January 2010
4 posts
Oscillator is Moving!
I’m super excited to be moving Oscillator over to ScienceBlogs! Make sure to update your bookmarks and visit me over at http://scienceblogs.com/oscillator!
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"Synthetic" Biology and Evolution by Symbiosis
I like using synthetic to mean “working together”, in “real” synthetic biology as bringing together (synthesizing) a lot of components from different living things in order to create a unique whole, and in “natural” biology in terms of how every living thing must live together with others in communities made up of complex interdependent relationships....
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Synthetic Sources of Natural Rubber
Rubber can be made chemically from fossil fuels, but natural rubber from tropical trees is still the best source, and in many cases the only usable one (car tires need a lot of natural rubber for the right combination of strength and elasticity). Besides being difficult to grow and relatively inefficient, rubber trees are also facing a fungal plague that could potentially wipe out natural rubber...
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Jonah Lehrer on Failure
A great article about failure and science by Jonah Lehrer in Wired, Accept Defeat: The Neuroscience of Screwing Up. I will quote the part about the work of Kevin Dunbar studying how scientists work in their “natural environment” at length because it is awesome:
Science is a deeply frustrating pursuit. Although the researchers were mostly using established techniques, more than 50...
December 2009
14 posts
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2009 Year in Review
2009 was a big year for synthetic biology in the academic press. Several journals had special issues devoted entirely to the topic, most recently Nature Biotechnology, but also Molecular BioSystems, The Journal of the Royal Society Interface, Systems and Synthetic Biology, and EMBO Reports with excellent research articles, reviews, and fascinating commentaries on economic, ethical, and social...
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The Top 100 Science Lecture Videos →
For people with lots of time on their hands, or a relaxing winter vacation coming up, the top 100 Science Lecture Videos from News Junkie Post, including Richard Dawkins, Kary Mullis, Steven Chu, Craig Venter, Stephen Hawking, E.O. Wilson, and a whole lot of other good stuff!
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What's in a name?
Synthetic biology has been used to describe many scientific activities for the past hundred years, and is still far from a concrete definition. Nature biotechnology asked 20 experts in the field how they define synthetic biology, leading to a great article that highlights many of the different pursuits of synthetic biology researchers as well as the common emphasis on engineering principles....
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“If biological engineering were aviation, it would be at the birdman stage: some...”
– Unbottling the genes, editorial from a special issue of Nature Biotechnology on synthetic biology
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Evolution, ecology and the engineered organism
Synthetic biology is fascinating and scary because of evolution. Evolution leads to the incredible diversity of biological systems that synthetic biology can draw from to create new designs, and evolution can be used in the lab to optimize synthetic biology pathways and make them better. However, because cells evolve and interact with the environment, synthetic biology is scary—what will...
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Cribsheet for Synthetic Biology
SEED magazine is one of my favorite resources for science news. They always have great articles, interesting perspectives, beautiful design, and useful content. Each issue has really fun pull-outable “cribsheets” about different trendy science topics, now available online as “downloadable tool[s] for living in the 21st century.” I’ve had the synthetic biology...
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“Are these microchips really behaving like neurons? Or has the simulation taken a...”
– Reverse-Engineering : The Frontal Cortex
November 2009
33 posts
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“As president, I believe that robotics can inspire young people to pursue science...”
– Barack Obama
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Algae Batteries! →
Cellulose is an amazingly versatile molecule, it helps plants and algae store energy, it feeds animals of all shapes and sizes, it’s the main ingredient in paper, it’s being used to make biofuels, and apparently it can also hold an electrical charge, essentially making a tiny, flexible, biodegradable battery. Different plants and species of algae have cellulose with different...
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“Adding decimal points to our irrationality doesn’t change much.”
– Seth’s Blog: The amateur scientist (that’s us)
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Biomaterials Insight
There’s a neat set of articles in this week’s issue of Nature on biomaterials. From the editorial:
Biomaterials research has come of age. Since antiquity, humans have been taking whatever substances are at hand — natural materials, glass, metals or polymers — and using them to replace body parts that have been damaged by disease or injury. But it is only recently, with the advent of...
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My Favorite German Human-Robots
via 3quarksdaily
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Electronic Noses
Biomimetic electronic noses are designed to mimic the olfactory system of mammals, with receptors that respond to certain chemicals, sending an electronic signal to a computer that can integrate the responses in order to identify the odorant. These systems are useful in industrial food preparation, where contamination by microorganisms must be detected as soon as possible. A fascinating new...
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Biology is Technology
Rob Carlson’s forthcoming book (<- Amazon link for pre-order), Biology is Technology: The Promise, Peril, and New Business of Engineering Life now has a blog with the first chapter posted online! It’s fascinating so far, I’m really looking forward to reading the rest!
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Plasmid Purification Technology
Purification of plasmids, circular pieces of DNA that replicate independently from the chromosome and can be engineered to carry and express any desired gene sequence, is a fundamental technique of synthetic biology and something that we take for granted in our lab. We use commercially available (and relatively expensive) kits that have been optimized to get a lot of DNA out of bacterial cells...
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“The bioartist as a creative prosthetic tissue in the societal fabric of the...”
– The Bioartist: Jester at the technoscience court? « Plastic Futures
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One Thousand Microbial Genomes
GenBank, the central public database for genomic information, just completed its thousandth microbial genome. An interesting Nature News article discusses how this isn’t nearly enough for many evolutionary scientists and microbiologists. According to one scientist: “There have been four billion years of evolution and we can really benefit from having some of that information in our...
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What is "boyish" anyway?
There’s been a lot of news today about a new study (that I can’t find online yet), reporting that prenatal phthalate exposure can make young boys act more “feminine.” Phthalates are chemicals found in some plastic products that have been shown to affect the endocrine system in rats, mimicking the effect of exposure to estrogens. The new study found that “Boys exposed...
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This Cyborg Life →
There’s an excellent set of articles from Gizmodo this week “exploring the enhanced human future,” including:
-an interview with Michael Specter, “Synthetic Biology: Why Not Pursuing Crazy Biotech is dangerous”
-an article about tissue engineering and skin grafts: “Meat Band-Aids and Mass Production of Living Tissue”
-human/machine interfaces to...
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Google Maps for Metabolism
A really neat new web-based metabolic network viewer was presented in today’s PLoS ONE: “Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API.” This is, for me, one of the most useful and intuitive new software systems for biological research. Through an easy to use web interface, you can search for and zoom in on specific metabolic reactions...
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Bioplastics Man § SEEDMAGAZINE.COM →
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The Scientist : Promises, Promises →
Last week there was an interesting discussion over at the Slate Book Club beetween Michael Specter, author of the new book “Denialism: How Irrational Thinking Hinders Scientific Progress, Harms the Planet, and Threatens Our Lives” and Chris Mooney that specifically talked about how to educate people about synthetic biology to prevent the irrational denialism that has affected other...
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Data Frenzy
Last night I went to see Ryoji Ikeda’s datamatics at Sanders Theater at Harvard and it was AWESOME. From wikipedia because I find it hard to describe (that’s Nick’s job), Ikeda:
is a Japanese sound artist who lives and works in New York City. Sometimes harsh, sometimes remarkably gentle, Ikeda’s music is concerned primarily with sound in a variety of “raw”...
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Gene Therapy Helps Blind Children See →
via Seed via ScienceNow
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“Bioelectronix can be much simpler still. Works involving bioelectronix can be...”
– What is biolectronix? « Hackteria
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iGEM Blogpost Roundup
Adam Bluestein:
One evident advantage of this compressed evolution is the opportunity, at iGem, for young students to engage directly with the Edisons of synthetic biology, sharing big ideas, tricks of the trade, and free sandwiches with the likes of Tom Knight, Randy Rettberg, Drew Endy, Pam Silver, and George Church (to name a few). How motivating must that be?
Rob Carlson:
iGEM is, at its...
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Gene-makers put forward security standards :... →
Several gene-synthesis companies yesterday finalized a code of conduct that outlines how to screen orders for synthetic DNA that could be used for terrorist activities.
The code, which has been in the works from the International Association of Synthetic Biology (IASB) in Heidelberg, Germany, for a year and a half, reflects for the most part what has become common practice in gene-synthesis...
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Vote for me! →
My essay on synthetic biology has made it to the finals in the scientificblogging.com graduate student writing competition! The winner is chosen through online voting on the site, so please click and vote for me (you can vote once a day until November 23rd!) and spread the word! Thanks!