Tag Archives: Science

General, Open Access, Science, Web 2.0

Who am I?

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I figure that I may be getting some traffic from the Huffington Post article so an introduction.

I’ve been working in the field of biotechnology since the early 80s, spending 16 years as a researcher at Immunex, the premier biotech in the Seattle area until it was bought by Amgen. It was an incredible crucible of top-notch researchers working with little money to find cures for important diseases. There were, I believe, less than 50 employees when I started and several thousand when I left. So I had first hand knowledge of many of the needs of a small biotech as it grew. I was a small part in the development of a biologic that changed people’s lives – ENBREL.

I left Immunex when Amgen finalized the merger and spent some time thinking about what to do next. Luckily Immunex stock options, which were given to all Immunex employees when I started, provided some economic buffer. I worked with the Washington Biotechnology and Biomedical Association on several projects and helped form a philanthropic organization called the Sustainable Path Foundation, where I am still a Board member.

I started a blog called A Man With a PhD, something I continue to this day, as well as a science-based blog called Living Code for Corante, that Forbes picked as the 3rd best Medical blog in 2003.

In 2004, I became the third employee of a startup biotechnology company called Etubics. As VP in charge of Research, I did everything from ordering lab equipment, growing cells, negotiating contracts and having to fly cross country to talk with suppliers. All while trying to raise money so we could have a hope of producing the vaccines that I believe can change the world.

So I got to see firsthand and at the highest levels, what it takes to start and run a company. I left last year as the company was entering a new phase, where clinical development and manufacturing were at the forefront and research was on the back burner. Not only were these areas I did not have a lot of expertise or interest, but I also was pretty well burned out. The stress of a small company is enormous, particularly in an industry where it takes over 15 years for a therapeutic to get from the research lab to the patient.

I left to pursue one of my real passions – how to understand why Immunex was such a powerhouse of research, why it is was one of the few biotech companies started in the 80s to produce a blockbuster drugs, along with several other good drugs, and whether this could be replicated.

That is what SpreadingScience is about – how to create organizations that are resilient to change, that can adapt in ways that increase the successful outcomes need. You can read some of the material or follow my blog to get an idea of how I am accomplishing this.


Knowledge Creation, Science, Web 2.0

My Op/Ed in Xconomy

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petri dish by kaibara87

The opinion piece I wrote for Xconomy has been published. Luke Timmerman asked me on Monday to examine the bill and the sections that impacted the Biotechnology industry. I had not even realized there were parts of the huge healthcare reform bill.

I started writing on Monday evening and got Luke my version by about 1 PM on Tuesday (I had to take my car to the shop for its 15,000 checkup or I would have been done sooner). Luke had some edits and it was ready by early evening.

Everything was done using online technologies. Even 5 years ago it would have been hard to put this all together in such a short time. I essentially started from zero on the specifics (I mean how many people have actually read any of the healthcare reform bill itself?), educated myself rapidly, used my background of 25 years in the industry to form an opinion and composed the piece. I then carried on a ‘conversation’ with Luke to get it into final shape.

I found the relevant parts using Open Congress’s interface, which allows you to link to specific paragraphs, as well as leave comments. It presents a unique way for citizens to interact with the legislation that our Congress is working on. Not only are there links to every piece of information one may want, there are also links to news stories, and other facts (Like the Senate version has over 400,000 words.)

Without this web site, it would have been very difficult to even find the sections dealing with biotechnology, much less try to understand them, It was very easy to search for the relevant sections and get an understanding of what they really said. I read a few articles online to get some other viewpoints and then wrote my opinion of the sections.

The fact that the biotechnology industry now gets 12 years of market exclusivity for its products, several years longer than for the small molecule drugs sold by pharmaceutical companies, is really a pretty big deal.

There has been uncertainty for several years over this time frame, with the FTC feeling there should be little or no market exclusivity outside of the patent time frame to the industry’s organization, BIO, which wanted at least 12 years without regard of patent considerations.

Not knowing just how long a time period a new biologic might be free of competition can have a large effect on determining which therapeutics make it to the market place. Now those who model the value of a product have much surer time frames to work with.

I do not think the bill is as friendly to those companies hoping to create ‘generic’ biologics called biosimilars. While it does delineate a path to government approval, the legislation does not make it easy. There are some substantial costs for getting approval of these products. They may not be very much cheaper than the original therapeutic itself. and they do not get any real exclusivity for their products in the end.

For many possible follow-on biologics it will simply be too expensive to take them to market. The large costs incurred while doing this will also make it harder for them to take market share away from a biologic, which has had 12 years of unfettered ability to market itself and its positive results to the customers. at least market share based on cost.

And, as I read the section dealing with patent issues, I became even more aware of the hard road for these follow-on generics. In order to get patent issues dealt with before the follow-on biologic is marketed, the patent holders/licensees of the original drug must be furnished the same information that is submitted in the application to the FDA – the results of clinical trials, assays to determine the follow-on biologic’s potency, stability, etc.

It seems to me that this could open up all sorts of shenanigans. And it appears to be more than regular generics have to do. From what I could determine, a company hoping for approval of a generic simply has to provide the patent numbers that cover the drug it is proposing to market. I could find nothing to indicate that it must turn over all the data of the generic to its direct competitor before going to market.

How many companies will be willing to provide their direct competitor with all the information present in its application to the FDA? It seems to me a place where some mischief could occur.

Now, I did not have time to review the complete history of these sections. I’m sure I could find all the committee testimonies on these parts. Perhaps someone out there has more detailed information. I’d love to pull an Emily Litella and say “Never Mind.”

So, this bill settled something really important for the biotech industry and, while bringing some clarity to the idea of biosimlars, also introduced some possible complications.

I have to say it was fun to use the power of the Web to investigate the issue and form some opinions. Using technology to move information around faster is part of what SpreadingScience does.

Knowledge Creation, Science, Web 2.0

The difference between the creative and the commonplace

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tufte by BruceTurner

Edward Tufte Presidential Appointment
[Via Daring Fireball]

President Obama has appointed Edward Tufte to the Recovery Independent Advisory Panel, “whose job is to track and explain $787 billion in recovery stimulus funds”. Outstanding.

[More]

This is pretty cool. Tufte is one of my favorite people, not only for his highly original books on data presentation but also for his sheer force of personality. He is one of the most entertaining, enlightening speakers I have ever heard.

I attended one of his workshops in Seattle probably close to 20 years ago. There was an interchange that has stuck with me ever since, because it so succinctly illustrates the divide between truly original, innovative change and the typical corporate response.

Tufte was discussing the different interfaces between the Mac OS and Windows. After going through a lot of the pluses he saw in the Mac and a lot of the minuses in Windows, he stated that the Mac looked like it had been created by one or a small group of people with a single purpose, a single view of how the information should be presented, while Windows looked like it had been done by a committee.

He then said that all the best presentations were this way – a single point of view forcefully pushed onto everyone. Someone in the audience then asked but what happens if your single point of view turns out to be wrong, to not work.

Tufte replied, simply, “You should be fired.” You could almost audibly hear the intake of everyone’s breath. That is exactly what they feared and why they would always want to retreat into committee decisions – they can’t be fired if the committee made the decision. FUD is what drives most people.

The creative, the innovative do not really fear failure, often because they are adaptable enough to ‘route around the damage’ quickly enough. They do not usually doubt the mission they are on and are certainly not uncertain about the effects. Read about the development of the Mac. They were going to change the world, no doubt about it. While you can see that there really was a focus of vision, there are also lots of ‘failures’ that had to be fixed. The key was to fail quickly, leaving time to find success.

And permitting committed individuals to find their own way to success rather than rely on committees to fix them.

Committees very seldom fail quickly, since failure is the thing they fear the most. They would rather succeed carefully than perhaps fail spectacularly. And they very seldom produce revolutionary change.

Single viewpoint, change the world, rapidly overcome obstacles, adaptable. All characteristics of successful change. They do not fear spectacular failure because the fruits of success will be so sweet.


Science, Web 2.0

Getting at data

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Four Ways of Looking at Twitter
 [Via HarvardBusiness.org]

Data visualization is cool. It’s also becoming ever more useful, as the vibrant online community of data visualizers (programmers, designers, artists, and statisticians — sometimes all in one person) grows and the tools to execute their visions improve.

Jeff Clark is part of this community. He, like many data visualization enthusiasts, fell into it after being inspired by pioneer Martin Wattenberg‘s landmark treemap that visualized the stock market.

Clark’s latest work shows much promise. He’s built four engines that visualize that giant pile of data known as Twitter. All four basically search words used in tweets, then look for relationships to other words or to other Tweeters. They function in almost real time.

“Twitter is an obvious data source for lots of text information,” says Clark. “It’s actually proven to be a great playground for testing out data visualization ideas.” Clark readily admits not all the visualizations are the product of his design genius. It’s his programming skills that allow him to build engines that drive the visualizations. “I spend a fair amount of time looking at what’s out there. I’ll take what someone did visually and use a different data source. Twitter Spectrum was based on things people search for on Google. Chris Harrison did interesting work that looks really great and I thought, I can do something like that that’s based on live data. So I brought it to Twitter.”

His tools are definitely early stages, but even now, it’s easy to imagine where they could be taken.

Take TwitterVenn. You enter three search terms and the app returns a venn diagram showing frequency of use of each term and frequency of overlap of the terms in a single tweet. As a bonus, it shows a small word map of the most common terms related to each search term; tweets per day for each term by itself and each combination of terms; and a recent tweet. I entered “apple, google, microsoft.” Here’s what a got:

twittervenn.jpg

Right away I see Apple tweets are dominating, not surprisingly. But notice the high frequency of unexpected words like “win” “free” and “capacitive” used with the term “apple.” That suggests marketing (spam?) of apple products via Twitter, i.e. “Win a free iPad…”.

I was shocked at the relative infrequency of “google” tweets. In fact there were on average more tweets that included both “microsoft” and “google” than ones that just mentioned “google.”

[More]

Social media sites provide a way to not only map human networks but also to get a good idea of what the conversations are about. Here we can see not only how many tweets are discussing apple, microsoft and goggle but the combinations of each.

Now, the really interesting question is how ti really get at the data, how to examine it in order to discover really amazing things. This post examines ways to visually present the data.

Visuals – those will be some of the key revolutionary approaches that allow us to take complex data and put it into terms we can understand. These are some nice begining points.

Science, Web 2.0

An interesting juxtaposition

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data by blprnt_van

Reaching Agreement On The Public Domain For Science
[Via Common Knowledge]

Photo outside the Panton Arms pub in Cambridge, UK, licensed to the public under Creative Commons Attribution-ShareAlike by jwyg (Jonathan Gray).

Today marked the public announcement of a set of principles on how to treat data, from a legal context, in the sciences. Called the Panton Principles, they were negotiated over the summer between myself, Rufus Pollock, Cameron Neylon, and Peter Murray-Rust. If you’re too busy to read them directly, here’s the gist: publicly funded science data should be in the public domain, full stop.

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and this

BBC News – Science damaged by climate row says NAS chief Cicerone
[Via BBC News | Science/Nature]

Leading scientists say that the recent controversies surrounding climate research have damaged the image of science as a whole.

President of the US National Academy of Sciences, Ralph Cicerone, said scandals including the “climategate” e-mail row had eroded public trust in scientists.

[snip]

He said that this crisis of public confidence should be a wake-up call for researchers, and that the world had now “entered an era in which people expected more transparency”.

“People expect us to do things more in the public light and we just have to get used to that,” he said. “Just as science itself improves and self-corrects, I think our processes have to improve and self-correct.”

[More]

It is important for Federally funded research to be in the public domain. But, Universities, who hope to license the results of this research, and corporations, who will not as likely commercialize a product if they can not lock up the IP, Both of these considerations must be accounted for if we want to translate basic research into therapies or products for people.

So, as the Principles seem to indicate, most of this open data should happen AFTER publication, so this would give the proper organizations to make sure they have any IP issues dealt with.

But what about unpublished data? What about old lab notebooks? The problem supposedly seen now has nothing to do with data that was published. It has to do with emails between scientists. Is this relevant data that should be made public for any government funded research?

Who determines which data are relevant or not?

And what about a researcher’s time? More time in front of the public, more time filling out FOIs, more time not doing research in the first place.

The scientific world is headed this way but how will researcher’s adjust? There will have to be much better training of effectively communicating science to a much wider audience than most scientists are now comfortable with.


General, Knowledge Creation, Science

Innovation on the cheap

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innovate by jordigraells>

Why Great Innovators Spend Less Than Good Ones

[Via HarvardBusiness.org]

A story last week about the Obama administration committing more than $3 billion to smart grid initiatives caught my eye. It wasn’t really an unusual story. It seems like every day features a slew of stories where leaders commit billions to new geographies, technologies, or acquisitions to demonstrate how serious they are about innovation and growth.

Here’s the thing — these kinds of commitments paradoxically can make it harder for organizations to achieve their aim. In other words, the very act of making a serious financial commitment to solve a problem can make it harder to solve the problem.

Why can large commitments hamstring innovation?

First, they lead people to chase the known rather than the unknown. After all, if you are going to spend a large chunk of change, you better be sure it is going to be going after a large market. Otherwise it is next to impossible to justify the investment. But most growth comes from creating what doesn’t exist, not getting a piece of what already does. It’s no better to rely on projections for tomorrow’s growth markets, because they are notoriously flawed.

Big commitments also lead people to frame problems in technological terms. Innovators spend resources on path-breaking technologies that hold the tantalizing promise of transformation. But as my colleagues Mark Johnson and Josh Suskewicz have shown, the true path to transformation almost always comes from developing a distinct business model.

Finally, large investments lead innovators to shut off “emergent signals.” When you spend a lot, you lock in fixed assets that make it hard to dramatically shift strategy. What, for example, could Motorola do after it invested billions to launch dozens of satellites to support its Iridium service only to learn there just wasn’t a market for it? Painfully little. Early commitments predetermined the venture’s path, and when it turned out the first strategy was wrong — as it almost always is — the big commitment acted as an anchor that inhibited iteration.

[More]

One problem of too much money is that bad ideas get funding also. In fact, there are often many more incremental plans than revolutionary ones. They soak up a lot of time and money.

Plus they create the “We have to spend this money” rather than “Where are we going to get the money to spend?”

Innovations often result in things that save money. But they are often riskier to start with. So how to recognize them and get them the money they need, but not too much?

Encouraging people to work on ‘back burner’ projects in order to demonstrate the usefulness of the approach is one way. Careful vetting can help determine whether it can be moved to the front burner or not.

Part of any innovator’s dilemma is balancing the innovative spirit with sufficient funding to nurture that spirit, without overwhelming the innovator with the debit of too much cash.

Knowledge Creation, Open Access, Science, Web 2.0

Updated: Short answers to simple questions

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fail by Nima Badiey

NIH Funds a Social Network for Scientists — Is It Likely to Succeed?

[Via The Scholarly Kitchen]

The NIH spends $12.2 million funding a social network for scientists. Is this any more likely to succeed than all the other recent failures?

[More]

Fuller discussion:

In order to find an approach that works, researchers often have to fail a lot. That is a good thing. The faster we fail, the faster we find what works. So I am glad the NIH is funding this. While it may have little to be excited about right now, it may get us to a tool that will be useful.

As David mentions, the people quoted in the article seem to have an unusual idea of how researchers find collaborators.

A careful review of the literature to find a collaborator who has a history of publishing quality results in a field is “haphazard”, whereas placing a want-ad, or collaborating with one’s online chat buddies, is systematic? Yikes.

We have PubMed, which allows us to rapidly identify others working on research areas important to us. In many cases, we can go to RePORT to find out what government grants they are receiving.

The NIH site, as described, also fails to recognize that researchers will only do this if it helps their workflow or provides them a tool that they have no other way to use. Facebook is really a place for people to make online connections with others, people one would have no other way to actually find.

But we can already find many of the people we would need to connect to. What will a scientific Facebook have that would make it worthwhile?

Most social networking tools initially provide something of great usefulness to the individual. Bookmarking services, like CiteULike, allow you to access/sync your references from any computer. Once someone begins using it for this purpose, the added uses from social networking (such as finding other sites using the bookmarks of others) becomes apparent.

For researchers to use such an online resource, it has to provide them new tools. Approaches, like the ones being used by Mendeley or Connotea, make managing references and papers easier. Dealing with papers and references can be a little tricky, making a good reference manager very useful.

Now, I use a specific application to accomplish this, which allows me to also insert references into papers, as well as keep track of new papers that are published. Having something similar online, allowing me access from any computer, might be useful, especially if it allowed access from anywhere, such as my iPhone while at a conference.

If enough people were using such an online application then there could be added Web 2.0 approaches that could then be used to enhance the tools. Perhaps this would supercharge the careful reviews that David mentions, allowing us to find things or people that we could not do otherwise.

There are still a lot of caveats in there, because I am not really convinced yet that having all my references online really helps me. So the Web 2.0 aspects do not really matter much.

People may have altruistic urges, the need to help the group. But researchers do not take up these tools because they want to help the scientific community. They take them up because they help the researcher get work done.

Nothing mentioned about the NIH site indicates that it has anything that I currently lack.

Show me how an online social networking tool will get my work done faster/better, in ways that I can not accomplish now. Those will be the sites that succeed.


[UPDATE: Here is post with more detail on the possibilities.]

Science

Red flags of understanding

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red flag by Luke Hoagland

Five Red Flags to Watch Out For in a Biotech, From Dendreon Co-Founder Chris Henney

[Via Xconomy ]

henneyc1 Luke Timmerman wrote:

Yesterday, we provided a rundown of the six hallmarks of a successful biotech company, according to Christopher Henney, the biotech pioneer who co-founded three of Seattle’s top biotechs—Immunex, Icos, and Dendreon. He made his remarks to an audience of about 100 investing professionals at the CFA Society meeting on Oct. 8 in Seattle.

Today, we follow up with the five red flags Henney advised investors to watch for when they evaluate biotech investments. Here’s what he singled out as warning signs:

—Top management without a scientific background. It’s not impossible for a biotech to succeed with a non-scientist at the helm, Henney said, but a smart investor must ask this non-scientific manager where the science comes from at the company. “The good answer would be, ‘It comes from my team of wonderful scientists who I recruited.’” A bad answer would be something like, “It comes from my scientific advisory board, which has two Nobel Laureates.” Henney added, “If you need to make an appointment to meet the guy who’s bringing you your science, then you don’t have much of a business.”

Henney wanted to make sure he wasn’t making a broadside attack against all non-scientific managers. One of his favorite biotech CEOs isn’t a scientist, but he adds, “You wouldn’t know it from talking to him.”

—No worries. An investor should ask what the management loses sleep over. “If they say, ‘I sleep like a baby,’ that’s a big red flag,” Henney said. All companies have their problems, and top management had better know them inside out.

—Hard-to-understand science. Ask the management to explain the science of their product in detail. “If they say something like the science is hard to explain, they can’t really explain it to you, that’s a big red flag.”

—Geographic remoteness. This provides some insight into Henney’s thinking on why two of the companies for whom he serves as chairman—Oncothyreon and AVI Biopharma—recently moved their headquarters from Edmonton, Canada, and Portland, OR, respectively, to the Seattle area. “You need a quorum of players,” Henney said. “You need access to talent, you need to be able to recruit people.” Seattle has more talent than the other places, and an ability to recruit more people, he said.

—Too many VCs. The board should be loaded with people that have experience running companies. “You shouldn’t have a board full of venture capitalists,” Henney said.

—Family members in key roles. “These aren’t family businesses. If you see a board dominated by siblings, or a couple of siblings in key management roles, I’d run, not walk.”

[More]

I have always had a soft spot in my heart for Chris Henney. Those of us at Immunex in the early days all have our hilarious Chris stories, often involving his confusion with our very weird phone system.

But when I first started at Immunex, it took a month to get our house closed. Because of the situation, I ended up staying in a fairly cheap hotel out in Issaquah (perhaps 15 miles away from downtown Seattle). This was an unexpected expense of moving and caused a little bit of hardship paying for before my first paychecks arrived.

So I talked with Chris and he got Immunex to pay for some of the cost as part of my moving expenses. It told me a lot about the culture at the company when a newly hired scientist could walk up to one of the founders and ask for money. And get it.

Most of his red flags deal with the inability to communicate the scientific reasons for the existence of the company. No science in the management’s background, no worries and nonsensical science all indicate a fatal lack of understanding.

If you do not understand the fundamental science in a deep way, you can not tell the story. An inability to tell the story in a way that resonates will make it impossible to shake some money loose.

This is not about hype, which is a snake-oil salesman’s approach to selling anything. In fact, hype indicates a total misunderstanding of the science because most biotechs are founded more on hope and strong egos than anything really solid. That is, often the company must begin development of the science for commercialization before the complete knowledge of the system is extant.

This means that the path to a commercial product will be littered with false starts and the company’s management had better understand the science enough to surmount these roadblocks.

I’m now going to tell a story. Perhaps some of the details may be a little off but it does illustrate why having a deep understanding of the science can be so important.

For example, Immunex, in large part, was started based on the hope that a molecule called interleukin-2 would be very important for medical protocols. See, IL-2 was also known as T-cell Growth factor and had been shown by some of Henney and Gillis’ work, to be absolutely required for the growth of T-cells in culture.

Now, T-cells are incredibly important in fighting off a whole slew of diseases, including cancer. So being able to manipulate T-cell levels seems like it would be a very good thing to be able to do. So, let’s clone IL-2 and produce it in large amounts. The we can sell it a s a therapeutic for a wide range of illnesses.

Turns out the IL-2 is not as useful as originally hoped. Not to say it does not have important uses, even commercial ones. But at the time, it seems like a critical molecule, one that would be core to our repertoire of tools.

Yet, when mice are bred which have no functional IL-2, they actually appear relatively normal. That is, the lack of any IL-2 is not fatal to the mice. There are some interesting immunological irregularities that have led to some interesting observations. But IL-2 is not absolutely required for a viable mouse. The mouse and its immune system find some other way to deal with T-cells.

Luckily for Immunex, our founders, and the scientists they recruited, had a deep understanding of the science and this allowed us to delve quite quickly into other aspects of the immune system as we worked on IL-2. For the same technologies that could clone IL-2 could be used to clone a wide range of immunoregulatory proteins.

By the time it could be shown that IL-2, while an important molecule, would not be the huge commercial product originally envisioned, we had a handful of other proteins cloned which presented even greater possible riches than IL-2. This deep understanding of the science eventually led to Enbrel.

Thus, a critical reason to have a deep understanding of the science is that no research venture, especially commercial ones, goes according to plan. But, if you understand the science, you can often be adaptable enough to find a successful solution.

Those that do not fundamentally understand the science will just be stuck when the inevitable roadblock appears. Then everyone, including the investors, are just stuck.