This innovative centrifuge that has been designed for Reading Biotech. What we are interested in is that it is simple, light, robust and portable. http://www.ncbe.reading.ac.uk/ncbe/materials/dna/microcentrifuge.html

It was designed by Millennium Products (http://www.ncbe.reading.ac.uk/NCBE/MILLENNIUM/centrifuge.html)

microcentrifuge is specifically designed for school use to give students and pupils access to ‘leading-edge’ biotechnology work. Several mains-operated microcentrifuges are commercially available but are designed for research level work. These typically cost £500+ and are beyond the needs and budgets of most schools. This microcentrifuge is designed and manufactured to sell for approximately £100, and has been developed by Professor John Cave of the Technology Enhancement Programme, and Middlesex University with help from Science and Plants for Schools and the NCBE.

Key features of the design

The centrifuge is simple, robust and has been thoroughly tested to ensure that it is safe. The centrifuge works at safe low voltages and – uniquely – can be powered from standard power supply units, batteries or a solar panel array. This makes the equipment suitable for the classroom or for field work. It also makes the equipment very suitable for developing countries. With batteries, it has a single speed of 6,670 rpm (2,236 g), but with a suitable mains adaptor a range of speeds up to 13,000 rpm (8,494 g) is possible.

A challenge to existing conventions

The equipment challenges several basic conventions. Most equipment is mains powered; the centrifuge works from just 6-12 volts . This invites a choice of power supplies such as batteries or even solar power. The equipment also challenges product design conventions for educational equipment by effectively ‘recycling’ or placing into an unintended context components and materials normally used in other applications. The centrifuge motor, for example, is a low-cost automobile unit; the centrifuge case is machined from high pressure mains water pipe and the motor housing is moulded from rubber normally used for acoustic damping in loudspeaker systems.

The equipment also uses innovative design principles. The microcentrifuge has a safety interlock consisting of just three extended screws. These complete the motor circuit via the metal lid when all are fastened down. They cannot then be unscrewed quickly enough to remove the lid before the motor has stopped turning.

Environmental considerations

The centrifuge uses fewer materials and processes in manufacture because of simplified design. Also, because the equipment is potentially solar powered, ‘conventional’ energy consumption can be zero; more importantly, perhaps, as science equipment for schools it carries an implicit message for students that pupils that important processes can be carried out using renewable energy.

The centrifuge from NCBE

Anyway it definitely is the year of DIYBio….. for me and at least 20 or so people around the world. In no order (off the top of my head) here are some of the people I have talked to around DIYBio

• Andy Gracie(UK)
• Marc Dusselier(CH)
• Yashas Shety(IN)
• Cathal Garvey (IE)
• Mac Cowell (US)
• Jason Bobe(US)
• Asa Calow(UK)
• Hwa Young(UK)
• Lisa Thalheim(UK)
• Bryan Bishop (US)
• Denisa Kera (CZ/SI)
• The guys at HONF Indonesia(Akbar, Venza and Togar)
• Tito(US)
• Meridith(US)
• Helen Bullard(UK)
• Anna Dumitriu(UK)
• tbc

Should you be on the list? Probably we haven’t had a long talk yet.

Did I get your geotag wrong? let me know, plus a link.

Dexy.it is the tool she has developed.

It may also be used in Literate Programming.

• cellcraft http://www.cellcraftgame.com/

This is an educational game that introduces people to a simplified idea of the components and processes that occur inside a cell, that is producing proteins, finding glucose, finding nucleotides and repelling infection. The conce3pts are ok, though the cell is a strange hybrid that doesn’t occur in nature.

• phylo http://phylo.cs.mcgill.ca/eng/play.html

An primary sequence alignment game where the idea is to beat the computer generated scores for similarity between different sequences.

• fold.it http://fold.it/portal/

A 3d protein folding game, in which humans try to improve the computer generated 3d structure(based upon the primary structure of amino acids)

• eterna http://eterna.cmu.edu/

a 2d rna folding game, in which humans try to generated a 2d structure from the bases of rna that match certain contraints. The idea is that the best will be printed in real life to see if it has novel functionalities.

What other biological based games have you seen?

“The Future We Deserve is a new book project about collaboratively creating the future we deserve. We will be working together at internet scale on internet time to brainstorm and barnstorm our way towards an image of a world we all believe in, a world of fairness, collaboration and living within a harmonious balance with nature. The book is open to all contributions — essays about technology, politics, working examples of better ways and fantastic ideas which just need to get done.”

Re-envisioning our relationship with Micro-Organisms

(and a lot more questions to answer)

Humans are topologically donuts, bacteria live on the surface, human cells on the inside. We are dwarfed by the number of genes that are in these bacteria. At last estimation there are only 23000 genes encoded in our genome (doi:10.1186/1471-2105-7-327) and up to 9 million of bacterial origin (doi:/10.1371/journal.pone.0006074). From this we need to consider the fact that this bacterial population forms a chronically understudied extrahuman organ.

Are we going to discover that there is a deep bacterial culture basis to human culture, that some cultural norms actually support a specific community of bacteria? We already recognise that fermentation outside the body has had a profound effect on what we as humans can eat or metabolize(coffee, cheese, kim cha etc). Now we have to recognise that this fermentation dosen’t stop on the outside of our body, it continues, as bacteria provide essential nutrients to us. Might there be communal rituals that are about keeping the ‘good culture’ alive in the community? When explorers introduce pathogens into a ‘naïve population’ what is really being lost? If there is a move away from the traditional foodstuffs, are we losing more than a human culture?

The adage ‘you are what you eat’ makes more sense when changing a diet could change suceptibility to modern diseases such as diabetes(doi:10.1371/journal.pone.0009085), Iritable Bowl Syndrome (doi:10.1371/journal.pone.0010507) by modifying our gut bacterial composition. The pectins in apple fruit skins has been shown to favour friendly bacteria within the gut (doi:10.1016/j.anaerobe.2010.03.005) and obesity (doi:10.1038/4441022a). As a last resort, colonic gut bacteria have been transplanted from a healthy person to cure a patient suffering from Clostridium difficile diarrhoea.

What will this mean for the Future We Deserve?

We hypothesis that there is a lot more going on in human culture that meets the eye. If we are carriers of ‘good’ as well as ‘bad’ bacteria, what does this add to human-human interactions, such as the rituals and customs of greeting? Are differences between cultures reflected in our microflora?

Can we have strategies that minimise the unintended evolution of bacterial pathogens by reducing the use of antibiotics? Can we investigate using other more specific technologies such as phage (a bacterial virus) therapy to knock out specific ‘bad’ bacteria such as C. difficile? In a wider context, does shared bacterial communities provide a method by which members are alike?

Can we ‘know our bacteria’ and gain guides on what foodstuffs we should be eating to maintain health? Can we envisage a Personalised Probiotics, that is not another mass produced commodity, or a ‘lite’ version of what actually works.

Lots of questions to answer, but that is part of the Future We Deserve, a culture that understands how it operates, where even the ‘lowly’ bacteria has a place, and not just as a causation of disease.

One of the great things about making the maker faire in Uk each year was catching up with Joris Peels. He speaks his mind, and this is refreshing. Formetrly of Shapeways (and not sure what hes hatching now), we have had a few discussions about what would be usefull for DIYBio.

Basically, how do we DIYBios make this a legitimate pastime, or pursuit, or calling. I welcome some regulation, but can currently see, that by not running a business, regulations do not necessarily apply, as most are dedicated to regulating WORKPLACE not homes.

At the moment I can’t see any regulations that apply, as we are not working with genetically modified organsisms, and keeping to type 1 (harmless) organisms. It does get interesting when people want to do GE in the garage. Next year the Biological agents and Genetically modified Organisms(Contained use) 2011 regulation comes into to force. This may impact on the iGem teams if they are working with organism new to the labs they are working in.

The problem with this hole in regulation I see, is basically, if not regulated to an extent, DIYBio may become illegal due to biosafety concerns.

A brief set of rules that I am working by

1) don’t bring persistant poisons into the house, look for the safest way of doing something, not the fastest. This is not much different to what is done with electronics in the house. If you want to etch using the ferric chloride way, you are left with a persistent poison. There are alternatives (http://hackaday.com/2008/07/28/how-to-etch-a-single-sided-pcb/)

MSDS tells you what poisons are, and their actions. there are many things in the laboratory that are incompatable with home labs. Ethidium Bromide comes to mind, its used to stain DNA, but now there are much safer alternatives. They may seem more expensive, but when you take into account waste disposal, i’d say they are much cheaper.

2) dont work with pathogens, its not worth it.

It does supprise me when people want to culture pathogens without the proper safety equiptment and risk analysis. There are so many other things to explore, like fermentation of beer, making yogurt, sourdough making, cheese making, that are all much more worthy of study and tasty.

3) cleaning hands before and after handling microbes. I have used bathrooms as a easy DIYBio lab for culturing glowing bacteria from seafood (see http://letters.cunningprojects.com/?p=97)

4) minimise waste, think about using slightly more expensive glassware than disposable plasticware

5) have a decontamination strategy, bleach and rinse

6) be very carefull about mixing strong chemicals, many are not compatible. (I would like to get a list of these)

DIY Bio.

This kind of science has at its base many of the concepts of signal processing.
Through mixing a known and unknown signal we can do some mathamatical operations of it.  Basically a transduction of a signal outside of us and our understanding (For an example see optics)
We need to separate the different ideas

1) citizen science = a citizen setting a science question and working out how to answer it
2) crowd sourcing = a scientist setting a question and getting everyone to participate. (big science framework)

What other types of science are there?

Harry Erwin talking about the types of behaviours he is modelling in silico

Last week I attended the second day of the Conference on Natural Computing and Intelligent Robotics at Sunderland University. This meeting was organised by NCAF (the Natural Computing Applications Forum)  meeting hosted by the Hybrid Intelligent Systems group at Sunderland.

An Approach to Developing a Library of Voltage-gated Channels by Harry Erwin (University of Sunderland).

This paper was a demonstration of the ability of a neuroscience-engineering collaboration to unravelling a complex process, in this case how sound is processed in the inferior collicular centre. The computational modeling arose out of the need to discover how the nerves in the IC worked. His group is using computational models to mimic the responses of four populations of nerve cells believed to be important in hearing in the IC.  Although not conversent with the algebra of the voltage-gated channels, I was interested in the explanatory potential of the models. One of the nice advantages over previous modelling of these channels was to anchor the models to DNA sequence terminology, thus providing a way to verify the in silico models in vivo. This would be by using genetic labeling technologies such as fluorescent proteins(see related articles), however it would only tell of the presence of the channel, not the activity.  This still needs to be addressed. His models provide predictions that can be checked in vitro, and give the engineers ideas of how to replicate hearing in robots. The insight that there is more than one behaviour in neurons in the IC, means that just using one type in robotic hearing is limiting.

From this and the other talks of the day, it is apparent that processing sound is computational intensive, having four populations of neurons that respond to different components of the sound means that immediate the processing is decreased. Each neuron ‘tags’ an input with sound, or vowel or consonant.

So what are scientists doing to reduce the amount of comutation needed? They look at simpler organisms, with smaller brains, to see if there are physical or neuronal structures that reduce the amount of computation needed. Lizards and Bats are being used for their use of sound in insect capture and object avoidance.

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