cagapakis

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May 7, 2010
I've been busily rubbing all sorts of things on bacterial growth plates after all the great suggestions I got yesterday. I want to present the data from the first big experiment suggested by JerryM, who wondered what kind of bacteria would be present on my hands immediately after washing them and…
May 6, 2010
Commenter JohnV asked me whether I had let any of my silkworms crawl on an LB plate (what microbiologists use to grow colonies of bacteria) to see what kind of bacteria is living on them in case I ever suffer from catastrophic experiment contamination. I hadn't thought of what kind of bacteria…
May 5, 2010
My semester in MIT's course on Documenting Science Through Video and New Media has drawn to a close. I've had a wonderful time and learned a lot about how films and science are constructed by different people in different times for different reasons. Most of all I've learned about how challenging…
May 4, 2010
So I had this great post planned about the Boston aquapocalypse but by the time I managed to get some water samples to the lab they had started heavily chlorinating the water and no bacteria were left! Since negative results don't make for good blog posts, please enjoy this video of my silkworms…
April 29, 2010
I got the chance to attend a panel discussion about science and the media presented by the UK-based charity Sense About Science. The audience was primarily scientists, many of whom were angry about how science is presented in the media: the outlandish claims, the hype, presenting "both sides" of…
April 27, 2010
Silks are incredible protein fibers produced by many different species of insects. Besides their use in making versatile textiles, silks are currently used in many different medical and engineering applications, from sutures to tissue engineering scaffolds to flexible electrode brain implants.…
April 22, 2010
Many people in synthetic biology, including myself and much of my lab, are working on using biology to make things more efficiently, renewably, and sustainably. Being able to make plastic replacing biomaterials, chemicals, medicines, and fuels in living cells from renewable resources (especially in…
April 21, 2010
By Patrick of Hydrocalypse Industries!
April 20, 2010
Light interacts with and controls biological systems in diverse and fascinating ways. Our eyes are made up of thousands of cells that respond to light, sending signals to our brain as light in different colors and shapes moves across them. Photosynthetic cells are full of receptors that can sense…
April 17, 2010
New in vitro fertilization technology is making it possible for someone to have two moms--one that provides the genome in the nucleus of the cell, and one that provides the rest of the egg cell, including the mitochondria. Since all mitochondria are passed down from the mother in the egg (sperm are…
April 14, 2010
As you can probably imagine, there are a lot of very interesting things that pop up when you have a google alert for "synthetic biology." Here is today's special find: a short dubstep song about synthetic biology by Dysoniq, featuring a voice talking about computer chips for your brain from this…
April 12, 2010
I got a lot of interesting responses to my post about DIYbio and how modeling innovation in biotech on computer hacker culture may lead to a science that is less "democratized" than what is being proposed. My friend Adam pointed me to Jaron Lanier's work criticizing the "open" and "free" culture…
April 10, 2010
My two great thesis project loves are hydrogen and symbiosis, and as such, the recent news of a multicellular organism that lives in a completely oxygen free environment and gets its energy from hydrogenosomes instead of mitochondria is totally fascinating. Hydrogenosomes are organelles that are…
April 7, 2010
An interesting paper in BioEssays last month looks at the potential future of xenobiology, totally orthologous biological systems made out of synthetic nucleotide and amino acid bases, new cells that use XNA instead of DNA. The author, Markus Schmidt, argues that while the design of such systems…
April 6, 2010
Last week's issue of Nature focused on the progress (or lack thereof) in genomics and related fields since the Human Genome Project (HGP) was completed ten years ago. In many ways, the era of genomics has yet to fulfill many of the promises made twenty years ago, but the investment in science and…
March 31, 2010
Because of my recent interest in autonomous, biologically inspired robots, my friend Tami sent me some fascinating links about designs and concepts for future flesh eating robots. From New Scientist, furniture that captures vermin and uses the biomass to power fuel cells that run small electronics…
March 29, 2010
Another Hydrocalypse Industries original production, the Beard-ome presents imaginary work on the genomics of the beard. What's lying beneath your beard?
March 25, 2010
Cellularity is a new project by James King, a speculative designer working on biotechnology and interaction design. The project focuses on the potential future of smart pharmaceuticals, drug molecules surrounded by membranes that over time as technology advances may come to more and more closely…
March 24, 2010
Happy Ada Lovelace Day! Today we blog to celebrate women in technology and science and remember Ada Lovelace, the woman considered to have written the world's first computer program back in the 1840's. So to celebrate, here's a clip of an interview with Rita Levi-Montalcini, one of my favorite…
March 23, 2010
I read R.C. Lewontin's Biology as Ideology: The Doctrine of DNA over the weekend and was struck in particular by one line in his wonderful diatribe against biological determinism and reductionism: "Intellectuals in their self-flattering wish-fulfillment say that knowledge is power, but the truth…
March 17, 2010
Synthetic biology deliberately equates genetic networks to electronic circuits, cells to machines, organisms to factories. In synthetic biology, every living can be thought of as a cyborg, a living machine that can be manipulated, changed to meet our needs, parts swapped in and out like a computer…
March 13, 2010
Carboxysomes are small compartments inside photosynthetic bacteria where the machinery for capturing carbon dioxide is concentrated. You can see carboxysomes and their characteristic virus-like shape when you look at slices of these bacteria under an electron microscope: Until recently, no one had…
March 11, 2010
The fight over genetically modified foods, whether they're safe, healthy, good for the environment, or just plain "unnatural," has been going on for a long time now. Most people in the scientific community agree that genetic modification in general is a good thing, able to create crops that need…
March 10, 2010
Animal cells are made up of many smaller membrane-bound compartments called organelles that perform highly specialized functions necessary for life. Incredibly, several of these organelles have been shown to be evolutionarily related to free-living bacteria, captured and incorporated inside a…
March 4, 2010
My paper, "Insulation of a synthetic hydrogen metabolism circuit in bacteria" just came out in the Journal of Biological Engineering! And it's open access! We designed a metabolic circuit in bacteria that produces hydrogen (a potentially useful fuel) from natural precursors in the cell. The…
February 28, 2010
My labmates and I love Lady Gaga. Like, love love love. Enough to make a parody fan video of Bad Romance. It is my pleasure to present to you "Lab Romance", a production of Hydrocalypse Industries. Enjoy! Lyrics after the jump! ø⸨°º¤ø⸸âø¤º°¨¸âø¤º°¨ ¨°º¤øâ¸LADYâø¤º…
February 26, 2010
Some of the responses to my post about synthetically expanding the genetic code have highlighted some of the weaknesses in my argument about the safety of using a different genetic code. Namely, that "life finds a way", that we can't really ever know for sure what will happen when we release a…
February 19, 2010
Here's my first little editing project for my documentary film class. A day in the lab, but much much faster paced.
February 18, 2010
Almost every living thing shares an identical genetic code, with three nucleic acids in an RNA sequence coding for a single amino acid in the translated protein sequence. While there are 64 three-letter RNA sequences, there are only 20 amino acids and degeneracy in the code allows some amino acids…
February 15, 2010
The future potential of synthetic biology is usually discussed in terms of applications in fields like medicine, food science, and the environment. Genetically engineered life forms are being designed to make medicines cheaply, to target tumor cells, to make more nutritious food, or to make…