Where Are My Bioengineered Ecologies?

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.

Where Are My Bioengineered Ecologies?


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.

Where Are My Bioengineered Ecologies?

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.

Where Are My Bioengineered Ecologies?


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.

Where Are My Bioengineered Ecologies?


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.