Bacterial Cell with a Chemically Synthesized Genome

[ViewsofMars]

I'm fasinated by this topic and would like to add a little bit more to the discussion about synthetic biology.

1. “If the methods described here can be generalized, design, synthesis, assembly, and transplantation of synthetic chromosomes will no longer be a barrier to the progress of synthetic biology. We expect that the cost of DNA synthesis will follow what has happened with DNA sequencing and continue to exponentially decrease. Lower synthesis costs combined with automation will enable broad applications for synthetic genomics.” (Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome – The J. Craig Venter Institute.
http://www.sciencemag.org/cgi/rapidpdf/science.1190719v1.pdf )


2. "Nat Rev Genet. 2010 May;11(5):367-79.

"Synthetic biology: applications come of age.
Khalil AS, Collins JJ.

"Howard Hughes Medical Institute, Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, Massachusetts 02215, USA.

"Abstract
Synthetic biology is bringing together engineers and biologists to design and build novel biomolecular components, networks and pathways, and to use these constructs to rewire and reprogram organisms. These re-engineered organisms will change our lives over the coming years, leading to cheaper drugs, 'green' means to fuel our cars and targeted therapies for attacking 'superbugs' and diseases, such as cancer. The de novo engineering of genetic circuits, biological modules and synthetic pathways is beginning to address these crucial problems and is being used in related practical applications."
http://www.ncbi.nlm.nih.gov/sites/e...ez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum

3. Howard Hughes Medical Institute, February '10/Vol.23, No.1
Cells Behaving Better by James. J. Collins
http://www.hhmi.org/bulletin/feb2010/pdf/Behaving.pdf
or
http://www.hhmi.org/bulletin/feb2010/perspectives/behaving.html
also
http://www.hhmi.org/research/investigators/collins.html

 

[rhody]

Heads up, tomorrow at 8:00 pm EST, Creating Synthetic Life on the Science channel, followed at 9:00 pm Creating Synthetic Life: Your questions

I have it programmed to record now.

Rhody...

 

[ViewsofMars]

Thanks rhody.

Science Channel Announces The Debut Of Exclusive Look Into Dr. J. Craig Venter's Creation Of Synthetic Life
May 20, 2010

Science Channel Documented the Five-Year Pursuit to Produce Life Synthetically for Creating Synthetic Life, premiering Thursday, June 3, 2010, at 8PM ET.

Discussion With the Experts, Creating Synthetic Life: Your Questions Answered, premieres at 9PM ET.

Watch video! [http://science.discovery.com/videos/creating-synthetic-life/]

Talk about this discovery and submit your questions for the experts on Science Channel's Facebook Page.

Washington, D.C. - Today, world-renowned scientist Dr. J. Craig Venter announced that he and his team at the J. Craig Venter Institute (JCVI) became the first in history to synthetically create a living, self-replicating cell. The news holds groundbreaking potential for solutions to a host of global challenges, including generating new food sources, pharmaceuticals and vaccines; cleaning up pollution; creating new energy sources; producing clean water; and more.

Now, Science Channel is exclusively bringing viewers inside Dr. Venter's pioneering quest to produce life synthetically in Creating Synthetic Life, premiering Thursday, June 3, 2010, at 8PM e/p. Over the course of five years, only Science Channel cameras captured the failures, successes and breakthrough moments of Dr. Venter, Nobel Laureate Hamilton Smith, Dr. Clyde Hutchison and JCVI researchers as they meticulously sought to create a synthetic single-celled organism.

What exactly does today's news mean for the human race? Where exactly will it take us? Could the technology be used for negative purposes? What are the ethical concerns we must weigh before using it? Following the premiere of Creating Synthetic Life, Science Channel delves deeper into the ethical and scientific implications of this discovery in Creating Synthetic Life: Your Questions Answered, premiering Thursday, June 3, 2010, at 9 PM (ET). This one-hour special is an open forum discussion featuring Dr. Venter, leading bioethicists, top scientists and other members of the scientific community discussing the breakthrough's ramifications and how it may change our world and the future.

Your Questions Answered allows viewers to ask the experts about how this technology will affect their lives. From now through May 26, submit your questions via Facebook, and they could be asked during the show. [It appears to me that they are no longer taking questions. May 26, 2010 is long gone. lol! I personally don't think it would be appropriate to submit a question(s) from this topic that was asked prior to or on May 26, 2010 and submit it without prior consent of the individual who asked the question here on this topic, which is on this website Physicsforums. Thanks, Mars]

"Science Channel brings viewers closer than any other network to scientific discoveries that are changing our world," said Debbie Myers, general manager and executive vice president of programming, Science Channel. "With Creating Synthetic Life, we're on the ground floor of cutting-edge science. We're giving audiences a platform to consider the issues and repercussions of this news, and directly question those leading the innovations."
[Please read on . . .]
http://science.discovery.com/tv/creating-synthetic-life/press-release.html

 

[rhody]

06/30 8:36 pm

Is anybody out there watching: "Creating Synthetic Life", I find it amazing that Ventor makes bold decisions, then his team somehow rises to the challenge, especially the decision to use the the twice as large faster replicating bacteria.

06/03 8:57 pm

I always find it amazing how small teams of intensely focused bright scientists driven by a leader with great vision can achieve great things, Burt Rutan who claimed the http://en.wikipedia.org/wiki/Ansari_X_Prize" and given us:

It is the first algorithm known to be suitable for signing as well as encryption, and was one of the first great advances in public key cryptography. RSA is widely used in electronic commerce protocols, and is believed to be secure given sufficiently long keys and the use of up-to-date implementations.

06/04 6:50 am

With the collection and sequencing of bacteria specimens in the Sargasso sea, what is Ventor's main purpose for doing so, genomic seed stock for new applications that involve his newly developed ability to create custom bacteria, and hopefully in the future more complex organisms ?

http://www.sciencemag.org/cgi/content/abstract/304/5667/66"

abstract:

We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.

Rhody...

 

[rhody]

a radical improvement in computing power, on the order of super exponential growth, tens of thousands of times faster then we have now...

From a recent http://www.ted.com/talks/henry_markram_supercomputing_the_brain_s_secrets.html" I know I am beating a dead horse, if I may direct your attention to the video:

7:00 New theory of autism, Intense World Theory​

7:30 Goal of Neuroscience: understanding the Neo-Cortical Column, reality, perhaps physical reality​

8:15 Built digital models of tens of thousands of neurons​

9:30 Most important design secret of the brain: diversity​

10:30 Pattern of HOW brain circuitry is designed, does not change​

11:40 Describe mathematics of how neurons communicate (a hand full of equations will do it)​

12:20 One neuron is assigned to each processor in a huge IBM supercomputer array, 10,000 in all​

13:00 New insight: ignore neurons, ignore synapses, instead look at raw electrical activity (electrical patterns)​

13:22 They produced ghostly like structures​

13:30 Electrical objects in a neo-cortical column (hold the info about what stimulated it)​

Any mathematical physicists out there interested in this ? If I had that skill set, I would be. What a great challenge...

Here is the Henry Markram interview by Sander Olson. [Note: there 14 questions and answers and a copyright by Dr. Markram at the end] Dr. Markram is the Project Director of the Blue Brain project, and Dr. Markram recently predicted that the Blue Brain project could have a human level brain simulation within a decade. Of note in this interview:

- The Blue Brain Project is not an AI project, but an attempt to unlock the mysteries of the brain. Dr. Markram is confident that Blue Brain models will eventually supplant AI.

-Knowledge of the brain is increasing exponentially. We are currently gathering as much information on the brain's structure and function each year as was gained in the entire 20th century. Neuroscientists are currently producing about 50,000 peer-reviewed articles per year. The Blue Brain project was launched in part to organize and coordinate this research.

-The Blue Brain project currently has the capability of electronically simulating 100 million neurons/100 billion synapse models, but is constrained by lack of funds to buy a sufficiently powerful computer.

-It currently requires 10-100 seconds of computer time to simulate one second of neuronal activity, but future computers should be able to simulate neurons in close to real time.

-A grid computing program to simulate and "build" individual neurons will soon be unveiled, and it will run on individual PCs as a screen saver.

- The blue brain project should result in extremely powerful "liquid computers" that can handle infinite parallelization.

Henry Markram Interview

Rhody...

 

[rhody]

From: http://www.sciencedaily.com/releases/2010/04/100426151638.htm"

ScienceDaily (Apr. 26, 2010) — Though scientists argue that the emerging technology of spintronics may trump conventional electronics for building the next generation of faster, smaller, more efficient computers and high-tech devices, no one has actually seen the spin -- a quantum mechanical property of electrons -- in individual atoms until now.

and

The study suggests that scientists can observe and manipulate spin, a finding that may impact future development of nanoscale magnetic storage, quantum computers and spintronic devices.

"Different directions in spin can mean different states for data storage," said Saw-Wai Hla, an associate professor of physics and astronomy in Ohio University's Nanoscale and Quantum Phenomena Institute and one of the primary investigators on the study. "The memory devices of current computers involve tens of thousands of atoms. In the future, we may be able to use one atom and change the power of the computer by the thousands."

Good to see basic research and that a possibility of progress in exponential processing power may be possible.

Rhody...

 

[rhody]

From: http://www.scientificamerican.com/blog/post.cfm?id=crystal-memory-allows-efficient-sto-2010-06-29"

The study's authors used a yttrium orthosilicate (Y2SiO5) crystal doped with the rare Earth element http://en.wikipedia.org/wiki/Praseodymium" , carefully tailored to have very specific absorption properties, as a quantum memory. Cooled to just three degrees Kelvin and held in an electric field, the crystal memory absorbs a pulse of laser light. But when the external electric field is switched, the memory produces an "echo" of the original photons, their quantum state intact.

"Light entering the crystal is slowed all the way to a stop, where it remains until we let it go again," lead study author Morgan Hedges, a student at the Australian National University's Laser Physics Center, said in a prepared statement. "When we do let it go, we get out essentially everything that went in as a three-dimensional hologram, accurate right down to the last photon."

The storage times demonstrated in the new research are rather short—measured in millionths of a second—but the researchers predict that even more efficient memories should be feasible, with storage times measured in seconds.

Properties of: praseodymium

Praseodymium is a soft, silvery, malleable and ductile metal in the lanthanide group. It is somewhat more resistant to corrosion in air than europium, lanthanum, cerium, or neodymium, but it does develop a green oxide coating that spalls off when exposed to air, exposing more metal to oxidation — a centimeter-sized sample of Pr completely oxidizes within a year.[2] For this reason, praseodymium is usually stored under a light mineral oil or sealed in glass.

Contrary to other rare-earth metals, which show antiferromagnetic or/and ferromagnetic ordering at low temperatures, Pr is paramagnetic at any temperatures above 1 K

Rhody...

P.S. After looking at the atomic structure with 59 protons and 82 neutrons, I knew they had to contain it in some way, or it would as the definition said, oxidize away. Makes me wonder how they came up with this one, got to hand it to those creative experimental physicists.

 

[rhody]

alxm,

One quick off topic question: http://en.wikipedia.org/wiki/Prion"[/URL]. I was under the impression that if you inhaled (through the nose) bone meal used for gardens, that just so happens to have prions in it from Mad Cow bones that in time you could develop CJD. I don't use bone meal to this day because of it. See text in blue from wiki link below.


Rhody...[/QUOTE]

Hmm.. findings on: [URL]http://www.nature.com/news/2010/100726/full/news.2010.376.html?s=news_rss"[/URL] from Nature News...
[QUOTE]After an epic series of experiments, a group of researchers has observed and reproduced what could be the spontaneous generation of prions — rogue misfolded proteins that have been implicated in the destruction of the central nervous system.[/QUOTE]
and
[QUOTE]In a typical experiment, they report, wires were placed with brain homogenate from either uninfected mouse brains or brains infected with scrapie prions. Out of 16 experiments, 9 had controls that were positive for prions. In total, 40 of 2,268 wells on test plates were positive. [/QUOTE]
and
[QUOTE]There is an alternative explanation to that of spontaneous generation.
Prions are believed to be a polymer of misfolded proteins. Collinge says that nascent 'seeds' of prions might be forming and being destroyed in brains all the time. The metal wire could have the effect of concentrating seeds, thus increasing the rate at which prions form.
[/QUOTE]

Interesting to say the very least, if prion's were not scary enough being transmitted from one animal to another, then spontaneous prion's with no known cause and appearing in low concentrations in mice brain tissue may occur (as a result of being exposed to the wire used in the experiment). The scientist's believe that prion's may be naturally occurring and being destroyed in mice brain's all the time, it's only when concentrations build to a certain number do disease symptoms develop. This was caused by introduction of the wire.

Have to keep and eye out for more research on this...

Rhody...