On metagenomics

So, I’ve returned from the ERTC (see previous post), and it was a gas. I think one of the more interesting things about the conference was that it was primarily Chinese and European scientists, and thus gave me some insights into how Americans tend to skew discussions. In any event, one of the coolest talks I saw was by Zhao Liping of Shanghai Jiaotong University (aside: this is where my most excellent graduate student, Xi Chen, came from; whatever you guys are doing there, you’re doing a great job!). Dr. Zhao talked about metagenomics of the gut as a function of diet. He makes a very good case that you are what you eat. Not so much in terms of the food, but in terms of what bacteria the food cultivate over time. To a first approximation, if you eat crap, you cultivate crap bacteria (pathogens), whereas if you eat well, you cultivate more gut-friendly bacteria. This is true even when you account for the genetics of the organism and its ability to utilize different foodstuffs. Some of this has already been reported in Li et al. (2008), PNAS 105:2117.

From a biodefense or intelligence perspective, though, what’s neat is that the bacteria associated with a given individual can be seen as a fingerprint of that individual. As the PNAS paper states: “At the species level, we found structural differences in the Chinese family gut microbiomes and those reported for American volunteers, which is consistent with population microbial cometabolic differences reported in epidemiological studies.” And as the cited epidemiological studies (Dumas et al. (2006), Anal Chem 78:2199) state, such “cross-population differences in urinary metabolites could be related to genetic, dietary, and gut microbial factors.”

Now, it’s perhaps not all that interesting that Chinese and Europeans, say, are different. Well, duh. What is interesting is if you consider the succession of microbial communities in the gut. This is older work, from Milkman amongst others, on “periodic selection.” Our guts are constantly roiling with different bacteria and even different allelic variants of the same bacteria. These bacteria rise to prominence and are extinguished depending on diet, even depending on a single meal. And they are passed between individuals. A family is likely to have more genetically similar gut flora, down to and including the pets of that family.

So, what if one was able to track the habits and associations of individuals based on their gut flora? Would that be useful (see also “On GATTACA and taggants”)? I would previously not have thought so. It would seem that the signal would be buried in so much noise that identification with any surety would have been impossible. But of course that was before we had so very, very much signal. There was another neat talk at the conference, by Yang Huanming, the “Chinese Craig Venter” (no offense to either party) who heads up the super Beijing Genomics Institute (BGI). The sheer scale of the BGI is breathtaking, with over 800 bioinformaticians dedicated to analyzing the data from their hundreds of NextGen sequencing machines (I think it’s not unreasonable to estimate this one Institute as being on the order of 100x University operations). In any event, a landmark event for the BGI was the publication of “a human gut microbial gene catalogue” (Qin et al. (2010), Nature, 464:59), which sampled 124 European individuals. One conclusion is that the genetic diversity of our gut flora dwarfs our own genetic diversity by a factor of ca. 100-fold. Or in other words: forget the 23-and-Me allelic analysis. If you really want to know about someone, ask about the bacteria that live inside them.

Is it possible that you’ll be able to peer into the detailed history, habits, and associations of an individual based on a fine analysis of their metagenome? Who knows? It’s not an unreasonable hypothesis. But I do know that given the scale of sequencing and analysis being carried out by the BGI, that they’ll know the answer long before we in the US do. From a purely Strangelovian perspective, there is most definitely a metagenome gap.

- originally posted on Sunday, October 24th, 2010

On futures

I’m at the Exploratory Round Table Conference in Shanghai, which is ostensibly a forum to discuss what directions synthetic biology will take into the future. As with most such forums, it frequently devolves into a discussion of what synthetic biology is (or is not). I am as happy to engage in such silly discussions as anyone else, especially given that I think synthetic biology is a buzzword rather than a discipline.

Arguments aside, it has been very good to see my friend Pam Silver here, and to hear her perspectives on the issue. As with many measured individuals (as opposed to zealots such as myself) she argues for a middle ground in which the good is maximized and the bad is minimized. In her view, the excitement and interest (at all levels) generated by the buzzword justify its use. More importantly, she sees the science and engineering that have arisen to be most useful for testing hypotheses about the nature of living systems. It is with Pam in mind that I submit to you two extreme futures:

The organism was one they really needed. And so it was good that it had been possible to synthesize this organism from the ground up. The years that had been required to painstakingly make and standardize the biological parts that comprised its critical circuits had been well-spent. These parts were robust, and worked consistently in a variety of genetic and environmental backgrounds. More importantly, though, they worked together in ways that were entirely predictable, allowing circuits with chemical and regulatory properties to be strung together and tested on the BioCAD prior to even laying them into carbon. This was especially true given the minimal chassis (UniOrg) that was being used, where there was little chance for unanticipated interactions or cross-talk (not that these were a problem even for the more Natural hosts, given the orthogonal building blocks and genetic elements that were being incorporated into the key pathway). The chemical and logical schemes may not have been ones that Nature would have ever chosen or even thought of, but the systematic characterizations that had been carried out over the years had shown that circuit and even organismal construction was indeed the sum of the parts (as it must be). The in silico testing had even revealed a feedback loop in genetic noise that might eventually lead to evolutionary loss of part of the key pathway, but this was quickly smoothed out by some nifty codon optimization and destructuring of mRNAs. Now the genome was spinning out on the Forge and its coat simultaneously crafted. A quick injection of starter materials (which degraded even as the organism’s new complement of proteins and self-sustaining metabolism came on-line), and life was breathed into the critical beast. Mankind was saved.

The organism was one they really needed. And so it was good that they understood where and how that critical bug delta could be changed. The microorganism had been retrieved from the Pharoah’s tomb itself, sequence had been acquired on the fly, the genome automatically annotated with precision, and the interactome and regulatory networks plotted based on analogy and a bit of extrapolation. The homology mapping from the vast repository of structural proteomics data and PhPh (phylo-physics)-based computational modeling had helped a great deal. Of course, it didn’t do quite what they needed, but it was close enough, with its thermo- and salt-tolerances almost perfectly balanced. It was just a matter of giving it a few new tricks. The synthetic pathway was laid carefully on top of the existing network, with a series of heterologous gene insertions scattered at key sites throughout the genome, and a few mutational changes to the bug’s own regulatory factors and signal transduction cascades. The changes were carried out quickly in parallel, and growth characterizations provided estimates of the fitness landscape surrounding each perturbation. This knowledge fedback onto the designs, and enhanced the ever-upgraded predictive evolutionary algorithms. Ultimately, genome editing of the bug by homologous recombination and targeted gene repair (the orthogonal operon that made the changes vanishing once the transfers had been effected) guided the critical beast to its new application. Mankind was saved.

Of course, both futures are open to us, and a good engineer will choose the pieces of these futures that allows her to save Mankind.

Or are they? We live in a world of limited resources and extraordinary competition. There is more than a little bit of ‘follow the zeitgeist’ where science is involved. The truly novel idea can be lost in the stampede towards perceived novelty. Perhaps this is ultimately not about which future is best, but about what type of scientific infrastructure produces the best future.

Choose wisely.

- originally posted on Tuesday, October 19th, 2010

On graduate students

As any faculty member knows, graduate students are our future. Or, more precisely, graduate students are the serf-like remnants of an ancient, hierarchical Germanic university culture that we continue to pretend drives innovation in the world. This pretense has some basis in reality, since graduate students are often very smart, very motivated, and very productive. Which ultimately is good for the faculty members who feed, vampire-like, off their productivity.

Graduate students are also great because they haven’t yet learned that they can’t really do anything important. This is a lesson most academics inculcate at some point in their careers (although of course the best ones do not). So, it’s fun when a graduate student comes to me with a Great Idea, shiny and new and ready to be shot down.

Most recently, a student in the extraordinary Marcotte lab, Jeremy O’Connell, came to me with an idea for how to use yeast to synthesize heroin. This warmed the cockles of my heart, because it’s about the fifth time I’ve heard this idea, dating back to when I also thought that I had uniquely thought of it, way back in, well, graduate school. Anyone who’s ever read anything about the wonders of secondary metabolism recognizes that organisms rule in terms of controlling regiospecific reactivity and carbon flux, and in turn find it surprising that the organic artistes make any money at all. However, in the absence of a centuries long breeding program to make addictive drugs something like 50% by weight of a leaf, it is actually hard to convince organisms to make complex metabolites, no matter what pathways may be known.

Nonetheless, metabolic engineering is big business, or at least is becoming big business, and the tools for convincing organisms to do things that they would not otherwise do are many and varied. Most recently, Hawkins and Smolke (Nat Chem Biol 4:564) had the clever idea that a commercially available compound, norlaudanosoline, looked something like a natural intermediate in relevant alkaloid biosynthetic pathways, and decided to try to convince yeast to use this compound for the production of a key intermediate, reticuline. The plant enzymes they used had enough play to allow this, and the yields were not bad (although starting a bit farther back, with dopamine, did not work so well). Even weirder and more interesting, a human enzyme could be used for a key transformation to salutaridine, which is getting reasonably close to morphine (and thus reasonably close to heroin; see also “On ingenuity”).

Now, Jeremy discounted the several, several steps from salutaridine to morphine, but let’s let that slide for the moment. What he did notice is that science marches on, and that researchers had identified a couple of key demethylases necessary to get from the intermediate thebaine to morphine (Hagel and Facchini, Nat Chem Biol, 6:273). That is rather interesting, given the aforementioned Hawkins and Smolke paper. It suggests that there may now just be a smallish gap left to bridge norlaudanosoline to morphine (that gap would be from salutaridine to thebaine, a measly two steps), and again from there to cocaine.

And keeping in mind that semi-synthesis involving both biology and chemistry is always a possibility, there may be pathways yet to be imagined that meld the street chemistries and chemists that were discussed in “On ingenuity” with the synthetic biology discussed herein. I again find this to be an especially intriguing combination, in that it goads the great minds with the invisible hand (or, as Jay Keasling wrote in a piece accompanying the Hawkins and Smolke work, “the worldwide sales of some of the most widely used alkaloids, including caffeine, nicotine, cocaine, and heroin, exceeded $US 4 billion in 2002″).

So, Jeremy, the ball is in your court. Finish the synthesis, and shake, shake, shake that goading invisible hand (or, as he put it in an E-mail to me: “At this point its probably just a matter of time.”). Now, I’m not really suggesting this, as I am not suicidally inclined to undercut the profit motives of large narcoterrorism empires. But Jeremy could have perhaps put it differently: “At this point its probably just a matter of who.” Not us (no, really), but someone. This of course ignores the many, many difficulties that yeast in a vat face relative to their sun-baked, highly bred green competitors (and don’t even get me going on price points), but where there’s a graduate student, there’s a way.

- originally posted on Sunday, October 17th, 2010

On predicting evolution

It sucked to be a dog in the late 1970s. It wasn’t just that your owners wanted you to wear cute, doggy-tailored wide-bottomed jeans, it was the fact that your historical enemies, the cats, had unleashed a devastating wave of biological warfare on you. Somewhere in Europe, the evil cats took a virus that was rampant in their own population, feline leukopenia virus, and mutated it to first infect wild animal populations (the sly minks are still suspect) and from there … to you. The wave of parvovirus infection spread around the world within years, quite literally decimating the worldwide dog population. Brave dog scientists helped humans create parvovirus vaccines to stem the tide of infection, and almost every puppy born today is vaccinated as a matter of course.

Of course, despite their feigned innocence it is unlikely that cats were actually able to carry out sophisticated molecular biology techniques. No, we were observing evolution in action, with natural mutations gaining traction in new animal populations. Viruses are mutating all the time, constantly testing the defenses of new prey, a process that Nathan Wolfe has nicely called “viral chatter.” This is the same process that has led to fear of ‘bird flu’ transiting into the human population in a form that will allow facile human-to-human transmission.

There are many levels of mutation that may be required for the zoonotic transfer of viruses, but it’s easy to focus on the first and most important one: entry of a foreign virus into a cell. Viruses normally enter host cells by binding to and exploiting one or more cell surface receptors. The process of binding is mediated by lock-and-key like interactions between the amino acids on the surface of viral proteins and the amino acids on the cell surface receptors. In the case of parvovirus, a relatively few amino acids had to change on the feline leukopenia VP2 protein to allow the virus to enter mink cells, and then again a few more mutations led to entry into dog cells.

When viewed from this perspective, feline bioterrorism is reduced to simple lockpicking. Which current amino acids must change to which new amino acids in order to gain entry into the new cell type? And if you could predict these new interactions, you could predict the evolution of viruses … or even guide their evolution for your own ends.

After mulling it over, there are really two good ways to predict / engineer viral evolution. First, you can look at the historical record, and second, you can do computer modeling. The historical record is of course the vast amount of sequence data available on virtually everything at this point, including viruses and their hosts. It is reasonable to assume that the predator:prey interactions between viruses and not-viruses have been going on for millions of years, and that many of the assaults have been recorded in the genes of both sides. This makes sense to me especially for viruses, which mutate on a fantastic time scale. I think one of the anecdotal stories that really brought this home to me was when I learned that in a given individual the virus would completely evolve around a single drug that was the result of billions of dollars of investment within just weeks. This is why we now give a drug cocktail (HAART) to treat HIV-1; it increases the number of mutations required for evasion to the point where the disease is managed over a person’s lifetime, rather than over weeks.

It was a series of conversations with my colleague Professor Sara Sawyer that has convinced me that we can also look back at viral-wrought changes in the host. Sara examines the positive selection of genes in mammals. She looks for positions in genes that are mutating much faster over time than might be expected (although keep in mind that the timescales are now on the order of thousands of years, rather than a month). She has found a number of such mutations that are best accounted for by assuming that they are the result of our slogging attempts to fight off the wave of viruses that continually confront us. For example, Sara noticed that one of the common cell surface receptors was undergoing accelerated evolution on its periphery. Examination of a crystal structure of the receptor with a viral protein showed that the mutations accumulating in primates were in the same regions that were touched by the viral protein. The genomes of the slow-growing mammals had apparently retained a record of fighting off the fast-moving viruses. But it is more than a record, it is a map, a map of what amino acid residues on the virus can be mutated to interact with what amino acid residues on the cell. It is a potential recipe for zoonosis or bioterrorism, depending on your point of view.

Now, it is amazing that Sara has discovered this faint signal in the sea of sequence data that has washed over our community. But even without it, it probably would have been possible (although much harder) to discover the lockpicking map. The fact is that in concert with the insane amount of sequence data that is accumulating, we have an equally daunting amount of structural data. It is now rare to find a protein whose basal structure cannot be predicted based on other, structurally similar proteins. And if you really want to know the structure of a given protein, the methods for obtaining it have been streamlined to the point where there are factories that literally produce hundreds of structures a month (it used to take an entire graduate student lifetime and then some to get just one structure).

In parallel with the acquisition of structure have come tools for understanding the energetics of that structure. Why does a protein fold this way and not that way? What keeps all the squiggly lines together rather than flying apart? These energetic methods are far from perfect, but again are much better than they used to be. Extraordinary practitioners of the art of computational protein design, like David Baker, Homme Hellinga, and Steve Mayo, have advanced to the point where they can let computers sift through a huge number of protein sequence variants, assessing the energetics of each and predicting new structures.

It is now pretty much like one of those scenes in a movie where a hacker (the person with glasses) clips some small device to an ATM or door or computer interface, and a bunch of numbers run across the face of the device, and then, voila, the electronic lock is picked. The device presumably just quickly ran through all the combinations and found the right one (and the idiot software designer supposedly did not see this coming and install protection against multiple incorrect inputs).

So, while viral evolution is really, really fast, it’s not quite light speed, and we can now nudge it up a notch by providing a map to what mutations need to be made to fit a new cellular receptor. We’ve now been running some of our own simulations of various virus:receptor pairs, and the results are either illuminating or chilling, again depending on your predilections. And with the ability to synthesize genes and even genomes now available, a new, evolutionarily accelerated virus, could potentially be ready for field-testing. Keep in mind, however, that the real threat here was not ’synthetic biology.’ Gene synthesis is just an enabler, the same way NextGen sequencing is now an enabler or molecular biology writ large is an enabler. Heck, it may not even be that much of an enabler: you could argue that a graduate student with a couple of QuickChange mutagenesis kits could get the job done faster. No, the real key is the computation. Bioinformatics is providing a new window not just on what life is, but where it is going. The question becomes: who will get there first? Ooh, that was suitably dramatic.

- originally posted on Tuesday, October 5th, 2010

On spoofing

This can be considered sort of a hybrid post, bringing together “On the threat of synthetic biology,” “On GATTACA and taggants,” and “On fear.” Or, in other words, I’m so boring that I can’t really write anything new.

My blanket scoff regarding the threat of synthetic biology has a few caveats, which I have indicated along the way. But the biggest caveat is this: given how primed we are to go nuts at the slightest provocation, it really wouldn’t take much in the way of synthesis to create a spoof of a disease. This is especially true given that the vast majority of biodefense assays at this point are based at some level on sequence (usually PCR, because of its power and adaptability).

Why assemble a mad scientist’s lair in the heart of a volcano to build smallpox from scratch when you could just as easily make a relatively small piece of smallpox that you know could / would be detected? Spread it around, call the media, and sit back and watch the chaos unfold. At the least, “government sources” would be unable to confirm or deny the nature of the threat for many weeks, as they attempted to find the other pieces of the virus. And even then there would be the issue of whether the terrorists were college-level pranksters or an Aum Shinrikyo equivalent, experimenting in place.

Now there are social memes other than educating the populace to try to curb bioterrorism. There is always the expedient of just deterring the population with a different kind of fear. This seems to be what we’re up to now, with increasing control over biological research, and life-altering consequences for those who do not conform to a rigid set of standards (see Butler, Thomas, for details). I think this is stupid, but it doesn’t matter what I think: the folks that sign my paychecks say do it, then I have to do it.

To my mind, this is now our bulwark against domestic spoofing: dire consequences. It will be interesting to see if this barrier holds, as DNA becomes more readily available, and as the pushback against what some see as the shift to being a police state increases. In order to overcome the dire consequences, you have to accept that they are worth overcoming … which is well beyond the prankster stage. That said, this country has a long history of civil disobedience. Again dating myself, I lived through one such era (although I was young at the time, really), and some of my constant companions were “Steal This Book” and other volumes available from the ever-reliable Paladin Press. I did not become a terrorist (although I did just about blow my foot off).

It seems quaint to talk about books in the age of instant information, but I’m reasonably confident that the Internet has actually decreased access to ‘real’ knowledge, rather than increasing it. This may be the subject of a future post.

Without completely second-guessing the government, I think that the “dire consequences” strategy in lockstep with the “youse kids don’t know nuthin’” strategy may be working. The disaffected nerds make computer viruses, rather than strands of Ebola. Perhaps the DIY Bio crowd will provide an outlet for rebels without a clue, although I hope not. Not because of the dire consequences to society, but because some poor suck is going to be behind bars forever, and I’ll have to endure another insane layer of bureaucracy.

None of the above has any relevance to foreign spoofing. The door is wide open, and Flying Spaghetti Monster help us all.

- originally posted on Monday, October 4th, 2010

On plasmids

Ever since I’ve been a practicing molecular biologist, we’ve used plasmids as vehicles for genetic engineering. Or, more accurately, episomes, encompassing the range of extra-genomic information that can replicate inside of cells. In parallel, viral vectors have been harnessed in both prokaryotic and eukaryotic cells. I sometimes wonder whether this predilection to eipsomes has driven perceptions of synthetic biology. If you want to engineer a cell of course you must add information to the cell in a somewhat orthogonal fashion, with its own origin and its own means of being maintained, separate from the chromosome. I think this is one of the reasons that the “Venter shunt” of synthesizing the whole genome has attracted so much attention (other than the obvious, of course: that it’s awesome!).

But given my biases regarding trying to either meld a synthetic system with a natural one, or with the limitations on being orthogonal, I think that we begin to see a much more realistic idea coming into vogue: the genome as the unit of synthetic engineering. Short of being Craig Venter (and wouldn’t we all like to be Craig … or maybe Bill Gates. Some days I just can’t decide), what do the hoi polloi do? Well, into the distant past the way was pointed by folks who originally did directed evolution at the unit of the cell. Barry Hall is a pioneer here, with evolved beta-galactosidase (ebg). Pim Stemmer is under-recognized (from my point of view) for his early successes in genome shuffling, including the uber-scary shuffling of HIV genomes (amusingly, synthesis of poliovirus drove folks nuts, while Stemmer’s earlier work on creating new viruses didn’t raise much of an eyebrow in the popular press). More recently George Church has developed MAGE, which allows the large scale, iterative alteration of the E. coli genome using synthetic oligonucleotides. Other recombinase-based methods are beginning to surge, and we have our own version of genome editing based on the Group II self-splicing intron. Folks have also recognized that naturally competent organisms such as Acinetobacter may provide traction for genome engineering.

Soon there will be tailored genomes that contain augmented genetic codes. And MAGE or its relatives will begin to be used regularly for phenotype evolution. I lived through the use of directed evolution for nucleic acids and proteins, and now we’ll have an age of directed evolution of cellular genomes. The corresponding readouts available from NextGen sequencing will make the analysis of the products of directed evolution relatively straightforward. And the tools available via systems biology will allow us to make sense of the glut of information that will become available. It could actually be argued that directed evolution is perhaps the best means of more fully understanding the interconnections that are being discovered by systems biologists.

I’m now wondering about a question that will be resolved by this age of directed evolution. What does the fitness landscape for a cell look like? Now, that’s a loaded question, given that the fitness landscape for anything is highly dependent upon the environment in which it finds itself. A cell (or protein or nucleic acid) in a laboratory environment has a very different available landscape than a cell (or protein or nucleic acid) in the wild. Still, it’s a legitimate question. One would almost have to believe that cells live on very large neutral plains. The genomes of cells have had to learn to get along over billions of years. If you’re the odd gene out, you get booted pretty quickly. That level of interconnection is probably only possible if the landscape for one mutation moves is very broad.

Of course, there are many places that one can climb or that one can fall on the landscape, but my guess is that the new optima (or nadirs) are relatively mild. I think that the directed evolution of cells will not produce the same range of phenotypes as the directed evolution of proteins. This would of course seem paradoxical, given that cellular machinery is of course for the most part made of proteins. Let me refine that musing: phenotypically, you will get more bang for your mutational buck by focusing on a single protein rather than the cell as a whole. You will eat lactose better if you mutate beta-galactosidase, rather than mutating a genome. Or maybe this is a futile attempt to compare apples and oranges, given that there are organismal phenotypes that have no counterpart in a single protein (you don’t eat lactose unless you first take it up, and beta-galacotisdase is not particularly good at that).

And this nicely brings me back to the start. On the one hand I think that genomes should be the unit of evolution, since they are already an integrated system. On the other, I think that the integrated system will only grudgingly provide new function. And hence we need to provide that new function orthogonally, either by having facile integration methods for new information (cells have already figured this out of course; see pathogenicity islands for details) or via … plasmids. And this brings into focus the question of how we best cross-adapt the older integrated systems with the newer functional information, a question I do not immediately have an answer to.

- originally posted on Monday, September 27th, 2010

On ingenuity

You have to admire drug dealers. Not for their ruthless savagery, moral depravity, or social uselessness, but rather for their ingenuity.

In comparison, I have colleagues in synthetic organic chemistry who are masters of the art (and synthetic organic chemistry is indeed an art). They spend lifetimes learning arcane reactions and coming up with elegant new transformations, all so that they can sculpt carbon and other elements into whatever molecules they want. Of course, this is big business, too, because the best artists can develop shorter, easier, cheaper syntheses of drugs, and in so doing can vastly reduce the costs of goods for the pharmaceutical industry. Even better, these wizards can make compounds never seen before, and can thereby potentially create new drugs.

As an example, my colleague Phil Magnus recently developed a quite brilliant synthesis of certain opioid intermediates, a synthesis that cuts several steps off of previously published syntheses. It seems likely that Phil’s synthesis will now prove useful for making Alzheimer’s drugs much more cheaply.

Now, some drugs do not just heal the chemistry of the body, they alter the chemistry of the brain. They are addictive. Without getting into whether addictions (and wars on addictions) are in and of themselves a good or a bad thing, they are nonetheless intensely profitable things. And the good old invisible hand of Adam Smith thereby drives ingenuity, whether that ingenuity is turned to good ends or otherwise.

So it occurred to me to ask whether or not this new synthesis might lead to the street production of opioids. Initially, I thought this was one of my less productive thought experiments. How could your average thug possibly reproduce what was done by my brilliant colleague and a cohort of highly trained students working in a state-of-the-art research lab? But I was curious, and this brings me full circle to my first sentence. It is amazing what not your average thug, but say a mid-level thug, can do. Take meth labs. A much simpler synthesis than the one for opioids, but still: Birch reductions with the lithium from batteries! Wow. Collection of adequate quantities of starting material by hiring armies of street people to overcome restrictions on the sale of pseudophedrine. Perhaps morally bankrupt, but still ingenious.

So, I reverse engineered Phil’s synthesis a bit, and … I think it’s still not a go for the street (see Magnusc, although I have removed the summary slide that summarizes “Andy’s bathtub synthesis of opioids;” I’ll just leave that one safely behind the curtain).

Nonetheless, the thought exercise was useful on another level, one that relates to other posts. If the invisible hand can make thugs into synthetic organic chemists of a sort … why would this not make street synthetic biologists, the “DIY Bio” crowd, a force to be reckoned with? My opinion of the current DIY Bio community is that it’s more than a bit laughable. But that is likely precisely because they are motivated only by curiosity, and not by screaming self-interest. Once synthetic biology is shown to produce an actual product, something that makes money, then there will be more than enough motivation for a host of imitations, innovations, and bastardizations.

And that perhaps is the only reason that I sometimes revise my own estimation of synthetic biology as a security threat. Usually I rank it really, really low on the totem. But every now and again I think: If gigantic pots of money can lead to quite sophisticated submersibles being built in jungles to run drugs into our country, then what will happen when similar pots of money are available to those who figure out how to make genes on the fly?

- originally posted on Saturday, September 25th, 2010

On Traitwise

You may or may not have noticed a button alongside these musings that links to Traitwise. I’ve been working towards installing a more cogent version of this feature, and may get to that at some point. In the meantime, some explanation may be required. As usual, it will be in the form of a story.

One of my favorite people is Zack Booth Simpson. I met Zack a few years ago because he started hanging around with my friend and colleague Ed Marcotte. The way I usually explain Zack is like this: you know how sometimes they just recruit NBA players directly from high school? Zack’s like that, except with programming. He never bothered to get a high school degree, he just went directly into Origins (EA Games) and rose through their ranks to the point where he became independently wealthy and now just pretty much does what he wants. Which fortunately includes working with us on bioinformatics and synthetic biology. His title at the University is something like “resident genius.”

Anyway, Zack has many other interesting friends, and they’ve been fun to meet. His friend Steve Moore was interested in expression chip-based approaches to diagnostics and disease discovery. Now, Steve did not initially know much about this, given that he was also a software guy and theatrical producer (I told you these people were interesting). But he believed, and wanted to start a company. It seemed that the best way to get going would be on the software side, and the notion was that as we all scream towards having our genomes sequenced, it sure would be nice to have correlative analysis of how genotype matched up with phenotype. This in turn led to the notion that phenotypes could be collected via a social networking approach. As I write this, I realize it all sounds much more rational than it actually was. As with many start-ups, ideas careened around, bouncing off one another, generally not going anywhere, but somehow moving the company forward. Full disclosure: I have some incredibly small piece of this company, for my role as Resident Evil.

In any event, I actually think this is a Really Good Idea. It should be possible to mine folks’ own perceptions of their health and other traits for correlations that will eventually reach down to the genetic level. And in this regard I encourage you to click on the associated button and answer some questions. The format is a ‘question stream,’ and you can choose to some extent how you want to direct the stream (especially if you have an account … a *free* account … yes, free, free, free, like all eyeball-capturing devices). The real power behind Traitwise is in part this ever-growing stream of user-based questions, and in part the extraordinary statistical engine that does the correlative analysis. As one bemused user said “Interacting with Traitwise is like having the perfect boyfriend, who always wants to know more about you, and always asks the right questions.” Yessssss.

So, since this is sort of a biodefense blog, what is the biodefense relevance? I think just the notion that social networking is probably now our first line of defense against zoonosis and terrorist attacks. When we get hit with something that is arguably new and different, how will we know? There are various information-gathering exercises that can be carried out via emergency room data and aspirin sales and googling flu and whatnot, but for the most part these are all very … passive. They do not involve the afflicted or the observers of the afflicted. The great thing about the Internet is that it is a true Democracy, in just about every sense of the word: everyone gets a vote, and everyone’s vote is pretty much useless (there is in fact a reason this country is a Republic with a representative form of government). The only folks who really get anything out of this cacophany are the ones that ride above it, sifting trends and making predictions. I think this is still difficult for Command and Control types to really get behind, although they’re pretty damn sharp. And I think it’s going to be even harder to develop an extended social network that not only gathers information but that can act on it. But I also think that our future as a Cheeseburger-Eating Empire depends upon it. We are just too vulnerable, can be taken down in too many different ways. And the only possible response is to … empower the folks who are really concerned about their health: us. Once we quit just using the Internet as a playground and start to have an extended sense of self that realizes we have a responsibility to our avatars … that’s when things will get interesting.

OK, I’m expounding beyond my knowledge and paygrade, time to shut up.

- originally posted on Tuesday, September 21st, 2010

On antibodies

I have begun to work with my friend George Georgiou on antibody development, and it’s really a kick. Basically, after having worked on functional RNAs for many years it’s sort of neat to be able to work with a biopolymer that actually has the ability to tightly bind ligands.

However, antibodies are more than just receptors. They represent our prime defenses against infection. And it has occurred to George and I and others that the new tools for dissecting sequence can now be used to dissect the immune response. Amazingly, you can immunize an animal with an antigen, wait a bit, and then sequence the mRNAs that encode immunoglubulins to determine what antibodies are the best (to a first approxiamtion). And because of our ability to synthesize genes de novo, we can go from immunization to sequencing to synthesis to build high affinity antibodies faster than if we were actually trying to clone the best antibody genes. Wild. I would never have believed that we could do this, a few years back. But now it seems poised to be the way in which many new antibodies will be made. More details on this method can be found in Reddy et al., Nature Biotechnology, 2010.

I think this tool will be especially useful in the biodefense realm, for a variety of reasons. One is that it is way easier to work with sequences from ‘hot’ immunizations than with the actual material. In this regard we have a great collaboration with Rob Davey at UTMB Galveston on identifying antibodies against proteins from Ebola.

Now, imagine that same scenario, but in a human, rather than an animal model. No, I don’t mean immunizing humans with Ebola. Sheesh. But what happens when we do have a zoonotic or bioterrorist event, and we don’t have the luxury of carrying out research against a completely novel pathogen. How do we fight it? We use our own immune responses. We sequence the repertoires of survivors (or even, as necessary, casualties) and determine what antibodies have come to the fore, make them, and use them as prophylactics and therapeutics against the disease. This is the ultimate ‘herd immunity,’ where we use our big brains and our fast machines to spread immunity throughout a population.

- originally posted on Sunday, September 19th, 2010

On GATTACA and taggants

OK, time for some more old people meandering. When I was a youngster, we sequenced by hand (actually, we also did PCR by hand, but that’s really sad). We ran our own gels, called our own bases, the whole 9 yards. The kits we used were a step above doing Maxim-Gilbert sequencing, but compared to today it’s still pretty weird.

Now, we have Engines of God that can sequence entire bacterial genomes in a day, and human genomes in weeks or less. What is wild to me is that not just within my lifetime but within my scientific lifetime we’ve gone from giving a Nobel Prize for the development of sequencing to having so much sequence data that we quite literally don’t know what to do with it all.

Clearly, there will come a point at which having your sequence information will be an important adjunct to health care, and we’ll have all sorts of privacy battles, yada, yada, yada.

But sequence is more interesting than biology. This, in my opinion, is a key concept. We often think of sequences as coming from biology, but that’s not the case. With the parallel revolution in DNA synthesis we can of course make any sequence we want, including massively unnatural sequences with no known counterpart in biology. And with the parallel-parallel revolution in sequence amplification, we have an unholy (or really cool, depending on your point of view) triad: make the sequence, amplify the sequence, acquire the sequence.

We have the ability to label anything we want with a code that scales to the 4th power, and can acquire that code with single molecule resolution. As I have previously predicted, written about, and been fascinated with for a long time, we have the ability to make taggants that can tell us anything about everything.

I originally got interested in taggants because of the OJ Simpson trial (and subsequent, much more legitimate demonstrations that forensics facilities don’t always do things right). Oh my, could we really have confused one DNA with another? How can we make sure of the chain of evidence? Obviously by tagging it with non-natural DNA, precontaminating it so that wherever the natural DNA goes so goeth the tagged DNA (although this would not guard against purposeful biological mixups by perpetrators, ala the plot twist in Presumed Innocent).

But now let’s expand on that concept. We can tag and follow forensic evidence. What else can we tag? Well, if we let our minds wander the answer is: anything. Any noun: people, places, and things. But more than just nouns, we can tag concepts: the time something occurred, where an event occurred, what interactions have occurred subsequently. Just layer on the DNA, and find it later, again at the single molecule level.

I guess the second time I began to fantasize heavily about taggants was after 9/11. Why didn’t we stop Atta? How could we have known? Now, presumably in this day and age the intelligence or homeland security apparatus would work, but as a technologist I’m of course going to hit the problem nail with a tech hammer. If I was into IT, I’d be pushing image analysis, which is quite good and probably less ridiculous than tagging an individual with DNA. Still … if we had known where the terrorists were meeting, and had some way of pre-introducing DNA, then we could let them disperse, let them carry the clues with them, and then had an easy way to pick up and analyze that DNA on the flip side … that would have done it. Not. There are too many slips twixt the DNA and the sequencer in that scenario. Nonetheless, it does set in motion thoughts about when would it be an appropriate tool.

And that was before the Engines of God began churning out their limitless supply of information. Now, now it is not so crazy to imagine that the scene from GATTACA where they vacuum up DNA and just randomly sequence everything in a room, in order to find a ‘borrowed ladder,’ is very possible. But instead of a borrowed ladder you could now be looking for the sequence evidence of what’s been there, where the DNA came from, what interactions have occurred. You’re setting up physical networks akin to the Internet, where you look for distribution from nodes, with the packets being DNA rather than electronic (or else you can just laugh at my view of the Internet as being only modestly superior to the now-deceased Senator who thought of it as a bunch of pipes).

Where will this first come to be? Government? Tagging piles of cocaine to look at distribution networks downstream? Tagging counterfeit money to plumb how it traverses economies? Or industry, where technological innovation usually starts? Many products are already tagged with RFID; will it in fact be cheaper to use DNA? I don’t know, I’ve never been a good futurologist, but I believe this is coming, if only because the network analysis required to understand dynamic distribution will be arcane enough (read: alot like modeling epidemics) to be counted as a trade secret by someone along the way.

- originally posted on Sunday, August 22nd, 2010