Late Night, Unedited Musings on Synthesizing Secret Genomes

By now you have probably heard that a meeting took place this past week at Harvard to discuss large scale genome synthesis. The headline large genome to synthesize is, of course, that of humans. All 6 billion (duplex) bases, wrapped up in 23 pairs of chromosomes that display incredible architectural and functional complexity that we really don't understand very well just yet. So no one is going to be running off to the lab to crank out synthetic humans. That 6 billion bases, by the way, just for one genome, exceeds the total present global demand for synthetic DNA. This isn't happening tomorrow. In fact, synthesizing a human genome isn't going to happen for a long time.

But, if you believe the press coverage, nefarious scientists are planning pull a Frankenstein and "fabricate" a human genome in secret. Oh, shit! Burn some late night oil! Burn some books! Wait, better — burn some scientists! Not so much, actually. There are a several important points here. I'll take them in no particular order.

First, it's true, the meeting was held behind closed doors. It wasn't intended to be so, originally. The rationale given by the organizers for the change is that a manuscript on the topic is presently under review, and the editor of the journal considering the manuscript made it clear that it considers the entire topic under embargo until the paper is published. This put the organizers in a bit of a pickle. They decided the easiest way to comply with the editor's wishes (which were communicated to the authors well after the attendees had made travel plans) was to hold the meeting under rules even more strict than Chatham House until the paper is published. At that point, they plan to make a full record of the meeting available. It just isn't a big deal. If it sounds boring and stupid so far, it is. The word "secret" was only introduced into the conversation by a notable critic who, as best I can tell, perhaps misconstrued the language around the editor's requirement to respect the embargo. A requirement that is also boring and stupid. But, still, we are now stuck with "secret", and all the press and bloggers who weren't there are seeing Watergate headlines and fame. Still boring and stupid.

Next, It has been reported that there were no press at the meeting. However, I understand that there were several reporters present. It has also been suggested that the press present were muzzled. This is a ridiculous claim if you know anything about reporters. They've simply been asked to respect the embargo, which so far they are doing, just like they do with every other embargo. (Note to self, and to readers: do not piss off reporters. Do not accuse them of being simpletons or shills. Avoid this at all costs. All reporters are brilliant and write like Hemingway and/or Shakespeare and/or Oliver Morton / Helen Branswell / Philip Ball / Carl Zimmer / Erica Check-Hayden. Especially that one over there. You know who I mean. Just sayin'.)

How do I know all this? You can take a guess, but my response is also covered by the embargo.

Moving on: I was invited to the meeting in question, but could not attend. I've checked the various associated correspondence, and there's nothing about keeping it "secret". In fact, the whole frickin' point of coupling the meeting to a serious, peer-reviewed paper on the topic was to open up the conversation with the public as broadly as possible. (How do you miss that unsubtle point, except by trying?) The paper was supposed to come out before, or, at the latest, at the same time as the meeting. Or, um, maybe just a little bit after? But, whoops. Surprise! Academic publishing can be slow and/or manipulated/politicized. Not that this happened here. Anyway, get over it. (Also: Editors! And, reviewers! And, how many times will I say "this is the last time!")

(Psst: an aside. Science should be open. Biology, in particular, should be done in the public view and should be discussed in the open. I've said and written this in public on many occasions. I won't bore you with the references. [Hint: right here.] But that doesn't mean that every conversation you have should be subject to review by the peanut gallery right now. Think of it like a marriage/domestic partnership. You are part of society; you have a role and a responsibility, especially if you have children. But that doesn't mean you publicize your pillow talk. That would be deeply foolish and would inevitably prevent you from having honest conversations with your spouse. You need privacy to work on your thinking and relationships. Science: same thing. Critics: fuck off back to that sewery rag in — wait, what was I saying about not pissing off reporters?)

Is this really a controversy? Or is it merely a controversy because somebody said it is? Plenty of people are weighing in who weren't there or, undoubtedly worse from their perspective, weren't invited and didn't know it was happening. So I wonder if this is more about drawing attention to those doing the shouting. That is probably unfair, this being an academic discussion, full of academics.

Secondly (am I just on secondly?), the supposed ethical issues. Despite what you may read, there is no rush. No human genome, nor any human chromosome, will be synthesized for some time to come. Make no mistake about how hard a technical challenge this is. While we have some success in hand at synthesizing yeast chromosomes, and while that project certainly serves as some sort of model for other genomes, the chromatin in multicellular organisms has proven more challenging to understand or build. Consequently, any near-term progress made in synthesizing human chromosomes is going to teach us a great deal about biology, about disease, and about what makes humans different from other animals. It is still going to take a long time. There isn't any real pressing ethical issue to be had here, yet. Building the ubermench comes later. You can be sure, however, that any federally funded project to build the ubermench will come with a ~2% set aside to pay for plenty of bioethics studies. And that's a good thing. It will happen.

There is, however, an ethical concern here that needs discussing. I care very deeply about getting this right, and about not screwing up the future of biology. As someone who has done multiple tours on bioethics projects in the U.S. and Europe, served as a scientific advisor to various other bioethics projects, and testified before the Presidential Commission on Bioethical Concerns (whew!), I find that many of these conversations are more about the ethicists than the bio. Sure, we need to have public conversations about how we use biology as a technology. It is a very powerful technology. I wrote a book about that. If only we had such involved and thorough ethical conversations about other powerful technologies. Then we would have more conversations about stuff. We would converse and say things, all democratic-like, and it would feel good. And there would be stuff, always more stuff to discuss. We would say the same things about that new stuff. That would be awesome, that stuff, those words. <dreamy sigh> You can quote me on that. <another dreamy sigh>

But on to the technical issues. As I wrote last month, I estimate that the global demand for synthetic DNA (sDNA) to be 4.8 billion bases worth of short oligos and ~1 billion worth of longer double-stranded (dsDNA), for not quite 6 Gigabases total. That, obviously, is the equivalent of a single human duplex genome. Most of that demand is from commercial projects that must return value within a few quarters, which biotech is now doing at eye-popping rates. Any synthetic human genome project is going to take many years, if not decades, and any commercial return is way, way off in the future. Even if the annual growth in commercial use of sDNA were 20% — which is isn't — this tells you, dear reader, that the commercial biotech use of synthetic DNA is never, ever, going to provide sufficient demand to scale up production to build many synthetic human genomes. Or possibly even a single human genome. The government might step in to provide a market to drive technology, just as it did for the human genome sequencing project, but my judgement is that the scale mismatch is so large as to be insurmountable. Even while sDNA is already a commodity, it has far more value in reprogramming crops and microbes with relatively small tweaks than it has in building synthetic human genomes. So if this story were only about existing use of biology as technology, you could go back to sleep.

But there is a use of DNA that might change this story, which is why we should be paying attention, even at this late hour on a Friday night.

DNA is, by far, the most sophisticated and densest information storage medium humans have ever come across. DNA can be used to store orders of magnitude more bits per gram than anything else humans have come up with. Moreover, the internet is expanding so rapidly that our need to archive data will soon outstrip existing technologies. If we continue down our current path, in coming decades we would need not only exponentially more magnetic tape, disk drives, or flash memory, but exponentially more factories to produce these storage media, and exponentially more warehouses to store them. Even if this is technically feasible it is economically implausible. But biology can provide a solution. DNA exceeds by many times even the theoretical capacity of magnetic tape or solid state storage.

A massive warehouse full of magnetic tapes might be replaced by an amount of DNA the size of a sugar cube. Moreover, while tape might last decades, and paper might last millennia, we have found intact DNA in animal carcasses that have spent three-quarters of a million years frozen in the Canadian tundra. Consequently, there is a push to combine our ability to read and write DNA with our accelerating need for more long-term information storage. Encoding and retrieval of text, photos, and video in DNA has already been demonstrated. (Yes, I am working on one of these projects, but I can't talk about it just yet. We're not even to the embargo stage.) 

Governments and corporations alike have recognized the opportunity. Both are funding research to support the scaling up of infrastructure to synthesize and sequence DNA at sufficient rates.

For a “DNA drive” to compete with an archival tape drive today, it needs to be able to write ~2Gbits/sec, which is about 2 Gbases/sec. That is the equivalent of ~20 synthetic human genomes/min, or ~10K sHumans/day, if I must coin a unit of DNA synthesis to capture the magnitude of the change. Obviously this is likely to be in the form of either short ssDNA, or possibly medium-length ss- or dsDNA if enzymatic synthesis becomes a factor. If this sDNA were to be used to assemble genomes, it would first have to be assembled into genes, and then into synthetic chromosomes, a non trivial task. While this would be hard, and would to take a great deal of effort and PhD theses, it certainly isn't science fiction.

But here, finally, is the interesting bit: the volume of sDNA necessary to make DNA information storage work, and the necessary price point, would make possible any number of synthetic genome projects. That, dear reader, is definitely something that needs careful consideration by publics. And here I do not mean "the public", the 'them' opposed to scientists and engineers in the know and in the do (and in the doo-doo, just now), but rather the Latiny, rootier sense of "the people". There is no them, here, just us, all together. This is important.

The scale of the demand for DNA storage, and the price at which it must operate, will completely alter the economics of reading and writing genetic information, in the process marginalizing the use by existing multibillion-dollar biotech markets while at the same time massively expanding capabilities to reprogram life. This sort of pull on biotechnology from non-traditional applications will only increase with time. That means whatever conversation we think we are having about the calm and ethical development biological technologies is about to be completely inundated and overwhelmed by the relentless pull of global capitalism, beyond borders, probably beyond any control. Note that all the hullabaloo so far about synthetic human genomes, and even about CRISPR editing of embryos, etc., has been written by Western commentators, in Western press. But not everybody lives in the West, and vast resources are pushing development of biotechnology outside of the of West. And that is worth an extended public conversation.

So, to sum up, have fun with all the talk of secret genome synthesis. That's boring. I am going off the grid for the rest of the weekend to pester litoral invertebrates with my daughter. You are on your own for a couple of days. Reporters, you are all awesome, make of the above what you will. Also: you are all awesome. When I get back to the lab on Monday I will get right on with fabricating the ubermench for fun and profit. But — shhh — that's a secret.

Biodefense Net Assessment: Causes and Consequences of Bioeconomic Proliferation

Revenues from biotechnology continue to grow rapidly around the world.  For several years I have been trying to assess these revenues, in part as a proxy metric for technological capabilities.  A couple of years ago, I received a commission from the U.S. government to explore this topic for the 2012 Biodefense Net Assessment (BNA).  I recently received approval to release the resulting report, which carries the title "Causes and Consequences of Bioeconomic Proliferation: Implications for U.S. Physical and Economic Security" (PDF).  As far as I am aware, this is the first publicly-released document from the BNA. 

There is a relatively small amount of information available about the BNA available on the web. The BNA is a quadrennial review required under Homeland Security Presidential Directive 10 (HSPD-10): "These assessments are meant to provide senior level decision makers with fresh, non-consensus, perspectives on key issues underlying the Nation's biodefense."  The first few pages of the report provide more information about the origin and use of the BNA.

My own motivation for doing this work is to better understand what is going on in the world.  When it comes to developing policy to improve security and safety, I unapologetically insist that data drive policy.  There are far too many people who develop policy in spite of data rather than in light of data.  That leads to messy thinking and demonstrably makes us less safe and less secure.  All that said, one conclusion from my work on this report is that nobody is doing a very good job of gathering and publishing the data necessary to understand the rapid technical and economic development of biotechnology around the world.

One final thought about the report: this particular document was funded by the U.S. government, and I was given a particular set of charges in the task (see pg iii-iv); the report is therefore tilted toward U.S. security concerns.  However, the basic analyses and conclusions are relevant to developing policy in any country, and for that matter to developing strategy for many private companies and other organizations.  I will continue work on this story, and look forward to engaging people around the globe in better understanding how our world is changing.

Here is the "Background" section of the report.  Please note that the report is now a few years old, and the bioeconomy has continued to grow rapidly around the world.

Biotechnology is becoming increasingly de-skilled and less expensive, leading to a proliferation of localized innovation around the world. In addition to major investments by growing economic powerhouses India and China, other developing countries such as Indonesia, Pakistan, and Brazil are equally intent on developing domestic biotech research and development capabilities. All of these countries are interested initially in producing drugs for diseases that predominantly affect their citizens, a project that requires a particular infrastructure and set of skills. Yet those same skills can be used to develop other applications, from fuels and materials to weapons, all of which can serve as a lever to increase power and presence on the world stage, thereby enabling developing countries to become rivals to the US both regionally and globally.

Economic demand will serve as a driver for ever greater proliferation of biotechnology. Today, in the US, revenues from genetically modified systems contribute the equivalent of almost 2% of GDP, and are growing in the range of 15 to 20% per year. China, among other countries, is not far behind and is following explicit government policy to substantially increase its independent, domestic development of new biological technologies to address such diverse concerns as healthcare, biomass production, and biomanufacturing. As is already the case in many other industries, trade between developing nations in biotech may soon exceed trade with the US. Therefore, among the challenges the US is likely to face in this environment is that the flow of technology, ideas, and skills may bypass US soil. Moreover, because skills and instrumentation are widely available, biotechnological development is possible in unconventional settings outside of universities and corporate laboratories. The resulting profusion of localized and distributed innovation is likely to provide a wide variety of challenges to US security, from economic competition, to intelligence gathering, to the production of new bio-threats.

Censoring Science is Detrimental to Security

Restricting access toscience and technology in the name of security is historically a losing proposition.  Censorship of information that is known to exist incentivizes innovation and rediscovery. 

As most readers of this blog know, there has been quite a furor over new results demonstrating mutations in H5N1 influenza strains that are both deadly and highly contagious in mammals.  Two groups, led by Ron Fouchier in the The Netherlands and Yoshihiro Kawaoka at The University of Wisconsin, have submitted papers to Nature and Science describing the results.  The National Science Advisory Board for Biosecurity (NSABB) has requested that some details, such as sequence information, be omitted from publication.  According to Nature, both journals are "reserving judgement about whether to censor the papers until the US government provides details of how it will allow genuine researchers to obtain redacted information".

For those looking to find more details about what happened, I suggest starting with Dorveen Caraval's interview with Fouchier in the New York Times, "Security in Flu Study Was Paramount, Scientist Says"; Kathleen Harmon's firsthand account of what actually happened when the study was announced; and Heidi Ledford's post at Nature News about the NSABB's concerns.

If you want to go further, there is more good commentary, especially the conversation in the comments (including from a member of the NSABB), in "A bad day for science" by Vincent Racaniello.  See also Michael Eisen's post "Stop the presses! H5N1 Frankenflu is going to kill us all!", keeping in mind that Eisen used to work on the flu.

Writing at Foreign Policy, Laurie Garrett has done some nice reporting on these events in two posts, "The Bioterrorist Next Door" and "Flu Season".  She suggests that attempts to censor the results would be futile: "The genie is out of the bottle: Eager graduate students in virology departments from Boston to Bangkok have convened journal-review debates reckoning exactly how these viral Frankenstein efforts were carried out."

There is much I agree with in Ms. Garrett's posts.  However, I must object to her assertion that the work done by Fouchier and Kawaoka can be repeated easily using the tools of synthetic biology.  She writes "The Fouchier episode laid bare the emptiness of biological-weapons prevention programs on the global, national, and local levels.  Along with several older studies that are now garnering fresh attention, it has revealed that the political world is completely unprepared for the synthetic-biology revolution."   As I have already written a book that discusses this confusion (here is an excerpt about synthetic biology and the influenza virus), it is not actually what I want to write about today.  But I have to get this issue out of the way first.

As far as I understand from reading the press accounts, both groups used various means to create mutations in the flu genome and then selected viruses with properties they wanted to study.  To clarify, from what I have been able to glean from the sparse accounts thus far, DNA synthesis was not used in the work.  And as far as I understand from reading the literature and talking to people who build viruses for a living, it is still very hard to assemble a functioning, infectious influenza virus from scratch.   

If it were easy to write pathogen genomes -- particularly flu genomes -- from scratch, we would quite frankly be in deep shit. But, for the time being, it is hard.  And that is important.  Labs who do use synthetic biology to build influenza viruses, as with those who reconstructed the 1918 H1N1 influenza virus, fail most of the time despite great skill and funding.  Synthesizing flu viruses is simply not a garage activity.  And with that, I'll move on.

Regardless of how the results might be reproduced, many have suggested that the particular experiments described by Fouchier and Kawaoka should not have been allowed.  Fouchier himself acknowledges that selecting for airborne viruses was not the wisest experiment he could have done; it was, he says, "really, really stupid".  But the work is done, and people do know about it.  So the question of whether this work should have been done in the first place is beside the point.  If, as suggested by Michael Eisen, that "any decent molecular biologist" could repeat the work, then it was too late to censor the details as soon as the initial report came out. 

I am more interested in the consequences of trying to contain the results while somehow allowing access to vetted individuals.  Containing the results is as much about information security as it is biological security.  Once such information is created, the challenge is to protect it, to secure it.  Unfortunately, the proposal to allow secure access only by particular individuals is at least a decade (if not three decades) out of date.

Any attempt to secure the data would have to start with an assessment of how widely it is already distributed.  I have yet to meet an academic who regularly encrypts email, and my suspicion is that few avail themselves of the built-in encryption on their laptops.  So, in addition to the university computers and email servers where the science originated, the information is sitting in the computers of reviewers, on servers at Nature and Science, at the NSABB, and, depending on how the papers were distributed and discussed by members of the NSABB, possibly on their various email servers and individual computers as well.  And let's not forget the various unencrypted phones and tablets all of those reviewers now carry around.

But never mind that for a moment.  Let's assume that all these repositories of the relevant data are actually secure.  The next step is to arrange access for selected researchers.  That access would inevitably be electronic, requiring secure networks, passwords, etc.  In the last few days the news has brought word that computer security firms Stratfor and Symantec have evidently been hacked recently.  Such attacks are not uncommon.  Think back over the last couple of years: hacks at Google, various government agencies, universities.  Credit card numbers, identities, and supposedly secret DoD documents are all for sale on the web.  To that valuable information we can now add a certain list of influenza mutations.  If those mutations are truly a critical biosecurity risk -- as asserted publicly by various members of the NSABB -- then that data has value far beyond its utility in virology and vaccinology.

The behavior of various hackers (governments, individuals, other) over the last few years make clear that what the discussion thus far has done is to stick a giant "HACK HERE" sign on the data.  Moreover, if Ms. Garrett is correct that students across the planet are busy reverse engineering the experiments because they don't have access to the original methods and data, then censorship is creating a perverse incentive for innovation.  Given today's widespread communication, restriction of access to data is an invitation, not a proscription.

This same fate awaits any concentration of valuable data.  It obviously isn't a problem limited to collections of sensitive genetic sequences or laboratory methods.  And there is certainly a case to be made for attempting to maintain confidential or secret caches of data, whether in the public or private interest.  In such instances, compartmentalization and encryption must be implemented at the earliest stages of communication in order to have any hope of maintaining security. 

However, in this case, if it true that reverse engineering the results is straightforward, then restriction of access serves only to slow down the general process of science.  Moreover, censorship will slow the development of countermeasures.  It is unlikely that any collection of scientists identified by the NSABB or the government will be sufficient to develop all the technology we need to respond to natural pathogens, let alone any artificial ones.

As with most other examples of prohibition, these restrictions are doomed before they are even implemented.  Censorship of information that is known to exist incentivizes innovation and rediscovery.  As I explored in my book, prohibition in the name of security is historically a losing proposition.  Moreover, science is inherently a networked human activity that is fundamentally incompatible with constraints on communication, particularly of results that are already disclosed.  Any endeavor that relies upon science is, therefore, also fundamentally incompatible with constraints on communication.  Namely developing technologies to defend against natural and artificial pathogens.  Censorship threatens not just science but also our security.

It is the End of the World as We Know it, and I feel Strangely Ambivalent: Synthetic Biology 5.0

Synthetic Biology 5.0 has come and gone.  I expected, as in previous years, to be busy liveblogging amid the excitement.  I tweeted some during the proceedings (here is Eric Ma's summary of #synbio5 tweets), but this is my first post about the meeting, and probably the last one.  I mostly just listened, took a few notes, and was delighted to see the progress being made.  I was not nearly as amped up about the proceedings as in previous years, and I am still trying to figure out why. 

Here are a couple of reasons I have sorted out so far.  It was the end of the beginning of synthetic biology.  The meeting was full of science and engineering.  And that's about all.  There were a few VC's and other investors sniffing around, but not nearly so many as in previous years; those who did show up kept a lower profile.  There were also fewer obvious government officials, no obvious spooks, no obvious law enforcement officers, nor any self-identified Weapons of Mass Destruction Coordinators.  And I only encountered a couple of reporters, though there must have been more.  I skipped 3.0 in Zurich, but at 1.0 at MIT, 2.0 at Berkeley (parts 1, 2, 3, 4, 5), and 4.0 in Hong Kong (part 1), there was much more buzz.  Synthetic Biology 5.0 was much shorter on hype than prior gatherings. 

There was substantially more data this year than previously.  And there was substantially less modeling.  All in all, Synthetic Biology is substantially more ... substantial.  It was like a normal scientific meeting.  About science.  No stunts from "civil society" groups looking for their next fear bullet point for fundraising.  No government officials proclaiming SB as the economic future of their city/state/country.  Just science.

What a relief.

And that science was nothing to sneeze at.  There were great talks for 3 days.  Here are a couple of things that caught my eye.

Jef Boeke from Johns Hopkins presented his plans to build synthetic yeast chromosomes.  I first heard this idea more than ten years ago from Ron Davis at Stanford, so it isn't brand new.  I did notice, however, that Boeke having all his synthetic chromosomes made in China.  Over the longer term this means China is getting a boost in building out future biomanufacturing platforms.  If the project works, that is.

As tweeted, Jack Newman from Amyris gave an update on commercialization of artemisinin; it should be on the market by the end of the year, which should be in time to help avert an expected shortfall in production from wormwood.  Fantastic.

Pam Silver and her various students and post-docs showed off a variety of interesting results.  First, Faisal Aldaye showed in vivo DNA scaffolds used to channel metabolic reactions, resulting in substantial increases in yield.  Second, Pam Silver showed the use of those scaffolds to generate twice as much sucrose from hacked cyanobacteria per unit of biomass as from sugar cane.  If that result holds up, and if the various issues related to the cost of bioreactors used to culture photosynthetic organisms are worked out, then Pam's lab has just made an enormous step forward in bringing about distributed biological manufacturing.

This is the sort of advance that makes me feel more sanguine about the future of MIcrobrewing the Bioeconomy.  It will take some years before the volume of Amyris' Biofene, or Gevo's bio-PET, or Blue Marble's bio-butyric acid begins to impact the oil industry.  But it is clear to me now as never before that the petroleum industry is vulnerable from the top of the barrel -- the high value, low volume compounds that are used to build the world around us in the form of petrochemicals.  Biology can now be used to make all those compounds, too, directly from sugar, cellulose, and sunlight, without the tens of billions of dollars in capital required to run an oil company (see The New Biofactories). 

So SB 5.0 was the end of the world as we know it.  Synthetic biology is now just another field of human endeavor, thankfully producing results and also thankfully suffering reduced hype.  I can see how the pieces are starting to fit together to provide for sustainable manufacturing and energy production, though it will be some years before biological technologies are used this way at scale.  Perhaps this is less in-your-face exciting for the attendees, the press, and the public, and that may be part of the reason for my ambivalence.  I fell asleep several times during the proceedings, which has never happened to me at SB X.0, even when overseas and jetlagged.  I have never before thought of achieving boredom as constituting progress.

Myriad's Lawyers Want to Patent the Periodic Table

Interesting arguments today before a Federal Appeals Court concerning the "BRCA 1/2" patents.  Recall first that the U.S. Government has filed an amicus brief supporting the trial judge's ruling that naturally-occurring genes cannot be patented (see "Big Gene Patent (Busting) News???" and "Surprise Outbreak of Common Sense in Washington DC").

The Appellate Court is going to decide whether two genes (BRCA 1 and 2), in which mutations are correlated with breast cancer, can be patented.  Myriad Genetics and its lawyers say yes, the ACLU and several groups representing patients, scientists, and clinicians say no.  So did the trial judge.  The basic argument is about whether a naturally-occurring gene sequence that is used in a diagnostic test can be considered an invention.

Nature's The Great Beyond blog has a bit of reporting from yesterday's proceedings.  There is a passage from the blog post I think is worth exploring a bit further for the way the litigants and the judges are talking about the nature of DNA and the nature of elements such as lithium:

Both the lawyers and the judges repeatedly compared the case to efforts to extract a valuable mineral from the ground.

"Why isn't the ingenuity [that justifies patentability] the process of extracting [the mineral]" rather than in the mineral itself, [Judge Kimberly Moore] asked [defendent's attorney Greg] Castanias. "God made it. Man didn't make it."

Castanias retorted: "What we have here are new tools [that are] the products of molecular biologists. They are not the products of nature. They are not the products of God."

If that's the case, [Judge William Bryson] pushed Castanias, are you saying that isolation of pure lithium is properly an invention?

"Yes," the lawyer replied.

That is extraordinary.  Castanias' assertion is contrary to more than a century of U.S. case law and administrative rulings by the USPTO.  Products of nature are explicitly excluded in laws, rulings, and administrative decisions from coverage by patents.  Castanias wants the Appellate Court to rule that the elements in the periodic table, along with any other naturally-occurring substance, are in fact patentable.

The mind boggles.  Following Castanias' reasoning pure oxygen, pure water, and pure gold could all be patented because some process was employed for purification.  If this sort of argument held sway, you could even patent the moon because you require a human invention to go visit and nab a piece of it.  Yes, yes, I know that other inconvenient case law would get in the way of patenting a celestial body, which really doesn't make any sense anyway.  But that is the point.  The trial judge in this case was actually the first to issue a ruling that patents on naturally-occurring genetic sequences are prohibited by law (see "Big Gene Patent (Busting) News???").

This argument revolves in part around the nature of DNA.  Here is another excerpt from the Nature blog post:

Chris Hansen, a staff attorney with the ACLU, told the judges: "Myriad's entire business is built on the proposal that isolated DNA and [naturally occurring] DNA are identical." They don't write to patients with their test results, saying: "You've got a mutation in your isolated DNA but I have no idea what's going on in your body," he said.

Judge William Bryson countered that the act of isolating DNA involves breaking covalent bonds, thus creating a product that does not exist in nature.

"With respect, your honor, I think not," Hansen replied. "DNA is DNA."

But Greg Castanias, a lawyer with the Jones Day firm in Washington DC who represented the defendants, begged to differ. "Isolated DNA does not exist in nature," and wouldn't exist at all without human ingenuity, he said. The entire biotechnology industry, he added, is built on interpreting existing law to say that DNA isolation is sufficient to show the human invention that is required for a patent.

I found the language quoted to be quite interesting.  The notion that "isolated DNA does not exist in nature" is based on the defendants' definition of "isolated DNA".  Judge Sweet spent three pages of his original decision dealing with Myriad's assertions about "isolated DNA", but it is hard to know from the Nature blog post whether this was part of yesterday's conversation.  Here is Judge Sweet's definition (p. 92 of his decision): "Isolated DNA is therefore construed to refer to a segment of DNA nucleotides existing separate from other cellular components normally associated with native DNA, including proteins and other DNA sequences comprising the remainder of the genome, and includes both DNA originating from a cell as well as DNA synthesized through chemical or heterologous biological means".

This is quite close to Myriad's definition of "isolated DNA", but Judge Sweet still found that because the isolated DNA is the same sequence, and therefore conveys the same information, as the sequence in vivo, it cannot be patented because it is a product of nature.

Incidentally, the definition of isolated DNA given above appears to include DNA that is free in the environment.  Free DNA is found in marine and terrestrial environments.  That DNA can be taken up by other organisms via horizontal gene transfer, which means that free DNA is perfectly funtional.  Here, for example, is an interesting little study looking at the uptake of free DNA by aquatic bacteria.

The point being that humans did not invent DNA that is "separate from other cellular components".  Humans may have invented processes to concentrate and purify DNA, or to extract DNA from complex structures, but that does not mean that isolated DNA is itself a human invention.

More Stem Cell Magic

How long will it be before we have replacement tissues made from in induced pluripotent stem cells (iPS cells, iPSCs, or sometimes iPSs)?  Progress in generating iPS cells in university labs has been rapid, resulting in a series of recipes that are spreading capability rapidly around the world.  About 18 months ago, in the wake of progress on creating iPSs from adult, differentiated tissues, I started wondering about how long it would take before someone tried this in a garage (see "Stem_Cells@Home or DIYStemCells?").

Accessible Is Not The Same As Easy

In what follows, please keep in mind that I am not asserting that producing autologous iPS cells will be easy for anyone.  It will be hard.  And it will be harder for those attempting the feat in settings like garages and small start-ups.  However, I visited a garage lab last spring in the SF Bay area that was more than adequately equipped to give producing iPS cells a go.  As the highly technical protocols become recipes, more people will have the opportunity to try them out.  This was my point in Carl Zimmer's piece in the New York Times last week.  Innovation requires the opportunity to fail. 

On the Path to StemCells@Home

This story starts, for me, with the demonstration in June of 2009 that recombinant proteins can be used to reprogram skin cells into iPSCs (see "Another Step Toward DIYStemCells").  Previously, this reprogramming step required genetic manipulation via viruses, which greatly lessened the utility of the resulting iPS cells for therapies.  With the demonstration that proteins themselves could be used to reprogram cells, anyone who wanted to spend ~$10K on synthesizing four genes and then another ~$10K on having the four corresponding proteins made in cell culture could have those proteins delivered by post a few months after the initial order.

As I commented last year when these results were announced (see "Another step toward DIYStemCells"), "if you wanted to do this at home, you could.  You should expect to fail many times.  And then you should expect to fail some more.  And then, assuming your human cell culture technique is up to snuff, you should expect to eventually succeed."  That is just the way it works in university and corporate labs.

But wait, it is now even easier to make iPS cells!  In September, a paper from researchers at Harvard showed how to use RNA to reprogram adult cells into iPSCs.  Writing in the Washington Post, Rob Stein described the advantages of the new method: "The technique converted the cells in about half the time that previous methods did, about 17 days, and with surprising economy - up to 100 times more efficient."

Here is the Warren et al paper at Cell Stem Cell: "Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA".  The team used a combination of chemical modifications of RNA, along with packaging of the mRNA in cationic lipids, to reprogram a variety of differentiated cells into "RiPS cells".  Most of the "chemical modifications" consist of changing a standard RNA synthesis recipe to include non-standard ribonucleotides, followed by a bit of enzymatic trickery.  The authors then used the same RNA programming trick to control the differentiation of those RiPS cells into a variety of different tissues:  "Our results demonstrate that modified RNA-derived iPSC clones from multiple independent derivations were fully reprogrammed to pluripotency and that the resulting cells very closely recapitulated the functional and molecular properties of human [embryonic stem cells]."

There are a few "Technical Notes" at the end of the paper.  Warren et all recommend that "all steps of the protocols described herein are followed rigorously and quality controlled."  They also observe that "Critically, the expression of proteins with modified RNAs must be confirmed by immunostaining."  Basically, this recipe sounds finicky and probably requires a great deal of practice.  (To say that I am oversimplifying here is to say that Hurricane Katrina was a wet sneeze.)  But oh what an improvement it is over the prior methods for making iPSCs.

Rob Stein, at the Washington Post, and Karen Weintraub writing in Technology Review, describe how the entire Harvard Stem Cell Institute is going to start using Rossi's recipe to make iPSCs, and how researchers at other institutions plan to try it out as soon as they can.

Although it is relatively technically complex, the methodology described here offers several key advantages over established reprogramming techniques. By obviating the need to perform experiments under the stringent biological containment required for virus-based approaches, modified RNA technology should make reprogramming accessible to a wider community of researchers.

In other words, Warren et al published a recipe.  A complicated, recipe, to be sure, but a recipe that is already being used (and probably improved) in a large number of labs around the world.  Does that mean we will see autologous stem cell transplants next year?  Probably not.  But we might.  The FDA, please recall, only regulates drugs and devices [thanks for the reminder, Bill], and only then through the Interstate Commerce Clause of the US Constitution.  The FDA is explicitly prohibited from regulating treatments, which are designed and implemented by doctors.  So as long as stem cells are used in procedures considered therapies, the FDA doesn't have anything to say about the use of RiPS cells in patients.

And regardless of progress in the clinic, at some point this technology is going to be tried by "the wider community" in the garage.  It is inevitable.  And when a garage protocol is successfully demonstrated, and perhaps shared in among people participating in Open Biology, then we will see a profusion of new therapies.  And also a profusion of mistakes and strange teratomas, because iPS cells will be used in contexts where nobody has any idea what the consequences will be.  But that is also inevitable.  Once producing stem cells truly moves from art to recipe, I don't think there is any way to stop people from playing with their own stem cells. 

So it is Magic, or Science?

Actually, it is starting to look a lot like engineering, or maybe even cooking.  By "magic", I mean not Harry Potter but art, or something that nobody really understands and works only in that hands of a small number of people.  "Science" in this context would be experiments that are designed to test particular hypothesis or to develop new methods, in both cases resulting in descriptions of nature or methods that require substantial reduction to practice before adoption is widespread.  But the RiPS method looks like it is being implemented widely just weeks after publication.  Nobody fully understands why RNA reprogramming works, or how RNA-directed differentiation works, to be sure, but this method is suddenly much closer to an engineering protocol than a mysterious incantation that only a few artists can implement.

Organs@Home or DIYOrgans.  More Likely DIYTumors.

So what are we going to use RiPS cells for?  Reaching back to news over the last year points the way.

Rob Stein, again writing in the Washington Post, described in July 2009 how mice were grown from iPS cells made from adult skin cells.  And in a news piece at Nature, David Cyranoski elaborates on the efficiency of the process as well as how many additional generations of mice were grown from the initial litter.  We've also now seen replacement teeth grown from stem cells (WSJ).  (Here is the Ikeda et al paper in PNAS: "Fully functional bioengineered tooth replacement as an organ replacement therapy".) 

In July of this year, the same sort of viral hack was used to make iPS cells from leukocyctes found in adult peripheral blood samples.  Laura Sanders at ScienceNews described the papers succinctly: "Blood drawn with a simple needle stick can be coaxed into producing stem cells that may have the ability to form any type of tissue in the body, three independent papers report in the July 2 Cell Stem Cell."

Shinya Yamanaka (who originally demonstrated the use of the 4 "Yamanaka factors" in producing iPS cells) wrote a very clear commentary accompanying the three papers.  First, here are links to the three papers: Seki, et al; Loh, et al; Staerk, et al.  The last paragraph of Yamanaka's piece is full of cautions about the utility of iPSCs derived from peripheral blood.  In particular, Yamanaka notes that his group showed that the safety of iPSCs in mice depends on the origin of the tissue used to generate the stem cells.

There are many hurdles to overcome before iPSCs are used in the clinic.  But the Seki paper in particular shows generation of stem cells from the T lymphocytes in just 1 ml of blood (becoming "TiPS cells").  That 1 ml of blood was put through a relatively straightforward Ficoll separation column to enrich the sample for T lymphocytes.  Obtaining these cells is pretty simple, and is in fact something I did myself, using my own blood, many years ago for an experiment for my doctoral work.  And most of those experiments were done with only a few hundred microliters of blood extracted from a finger stick.  In other words, I can imagine at least starting down the road surveyed by Seki et al with just a lancet (a sterile needle would do), a Microtainer with heparin from BD, and microcentrifuge.  In fact, here is a protocol from Ohio State (PDF) that looks like it would do fine to derive your own T cells, though you could probably skip the red blood cell lysing step.

The initial separation is followed by culturing the T cells in a dish, which also isn't so hard as long as you have the proper equipment.  However, thereafter the Seki et al recipe starts to get a little hairy, including multiple steps of culturing on feeder cells and incubation with very specific kinds of cell extracts.  If you try this in your garage, you are likely to fail many times.  But that is to be expected, because Seki et al failed many times, too.

Seki suggests one reason for the low efficiency of conversion T lymphocytes to iPSCs is due to the low rate of gene transfer by viruses.  Now, presumably, you see where this is going:  Re-enter Warren et al and their RNA induced pluripotent stem cell method described above.  Recall that this method works in about two weeks and is ~100 times more efficient in generating iPSCs than is gene transfer.  No doubt there will be some hurdles to overcome before putting all these pieces together, but I would be greatly surprised if there we didn't see RiPS generated from adult peripheral blood cells by the middle of next year.  Undoubtedly that paper will also demonstrate some streamlining of the protocol.  And then people will have another recipe to play with.

Seki et al demonstrated that human TiPS cells implanted into immune compromised mice can differentiate into many different tissue types.  They also showed that the TiPS cells can become teratomas, which means unless you are careful with the implantation of these cells you are going to wind up with strange tumors.

That said, Warren et al show that subsequent RNA reprogramming can direct RiPS cells to become all sorts of interesting tissues.  So if you want to try all this in your garage, and if you have the appropriate cell culture skills and equipment, you can give it a fair go.  Access to the appropriate strains of feeder cells, as well as the modified RNAs, could be a stumbling block.  But I have to imagine 1) that those cells and the RNAs are going to be available commercially as a package at some point or 2) that you will be able to get the cells from a supplier and contract out the RNA production for no more than a few thousand dollars.

Derek Rossi, the Harvard professor who is the senior author on the Warren paper has, according to the acknowledgments on the paper, started a company "dedicated to the clinical translation of this technology".  Whether that means there will be a monopoly on the methods and materials is unclear to me at the moment.  If you want to generate your own RiPS cells from T lymphocytes, who is going to stop you?  And if you use those cells to produce tissues, and even to attempt treating yourself?  Even then, it isn't clear that there is any rule, law, or regulation that can be used to stop you; recall that the FDA, at present, has not yet decided to try to regulate stem cells as drugs.  Please note that I don't think self treatment is a very good idea, just yet.  But nobody who is interested in playing with these technologies is likely to listen to me on this point anyway.

However, if you did something that looked like treating another person, then all hell would probably break loose because you could be accused of practicing medicine without a license.  And then there are the consequences of getting this wrong, whether you are treating yourself of somebody else.  About a year ago, on an airplane, I happen to sit next to the CEO of one of the largest health insurance companies in the US.  At one point in the conversation, I asked him what his company would do if people started showing up needing treatment for tumors they gave themselves by injecting their own iPS cells.  He just stared at me, stunned, with his jaw agape.

That is the right response, I suspect.  The world is changing very quickly, and even if you spend your days trying to understand what is coming you are guaranteed many surprises that will just leave your jaw agape.

Surprise Outbreak of Common Sense in Washington DC

News today that the Justice Department has filed an amicus brief outlining a new position that naturally occurring genes should not be patentable.  The New York Times is reporting that "while the government took the plaintiffs' side on the issue of isolated DNA, it sided with Myriad on patentability of manipulated DNA."  The change in position was evidently prompted by the decision of a federal judge this past spring that certain claims in what are known as the BRCA 1/2 patents should be overturned because those genes are preexisting in nature.  Perhaps Jon Stewart has more influence in DC than we all thought.

I am largely on board with the line taken by the Justice Department.  It is pretty close to my own analysis, as described in my post from last spring: "Big Gene Patent (Busting) News???"  There are, however, a few bits that I am still chewing on, which I will get to later.

First, in broad strokes, the government's brief supports the decision of District Judge Robert Sweet that naturally occurring gene sequences are not patentable, but weighed in against Judge Sweet's analysis that DNA coding for natural genes is not patentable if it has been restructured in an artificial construct but is still the same sequence as occurs in nature.  The most obvious example of the latter is a coding sequence with all introns removed and packed in a plasmid as a cDNA.

Here is the Justice Department's language (the text of the brief is available via the NYT page):

The district court erroneously cast doubt on the patent-eligibility of a broad range of man-made compositions of matter whose value derives from the information-encoding capacity of DNA. Such compositions -- e.g., cDNAs, vectors, recombinant plasmids, and chimeric proteins, as well as countless industrial products, such as vaccines and genetically modified crops, created with the aid of such molecules -- are in every meaningful sense the fruits of human ingenuity and thus qualify as "'human-made inventions'" eligible for patent protection under section 101. (p.9)

...The district court correctly held, however, that genomic DNA that has merely been isolated from the human body, without further alteration or manipulation, is not patent-eligible. (p.10)

...Indeed, the relationship between a naturally occurring nucleotide sequence and the molecule it expresses in a human cell -- that is, the relationship between genotype and phenotype -- is simply a law of nature. (p.10)

Here is the meat:

The chemical structure of native human genes is a product of nature, and it is no less a product of nature when that structure is "isolated" from its natural environment than are cotton fibers that have been separated from cotton seeds or coal that has been extracted from the earth.

The scope of Section 101 is purposefully wide and its threshold is not difficult to cross.  See Bilski, 130 S.Ct. at 3225.  New and useful methods of identifying, isolating, extracting, or using genes and genetic information may be patented (subject to the prohibition against patenting abstract ideas), as may nearly any man-made transformation or manipulation of the raw materials of the genome, such as cDNAs. Thus, the patent laws embrace gene replacement therapies, engineered biologic drugs, methods of modifying the properties of plants or generating biofuels, and similar advanced applications of biotechnology. Crossing the threshold of section 101, however, requires something more than identifying and isolating what has always existed in nature, no matter how difficult or useful that discovery may be. (p.11)

It might seem that the Justice Department gives back a lot of power to those who hold patents on natural genes by including cDNAs (with introns removed) as patentable material.  This would seem to give patent holders a lock on the human proteins those genes encode, because the most common way to make a protein is to use a cDNA (or similar) to express a protein in a host like E. coli or yeast.  So unless people come up with a good way to cause overexpression of human proteins from native genes via mechanisms that chop out the introns -- and some methods like that do exist -- the patent seems to block use of the protein.

But I am not sure that this brief gives any succor to those hoping for patent protection of a genetic diagnostic.  Those diagnostics generally work by using a short sequence of the gene in question as a PCR primer to find (or exclude) particular sequences of clinical interest in a patient's genome.  Those primers generally can be found in regions of DNA not interrupted by an intron, or can include the intron in the primer sequence, which means that the primer can consist of sequences that were preexisting in nature.  Only if the primer has to be composed of a sequence that -- in nature -- is interrupted by an intron but is only found in somebody's edited cDNA library without that intron would a patent protect the diagnostic assay.

A penultimate thought on the brief: I am still pondering whether the Justice Department lawyers, in their extended discussion of DNA as information carrying medium, got their analysis right.  I will have to read the brief again.  And perhaps again after that.

Finally, the brief leaves most of my previous conclusions intact, namely that the biggest impact of Judge Sweet's ruling that natural sequences cannot be patented may be for work in organisms other than humans.  From my post last May:

...the rest of the biotech industry shouldn't be concerned about thisruling, frankly.  They might even celebrate the fact that they now have access, potentially, to a whole bunch more genes that are naturally occurring.  Not just in humans, mind you, but any organism.  This opens up a rather substantial toolbox for anybody interested in using biological technologies derived from viruses, bacteria, plants, etc.  If it holds up over the long run, Judge Sweet's decision should accelerate innovation.  That is definitely a good thing.

Now we wait for what the appellate court has to say.

"National Strategy for Countering Biological Threats"

I recently had cause to re-read the National Strategy for Countering Biological Threats (Full PDF), released last fall by the National Security Council and signed by the President. I think there is a lot to like, and it demonstrates a welcome change in the mindset I encounter in Washington DC.

When the document came out, there was just a little bit of coverage in the press. Notably, Wired's Threat Level, which usually does a commendable job on security issues, gave the document a haphazard swipe, asserting that "Obama's Biodefense Strategy is a Lot Like Bush's".  As described in that post, various commentators were unhappy with the language that Under Secretary of State Ellen Tauscher used when announcing the Strategy at a BWC meeting in Geneva. According to Threat Level, "Sources tell this reporter that the National Security Council had some Bush administration holdovers in charge of editing the National Strategy and preparing Ms. Tauscher's script, and these individuals basically bulldozed the final draft through Defense and State officials with very little interagency input and with a very short suspense." Threat Level also asserts that "Most are disappointed in the language, which doesn't appear to be significantly different than the previous administration." It is unclear who "Most" are.

In contrast to all of this, in my view the Strategy is a clear departure from the muddled thinking that dominated earlier discussions. By muddled, I mean security discussions and policy that, paraphrasing just a little, went like this: "Biology Bad! Hacking Bad! Must Contain!" 

The new National Strategy document takes a very different line. Sources tell this reporter, if you will, that the document resulted from a careful review that involved multiple agencies, over many months, with an aim to develop the future biosecurity strategy of the United States in a realistic context of rapidly spreading infectious diseases and international technological proliferation driven by economic and technical needs. To wit, here are the first two paragraphs from the first page (emphasis added, of course):

We are experiencing an unparalleled period of advancement and innovation in the life sciences globally that continues to transform our way of life. Whether augmenting our ability to provide health care and protect the environment, or expanding our capacity for energy and agricultural production towards global sustainability, continued research and development in the life sciences is essential to a brighter future for all people.

The beneficial nature of life science research is reflected in the widespread manner in which it occurs. From cutting-edge academic institutes, to industrial research centers, to private laboratories in base­ments and garages, progress is increasingly driven by innovation and open access to the insights and materials needed to advance individual initiatives.

Recall that this document carries the signature of the President of the United States.  I'll pause to let that sink in for a moment.

And now to drive home the point: the new Strategy for Countering Biological Threats explicitly points to garage biotech innovation and open access as crucial components of our physical and economic security. I will note that this is a definite change in perspective, and one that has not fully permeated all levels of the Federal bureaucracy and contractor-aucracy. Recently, during a conversation about locked doors, buddy systems, security cameras, and armed guards, I found myself reminding a room full of biosecurity professionals of the phrase emphasized above. I also found myself reminding them -- with sincere apologies to all who might take offense -- that not all the brains, not all the money, and not all the ideas in the United States are found within Beltway. Fortunately, the assembled great minds took this as intended and some laughter ensued, because they realized this was the point of including garage labs in the National Strategy, even if not everyone is comfortable with it. And there are definitely very influential people who are not comfortable with it. But, hey, the President signed it (forgive me, did I mention that part already?), so everyone is on board, right?

Anyway, I think the new National Strategy is a big step forward in that it also acknowledges that improving public health infrastructure and countering infectious diseases are explicitly part of countering artificial threats. Additionally, the Strategy is clear on the need to establish networks that both promulgate behavioral norms and that help disseminate information. And the new document clearly recognizes that these are international challenges (p.3):

Our Strategy is targeted to reduce biological threats by: (1) improving global access to the life sciences to combat infectious disease regardless of its cause; (2) establishing and reinforcing norms against the misuse of the life sciences; and (3) instituting a suite of coordinated activities that collectively will help influence, identify, inhibit, and/or interdict those who seek to misuse the life sciences.

...This Strategy reflects the fact that the challenges presented by biological threats cannot be addressed by the Federal Government alone, and that planning and participation must include the full range of domestic and international partners.

Norms, open biology, better technology, better public health infrastructure, and better intelligence: all are themes I have been pushing for a decade now. So, 'nuff said on those points, I suppose.

Implementation is, of course, another matter entirely. The Strategy leaves much up to federal, state, and local agencies, not all of whom have the funding, expertise, or inclination to follow along. I don't have much to say about that part of the Strategy, for now. But I am definitely not disappointed with the rest of it. It is, you might say, the least bad thing I have read out of DC in a long time.