three lines or 135 characters including spaces.

Why aging is an unnatural process? An argument from Atul Gawande

There is a formulation of the argument on why aging should be considered as an unnatural process by Atul Gawande in the current The Way We Age Now report in The New Yorker:
“..scientists do not believe that our life spans are actually programmed into us. After all, for most of our hundred-thousand-year existence—all but the past couple of hundred years—the average life span of human beings has been thirty years or less. (Research suggests that subjects of the Roman Empire had an average life expectancy of twenty-eight years.) Today, the average life span in developed countries is almost eighty years. If human life spans depend on our genetics, then medicine has got the upper hand. We are, in a way, freaks living well beyond our appointed time. So when we study aging what we are trying to understand is not so much a natural process as an unnatural one.”

Update: Derya Unutmaz‘s critic of this argument on FightAging! and more: “This is gross misconception. The reason why the average life span was so low was because most of the deaths occurred during childhood and through infections during adulthood. If one corrects for the infection survival and looks at life expectancy at older age, there has only been about 6-8 years increase in overall life extension in the last 100 years. Thus, the data strongly argues for biological program of aging, and that at current time we are not yet freaks living much beyond our appointed time, just that many more of us reaching the near maximal set program.”

BioTech(nically), Business 2.0′s new biotech blog

Business 2.0 Blog Beta Network‘s new blog BioTech(nically) was launched written by Marie Cannizzaro who says about herself in the intro post, March 27: “Before joining Business 2.0, I wrote for Dow Jones VentureWire and Stanford Magazine. I have a degree in Human Biology with a concentration in Biotechnology and Bioethics from Stanford University.”

At the present moment, the blog is in an experimental condition, and it takes time for the blogger to form an idiosyncratic style with special topic selection and get a highly targeted stable audience. But as BioTech(nically) is a member of a very prestigious blog network of professional journalists, it is a superb advantage that could easily shorten the experimental period. Good luck to Marie and welcome to the emerging biotech blogdom.

Truth to be told: I would be really happy to do this biotech blog job for Business 2.0. In fact I did try to apply this job even when it was non-existing, but I was sure this fits into Business 2.0′s web and high tech focused profile. Here are some sentences from my pushy mail to Erick Schonfeld, from October, 2006 with the subject: joining Business 2.0 Beta as a biotech blogger: “I found the Business 2.0 Beta aggregator idea fascinating but what I really missed out of the blogs you have is an uptodate and cool biotech-regmed blog.

Blogxperiment: What are the good ways to summarize peer-review articles?

In future posts I’d like to do a blogxperiment based on comments feedback. My general question is: What is the best way to summarize peer-review articles for a more general readership and transmit scholarly knowledge and literature? What are the opportunities used in blog posts? Figures, abstracts, dense citations, other summarize options, journalist lingo, superficial metasentences, more original contributions from the blogger? My sample article will be a review first, not an original publication on mitochondrial division: The Machines that Divide and Fuse Mitochondria

And simply start the experiment with the abstract:

I also might have asked: What are the good ways to popularize peer-review articles?

Bodyhack’s merging with Wired Science Blog

Bodyhack, Wired’s pioneer biotech and stem cell focused blog is folding into Wired Science Blog. Thank you Kristen et al.

The bodyhacknorati profile:

How much do you think a scientific blog post is worth (in US dollars)?

Ok, this is the question I asked yesterday at LinkedIn Question&Answers service: How much do you think a scientific blogpost article of 300 words is worth (in US dollars)?

Next big thing at Darpa after the Internet: biology, of course!

When ordinary folks hear the name of Darpa, Defense Advanced Research Projects Agency, Pentagon’s science division, the next association is usually not a military one, but the the insituiton’s role in the nascent Internet. Indeed as Wikipedia inform us: “its original name was simply Advanced Research Projects Agency (ARPA)…and had a major impact on the world, including computer networking (starting with the ARPANET, which eventually grew into the Internet).”

Recent days, Darpa researchers are into the next big thing in high technology, which is not pure information technology, but rather biotechnology and bionics. Wired magazine has an article on the topic by Noah Shachtman called Be More Than You Can Be: “The agency had mostly avoided the life sciences. Darpa’s directors in 1980s and 1990s weren’t interested — and were happy to avoid the tangled ethical issues that often go along with research on human beings. Then, from June 2001, under Tony Tether‘s guidance, Darpa’s embryonic biology efforts began to multiply and expand. Research on biodefense led to research on the immune system, which led to more general research on the human body.”

The report emphasizes the amazing Cooling Glove project (see cartoon) and the hibernation project on “metabolic flexibility”.

Unfortunately I did not see a word on probable stem cell and regenerative medicine projects at Darpa, although it is known for example, that there was an awarded a $3.7 million Darpa grant to the University of Pittsburgh’s McGowan Institute for Regenerative Medicine on wound healing and tissue regeneration.

Artifacts from the past: Wiredophilia

Once upon a time in 2005 I wrote an article on Wired magazine published in a language you probably do not understand. This photo was shot by Daniel Nemeth in my appartment, so if you are curious, you can see three little pieces of carpet in my living room. Have a nice weekend!

TierneyLab: new science blog hosted by The New York Times

TierneyLab, the science blog of the professional journalist John Tierney was launched one week at January 15 hosted by The New York Times website with this intro: “I’m hoping to follow the scientific method: experiment to see what works and what doesn’t. I want to give you a chance not just to discuss science but to participate in it. I’ll be guided by what’s in the news, what’s intriguing, what’s fun.” From the about section: “John Tierney always wanted to be a scientist but went into journalism because its peer-review process was a great deal easier to sneak through.” The 2 founding principles behind are tricky enough: 1. Just because an idea appeals to a lot of people doesn’t mean it’s wrong. 2. But that’s a good working theory. Self-reference is a compelling logical principle, so I suggest to apply these 2 principles to TierneyLab too: 1. Just because a blog belongs to The New York Times doesn’t mean it’s bad. 2. But that’s a good working theory. Anyhow, I am curious about the output of an experiment based on the mix of popular science and high end journalism in the medium of blogs.