Molecularist

So, I’ve been talking about trends in biology that I think are significant (maybe because I’ve only started following biology again in the past year). In any case, I’ve said the trends were synthetic biology, the future of scientific publishing, and personal genomics.

Personal genomics is where individuals have detailed access to their genomic information (your genotype). To put us all on the same page, your genome is the totality of all your DNA – your nuclear DNA and your mitochondrial DNA. I claim that it also needs to include your micro-organismal biota DNA, as well. But, what the genomic information gives you is the programmatic basis for who you are, where you’ve come from, and what you might pass on.

Genetics 101

To be frank, you already have a clue as to what your genotype is, through observation of your phenotype (how your genotype is expressed in an observable attribute). For example, if you have blue eyes and only one of your parents do, you know that the non-blue eye parent is carrying a blue-eye gene (in normal cases, of course, but you get the idea). Indeed, the long list of questions of parental and family history that doctors ask are a sort of genetic profiling to give an idea of your own hereditary susceptibility to diseases.

Knowing all your DNA code at this time (through sequencing) is unlikely, mostly due to cost (unless you are on this list, or this program, or are this guy). Sure, it will come (and on the way, someone will win a prize). But for now, you need to be satisfied with just the direct sequencing of known stretches of DNA.

Another way is to look for indicative SNPs (pronounced ‘snips’, small nucleotide polymorhphisms, basically differences in code at a certain position of the genome). These SNPs are used as markers associated with a gene or phenotype. Hence, knowing SNPs, which are easier to scan for than sequencing the whole genome, are the state of the art in whole genome understanding.

Booming area?

While the dream of personal genomics is to drive more targeted pharmaceutical treatments, I think where it will really boom is in giving people their information to do what they want to.

I have seen a few companies pop up that offer various forms of DNA tests for regular folks, for curiosity or what. It definitely sits in a general self-knowledge, self-measurement trend that new sensors and tools have begun to provide.

One company I have been following is 23andMe (a play on humans having 23 pairs of chromosomes). In a nice twist, the genetic testing (they scan one million SNPs) is really just a conversations piece, a social object that customers discuss on 23anMe’s socially-driven service. Yep. Social sharing meets biological diagnostics.

How much can it cost? 23andMe used to charge about $1000 per test (and I think that was for 500k SNPs). Recently they lowered the price to $400 and cover over one million SNPs. I suppose, at some point, the price will level off to ensure business profitability. Well, so long as profitability is based on selling tests. Which I probably suppose it won’t be, since these are smart folks running the company.

Thoughts on this

While I am still trying to get a feel for how 23andMe is positioning itself, I do think that the drive in personal genomics will come from people wanting to know more about themselves, to help them make lifestyle decisions, and to feel more secure about their potential health future and of their children. And having the information before knowing what it means is fine, since companies like 23andMe keep combing the literature to add meaning to the data.

Also, pulling on the self-quanitification thread, one might want to marry this with other whole-organism tests. Metabolomics, the sum total of your metabolites, gives a great understanding of your current physiological make up. Marry a string of metabolic analyses with the understanding of your genome, and you have a powerful whole-body understanding. And metabolomics is a mature field with a good technological and informatics underpinning. And it is not expensive.

And and and, what’s more. If you think of the genomic data 23andMe are sitting on, they stand a lot to gain from adding further info to the genomic set. They are already doing surveys that they can match to customer genomic profiles. Imagine if they had detailed metabolic information? Then they have a powerful repository of information to mine about health and genetics. Ripe enough to make oodles of money on, without violating anyone’s privacy.

Hm.

Image by Image Editor

Synthetic biology is the design and building of novel organisms or biological systems. Sounds amazing, but we have been doing it to some degree for millenia, through husbandry of plants and animals, evolving them over time to drop the traits we didn't want (say, poison, aggression, horns) and promote the traits we did want (say, domestication, wool, meat, seeds).

With the advent of recombinant biology (where genes from one organism are added to another organism), we've been able to modify all sorts of creatures in important or bizarre ways. And, of course, genetically modified crops scare the Jeebus out of some fokls.

Microorganisms are commonly used to grow recombinant proteins, say, human proteins in E coli. But the current spirit of synthetic biology is to rebuild or build (micro)organisms to do some specific tasks or work.

I've spoken about Craig Venter many times. The work he's doing now, that should win him his 4th Nobel, is to specify a microbe that makes biodiesel. Indeed, we already use microorganisms to create biodiesel from various feed-stocks. But Venter takes it up a notch, to the point of specifying the _whole_ microorganism to do exactly the biochemical pathways he wants, rather than mutating or adding or subtracting a gene here or there.

Another person I'm watching is Drew Endy*, from MIT. He and a bunch of other adventurous bioengineers are creating a catalogue of genes that can be used as parts to easily build specific functions in microorganisms. Along with his cohorts, he's been running the iGEM competitions and creating a foundation called BioBricks. There's already a spinoff from these iGEM folks, called ginkgobioworks.

While many of the things I see coming out of this bioengineering seems like trying to shoe-horn a digital thinking onto analogue structures, the breath and depth of the creations, many of them just brilliant in their ingenuity or play, makes me overlook such a anti-digital peeve of mine.

Really, things are just beginning in this new age of synthetic biology. And it'll be really exciting for folks entering it at this stage. I'm looking forward to see how these bioengineering companies flourish.

BTW, the Boston Globe has a good write up of this new breed of bio-hackers.

Image from lofaesofa

*Endy is giving a Long Now seminar on 17 Nov 02008.