It's almost the end of the year and it seemed like it's been for ever
since I sent out any kind of "I'm alive and well" kind of e-mail.
Lots of people rely on the steady stream of humour peppered with the
occasional scientific article sent from my mailbox as a sign of life,
but the lovely collection of Christmas cards, newsletters, great pictures
of people's children and family etc reminded me that I should write
something, although in this day and age it seems very old-fashioned to
"push" information out. It seems more appropriate to just publish and
wait for somebody to download but I digress.

I just spent my first San Francisco Christmas with mum and dad and a
few friends.  I have come to associate travelling with Christmas and it
was strange working right up to the date.  Christmas in San Francisco
is kind of wet.  Not cold, not warm, just kind of overcast.  It's also
quite anticlimactic because by the time it arrives here, everybody
has been ringing up for over 24 hours and saying "Merry Christmas",
so it feels somewhat belated.  It was great to have friends and family
together though, and that's most of what Christmas is about along with
custard and Christmas pudding.

So I've been working for the US government for nine months, specifically
at the Joint Genome Institute.  I am actually a Lawrence Livermore
employee (their main business is nuclear weapons design, but they have
lots of other scientific interests including genomics).  Livermore is
physically a long way from San Francisco, so fortunately I am sited at
a different facility out in walnut creek which is jointly run by both
Livermore and Lawrence Berkeley.  The Department of energy (which runs
all of this) started the human genome project believe it or not and
ended up finishing three chromosomes.  Nowadays, they are much more
interested in organisms that can help with energy production, regulate
the environment or help cleanup contaminated environments.  They are
sequencing the equivalent of a human being in 8 months and actually
dealing with hundreds of different organisms.  I actually started
interviewing with them in October 2004 and after hearing I didn't get
the job, started interviewing again and second time round they made
the right :) decision around about the time I was ready to settle down.
I started in March and after 72 hours of mostly safety training, I was
unleashed on the JGI.

 It's quite a culture change after working for a startup/biotech company.
 For a start, the organisation is several hundred people, Livermore
 is 7000 and the US government is huge and sprawling, so there are
 many more rules, interacting pieces, and overall quite a different
 culture.   I've been through three audits/reviews since arriving. The
 other difference was that  Exelixis went from roughly 30 employees
 when I met them to over 600 and I was there as it grew up.  This felt
 much more like parachuting down into a completely alien landscape .
 People were really good about giving me time to get to know them.
 For literally months, I would wander the corridors and run into
 people I'd never met, only to find out later that they worked for me.
 I'm responsible for about 55 people and I'm sure if they had seen the
 state of my apartment they would have thought twice about giving me
 the job .  It's an interesting mixture of management (particularly
 lots of change management) and science/technology.  I've done lots
 of DNA sequencing, and it's interesting to come back after a bit of
 a break and see what's changed and what hasn't.  Some really basic
 problems remain and everything else is just so much faster and cheaper.
 The organisation has gone through a lot of change adjusting to the post
 human genome era and it's hard work but also very rewarding making that
 all function properly.

The other big adjustment for me was the commute.  I travel probably 500
km per week, ride 50 km of that, and spend 2.5 hours commuting per day.
Work is about 50 km east of San Francisco, over a mountain range.
That's the bad news.  The good news is I still don't have a car, so most
of that is useful time.  I get a lot of work done on the train and have
a folding bicycle which is very convenient for commuting.  I was riding
along the (stunningly beautiful) 2 mile bike trail at the Walnut creek
end this morning in heavy rain, wrapped up in Gore-Tex with an iPod
listening to a German podcast called "Filme und So" which comes out of
Munich, catching up on film reviews in German, so every minute is put to
a good use.  Oddly enough the commute really has been quite pleasant.
I do notice that my day is shorter and along with German classes which
I'm still taking and getting to the gym regularly, I don't have as much
time for socialising and I used to.  The other strange thing about
making this community is that I am in a totally different climate.
The hills between San Francisco and Walnut Creek block much of the sea
climate, so I commute from "winter" as we affectionately call summer in
San Francisco, to "summer"  as they refer to it in Walnut creek.

Time spent not working and learning German is usually split between a
variety of outdoor recreation (a lot of hiking in the Sierras, some
cross-country skiing, and a little recreational biking), time with
friends, and dating.  Dating in particular is one of those lifestyle
things you just have to learn to enjoy.  I can't say I've stayed out
of trouble this year, but I have discovered that I like meeting people
which is a good thing.  Everybody is unique and in some way interesting.
Unfortunately not always interesting enough or available, or compatible.
I'm reminded of that great poster on which talks about the
importance of enjoying the journey (you should look through those if
you haven't), with a guy just sitting in an empty stadium, and arguing
you shouldn't rush the journey.  So I am still unattached and will put
out my annual plea for interesting, single women you might know about.
Please feel free to send them my way.  I'm still quite content living in
San Francisco.  I did think in the end of that a change would have been
fine as well.  I had mentally gotten to a point where I could imagine
living in Singapore, but at the end of all of my travels, I arrived
back in San Francisco one cool morning and grabbed a bagel at my local
cafe and everything was just beautiful and perfect.  Incidentally, if
you are ever thinking of moving away from San Francisco, don't try to
make the decision in September October or November.  I think actually
something like February would be ideal when it just rains and rains,
or maybe July when the fog destroys any hope of ever seeing the sun again.

I still get regular political feedback from those of you based outside
the United States and I have to say there has been a lot of discussion
within the country about the state of the US/world/economy etc.  I don't
know really what to think any more.  It's been interesting reading
lots of German news, because you do realise how your culture affects
what is considered news and how it is reported.  I should probably
be doubly careful now that the NSA is probably spying on all of our
domestic conversations ;) Actually one of the more interesting parts of
the Livermore job application process is the background security check.
If you can imagine someone from Georgia in a deep Southern drawl calling
up one of my friends and asking if "Mr Platt has it had been known to
be a member of any organisation and may not be working in the best
interests of the United States", and my friend replying "well he is
an Australian.".  The follow-up question was " should I write anything
other than the Australian thing?".  Ironically this organisation doing
the checks was choice point security which had just accidentally handed
out the personal data on 400,000 people/organisations to criminals.  I was
asked in the interview process if I would contemplate becoming an American
which would be a prerequisite for the next level of security clearance.
Something I'd have to think about ;)  As I was saying, the world seems
like an increasingly complex place and there is a lot of conflicting
information/debate in particular on how the US is doing economically.
It's still very hard for me to judge as same relative newcomer how bad
things really are, not having lived through the 80s or previous decades
here but I have a sense that we are living in interesting times.  I can't
say Australia appears as the Paradise I once used to think of it as.
The news coverage isn't always flattering any more.  The relatively
peaceful neutral multicultural environmentally aware country I left behind
usually appears in newspapers under articles about the Kyoto treaty,
treatment of refugees and most recently race rioting, so I can't say
the government has done a good job, at least on the marketing front if
not the substance behind it.  Schwarzenegger seems to be well past the
end of his honeymoon period and is slowly showing his true conservative
colours. The next (scheduled) election should be eventful.  I'm now
going on over a decade outside Australia and other than voting for
Blair in the 97 election, have not participated any form of democracy.
Taxation without representation was ironically the issue around which
the US was established.

So on a more interesting/upbeat note, we are doing something about
alternative energy at work and I've clipped out a small section of a
recent press release about termites (below).  We're basically planning
to sequence the bacteria living inside termites and it's totally cool to
be involved with something like this.  I'm still very much enjoying my
work and still thinking long-term I'm interested in synthetic biology.
I attended a symposium on artificial life earlier this year and there
are so many fantastic applications for engineered bacteria around the
corner that we will live through a very exciting time.  Some students as
part of a synthetic biology competition built a camera using bacteria
that would capture any image shone onto the plate of live bacteria.
They actually started out with the more ambitious goal of just catching
the outline of the image.  It was very eerie and exciting seeing the
outline of "Hello World" written on the bacteria, right down to the edges
of the pixels.  There are many more serious applications in human health
and also on the DNA sequencing front, many new technologies that promise
to sequence all of our individual genomes.  I'd be very surprised if we
don't all have our genomes sequence in the next 10 to 20 years (with
our permission of course), so it is a great time to be in this field.
There is obviously a lot of anxiety around this if you aren't in the
field, but I am confident that the benefits are going to phenomenally
outweigh any mischief, but that of course remains to be seen.

Please stay in touch, it's always great to hear what everybody is up to.
I  still have two futons and wireless Internet for any visitors and am
conveniently located in San Francisco near public transport, so please
drop by!

Hope you have a great 2006,

JGI home page

Sequencing Termites
> One of DOE’s most enduring goals is to replace fossil fuels with
> renewable sources of cleaner energy, such as hydrogen produced from
> plant biomass fermentation. The lowly termite is actually one of the
> planet’s most efficient bioreactors, capable of cranking out two
> liters of hydrogen from fermenting just one sheet of paper. Termites
> accomplish this Herculean task by exploiting the metabolic
> capabilities of microorganisms inhabiting their hindguts. DOE JGI will
> be sequencing this community of microbes to provide a better
> understanding of the biochemical pathways used in the termite hindgut,
> which may lead to more efficient strategies for converting biomass to
> fuels and chemicals. Similarly, an ability to harness the pathways
> directly involved in hydrogen production in the termite gut may one
> day make biological production of this alternative energy source a
> viable option.
 More info on termites