Month: November 2011

Synthetic Biology: It’s life Ben, but not as we know it.

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Synthetic biology is a new area of biological research that combines biology and engineering in order to design and build ("synthesize") new biological functions and systems in cells.

synthiaThe controversial scientist Craig J Venter and his team built the first synthetic organism “Synthia” last year after 10 years of research. They took a commonly occurring bacterium, stripped out its genome (DNA) and then replaced it with their own synthetic DNA produced in the lab. Although these synthetic cells had only just enough genetic material to allow it to survive, this amazing achievement is proof that genomes can be designed by a computer, made in the laboratory and transplanted into a recipient cell to produce a new self-replicating cell controlled only by the synthetic genome.

But why would anyone want to create an artificial cell? Well the aim is to take a cell that has the basic function necessary for it to ‘live’ and then ‘add’ new features to it, allowing it to produce specific products. Sounds complicated, but it starts to make sense when you look at it like this.

In synthetic biology you can think of a cell almost like a computer: in a computer, there are a whole lot of individual parts, like memory, CPUs, and video cards, which work together to provide different functionalities. In cells, there are also a lot of different parts – things called membranes, mitochondria, ribosomes, enzymes etcetera – that work together, providing different functions to make the whole cell work.

All of these different parts are coded for by the cell’s genetic material, DNA, the same way computer programs have code to make them work. And in the same way we use different bits of code in different computer programs, we can also use different bits of DNA to program a cell. We call these bits of DNA ‘BioBricks’.

These bio-bricks code can then be connected like computer circuitry inside the cell by a Synthetic Biologist. These codes can then be arranged inside a modified bacteria or yeast cell that has had most of its natural genetic material or production lines removed – just like an empty factory. The genetic plans for the new production line can then be installed inside the chassis cell and the brand new cell factory will then be ready for operation.

dnaBut what makes synthetic biology different from plain old genetic engineering? Well, in genetic engineering, a few genes might be added or deleted from a cell, but these genes already exist in nature. In synthetic biology, we are making biological parts and devices that don’t already exist in nature: either extensively modifying existing DNA code, or creating entirely new bits of code that produce new components. This is like writing a new program for the cell and getting it to work properly with existing DNA and cell parts.

This difference between synthetic biology and genetic engineering is as subtle as it is profound. Synthetic engineering is effectively the creation of life through totally artificial means. For some this might sound scary, but the reality is there are many aspects of this process that are still quite natural. Because of our large size, complex cellular structures and sentient qualities we often over look the fact that the organic life around us exists because at the smallest scale, each atom inside us obeys of the fundamental laws of chemistry and physics. Artificially created or not, organic life will only exist if its base components are arranged in a similar way to what we would expect in any naturally occurring system.

As yet, we’ve not seen synthetic biology used as a plot device for a Hollywood film- probably due to it only being an emerging technology. Genetic engineering however has had a great run in the horror genre, responsible for everything from disease epidemics, mutant creatures and the return of the dinosaurs. As far as synthetic biology goes FLUBBER may well qualify as a product of artificial life- can anyone out there think of another film with a star that qualifies?

But back on topic- so what might synthetic biology used for? One example is creating cells that produce special hi-tech products that humans can harvest and use. Currently Synthetic Biologists are exploring ways to make low cost drugs that will overcome global shortages for diseases such as malaria. They are also investigating ways to turn sugar cane into jet fuel and create super fibres like spider silk.

Artificial organisms produced with these techniques could be used to alert us to the presence of environmental toxins, produce carbon neutral fuel sources, create super strong/super light textiles and help us diagnose and protect us from disease. Right now however, there is still a lot to learn because although we know how to read and write the genetic code, we still don’t know how to use it to solve a particular problem.

But as we learn more about synthetic biology we will be able to design more complicated cell systems and tackle many of the problems facing our modern world today. In theory, the uses and applications of Synthetic Biology are only limited by our imagination.

Watch FiST Chat 48: Synthetic Biology & Biotechnology for more on this topic.

A Trip To Mars: Hollywood Or Hell?

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On November 4th 2011, after 520 days in a sealed containment vessel in Russia, 6 would be astronauts completed their simulated mission to Mars.

The Mars500 study, a collaboration between the European Space Agency and Russia’s Institute for Biomedical Problems was designed to determine the human capacity to cope with a long haul space flight and its physiological and psychological demands. The simulated mission included a launch, a mars landing and a return to earth, allowing the crew to experience every aspect of long range space travel except zero gravity.

mars500-2The crew’s health and mental state were constantly monitored over the 17 months they lived in the cramped confines of their space craft, on its lonely journey through deep space. You can find out more about this amazing mission here:

But it begs the question how would a real flight to Mars (or elsewhere) in the Solar System compare with Hollywood’s film representations and what would it be like to be a real astronaut on a mission into deep space?

If we start with APOLLO 13 and the award winning SHADOW OF THE MOON – a documentary based around the highly successful Apollo missions in the 60s and 70s, we can see how early space exploration captured the imagination of (Ron Howard and) a whole generation. From a historical perspective these films show exactly what early space flight was like. With barely enough room to move, in early moon missions the astronauts were jammed together in a claustrophobic metal can for almost a week, with the only compensation being the zero G environment.

The now retired Space Shuttle and the International Space Station (ISS) ushered in the modern era of space travel. The Imax film, SPACE STATION is a fantastic insight into what life in space is like for astronauts, and probably will be for the foreseeable future. The ISS has a pressurised atmosphere similar to Earth’s, and an array of work and recreation areas, allowing a crew of 6 to live and work in zero gravity in an area similar to that of a 5 bedroom house.

The Mars500 mission recreated a very similar environment to that of the ISS with roughly the same amount of living space. For the record Cosmonaut Valeri Polyakov currently holds the record of 437 continuous days in space, still well short of the 520 days required for a successful Mars mission.

At least in our lifetime, any real-life journey to Mars wouldn’t differ much from life on the ISS, and to that extent the Hollywood interpretations in MISSION TO MARS or RED PLANET tend to get some aspects of space travel right. Although MISSION TO MARS had a scientific advisor credited in its making, the plot is so poor, the clunky expositional dialogue that dominates the journey to Mars manages to recreate for the audience the painful boredom an astronaut might suffer on a long haul mission.

redplanetRED PLANET on the other hand is quite accurate in its operational portrayal of the mission, featuring everything from a spaceship constructed in earth orbit, a crew of 6, a Mars style cushioned surface landing and the design of the pressure (space) suits. But even then, the most interesting aspect of this film was the on-set brawl between stars Kilmer and Sizemore which almost stopped completion of the film, and which if had happened on a real life Mars excursion would have put the entire mission in similar peril.

Perhaps the two films that best capture the realities of space travel are 2001- A SPACE ODYSSEY and MOON, both of which are intensely realistic in their depiction of life in space. The use of predominantly white sets and silence in both these films emphasise the artificial environs and isolation space crews will experience in the lonely depths of space. This is one of the reasons astronauts are kept busy working and exercising in space, just to combat the tedium.

The other reason for all this activity is to keep their strength up, as muscles waste quickly in the absence of gravity. Both RED PLANET and 2001 include artificial gravity as a feature in their space-craft, and although no one at NASA seems to have a real life solution for this yet, this will be an important adaptation if we are to one day ‘live’ in space. Interestingly the next generation of space travel as depicted in Hollywood films set 50 years in the future like SUNSHINE, EVENT HORIZON and ALIEN all have artificial gravity; perhaps Hollywood knows something the rest of us don’t?

Hollywood is an industry that is very good at helping us ordinary mortals imagine what something special might be like, and these films do a fantastic job of helping us imagine life in space. For all their flaws, they are still worth watching if you are a sci-fi fan, a space enthusiast or even dream of joining the astronaut core.

But for those that just want to bypass reality and don’t mind their science mangled by a journey through hyperspace, Hollywood offers even more. Films like LOST IN SPACE, STAR TREK and STAR WARS, are of course pure fantasy, but all offer the film fan something special to think about.

Will robots, cyborgs and crazy looking aliens all be a normal part of life for the human space farer 1000 years from now? Will leaving Earth never to return be just one of those things you do? And will humans ever live on giant megacity style spacecraft that seem to wander aimlessly around in space waiting for the next combative encounter? The questions are a plenty, but the answers will only come when human endeavour takes us further than we have been before, to places we are yet to travel.

Congratulations to all involved in the Mars500 mission for their role in what history will one day record as humanity’s greatest journey.

Watch FiST Chat 47: Mission To Mars On Earth for more on the Mars-500 experiment.

Population 7 Billion: A Cause For Celebration?

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This week the UN’s population division announced the 7 billionth human has been born.

7 Billion Population

Now 7 billion is a BIG number by any terms but just how does a population of 7 billion humans compare to other species and more importantly what does the size of our population mean for our planet?

We might begin putting these sorts of numbers in perspective by ranking the human population against others with a little help from wikipedia.

By far and away the most populous species on the planet are bacteria with numbers in the vicinity of 4 quadrillion quadrillion (4×1030) easily outnumbering all other animal populations combined. In the oceans there are an estimated 500 trillion krill, and while that is still an impressive number, their biomass is only around 50% of that of humans.

chickensIf we then move onto larger beings there are an estimated 10 billion billion ants in the world- (who counted them all?), with a combined biomass of almost 10 times that of humans. And who would have thought there are more than 20 billion domestic chickens wandering around providing humans with a significant source of their daily nutritional requirements?

Interestingly but not surprisingly the top ten mammalian populations are held exclusively by humans and their domesticated friends. As modern civilisation has allowed human populations to expand well beyond those of subsistence level, the associated agricultural production of livestock has seen populations of cattle (1.4 billion) and sheep (1.1 billion) far exceed what would be expected in wild ecological systems. Likewise, domesticated pets like cats and dogs are estimated to have populations of around 500 million each, due to their close association with humans.

But it becomes a little more controversial as to which species is actually number one. Although there is no real way of knowing, there is an over-riding body of evidence that would suggest that humans might be third on this list after mice and rats, which although not domesticated strictly speaking, have a liking for human’s domesticated lifestyles.mice

By comparison populations of non- domesticated large mammals struggle to get into the tens of millions and although kangaroos are highly successful at 60 million- most wild mammal populations are in the single millions or lower due to human encroachment on their habitat. Make no mistake, that when you see the population sizes of large terrestrial mammals falling (500 000 elephants, 200 000 chimpanzees, 120 000 for all big cat species and 20 000 polar bears), the growing human population is directly responsible for their decline.

So when it comes to numerical superiority humans are right up there, and we probably should be celebrating our success. But rather the tone this week has been somewhat circumspect. In general there seems to be some concern with the size of our (over) population and the challenges we now face on a global scale. Not the least of which is providing on going food security, not for the 7 billion people alive today, but the 9 billion people expected to inhabit the planet by 2050.

Most experts seem to think that feeding 10 billion people is well within the capacity of modern agriculture. However the major problem will be changing the attitudes of first world societies towards food. There will have to be a radical shift in thinking across a range of issues if we are to achieve food security for the global population. And of course providing safe drinking water for all these people is just as important an issue.

Then there is the question of other vital resources. Raw materials now are being mined at an ever increasing rate to feed an increasingly wasteful consumer economy. If global growth was to continue to rely these principles it would take 1.5 earths within 30 years just to keep up the supply. Perhaps its time for the whole world to have a serious look at making recycling part of our lives?

Powering our modern lifestyles is also proving to be a challenge for the future. Fossil fuels might have seemed infinite 100 years ago, but we have now discovered that there are only finite ways to access them. This once inexpensive and easily produced source of energy is now becoming more and more complicated in its supply and its cost. solarpowerAdd the fact we are now endangering important ecosystems and prime agricultural land to access it, is just another reason to transition away from it to more efficient sources like nuclear, solar and geothermal.

So its no wonder the 7 billion celebration was muted- especially when the problems our species face are mainly of our own making. Yet, perhaps we should tackle these problems with a sense of optimism- overcoming them is represents a challenge that might finally unite all of humanity. As a species humans have notched some pretty impressive achievements along the journey. After all, it was our oversized brains that got us into this situation, and if we put the collective mental capacity of 7 billion people to the task, not only will we solve these problems but we might even make the world a better place.

Steve discusses this topic along with co-host Ben Warner in “FiST Chat” episode POPULATION: 7 BILLION.