Biotech Oases -- your gas purchases at work.

Hot on the heels of news about serious biotech investment in Kazakhstan comes an update on similar efforts in the Middle East.  In the latest Nature Biotechnology, Cormac Sheridan describes (PDF only) initiatives in Dubai, Abu Dhabi, Qatar, and Saudi Arabia to nucleate biotech business and education.

Tax incentives, government sponsored facilities and infrastructure, and multi-billion dollar endowments for training and scientific grants are all part of efforts to bootstrap local technology development.  Strong, well-funded connections are being built with western educational institutions.  The story notes that countries in this region do not have a strong history (recently, anyway) of scientific research, and that part of the challenge will be to create a culture of innovation and competition to produce new results.  Oil money is paying for all of this, and I have to say that I am not unhappy some of the profits from filling my gas tank will go to this sort of investment.

In the long run, I wonder what will be the domestic social and political impacts of encouraging inquiry and increased contact with western scientists.  It's also worth asking, given historical Arab leadership in education and scholarship, about the local mores (Islamic or otherwise) regarding cloning, stem cells, genetic modification, and cell based therapies.  Does anyone have suggestions for reading along these lines?

Commentary on Flu Vaccine News and Epidemiological Models

I've been mulling whether to wade into the fray generated by recent reports of "effective" H5N1 vaccines and computer models that suggest a pandemic might be stoppable.  Fortunately, I see that the folks at EffectMeasure took care of most of what I wanted to say.  Basically, the media is distorting news of minimal (and possible irrelevent) progress on the vaccine to make it sound like we are all set and ready for whatever comes, while the models show that only if we are very lucky will anti-virals and quarantines slow a pandemic (the comments on both posts are worth reading, too).  I feel so much safer.

454's Microfabricated Pyrosequencer

Today, Nature published online an article entitled, "Genome sequencing in microfabricated high-density picolitre reactors," by Margulies et al.  The paper describes embedding beads coated with DNA in 1.6 million wells etched into the end of a fiber-optic slide, where the slide is produced by repeatedly folding and drawing a fiber-optic cable.  Each well serves as a reaction chamber for the sequencing-by-synthesis method known as Pyrosequencing.  The research utilized an instrument built by 454 Life Sciences.

My email is ringing off the hook today with questions about how this fits into my estimates of sequencing and synthesis productivity ("Carlson Curves").  Thanks for your interest, everyone.

A few comments.  The first thing to note about the article is that the authors state they sequenced "25 million bases, at 99% or better accuracy, in one four hour run."  So at 6.25 million bases per hour, they appear to be doing quite well compared to a Sanger-based 96-capillary instrument, which the authors assert reads out 67,000 bases per hour.

Digging into the text a bit, we find that the average length of the DNA the authors were able to read was about 100 bases, which they note is far shorter than the ~750 bases standard in Sanger sequencing.  The article also notes that prepping the DNA samples required 10 person-hours; 4 hours for fragmenting genomic DNA into bite-sized pieces and generation library from those pieces, and 6 hours to put that DNA on beads and then put the beads on the sequencing chip.

So, that's roughly 14 hours from start to getting sequence data, which puts the productivity number at about 10 million bases per person per day.  This is better than running a couple of capillary-based instruments, it's true, but there is still an enormous amount of skilled labor in that 10 hours of sample preparation.  If you have look at the supplementary information, documents s1 and s3 in particular, the processing is by no means trivial.  Actually, the enzymatic rigmarole is quite impressive.  But I wouldn't want to do it myself.  Looking ahead, I don't see any reason it can't be automated.  Given time, patience, and some effort at the microfluidics, the whole process should require only minimal human attention.  That will definitely make an impact on productivity.  No doubt 454 is planning for this eventuality.  The upshot is that this paper puts a point, more-or-less, right on my previously published curves.  It is consistent with progress made with previous technologies, but is actually a bit slower than the estimate Mostafa Ronaghi gave me in 2003.  That's life.

Here's a bit more info.  The New York Times is reporting that;

Jonathan Rothberg, board chairman of 454 Life Sciences, said the company was already able to decode DNA 400 units at a time in test machines. It was working toward sequencing a human genome for $100,000, and if costs could be further reduced to $20,000 the sequencing of individual genomes would be medically worthwhile, Dr. Rothberg said.

We'll see.  We are still a long way from the Thousand Dollar Genome, and this paper appears to be keeping the pace.  All in all, it looks promising, though I wince at the current $500,000 instrument cost.  I don't have enough information at hand to make my own estimates of per base sequencing cost, and I haven't had a chance to contact anyone at the company to suss out the productivity issues better.  I'll update this if and when such conversations take place.

UPDATE (5 Aug 05):  The $500,000 per instrument cost comes from the NYT article:

The Joint Genome Institute, a federal genome sequencing center in Walnut Creek, Calif., has ordered one of 454's $500,000 sequencing machines but has not yet installed it. Paul Richardson, the institute's head of technology development, said the new approach "looks very, very promising" and could reduce sequencing costs fourfold.

The machine's limitation is that at present it can only read DNA fragments 100 units or so in length, compared with the 800-unit read length now attained by the Sanger-based machines. The shorter read length makes it harder to reassemble all the fragments into a complete genome, Dr. Richardson said, so although microbial genomes can be assembled with the new method, mammalian genomes may be beyond its reach at present.

Dr. Fraser, director of the Institute for Genomic Research in Rockville, Md., also said that the new machine's short read lengths "limit its overall utility at this point."

 

Global Distribution of Commercial DNA Foundries

(UPDATE, 22 November 05: Wired Magazine has now published a version of this map.)

Given recent discussions in the press and at the NSABB meeting concerning licensing DNA synthesis instruments and related professional skills, it seems like a good idea to make an estimate of how big the problem is by assessing the distribution of the technology.  Prompted by Jerry Epstein at the Center for Strategic and International Studies, I headed out on the web to make a list of Commercial DNA Foundries.  Here is a map we came up with to represent access to commercially synthesized oligos.

(UPDATE, 19 July 05: I've replaced the .gif with a higher resolution .jpg.)  (UPDATE: Note that these are Foundries -- that is, the building where DNA actually gets synthesized -- and that the associated distribution/marketing networks are actually considerably more widespread.)

Dna_synthesis_foundries_rob_v1d

This is just a first pass, though given how many companies there are I don't know if we will spend a lot of time trying to be encyclopedic.  A few notes:  there are no academic foundries on here, save the Zelinsky Institute in Moscow (which I included because it is quite interesting that a government facility in Russia is operating commercially -- fascinating implications for proliferation).  The number of academic foundries suggests that both instrumentation and skills are quite widely distributed.  The companies are numerous enough.  I gave up trying to fit more companies into the maps of US and Western Europe -- if I left out your company, my apologies.  Perhaps if we figure out a more clever way to keep track of, and represent, all the data, we can include all comers.  I suspect there are more companies in Russian and China, but the language barrier defeats my first pass with Google.

So now, a couple of thoughts.  The net capacity of all these foundries looks to be pretty impressive (though I have yet to add it all up).  Who is ordering all this DNA?  The estimates I've heard for the size of the synthesis market are in the low tens of millions of dollars annually.  Either many companies are ekeing out existence on wee small pieces of the total, or the market is much bigger than people think.  How is it split between short oligos, perhaps primarily used as PCR primers, and larger constructs used to build genes for recombinant proteins?  Does it make a difference, even now?  If so, given the increasing capability demonstrated in assembling short pieces of DNA, is it worth trying to distinguish between short and long oligos?  That is, will regulation of either short or long pieces of DNA be feasible and will it increase security?

Finally, I haven't yet charted the cost per base of synthesis as a function of geography, but I'm sure the results will be provocative.  I was surprised to see that the biotechnology industry in India is supporting at least three commercial synthesis foundries, and I'll bet those companies are charging less than I recently paid for gene synthesis domestically.  How soon are North American and European DNA foundries going to have to compete against Indian labor and FedEx?

More to come as I ponder this.  Comments and suggestions?

Kazakh Biotech Empire

The 24 June issue of Science contains a story (subscription required) by Richard Stone describing efforts to build up biotech in Kazakhstan.  They aren't thinking small; "The government has approved plans and is now reviewing financing for a $50 million Life Science and Biotech Center of Excellence, supported in part by the World Bank."

I think this is interesting for a couple of reasons.  The first is that the article describes U.S. Department of State hopes that the endeavor will keep former bioweapons scientists engaged in less threatening activities.  The second is that the World Bank is helping finance what could be at minimum a regional biotech power.  Given a few years to build up the infrastructure, combined with the expertise developed at Stepnogorsk in manipulating and manufacturing biologicals, they could be a global technological and economic power.

The Death of Innovation, or How the NIH is Undermining Its Future

Donald Kennedy's latest editorial in Science notes that the vast majority of NIH grants are going to older investigators.  Writes Kennedy;

In 1980, despite a tightened academic job market..."new" investigators held 50% of competing new grants, and 23% of all awards were going to scientists under 35. Now, alas, that percentage has shrunk to less than 4%, with a huge corresponding increase in the proportion going to older researchers.

This despite the fact that the NIH budget has at least doubled since 1980.  (The figure is from an interesting article on how to fund science and innovation by Kei Koizumi for the AAAS.)  A rough Google search suggests 80% of PhD's in the US are held by people under 40 (does anybody have good numbers for biology?), which means that the vast majority of NIH dollars are going to investigators who have been around awhile.

Now, of course, I don't mean to imply that "older researchers" aren't innovating.  Few brand-spanking new PhD's can keep up with Sydney Brenner.  A characteristic of biology that distinguishes it from theoretical physics is that doing good biology requires the grasp of a great many facts and stories.  Whereas a the guts of a PhD in physics can be derived over a weekend (or so I was told upon arriving at Princeton -- mine took rather longer) the combination of biological lore and experimental art accumulates over time.  But if we aren't funding young scientists with new ideas then we are missing out.  New methods and tools are the key to progress in biology.

Why should young scientists from abroad bother to come here?  Why should any young scientist bother to stay here?  Yes, yes -- the US still has the biggest budget and a tremendous diversity of research.  But even Sydney seems to be spending most of his time in Europe and Asia these days.  If we fail to ensure proper funding and opportunity for young biological scientists, then the innovation is simply going to happen elsewhere. 

The Challenges of International Regulatory Regimes for Biological Technologies

Arriving in my mailbox this morning was a story from the Washington Times Post (Thanks, Oliver), dated 18 June 05, "Bird Flu Drug Rendered Useless: Chinese Chickens Given Medication Made for Humans", by Alan Sipress.  Chinese farmers, encouraged by the government, have since the late 1990's been feeding the antiviral drug amantadine to chickens infected with H5N1.  (Update: Recent news stories in Science and Nature carry claims from the Chinese gov't that this usage was most certainly not officially sanctioned or  encouraged.)  The story notes that this usage is in violation of international agreements on the treatment of livestock with drugs, and that the resulting long term selective pressure is the reason amantadine is no longer effective in treating the influenza strain currently causing concerns about a pandemic.  This sets up China (and due to growing economic interdependence, the rest of the industrialized world) for serious woe, amplified by the fact that the most populous country on the planet is not prepared for a pandemic

In summary, an important tool in dealing with a potential pandemic outbreak in humans has been rendered useless despite an international agreement aimed specifically at preventing that sort of occurrence.  Writes Sipress;

The Chinese Agriculture Ministry approved the production and sale of the drug for use in chickens, according to officials from the Chinese pharmaceutical industry and the government, although such use is barred in the United States and many other countries. Local government veterinary stations instructed Chinese farmers on how to use the drug and at times supplied it, animal health experts said.

Amantadine is one of two types of medication for treating human influenza. But researchers determined last year that the H5N1 bird flu strain circulating in Vietnam and Thailand, the two countries hardest hit by the virus, had become resistant, leaving only an alternative drug that is difficult to produce in large amounts and much less affordable, especially for developing countries in Southeast Asia.

The scientific evidence that using antivirals in poultry is a bad idea has been around for quite some time, and international policies regarding veterinary application of the drugs is based on clear evidence: "In 1987, researchers at a U.S. Department of Agriculture laboratory demonstrated that bird flu viruses developed drug resistance within a matter of days when infected chickens received amantadine."

So we have a situation where scientific, technical, and policy components were all directed towards a particular regulatory goal, and all were ignored.  There is one more key piece to this story, and that is the number of years it has taken to confirm the information.  Sipress, again;

Health experts outside China previously said they suspected the virus's resistance to the medicine was linked to drug use at poultry farms but were unable to confirm the practice inside the country. Influenza researchers at the U.S. Centers for Disease Control and Prevention, in particular, have collected information about amantadine use from Chinese Web sites but have been frustrated in their efforts to learn more on the ground.

This is truly the crux of our challenge over the coming decades.  Despite efforts determine the extent of veterinary use of amantadine within China, even widespread government sanctioned (recommended, according to the story!) use that violated explicit international agreements continued unabated.  Even if the relevant intelligence had been confirmed, it isn't clear that the Chinese government would have changed its policies.  Regulation failed in this case, and because information was hard to come by our response to the problem is further impaired.  (Update:  Regardless of the involvement of the government, my point about the importance of good information stands.)

This is why I have been arguing so strenuously that open and distributed networks of people using and developing biological technologies are strongly preferable to closed ones. In my recent essay "Synthetic Biology 1.0", I discussed the effect of regulation on preparedness for natural and artificial biological threats, in part with conditions in China in mind.  Though many states and organizations will be pushing biological technologies in the coming years, China is front and center because of its growing economic might and educated population.  It is clear they are going their own way, developing and, more importantly, using technology as they see fit.

In the year 2000, Jiang Zhemin, the former President (Premier? I can never remember which) of China, said in no uncertain terms that in order to deal with their health care crisis they would use all tools at their disposal.  He specifically mentioned genetically engineering the population (this story is now finally on the record in Gerald Epstein's recent report from CSIS, "Global Evolution of Dual-Use Biotechnology").  Such efforts will explicitly require sophisticated biological technologies, in particular those related to DNA synthesis and sequencing.  Countries throughout Asia are already pushing the technology without much, if any, concern for what we decide to do here in the states.  Creating and enforcing regulatory regimes for this sort of thing would require an international effort that historically doesn't work so very well for just about anything else.  Witness the amantadine problem.

Then there is the problem that the technology and skills do not respect borders.  Synthetic genes can be ordered from companies in Seattle, San Francisco, throughout western Europe and Russia, Dalian, Tehran; the list goes on.  How do we monitor the flow of Epindorf tubes full of lyophilized DNA around the globe?  Used synthesis instruments are not only available worldwide, but the parts for a new 192 channel instrument (styled after ABI or Gene Machines) can be had for about $10,000.  The plans and process specs were published long ago.  Yes, it requires some skill to assemble the instrument, and yes, it requires some skill to write the software, but most people with undergraduate degrees in engineering or physics have this skill or can fumble their way to it in a relatively short period of time.  Reagents are available worldwide, and I don't understand how we can track those reagents any better than we do it now for industrial chemicals or drugs.  The grey and black markets for everything from drugs to fluorocarbon coolants are thriving around the world.  I don't understand how reagents, short oligos, genes, or even synthetic genomes can be controlled any better.

This raises two main issues.  The first is that I suspect regulation will only slow down scientific and technological progress here in the US.  Other countries (and organizations) are likely to explore the relevant fields a their own pace.  This resulting technology gap constitutes the second issue, which is that we will be unprepared for surprises.  Given the history of technology from the last century, I do not believe we can control the pace of development of biological technologies.  If we, here in the US, are not in the lead, somebody else is.  And we will thus experience surprise on a regular basis.  Our choices about developing biological technologies will determine whether we are willing to let potential adversaries be in the lead.

The above arguments are primarily directed at our physical security, but I am equally concerned about our economic security.  It is clear that China and India are pushing ahead with biological technology.  The sheer numbers of talented and smart students in these countries is to me mind boggling.  I am not sure that we can maintain our economic vitality even if we keep going at the current rate, but I am certain we will lose out if we decide to slow down.  We absolutely require increased government investment in technology and increased numbers of skilled people.  If you don't believe me, then the interviews Bio-ERA has been doing for our DOE-funded Synthetic Biology project clearly indicate that our global competitiveness is already at risk.  There is absolutely no reason European or Asian scientists and businesses should order synthetic genes from the US.  More specifically, my experience at a Global Business Network meeting a few weeks ago indicates that even though China is likely to experience some internal disruption over the coming decade or two, they are pushing hard not just to be competitive, but to take the lead.  In everything.

In summary, given my historical study of other technologies and my experience developing new biological technologies, I do not believe that regulation will result in improved security.  On the contrary, I believe it will impair our preparedness, reduce our security, and reduce our economic competitiveness.  Independently from these issues, I do not see how international regulatory regimes for biological technologies are workable, even if agreements are reached and are implemented -- by no means trivial efforts in themselves.

Finally, I would observe that no regulatory regime is perfect, and regulation is in actuality more a problem of managing barriers (to entry and use) that are inherently leaky.  Implementation of regulations always seeds resistance.  Given the power of biological technologies how many surprises can afford?

Synthetic Biology 1.0

I have a new essay, "Synthetic Biology 1.0", just published on Future Brief.  Here are the first few 'graphs:

Open development of biological technology is crucial to US domestic security and to the health of our economy.

Misuse of this technology in bioterrorism is a clear threat. Our first response to recent domestic bioterror attacks, and to evidence of bioweapon programs abroad, has been to pursue safety in regulation. However, it is already clear that action to limit domestic access to materials and methods will produce only illusory safety. Reagents required for genetic manipulation are available from manufacturers outside the U.S. Synthetic genes can be ordered with equal ease from fabrication labs in Seattle and Tehran .

Beyond access to the infrastructure of sequencing and synthesis, which enables attempts at state-of-the-art genetic manipulation, the practical knowledge required to assemble objects and processes in cellular and molecular systems is proliferating globally. Moreover, biological technologies are being developed globally, and they will be as useful worldwide in developing new crops, drugs, and industrial products as they will be in producing weapons. These factors considerably expand the scope of our security problem.

Ensuring domestic physical security and economic competitiveness requires a long-term plan to integrate public and private sector interests. Serious consideration should be given to the role of government in establishing the design and production infrastructure for biological engineering. In particular, investing in engineering tools as a goal of federal research policy will enable safer and more rapid progress in all areas of biology...

Follow the link to Future Brief for a PDF.  The link only just went live today, and there is already some nice commentary over at WorldChanging.

"Influenza Pandemic: Challenges Remain in Preparedness"

On 26 May, 2005, Marcia Crosse, Director of Health Care at the Government Accountability Office(GAO), testified (PDF) before the Subcommittee on Health, and the Committee on Energy and Commerce of the U.S. House of Representatives on pandemic preparedness in the US.  The news is not good.

Some of the choicer comments:

Challenges regarding the nation’s preparedness for and response to an influenza pandemic remain. Specifically, our prior work has found that although CDC participated in an interagency working group that developed the U.S. plan for pandemic preparedness that was posted for public comment in August 2004, as of May 23, 2005, the plan had not been finalized. Further, we found that the draft plan does not address certain critical issues, including how vaccine for an influenza pandemic will be purchased, distributed, and administered; how population groups will be prioritized for vaccination; what quarantine authorities or travel restrictions may need to be invoked; and how federal resources should be deployed. At the state level, we found that most hospitals across the country lack the capacity to respond to large-scale infectious disease outbreaks.

...The draft plan delegates to the states responsibility for distribution of vaccine. The lack of a clearly defined federal role in distribution complicates pandemic planning for the states. Furthermore, among the current state pandemic influenza plans, there is no consistency in terms of their procurement and distribution of vaccine and the relative role of the federal government. Approximately half of the states handle procurement and distribution of the annual influenza vaccine through the state health agency. The remainder either operate through a third-party contractor for distribution to providers or use a combination of these two approaches.

Most annual influenza vaccine distribution and administration are accomplished within the private sector, with relatively small amounts of vaccine purchased and distributed by CDC or by state and local health departments. In the United States, 85 percent of vaccine doses are purchased by the private sector, such as private physicians and pharmacies. HHS has not yet determined how influenza vaccine will be distributed and administered during an influenza pandemic.

There are many issues surrounding the production of influenza vaccine, which will only become exacerbated during an influenza pandemic. Vaccines, which are considered the first line of defense to prevent or reduce influenza-related illness and death, may be unavailable or in short supply. Producing the vaccine is a complex process that involves growing viruses in millions of fertilized chicken eggs. Experience has shown that the vaccine production cycle takes at least 6 to 8 months after a virus strain has been identified, and vaccines for some influenza strains have been difficult to mass-produce, causing further delay. The lengthy process for developing a vaccine may mean that a vaccine would not be available during the initial stages of a pandemic.

Here is a wee bit of good news, namely that the US Government is spending money to guarantee purchase of vaccine so that manufacturers will maintain more production infrastructure:

...The agency’s fiscal year 2006 budget request includes an increase of $30 million for CDC to enter into guaranteed purchase contracts with vaccine manufacturers to ensure the production of bulk monovalent influenza vaccine. If supplies fall short, this bulk product can be turned into a finished trivalent influenza vaccine product for annual distribution. If supplies are sufficient, the bulk vaccine
can be held until the following year’s influenza season and developed into vaccines if the circulating strains remain the same. In addition, according to CDC, this guarantee will help to expand the influenza market by providing an incentive to manufacturers to expand capacity and possibly
encourage additional manufacturers to enter the market. In addition, the fiscal year 2006 budget request includes an increase of $20 million to support influenza vaccine purchase activities.

But, of course, the testimony basically ends on a downer:

Even if sufficient quantities of the vaccine are produced in time, vaccines against various strains differ in their ability to produce the immune response necessary to provide effective protection against the disease. Studies show that it is uncertain how effective a vaccine will be in preventing or controlling the spread of a pandemic influenza virus.

At least with this testimony, and the remarks  of Senate Majority Leader Dr. Frist at Harvard Med School last week, it seems the right noises are being made in Washington DC.