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What’s next for synthetic life?

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synthetic life genome next step dinosaurs venterCOLD SPRING, N.Y.— J. Craig Venter and his colleagues recently announced that they had created the first cell to run on a fully artificial genome. So what’s next for this synthetic strain of microscopic Mycoplasma mycoides and the new technology?

The "synthetic cell" achievement has been lauded, condemned and undercut, but it has yet to fully demystify life’s underlying code, the genome. "It’s amazing how little we know about genomics," Venter said June 1 at the Cold Spring Harbor Symposia on Quantitative Biology in Cold Spring, N.Y.

Researchers built much of the bacterium’s genome without fully understanding the function of many of the million-plus base pairs involved. About half of the genes, in fact, are still "a complete black box," said Richard Roberts of New England Biolabs, Inc., in a commentary after Venter’s talk.

But a bit like complex erector sets can help illuminate some of the basic rules of physics and engineering, scientists are hoping that constructing—and deconstructing and reconstructing—whole genomes will help them better understand genomic principles. "We have to find what the rules are," Roberts said. Scientists, for instance, don’t yet know what role or importance the order of genes in the genome plays. They have seen that in some cases, genes can have their order swapped with little visible outcome on life, whereas, specific sequence might be more important elsewhere on the genome.

Although the researchers based their synthetic genome on the natural one, their cell did not behave exactly the same, Venter noted. Usually when you mess around with the inner workings of a cell, especially its genetic code, growth rate tends to slow. With this one, however, there was a substantial increase in the growth rate. "That was a surprise," Venter said. "We have no idea why the cells grew faster."

Future studies will examine the behavior of the microbe and its progeny to see how these behavioral changes match up to genetic changes. The initial paper was only intended as a proof of concept, Venter pointed out. Nevertheless, he said, "people are disappointed that it doesn’t sing and dance."

So how long will it be until scientists can synthesize genomes for other, more complex forms of life? Even expanding the capability to various kinds of bacteria will likely take a long time, Roberts noted. "Maybe we’ll even be able to take the Jurassic Park scenario," but he said, happily, that there wasn’t much chance of crossing paths with a recreated dinosaur—in his lifetime anyway.

One of the group’s long-term goals, said Venter (who has "never been known for his extreme modesty," Roberts, a long-time acquaintance, said at the symposium), is to develop a universal recipient cell, into which researchers can plug a variety of synthetic genomes and see how they run. And in the future, he proposed, it might be cheaper for scientists to synthesize simple organisms than to grow them.

Roberts is happy to see the synthetic genome advance as a way to refocus research interest and attention on bacteria, which he calls "cute…lovely little organisms." In particular, being able to better understand the genomes of bacteria can have broad health implications for people, who host some 100 trillion microbial cells in and on their bodies.

The field of genomics, however, can be slow-going and riddled with many costly mistakes. Just one error small in earlier attempts to assemble a synthetic code set the researchers on Venter’s team back months. But James Watson, former head of Cold Spring Harbor Laboratory whose co-discovery of DNA more than 50 years ago helped to lay the foundation for this work, was pleased by the speed of progress. "We’ve been so much more successful that you might have predicted," he said at the symposium.

And for those keeping score, the synthetic genome, which contains coded Web and email addresses, has been cracked by 26—and counting—scientists so far, Venter said on Tuesday.

Image of Venter courtesy of Wikimedia Commons





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  1. 1. robert schmidt 2:47 pm 06/3/2010

    As the first article indicated the next step is to start chopping genes to find out what does what. I’d like to see an annotated version of the genome they are using.

    I am just beginning to get into bioinformatics for a project. To me gene expression and cell biology looks like a fuzzy state machine. I’m wondering if others have seen this and if there are any resources that illustrate this in more depth. If you think this isn’t the case, I’d be interested in hearing your opinion why gene expression can’t be modeled as an FuSM. This discovery brings us closer to the point where we will be able to program cells like we program computers. I am interested in the structure and syntax of that meta-code. I know they use a regular expression like syntax for proteins and have used the 2D HP model for protein folding but how would you structure a computer language to model gene expression and cell biology?

    Link to this
  2. 2. rlanzara 7:48 am 06/4/2010

    Unfortunately Dr. Ventor & Synthetic Genomics should be temporaliy stopped before a terrible mistake occurs. Dr. Ventor’s lab isn’t taking appropriate precautions with its synthetic life program. Synthetic Genomics should use a level 3 containment lab and dispose of the yeast cultures very carefully.

    Link to this
  3. 3. rlanzara 10:59 am 06/4/2010

    (Correcting the spelling of Dr. Venter’s name – not "Ventor".) Unfortunately Dr. Venter & Synthetic Genomics should be temporaliy stopped before a terrible mistake occurs. Dr. Ventor’s lab isn’t taking appropriate precautions with its synthetic life program. Synthetic Genomics should use a level 3 containment lab and dispose of the yeast cultures very carefully.

    Link to this
  4. 4. Fumaca St. louis 11:42 pm 06/9/2010

    It’s all very complicated to me as a layman, but none the less extremely exciting. I only have one question that maybe someone here may provide an answer, what is this creatures energy source, does it synthesize it’s on or does it consume, and if it eats what does it eat???

    Link to this
  5. 5. Fumaca St. louis 12:05 am 06/10/2010

    As a layman I find Dr. Venter’s breakthrough exciting and full of possibilities. As with all new things in science caution and prudence should be exercised as it proceeds, to quote a cliche ‘I haven’t seen a miracle of science go from a blessing to a curse’. The one question I have about this new creature is simple but I haven’t heard the answer. What is this life forms energy source?

    Link to this
  6. 6. Dov Henis 4:27 am 07/9/2010

    Life Is Just Another Mass Format

    Synthetic Cell Is An Organ Transplant Affair
    Life, WE, Are Just Another Mass Format

    A. "Is the Synthetic Cell about Life?"
    http://www.the-scientist.com/2010/7/1/27/1/

    B. "Is Life A Conglomeration Of Mechanisms?"
    http://www.the-scientist.com/community/posts/list/300/122.page#5864

    - The JCVI feat is an impressive technological feat of mastered life mechanisms technologies, coupled with an impressive novel organ transplantation technology.

    - Is it human nature, or just "scientist" nature, to accept-prefer the complicated-complex rather than the obvious-rational conception?

    - "Genes’ Expression Modification"
    http://www.the-scientist.com/community/posts/list/200/122.page#3649

    Life is just one of the mass formats in the universe. Life’s is the ubiquitous cosmic evolution mode. The mode of a gene’s response to the organism culture’s feedback signal, i.e. "replicate without change" or "replicate with change" in case of proven augmented energy constrainment by the offspring, is the mode of Life’s normal evolution, which is the mode of evolution universally, the mode of cosmic evolution.

    Dov Henis
    (Comments From The 22nd Century)
    03.2010 Updated Life Manifest
    http://www.the-scientist.com/community/posts/list/54.page#5065
    Cosmic Evolution Simplified
    http://www.the-scientist.com/community/posts/list/240/122.page#4427
    Gravity Is The Monotheism Of The Cosmos
    http://www.the-scientist.com/community/posts/list/260/122.page#4887
    EOTOE, Embarrassingly obvious TOE, expanding the horizon beyond Darwin And Einstein
    http://www.molecularfossils.com/2010/05/formal-test-of-theory-of-universal.html

    Link to this
  7. 7. Dov Henis 2:36 am 12/5/2010

    On Genes And Genomes, Concepts And Terminology
    http://darwiniana.com/2010/11/11/epigenetics-9/comment-page-1/#comment-355245

    Dispel Some Figments Of Present Science Imagination

    "Galaxies pin down dark energy"
    http://physicsworld.com/cws/article/news/44468

    - Dark energy and matter YOK. Per E=Total[m(1 + D)] all the energy and matter of the universe are accounted for.

    - Higgs Particle YOK. Mass begins to form below some value of the above D.

    - Sleep is inherent for life via the RNAs, the primal Earth ORGANISMS formed and active only under direct sunlight in pre-metabolism genesis era.

    - Natural selection is ubiquitous for ALL Mass Formats. It derives from the expansion of the universe.

    - Epigenetics: Where Life Meets the Genome
    http://www.bionews.org.uk/page_66997.asp?dinfo=rWfnKzZO4tkhJf38jsJ5EeJo

    Epigenetics =
    a) the study of heritable changes in gene function that do not involve changes in DNA sequence
    b) the science of enduring changes in the pattern of gene activity, during embryo development and beyond, that do not involve alteration of the DNA sequence.

    The "heritable or enduring changes" are epiDNAtics, not epigenetics. Alternative splicing is not epigenetics, even if/when not involving alteration of the DNA sequence. Earth life is an RNA world.

    It’s the RNAs that evolve proteins. AND IT’S THE RNAs THAT HAVE EVOLVED AND PRODUCE AND EMPLOY THE DNA ( and RNA ) templates to carry out life processes, for enhancing Earth’s biosphere, for augmenting and constraining as long as possible some energy by augmenting its self-propagation, constraining some of the total energy of the universe, all of which is destined to fuel the ongoing cosmic expansion.

    IT HAS ALWAYS BEEN AND IT STILL IS AN RNA EARTH LIFE.

    Science should adjust its vision, comprehension and concepts.

    Dov Henis
    (Comments From The 22nd Century)
    http://www.the-scientist.com/community/user/profile/1655.page

    Seed of Human-Chimp Genomes Diversity
    http://pulse.yahoo.com/_2SF3CJJM5OU6T27OC4MFQSDYEU/blog/articles/53079
    03.2010 Updated Life Manifest
    http://www.the-scientist.com/community/posts/list/54.page#5065
    Cosmic Evolution Simplified
    http://www.the-scientist.com/community/posts/list/240/122.page#4427
    Gravity Is The Monotheism Of The Cosmos
    http://www.the-scientist.com/community/posts/list/260/122.page#4887
    Evolution, Natural Selection, Derive From Cosmic Expansion
    http://darwiniana.com/2010/09/05/the-question-reductionists-fear/

    Link to this

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