by seanmcgrath
Goldman’s pool for drug research:
[Via business|bytes|genes|molecules]

And while we are on the subject of blog posts by Derek Lowe, here’s one where he points to news about Goldman Sachs funding a large pharma company and using a “new” business model

(The model involves) a different approach, creating a “research pool” into which pharma companies would place a range of experimental drugs in a single therapeutic area in early-stage phase 1 and 2 trials, where their specialists would work alongside external experts including scientists, chemists and clinical research organizations.

By the time an experimental drug is in Phase I or II trials, little ‘research’ is really being done. It is mostly development, at least with regard to dosing and such, as well as production methods. The failure rate of drugs at this late stage is much lower than during the pre-development stage, which really is what most people would call research.

But the large costs for drug development comes at the clinical trial stages. So it makes sense for Big Pharma to pool resources here to save some money.

That’s a model that I am sure I’ve heard being mentioned somewhere else, although I can’t remember. The concept is one that does appeal to me in general, but is phase 1 or 2 the correct time? A lot of the attrition occurs in pre-clinical work. Isn’t that the best time to share some risk and make some bets? I still like the idea of a company whose task it is to find interesting drug candidates and connect that candidate to pharma, biotech, academic researchers and funding, or a model where there would be a marketplace that early stage candidates could be placed into and companies could form collaborations or bid for the ability to take the drug forward. This isn’t that far removed for those ideas. I think the distribution fosters innovation, but having someone orchestrating the network is also critical otherwise you won’t get anywhere.

Anyhows, will be following this story and see if we can find out more. A quick google search really didn’t shed any additional light.

Pre-development, on the other hand, is something Big Pharma has not been as innovative at. That can be seen in the areas of research seen in many non-profit research institutions and small biotech companies.

In many cases, technology moves out of basic research facilities at universities and research institutions too early, with a very risky economic future. The pressures of raising money often hampers effective investigation of novel approaches, especially today when almost every small company wants to demonstrate a ‘proof of concept’ so it can sell out to a larger company.

Either the technology should be held longer and investigated by non-profit research institutions (and we see this with some of these organizations moving all the way to production methods) or for a similar basic research pool for companies to fund interesting technologies. Luke Timmerman wrote about one such possibility in Boston earlier this year, Enlight.

Technorati Tags: Science, Web 2.0

On Thursday, Xconomy held an event in Seattle where a panel discussed Vaccines 2.0. It was very interesting and I will wrote up more later. In the meantime, here are some photos:


Well, I spent too much time talking out front and did not get a great seat.

There was a full room here, with some standing room only in the back.


The networking session afterwards lasted well over an hour with people still talking after 9 PM. This was a really nice first event with a potential to bring together quite a wide range of people.

Technorati Tags: Biology, Science, Technology

by Vik Nanda
Soon it will be time to start over, again:
[Via Scripting News]

Here’s how the tech industry cycle goes.

A new generation of young techies comes along, takes a look at the current stack, finds it too daunting (rightly so) and decides to start over from scratch. They find that they can make things happen that the previous generation couldn’t cause they were so mired in the complexity of the systems they had built. The new systems become popular with “power users” — people who yearn to overcome the limits of the previous generation. It’s exhilirating!

Some of those power users are venture capitalists, they’re hanging around looking for things to invest in, and they pick a few things that look like winners. When I was fresh and dewy, part of the new crop of techies, these people were Mike Markkula who funded Apple, and Ben Rosen who funded Compaq and Lotus. In later generations they were different people, of course.

So the new folks, freshly funded, hire lots of people, young’uns like themselves who are doing it The New Way. They ship some products, and while the users are happy and excited about all the cool new things they can do with the new generation, now that they’re freed of the limits of the previous one, they still want all the features they had come to expect in the old days. No problem! The new companies hire more people and they add all the features of the old generation. Feature wars follow, and the users get bored, and a new generation of techies comes along, takes a look at the current stack, finds it too daunting (rightly so) and decides to start over from scratch.

[More]

Dave has been around for quite a while and he is absolutely right about this sort of innovation cycle. Read the entire post. Complexity is what we fight. But the simplifying solutions are usually inherent in the complexities we have created.

It will be interesting to see what the next cycle will bring. Innovation is always exciting but never more so than when the world is in turmoil.

Technorati Tags: Technology, Web 2.0

Supporting the Commons: Jesse Dylan and Richard Bookman:
[Via Science Commons]

Today, we are proud to announce the release of Science Commons’ first informational video. The video was directed by renowned director Jesse Dylan, the director of the Emmy- award winning “Yes We Can” Barack Obama campaign video with musical artist will.i.am from the Black Eyed Peas. The video can also be seen on the front of sciencecommons.org.

“I believe Science Commons represents the true aspiration of the web, and I wanted to tell their story,” Dylan said. “They’ve changed the way we think about exploration and discovery; the important and innovative ideas need to be shared. I believe it’s vital to revolutionizing science in the future. I hope this is just the beginning of our collaboration.”

This video is launched in conjunction with a letter of support from Richard Bookman, the Vice Provost for Research and Executive Dean for Research and Research Training at the University of Miami. Bookman joins a group of esteemed Commons supporters featured in this year’s “Commoner Letter” series, including this year: Eben Moglen of the Software Freedom Law Center and Columbia University, Renata Avila - CC Guatemala Project Lead, and singer/songwriter Jonathan Coulton. More information and an archive of past letters can be found at http://support.creativecommons.org/letters.

In his letter, Bookman writes:

“We need to find ways to make sharing research results and tools easy, trackable, and useable by scientists on a day-to-day basis. Science Commons is working on these problems in a way that few other projects contemplate: they don’t write papers, they release “running code” like contracts for sharing biological materials and open contracts for biological tools like stem cells and genetically modified mice. [...]

I support SC/CC because I think it’s the right approach at the right time. It’s vital that we as a community support the organization - the interstitial nature of what gets done at CC makes it harder than many might think to raise money, which can leave the most important work dying for lack of funds.

I hope everyone in the community can dig deep and support CC during this campaign. When you support CC, whether because of the cultural work, or the education work, or the science work, you’re supporting an organization that is much more than contracts and websites and videos. You’re supporting an umbrella organization working around the world that lives and breathes the “some rights reserved” philosophy.”

Our thanks to Jesse Dylan, Professor Bookman, and the broader CC community for their ongoing support. For more information about the campaign, or to show your support, visit http://support.creativecommons.org. Every little bit counts. Help support the Commons.

Science Commons has a very strong role to play in getting scientists to actively develop the web in ways that can benefit everyone, including themselves. In particular, Health Commons is a project that may provide a place for biologists to ‘remix’ their data in profound ways. If we can only get them to think about the Commons in the pursuit of their work.

Technorati Tags: Social media, Web 2.0

by even.
Typealyzer says my blog is INTJ:
[Via Knowledge Jolt with Jack]

Typealyzer says that this blog appears to be of the Myer-Briggs type INTJ.

The analysis indicates that the author of http://blog.jackvinson.com is of the type:
[More]

Myers-Briggs is a useful tool for demonstrating that different people have different strategies for solving life’s problems. It is based on Jungian archetypes that, while sometimes simplistic, can offer insights that may be useful. The danger is that people make the analysis definitive, much like some people make genes the final arbiter of all behavior. People are not archetypes and can easily change depending on circumstances.

I have taken MB tests several times. What I find interesting is that, for me, there often seems to be only one reasonable answer. I figure everyone feels this way. I am usually an ENFP (Extraverted iNtuitive Feeling Perceiving).

While ignoring some of the astrological vagueness of the description, it does come pretty close to describing some important traits of mine. But all of us can act in a different fashion of we need to. We can adapt our ’style’ for the particular venue we find ourselves.

For instance, this blog, when run through Typelyzer, gives an INTJ type. Now this could just be real hokem, but this does come closer to the style I have tried to apply to this site - a little more grounded and focused on specifics.

But care must be given. Daily Kos, the largest progressive political site, comes out as ISTP - the mechanics

The independent and problem-solving type. They are especially attuned to the demands of the moment are masters of responding to challenges that arise spontaneously. They generally prefer to think things out for themselves and often avoid inter-personal conflicts.

The Mechanics enjoy working together with other independent and highly skilled people and often like seek fun and action both in their work and personal life. They enjoy adventure and risk such as in driving race cars or working as policemen and firefighters.

while RedState, one of the largest conservative, comes out as INTP - the thinkers

The logical and analytical type. They are espescially attuned to difficult creative and intellectual challenges and always look for something more complex to dig into. They are great at finding subtle connections between things and imagine far-reaching implications.

They enjoy working with complex things using a lot of concepts and imaginative models of reality. Since they are not very good at seeing and understanding the needs of other people, they might come across as arrogant, impatient and insensitive to people that need some time to understand what they are talking about.

I am sure there would be some disagreement in these designations but it sure would make for an interesting discussion.

Technorati Tags: Education, General, Technology

Does my sequence have a new homolog?:
[Via business|bytes|genes|molecules]

Image via Wikipedia

Here’s an interesting service I discovered during a snoop on the web. PDBalert is a web-based system that alerts users as soon as a pdb structure with homology to a protein of interest becomes available. Users can upload protein sequences of interest and ever Wednesday, when the PDB releases new structures, the service compares sequences to all the new proteins. Simple enough. I suspect many people have their own scripts which do essentially the same.

The thing that jumped out at me was how easy it could be for the PDB to create a service that does the same. You point the service to a source file(s), choose an appropriate algorithm (they could give you some choices), etc. In a perfect world, you could even mash this up with some kind of function prediction engine, etc. The way I see it, more services the better, esp if they can talk to each other. Some day. I still believe there is room in the science space for an API management service which allows developers to build tools upon existing resources like the PDB.

Deepak is absolutely correct. There has to be greater attention to scientific APIs, especially providing users with the abilities to manage these APIs and to perform more complex mashups.

So how about getting a tweet on twitter instead of email, or even have it appear on a Facebook page? Then have it hit pubmed and provide useful papers dealing with the new protein. Why not then directly provide DNA sequence homologies, etc?

Technorati Tags: Science, Web 2.0

by · YeahjaleaH ·
Gifted few make order out of chaos - 06 March 2002 - New Scientist:
[Via New Scientist]

Some people have a special gift for predicting the twists and turns of chaotic systems like the weather and perhaps even financial markets, according to an Australian psychologist.

Richard Heath, who has now moved to the UK’s University of Sunderland tried to identify people who can do this by showing volunteers a list of eight numbers and asking them to predict the next four. The volunteers were told that the numbers were maximum temperatures for the previous eight days. In fact the numbers were computer-generated: some sets were part of a chaotic series while the rest were random.

Random sequences are by their nature unpredictable, whereas chaotic sequences follow specific rules. Despite this, chaotic sequences are very hard to predict in practice because of the “butterfly effect” - even an unmeasurably small change in initial conditions can have a dramatic impact on their future state.

Nonetheless, Heath found that a quarter of the people he tested could predict the temperature for at least the next two days if the sequence was chaotic, rather than random, even though there is no obvious pattern to the figures.
[More]

The above link is a 6 year old article from New Scientist. It is about one of my favorite papers: Can People Predict Chaotic Sequences?

My post on Friday about entrepreneurs and their ability to make decisions under stress reminded me of it. Heath’s paper was a small study but I was intrigued by the possibility that a fraction of the population, about 25%, might be capable of seeing a pattern in information that the rest of the population sees only as random noise.

I wonder how a group of entrepreneurs would do with his tests?

Technorati Tags: Science, Social media

by Jordi Armengol (Xip)

Clarity of vision:
[Via business|bytes|genes|molecules]

Be stubborn on vision and flexible on details
– Jeff Bezos

Those words, which I heard recently, have stuck in my head (or rather in Evernote, as I typed them on my iPhone furiously as I heard them).

Over the years, I have seen too many in the life science industry, even pharma in recent years, lurch around, almost trying to figure out what they need to be doing as companies as they go along. That’s why so many fail. Let’s say you are running a small biotech or bioinformatics shop. You need to be sure what your vision is, identify the actionable milestones that you need to achieve and then figure out what you need to do to hit each milestone. It’s not just for a company. If you’re a product manager, think about your product line, and so on. The times I have been successful were times where I had a clear vision about where I wanted to be, and then figured out a path (stress on “a path”) to get there. When you’re too reactive, it just doesn’t work.

Having worked at a couple of Biotechs I know some of the pitfalls. Vision is great and actionable milestones are a must but in biology both are usually based on extremely limited knowledge of very complex information.

Enbrel is a great example. Originally developed to fight septic shock, it passed every milestone but one. It failed in clinical trials, to have an ameliorative effect. But, rather than toss it away, Immunex was able to rework it into a premier rheumatoid arthritis drug. Flexible on the details.

Flexible means working for a successful failure. That can be the best win of all.

Technorati Tags: Science, Social media

by notsogoodphotography
Are scientists missing the boat?;.:
[Via Bench Marks]

….or has that boat already sailed?

I’ve read many a blog posting or magazine article declaring that scientists are behind the curve, and we biologists have been slow to pick up the new online tools that are available. I’ve repeatedly asked for examples of other professions that are ahead of the curve that we can use as models (are there social networks of bakers sharing recipes and discussing ovens?), but haven’t seen much offered in response. I tend to think that it’s not a question of scientists being slow, it’s that the tools being offered aren’t very appealing. Note how quickly scientists moved from paper journals to online versions, which only took as long as it did because of the slow progress on the part of journal publishers getting their articles up on the web. The advantages of online journals were obvious, and in comparison, the advantages of joining “Myspace for scientists” are less evident.

Are social networks )”Meet collaborators! Discuss papers!”) ever going to see heavy use from the biology community? Or are we starting to see that they’ve run their course in general, and scientists were prescient in not wasting their time?
[More]

There are too many advantages that arise from using many of these Web 2.0 tools (i.e. the ability to leverage human social networks in order to examine large datasets). However, the race will not be to have 5000 friends, as often seen out in the wild.

I don’t think the next generation will shun these tools. They will just have a better idea of how to interact with them more usefully, with a focus that can really help their workflow.

Technorati Tags: Science, Web 2.0

by dalbera
Is Science Being Distorted?:
[Via The Scholarly Kitchen]

A recent PLoS Medicine article claims that information economics distort science. But maybe it’s an obsession with journals distorting the views of the authors.
[More]

As I said earlier, I thought there would be some interesting discussions. I guess one way of looking at it is that all the ‘good’ data gets published in the prestigious journals and there is nowhere for the ‘bad’ data to be published until after a clinical trial fails. Whether this is a real bias problem is difficult to assess.

I think any problem is due more to the complexity of human health studies than any bias but we have to keep moving forward as best as we can.

Technorati Tags: Science