Embedding the Future: the X2 Project goes public!

With the public launch of the X2 project, Alex Soojung-Kim Pang realized one of his dreams. Alex is the research director of The Institute for the Future (IFTF), an independent nonprofit research group headquartered in Palo Alto, Silicon Valley. He writes:

The project is called X2, and its aim is to forecast the future of science, technology and innovation. The name may sound like science fiction, but it’s actually an historical allusion. In my previous life as an academic historian, I studied the X Club, a group of Victorian scientists who were very interested in the future of British science. The Club formed when its members were still young, ambitious outsiders, fighting to establish their reputations in a world in which social connections and privilege mattered more than scientific achievement; by the time they retired, its nine members were among the leaders of British science.

That said, dear ‘still young, ambitious outsiders’ you can now sign up for the project and join the groups you’re interested in. I suggest you starting with Quick Start. Disclaimer: I am the so called “steward” of the embryonic group Biomedical Sciences and Biotechnology. Continue reading

BioBarCamp in the Valley before the SciFoo Camp!

It seems that my favorite ever unconference, the SciFoo Camp will be aroundunconferenced by a BioBarCamp this year. The whole idea of the BioBarCamp is based upon the SciFoo Camp, so it is by no means a competitive but a complimentary event.

From the BarCamp wiki: “The BioBarCamp is an idea (fed by the tweets of the BioTwitterer community) to organize a life sciences – biotechnology – personalized genomics & medicine – bioinformatics unconference at the Bay Area around the 3rd SciFoo Camp time, which is 8-10th August. The SciFooCamp generates a lot of enthusiasm & activity but not just for those who are invited (only 200). On the other hand, it would be nice to organize a bio-related BarCamp, just like the Cambridge BarCamb, in which the bio-related SciFoo Campers and all the other biogeeks could gather together.”

The main activity is happening right now at the public BioBarCamp Google Group. If interested please join there or just follow the discussions. We are right now in the process of finding a proper venue and sponsors and any help would be most welcome. Right now 6 or 7 August seems to be the consensus day and we have a very generous offer from The Institute for the Future via Alex Soojung-Kim Pang in Palo Alto (no response from 23andMe so far, see below).

It’s against a classic Twitter story, just like this before. You can reconstruct the whole conversation with Twitter Search Engine Tweet Scan by searching for terms SciFoo, BioBarCamp, SciBarCamp but here are my selected tweets:

Scene One, 04/10/08 How the idea was born on that day in reverse chronological order:

Scene Two 04/22/08 How the biospecificity and name was born alongside with a possible venue idea: Continue reading

3rd SciFoo Camp, Googleplex, August 8-10, 2008!

The 3rd Science Foo Camp, organized by Nature, O’Reilly Media, and Google will be held on August 8-10 and hosted at the Googleplex in Mountain View, CA.

From the mail: “Now in its third year, Sci Foo is already achieving cult status among those with a passion for science and technology. The Economist said that it “capture[s] the essence of innovation”; in a photo essay for Edge, George Dyson wrote of the “the impossible choice” when deciding which sessions to attend; another attendee described it simply as “The best gathering ever. Period.”

Also check the strongly related BioBarCamp idea.


Human proteome project: 21000 genes/1 protein, 10 years, $1 billion?

In order to have the slightest change to design a robust, systemic life extension technology, we need to accumulate every systemic macromolecular, cellular, tissue- and organ level data of the normal, physiological human body, connect the trillions of nodes with scalable software algorithms and suck out the draft of the proper sequence of consecutive treatment/regeneration steps later. Fortunately not only life extension technology needs systems biology projects (this is not enough for getting grants), but more importantly the effective design of new drug targets and the discovery of disease biomarkers are clearly crying for the systemic level. The urgent diagnostic and therapeutic demands are sufficient to launch international, many-lab projects.

Finally a complete ‘Human Proteome Project’ is in the pipeline (illustration via BioMed Search). It aims the tissue-level complete knowledge of the human proteome revealing “which proteins are present in each tissue, where in the cell each of those proteins is located and which other proteins each is interacting with”. Keep in mind also that around 21’000 human genes encode 1 million different proteins and that the effort cannot localize exactly which cell types in a given tissue is producing which protein. According to Nature’s Helen Pearson: Biologists initiate plan to map human proteome

“Those involved in the draft plan say that a human proteome project is now feasible partly because estimates of the number of protein-coding genes have shrunk. It was once thought that there might be around 50,000 or 100,000, but now, just 21,000 or so are thought to exist, making the scale of human proteomics more manageable. And the group plans to focus on only a single protein produced from each gene, rather than its many forms.

The plan is to tackle this with three different experimental approaches. One would use mass spectrometry to identify proteins and their quantities in tissue samples; another would generate antibodies to each protein and use these to show its location in tissues and cells; and the third would systematically identify, for each protein, which others it interacts with in protein complexes. The project would also involve a massive bioinformatics effort to ensure that the data could be pooled and accessed, and the production of shared reagents.”

The idea is to analyze and list all the proteins manufactured by chromosome 21 within 3 years as a pilot study and then finish the whole project within 10 years. Chromosome 21 is the smallest child in the family and likely contains between 200 and 400 genes, so the pilot study can yield us a couple hundreds proteins. Another powerful idea (actually I prefer this) is to start with the human mitochondrial proteome which is around 1000-1500 proteins as far as I know, that is at least 3 times as many as encoded by chromosome 21. Continue reading

How to predict the future via Twitter: Google invests in Navigenics

Wow, I guess it’s time for me to move into the stock market business! Here’s the story via David Bradley’s tweet: Julie Kent, Search Engine Journal, April 21st, 2008: Google Wants to Index Genetic Information, Invests in Second DNA Start-Up

In 2007, Google made headlines when they invested $4.4 million in 23andMe, a genetic screening start-up company began by Anne Wojcicki, the wife of Google co-founder Sergey Brin, and a business partner. But if you thought that was Google’s only interest in genetics and DNA, you’re wrong. Google has also been investing in a second DNA start-up called Navigenics, which for $2,500 and a small bit of saliva will provide you with genetic test results delivered securely online containing information about the likelihood for 18 medical conditions.

What’s really funny here is that I predicted this investment last Friday, on the 18th, on Twitter. The original idea was Aaron Swartz’s Google thought experiment: Imagine you were suddenly put in charge of Google. What would you spend your time doing? I came up with this answer (picking Navigenics because of ther profile and location) on behalf of Sergey Brin:

The whole tweetstream: Continue reading

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 Continue reading

Follow @biotecher, a solution to find all biotwitterers in 1 place!

Twitter effects blogging habits in many ways (see the term microblogging) and it is frequently the premier source of fresh web information. The number of biology and science related Twitter users are steadily growing, so today I created the @biotecher account in order to find every biotech, biology, medicine, bioinformatics related twitterers at one place and follow them. That is a guide for newly registered Twitterers who want to find their professional community on Twitter too.
How does it work: at this point, manually, everyone who follows @biotecher will be reciprocally followed by @biotecher and the account info will be shared in order to expand the biotwitter bubble.

Update: A person that uses Twitter is a Twitterer rather than a Twitter.

Thesis live: 1.2 Liver, regeneration and stem/progenitor cells

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

1.2. Tissues, organs with different turnover and regenerative potential

/bioenergetics data missing/

Liver

During organogenesis the hepatic endoderm epithelium invades the surrounding mesenchyme to form the liver bud and continued epithelial/mesenchymal interactions stimulate cell proliferation and morphogenesis. Consequently, the liver is largely of endodermal origin – including cells with a mesodermal origin and – and contains many different cell types: two epithelial liver cell types, the hepatocytes and bile duct cells, stellate cells (formerly called Ito cells), Kupffer cells, vascular endothelium, fibroblasts, and leukocytes (Desmet 1994). Hepatocytes are the main funtional liver cells accounting for ~70% of the cells in the liver and form the bulk of the liver weight (90%), yet only ~60% of total liver DNA is hepatocyte-derived (many of them with 2n, 4n, 8n DNA content). An adult human liver contains about 80 x10(9), hepatocytes. Hepatocytes are in a quiescent state and the turnover rate is low, 1-2 times/year[]. The remarkable regenerative potential of liver is well-known, in humans the liver almost completely regenerates in about 1 month after two-thirds (up to 75%) partial hepatectomy and this process can occur repeatedly in contrast to most other parenchymal organs, such as kidney or pancreas. In the literature the term liver or hepatic stem cells is used for precursors of the hepatocytes and the bile duct epithelial cells. On the other hand liver stem/progenitor cells can be define in different ways. Continue reading

Thesis live 1.1 The stem cell niche

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

1.1 Stem cells and regenerative medicine

The concept of the stem cell niche was first proposed theoretically by Schofield exactly 30 years ago in the context of hematopoietic stem cells: “a hypothesis is proposed in which the stem cell is seen in association with other cells which determine its behaviour. It becomes essentially a fixed tissue cell. Its maturation is prevented and, as a result, its continued proliferation as a stem cell is assured. Its progeny, unless they can occupy a similar stem cell ‘niche’, are first generation colony-forming cells, which proliferate and mature to acquire a high probability of differentiation, i.e., they have an age-structure.”

Niches are restricted and specialized tissue microenvironments that integrate local and systemic signals for the regulation and maintenance for resident stem cells. The elements of the stem cell niche include the constraints of the architectural space, cellular components like stromal supporting and descendent/progenitor cells and acellular elements, like soluble and membrane bound molecules, paracrine and endocrine signals from local or distant sources and neural input [Figure by Jonas].

Niches are dynamic entities, could be redistributed and ideally “a candidate niche Continue reading

The Tweet Cloud of a biotech geek blogger

With TweetClouds (scripting: John Krutsch design: Jared Stein) people can generate the Tweet Cloud of a Twitter user. In case of bloggers/Twitters it is an interesting question whether there are any strong differences between the category cloud/Tweet Cloud of the same person suggesting patterns in web behavior. I’ve just generated mine. One obvious difference is that with TweetClouds including replies to other Twitters (there is an option to suppress @replies, but why would you?) there is also a social/networking component (check the names after @) instantly visible on the generated cloud.

Thesis live: 1.2 Kidney and stem cells

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

1.2. Tissues, organs with different turnover and regenerative potential
In the adult kidney the nephrons (approximately 500 000 nephronic units/kidney) develop from the metanephric mesoderm/mesenchyme while the collecting ducts are coming from the ureteric bud. The kidney is a complex structure with at least 26 different cell types. The renal function is particularly age-dependent (loss of functional renal mass up to 25%). The kidney is an active tissue with high energy demand and contains a lot of mitochondria (especially in the proximal tubules). On the other hand, while the turnover rate is low, there is a robust although limited regenerative response to acute kidney injury. The candidate cellular sources of recovery, replacement: adjacent, less damaged tubular cells, resident adult kidney stem/progenitor cells and circulating mesenchymal cells from the bone marrow. Amongst others the following cell surface markers were used for isolating/enriching stem cell/multipotent renal progenitor populations: CD133, stem cell antigen-1 (Sca-1), CD24, CD90, Pax-2, Oct-4, Rex-1 (see table).

One such population was isolated from the cortical interstitium making up 0.8% of all cortical cells and were capable to differentiate into epithelial and endothelial like cells in vitro forming tubular structures in SCID mice [Bussolati et al, 2005]. In the lack of definitive markers of kidney stem cells not much certain could be said on the kidney stem cell niche.

Literature: Gupta S, Rosenberg ME. (2008) Do Stem Cells Exist in the Adult Kidney? Am J Nephrol. 19;28(4):607-613

Percy CJ, Power D, Gobe GC. Renal ageing: changes in the cellular mechanism of energy metabolism and oxidant handling. Nephrology (Carlton). 2008 Apr;13(2):147-52.

Bussolati B, Bruno S, Grange C, Buttiglieri S, Deregibus MC, Cantino D, Camussi G. (2005) Isolation of renal progenitor cells from adult human kidney. Am J Pathol. 2005 Feb;166(2):545-55.

Dear StartupSearch: Is 23andMe a web-based startup or not?

1. A start-up is a company with a limited operating history (Wikipedia).

2. Startup search

“tracks the web technology ecosystem commonly referenced as “Web 2.0.” We collect facts and figures about new web products, startup companies, key startup employees, and the funding dollars powering their growth.”


3. 23andMe is a pioneering web-based, personalized genomics startup (founded in April, 2006) with a high-tech service, a definitely “Web 2.0″ website & investors most Web 2.0 startups only dreaming of.

4. Why is 23andMe not tracked by StartupSearch? Continue reading

Thesis live: 1.1 Turnover or Every cell has a lifespan

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

1.1 Stem cells and regenerative medicine: basic concepts

/turnover: cellular turnover/

The concept of biological turnover (rate) can be interpreted on many levels: molecules, molecular pathways (signaling), organelles, cells, tissues, organs. The turnover rate by which a biological entity is replaced can be quantified by measuring its half-life. /In abstract form “the half-life of a quantity whose value decreases with time is the interval required for the quantity to decay to half of its initial value” (Wikipedia) I have to check whether it is problematic to explicitly use a Wikipedia entry – I am sure it is used implicitly – in a PhD thesis/ The concept of half-life refers to the time required for an initial quantity of entity E to decay half of its initial value. According to Caplan [reference]: “Every cell in the body has a specific half-life; every cell comes to maturation and will, predictably, drop dead in due course.” For instance erythrocytes have half-lives of 60-90 days and the turnover rate of hepatocytes is 1-2 times/year. On Figure 1 from Caplan the lineage development of a differentiated cell and its replacement cell is delineated. The relative position of these two curves to one another defines growth, steady-state, or atrophy depending on when the first cell dies and when its replacement, the second cell, comes online. /I am not sure here how to solve the problem of legends in the case of figures coming from the literature but I figure it out, here is/

caplanturnoverfigure

Continue reading

Thesis live: 1.2 tissue/stem cell introduction scheme

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

When producing a text, a post my building strategy is not linear, but heavily non-linear (I wouldn’t say it’s circular): I’d like to jump to the part of the story where there is something instantly to write/edit; be it the beginning, middle or end. In case of scientific articles frequently the first part to be build are figures/methods, which forms the bulk, the middle of the story after introduction, before discussion.

1.2. Tissues, organs with different turnover and regenerative potential

In order to discuss the different adult tissues in a unified manner, from a systemic point of view, I use the following tissue/stem cell introduction scheme where data are available: development of particular tissue, number of cell types, bioenergetics (high/intermediate/low energy demand), turnover (high/intermediate/low), regenerative potential (high/intermediate/low), resident stem cells, niche, markers, cell sources from other tissues that can contribute to the particular tissue during normal turnover or chronic/acute injury.

Leigh syndrome – where are those mitochondria replacement therapies?

Dear Sir: I came across your blog after reading Stanley Bing’s recent article in Fortune Magazine. I will try to be brief.

I have a 4 year old son who was diagnosed 1.5 years ago with a form of Leigh’s disease; one of the most devastating forms of mitochondrial disease. While he is receiving care from some of the most experienced doctors in the area of mito disease, as you are probably aware the general approach is to prescribe a vitamin regimen and “keep him comfortable.” That is to say, there is no cure or treatment for the disease, and the few centers that are researching the disease are not close to finding one. Since the disease is degenerative, this is a hard pill to swallow.

I am writing to you in hopes that you can recommend doctors or research centers that are applying experimental techniques to treat the disease through systemic regmed, stem cell or other methods. If I wait for traditional medicine to find a treatment (and especially the FDA), I fear it may be too late for my son.

Any help or advice would be appreciated.

Best regards -

Joe Mileti
[miletijoe][at][hotmail.com]

Dear Mr. Mileti,

thanks for your honest mail. The kind of organellar, mitochondrial therapy that would be needed in order to replace the Continue reading

Thesis live: 1.1 Basic concepts: Let’s roll!

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

After the Introduction draft it’s time to actually start to fill in the text and that’s really the hard part. In the text I mix complete sentences, paragraphs (source code, object language) with fragmented metacomments (labeled as /draft, comments are here/) as a GTD technique. Used literature, links come after the text in a reference form like: Rando TA. Stem cells, ageing and the quest for immortality. Nature 2006;441:1080-1086. or Rando TA. (2006) Stem cells, ageing and the quest for immortality. Nature 441:1080-1086. (maybe I should check the official rules here)

Figures, diagrams will be included and I don’t promise to figure out brand new ones (but promise to find good ones), but that’s not a necessary job for thesis writers.

Expect me to start with a low quality (including older texts of mine) material and progress toward something more valuable.That is a trend people usually would like to follow throughout their professional careers.

1.1 Stem cells and regenerative medicine: basic concepts

Looking for the exact definition of stem cell is sometimes the source of endless semantical debates, but at least we do know two generally accepted criteria: stem cells are able to renew themselves and could differentiate into other type of cells. First, they are unspecialized, mitotic cells that renew themselves for any (i.e. long) periods through series of cell divisions, which result in similar unspecialized stem cells. This is the so called and overstated “immortality” characteristics. Continue reading

Oxygen control of stem cell niches and cell fates

Did you know that physiological normoxia generally falls in the 2-9% O2 (14.4-64.8 mm Hg) range for most adult cells in vivo? 3 remarkable exceptions are thymus, kidney medulla and most importantly bone marrow which can exist at 1% O2 (7.2 mm Hg). On the other hand, stem and progenitor cells are frequent residents of hypoxic niches and low O2 regulates their differentiation. Conclusion?

Although most cells are maintained in culture conditions at 21% O2, this is unlikely to be optimal for maintaining their normal proliferative or developmental state. The derivation of novel stem and undifferentiated cell populations should therefore be enhanced by culture in the range of 3–5% O2.

More on this very important and usually neglected oxyphsiological angle on stem cells, development and culture in the very uptodate review: The role of oxygen availability in embryonic development and stem cell function by Simon@Keith in Nat Rev Mol Cell Biol. 2008 Apr;9(4):285-96.

stemnicheoxydiff

Some stem cells (such as those in the endosteal bone marrow compartment) occupy extremely low O2 microenvironments (<0.5% O2) Continue reading

“What is the meaning of life?” for a life extensionist

In No kidding, I am a cum laude philosopher, and so can you! it turned out that finally I got a philosophy diploma. That said, from now on I am officially qualified to think on the big questions of life. For instance, I can find out new arguments and concepts and I can answer (or at least fine-tune) questions like: ‘what is the meaning of life?’. (The best analysis of this question for me was Robert Nozick‘s Philosophy and the Meaning of Life in the last chapter of his book Philosophical Explanations, for an official intro see Stanford Encyclopedia of Philosophy)

So here is a short analysis and an answer of mine to this most important philosophical question from the point of view of a life extension supporter:

1. premise: this question could be answered only if it not about the general meaning of all life, but the particular meaning of individual human lives.

2. analysis: let’s fill the question up to show the variables in it: ‘what is the meaning of an individual human life (x) for somebody individual (y)?’ Continue reading

Michael Kingsley on competitive, bitter, boomer longevity

mineislongerthanyoursnewyorkerMichael 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): Continue reading

36 Life extension idea killers: mental practice for the pros!

Today’s meditation is for serious healthy life extension supporters to consider the following 36 – general and sometimes corporate – idea killers concerning our little project:

1. We tried that already
2. We’ve never done anything like that before.
3. Has anyone ever done anything like that before?
4. That never works
5. You’re fired
6. We will actively work against you
7. Laughter
8. Not in our budget
9. Not an interesting problem
10. We don’t have time/We’ll never find the time to do it. (I specially liked this one.)
11. Execs will never go for it
12. Out of scope/Not in our business
13. But its the law
14. Too blue sky / Holy grail
15. Wont make enough $$
16. That isn’t what people want
Continue reading