New life for science

A few weeks ago I opened up The New York Times to find the claim by J. Craig Venter that his laboratory (the institute named after him) had created life. It was not a long or involved article. I saw very little about this on the news, and I’m including the internet.

Of course, there are some articles on it, but I suppose the most important one is found at http://www.sciencemag.org/cgi/rapidpdf/science.1190719v1.pdf, which is the Science article in which it was announced by the creators. I did my best to read it, and hope I got the gist, but I'm not going to pretend I understood the details. Some things you don't have to go to school for. That you do.

But, I saw so little commentary on it that I wondered if most people even have a clue that this had happened. A few educated people I've spoken with had no idea at all. It seems like an event of cataclysmic proportions, over time much more important than what is going on in our government or world affairs. Freeman Dyson, the now elderly physicist who seems to be some people’s idea of a scientific genius wrote: “I feel sure of only one conclusion. The ability to design and create new forms of life marks a turning-point in the history of our species and our planet”

I find it hard to disagree. However you want to limit his achievement, and it is a step, not the whole enchilada, it seems remarkable enough and I feel like everyone should be jumping down saying “Oh, my God, Oh, my God, Oh, my God,” but instead we have a parade of yawns looking not unlike the pointless “gates” set up in Central Park a few years ago imitating art, an event that so offends my aesthetic sensibilities I had to make this unnecessary mention of it.

Let me start with some basics you probably don’t need – Who is J. Craig Venter? He is the biologist who a few years ago took on the federal government in a race to sequence the human genome – that is – read the chemical code which makes up the human genome or DNA. His approach to doing so – the shotgun sequencing method - was less accurate than the government's method, and controversial, but much faster. And, he was right; it was accurate enough. Soon, the government and his team were working together and accomplished the task much faster than either would have done alone.

Now, he and his new group have succeeded in creating the dna for a simple micro-organism synthetically and introducing it into the shell of another micro-organism. They claim they have created life.

If I’ve done a poor job of explaining what they did – I want to try again. DNA is the code of life - I know you know that – but bear with me so I can get to what I really want to talk about. This is from Wikipedia:

“Deoxyribonucleic acid . . . is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints, like a recipe or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.”

Venter (who despite some popular opinion is not just the money man but a highly cited scientific researcher) and his team created a long strand of a DNA molecule which makes up the genome of a certain type of bacteria in the laboratory and successfully inserted it into another cell (which they did not create).

Some argue already that this is not creating life because they did not create the cell into which the dna was inserted. But, they do not claim to have created an entire organism. But, they do claim to have created synthetic, or man-made, life form – Mycoplasma laboratorium. Even if the original specimen partially existed before, the cell has replicated itself over and over again based on the synthetic dna. Did you read that? Each new cell has the synthetic DNA.

In order to keep tabs on the synthetic lines of cells they actually put a chemical watermark in it – things like the alphabet (or a code for it – again, don’t ask me), the names of the scientists, the cell’s own website and I forget what else.

The implications for this are astonishing, however inevitable it might have been to happen someday, and I doubt anyone can even now conceive the developments that will come out of it. I remember sitting in an IHOP many years ago with a friend who asked me what I thought would come out of the internet. We both agreed that it would change the world, but we couldn’t figure out how. Now, I’m no entrepreneur, but no one else seemed to have the answer to the many ways it would change the world either. There are now many thousands of applications now available to us, and it changes faster than anyone can even keep up with. Indeed, it is computer power that Mr. Venter suggests in the Science article that is the reason for the new developments ("Our ability to rapidly digitize genomic information has increased by more than eight orders of magnitude over the past 25 years.")

MIT's chief robotocist and artificial intelligence expert, Rodney Brooks writes that on one hand we can say the Venter bacterior is synthetic life, because the genome is synthetic, but on the other hand, we can't, because the ancestor was not synthetic. I think he misses the point. Yes, maybe the original creation was is only partially synthetic - but it lives. Remember, Frankenstein's monster was made up completely of a human being and its fictional re-animation was considered pretty exciting. Besides, its descendants were not only alive but all had the DNA that was man-made, including the water-marks.

Actually, Brooks also claims that Venter's genome decoding and his lab's removing of "100 out of 485 protein coding genes of what was already the shortest known genome of an organism capable of independent growth, and still the new genome supported continued growth and reproduction" were both much bigger surprises.

More, he writes, will need to be discovered before ethicists have something to worry about. First we need to discover -

"• a viable synthetic genome which mixes and matches genes from many species

• a viable synthetic genome which includes genes which have been designed rather than copied from existing species

• a bacterial line where the RNAs that decode the genome are also synthetic and which use a different encoding mapping three base pairs to amino acids — a bacterial line that uses new and different amino acids for the construction of proteins

• a eukaryote line that uses a synthetic genome, and all of the above innovations."
 
Again, I think he misses the point, even if he is a hundred times more adept than me at science - of course, this is a step. You read the Science article and you get that immediately. But, it is a magnificent step. I'm reminded of the Neil Armstrong quote - "One small step for man; one giant step for mankind." The theory of relativity did not come from nothing but from Einstein's trying to understand why existing theories seemed contradictory at points. All great scientists talk about standing on the shoulders of giants. The Greek who first thought, "hey, how about using letters for vowels too" already had an alphabet to work on too. The moon landing was a step, but wow!
 
Naturally, where there are stunning technological developments, there are ethical concerns. Some may fear the power to couple synthetic DNA with cloning and create new types of creatures, even super-humans who never age, never get bored, sneeze, nod off, worry and who can work indefinately. Of course, before they get to that we have to worry about the 6 foot tall house cats chasing pit bulls down the street and the like. With the recent work on the Genome of Neanderthal man (60 percent complete, as I understand it), we might just find out if they had speech, and given a second chance at life, prevail by making incredible lineman and tight ends.

NYU-Polytechnic's Nassim N. Taleb, whose pompous Black Swans I am now reading is an expert on "risk engineering" (trying not to laugh here - what the f*** is that? - although a lot of people find him quite important). Another day I will challenge, at least to some degree, his central thesis that unexpected events of the Jurassic Park variety are more important than the inductive reasoning (but I really should finish the book first, don't you think), so despised by philosophers and scientists, but for now, he writes:
 
"If I understand this well, to the creationists, this should be an insult to God; but, further, to the evolutionist, this is certainly an insult to evolution. And to the risk manager/probabilist, like myself & my peers, this is an insult to human Prudence, the beginning of the mother-of-all exposure to Black Swans. Let me explain.

Evolution (in complex systems) proceeds by undirected, convex bricolage or tinkering, inherently robust, i.e., with the achievement of potential stochastic gains thanks to continuous and repetitive small, near-harmless mistakes. What men have done with top-down, command-and-control science has been exactly the reverse: concave interventions, i.e., the achievement of small certain gains through exposure to massive stochastic mistakes (coming from the natural incompleteness in our understanding of systems). Our record in understanding risks in complex systems (biology, economics, climate) has been pitiful, marred with retrospective distortions (we only understand the risks after the damage takes place), and there is nothing to convince me that we have gotten better at risk management. In this particular case, because of the scalability of the errors, you are exposed to the wildest possible form of informational uncertainty (even more than markets), producing tail risks of unheard proportions.

I have an immense respect for Craig Venter, whom I consider one of the smartest men who ever breathed, but, giving fallible humans such powers is similar to giving a small child a bunch of explosives."

To the contrary, PZ Myers, a professor at the University of Minnesota writes that what we really have to worry about is not the problems coming from our infant-stride developments in genetics, but the little buggies who have been strengthened by natural selection for millions of years and want to eat us. He may be right about the buggies, but can't both things be a worry?

I believe that Taleb and Myers are both wrong, at least, potentially wrong - Taleb's black swan events could be positive as well as disastrous. We have something to say about that, if we manage our technology. On the other hand, Myers' may underestimate, for example, the damage a genetically altered honey bee might do, it got rid of all the other honey bees and then fizzled out.

We don't know. That's one of the great things about being a human in this amazing age. You just don't know what is going to happen next and the ability of us to transform ourselves and the future world may be extraordinary or disastrous, but probably both if history is a guide (Taleb would scoff at that thought). But, as a whole, humans are Vikings at heart, or at least Polynesians, and we don't just sit home. We keep doing new things. Does Nassim Taleb think that air conditioning was a bad thing? Because his black swans could have made that that a disaster too.

But, what of Taleb's comment about this being an insult to God (not to mention to evolution). What if scientists can in the near future actually create living organisms from scratch? Those believers should be careful in saying it can never happen, because one day, it is going to? And what if someday that creation includes a human? Will there be an argument made that it isn't human because, even if it has every wonderful saint-like quality you can imagine, it doesn't have a soul? 

Venter's triumph is just one of the developments that is going to so change the world that even the children today who grow up with the wonders of the internet as a given, will not recognize the world 50 years from now. I plan on being dead, of course, but I still think I will see changes that will be as astonishing as the moon landing was to people born in the 19th century.

One of the baby steps that I find marvelous is research on brain-machine interfaces. About seven years ago Duke University demonstrated rhesus monkeys controlling robot arms with their minds. More important, they showed that the monkey's brain adapted to treat the arm as if it was part of the monkey. It has been repeated elsewhere.

This research started in the 90s but has exploded. It is now possible with electrodes insterted into the brain's thalamus to digitally recreate what people are seeing. If this sounds like science fiction, it is not - it is just science.

Star Wars fans remember Luke Skywalker getting a synthetic hand, which immediately worked. That's not far fetched anymore. We also remember the character on Star Trek: The Next Generation where Jordy was able to see with special glasses. In the early 2000s, a man was already able to drive around a parking lot with the help of electrodes and glasses. Only a few years before his predecessor had to be hooked up to a two ton machine. How soon before it is possible to do it with a simple pair of glasses and a wireless device?

And, of course, they now have succeeded in having parapalegics move computer cursors. If parapalegics can do it, probably almost anyone can do it. And if we can move a cursor, we can make anything happen that is connected to the computer.

I'm not going to go on much of a fantasy flight here as to what might occur in the future. But, it occurred to me that my daughter's child, or at least her child's child, will someday have a computer chip implanted when she is born, and probably right into the fetus someday. I will suggest that we are on the verge of science outstripping or at least running alongside science fiction. At the very least, the writers are going to have to get more creative.

Bonus material:

Below has nothing to do with DNA. It is Louis Prima's band with Sam Butera doing Night Train. They were the best. I love watching Keely trying not to laugh. I'm so sorry I missed them. If only my time machine wasn't still broken.