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Starting at the Beginning

The views expressed are those of the author and are not necessarily those of Scientific American.


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Welcome! I’m thrilled to be joining this brand new blog network and to be part of this new collection of voices! Since I hate blogging about blogging I’m going to just jump right in, and what better place to start than right at the beginning? I work on synthetic biology, a mix of biology and engineering that emerged in its most recent form about ten years ago. Most people trace the first use of the phrase “synthetic biology” back to a 1978 note in the journal Gene by Waclaw Szybalski and Ann Skalka about the Nobel prize awarded for restriction nucleases, enzymes that can cut DNA in ways that allow the gene cutting and pasting of genetic engineering. Szybalski and Skalka write:

The work on restriction nucleases not only permits us easily to construct recombinant DNA molecules and to analyze individual genes but also has led us into the new era of “synthetic biology” where not only existing genes are described and analyzed but also new gene arrangements can be constructed and evaluated.

But synthetic biology has a much longer history that starts well before people knew what DNA was, let alone how to cut and paste gene sequences together. In 1910, the French scientist Stéphane Leduc published “Théorie Physico-Chimique de la Vie, et Générations Spontanées” where he described his vision of La biologie synthétique: creating artificial, simplified models of living processes in the lab in order to better understand the origin of life. Leduc focused on the physical behavior of liquids and salt solutions, believing that the osmotic forces he could observe moving ink blobs in test tubes were the drivers of life. He writes, as quoted by Joost Rekveld on Light Matters:

The study of synthetic biology is therefore the study of the physical forces and conditions which can produce cavities surrounded by osmotic membranes, which can associate and group such cavities, and differentiate and specialize their functions. Such forces are precisely those which produce osmotic growths, having the forms and exhibiting many of the functions of living beings. Of all the theories as to the origin of life, that which attributes it to osmosis and looks on the earliest living beings as products of osmotic growths is the most probable and the most satisfying to the reason.

To synthesize life based on these physical principles, he mixed together inks and salt solutions that would swirl and clump together, creating “osmotic growths” that resembled living forms.

 

 

These shapes could move and grow, changing shape as the solutions pushed against each other. The ink drops could be made to look like macroscopic organisms and startlingly like the microscopic processes going on inside cells.

 

 

Salt solutions also played an important role in the work of Jacques Loeb a decade earlier, with the goal of “constructive or engineering biology in place of a biology that is merely analytical.” Loeb was interested not in the origin of all life, but in the development of individual organisms starting from a fertilized egg. He placed sea urchin eggs in different concentrations of salts and found that with just the right mixture the eggs would start to divide and develop into the urchin embryo without being fertilized by sperm.

 

 

The concurrent success of genetics and molecular biology kept this kind of engineering biology on the sidelines, but by the 1980′s and 1990′s a new crop of engineer/biologists was popping up with new sets of tools. Instead of ink drops, computer scientists in the 1980′s experimented with artificial life in computer programs, designing programs that would self-generate pixels on a screen that could interact, compete, reproduce, and evolve. These cellular automata are as un-biological as Leduc’s ink drops, but they displayed the characteristics and properties of life that the researchers were interested in, often making the automata “alive” in their eyes.

 

 

Drops of oils and salts in water today form protocells that resemble the what researchers imagine the earliest cells looked like. The illustration below is by Janet Iwasa, a scientist and animator working with Jack Szostak’s lab at Harvard to visualize the lab’s work on trying to use a synthetic approach to understanding the origin of life on earth.

 

 

Loeb’s legacy lives on as well, in researchers working on cloning animals and reprogramming stem cells. Starting from one cell type and inducing it to divide and change with the addition of different chemicals; turning adult cells into stem cells that have the potential to become any cell in the body or into a whole animal.

 

 

“Synthetic biology” today is usually used to describe three independent but interrelated research programs aiming at engineering life for applications in alternative energy, medicine, and the environment–building genetic circuits and devices based out of interchangeable biological “parts”, chemically synthesizing genetic pathways or whole genomes, and trying to recreate the earliest life forms with protocells. The past and present of engineering inspired biology is much broader and wackier than most literature reviews of the field can cover and this blog is devoted to all sorts of synthetic life forms and artificial forms of life.

As an active participant in synthetic biology my goal in writing this blog is never to just promote the acceptance of new science and technology, but to celebrate the creativity of biology and engineering and all strange blends thereof, to try and engage critically with new developments and new promises, and to be one very small part of the very complicated way that society and technology are interconnected.

Christina Agapakis About the Author: Christina Agapakis is a biological designer who blogs about biology, engineering, engineering biology, and biologically inspired engineering. Follow on Twitter @thisischristina.

The views expressed are those of the author and are not necessarily those of Scientific American.



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  1. 1. ewintermute 12:59 pm 07/5/2011

    Supercool! This also reminds me of Alan Turing’s reaction-diffusion models of morphogenesis. You can write like two simple equations for molecules diffusing around in a mixture and create patterns that look like life. This page has a fun applet to play with.

    http://cgjennings.ca/toybox/turingmorph/

    Link to this
  2. 2. drkahaynes 1:51 pm 07/5/2011

    Excellent writing. Glad to see you featured at Scientific American.

    “He placed sea urchin eggs in different concentrations of salts and found that with just the right mixture the eggs would start to divide and develop into the urchin embryo without being fertilized by sperm.”

    This ties in directly to a section if an undergrad Bio111 course I taught (fertilization), but I wasn’t aware of the history of manipulating calcium gradients. Could you post a reference article or two?

    Link to this
  3. 3. mrund 2:38 pm 07/5/2011

    Yay Christina, congrats!

    Link to this
  4. 4. Kevbonham 4:08 pm 07/5/2011

    Sucks that they got you guys started without links to RSS feeds. For anyone else that’s curious, it’s just the normal-url/feed

    Glad Christie Wilcox gave the link in her first post :-)

    Link to this

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