How Science is Reinventing Life Itself

Adam Rutherford, 2013

This book, along with Life at the Speed of Light by J. Craig Venter, and Regenesis by George Church and Ed Regis, are three looks at recent advances in synthetic genomics, the creation of artificial life. Both accomplished scientists, Venter is the Adventurer Captain and Church is the Academic Collaborator. Rutherford ("no relation to Ernest") is a science-trained British journalist, fighting to balance enthusiasm with the cynicism expected of his nationality and profession. This webpage concerns Rutherford's book.

Schroedinger asked "What Is Life?", and unless one believes in miraculous, abrupt discontinuities, there will never be an crisp dividing line. Fusion made atoms, geology made chemicals, and chemicals made life, over billions of years. If we see sharp distinctions between living and dead chemicals, it is because the gradual separation, like that between species, occured in the invisible past.

Everyone and everything is connected - we share the same ancestors as those who die crossing our borders. If those ancestors were still alive, they would beat the crap out of us for attacking our cousins - that is, if they weren't so busy attacking their own cousins. This shit (as they say) never ends.

Part one of Rutherford's book is "The Origin of Life", with fascinating experiments showing how the simplest replicating short RNA strings now in the lab could lead to something like the first "life" and L.U.C.A., the Last Universal Common Ancestor of all bacteria, archaia, and eukariotes (plants and animals ... us). Unless we encounter space aliens who watched and took notes, Luca is lost to history, consumed by her descendants; but if we can plausibly generate a series of lifeforms that could lead to further evolution, we have demonstrated that there is no sharp boundary between the chemical and organic worlds, and that the latter almost certainly sprung from the former. We can also better estimate how often this occurs in the universe, and whether we can expect separate beginnings on nearby planets.

Part two of Rutherford's book, "The Future of Life", springs from Feynman's aphorism "What I cannot create, I do not understand". We will never fully understand life unless we create homologues of what we see around us, as well as "what if" experiments that tinker with the machinery and observe the results, calibrating our predictive machinery with real examples. These chapters discuss the "open source" Biobrick movement, student competitions, and the production of materials and behaviors unlike any existing in nature.

Humans have modified life since we first unconsciously domesticated (and were domesticated by) plants and animals, developing "un-natural" genetic lines we are quite dependent on. After millennia of artificial selection, described by Darwin and Mendel, around 1900 we began to use chemical and radiological mutagens to create variations from which we more carefully selected, sparking an accelerated second wave of genetic modification. The third wave began around 1980, building on knowledge of DNA from Monod and Watson and Crick and countless others, using the early tools of gene splicing to intentionally copy genes between species, accelerating and taking control of the accidental processes of viral gene vectoring that nature has always used.

Most anti-GMO protesters reject this even-more-intentional third wave, while touting the accidental creations of the second and first waves - they want second-wave grains and "heirloom" first-wave tomatoes, and want all the rest of us to make the same choices. Few forage in the wilderness for plants untouched by human interaction, and that foraging changes the wilderness forever. Every lifeform on the planet is a unique and accidental experiment of genome and environment; perhaps the constrained creations of the lab call too much frightening attention to the completely unpredictable accidental creations of nature.

Even before the third wave is completely accepted, the fourth wave is upon us, the de novo creation of genes and genomes, the "reinvention of life itself" of Rutherford's subtitle. No longer constrained to observe and select, the fourth wave is characterized by first-principle design and construction. We decide what task we want to accomplish, we design a set of protein machines to do the task, we analyze and debug them on computers, then synthesize DNA sequences to produce them. We are still in the early stages. Accurate prediction is difficult. But the trend is clear - we will have a much better idea of what will sprout out of our farm fields in a few decades, because we will have watched those plants grow in a computer beforehand. The frightening thing is not food that will turn us into monsters, but food that is the expression of the monsters already within us. Problems will increasingly stem, not from accident or hidden agenda, but from willful self-destructive personal choice.

Bioengineered products can result from tinkering with natural organisms, but we have more control if we build our own organisms de novo. J. Craig Venter calls his Mycoplasma mycoides JCV1-syn1.0 the first synthetic lifeform, since its entire genome was produced from a sequence in a computer. Rutherford disagrees - almost all the genes are copied from Mycoplasma mycoides and inserted into a related Mycoplasma. However, subsequent steps will introduce new genes unlike any in nature, and a sequence of such changes will lead to an "engineering substrate" bacterium that is both unable to survive outside the lab (good for safety) and capable of being modified into many different forms, for many different tasks. The fact that there is no "giant leap" is true of all new technologies - the cars driving past in front of me right now resulted from a long sequence of small changes backwards in time, through the model T and Stephenson's Rocket and the horse-drawn cart, all the way back to the first rolling log used to move a load. As with the first life, the branch point to first "artificial life" will be a series of steps. The step made by Venter's team is a far more artificial and discontinuous one than the step that produced Luca; with much more knowledge and the exact same techniques, a series of further steps could take artificial life a long, long way, to something that is unquestionably distinct from evolved bacteria. If there is anyplace along that trajectory to draw the boundary to artificial life, it is JCV1-syn1.0 . Otherwise, we dispense with sharp boundaries altogether, and use different language for the continuum of all things.

Creation (last edited 2014-02-06 00:55:39 by KeithLofstrom)