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paleoanthropology, genetics and evolution

synthetic biology

  • Synthetic biology explainer

    Sat, 2012-01-14 14:47 -- John Hawks

    Nice piece on synthetic biology by Adam Rutherford:

    But Freckles is a long way from normal. She is an extraordinary creation, an animal that could not have existed at any point in history before the 21st century. She is all goat, but she has something extra in every one of her cells: Freckles is also part spider.

    UPDATE (2012-01-14): A knowledgeable reader writes:

    Ah, journalists! What do transgenic animals have to do with synthetic biology? Absolutely nothing, in fact. And the hyperbole fails, too. If the protein was human instead of arachnid (as is the with many cows now), that goat would be part human then? Which would then mean that a lot of bacterial, insect and mouse cells I grow in the lab are part human, too! Woo-hoo! Meet Dima Klenchin, a synthetic biologist...

    And Venter Institute's bacterium is not a synthetic life by any stretch of imagination and neither is anything else described in the article (modifying microorganisms for industrial production is about two decades old news). In fact, "synthetic biology" seems to be simply a new buzz word to get funding easier. You see, "transgenic organisms" is getting too routine and stale from the funding point of view and "nanotechnology" too has been overused to the point of losing much of its buzz power as well. So pharmacology is now "chemical biology" and gene engineering is now "synthetic biology".

    As for the truly synthetic life, we are finding that it is a very hard going. Everyone would be enormously impressed by a single brand new enzyme or a metabolic pathway (no aping from existing prototypes in nature). Alas, even that turns out to be easier said than done. But fear not - all those computer scientists and physicists will soon, veeeery soon, come to the rescue. :-)

    I thought it was a fun article but your points are well taken. I think that there is a faction who are trying to "define down" the term synthetic biology so it applies to everything from recombinant DNA upward. Venter obviously hasn't helped matters by trying to lower the bar for an artificial life form.

    But maintaining any useful distinction may become impossible anyway if molecular machines can be made to interact in any useful way with endogenous genomes. Of course if they make spider silk comes straight out the goat's udder it would be more awesome than tomacco!

  • Bloggingheads: Synthetic biology and Neandertal genomics

    Sat, 2010-05-29 01:14 -- John Hawks

    I got to return to bloggingheads.tv this week for Science Saturday, with a conversation between me and Christina Agapakis, of the Oscillator blog.

    Here's a non-embedded link to the diavlog. Christina's work is in synthetic biology, and we talked a lot about the recent announcement from the J. Craig Venter Institute, with some background on what synthetic biology is, and how the newsmaking work fits into the field as a whole. I learned a lot from our conversation. We got to the Neandertal genome in the second half of our conversation, and we found several common links -- and neither of us mentioned synthetic Neandertals once!

  • Quote: Jim Collins on synthetic biology

    Mon, 2010-05-24 23:13 -- John Hawks

    Bioengineer Jim Collins, quoted in Nature on the "synthetic cell" story:

    Frankly, scientists do not know enough about biology to create life. Although the Human Genome Project has expanded the parts list for cells, there is no instruction manual for putting them together to produce a living cell. It is like trying to assemble an operational jumbo jet from its parts list — impossible. Although some of us in synthetic biology may have delusions of grandeur, our goals are much more modest.

  • Synthetic code

    Sun, 2010-02-21 07:30 -- John Hawks

    The Oscillator's Christina Agapakis reviews some work in synthetic biology -- "Expanding the genetic code"

    But what if instead of mutating individual tRNAs, you could make a whole parallel genetic code in a living cell? An awesome paper in this week's Nature makes progress towards this goal, by using directed evolution to design a ribosome that reads four letter codons instead of the normal three. With a four letter code, you could potentially program 256 different amino acids, to create altered proteins or entirely different biological polymers.

    This seems like the kind of thing that ought to be encouraged. You know, so synthetic organisms won't be able to eat us so easily. Of course, that's what they thought about engineering lysine-deficient dinosaurs in Jurassic Park.

  • BioBricking

    Mon, 2010-02-15 10:58 -- John Hawks

    A couple of long stories in the New York Times Magazine this weekend caught my interest. One of them covers the emerging world of university competitions in synthetic biology:

    Over the past five years, iGEM teams have been collaboratively amassing a centralized, open-source genetic library of more than 5,000 BioBricks, called the Registry of Standard Biological Parts. Each year teams use these pieces of DNA to build their projects and also contribute new BioBricks as needed. BioBricks in the registry range from those that kill cells to one that makes cells smell like bananas. The composition and function of each DNA fragment is cataloged in an online wiki, which iGEM’s director calls “the Williams-Sonoma catalog of synthetic biology.” Copies of the actual DNA are stored in a freezer at M.I.T., and BioBricks are mailed to teams as red smudges of dehydrated DNA. Endy showed me a set stuck to paper, like candy dots.

    The article follows a team from a community college in San Francisco that competes with the "big boys" -- I love the fact that one of the real powerhouses, from Slovenia, gets all kinds of local media attention.

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.