Biodesign Projects

DNA Encoding Program

A quick sketch of a program that will allow users to encode messages into RNA codons.

What will be the impact of biological data storage if it becomes commoditised?

Biodesign Projects

Algae, People and Design


The term ‘algae’ represents a large range of photosynthetic organisms.

Seaweed is a type of algae, sometimes known as micro algae and generally live attached to rock or other hard organisms in coastal areas. It’s primary requirements are  seawater and light (for photosynthesis). The presence of algae in an ecosystem is imperative as seaweed removes undesired nutrients from water and is a natural filter.

Algae farming: Growing cyanobacteria ( a group of bacteria that obtain their energy through photosynthesis) and algae does not require arable land. Researchers say that algae could be 10 or even 100 times more productive than traditional bio energy feedstocks. Furthermore, algae fuel is now known to be an alternative to liquid fossil fuel.

Algae is a bioindicator of water pollution as they change and adapt in relation to water chemistry, an intelligent reaction to problems that eco systems and humans face. Certain algae species’ flourish in polluted water. Many blue green algae occur in nutrient poor water, while some grow well in organically polluted waters..

Stigeoclonium tenueis- heavily polluted water

Nitzschia palea- mildly polluted

Cocconeis + Chamaesiphon- unpolluted

Navicula Accomoda- presence of sewage and organic pollution (this species occurs in the most heavily polluted water

How do we percieve algae?


The presence of algae is perhaps often seen as negative; dirty water that is unclean to enter and is unhealthy.

Biodesign Projects

Acellular Slime Mould

Background information

  • Slime moulds are catagorised in two distantly related families: “cellular” and “acellular”.
  • Cellular slime moulds spend the majority of their life cycles as individual, single celled amoebas. Once they have exhausted the resources of their immediate environment the individual cells join together to form a slug which travels to fresh pastures before fruiting and dispersing spores.
  • Acellular slime moulds have a “plasmodium” stage in their life cycles. Plasmodium is made up of millions of nuclei which share a single, gigantic cell without any membranes to separate them.
  • Much of the research around slime moulds is focused on the acellular variety (usually Physarum polycephalum), as it is a much more unusual life form, with many unexpected properties. For the remainder of this research, the term slime mould is used to refer to acellular slime moulds.


  • Although it lacks a brain or a central nervous system, polycephalum is capable of performing complex behaviours such as finding the shortest path through a maze, solving computationally difficult puzzles and making decisions based on multiple objectives.
  • polycephalum is part of the Protista kingdom, which contains a variety of unicellular eukaryotes (an organism with a complex cell or cells) that do not fit into the other kingdoms.
  • They are where the world of cellular biology collides with the macroscopic world.

How we perceive them

  • Due to their unusual biological properties and ease of culture, the acellular slime mould Physarum polycephalum is a favourite amongst cell biologists.
  • More recently, due to the way it constructs networks, it has become the become a model organism for a variety of disciplines including behavioural ecologists, town planners, computer scientists and artists.

How it grows, how it nurtures itself

  • Life cycle diagram
  • Plasmodia of acellular slime moulds form a fan-like sheet at the front, followed by a network of interconnected veins through which cytoplasm flows.
  • Because it forms a network with several fronts, polycephalum can feed from multiple food sources simultaneously.
  • Under nutritional stress and when exposed to light, vegetative growth stops and the slime mould fruits, releasing male and female sexual myxamoebas into the environment.
  • The myxamoebas feed and divide, and when a male and female amoebas meet they fuse to form a binucleate cell, which develops into a plasmodium.
  • In the natural environment slime moulds feed on bacterium, fungi and detritus.
  • In labs they are cultured on moist filter paper, agar or rolled oats.
  • Their optimal diet consists of 2 parts protein to 1 part carbohydrates.
  • Plasmodium are self-repairing, and can regenerate when part of it is cut away.
  • Slime moulds grown from different inoculations are repellant to each other, but can merge if the environmental factors force them to.

How it lives, how it interacts with its surroundings

  • When a vein contacts a food source, biochemical oscillators give rise to propagating waves, redirecting cytoplasm to that vein. The vein becomes thicker at the expense of those which do not form a direct link between the two parts of the organism. This combination of positive and negative feedbacks allows the organism to connect food sources via the shortest path.
  • Slime mould leave a thick mat of non-living, extracellular slime behind their path. It uses this as an external memory to avoid areas where it has been before. Using this, it is capable of solving the U-shaped trap problem, a test of autonomous navigational ability used in robotics.
  • The slime mould is capable of using a hierarchy of rules, for example: it will crawl across extracellular slime if they detect the presence of food.
  • There is evidence that slime moulds also have an intracellular memory which allows them to anticipate periodic events. A slime mould will rhythmically reduce their speed of movement if they become attuned to a light flashing on and off – even once the light remains permanently off.
  • Slime moulds are capable of making intelligent decisions. When offered a choice between food sources of differing quality (concentration of oatmeal), it is capable of choosing the source with the highest concentration.
  • Plasmodia trade off risk against food quality, a food needs to be 5 times higher in concentration before the slime mould will forage in the light.
  • Speed of decision making affects the accuracy of those choices. Then stimulated to make a fast decision between two food sources of differing concentration by the presence of light, it was less likely to make the correct choice.
  • Slime moulds also alter their search pattern depending on the quality of food sources they are already exploiting. When consuming a high quality food source the plasmodia will perform an area-restricted search. When feeding from a low quality source it will move away from the source before sweeping the area for alternative food sources.
  • Plasmodia can distribute their biomass proportionally across multiple food sources of differing nutrient quality to receive an optimal diet.

What affects its health in positive and negative ways

  • The distribution of a slime mould’s biomass across an environment displays the organism’s relative comfort level in each location. By observing this, researchers have been able to isolate which factors encourage and inhibit the growth of a slime mould.
  • Attractive substances such as oats increase flow of cytoplasm to a location, repellant substances such as salt reduce it.
  • Low light levels and high humidity increase flow, high light levels and low humidity reduce it.

How it eventually dies

  • When the resources in the slime mould’s environment become exhausted, or it becomes too large to maintain itself the plasmodia diverts all its energy away from growth and into producing spores.
  • The spores spread out, leaving the slime mould to decompose.

Additional properties

  • Cytoplasm veins are conductive and can carry voltages high enough to power an LED without killing the slime mould.
  • Nano particles can be picked up by the plasmodia and transported along it’s veins.
  • Magnetic nanoparticles (barium hexaferrite crystalline nanoparticles) are bio-compatable with the slime mould. Magnetic fields can be used to deflect the path of magnetized slime moulds in order to control their path.
  • Plasmodia have been found to have memristive properties.
  • Because separate colonies of slime moulds repel one another, multiple inoculations on nutrient rich agar spread out and form voronoi diagrams where their boundaries meet. Voronois are materially effiecient – potentially load bearing structures.
  • This semi-self-repelling nature also allows physical Boolean logic gates to be made.
  • Physarum is photo-sensitive, and experimental data suggests it can tell the difference between red and blue light.
  • When a plasmodia’s vein is heated up to 40oC its resistance increases 1000 times, making it a biological thermic switch. In about 10 minutes the slime mould reforms and continues unharmed.
  • To produce biodiesel efficiently an organism requires a high concentration of lipids in their bodies, which is true of slime moulds. Because they produce biomass at a rate that exceeds algae, they could be an alternative biological factory for the fuel.

Its applications in the world

  • polycephalum can be used to model network formation in a biological system.
  • Network performance involves a trade-off between cost, transport efficiency and robustness.
  • Inspired a mathematical model “The Physarum Solver” which is able to find the shortest path between many points in a real world network, such as the Tokyo subway.
  • The slime mould’s ability to anticipate periodic events hints at the cellular origins of primitive intelligence.
  • The slime mould’s networking behaviours have been used to explore and model creative thinking.
  • People migrate towards sources of safe life and higher income. Physarum migrates into environmentally comfortable areas and towards sources of nutrients. Plasmodium have been used to model pathways of migration from Mexico into the USA.
  • Slime moulds have been used as biological sensors, using their aversion to light to steer a small hexapod robot. 
Biodesign Projects

Research into Coral and Algae:

When I started this project I looked into various micro-organisms ranging from slide mould to forms of fungi. I found myself particularly interested in ‘Algae’. The first thing I did was type  ‘Algae’ to Google and it gave me an array of definitions, wikipedia’s was the easiest for me to understand: a simple non- flowering, and typically aquatic plant part of a large assemblage that includes seaweeds and many single- celled forms. Algae is very popular, diverse and found all over the world, just from this initial research I wanted to explore more.

Algae is photosynthetic which means it releases oxygen because of this quality, the organism makes up a high percentage of the earths oxygen supply. This helps plants and marine life grow while also being many animals main food and oxygen source. Algae are single celled and  float on water, they absorb food through their cell walls. They can multiply and that’s how they can cover large surface areas.

Algae is a very large and there are many different groups. subgroups and forms of this organism. The two largest sub groups were red algae and green algae.  Green algae is most commonly land plants from marine and fresh waters. There are many various forms in this group such as Eugkenoza, Cecoza and Glaucopyta. Red Algae always inhabits marine environments and is multicellular.

This is a diagram which show’s the different groups of Algae

Morover, algae is not only common in sea and lakes but can even be found on animals (like turtles), it is essential to some underwater animals as it can provide shade to them when needed. Some forms of algae have high levels of unsaturated fatty acids, this is eaten by many types of fish. Fish oils contain omega three which is surrounded by algae, it is eaten by the animals and passed up the food chain

 Having lots of types of algae is good and healthy for the eco system, the ocean being one of the largest. Algae absorbs nutrients, ammonia and phosphorus as too many of these can be bad for the overall health of water. From this I wanted to focus on something that heavily depends on algae to survive, I looked into coral due to the fact it is necessary to our oceans eco system and how coral reefs face many threats.

coral bleaching
Diagram illustrating the effects of coral bleaching

Initially, I looked into the relationship that the algae and coral have. A healthy coral relies in the algae to survive, they depend on each other. Once the coral begins to get stressed to due ‘coral bleaching’ then the algae will leave the coral. The coral is then left bleached and vulnerable, without the algae it looses its food source, causing it to turn pal and more to susceptible diseases. The main causes of coral bleaching are:

  • Change in the ocean temperature– This is the number one cause for coral bleaching and it is due to climate change and the increased temperature.
  • Run off and pollution– storm generated precipitation can rapidly dilute ocean water and runoff can carry pollutants, these can bleach near shore corals.
  • Exposure to sunlight– when the temperatures are high, high solar irradiance contributes to bleaching in shallow water corals.
  • Extreme low tides– exposure to the air during extreme low tides can cause bleaching in shallow corals

In coral polyps there is a symbolic relation between the algae and the coral and this relation is called zooxanthellae. The coral provides the algae with a protected environment and the compounded needed for it to photosynthesise. This is described as a yellowish brown dinoflagellate in large numbers in the cytoplasm and many marine invertebrates, including coral polyps. This ‘zooexanthellene’ lives in the coral tissues and when coral becomes stressed the relationship is broken.

This image shows the ‘zooxanthellae’ in the coral

Finally,  E.chromi, this is an idea of based of synthetic biology which theres a colour indicator added They engineered bacteria into produce a variety of coloured pigments, visible to the naked eye. This can help detect diseases and hopes in the future to help warn people about excess pollution in the sky. I could relate this idea to coral bleaching, if the coral is showing signs of being stressed it could change colour and this could somehow be communicated to marine life and not harm the eco system.


Algae, Edible Culture, and Contemporary Design

The vast fields of deep sea grass and thick diffused fog of iridescent river microbes share a common ancestry – both of Familiae Eukarayota, or Algae, in a partnership going back 1,600 million years.

Human interaction with algae came after hundreds of million years of evolution, first introduced as edible seaweed to Chinese nobility around 2700BC – alongside the birth of the silk trade and the Pyramids of Giza.

Algae has been found in pre-Christian fabric dyes along the Mediterranean coast, and in medieval fertiliser along the Irish sea – with Victorians even finding art in leaves of seaweed, the first photo-book published in 1843 featuring cyanotypes of pressed algae samples collected around the Kent coast. Diatom Arrangement even became quite popular during the later 19th century, being the practise of arranging micron-sized algae into patterns under a microscope.HistoryofAlgae1


So from the fields of shallow water surrounding Yokohama Bay to the scrapbooks of Victorian housewives, algae has been found woven into a number of historical uses, cultural narratives and practises.

Algae is therefore safe from the public eye and will likely continue to be used within cuisine, fabrics – but the emerging talents of synthetic biology and design will be amongst the first to promote new uses for algae.

The field, however, suffers from an image issue – conceptual projects are too elitist and abstracted for the non-designer, attracting parody and mockery instead of provoking serious discussion. It is a disgrace to the synthetic biology industry that great ideas are hindered by public perception – both due to collective ignorance of the subject from the public, and the arrogance of the scientists and designers that work with synthetic biology.

Realistic design futures make them selves known in developed steps, rather than leaps of imagination – as William Gibson famously said of first-world development; “The future has already arrived, it’s just not evenly distributed yet”.





Syn Bio… On MARS?!

I’ve been really interested in Elon Musks mission to Mars idea that he spoke about just recently at one of Space X’s conferences. He has an in depth, ambitious plan to get us to Mars within the next 6 years… It’s totally mental, but also a lot sooner than the current 100 year plan that Nasa had predicted. It’s inspired me however, to look at our brief from a different perspective, and think about how to redefine peoples understanding of synthetic biology by using it to make living on Mars in the not so distant future an actual probability.

Its tricky, however, as I’m not a scientist, and don’t want to sound like I’m claiming to be. But I’ve looked into a couple of ways of integrating synbio into creating a ‘better’ living space on the currently uninhabitable climate of Mars. I’ve looked a lot into algae, and its many benefiting factors, and finding that it is the main reason Earth has oxygen in its atmosphere today all started from algae and similar bacteria millions of years ago. I firstly, looked into how we could try reconstructing that on Mars to eventually change its atmosphere to a hospitable and breathable environment. However it turns of that a lack of oxygen isn’t the only factor that makes Mars inhabitable, and going about terraforming Mars would take 1000’s of years… a good long term solution but something to leave to the professionals.

So after more research of other benefits of algae and a couple other types of helpful bacteria – and also a quick read of “The Martian”, which goes into amazing scientific depths of a man stranded and left to live on Mars – I’ve tried to think of other ways that synbio could be of use on a much smaller scale.  Currently I’m considering a couple routes; Could we start terraforming on smaller scales, just small parts of land to create biomes of good climate without the need for machines to create our atmospheres for us? This could lead down to designing algae tanks or photobioreactors to cultivate bacteria. Or instead of trying to purify the air, use it to purify the water extracted from Martian soil? Perhaps then just using algae, or cyanobacteria to act as fertilisers or ‘soil conditioners’ with Martian soil. Now as I OBVIOUSLY don’t have access to Martian soil or really any way of recreating it, it would mainly focus on what the best conditions would be for the specific plants one would need in small areas dedicated to growing crop. So could I design these areas for optimised plant growth? Or could I design a fertilising machine that uses genetically enhanced bacteria? Would that be for adapting to Mars atmosphere or for in biomes?

I need a push in the right direction with this project though. I’m wiling to follow a different microorganism if it would fit the narrative better, its just finding the right approach that is convincing. It’s a crazy narrative to follow, but I like it, and I think it could go some where fun and challenging. Also the fact that it is at first seen as an unrealistic approach, might make it a successful project for redefining people perspective of synthetic biology, and just how much of a change it could make… If a stranded astronaut can make potatoes on Mars – supposedly – why can’t we design a way of starting life on mars the right way, through bacteria?

Here are just some of the websites I’ve used in my research:




In the beginning…

Started diving into the world of fungi and mycelium…first things first: what does a fungi family look like? Knowing the basics about the material we’re working with will help along the way, as well as learning how it interacts with its environment and other organisms. This is Transactions on a micro and macro scale.Fungi Family Hunting for fungi in Roslin Glen