(bio)logical

Paul Raven @ 14-12-2010

Organic computing, anyone? Ars Technica reports on a paper published in Nature, wherein the authors describe the creation of bacterial colonies that can act as logic gates:

The key to the new work is stretches of DNA that act as logical OR and NOR functions. Both of them rely on small stretches of DNA called promoters that control the activity of nearby genes. In this case, the authors used promoters that activate nearby genes in response to simple chemicals (arabinose and tetracycline for these two promoters). By putting both promoters next to a reporter gene, the system acted as an OR gate: when either of the chemicals was present, the reporter was on.

[…]

the authors set up small clusters of bacterial colonies (small lumps of genetically identical cells). Each colony had a single logic gate (the authors used NOR, OR, and NOT gates). Depending on the arrangement of the colonies, each one could signal to only one or two neighbors, and each could only take input from one or two. The authors demonstrated a functional XOR gate built from four colonies, showing that all logical functions can be built from similar combinations.

The nice thing about using populations of cells is that this averages out some of the chaotic behavior typical of systems based on single cells. At a minimum, the systems they tested showed a five-fold difference between their on and off states. The downside is that, relative to a single cell, these systems are huge. The authors suggest that it might be possible to adapt their system to single cells, but it’s not clear that the same sort of performance could be maintained.

Boole meets biology. Maybe one day we’ll grow computers instead of building them from silicon slices…


BioBricked bacteria glow in the presence of landmines

Paul Raven @ 18-11-2009

landmine warning sign, CambodiaAn alarmingly large amount of the world’s surface is strewn with landmines left behind after conflicts of one sort or another, leaving the locals at risk of death and mutilation long after the dispute that caused them to be laid down has ended (or moved elsewhere).

Scouting for landmines is a risky job for humans (and, sadly, not everyone has a bomb dog like UXO)… but a student project at the University of Edinburgh may have found an easier and safer way of locating the mines so that they can be defused:

Bacteria which glow green in the presence of explosives could provide a cheap and safe way to find hidden landmines, Edinburgh scientists claim. The bugs can be mixed into a colourless solution, which forms green patches when sprayed onto ground where mines are buried. Edinburgh University said the microbes could be dropped by air onto danger areas. Within a few hours, they would indicate where the explosives can be found. The scientists produced the bacteria using a new technique called BioBricking, which manipulates packages of DNA.

Sounds like the perfect solution… although, as Inhabitat points out, we could do with being sure that the bacteria are thoroughly benign and unlikely to spread beyond the target area, lest we simply swap landmines for a form of unintended biological warfare. [via SlashDot; image by karl simourd]


Karl Schroeder deflates further Mars FUD

Paul Raven @ 02-11-2009

After dismantling the suggestion that a Mars mission is too inherently dangerous for humans to undertake, Karl Schroeder has a new targetScience Daily announces a paper that claims that we can’t go to Mars because the spacecraft will fill up with nasty bacteria and make everyone sick [via SlashDot]:

Frippiat and colleagues based their conclusions on studies showing that immune systems of both people and animals in space flight conditions are significantly weaker than their grounded counterparts. They also reviewed studies that examined the effects of space flight conditions and altered gravity on virulence and growth of common pathogens such as Salmonella, E. coli and Staphylococcus. These studies show that these bacteria reproduce more rapidly in space flight conditions, leading to increased risk of contamination, colonization and serious infection.

The basic facts there are quite true, but they’re being deployed alongside some invidious assumptions, as Schroeder points out:

This doesn’t mean that space flight is intrinsically dangerous.  It means that badly shielded tin-can environments that aren’t spun for gravity are a bad idea.  And that is quite a different conclusion.

Prolonged exposure to zero gravity weakens the immune system, so don’t expose astronauts to prolonged zero gravity.  Invest in some research into how to spin the spacecraft.  Then spin the spacecraft.

Secondly, shield the damn things.  The only reason why radiation is considered an issue is because it’s expensive to transport heavy shielding into orbit. One solution would be to use lunar water; simply put bags of the stuff around the ship.  That makes it heavier and hence requires more fuel… but now the problem can be seen for what it is, a simple problem of launch costs.

Spaceflight is not bad for our health.  Cut-rate spaceflight that avoids the obvious solutions is.

Those obvious solutions are, of course, a function of the launch cost issue – there’s a solution for pretty much everything if you can just get the necessary hardware up into orbit, but that’s not an option while we’re constrained by the limitations of rocketry.

I suspect that we’ll get there eventually, provided we survive our short- to medium-term future. After all, sailing ships were almost impossible to keep disease-free at first, until some smart minds got focussed on fixing the problems – and the motives for those fixes were profit and colonial expansion, which are likely to be exactly the same factors that propel us out of the gravity well. Perhaps the commercial space operators will break out of the rocketry box, given the chance.


A spoonful of friendly bacteria helps the medicine go down

Tom James @ 21-08-2009

pillsGenetically engineered bacteria have been used to deliver therapies for bowel disorders like inflammatory bowel disease:

The bacterium is able to deliver the protein, a human growth factor called KGF-2, directly to the damaged cells that line the gut, unlike other treatments which can cause unwanted side effects. Also unlike other treatments, it is envisaged that patients will be able to control the medication themselves by ingesting xylan, perhaps in the form of a drink.

I am not 1 of the 400 Britons who suffers from IBD but it is wonderful to see that genetic engineering has such excellent medical applications.

[from Science Daily][image from Deco Fernandez on flickr]


Bacterial computers to solve complex mathematics problems

Tom James @ 24-07-2009

bacteriaWe’ve seen viruses used to help treat cancer, and help building electrical components, now bacteria are being used to solve hitherto intractable mathematics problems:

Imagine you want to tour the 10 biggest cities in the UK, starting in London (number 1) and finishing in Bristol (number 10). The solution to the Hamiltonian Path Problem is the the shortest possible route you can take.

This simple problem is surprisingly difficult to solve. There are over 3.5 million possible routes to choose from, and a regular computer must try them out one at a time to find the shortest. Alternatively, a computer made from millions of bacteria can look at every route simultaneously. The biological world also has other advantages. As time goes by, a bacterial computer will actually increase in power as the bacteria reproduce.

These developments in synthetic biology are really amazing: it is just another example of how researchers are looking at pre-existing biological structures to solve problems (albeit somewhat abstract problems in this case) instead of building technologies from scratch.

[from the Guardian][image from kaibara87 on flickr]


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