Favorite Books of 2010

Biology is Technology is on the favorite books of 2010 list at Foreign Policy:

Mankind is at the threshold of a new leap forward in our understanding of how life works, and this book shines a light on the path ahead by approaching the subject as a series of engineering and technology problems. The book is sophisticated, clear, and eye-opening in explaining the promise, and peril, of a profound revolution in genetics and molecular biology.

Fly On the Wall: 2010 Meeting of States Parties to the Biological Weapons Convention

Last week I made it through the snow in Europe to attend meetings in Paris and Geneva.  In Paris I spoke at a joint meeting of the OECD and the ESRC Genomics Network, Delivering Global Promise Through the Life Sciences.  (I'll post a link to the slides when the conference puts it online.)  Then I hopped a TGV to speak at the UN at the 2010 Meeting of States Parties to the Biological Weapons Convention.

After giving my talk in Geneva, (here is my slide deck, "Engineering a More Secure Future") I sat in the back row of the official Meeting of States Parties.  I spent some time listening to the simultaneous translation of the public session on building national capacity for public health, watching the diplomatic sausage get made.

Among the interesting things I heard: the Russian representative emphasized their position on the need for a standing body for national inspection and enforcement of the Convention.  This from a country that, even after signing the BWC, maintained an extensive offensive biological weapons program until relatively recently.

Also, Iran asserted that it is having difficulty obtaining standard infectious disease strains due to various international restrictions and sanctions.  Noted that trust is a basis of all relationships.  Indeed.  Elsewhere in the building, Iran was simultaneously stating there would be no discussion of its uranium enrichment program in upcoming talks.

Finally, a minor tiff as Armenia made mention of the disputed region of Nagorno-Karabakh (NK), whereupon Azerbajan, within whose borders that region is presently located, then exclaimed that discussing NK has no place at the BWC Conference.  Armenia returns with, approximately, 'Regardless of who owns land, all people deserve care.'  Can't argue with that.

Okay, then.  That's more than enough sausage for one day.

Dipping My Toes in International Diplomacy, or Simulating Combat Flying in a British Taxi

In late September I spoke at a warm-up meeting for the 2011 Review Conference of the Biological Weapons Convention (BWC).  The BWC, as I understand it, is administered by the UN but is a direct agreement between the signatories, otherwise known as "States Parties".  The Review Conferences take place every five years.  The meeting was held at Wilton Park, an independent, academic branch of the British Foreign Office.  The venue was founded by Winston Churchill in 1946 as a "a forum for democracy building, post-conflict reconciliation and international dialogue".  Wilton Park is now housed at Wiston House, the initial construction of which dates back to the sixteenth century, and the style of the place certainly gives a unique air to proceedings there.  Here is a BBC story from a few years ago that provides more history.

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The meeting was attended by a very interesting collection of ambassadors, diplomats, scholars, and foreign-office types from around the world.  Definitely not my usual drinking buddies.  But more on that later.  Before continuing, to be clear: I was there in a personal capacity, invited by the organizers and meeting sponsors (Wilton Park and the British and Dutch Foreign Offices), and I was in no way representing the US government.

I gave the opening talk, during which I focused on how biological technologies have advanced in the last five years, who is investing and how revenues are apportioned worldwide, and what we may see in the bioeconomy over the next five years.  Much of what I said was evidently new to the assembled crowd, which led to some interesting conversation.  Time for another pause: According to the Wilton Park Protocol, under which the meeting was held, "participants are free to use the information and views discussed in the conference, but no individual speaker or participant should be quoted", so I will do my best to tread carefully.

There are, in fact, only a couple of things I think are worth passing on in this post because they may have some impact on public policy discussions more broadly.  My personal predilection is to measure what I can about the world and then figure out where to go once I have established an understanding of where we are.  In particular, I have been trying to understand the global bioeconomy because many countries around the world are investing heavily in biological technologies in order to be dominant players in the 21st century.  Most of those technologies and related skills are explicitly dual use; that is, they can be used to create good or cause harm.  It simply makes sense to me to figure out what those countries are up to and what the consequences are before taking any action, political or otherwise.

Not everyone thinks that this procedure is the way to make public policy.  After I presented data on how various countries are investing, and on how fast their domestic skilled biotech labor pools and domestic biotech revenues are growing, this was waved away by one group with (very approximately) 'Do not tell me about revenues and economic activity: we should decide on how we want the world to be and then implement it!'  This left me somewhat at a loss for words.  I was surprised at the notion that any one of the States Parties might feel, in today's geopolitical and economic climate, that it could dictate terms to any other Party.  Particularly in a technological area that is deemed crucial for economic competitiveness and success.  More generally, I am confused by the notion that a qualitative goal in an area of policy can be set before an effort is made to understand, and to quantify if possible, the size and shape of that area.  What if proposed qualitative goals are already irrelevant, or even misguided, given the current state of the world?

Somewhat later in the meeting, I observed that the National Strategy for Countering Biological Threats -- written by the National Security Council and signed by the President -- states that garage biology is good and necessary for the political and economic security of the United States.  I then made my usual observation that garages are the source of most of the innovative technologies in the global economy.  The response to this from one group was also interesting (again, very approximately): 'This garage or DIYBio is only a problem in the US.  In our country it is illegal to do such things.'  I managed to bite my tongue at this juncture -- recalling the setting, and aided by the fact that the session chair forgot to give me a chance to respond (for which he apologized later, though I silently thanked him at the time). But what I really wanted to observe aloud was that it must be very nice to live in a country where nothing bad happens because all bad things are illegal; I will try to remember that next time I get off an airplane or train there to be greeted by paramilitary troops with their fingers on the triggers of sub-machine guns.  Fortunately for me, at this point the conversation wandered off into a very apt discussion about intent and misuse, as opposed to dual use, a characteristic that biology shares with many other technologies.

Which brings me to my second confusion, which is that while it is all very well and good to define areas of misuse, perhaps by making it 'illegal', and to define potential responses to that misuse, simply defining that misuse does little to prevent it.  That is, with biological technologies already spreading around the world at a rapid clip, and with innovation in those technologies taking place in countries that may care little about any given definition of misuse, those definitions amount to security theater of the worst kind.  I have yet to hear any proposal for biosecurity that recognizes the futility of physical prohibition or containment of using biological technologies.  Preventing access to technologies by the wrong sort of chap sounds great, but in this context it is unlikely to work, and therefore only makes it sound like we are safer rather than actually making us safer.

Perhaps admitting the above in print here means my future as a diplomat is limited.  Oh well.  And with that I must curtail any further description of the discussions. 

While I can comment on only a small fraction of what was said at the meeting, I can relate a few other anecdotes from the trip.  The Wilton Park experience lives up to one's expectations: formal dinners, preceded by cocktails; a formal group photo in which you might find yourself standing next to an ambassador; nightly excursions to the bar, during which discussions continue amidst libations.  I have never been much of a scotch drinker, but one must, after all, be adaptable.  Particularly when, upon learning of this educational deficiency, an Ambassador takes you aside and does the buying.  "Young man, you should really give this a try."  I could be a convert.

The most memorable bit of the trip, however, was what happened the next afternoon, upon the close of the meeting.  Just after a rather large English lunch (can you say, "foreshadowing"?),  the American delegation shanghaied me for the ride back to London.  This ride took place in one of those tall, European passenger vans.  The ones that look somewhat unstable and that one might expect to sway considerably going around corners.  There were seven seats in the van.  One up front with the driver, three in the back facing forward, and three more facing backward.  I believe everyone in the van ate approximately the same, large English lunch.

Facing forward were three officials from the US State Department (hereafter State 1, State 2, and State 3).  Facing backward were myself, (following the naming convention) White House 1, and Defense 1, who is a PhD who spent an earlier life jumping out of helicopters with bullets flying.

The trip began slightly ominously, because I was originally seated facing forward, and State 1, who was last into the van and thus got a seat facing backward, politely asked to switch with me because she was prone to motion-sickness.  How could I refuse?  I had been motion-sick exactly once in my life, and never at sea, and that one time only because my lovely wife was sitting next to me on the airplane and led the way.  But I digress.

The taxi set off, and I was surprised to be included in conversations about potential diplomatic breakthroughs with various attendees at the meeting.  We had a jolly good time as the taxi driver wound his way through the English countryside, eschewing the nearby straight-as-an-arrow motorway for as many narrow, winding country lanes as possible.  This being England, the driving is on the left side of the country lane.  This being England, those country lanes intersect at roundabouts, wherein a taxi making a right turn involves first throwing passengers through a hard left to get into the roundabout, slamming the wheel over and accelerating hard to the right for 270 degrees around the circumference, followed by a short hard left to get onto the next country lane.  And repeat.  This particular driver evidently set about finding as many roundabouts as he could.  And then seemed to traverse some of them several times.  Just for kicks.  To my inner ear.

Where was I?

Ah, yes; diplomatic breakthroughs, discussions of how much various countries are investing in biotech, and what the medium- to long-term consequences are for the physical and economic security of the US.

And then another roundabout.  Whereupon State 1 suddenly -- for reasons I simply cannot fathom -- changes the subject and the following conversation ensues:

State 1: "Are you fellows feeling alright?

Myself, White House 1, and Defense 1: "Oh, fine."

State 1: "You are all looking a bit green."  Pause.  "Smint?  They help settle the stomach."

Me: "Nah, I'm fine."

White House 1 and Defense 1 (hereafter to be thought of as "The Sensible Ones"): "Sure."

<intervening roundabout>

State 1: "Smint?"

Me: "Uh, sure."

State 2: To the driver: "Can we get some windows open, please?"

White House 1: "I have a bag, just in case."

Me: <breathe in, breathe out> <breathe in, breathe out>  Out loud: "Um, no thanks."

Me, out loud, in a half-hearted attempt at humor: "It's a giant shopping bag: You prepared for this?"  To myself: Put the fucking bag away White House -- are you nuts?!?  Six people, confined space, big lunch: If one of us goes, we all go.  Don't even give anyone the option!

State 1: "So about country X..."  Pause.  "Are you sure you guys are alright?"

Defense 1: Enthusiastically: "This is just like flying in the back of a helicopter!"  With even more gusto: "I'm ready to go into combat!"

White House 1: Remember his own days in uniform: "Um, I was just thinking that."

Me: <breathe in, breath out>

State 1: "Smint?"

Somehow, just about then, or quite possibly many hours later, we arrived in central London.  At least some of us talked about business for at least part of that taxi ride.  The bag remained empty.

I'm headed to Geneva for the next BWC event, the Meeting of States Parties from 6-10 December.  There I will be speaking along with Andrew Hessel and Drew Endy in a session on "Synthetic Biology: Building a Secure Future".  I don't know if there will be any more late night scotch on this trip, but I certainly hope to avoid more taxi rides that simulate riding a helicopter into combat.

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.

iGEM 2010: Finalists are Announced

iGEM 2010 finalists: Slovenia, Cambridge, Peking, TU Delft, BCCS-Bristol, Imperial College London. No US teams in the finals for the first time... (Drew Endy corrected my faulty memory via email to note that no US teams made it to the finals last year, either...)

The teams are starting their presentations now.

iGEM 2010: Midway

All the talks are over for this year's iGEM, with the final poster session to go and then the annual marathon judge's meeting.  Alas, there is no chromo-poo this year, but there is one team running around in wonderful light-blue leisure suits.  There are from Paris, I think.

I have been very impressed with the sophistication of the component and device design this year.  More on this after the finals tomorrow.

Of general note, Uni Freiburg Bioware biobricked a bunch of parts for packaging up therapeutics in adeno-associated viruses (AAVs).  They showed targeting toward specific cancer cell lines, and also showed the means to build various adapters to target any number of cell-specific markers. There is a very nice 150 pg manual describing protocols for design and use of the AAVs for delivering genes and pro-drugs, with an emphasis on personalized medicine.  All the sequences are online, and even if you can't get the parts from the Registry of Standard Biological parts you can have Blue Heron or somebody else synthesize them for you.  In other words, it appears that Uni Freiburg has enabled DIY Garage Therapeutics.  Got cancer?  Now you've got a personalized therapy.

This is not to say that every Tom, Dick, and Andrew Hessel will be able to generate a personalized cancer therapy on the first try.  But it steps like this gives people an opportunity to fail in a new way, which is a prerequisite to, and always precedes, success.  Failure is the first, and most important component of innovation.

And people will fail -- I am not entirely comfortable with the thought of people attempting their own therapies at home.  But I do think it is inevitable, and I don't think there is any way to stop it. That is the world we live in.