Tag Archives: biochemistry

Genesis reloaded: are there forms of life on Earth we’ve missed?

It’s a well-used riff, but it seems to be making a comeback in recent months: is there a “shadow biosphere” of lifeforms on Earth that don’t obey the known rules of biochemistry? And if so, how might we find it – let alone recognise it when if do? A nice long article; you should go read the whole thing, but here’s a few snippets:

To investigate a species of microbe fully, you first need to culture it in the laboratory and then study its biochemistry by sequencing its genome to position it on the tree of life. This technique, while undoubtedly important, has its problems.

Many microbes don’t like being plucked out of their natural habitat and cannot be cultured easily. Some resist gene sequencing.

And, because the chemical techniques used to analyse microbes are customised and targeted to life as we know it, they wouldn’t work on an alternative form of biology. Should there be a different type of microbial life out there, it is very likely to be overlooked, simply because it would be unresponsive to the biochemists’ probes used so far. In a laboratory sample it might well get thrown out with the garbage.

If you set out to study life as we know it, then what you find will inevitably be life as we know it. It’s therefore an open question whether some microbes might actually be the descendants of a different genesis.


Notwithstanding their exotic nature, to date all extremophiles that have been analysed are standard life: they belong to the same tree of life as you and me. Their existence proves that the range of conditions under which standard life can survive is much broader than previously suspected. Nevertheless there are limits.

If there is a shadow biosphere, it might be occupied by weird ‘hyper-extremophiles’ inhabiting environments beyond the reach of even the hardiest form of standard life, and have so far escaped detection because nobody thought to look for any form of life under such extreme conditions. A good example is temperature: standard hyperthermophiles seem to have an upper limit of about 130˚C – and for good reason. The intense heat disrupts vital molecules, and even with a host of repair and protection mechanisms, DNA and proteins start to unravel and disintegrate if they are subjected to temperatures much in excess of 120˚C.

Suppose we find nothing living between 130˚C and 170˚C in a deep-ocean volcanic-vent system, but then discover microbes thriving there between 170˚C and 200˚C? The discontinuity in temperature range would be a strong indicator that we were dealing with weird life as opposed to standard life that had simply pushed the temperature envelope higher.


There are plenty of other places that could be home for isolated weird extremophiles. The inner core of Chile’s Atacama Desert is one place – it is so dry and oxidising that bacteria can’t metabolise. The U.S. space agency NASA has a field station there, but so far there is no evidence for any carbon chemistry that could be attributed to weird life.

Other possible locations include the upper atmosphere, cold dry plateaus and mountain tops (where high-ultraviolet flux is a problem for standard life), ice deposits at temperatures below -40˚C, and lakes heavily contaminated with metals toxic to known life. We don’t need to confine our search to a single parameter such as temperature; it’s possible that some combination such as temperature and acidity together is more relevant.

Very speculative stuff, as science goes: it’s basically hinging on the old “white crow” aphorism, which says that the fact that you’ve never seen something doesn’t prove that the thing doesn’t exist. But we’re friends of informed speculative science around these parts, so… 🙂

First artificial organelle

artificial_organelleResearchers have developed an artificial cellular organelle to aid in the development of artificial synthesis the life-saving anti-clotting drug heparin:

Scientists have been working to create a synthetic version of the medication, because the current production method leaves it susceptible to contamination–in 2008, such an incident was responsible for killing scores of people. But the drug has proven incredibly difficult to create in a lab.

Much of the mystery of heparin production stems from the site of its natural synthesis: a cellular organelle called the Golgi apparatus, which processes and packages proteins for transport out of the cell, decorating the proteins with sugars to make glycoproteins. Precisely how it does this has eluded generations of scientists.

To better understand what was going on inside the Golgi, Linhardt and his colleagues decided to create their own version. The result: the first known artificial cell organelle, a small microfluidics chip that mimics some of the Golgi’s actions.

As well as the utility of being able to produce drugs in this way, it is impressive the degree of control that can be exerted over the matter:

The digital device allows the researchers to control the movement of a single microscopic droplet while they add enzymes and sugars, split droplets apart, and slowly build a molecule chain like heparin.

[from Technology Review, via KurzwailAI][image from Technology Review]

Plastic fantastic: plastic from trees

leafIn preparation for when the oil runs out (or becomes economically unviable to extract – as detailed in The End of Oil by Paul Roberts) scientists have started developing alternative methods for making plastic. In this case from trees:

Some researchers hope to turn plants into a renewable, nonpolluting replacement for crude oil. To achieve this, scientists have to learn how to convert plant biomass into a building block for plastics and fuels cheaply and efficiently. In new research, chemists have successfully converted cellulose — the most common plant carbohydrate — directly into the building block called HMF in one step.

HMF, also known as 5-hydroxymethylfurfural, can be used as a building block for plastics and “biofuels” such as gasoline and diesel, essentially the same fuels processed from crude oil.

Given that so much of our industrial infrastructure rests on oil it is reassurring that alternative sources of basic materials are being developed.

[from Physorg][image from linh.ngân on flickr]

Does the Earth harbour a ‘shadow biosphere’?

alien desertDoes the Earth harbour forms of life unrelated to the carbon-based DNA-powered stuff we know about? “Impossible,” you might say, but as pointed out by astrophysicist Paul Davies, we wouldn’t know – because we’ve never looked for it.

“Our search for life [has been] based on our assumptions of life as we know it. Weird life and normal life could be intermingled, and filtering out the things we understand about life as we know it from the things we don’t understand is tricky.”

The tools and experiments researchers use to look for new forms of life – such as those on missions to Mars – would not detect biochemistries different from our own, making it easy for scientists to miss alien life, even if was under their noses.

Alternative biochemistry is inherently a speculative field, which is why it has made plenty of appearances in science fiction – Rudy Rucker has dealt with similar ideas before, for example, and Futurismic columnist Mac Tonnies has theorised about the potential of Earth being home to beings we are not able to recognise as such.

Finding examples of alien life here on Earth might add credence to theories like panspermia – but, more importantly, it would suggest that the likelihood of life developing elsewhere in the universe is closer to one than to zero. [via SlashDot; image by Haeroldus Laudeus]

Productive Nanosystems – The Movie

Most of us are aware that DNA and RNA are the molecular machinery that synthesise proteins and allow the complex reactions of life to take place, but actually visualising the processes is a considerable mental leap.

Most such visualisations rely on visual simplifications that actually present a false impression of the processes involved, but via Eric Drexler we discover the following examples by Drew Berry, which are apparently much truer to the actual processes that occur. Take the seven or so minutes needed to watch this, and you’ll be set up for your daily dose of scientific sensawunda for the rest of the week – biochemistry is incredibly awesome:

Aside from the sheer wow-factor of seeing molecules acting like high-precision machines deep at the cores of our cells, it’s worth bearing in mind that there’s no magic involved, and that we’re constantly getting better at understanding how these processes work.

Which, I expect, is why Drexler is so fascinated by them: once we know how the body’s nanomachines work, we’ll be properly equipped to start building new ones.