Synthetic Biology
My goal is to be able to design a synthetic bio project regarding quorn or corn within three weeks.
Contents
Definition of Syn bio
Definition from Synthetic Biology: Tools and Applications (2013) by Zhao Huimin "Synthetic biology is the design, construction, and characterization of improved or novel biological systems using engineering design principles"
Definition from Synthetic Biology: Industrial and Environmental Applications (2012) by Markus Schmidt: "Synthetic biology is the design and construction of biological devices and systems for useful purposes."
Definition from Synthetic Biology Engineering Research Center (SynBERC): Synthetic biology is the design and construction of new biological entities such as enzymes, genetic circuits, and cells or the redesign of existing biological systems.
Definition from ERAsynbio (EU's synthetic biology network): Synthetic Biology is the engineering of biology: the deliberate (re)design and construction of novel biological and biologically based systems to perform new functions for useful purposes, which draws on principles elucidated from biology and engineering.
- Polish geneticist said in 1974 Wacoaw Syzbalski: "Up to now we are working on the descriptive phase of molecular biology… but the real challenge will start when we enter the synthetic biology phase of research in our field. We will then devise new control elements and add these new modules to the existing genomes or build up wholly new genomes…. a field with unlimited expansion potential and hardly any limitations to building 'new better control circuits' and finally other' synthetic' organisms, like a 'new better mouse'.
- syn bio is sometimes confused with systems biology or metabolic engineering. the difference is that system biology forces more on the characterisation of complex interactions within biological systems using a more holistic perspective, so sys bio and syn bio are like two sides of the same code. metabolic engineering focuses on engineering of cellular metabolism to product a certain substance using recombinant dna tech. however metabollic engineering is limited to singe cells and to maximise the formation of specific product. the difference between that and synbio is that it deals with a biological system which could be anything from a genome, a cell, a tissue, and an ecosystem. synthetic biologists also address broader issues - and are not limited to recombinant dna technology.
- key tools for synbio include dna synthesis, construction of large size dna molecules, and bio-orthogonal systems such as the introduction of unnatural amino acids into proteins
various discursions
- The DNA can be cut with restriction enzymes to look for single nucleotide polymorphisms (SNPs) which can tell the identity of a person. This is how forensics scientists identify a person based on DNA evidence, and also how paternity can be determined (a child will have combination of SNPs from mom and dad) SNPs can also tell you if someone is prone to a certain genetic disease in some cases.
- DNA can be sequenced - you can get the exact base pair sequence. Again, this can tell you about the persons genetic make up... different versions of different genes they have, etc. In an experimental lab, it can verify that you are working with the DNA that you think you are.
- DNA can be put through chromation immunoprecipitation assays (ChIP) In this test, you are looking for a protein that bind to a particular sequence of DNA. This is often use to determine transcription factor - promoter interactions...
- you can cut the DNA with a restriction enzyme and run it through an electrophoresis chamber
- you could put into a plasmid gene and transfer it to a bacteria
Fish forensics
To identify a piece of fish, AFT staff slice off a tiny sample from a fillet, heat it up to break down the tissue and open up its cells, and spin it in a centrifuge to extract the DNA. They put this genetic material through a technique that uses polymerase chain reactions (PCR) to produce many copies of a particular DNA segments. By amplifying just a few different genes—most often, the COI gene—researchers can readily distinguish similar-looking pieces of fish and determine their species.
Using water in mouth to flush out excess urea (turtles urinate through their mouth, solution for kidney patients?)
Urinating Through Your Mouth Is Great. Ask This Turtle. - See more at: http://inkfish.fieldofscience.com/2012/10/urinating-through-your-mouth-is-great.html#sthash.8lKGOL7k.dpuf http://inkfish.fieldofscience.com/2012/10/urinating-through-your-mouth-is-great.html
Ip writes in the Journal of Experimental Biology that turtles on dry land dunked their heads in water for 20 to 100 minutes at a time. While submerged, they repeatedly "rinsed" their mouths with water while rhythmically pulsing their throats. He discovered that this motion simultaneously pulled oxygen out of the water, so the turtles could keep breathing, and expelled urea into it.
Looking at the turtle's DNA, the researchers found what looked like a gene for a urea transporter, a protein that carries urea molecules across membranes. The gene was active in the turtle's mouth and the gill-like BVPs, but not—as it would be in humans or almost any other vertebrate animal—in the kidneys.
Ip thinks the Chinese soft-shelled turtle's strategy is not, unlike most cases of misplaced urine, an accident. He notes that P. sinensis and other soft-shelled turtles often live in salty marshes and swamps, or even in the sea. If they excreted urea in the usual way, they would need to continuously drink the water around them to make urine. But like human castaways in the ocean, the turtles would be ill-advised to drink this water; their kidneys can't handle that much salt. So instead, P. sinensis—perhaps along with the other soft-shelled turtles—sends urea back toward its mouth after filtering it from its blood. To dispose of the urea, the turtle only has to rinse its mouth with water, not drink it.
Chinese soft-shelled turtles aren't the only animals that know the taste of urea. Cows and other ruminant animals excrete some urea into their saliva. Their reasons are quite different: they use nitrogen in urea to feed the friendly bacteria that live in their guts and help them digest plant matter. By swallowing their urea-carrying saliva, cows send it to their stomach and keep their microbes alive.
You may find this trick unappealing, but to Ip it's inspirational. Hypothetically, he says, doctors could one day treat patients who have kidney failure by turning on genes for urea excretion in their mouths, just as these genes are turned on in turtles. "Urea excretion can still occur through rinsing the mouth with water, just like the soft-shelled turtle," he says, "without having to go through blood dialysis." Then we'll be able to ask them just how great it is. - See more at: http://inkfish.fieldofscience.com/2012/10/urinating-through-your-mouth-is-great.html#sthash.8lKGOL7k.dpuf
Apples which do not brown
To scientifically breed Arctic apples, Okanagan Specialty Fruits’ science team turns down the expression of the apple PPO genes in a process called gene silencing, which utilizes low-PPO genes from other apples. Gene silencing is a natural process that all plants (and animals too) use to control expression of their genes. This apple-to-apple transformation is aided by time-proven biotechnology tools. In the end, Arctic apples produce too little PPO to brown. (For an even more detailed description of Arctic apple science, visit the OSF website.) No frankenfood here, folks – just apples, now with suppressed PPO to stop enzymatic browning. http://www.arcticapples.com/arctic-apples-story/how-we-keep-apples-from-turning-brown
Pigeon which poops soap
More notes for later
- “THE GALLERY SPACE IS NOT A NEUTRAL CONTAINER, BUT A HISTORICAL CONTRUCT”
- Demo or die - 'Demo or Die' is a dogma. The belief that technical prototyping is the only way of developing an idea quickly becomes a problem when it prevents designers from engaging with technologies beyond their level of ability, budget or means. The result of this dogma for people without the luxury of a lab will always be small scale, craft-like objects: a form of digital craft. There's nothing wrong with this, but sometimes we need to turn our attention to problems and ideas that are bigger and more complex than we can handle individually or make ourselves, these skills are important too.
- Unlike many other areas of engineering, biology is incredibly non-linear.
- food which play with my cutlery and create hyper-sensations in my mouth - but are those things actually edible and palatable, or is it just an exercise in making unliving stuff move?
- http://fandomania.com/defining-the-genre-utopia-and-dystopia/
- http://en.wikipedia.org/wiki/The_Man_in_the_White_Suit
- http://www.leverhulme.ac.uk/funding/grant_schemes.cfm
- Circular Walks Around Rowley Hall - Andrew Lanyon
- WHy not use wood panelling on everything - There is a part of the story missing. Real wood paneling was expensive and a sign of status. The look became unfashionable because many electronic and furniture manufacturers moved away from real wood veneer toward cheaper wood-looking laminates made of particle board cores and paper, vinyl, or resin/paper top layer combinations (think today's laminate flooring). These laminates could be processed in mass production lines and resulted in everything having a "wooden" look: Cheap TV's, Sound speakers, IKEA furniture, the inside of mobile homes, kitchen cabinets. This trend not only "cheapened" the wood look, but it also gave it a low quality reputation since many of those cheap laminates peeled off or ripped with heavy use. Thus the move away from the wood look to "expensive looking" black plastic.
- How kale may not be the answer - http://mobile.nytimes.com/blogs/opinionator/2014/01/01/kale-juicing-trouble-ahead/?_r=0
- “In my early twenties, I felt that my life could be one big experiment, and in my mid-twenties I am coming to terms with the fact that no, my life is actually my life,”
- A modern version is known as the "Sheffield rack" or "Sheffield stand" after the city of Sheffield in England where these were pioneered.[7] These consist of a thick metal bar or tube bent into the shape of a square arch. The top part is about level with the top bar of the bicycle frame, and thus supports the bicycle and allows the frame to be secured. The origin of the racks was when the frugal citizens of Sheffield had to decide what to do with some old gas piping. Local cyclists suggested the cycle rack idea and two simple bends later, and a little concrete in the ground, the rack was born. At the time this was a revolution in a world of 'single-point holders' that bent wheels and offered little lockability for frames. A version of this design feature a second, lower horizontal bar to support smaller bikes (this version is also known as “A stand”), and are coated to reduce their surface hardness and to not scratch the bike's paintwork.
- As you know, ‘experimental’ can live on a fine line between being a true artist and
simply using it as an excuse to avoid the difficulties of plotting a work.
- Many people respond to the violent destruction of books and libraries with deep emotion. The sadness and fear in eyewitness accounts convey a sense that the destruction of texts signifies not only the immediate breakdown of order and peace but also a compromised future (…)
Popular historian Barbara Tuchman's 1980 address at the library of congress describes the humanist attitude towards books: "Books are the carriers of civilization. Without books, history of silent, literature dumb, science crippled, thought and speculation at a standstill. Without books, the development of civilization would have been impossible. They are engines of change, windows on the world, and (as a poet as said) 'lighthouses erected in the sea of time'. They are companions, teachers, magicians, bankers of the treasures of the mind. Books are humanity in print" (Tuchman 1980, 13). This notion is a cornerstone of twentieth-century humanism. The well-being and future of people is linked with the well-being and future of books and libraries. Like an article of faith, Tuchman's words have emotional and rational resonance. The angst in humanists' accounts of the destruction of libraries carries a sense of personal trauma akin to the accounts of the destruction of groups of people (especially of children). Books, like children, are objects of affection, vessels for society's hope and aspirations, links between past and future, and barriers to morality….
- Microbes in air - Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches.
