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Reverse the Biosphere


Will Dunham, Reuters, Scientists propose project to build synthetic human genome, here. Not booting it up. Not going to do it. No plans.

The group also includes experts from Harvard Medical School, the Massachusetts Institute of Technology, the U.S. government’s Lawrence Berkeley National Laboratory, Johns Hopkins University School of Medicine, Yale University, the University of Edinburgh, Columbia University, the University of California at Berkeley, the University of Washington, Autodesk Bio/Nano Research Group, Bioeconomy Capital and other institutions.

Scientists not involved in the project cited potential benefits from the work, including learning the function of vast parts of the genome that remain mysterious and helping better understand how genes are regulated and why there is so much genetic variation among individuals and human populations.

“It will also provide technologies for advanced gene therapy and lead to a much greater understanding of how the genome is organized and how in disease cells this becomes altered,” said Paul Freemont, co-director of the Centre for Synthetic Biology and Innovation at Imperial College London.

“The project is not as controversial as some observers might be saying,” added University College London professor of synthetic biology John Ward. “There is no call to make an entire human being.”

Karen Weintraub, Scientific American, Taking Gene-Editing to the Next Level, here. Can we just find out if the CRISPR stack of viral DNA snippets can count from 0 to k reliably? Is there only one stack or are there multiple stacks? Do they all have the same data in the stack frames? Are the stack frames fixed length or variable length? I understand that it is super good to have a precision cut for DNA and RNA. But if there really is an accurate implementation of a push down stack in the native DNA, that is a really big deal as well, no?  What happens if DNA has some Reed-Solomon error correction in the native code that can be cited as prior art from the year 10,000,000 BC to avoid paying royalties?  Do we have to assume that somebody like Craig Venter synthesized the DNA we are testing?

Researchers who discovered a molecular “scissors” for snipping genes have now developed a similar approach for targeting and cutting RNA. The new cutting tool should help researchers better understand RNA’s role in cells and diseases, and some believe it could one day be useful in treatments for illnesses from Huntington’s to heart disease.
To develop the “blades” for the process, researchers led by Feng Zhang at the Broad Institute used CRISPR (clustered regularly interspaced short palindromic repeats)—a system that bacteria evolved to fight off pathogens. CRISPR has previously been used to edit DNA but had been theorized to work on RNA as well.
The new findings, reported Thursday in Science, came from systematically exploring different aspects of that natural defense system that protects bacteria—and may eventually be put to use helping people. “Nature has already invented all these really interesting mechanisms,” Zhang says, comparing himself with a treasure hunter. “We’re just trying to play with that and learn how they work…then turn them into tools that will be useful to us.”

Erik Arends,, Second layer of information in DNA confirmed, here. I think you simply want a result that shows DNA is equivalent to some K tape Turing machine so you get on with the business of  reversing the native program in the original DNA.  It is great to boot up entirely synthetic DNA and see what happens. But it is really more interesting to reverse the actual native code. Look at it this way if you can reverse the native code in the DNA you have a chance that you get to call up George Church at Harvard with a “Soylent Green is people” or ” What are the 39 steps?” kind of message that you reversed from the native DNA code.

For the first time, Leiden physicist Helmut Schiessel and his research group provide strong evidence that this second layer of information indeed exists. With their computer code, they have simulated the folding of DNA strands with randomly assigned mechanical cues. It turns out that these cues indeed determine how the DNA molecule is folded into so-called nucleosomes. Schiessel found correlations between the mechanics and the actual folding structure in the genome of two organisms—baker’s yeast and fission yeast. This finding reveals evolutionary changes in DNA—mutations—that have two very different effects: The letter sequence encoding for a specific protein can change, or the mechanics of the DNA structure can change, resulting in different packaging and levels of DNA accessibility, and therefore differing frequency of production of that protein.



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