Craig Venter and the life extension drive: blogterview questions

One strategy (call it Life Extension Gets Personal) to raise awareness for the idea and technology of healthy life extension is to publicly encourage life extension “coming outs” on behalf of mainstream celebrities. In order to get an academic legitimacy for LE (which is one of the most important aim of Pimm) I am interested specially mainstream or at least well established scientific celebrities. To accomplish this project a man needs to identify target persons to interview (finding hints that the person is positive about LE), contacting these persons and publish the final piece somewhere.

As a first target Craig Venter, the genomics pioneer seemed unconventional and free minded enough to approach with the idea of a LE blogterview. On the other hand I found definite signs of his interest in longevity and life extension suggesting that if Craig Venter had been given a technological-medical chance to extend his healthy lifespan significantly he would definitely not like to die due to accumulating functional declines associated with aging within the next, say hundred years. Maybe I am wrong here, maybe I am not but to figure this situation out I translated these signs into the following blogterview questions and tried to contact him in early December, 2007. So far I reached only his nice and diplomatic PR agent, who said that maybe we have a chance to get the blogterview done in the near future. Till we get there below please find my targeted questions to Craig Venter:

1. Once I’ve read somewhere but was unable to recall later that one particular motivation behind the sequencing of your own genome was your serious life extension commitment and the belief that genomics has something to say about life expectancy. Is it true? If yes, what is the story of your life extension commitment? Is it a commitment for moderate or maximum life extension? In A Life Decoded I’ve found only one paragraph in your molecular biography explicitly on Long Life about the I405V of the CETP gene but no more hint to this important topic.

2. What do you think about Aubrey de Grey’s SENS approach? You’ve been one of the judges on the The SENS Challenge Prize organized by the Technology Review in 2005 for those “who could prove that SENS was “so wrong that it is unworthy of learned debate.” ? Who got the point there?

3. What do you think about the mitochondrial theory of aging? I was a little surprised when I’ve found that your circa 16.5kb mitochondrial DNA sequence was not published in the PLOS Biology paper: The Diploid Genome Sequence of an Individual Human Obviously it is not part of the diploid genome but I expected it at least as an appendix as those 37 genes and D-loop region can give important genetic information. Have your mitochondrial genome been sequenced already?

4. In a recent Rolling Stone interview you are saying that “There is probably nothing more important to study about human biology than stem cells.” What do you think about regenerative medicine’s role in a robust and healthy life extension technology?

23andMe on the biparental inheritance of mitochondrial DNA and more

In my former blog post inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa? I meditated on 23andMe’s capability of detecting paternal mitochondrial DNA in their customers’ saliva with their Illumina microarray chips scanning around 2000 mitochondrial single nucleotide variants. Published here the initial answer of the 23andMe Editorial Team to this fairly technical, but nevertheless crucial question with permission granted. Besides, I am happy to report that I am working on a blogterview with one of the key member of 23andMe’s Research Team. Hopefully I’ll be able to get back to you with some first-hand information on the science and technology behind the personal genome service of 23andMe and on how 23andMe can facilitate academic research.

Dear Attila Csordas,

Thank you for your interest in 23andMe’s research mission. The question of paternal inheritance of mtDNA is a fascinating one, and the debate in the literature has continued over the past couple of decades. Currently, there is little evidence for paternal inheritance of mtDNA, outside of isolated individuals. However, the array platform lets us resolve multiple SNP states independently. 23andMe’s technology and throughput may indeed provide a novel way to address the question. We will include the question in our consideration of research projects. In the meantime, here are a couple of articles discussing the subject:

Bandelt et al., “More evidence for non-maternal inheritance of mitochondrial DNA?”
Chinnery, “The Transmission and Segregation of Mitochondrial DNA in Homo Sapiens” in Human Mitochondrial DNA and the Evolution of Homo Sapiens.

Sincerely,

The Editorial Team at 23andMe

The question is crucial for a personalized genetics company like 23andMe providing Maternal Ancestry Tree service for the customers based on the exclusively maternal inheritance of mitochondrial DNA. As one of my correspondent partner wrote:

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).

What is your (science) blogging writing style, Maxine Clarke?

I met Maxine online first when she commented my post on the The problem of online “supporting information” in peer-review articles and then interviewed her on Nature policies concerning the same problem. Then I met Maxine offline in London and learnt a lot on how every issue of Nature is born and other insights I hope I can share with my readers here later. The following is Maxine’s answer to my stylish question and I would also like to offer her culture rich personal bookblog, Petrona.

My professional blogs (Nautilus, Peer to Peer and From the Blogosphere) are addressed to a particular group of people: scientists who read, review and publish, or would like to publish, in our journals. Therefore, the style I try to achieve is helpful, informative and stimulating, yet not didactic or dull. I aim to highlight the benefits of publishing at Nature Publishing Group and provide assistance to those wishing to do so, in a way that is not too directly promotional, but which is constructive to authors and interesting to them and other readers, as well as encouraging their feedback. Therefore I write about news concerning journal policies and format, as well as announcements of new journals, projects, conferences and online tools of interest to authors and reviewers. I also highlight when journal content is free for some reason, because this means that the authors of those articles are achieving greater “reach” for their articles (as well as making it possible for more people to read them, by my announcement). I also highlight news from the wider world of science communication, for example about quality indicators (citations tools and impact factors, for example), ethics, peer-review and so on, in the hope of stimulating community discussion of these issues, as this can help us decide on our journals’ evolution. Finally, I blog to provide an approachable forum for potential authors to ask questions about our publication policies, and to have them answered quickly in a way that can also benefit others, as they can see the responses.

Next blogterviewee is the number one scientific aging blogger, Chris Patil of Ouroboros.

Earlier:

Deepak Singh

me

What is your (science) blogging writing style, Deepak Singh?

Actually the idea of asking science bloggers about their style came to my mind reading one email remark of Deepak on the writing style. Deepak is the guy behind business/byte/genes/molecules and he was a Sci Foo camper this year. He is one amongst the few bloggers who are standing at the intersection of science and technology and being the founder of Bioscreencast he is actively experiencing the life of a bioweb entrepreneur.

My style is a heady mix of spontaneity, continuous partial attention, a total lack of time, the random connection of ideas formed at different times, semi-formal essay-style writing, attempts at humor, deep thought, tempered enthusiasm, and unbridled passion.

Uncensored gmail chat between 2 science bloggers on adult issues

me: Hi Bora, can you send me the Nature piece on the Blogging Anthology?
I am not in the Institute and do not have subscription
http://www.nature.com/nature/journal/v447/n7146/full/447779b.html
Sent at 8:58 PM on Wednesday
me: cheers
Bora: No problem. Thanks.
me: wait that is some old stuff.
Published online: 22 January 2007; | doi:10.1038/news070122-I’ve read that
I have in mind the current one: Bloggers unite p779
Paul Stevenson reviews The Open Laboratory: The Best Writing on Science Blogs 2006
doi:10.1038/447779b
Full Text | PDF (207K)
See also: Editor’s summary
Bora: Wow! That is news to me!
me: ok, who posts first?
do you have access to it right now?
Bora: No. I should have it in minutes/hour as soon as one of the sciblings check the forums and sees my query.
me: ok
I am curious how positive, or critical it is
Sent at 9:04 PM on Wednesday
Bora: http://neurophilosophy.wordpress.com/2007/06/13/open-laboratory-reviewed-in-nature/
me: good
Sent at 9:07 PM on Wednesday
me: I think, the science blogosphere now reached its adult stage

Stem Cell Lab Monitor: the Bernstein Laboratory at UCSF

The first lab of Pimm’s new series turned out to be the Bernstein Laboratory at the University of California, San Francisco focusing on heart muscle regeneration. Unlike other professors, Harold Bernstein is extra fast, he answered my questions within 8 hours. This web-availability, rare within academic circles, positively correlates with the design and functionality of the Bernstein lab webpage, which was the first candidate of the lab website competition. I especially like that it is not a lab site built around the PI only, but it focuses on the team at work which is quite big (more than 30 members, 8 postdocs). The lab got a $2,229,140.00 California ESC grant (first year $531,88 on Modeling Myocardial Therapy with Human Embryonic Stem Cells.
The answers of professor Harold Bernstein’s are as follows:

1. What is your scientific background and how did you get immersed into stem cell research? What was the motivation behind that?

I trained in human genetics, receiving a Ph.D. Toward the end of my graduate studies, I realized that I wanted to know more about human biology, and so I entered medical school, and subsequently received an M.D. I have always been interested in the regulation of cell proliferation versus differentiation, since that is a key decision point in the formation of many mammalian tissues. Especially in some organs, such as brain, muscle and heart, the paradigm has been that once the decision to differentiate has been made, there is no turning back, hence, “terminal differentiation.” Stem cells seemed like the most likely model system in which to pursue our questions, and the advent of human ES cell technology has provided an unprecedented opportunity to examine human tissue development.

2. Who were your masters and supervisors?

Nature Publishing Editor on the idea of a public scientific multimedia site

Maxine Clarke, Publishing Executive Editor of Nature and blogger of Peer-to-Peer got interested in the problem of “supporting information” and in the idea of an open access, peer-review supporting information aggregator website. She shared with me her valuable thoughts and informations by mail, from which I now publish parts with the permission of Maxine Clarke (emphasis by me).

On the possibility of a community-approved public multimedia site (videos, audios, pictures) with open access supporting information from peer-review journals.

It would indeed be nice for authors and readers to have such a facility. If there were to be a multimedia database, accepted by the community, we’d be happy to consider making deposition mandatory. Our principle is that data described in our papers are freely available, so if there were a community-approved public multimedia site, which included annotatation and curation, we’d be happy to consider making it a condition of publication for movies etc to be deposited in it. It would need to be publisher-independent to work, so that authors could upload multimedia data wherever they’d published their paper.

The main point for us at Nature is that as a publisher we have to be confident that material published off our website is properly curated, archived and preserved. For example, when we introduced the microarray deposition policy we ensured that there was full community support for the two databases (in one of which, authors’ choice, we require deposition) before implementing the policy. So for this video idea to work, the “database” concerned would need to be publicly accessible (not commercial), curated, annotated etc.

On the status of online supporting information at Nature:

Supplementary Information on the Nature website is free, though you have to register. (Confirmed, see screenshot of a 3D supplementary animation showing that the gut-associated lymphoid tissue comprised of different subsets of haematopoietic cells, Veiga-Fernandes et al.)

On the problem and handling of online supporting information:

Biosingularity’s Derya Unutmaz: a T cell expert on life extension

As many other heavyweight bloggers Derya Unutmaz has an A life and a B life. His A life is focusing on the molecular machinery of T cell activation, differentiation, survival and its explotation by HIV as he is an Associate Professor at Department of Microbiology at New York School of Medicine. Briefly, he is an immunologist researcher. In his B life he edits Biosingularity, which - according to the subtitle - is a weblog on advances in biological systems. It gives an uptodate and detailed review of the current biological research from a very broad range on a quality level rare in the blogosphere. As in the case of lucky science bloggers, Unutmaz’s A life motivates his B life and vice versa. I am now pleased to report that he was kind enough to answer some life extension questions as he is really supportive of that topic (emphasis added by me). Fortunately the degrees of freedom in the blog genre is higher than in mainstream journalism, so although I realized that my old questions (they were sent in last October) are not enough, the answers were so deep, that I publish them now, and set some other questions later. I am really happy to share my point of view with Professor Unutmaz concerning the role of systemic regenerative medicine in indefinite or big-scale life extension. I’d like offer his words for every life extensionist: “The most important thing to remember though is to filter the hype from truth and solid science while both raising the awareness about the possibility of human life extension and also brain storming about the ideas on how to do this best.”

1. What is the story of your life extension commitment? The story of my commitment to life extension began as I became passionate about biology and science while I was still a kid. I realized then, (about 25-30 years ago) the technology was going to keep advancing and started to think why we could not come to a point when we have the knowledge to treat all diseases, and then why not stop aging? During medical school as I learned more about the physiology and pathology I realized the complexity of biological systems. It seemed intractable but at the same time biology followed rules, it wasn’t something magical that we can not conquer. I decided my life long commitment was going to be try to figure out how biological systems worked and how we can eventually master them to a point where we can reprogram our biology.

Life extension blogterviews in 2006

What can/will You do for life extension? Answer these questions first.

Interviews in a temporal order: Reason, Chris Patil, Jim Craig, Aubrey de Grey, John Cumbers, Kevin Dewalt, Nick Bostrom, James Clement, David Kekich, Huber Warner, Mark Hamalainen, John Schloendorn.

For me it is important to introduce here people with different professional background who are life extensionists, but being a biotech blogger I would like to focus more on life scientists, stem cell researchers, biologists, biotechnologists, medical doctors, since they (we) are the ones who have a chance to realize any little piece of life extension technologically. In my opinion this is the stable way to make life extension acceptable in front of decision makers and the public. So I’ll continue the interviews, try to evoke mature scientists, and try to be more and more disciplinal except when I am not.

The story of my life&extension commitment

Now I start to answer my blogterview questions concerning life extension. Here is the first:

1. What is the story of your life extension commitment? since the age of 15. I started my first offline diary at that age with a sentence something like this: I have eventually find the aim and meaning of my life which is the extension of human life, understanding