MainlyMartian

Phoenix descending

Having witnessed two Mars lander failures, Mars Polar Lander before this blog was even born and Beagle-2 back when it was young and active (Landing and prelanding in the December 2003 archive, and the whole sad story in the Beagle-2 archive), and having been absent for all the other attempts that have proved successful, it seemed to me only prudent not to cover the landing of Phoenix this weekend (and, yes, the fact that Pete Smith has bribed me heavily not to bring my big dead martian albatross anywhere near his nice shiny mission does play a role in this...).

However my excellent colleague Eric Hand is taking up the challenge -- he's down in Tucson now, embedding himself with Pete's science team, and will be blogging at Nature's In the Field blog. So if this post turns up unexpectedly in your RSS feed (I can't believe anyone looks at a blog this defunct) I advise you to  turn your attention to what he has to say...

Oh yes: for more on what it was like to cover the loss of Mars Polar Lander, debates over where to send the spacecraft which eventually became  Phoenix, and a few apercus from Pete Smith, and the significance of ice on Mars you could do worse than turn to Mapping Mars, now invitingly cheap at Amazon US and not that much pricier at Amazon UK

Global warming across the solar system

There's a nice new paper in Nature by some NASA Ames and USGS people (including Bob Haberle, who used to have a sign saying "Commander of the Solar System" taped to his office door) on the link between climate and albedo on Mars. As my colleague Katharine Sanderson reports, they found that warming of darker patches creates winds that move the lighter dust around so that the darker patches grow and get warmer still -- a nice positive feedback that is presumably reset by global dust storms and the like.

This provoked me to a little venting on the Nature website about the absurd climate skeptic riff that there's warming going on all over the solar system and that since the thing all the warming places have in common is the sun that must be the cause.

My conclusion:

What's saddening is that people should miss what these various phenomena really have in common — their explicability. They show that our ideas of atmospheric physics are applicable and useful on bodies that range from the tiny (Pluto, the atmosphere of which is hardly worth mentioning) to the gigantic (Jupiter, the atmosphere of which outweighs a hundred solid Earths). And computer models based on the ones used to study the climate on Earth provide results even when applied to the hugely different conditions on Mars. That is truly impressive.

So what these disparate observations actually tell us is that the scientific community — the scientific community that enjoys a firm consensus on the causes of Earthly climatic change — has a fairly impressive grasp of the fundamentals of how weather works elsewhere, as well. It's a rather inspiring insight. But it is not the lesson that climate sceptics want their readers to learn.

It would be remiss of me...

... on this, Spirit's 1000th sol, not to point you towards this.

The Pluto controversy

Just to say that my magnificent Nature colleague Jenny Hogan is blogging the IAU's decision on Pluto's planetdom, or lack of it, more or less live here. I'm all for the planetinos myself.

Update: Pluto is out!

Mainly Marc

This is really a placeholder post to tell people that:

1) This is still Oliver Morton's blog, but is currently being used very rarely and fitfully. It is still in principle devoted to matters martian, but for the time being I'm not updating. The set of posts on methane on Mars can be found here, and observations on the life and death of Beagle 2 can be found here. The big wodge of stuff on synthetic biology from May 2006 is here because of a snafu that stopped me blogging live to the Nature Newsblog over the relevant weekend. It is of little or no planetary science value, though interesting in other ways.

2) If you're a friend, associate or indeed enemy who has lost track of me, perhaps due to the interruption of my abq email address, you can reach me via gmail as oemorton, or at nature.com as o.morton.

3) The Marc made by the Domaine Ott is I think the best truly strong (>50%) liquor I have ever drunk. Or at least it seemed so on Sunday night.

Synthetic Biology 2.0: Nature product

I meant to do a wrap-up post, but travel and poor connectivity intervened. Rob Carlson had a last post on the conference that I found intriguing, but  I will content myself by pointing to Erika Check's news report on the meeting in Nature, and an editorial that accompanied it. Here's the nub of the argument:

Self-governance need not and should not be exclusive — it does not preclude other forms of governance, any more than the possession of conscience makes redundant the strictures of law. It is hard not to suspect that the problem with self-governance from the point of view of the letter-writers is that it could go some way to addressing potential problems that would make good campaigning issues.

The ability of human societies to modify and transform biological systems will increase more in this century than it has in the hundred centuries since the dawn of agriculture, regardless of whether the transformation unfolds under the rubric of 'synthetic biology'. Or, at least, we must hope that it will — as the only credible alternative is a future in which massive social upheaval, armed conflict or natural disaster halts the progress of scientific knowledge. The challenge is to foster a matching, or at least sufficient, increase in the wisdom and accountability with which these abilities are used.

That challenge will require changes in the law and customs, in ideology and theology, and in education and economics. No scientific community can be expected to shoulder all that on its own, and nor should it. Scientists who are alive to the possibilities of change, anxious to keep their house in order and be seen to be doing so, and keen to discuss the issues with the world, are part of the solution, not part of the problem.

Update: I'm informed by the excellent Kevin Costa that the webcast of the SB2.0 talks is now archived for online viewing here, and will soon be added to Google Video for podcasting. The community declaration, which is still a work in progress as of June 13th,  can be viewed here.

Synthetic Biology 2.0: More bloggers

Crossposted from the Nature Newsblog; to comment, please use the version there.

Alex Mallet, from Drew Endy's lab, gives his take on the whole meeting here. And a student at Davidson college has lots of entries summarising specific talks on cis-action. In the long run, I expect the easiest way to browse them will be on the May archive.

Four active bloggers at a small biology meeting: the shape of things to come? or an outlier produced by an over-representation of geekiness in this very specific field?

Synthetic Biology 2.0: Medicine (and its malcontents?)

A big difference between this meeting and the one two years ago is the stress on medicine, which has been taking up quite a lot of Sunday. Wendell Lim, of UCSF, chairing the session, started it off with a serious, provocative vision. The medical implications of synthetic chemistry have been in making small molecule therapies; the medical implications of synthetic biology will lie in making "living therapies". Living therapies are creatures designed, with the help of synthetic genomes or parts of genomes, to do medicinal stuff. Examples from today: therapeutic bacteria that target tumours (bacteria seem attracted to tumours, which I didn't know before, and I'd be interested in finding out if anyone knows why), viruses for delivering genes, engineered immune system cells.

The immune cells came from David Baltimore, speaking this afternoon, who talked about various aspects of his project to "engineer immunity". The logic here is that it is difficult to develop vaccines against diseases such as AIDS and malaria because the immune system just isn't very good at dealing with them; if it were, the diseases wouldn't be such a problem. The fact that the natural immune response is so poor makes it hard to provoke a good response using vaccines. Wouldn't it be nice, goes Baltimore's argument, if we could get round this by going in and telling the immune system exactly what it should be doing, rather than just giving it a sketch of the problem -- that is, a vaccine -- and leaving it to its own insufficient devices. So, for example, give it blueprints of specific antibodies that are known to have a neutralising effect on HIV, rather than make do with the less impressive specimens it comes up with on its own. Or give it some stem cells that will make T-cells that we know will deal with a specific tumour.

Baltimore admits that this is ambitious stuff; it effectively combines immunotherapy, stem cell therapy and gene therapy, none of which, to put it kindly, are exactly established successes. But there are some encouraging results, and the potential pay offs are obviously vast.

Two thoughts here: one is that Baltimore's project, which has attracted the attention of the Bill and Melinda Gates Foundation, might be seen to some extent as old wine in new bottles -- ideas that have been around for a while and perhaps lsot some lustre rebadged in shiny up-to-date livery. Gene therapy has, after all, been in trials since 1990. In fact, though, I think re-examining the idea as synthetic biology makes sense. Synthetic biology is largely about reprogramming biological systems, and that's what gene therapy tries to do. If including gene therapy makes you reexamine what you think synthetic biology is, then maybe it should -- maybe synthetic biology is a bigger, broader thing than people are mostly taking it for.

Second thought: as these technologies get nearer to medicine, they also get scarier. Making viruses less likely to be recognised by a pre-existing immune response is a good idea for gene therapy, but it obviously has other potential implications. Likewise getting bacteria to last longer in the bloodstream and to express new proteins, such as invasin, that get them into cells, as described in one of the talks, is something that might be quite unpleasant in the wrong hands. So might associated systems that trigger pathogenic behaviour with an external cue. Imagine a harmless bacteria that could be spread through a population unobserved and then be triggered to turn nasty by a gas -- a gas that was not in itself a weapon, and so not recognised as such. That would be seriously nasty stuff.

The people doing this work are devoted to trying to do good. But systems for getting "living therapies" into the body to do good are obviously going to have overlaps with techniques for getting living weapons in to do harm. As I argued last year, biology has a dark side. This is not a reason for not doing such research -- but it is a reason for staying careful and thoughtful while doing so. This is something that the meeting will be returning to tomorrow.

(There are other worries, too. As Baltimore pointed out when he was talking about his expectation that lentiviruses would not have the leukaemia-causing problem that has dogged some gene therapy, it seems possible that the gene which was used in those trials was itself an oncogene. As Baltimore said, this was unfortunate. Also a little sobering.)

This has now been crossposted onto the Nature Newsblog. If moved to comment, please do so there.

Synthetic Biology 2.0: Also blogging the meeting...

...is Rob Carlson, a friend who I met at the first of these meetings. Rob, like Drew Endy, used to work at Roger Brent's Molecular Sciences Institute, just down the road from here, and he's now at the University of Washington. He may well be the only person in this pretty eclectic audience whose interests roam from detecting single proteins in cells to building space elevators. More on Rob here.

Rob's latest post from the meeting points out its commercial vibe. I must say that I wish I'd noticed Craig Venter and Vinod Khosla talking over lunch -- or indeed heard what they were saying... Rob also catches up with a couple of this morning's chemistry talks, so for the time being at least I won't.

Posting on Rob reminds of something I wrote about the biosecurity implications of synthetic biology in the New York Times last year. It seems particularly apposite right now, because the past two talks have been about designing bacteria and viruses for therapeutic purposes, part of which might involve making them less susceptible to the immune system. Subscribers can find it here, and everyone else can apparently find it for free here, but I should point out that the free version contains an error that crept into my copy through miscommunication with the Times, and which the Times itself has corrected: though Rob was a key player in the conception of very sensitive detection molecules called "tadpoles", there are a bunch of other people who should share credit, most specifically Ian Burbulis. The relevant paper is Burbulis, I.E., Yamaguchi, K., Carlson, R., and Brent, R. "Using protein-DNA chimera to count small numbers of molecules". Nature Methods Vol. 2, 31-37, 2005

Update: the shadow version of the Times story has been corrected to list all authors

Synthetic Biology 2.0: Opposing views

Tim Gardner, of Boston University, gave an interesting talk this morning on the "network biology" approaches he's using in his lab. Interesting in two distinct ways.

One: interesting in itself. Looking for networks by comparing the RNA expression of cells in different conditions and looking for correlations (or, more precisely, according to Gardner, "mutual information") between the expression of regulatory sequences and genes is a neat way of learning more about how cells actually work, a subject on which we are often remarkably ignorant. Key factoid (if I understood it correctly): in E. coli, the best studied bacterium, researchers currently don't have any idea of how three quarters of the genes are regulated. And that shouldn't be taken as meaning that we understand fully how the other quarter is regulated -- just that in those cases we have some leads on the subject (and, to be fair, in some of those cases much more than that).

Second interesting thing: Gardner's take-home message is the exact opposite of the view taken by Drew Endy and his colleagues. Gardner argues that because we have very few well characterised "components" with which to build entirely novel mechanisms and don't really understand how to do so we should concentrate on learning how natural cells work through building network models and get our miracles by tweaking these natural systems. Endy's position is that working out how natural systems actually work is extraordinarily hard (remember that ignorance over three quarters of E. coli) and that we should instead try and build simple things which we do understand. In this respect synthetic biology exists as a counterpoint, or alternative, to systems biology, network biology and other attempts to uncover the ways life actually works.

In part, this is the division between science and engineering. Endy and many of his colleagues at MIT are engineers, and they think in terms of designing well characterised systems, not of understanding very poorly characterised systems such as those that four billion years of evolution have left littering the face of the earth. As Endy puts it, if you were faced with a very complex, very buggy, awesomely antique software system which had been re-worked billions of times, with no notes at all to reveal what all that rewriting was meant to accomplish, or any really well understood sense of what its operating principles were, wouldn't you rather design something new from scratch?

The idea that synthetic biology offers that ability to do wholly new things is often seen as underwriting its practical or commercial possibilities. But it is also, at a more fundamental level, an epistemological distinction that sets this new discipline apart from its predecessors, offering real intellectual novelty. If, that is, Endy and his engineering colleagues can really deliver. Otherwise, it's biology as usual -- even if that biology is, as Garnder's talk was, very interesting in its own right.

I'll try and get a sense of which side of this debate the people attending the conference can be found on; if I turn up anything, I'll report back.

Update: I originally characterised the "mutual information" approach as a way of looking at things "more loosely but more productively", but Rob put me right.

This has now been crossposted onto the Nature Newsblog. If moved to comment, please do so there.