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.”
Anna and me are visiting New York City from 8th to 11th, Sunday this week. We are eager to meet geeky figures particularly as our current location, New Orleans is not really a heaven for tech-savvy people. If interested to meet with us, drop me a line: [attilacsordas][at][gmail.com]
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.
It seems that my favorite ever unconference, the SciFooCamp 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:Read the rest of this entry »
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.”
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.Read the rest of this entry »
“Skull is in the game zone, right now. And you don’t want to mess with him when he is in the game zone. He once played for 4 days straight on 1 quarter, a gallon of chocolate milk and an adult diaper.”
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:
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 cooperatorsRead the rest of this entry »
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.
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.Read the rest of this entry »
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].
With TweetClouds (scripting:John Krutsch design: Jared Stein) people can generate the Tweet Cloud of a Twitteruser. 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.
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 st
