It seems quite likely that future historians of science will divide biology into the pre- and post-genomic eras.
In one way, post-genomic biology—biology 2.0, if you like—has finally killed the idea of vitalism, the persistent belief that to explain how living things work, something more is needed than just an understanding of their physics and chemistry. True, no biologist has really believed in vitalism for more than a century. Nevertheless, the promise of genomics, that the parts list of a cell and, by extension, of a living organism, is finite and cataloguable, leaves no room for ghosts in the machine.
Viewed another way, though, biology 2.0 is actually neo-vitalistic. No one thinks that a computer is anything more than the sum of its continually changing physical states, yet those states can be abstracted into concepts and processed by a branch of learning that has come to be known as information science, independently of the shifting pattern of electrical charges inside the computer’s processor.
So it is with the new biology. The chemicals in a cell are the hardware. The information encoded in the DNA is the preloaded software. The interactions between the cellular chemicals are like the constantly changing states of processing and memory chips. Though understanding the genome has proved more complicated than expected, no discovery made so far suggests anything other than that all the information needed to make a cell is squirreled away in the DNA. Yet the whole is somehow greater than the sum of its parts.
More on artificial or synthetic life: An ‘Edge’ Symposium with Richard Dawkins, PZ Myers, Daniel Dennett and others
ON “CREATION OF A BACTERIAL CELL CONTROLLED BY A CHEMICALLY SYNTHESIZED GENOME” BY VENTER ET AL” [5.20.10]
On May 20th, J. Craig Venter and his team at J.C Venter Institute announced the creation of a cell controlled by a synthetic genome in a paper published in SCIENCE. As science historian George Dyson points out, “from the point of view of technology, a code generated within a digital computer is now self-replicating as the genome of a line of living cells. From the point of view of biology, a code generated by a living organism has been translated into a digital representation for replication, editing, and transmission to other cells.”
This new development is all about operating on a large scale. “Reading the genetic code of a wide range of species,” the paper says, “has increased exponentially from these early studies. Our ability to rapidly digitize genomic information has increased by more than eight orders of magnitude over the past 25 years.” This is a big scaling up in our technological abilities. Physicist Freeman Dyson, commenting on the paper, notes that “the sequencing and synthesizing of DNA give us all the tools we need to create new forms of life.” But it remains to be seen how it will serve in practice.
One question is whether or not a DNA sequence alone is enough to generate a living creature. One way of reading the paper suggests this doesn’t seem to be the case because of the use of old microplasma cells into which the DNA was inserted — that this is not about “creating life” since the new life requires an existing living recipient cell. If this is the case, what is the chance of producing something de novo? The paper might appear to be about a somewhat banal technological feat. The new techniques build on existing capabilities. What else is being added, what is qualitatively new?
While it is correct to say that the individual cell was not created, a new line of cells (dare one say species?) was generated. This is new life that is self-propagating, i.e. “the cells with only the synthetic genome are self replicating and capable of logarithmic growth.”
Prof. Daniel Geschwind seminar: Thursday 22nd April: “A framework for functional genomic investigation of human higher cognition”
From my colleague, Kevin Mitchell:
With any luck, Dan Geschwind will be visiting tomorrow and giving a seminar, in the TCIN building at 4pm.
Prof. Geschwind is a world-leader in the genetics and neuroscience of autism and in the study of the development and evolution of gene networks underlying human cortical structure and function and the evolution of human cognitive abilities, including language. Please see below for a list of some of his papers related to the latter topics.
” A framework for functional genomic investigation of human higher cognition”
Prof. Daniel Geschwind
University of California, Los Angeles
Thursday 22nd April
4pm, LB11, Lloyd Building
Human-specific transcriptional regulation of CNS development genes by FOXP2.
Konopka G, Bomar JM, Winden K, Coppola G, Jonsson ZO, Gao F, Peng S, Preuss TM, Wohlschlegel JA, Geschwind DH.
Nature. 2009 Nov 12;462(7270):213-7.
Neuroscience in the era of functional genomics and systems biology.
Geschwind DH, Konopka G.
Nature. 2009 Oct 15;461(7266):908-15. Review.
The organization of the transcriptional network in specific neuronal classes.
Winden KD, Oldham MC, Mirnics K, Ebert PJ, Swan CH, Levitt P, Rubenstein JL, Horvath S, Geschwind DH.
Mol Syst Biol. 2009;5:291. Epub 2009 Jul 28.
Functional organization of the transcriptome in human brain.
Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH.
Nat Neurosci. 2008 Nov;11(11):1271-82. Epub 2008 Oct 12.