io9: synthetic biology

Final Reminder! Build a Lifeform and We'll Send You to Hong Kong or Give You $1000

Annalee Newitz — Mon, 25 Aug 2008 11:20:27 PDT

You've got until midnight tonight to enter io9's mad science contest to build a new lifeform. Building new lifeforms is the science of the future and therefore you can never have too many garage laboratories and mad scientists devoted to it. That's why io9 is sponsoring a contest to find two of the best synthetic life forms you can design for us. You've had almost two months to build that lifeform, and now the contest deadline looms! You've got until tonight, Aug. 25, at midnight to hand in your contest entry.

The winners in our two categories will get either an all-expenses-paid trip to the kickass Synthetic Biology Conference in Hong Kong this October, or $1000 and a chance to have their creature drawn by a cool comic book artist. Find out more below.

There are two categories in the contest, each with their own prize. The important thing to remember is that this contest is about creating cool new lifeforms that are also, in some way, entertaining. So each entry will be judged for plausibility (i.e. whether it is scientifically justifiable), creativity, usefulness, and entertainment value.

Our esteemed judges include synthetic biologist Drew Endy (MIT), evolutionary biologist and PLoS co-founder Michael Eisen (UC Berkeley), Spore game developer Jason Shankel (EA/Maxis), and biology researcher/io9 "ask a biogeek" columnist Terry Johnson (UC Berkeley).

Category One: BioBricks Lifeform
Using the BioBricks registry of standard biological parts, propose a lifeform design that you could conceivably create in a lab. Must include a complete description of how you would make the lifeform, what it would do, and what possible hazards might be involved in creating it. You may design this creature with a team, but only one of you can claim the prize. You may enter lifeforms that you have entered in other contests, but you must state in your entry which contest(s) you've already entered. Your entry should be in the form of a short scientific paper (no more than 3000 words), with illustrations. More points given if you've actually got a working organism.
Prize: All travel and hotel expenses paid trip to the Synthetic Biology Conference in Hong Kong in October, as well as the chance to present your research there.

Category Two: General Synthetic Lifeform
This lifeform can be more creative. Propose a scientifically justifiable lifeform, which could conceivably be created using current technology. Explain how you would create it, what it would do, and hazards involved. Unlike the BioBricks lifeform, this lifeform can be more speculative. It should be science fictional, but must remain scientifically plausible. Your entry should be less than 3,000 words, please. Illustrations and diagrams are a good idea.
Prize: $1000, plus a cool comic book artist will draw your lifeform and you'll get a signed copy of the original art.

DEADLINE FOR ALL ENTRIES IS AUGUST 25 AT MIDNIGHT PST.

General Rules

1. Send queries and completed entries to madscience@io9.com.
2. On entries, please include your full name, an email and phone number where we can reach you, plus any information about other contests you may have entered your lifeform in.
3. Winners will be announced September 8.
4. All general Gawker contest rules apply.

Deadline Approaches! Build a Lifeform and We'll Send You to Hong Kong or Give You $1000

Annalee Newitz — Thu, 21 Aug 2008 10:00:00 PDT

io9 wants to encourage mad scientists in every field, but especially in the area of synthetic biology. That's because synthetic biologists are the people who are going to build new life forms, like ligers and unicorns and people with claws and glowing eyes. OK, they might build bacteria that can clean up oil spills and repair damaged kidneys too. The point is, building new lifeforms is the science of the future and therefore you can never have too many garage laboratories and mad scientists devoted to it. That's why io9 is sponsoring a contest to find two of the best synthetic life forms you can design for us. You've had almost two months to build that lifeform, and now the contest deadline looms! You've got until Monday, Aug. 25, at midnight to hand in your contest entry. All the details are below.

DEADLINE FOR ALL ENTRIES IS AUGUST 25 AT MIDNIGHT PST.

General Rules

Mad Science Contest: Build a Lifeform and We'll Send You to Hong Kong or Give You $1000

Annalee Newitz — Mon, 07 Jul 2008 12:11:25 PDT

io9 wants to encourage mad scientists in every field, but especially in the area of synthetic biology. That's because synthetic biologists are the people who are going to build new life forms, like ligers and unicorns and people with claws and glowing eyes. OK, they might build bacteria that can clean up oil spills and repair damaged kidneys too. The point is, building new lifeforms is the science of the future and therefore you can never have too many garage laboratories and mad scientists devoted to it. That's why io9 is sponsoring a contest to find two of the best synthetic life forms you can design for us. The winners in our two categories will get either an all-expenses-paid trip to the kickass Synthetic Biology Conference in Hong Kong this October, or $1000 and a chance to have their creature drawn by a cool comic book artist. Find out more below.

DEADLINE FOR ALL ENTRIES IS AUGUST 25 AT MIDNIGHT PST.

General Rules

Where Are My Bioengineered Ecologies?

Terry Johnson — Thu, 05 Jun 2008 09:00:00 PDT

It's another installment of Ask a Biogeek, a column where UC Berkeley biology researcher Terry Johnson answers all your questions — especially the weird ones.

Reader Daniel wonders:

As a biologist who studies whole organisms and populations, I find that more and more of biology (in terms of funding, positions and emphasis) is going to the sub-organismal level. We now have lots of cell biologists, geneticists, neurologists, biochemists, biomechanics, bioengineers and so on, but not a lot of behaviorists, population ecologists, biodemographers and others who study the emergent properties that arise at the higher levels of organization. What role, if any, do you foresee for understanding of these higher level biological phenomena in the future sci-fi-ish stuff?

I believe we're rapidly reaching the point where scientists will be both ready and able to consider artificially-induced emergent biological properties — in other words, terraforming. Let me take you on a tour of today's state-of-the-art in this emerging field.

As far as emerging biotechnology goes, science fiction grapples more frequently (if not always very seriously) with issues of organismal or ecological impact than the scientific establishment. There are good reasons for this. Ecological ruminations are a tradition for the authors, and the scientists have - until quite recently - been limited by technical considerations. As a scientist, I hope the title Planetary Ecologist will go on someone's tax return someday.

A Sandworm of Arrakis, from Frank Herbert's Dune.

Some would say that Frank Herbert's Dune was the beginning of ecological science fiction, but its roots go much deeper than that. Every time an author has imagined an alien world and then tried to fill it with beings capable of surviving on it, that author is grappling with issues of ecology, and every time an author has decided how those aliens would act, they were engaging in a bit of recreational behaviorism. Herbert elevated the tone and raised the bar, no doubt, but there is a long-standing tradition of biological and behavioral what-if in SF. The rise of environmentalism coupled with another favorite SF theme - dystopianism - brought us the environmental disaster subgenre, from the ridiculous The Day After Tomorrow to more thoughtful treatments like David Brin's Earth or the works of Kim Stanley Robinson.

Mars (with a little terraforming and a lot of luck).

While there are (of course) ecologists in the scientific community, there are very few thus far that bridge the gap between research at the molecular level and ecologies larger than a tissue culture dish. This is not to imply that ecologists are ignorant of molecular biology; the field has generated far too many useful tools for that. The bioengineers and cell biologists who are designing new organisms at the molecular level, on the other hand, are not always well versed in the basics of ecology and evolution. They are necessarily focused on what one scientist has called the molecular sociology of the cell.

Up until quite recently it would have been ludicrous to expect a molecular biologist to consider the higher-level environmental interactions of, for example, a particular gene, because he or she was still trying to figure out (at a molecular level) what the damn gene did to the cell itself. Take a peek at the inner life of a cell (if you haven't seen if before). A single cell is a giant bag of confusion. Trying to sort out web of interactions between the thousands of molecules present in hundreds of compartments using the technology at hand has been compared to figuring out the rules for a game of football using only pictures of the field (that only show certain players) at various times. This is why many researchers like to work with single cells instead of a cell in its natural environment, whatever that is - the cell alone is complicated enough. Experimental limitations or therapeutic concerns often require an intimate knowledge of a single organism's physiology, effectively tying a researcher to a single animal. Heinlein said, "Specialization is for insects". I would add grad students to the list.

Take E. coli as an example. We've had its genome sequenced for over a decade. Type its name into Google Scholar and you'll find over 1.5 million hits. Yet programming this bacteria - synthetic biology - is still a difficult and time-consuming process. When The University of Texas at Austin's entered their light-sensitive pigment-producing bacteria biofilm in the intercollegiate Genetically Engineered Machine (iGEM) contest, they realized that their achievement barely scratched the surface - that the "program" they'd written into the bacteria was relatively simple compared to the programming it already used to survive. In recognition of this fact, they produced perhaps my favorite "Hello world" program ever.

10 GOTO e. coli 20 Hack it genetically to turn it into a light-sensitive film

It's also important to note that almost all of the engineered cells and organisms made today are never meant to be released in the environment (and wouldn't be likely to survive in it if they did). Those that aren't created purely for research purposes are typically meant to live in small, artificial, and easily replaceable ecologies, like bioreactors in a pharmaceutical company or fermenters in a winery.

Either the bacteria are doing what they've been programmed to or we have a serious Cthulhu problem.

Genetically modified foods are a special case, but as a special case they've already received the most attention by ecologists. GM organisms that are designed to move outside of the lab enter the purview of the ecologists.

While disciplines like bioinformatics combine computational and molecular biology with evolutionary studies, increasingly complicated bioengineered organisms designed for the wild will require the ability to effectively model the ecologies they were designed for. In brief, once we're good enough at figuring out how to make a cell jump or play dead, the next frontier of design will be figuring out when we want a cell to jump or play dead, considering its surroundings. Top image via Electro-Plankton.

Do you have questions you've always wanted to ask a biogeek? You can email me at tdj@io9.com.

This Weekend, Start Building a New Life Form

Annalee Newitz — Fri, 29 Feb 2008 16:25:17 PST

In a few years, your weekend hacking project will involve bits of DNA and a PCR machine instead of a soldering iron or glue. With the help of the Open Wetware Project, and the Registry of Standard Biological Parts Wiki, you too can become an amateur synthetic biologist. But this isn't about evil mad scientist stuff. People using these new open-source biohacking tools are trying create helpful life forms, like insulin-producing bacteria or drought-tolerant crops. Here's a quick introduction to the biohacking tools everybody will be using tomorrow.

Registry of Standard Biological Parts [a wiki]. Start with the tutorial, just to get a flavor of what it means to take standard biological parts from a registry and put them together into a new organism. It's actually a lot simpler than you might think. This parts registry is a tool repository, but also a repository of information about biological parts that people have standarized, codified, and registered. A "part" isn't something like an arm — it's going to be something small, like an enzyme that affects a gene, or a protein that causes a particular biological state. Or perhaps a gene that will make you grow an arm.

Open Wetware Project [a community]. This is a clearinghouse community site for academics, students, and the public to share information about synthetic biology and biological engineering projects. You'll find classes, tutorials, and massive lists of laboratories working on biohacking. It's a great place to poke around and find out what people are really doing to create new life forms — and what their motivations are. Also, if you've got your own project or want to know more about an ongoing project, this the place to go to share ideas.

Programming DNA [a lecture] As we've mentioned before, MIT professor Drew Endy gave a smashing and fun introductory lecture about biohacking a couple of months ago at the Chaos Computer Congress in Berlin. If you want a crash course in how hacking a biological system can be like hacking a machine, load this one into your portable media device of choice and watch it during your commute (but only if you're not driving).

BioBricks Foundation [a standards body]. This is a non-profit formed by people from Harvard, MIT and UCSF in order to create standards for what counts as a "biological part." They're tackling legal and ethical issues, as well as strongly supporting the idea of making all information about biological parts and synthetic biology available for free to the public.

Open Biohacking Kit [via Sourceforge]. Get started on your biohacking project with this free software package. From the Sourceforge description:

This open, free synthetic biology kit contains all sorts of information from across the web on how to do it: how to extract and amplify DNA, cloning techniques, making DNA by what's known as oligonucleotides, and all sorts of other tutorials and documents on techniques in genetic engineering, tissue engineering, synbio (synthetic biology), stem cell research, SCNT, evolutionary engineering, bioinformatics, etc.

Image above is of a creature created with Maxis' forthcoming game Spore.