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Structure Programmable Biofactories in Industry




The Glucossification of lignocellulose offers the ability to support 70 billion humans on planet Earth with a lower eco-footprint than today.


























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Biofilms Kinkajou

The concept of biofilms introduces a new method of biological industrial processing. Single bacteria have long been used as biological chemical factories with specific end products: notably in alcoholic beverage production or baking. (One germ: one predetermined range of outputs).

With biofilms, where a biological industrial process involves a number of different steps or multiple desirable end products, a different microbe can be optimised to give maximum yield for each of the separate steps.

Probably the most obvious example in which humanity absolutely must achieve a success, lies in the production of biological molecules especially glucose from plant materials, notably lignocellulose. In science fiction we are quite familiar with the example of Trantor, the capital of the first Galactic Empire. It was reputed to have a population of 40 billion. The cities tunnelled into the ground up to a kilometre and extended out under the ocean floor. The burgeoning human population required the output of a dozen agricultural worlds to support it.

Dr Xxxxx has suggested that circumstances may well make our earth quite easily reach a population of up to 70 billion. The mechanism: humanity achieving successful life extension for its populations.

The key biological industrial process which would enable humanity to support such a population on this planet, critically with a smaller human footprint on the planet than we have today, is the extraction of glucose and other biological molecules from lignocellulose.

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Biofilms are critical to the process. One bacterial species can be selected for its enzymatic ability to break down lignocellulose strands. Another bacterium can be selected to specifically produce an entire range of biomolecules which would be required for human technological civilisation on this planet to continue. To maintain a technical civilisation, we need a range of biological feedstocks for our industrial processes, which individual microbes can be optimised to produce. Such specialisation allows better control. It also reduces the risk to the environment posed by the escape of clever biologicals.

If we are to stop the burgeoning human population from choking the planet, we need to become much more efficient in our agricultural production. Food production using plant products such as grains or fruits will be unable to support a human world drowning in flesh.

But there are more issues than simple bio- molecule production as well. In our Galactic Travelogue, we have the example of Loo Macklin’s birthplace: Cluria. Cluria is a world so polluted that the humans have encased themselves in transparent tunnels on the surface of the world, excluding the pollution and waste that they generate.

With clever biologicals, this future does not need to happen.

It becomes obvious to us in looking outside through our own windows, that life enables life. A form of waste from one organism or factory can become a food source for other organisms. Pollution can be broken down by the cycle of life. Materials are recycled. It is  the need for the processing of "industrial" quantities of waste that requires human intervention. Yes nature can “recycle”. But to process bulk waste quickly - requires fast and bulky solutions- usually in excess of  the capacity of “natural” cycle to cope with.

We exist in our infancy in using biological agents to assist us in controlling pollution and to enable recycling.

Smades TavernThe next example from science fiction is the example of Smade’s Tavern. Smade has set up his Tavern on an isolated planet. And yet strangely, the introduced biota shows little inclination to overrun the planet. This example is very interesting. It makes sense that it requires a web of life supporting organisms to create a sustainable functioning ecosphere. The deficiency of a critical component, such as nitrogen fixing bacteria could well limit plant growth and expansion. I personally have seen potted palm trees persist at the same stage of growth for years. The poor nutrient content of the potting mix essentially almost completely stifles plant growth. They survive, but they certainly do not thrive.


Where the ecosystem can support introduced species, much of our experience points the opposite way. In Australia, introduced rabbits destroyed millions of square kilometres of low treed mallee scrub in the Great Australian Bight. Now a scrub like desert covers much of this area. This is not a natural occurrence. At the turn of the century, Australians in these areas witnessed rabbit plagues 20 to 30 km wide, and up to one kilometre deep migrating across the landscape and devastating it to an extent that 100 years of time have not shown any signs of erasure. The desert existing in this part of Australia, is a recent event.

BlobThe Blob from science fiction is a stupid if awesome horror. If the thing would stop eating people, it is probably one of the greatest recycling tools we have ever discovered. If such an organism could be worked with safely, household rubbish and pollution would almost become a thing of the past on this planet.


We see the example of the chitin insects of Fenrille developing a sort of "insect biofilm". In this instance the communication biomolecules themselves synthesized naturally  by these insects are incredibly valuable to humans in extending life. The "insect biofilm" allows the insects to attain a form of intelligence.

The other example we talk about in our Galactic Travelogue is the “Green Brain”, an entity unlikely to ever be a reality I feel. While insects may indeed be able to culture and grow neurones and their supporting cells, bacteria and fungi are extremely likely to attack and destroy undefended eukaryotic mammalian cells. However it is quite possible that we may ourselves in the future be able to develop composite cell biofilms with the capacity to function together in some way.

Is interesting to consider that bacteria are in their own way as biologically complex as mammalian cells. What we call colonies, they may well call cities. And we’re coming to the realisation that bacteria may not just crowd together in the disorganised fashion dictated by explosive reproduction. They may in fact cohabit according to a complex DNA coded set of rules, allowing the interaction of a range of microbial inhabitants in a fashion to support substantial and complex bacterial cities.

So what images in Brisbane are conjured up by the word biofilms?

Taking a car across the ferry to South Stradbroke Island is one image. The crystal clear pristine waterways beckon. It is an experience to see how pure nature can really be.

On the technical note I think that the appearance of the crystal clear water probably relates more to the proximity of Deep Ocean to the island, than to lack of pollution. In shallow bays, sediment discolouration the water persists because it is not swept away. South Stradbroke exists very close indeed to the Pacific Ocean.

Cylinder Beach Stradbroke

I would suggest walking along some of the picturesque isolated beaches. I would also suggest staring at the dense star filled sky at night away from the village lights. We must never lose our sense of awe at the magnificence of our planet.

I think a more cogent example of biofilms can be seen simply on the city riverside walkways. These walkways  bypass Southbank and its gardens, mangroves and the botanical Gardens in the city areas, and many simple open pathways along the remainder of the river. Currently it is free to cross the river on the little red Hopper ferries. You can readily cross the river for a few dollars anywhere else in any case. The city Hopper ferries are promised to run every 10 minutes, pretty good for a city like Brisbane.

Clever new applications:

  • Altered medical treatments and processes for many diseases.
  • Recycling
  • Industrial Processing
  • Bio- molecule production
  • Lignocellulose Breakdown and Bio- Glucose Production: The most important breakthrough needed to enable the survival of the human bio-mass on the planet.



Other examples of books referring to this technology or variants

Greg Bear: “Blood Music”.

In this book human lymphocytes attain intelligence using DNA as coded memory. They explore their human habitat, grow to alter and optimise their habitat and then begin to explore the outside world – lymphocyte spaceships. The lymphocytes in effect form a eukaryotic biofilm.

Personally I think using DNA to code memory is like an accident waiting to happen . Perhaps a good Dr Who script beckons. Aliens trapped in another dimension communicate via DNA to escape their prison across the "Brane".
Virgil Blood Lymphocyte SigmaPsiVirgil Ulam


David Brin  : “Star Tide Rising”

Biofilms in this book are best represented by the Jophur. These aliens are in effect a composite of independently viable toruses, capable of combining to form a much larger , more powerful and more intelligent organism. Each torus performs a specialised function for the composite being. There are toruses with legs capable of running for ever. There are toruses which store information as memory wax. The memory wax can then be accessed to retrieve the memory. There are toruses that command. These change the nature of the peaceful beings, creating an aggressive and competitive new organism, but losing an aspect of their former “humanity”.
Tom Orley Terragens Agent SigmaPsiTom Orley Gillain Baskin SigmaPsiGillian Baskin
Hikahi Dolphin Spacer SigmaPsiHikahi 2IC Dolphin Spacer



Max Brooke: “World War Z”

Zombies could possibly be interpreted as a biofilm of “something”. They are capable of “life”. They move. They act. They are capable of changing their environment albeit in a simplistic way.
Zombie SigmaPsiZombie



Star Wars

In this movie series, Millicurians reside in and combine with all living biological life. They create a power or force which can be used for good or for evil. The "galactic Biofilm" - represented by "the Force" becomes a composite of plant and animal life and the Millicurians.



Alan Dean Foster: “Mid World”.

In this book the plant and animal life cooperate through a sense of united entity to create a single living organism encompassing a planet. Each sub component of the overall contributes something to the whole. The trees being the “They Who Keep” work by harvesting human neurones and integrating them into their structure, acquiring intelligence for the planet spanning life form. Beware universe – the child in green bunting. Here again the biofilm becomes a composite of plant and animal life.

FlinxTravellorPsi SigmaPsiFlinx Thranx SigmaPsiThranx


Julian May: “Orion Arm”.

Gene splicing allows beings to be built from composite of their own cells. A biofilm of sorts. These types of organisms do exist naturally – human chimeras in fact being relatively common. It is not unheard of for individual people to have normal cells as well as cells missing a chromosome in their constituent structure.

Helmut Icicle SigmaPsiHelmut Icicle



Thomas Harlan: “A Wasteland of Flint”.

Here the biofilm is a nano tech composite. It can analyse and copy any structure, subsuming even its memories and intelligence. It cannot form organic structures such as “fuel”. The book is somewhat disturbing in the insidious nature in which the nano tech subsumes the humans exploring the planet.
Captain Chu-sa Hadeishi SigmaPsiCaptain Chu-sa Hadeishi



Frank Herbert: “Dune”.

In this book, worms and their predecessors can act as composite lifeforms with disturbing properties and create the “Spice”.
Duncan Dune Warrior SigmaPsiDuncan Idaho



Charles Stross : “Saturn’s Children”.

I think this book comes closest to defining robotic life as a mechanical biofilm. The robots are built from mechanocytes, and are capable of sharing many aspects of themselves with others of their ilk. The mechanocytes reside in the marrow techne. They are sensitive to radiation and to damage. But they are incredibly robust, much more so than the organic structures of plant and animal life on earth. It allows the robots to colonise the solar system and to look further into space.
SexRobotFreya SigmaPsiFreya Nakamachi- 47



Joan Slonczewski: “Brain Plague”.

Biological entities form the Brain Coral which live within the ventricles and subarachnoid spaces of the human brain, creating cities, intelligence and able to communicate with their greater human host. They can take over the human host, destroying or subverting the body. They live at an accelerated pace of life and are capable of enhancing many human functions most particularly intelligence – making them valuable commodities in the world of the future.
Eleutherians Brain Citizen SigmaPsiChrys



Brian Stableford: Halcyon Drift.

The biofilm in this story is the coalescence of the alien “The Wind” and a human being. Each exists separately but within the same body. Each can affect the other, but both must work together for the benefit of the body. If you die, I will die also. “The Wind” is one alien with whom I have some sympathy and understanding.
Grainger and The Wind Starship PilotsSigmaPsiWind”