Mapping neurons without glial cells ~ SNP genotyping w/o whole sequencing?

Nature’s Journal Club column is usually a good & always a short read providing exciting angles on scientific topics/papers from good researchers. Recently ‘neuroscientist’ Dave Featherstone argued for a broader approach to brain mapping by not restricting it only to the connectome between neurons. Neurons are making up less than 10% of the human brain while most brains cells are glia neglected by scientists making the wiring diagram of a ‘complete’ human brain.

For example, consider the recent study of adenosine and sleep led by Philip Haydon and Marcos Frank at the University of Pennsylvania in Philadelphia (M. M. Halassa et al. Neuron 61, 213–219; 2009). Adenosine binds to receptors on neurons, thereby regulating neuronal signalling. Interestingly, adenosine seems to represent ‘sleepiness’: it accumulates during wakefulness and dissipates during sleep. Where does it come from? It is generated from adenosine triphosphate (ATP), which is secreted by astrocytes — a major type of glia.
Therefore, if we want to map the functional brain connections controlling sleep, we need to include glia and the extracellular space between glia and neurons. If we’re going to understand brain function by mapping the brain, we need to include most of the brain in our map.

I tried to draw an analogy between the situation in brain mapping and personal genomics on FriendFeed:

brainmappinganalogy

Update: it seems Dave Featherstone had something similar in mind as an analogy, he answered my email the following way:

Yeah, that’s a good analogy. The original version of my column said the connectome would be like if the human genome had only sequenced exons. But that sentence was cut for space considerations.

Nature Insight: The complex trait of quantitative genetics

Nature’s newest issue has a Quantitative genetics supplement with 3 free access pieces included out which I find this review the most interesting: Reverse engineering the genotype–phenotype map with natural genetic variation by Matthew V. Rockman. There’s a lot information to digest and many patterns to understand in this background field in order to approach the future of (personal) genetics/genomics.

naturequantittivegenetics

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.

naturepersonalgenomes

“blogs.nature.com v1 is live” and beyond

A new, completely rewritten, integrated nature.com website blogs.nature.com has been launched by the Natureplex people – informed his Twitter pals Euan Adie:

Also, blogs.nature.com v1 is live! Tequila and donuts all round. Early n’ often release v2 coming on the 18th so get any bug reports in now.

natureblogs

Suggest good science blogs that are not listed on the Nature Blogroll yet.

Compare scientific websites with a new Google Trends layer!

I always had the feeling that the Natureplex (the web division of the Nature Publishing Group headed by Timo Hannay) is ahead of most scientific journal publishing conglomerate’s similar departments. Now with the help of a new Google Trends layer that compares websites in terms of traffic this impression was confirmed again without strict numbers. I hope that more and more scientific journals gain incentives finally to experiment with new web technologies. Also a quick look to the Regions comparison on the bottom left helps you give up the history based conclusion that Science is the number 1 on the web in the US compared to Nature while Nature is so UK and Europe centric.

“Today, we add a new layer to Trends with Google Trends for Websites, a fun tool that gives you a view of how popular your favorite websites are, including your own! It also compares and ranks site visitation across geographies, and related websites and searches”

Source: Official Google Webmaster Central Blog via Webmonkey

The same comparison with Alexa: Continue reading

What path would you follow: Shumway or Barnard?

Monya Baker has an excellent Q&A with the authors of the recent Nature Insight: Regenerative Medicine over at The Niche blog. Ken Chien, the author of Regenerative medicine and human models of human disease – see earlier postrecalls the paradigmatic story of heart transplantation and the 2 main surgeons behind, Norman Shumway and Christiaan Barnard, who are perfect representatives of the different paths of pioneering clinicians:

Sometimes in looking forward it’s good to look back. In cardiac regenerative medicine, probably the only clear success to date is heart transplantation. From the initial grant that Norman Shumway received in 1958 [to study the possibility of heart transplantation] it took more than two decades before the procedure became routine.

Shumway was a careful, thoughtful man. He not only didn’t do the first heart transplant; he didn’t do the second. He was slowed down in the United States because of the regulatory barriers and ethical concerns. Christiaan Barnard, on the other hand, went back to South Africa and decided to just go for it. Sounds familiar?

We realized very quickly that this was not working, that the science was not there. In 1968, a year after his first attempt, Barnard gave up on the procedure and considered it a failure. Everyone gave up, except Shumway. He went back to the lab and spent the next ten years figuring it out. He realized that the issue was rejection. Continue reading

Problem: embryonic stem cell lines vary & iPS lines too

Finally I started to digest all the articles (usually on the streetcar on my way to work and home) from the recent Nature Insight: Regenerative Medicine and I try to pick up some stories for you (& interesting enough for me) from that, in case you are not lucky enough to have an available copy.

For clinicians, the lack of gold standard embryonic stem cell lines with the measurably same regeneration potential will be a huge technological problem later while this variability is an interesting basic science problem today.

Kenneth R. Chien: Regenerative medicine and human models of human disease

A central challenge to the development of human stem-cell-based models of disease lies in the need to isolate and expand rare cell populations reproducibly and then to fully differentiate enough of the cells of interest. In this regard, one of the main obstacles to establishing human ES-cell-based models is that ES cell lines vary. All lines do not have the same potential to differentiate into cells of a particular lineage, most probably as a result of inherent epigenetic, genetic and developmental differences at the time of their isolation. For example, a study of 17 independent human ES cell lines showed that 7 of these lines had little or no capacity to enter the cardiovascular lineage, and the level of cardiovascular markers expressed by 2 of the 17 cell lines was an order of magnitude or more higher than that of these 7 lines. Similar variability between human ES cell lines was observed for entry to the pancreatic lineage, and cell lines that were optimal for generating cells of endodermal lineages were extremely poor for generating mesodermal lineage cells in many cases. Thus, new human ES cell lines that are optimal for generating specific lineages of interest need to be produced. In addition, iPS cell lines might be similarly variable. Continue reading

Personal genetics test-takers are future risk-takers

A good introduction in Nature on the risks and advantages of letting people know their genetic risk information via personal genetics services. I do hope that the test-takers will finally become the risk overtakers.

Helen Pearson: Genetic testing for everyone

Direct-to-consumer genetic testing is a rapidly growing market — the past year has seen the launch of companies, such as Navigenics and 23andMe in California and DeCODEme in Iceland, that offer DNA screening for a range of common genetic variants linked to disease. The testing outfits have created a buzz in the business and research communities as well as in the wider public: Google has invested in two of them and Navigenics briefly opened a store in New York’s hip SoHo district.
“It’s an intriguing idea that you can peel back your genome and reveal your future.”
The idea is that test-takers will be alerted to risks and so take preventive action where possible. But psychosocial scientists who study how people respond to risk information say there is scant evidence that people are affected deeply by genetic test results, or that such tests spur much change in behaviour.
Continue reading

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

Nature’s Great Beyond on the Warda-Han-Proteomics-Creator paper

Peer review, ‘a mighty creator’ and an almighty row

However the paper was only retracted for “a substantial overlap of the content of this article with previously published articles in other journals.”, not for the strange “mighty creator” line. Peer review isn’t perfect but you’d hope it would catch something like this.

Stat freaks, are you ready to play with the SCImago Journal & Country Rank?

Finally the Google PageRank algorithm, the core analysis tool of the current web is back to where its idea is originated from, scientific citation analysis. The recently launched SCImago Journal & Country Rank database uses an algorithm very similar to PageRank. It has a new metric: the SCImago Journal Rank (SJR). According to Nature:

A new Internet database lets users generate on-the-fly citation statistics of published research papers for free. The tool also calculates papers’ impact factors using a new algorithm similar to PageRank, the algorithm Google uses to rank web pages. The open-access database is collaborating with Elsevier, the giant Amsterdam-based science publisher, and its underlying data come from Scopus, a subscription abstracts database created by Elsevier.

The SJR also analyses the citation links between journals in a series of iterative cycles, in the same way as the Google PageRank algorithm. This means not all citations are considered equal; those coming from journals with higher SJRs are given more weight. The main difference between SJR and Google’s PageRank is that SJR uses a citation window of three years.

From now on every stat geek can compare journals to journals, countries to countries based on different metrics like citable documents, cites, self-cites or the new h-index and get a ticket to recursive heaven. Of course I started with the comparison of Nature and Science to find something very different. I couldn’t. I predict that self-cites will show a lot on how things are going on at different scientific journals and the stats will be used as serious arguments in many blog posts. But here let me share some graphs on the quick comparison of USA, UK and China in the category of Aging.

SJRcompare

First graph: citable documents Continue reading

Nature Editor-in-Chief’s changed mind on enhancement drugs for healthy people

philip campbellPhilip Campbell, the open editor-in-chief of Nature was asked by John Brockman under the cover of the 2008 Edge Annual Question: WHAT HAVE YOU CHANGED YOUR MIND ABOUT? WHY?

Campbell writes in his thoughtful answer:

“I’ve changed my mind about the use of enhancement drugs by healthy people. A year ago, if asked, I’d have been against the idea, whereas now I think there’s much to be said for it.”

Before citing further the argument of Campbell I’d like to remind the analogous problems of biotechnological life extension products targeted for healthy people in a “normal” physiologic state. Good example are the resveratrol-like but more effective sirtuin activators with a probably positive healthy lifespan extension effects developed by David Sinclair and his group at Sirtris. The trick is to market Sirtuin activators as anti-diabetes drugs, or find other registered diseases to target with the drugs. According to Mass High Tech:

“Aging is not a disease to the FDA,” Sirtris co-founder Christoph Westphal said, so Sirtris is focusing on drugs to treat ailments of old age.

With this story in our changed and future focused mind it is very promising to read for healthy life extension supporters what Campbell, a mainstream academic science representative has to say on cognitive enhancement drugs:

New cognitive enhancing drugs are being developed, officially for therapy. And the therapeutic importance — both current and potential — of such drugs is indeed significant. But manufacturers won’t turn away the significant revenues from illegal use by the healthy.

That word ‘illegal’ is the rub. Off-prescription use is illegal in the United States, at least. But that illegality reflects an official drugs culture that is highly questionable. It’s a culture in which the Food and Drugs Administration seems reluctant generally to embrace the regulation of enhancement for the healthy, though it is empowered to do so. It is also a culture that is rightly concerned about risk but wrongly founded in the idea that drugs used by healthy people are by definition a Bad Thing. That in turn reflects instinctive attitudes to do with ‘naturalness’ and ‘cheating on yourself’ that don’t stand up to rational consideration. Perhaps more to the point, they don’t stand up to behavioral consideration, as Viagra has shown.

Research and societal discussions are necessary before cognitive enhancement drugs should be made legally available for the healthy, but I now believe that that is the right direction in which to head.

The received view in 3.5 paragraphs on Ending Aging in Nature (part 1)

In the 15 November Nature issue Judy Illes neurology professor turned neuroethics expert reviews Enhancing Evolution: The Ethical Case for Making Better People by John Harris and Ending Aging: The Rejuvenation Breakthroughs That Could Reverse Human Aging in Our Lifetime by Aubrey de Grey & Michael Rae.

From the review:

“Ending Aging is a more “new wave” treatment of enhancement, longevity and immortality…. The authors rather unnecessarily brand ageing as repugnant and curse, and use their book to preach on fund-raising opportunities.
The freedom to pursue ways to enhance human mental and physical capacities and to eliminate negative aspects of the human condition, such as suffering and death, is a fundamental tenet of the trans-humanist movement. Although seemingly worthy, there are problems ahead for the futurists, including for Harris, de Grey and Rae….

…Let’s not throw away today for tomorrow. Ending Aging is likely to appeal to those already converted to the author’s views, and perhaps will find some traction among those who are more curious than interested in deeper scientific engagement.”

Unfortunately Illes completely mixes transhumanism with the belief that robust life extension is possible and desirable due to handling the 2 books together and I think this is not a fair angle on life extension. Consequently she can say on the whole that those beliefs are “going well beyond what might be imaginable, or ethical today.”
But most life extension supporters are simply not transhumanists at all and it is a simple logical fault to think that ‘if A then B’ is true (every transhumanist is a life extension supporter), than it follows that ‘if B then A’. For instance, most life extension supporters that I’ve met, say in the SENS3 conference, are not transhumanists, but simply young life scientists for whom life extension is just the technological frame (the highest aim) of their translational science. Think systems biology: human organismal aging is a complex dynamics of a complex system and if you want to modify it you should think on the systemic level. Continue reading

23andMe: Genetics brings people together, rather than differentiate

“We are all from the same seed” – Kara Swisher summarizes what she heard from Linda Avey, co-founder of web based personal genome service 23andMe in the video interview below. Linda and the other founder Anne Wojcicki just talked about the company’s ancestry, genetic comparison and similarity seeking services, the ones that will technologically turned into a social networking service later based on shared genotypes backed by the genetical connectedness of all people (in this case all 23andMe customers). I called this idea the social networking XY.0 yesterday.

Linda’s thought was the following: “If genetics has the basis to bring people together, rather than differentiate them, that’s gonna be really interesting.” (Thanks Deepak for finding the videos)

In a recent Nature report by talented journalist Erika Check Hayden called So similar, yet so different we can find the following expert opinions on the very same topic that is commercialized and envisioned now by 23andMe (citing lengthy here, emphasis by me): In his 2000 State of the Union Address, President Bill Clinton chose to emphasize something he had recently heard from a genome researcher: that humans are all, irrespective of race, 99.9% the same genetically. “Modern science,” he told his country’s legislators, “has confirmed what ancient faiths have always taught: the most important fact of life is our common humanity.” Seven years on, and four years after the final publication of the sequences from the Human Genome Project, new technologies and larger data sets are allowing genome biologists to answer a conundrum embodied in that unity-inspiring percentage: if our DNA is so similar, why do we seem different in so many ways? Continue reading

Interdisciplinarity explained: “Eclectic others, who are smart and fun to have around”

brainnatureI’ve found the following perfect quote in Paul Smaglik’s NatureJobs report on the current human brain mapping efforts of scientists all around the world (emphasis by me): Interdisciplinary groups are trying to combine imaging approaches and analyse them with statistics, and computational and mathematical modelling. Nikos Logothetis, a professor in physiology and cognitive processes at the Max Planck Institute for Biological Cybernetics in Tübingen, Germany, has combined data from fMRI and electrophysiology and wants to do both approaches simultaneously, then use “lots and lots of mathematics” to build circuit diagrams.

Karel Svoboda, a group leader at the Howard Hughes Medical Institute’s Janelia Farm campus, says that all 15 neuroscience groups there take a similar approach, but concentrate on specific regions of the cerebral cortex. Janelia plans to add 10–15 more leaders, says Svoboda: investigators examining neural circuits who use imaging tools; physicists, engineers and computational scientists who are building tools; and “eclectic others, who are smart and clever and fun to have around”.

Finally I understood the essence of interdisciplinarity in a sentence fragment. Thanks, Karel Svoboda.

Tim O’ Reilly at Nature: science meets bored tech-savvyness to find new things

timandtimoAs a biotech geek blogger and occasionally Make contributor, who stands at the intersection of science and technology with a (life) science bias, it is more and more exciting to see how the attractive brands of the 2 sides are building the bridge and creating a shared channel. So far, the biggest manifestation of this shared channel was the SciFoo Camp, organized by Nature and O’Reilly, hosted by Google. Now Tim O’Reilly, a native of Cork, Ireland turned Californian tech publisher visited the Nature Headquarters and talked about his angle on the web and tech publishing (giving me an incentive to finish the story of my earlier visit at Nature at September). You can read the informal account of Timo Hannay on the meeting at Nascent (picture: my shot on Tim and Timo summarizing the SciFoo experience at the Googleplex).

One thing seems more visible to me: Tim is bored about his original business and industry and is looking for some new which he seems to find in…. science (see Craig Venter and Tim O’Reilly chat: when 2 worlds meet).

The computer industry was a very exciting place, and then it became boring, because it became consolidated. ..There is going to be a lot of consolidation, the man will take over (he might be idealistic like google), it is going to get a lot more boring. The interesting question is what will happen when google’s growth slows down?
But you have to have a belief in people’s ability to find new things. There are going to be a lot new areas coming out of science, one thing we can do is to help to birth the future.

or: What happens when folks from synthetic biology meet hedge fund hackers meet roboticists and makers?

Tim’s boreness is really good (not the burned out part) for scientists like me. For instance, one of my ideas (an idea briefly communicated to Phil Torrone at the Austin Maker Faire) is to collect enough bioDIY projects like the “Make stem cells from the placenta at home” together, that is enough to set up an exclusive “sciencey” BioMaker Faire. Continue reading

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. Continue reading

The Laboratory Website and Video Awards by the Scientist!

LaWVas logoLaWVas nominateHere is a classical web story told in links: a niche blogger got an idea and tries to outsource it, it is popularized by other bloggers, then goes mainstream with the help of a science journal, grows over little blogger’s head and get realized by another powerful science institution.

That’s what happened with my unofficial lab website competition idea, which was featured in Nature back in May.

Let me introduce you to the Laboratory Website and Video Awards or LaWVAs (pronounced like “lava) hosted by The Scientist. (Disclaimer: I am a consultant to The Scientist on the LaWVA project and a member of the judging panel.)

The algorithm is as follows:

1. readers nominate their favorite academic or industrial lab websites

2. editorial team will review the nominations and provide up to 30 outstanding sites to the panel of judges

3. panel of judges (e.g. Elizabeth Kerr from Apple Inc. amongst others) will then carefully review these nominations, ranking their top choices in each category (design, usability, content, community), as well as making a selection for our “Judging Panel’s Best of the Web” award.

4. Once the panel of judges has completed their review, it’s time to turn the voting back to you. The winning sites as selected by the editorial team, judging panel and the readers will be announced in this December.

Wow! Let’s make together a web-savvy laboratory culture!

Visiting the Nature Headquarters, part 1: the internal Nurture blog

MacmillanBuildingLondonMacmillanBuildingwholeEven those scientists, who don’t have any journalism, or out of niche discipline interests (the vast majority), would be eager to take a closer look at how Nature, the number one scientific weekly journal is made, how the articles are peer reviewed, how the column structure looks like, what are the future perspectives of Nature Publishing Group, how they are doing in the new web age, what the main problems are.

On the 10th, September I spent around 6 hours at the Nature Headquarters in London. The Macmillan building is an old Victorian house near King’s Cross at the Crinnan street.

For lunch I was happy to get the company of Nature’s Web Publishing group’s brain trust: Timo Hannay, Euan Adie, Ian Mulvany and Joanna Scott (pictures in the next post).

We started to talk about how work at NPG is organized and I asked the guys how functional the Nature email system (@nature.com addresses) is. It turned out that the mail storage capacity is poor (still in the MB range), so heroic manual delete fight is needed against full mailboxes. But instead of an efficient email system, there is an internal, email killer corporate blog called Nurture (don’t mix it with the Nurture’s magazine for Nature authors) which works perfectly well.

Ian Mulvany, Connotea experimenter, was kind enough to send me the first post of Nurture by Ben Lund (former Connotea project manager turned freelancer) from 2003 in the name of radical transparency. So here I am pleased to blog this historical first post accompanied by the current tag cloud of the Nurture blog. As Ian says retrospectively: By placing it on a blog the readership can self-select. It also allows for consumption independent from interruption. Continue reading

Pimm’s Pubmed filter post in Nurture’s “Science 2.0″ issue

The edited version of Pimm’s January 30th, 2007 post How to filter and read PubMed articles through RSS feeds? was published in The Summer 2007 issue of Nurture, the magazine for past and present Nature journal authors. According to Maxine Clarke, Nurture editor: The Summer 2007 Issue of Nurture celebrates our blossoming “science 2.0″ activities, which invite authors and reviewers to participate with Nature Publishing Group in an interactive, global scientific community. Indeed, there are quick intros to Nature Precedings, Nature Network London, Nature Report Stem Cells, Scintilla, but besides that my favourite reading are the personal editor and author profiles. (On the cover of Nurture you can find one of my confocal microscopy pictures out of the Nature Precedings poster.)

pimmn

Mitochondria in the tubes of stem cells poster on Nature Precedings

naturemainwebsiteexploreBack in June I was a happy beta tester of Nature Precedings, Nature’s own free preprint server. I uploaded a poster of our group called Intact mitochondria migrate in membrane tubular network connections formed between human stem cells by Csordas, Attila, Cselenyák, Attila, Uher, Ferenc, Murányi, Marianna, Hennerbichler, Simone, Redl, Heinz, Kollai, Márk, and Lacza, Zsombor. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2007.44.1&gt; (2007).

Meet the nodes, “clustered hubs” and links of clathrin-mediated endocytosis

vesicleformation2Network biology is a way to integrate fragmented benchwork data in order to understand complex biological phenomena. In a recent Nature paper, entitled Integrating molecular and network biology to decode endocytosis Cambridge (UK) researchers authors Eva Schmid and Harvey McMahon of MRC, Cambridge give a good example of a predictive and experimentally useful systems biology approach. As in many cases in the current literature, the formal, printed article is just the tip of the iceberg, and the “supplementary informationsection is as crucial.

Clathrin-mediated endocytosis (CME) is an important vesicle biogenesis pathway. Cargo is packaged into vesicles that are surrounded by a coat predominantly made of the protein clathrin and adaptor protein complexes. For instance at the synapse, clathrin-coated vesicles (CCVs) participate in retrieval of synaptic vesicles following exocytosis.

vesicleformation3Authors identify 2 hubs in this pathway: AP2 and clathrin triskelion and instead of putting them into the existing hub subtypes (‘date’ and ‘party’ hubs) they argue that neither are hubs at the beginning of CME, but mature into hubs by clustering either on the membrane or through polymerization. It is likely that many pathway/party hub proteins will oligomerize or cluster to function as pathway hubs. ‘Clustered hubs’ are a new subtype of hubs not previously described

I found Figure 3 particulary refreshing which depicts functional and connectivity views of vesicle formation in nerve terminals. (2 pieces included)

Experimentally testable consequences of the study: Continue reading

Trends in Nature’s July top ten PDF downloads: 5 stem cell papers!

Maxine Clarke over at Nature’s Nautilus blog published Nature’s July top ten PDF downloads.
July was a particularly strong month for Nature concerning pluripotency and embryonic stem cells as 5 out of the 10 top ten downloads, that is 50% of the most popular articles are tinkering with stem cell biology. The other trend: microRNAs, 2 papers. I wonder which could be the last research trend that reached that maturity and which will be the next.

SciFoo Camp, 2007: data (Google) publishing (Nature) geeks (O’Reilly)

SciFoo is over, and I’ve just arrived back to New Orleans from SF. First of all: a big thanks for the organizers (Chris DiBona, Timo Hannay, Tim O’Reilly, Google, Nature, O’Reilly) and campers, it was really the highest end. Here is a quick SciFoo key terms summary (photos, detailed accounts later):

“scientific data”

One of the most frequently used key term was “scientific data”. And the question is: how to collect, upload, organize and index them. With the exponentially increasing data sets, that are produced by scientists worldwide, it is obvious that we need really powerful tools to benefit them. After a couple of beta years it is highly probable that Google (according to its mission statement) will offer new ways to manage the enormous amount of valuable scientific data. Without that, the efficiency of the science industry will dramatically decline.

“science publishing”

Yes, the old question ranging from open access science to different pre- and post publishing opportunities, addressing peer-review tools. A new and clear vocabulary is needed. Nature people were honest about the problems, asking for the optimal solutions.

“the geek factor”

Mainstream scientists are rather conservative folks, they can easily have revolutionary thoughts in their niche research fields, but are not too open minded and experimental when it is about new web and technology tools. The alpha geeks from the O’Reilly Media reminded the science population of the SciFoo (not the typical technology neutral mainstream scientists) that there are many innovative things that could be done in and out of science too. (You don’t necessarily need the newest Mac gadgets for that, just try out some mind performance hacks)

The architecture of the scientific web, a must read/see from Timo Hannay

Natureplex boss Timo Hannay published a landmark article draft on the web opportunities for the (more and more NPG boosted) scientific web. He highlighted 3 areas: audio-video content, databases (my emphasis), social software and summarized the science webspace with an artistic figure:

scientificwebhannay

Nature’s Superb Many Worlds Retro Cartoon Cover, quantum physics and SF

The current issue of Nature looks like something especially targeted for geeks with a high end content. Consider again the role of comics in science popularization. Is this Nature, not Wired?
From the Editor’s Summary: “Yes, this is Nature. The cover art, by David Parkins, salutes a big year for quantum physics: 50 years ago, Hugh Everett III proposed what came to be known as the ‘many worlds’ hypothesis. He took quantum physics at face value, and imagined what it really meant. He aimed to resolve the paradoxes of quantum theory by allowing every possible outcome to every event to exist in its own world. In a News Feature, Mark Buchanan reports on modern reactions to the ‘many worlds’ idea…. Life sciences also have their place in this fiction-inspired issue and the whole is brought together in an Editorial.”

Nature’s Many Worlds Retro Cartoon Cover

I first heard about the Many-World interpretation of quantum mechanics (proposed by Hugh Everett III) as a philosophy undergrad writing a bigger essay on the modal realism of my favourite analytic philosopher David Lewis. This philosophical-logical theory argues that possible worlds are as real and irreducible as the actual world.

Nature Precedings: a free preprint, poster and presentation sharing science service

Nature Precedings is “a free online service that enables researchers to rapidly share, discuss, and cite their early findings” launched on 18th June. I was really happy to be a beta tester, contribute and help to clear out some bugs. This line is from one of my mails 2 weeks before: “I find the idea of Nature Precedings the most advanced in 2007 on the academic Web.”

Well it is not the most advanced in the sense that it is based on a brand new idea (think about arXiv.org) but it is really advanced in realization, power range and timing as it is the product of the Natureplex, the web 2.5 flagship of mainstream science publishing. Also the poster/presentation uploading option seem quite new (correct me, if I am wrong). Posting posters and presentations is a good idea since a massive portion of scientific results is materialized only in the truly interactive poster/presentation form.

bradleyonnatureprecedings

I strongly hope that Nature Precedings won’t be the cemetery of finally unpublished and rejected paper seeds (a working voting system and a focus on posters/presentation can balk this) but the first distribution point of essential science results.

Coverages on Nature Precedings: Continue reading

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

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Scintilla, a science aggregator and recommendation engine freshly from the Natureplex

The Natureplex (Nature Web Publishing Department on the second floor of a renovated warehouse with around 25 people near at King’s Cross, London) nerds are still busy: Scintilla, a science recommendation engine was launched based on aggregating science content from RSS/Atom feeds of various websites. How could Scintilla (check what the term scintillation refers to, it is a good name) be harmonized with other products of the NPG, like Postgenomic, Connotea, Nature Network…is a future question. For me it seems that the developers would like to convince me to use Scintilla feeds (in the long run) instead of Google Reader feeds when the content is about science in general and in details. The key word is personalization and personal filtering and in that respect maybe it is worth to think of Google’s personalized search trials and web history. More info (including the mail of Euan Adie, developer): Scintilla and Scintilla brings personalization to science

scintilla

Biotech Geek Blogger goes Nature Stem Cell Blogger at the Niche

thenichelogoIn 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. Continue reading

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.”

theNiche

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

Nature Reports Stem Cells is live from now on…for stem cell enthusiasts

No more waiting: Nature Reports Stem Cells (NRSC) launched today, and so finally there is a fully web native, scientifically high-end (naturally), freely accessible, all-in-one stem cell research hub site for everyone (especially for the researchers) to read, share, contribute and turn the acquired insights back into new experiments, policies, ethics, businesses and clinical trials.

NRSClaunches

Edited by the devoted small team Natalie DeWitt (Editor at Large), Monya Baker (News Editor) and Jessica Kolman (Editorial Assistant), based in Nature’s San Francisco office, California (where else?) NRSC has a bunch of usual and unusual ways: news, featured editor, journal club with user recommended articles and voting system, interviews, events and the really exciting and experimental Insider the paper section. From the first editorial of NRSC: Inside the Paper posts edited discussions between authors and reviewers during peer review. Such transparency should not only deepen readers’ understandings of individual research publications, it will expose the workings of peer review itself. In the coming months, we plan to launch a Toolbox section will aggregate information on stem-cell protocols, reagents, and cell lines that would otherwise require trawling through literature or having serendipitous conversations at conferences.”

insidethepaperembryonic

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Industry and career focused stem cell report in the current Nature volume

Positively tuned (for the most part) report on stem cell science by Ricki Lewis: The hard cell Nature 447, 748-749 (June 2007) Excerpts, emphasis added by me:

research in the field is thriving globally. At least 500 companies and collaborations have sprung up, 100 of them in the past year alone

A solid background for a researcher includes a doctorate in molecular, cell or developmental biology, as well as skills to work with specific cell or tissue types… Continue reading

Forget about submitting your scientific papers written in Word 2007

Wow, I feel fresh air, although I am not sure whether the following news is a beginning of any deeper changes or not: From Science Authors Guideline: “Because of changes Microsoft has made in its recent Word release that are incompatible with our internal workflow, which was built around previous versions of the software, Science cannot at present accept any files in the new .docx format produced through Microsoft Word 2007, either for initial submission or for revision. Users of this release of Word should convert these files to a format compatible with Word 2003 or Word for Macintosh 2004 (or, for initial submission, to a PDF file) before submitting to Science.”

Tips: Undernews: SCIENCE PUBS REJECT ARTICLES WRITTEN IN WORD 2007
O’Reilly Radar: Science and Nature rejecting Word 2007 Manuscripts

One commenter in Undernews said: “This isn’t just Science and Nature. All Wiley journals now include the instructions: “[Journal] does not accept Microsoft Word 2007 documents at this time. Please use Word’s “Save As” option to save your document as an older (.doc) file type.” So don’t think it’s a singular problem — I’m sure if you visited all the science journal publications, you’d find similar instructions as well.”

What can I say: Prepare for the age of Google Office manuscripts and figures! All you need is a gmail account.

P.S. I made an attempt to coedit my ongoing first author article (desperately waiting for submission) by publishing the draft on Google Docs and adding the coauthors as collaborators, but only one coauthor (a med student) was kind enough to make one little correction this way. The rest is….well the majority of science people are living within the narrow world of Microsoft Office.

Editing my doctoral thesis on stem cells in a blog: Why not?

marie curie’s doctoral thesisOK folks, after reading the official rules about how to get and manage a doctoral thesis, and after speaking with my supervisor asking for his permission, I’ve decided to edit my ongoing doctoral thesis in Pimm. Or at least the introduction of it, which is intended to be no other than a review-like summary of some current results in the stem cell biology of different tissues, organs. What will remain hidden in the first round (but can follow later): the data-heavy yet unpublished results and the discussion, conclusion session. Objectives, Materials & Methods: we shall see it. Sounds like there are complete parts of the thesis, but that’s dead wrong, at this time my doctoral thesis is in an embryonic form. Also no idea on how challenging, meaningful this project, a sub-series in Pimm, will be. What I know is that continuous experimentation with genres and frames is the essence of free blogging!
After all, what do I risk here? If someday I’d like to write a review out of the published introduction, can this cause a publishing problem? According to Maxine Clarke, Publishing Executive Editor of Nature (i.e. peer review and publishing policy expert) the status of a thesis is: “No, a doctoral thesis does not count as “previously published” and yes, you can submit work that was part of your thesis, with an appropriate citation.”

I also asked Maxine by mail and she was kind enough to enlighten me: There is no problem with you publishing your thesis in this way, so far as consideration for publication of any part of it for a Nature journal is concerned (or any NPG journal). We encourage communication between scientists via discussion of work and unpublished drafts in the form of theses, meetings, preprint servers, online scientific forums (between scientists) etc. Continue reading

Laboratory website culture and Pimm in Nature: the real digital windows

Paul Smaglik, Naturejobs editor wrote a Prospects piece in the current Nature (yeah, the big one) in his column on laboratory website culture apropos of the highly unofficial lab website competition of Pimm. Read it, think it over and build better and more professional lab websites. Oh yes, and don’t forget to allocate the resources (see the comment of Anonymous Prof).

Nature 447, 347 (May 2007) Paul Smaglik: Creating better lab websites gives potential collaborators and recruiters a clearer window into your world.

smaglikpimmprospects

Maybe it’s the proper time to ask once again the question: Who wants to host the best laboratory website competition?

Nature Network Global Beta and social networking 2.0 for scientists

naturenetwork profileIf you are busy building a professional career and want things to get done, it’s time to forget MySpace, Facebook or any other social networking 1.0 sites, that are focusing on friendship, love, spam whatever with a general membership. What you need is social networking 2.0, which is based on the special profession you’re in, or is centered around a special topic. Ning, for instance, is a tool for creating your own social network for anything specifiable.

For the business and technology (mostly IT) sector LinkedIn is a more and more frequent destination. And, at last, there is a social networking starting point for every English-speaking (natural) scientist called the Nature Network (NN), which went global in February, after 7 testing months in the local hub Boston. It is still in Beta, just like all good “web 2.0 and more” apps.

First, I was informed about the plan of Nature Network Global from a comment of Corie Lok, main editor on NN, in the comment section of a Nature Blog in January. Corie was kind enough to share with me some recent initial stats on NN: We have more than 1800 registered users. When we relaunched in mid-February, we had 400. We’ve been growing steadily since February by about 100 to 150 new users registering every week. We’re now at about 100,000 total page views across the whole website. We had about 20,000 in February.

According to the numbers, Nature Network is currently a very small but organically growing strong online community. This is exactly the most exciting period in the life cycle of every forming network, so it is a guaranteed experience and challenge to join and participate – now at least – for people like me, who are eager to test and modulate every flexible beta product.

To get the key parameters and shed light on the prospects standing before NN, I’ve made the following table, which is a comparison of NN with relative and rival professional networking site LinkedIn:

natlink

As Gavin Bell neatly summarized the core architecture and aims of NN while writing on Nature Network Boston launches: “Some of the key features of the site are the groups, which allow individual communities to have their own spaces within NNB. Continue reading