Bacterial Cell with a Chemically Synthesized Genome

[Ygggdrasil]

Not working in the biological field, the mention of: proteomics, metabolomics, immunomics, epigenetics is news to me. Did these fields even exist, say 5 to 10 years ago ?

All of the "omics" fields really started taking off only in the late 1990s-2000s.

Finally, a question for ygggdrasil, are all of Venter's experimental data and methods open for peer review by other Genome Companies/NIST/DOE, etc.. ? and if not, why not

All of the experimental data and methods for the results the institute has published are available in their papers (in addition to the Science papers, the institute has some methods papers in other journals describing the methods in more detail). Also, the sequences used in all of the published projects are available in the Genbank sequence database (for example, the sequence of the synthetic DNA implanted into the cell in this most recent paper is available at http://www.ncbi.nlm.nih.gov/nuccore/296455217).

 

[ice109]

Here are some writeups from the popular press:
http://www.wired.com/science/discoveries/news/2008/01/synthetic_genome
http://www.nytimes.com/2008/01/24/health/24iht-24genome.9483638.html

And a short perspective on the paper by Biological Engineer Drew Endy (subscription required):
http://www.sciencemag.org/cgi/content/full/319/5867/1196

i was hoping for something that was actually expository. the popular write ups aren't detailed enough and gibsons paper assumes too much. the problem is that I'm not trained as a biologist and while i can look up the words and understand them i don't know why he's using the techniques that he is. for example i don't understand why he gets the cassettes synthesized then puts them into a BAC vector plasmid then cuts them out again with a type 2 restriction exonuclease.

 

[rhody]

Good article in the Wall Street Journal yesterday: http://online.wsj.com/article/SB10001424052748704026204575266460432676840.html?mod=googlenews_wsj"

Interesting approach, divide, overlap, reassemble at overlap points in three stages.

excerpts:

We started with the more than one million letters of genetic instructions for Mycoplasma mycoides, and then made slight modifications to its DNA sequence. First, we deleted 4,000 letters, which removed the function of two genes. We then replaced 10 genes with four "watermark" sequences. These watermark sequences are each over 1,000 letters in length and can be decoded to reveal the names of people, famous quotations and a website address. The entire sequence of DNA letters was then partitioned into 1,100 pieces, and each was synthesized using four different bottles of chemicals that make up DNA. These DNA fragments were designed such that adjacent pieces contained an 80-letter overlap, which facilitated the assembly process by providing unique regions where the synthetic pieces could join.

and

The synthetic Mycoplasma mycoides genome was assembled by adding the overlapping DNA fragments to yeast. Once inside a yeast cell, the yeast machinery recognized that two DNA fragments had the same sequence and assembled them at this overlapping region. The genome was not assembled from all 1,100 pieces at once but rather in three stages: 1,000 letters to 10,000 letters, 10,000 letters to 100,000 letters, and finally 100,000 letters to complete the 1.08 million letter genome. This assembled genome is the largest chemically defined structure ever synthesized in the laboratory.

Practical applications of this research:

We are currently working on the design of new cells that can much more efficiently capture carbon dioxide and "fix" (or incorporate) the carbon into new fuel molecules, new food oils, and new biologically derived sources of plastic and chemicals. We already have funding from the National Institutes of Health to use our synthetic DNA tools to build synthetic segments of every known flu virus so that we can rapidly build new vaccine candidates in less than 24 hours. We are also being funded to see if we can take sets of genes out of bacteria to design new synthetic pathways to make antibiotic compounds that are currently too complex for chemists to make.

Finally, a question for ygggdrasil, Andy Resnick,

It would seem that research (this question applies to the US) is well underway with work on "artificial life", a large number of Google hits confirm this. Do either of you know if said research is being done in the strictest of environments ?

I mean Biohazard Level IV (Doubly sealed, negative pressure buildings buried deep underground) Highly Secured Containment Facilities, and if so with oversight from official US agencies, NIST, DOE. One would hope so...

Rhody...

 

[Andy Resnick]

If understood your point, you are saying that not only is computing power an issue, but intelligently designed software to analyze the results (as applied to the emerging fields of study listed above), correct ? What are the major software players that exist today ? Say the top five in analyzing genomic data. What new software is being considered ?

I think that's about 1/2 right. Here's an interesting recent development:

http://www.livescience.com/technology/090402-robot-scientist.html

I'm not expert enough to say much more than that. I guess my claim is that the complete analysis of data requires insight and creativity, features currently not sufficiently developed in software.

 

[Andy Resnick]

It would seem that research (this question applies to the US) is well underway with work on "artificial life", a large number of Google hits confirm this. Do either of you know if said research is being done in the strictest of environments ?

I mean Biohazard Level IV (Doubly sealed, negative pressure buildings buried deep underground) Highly Secured Containment Facilities, and if so with oversight from official US agencies, NIST, DOE. One would hope so...

Rhody...

I defer to ygggdrasil, but I do know that it is common to use Ebola and HIV virii bodies as carriers for DNA transfections, specifically because they are so infectious. One needn't get all "Andromeda Strain", either.

Plus there's research on the actual nasties themselves: ebola, anthrax, prions, etc., also not in highly secure labs.

 

[zomgwtf]

I defer to ygggdrasil, but I do know that it is common to use Ebola and HIV virii bodies as carriers for DNA transfections, specifically because they are so infectious. One needn't get all "Andromeda Strain", either.

Plus there's research on the actual nasties themselves: ebola, anthrax, prions, etc., also not in highly secure labs.

Indeed, however I'm pretty sure that they implement a 'kill-switch' into their organisms. There are many ways to make this work but I believe the 'popular' one is to make the organism somehow environment dependent. If it leaves the specific environment conditions of the lab, it will die. Or if it runs out of a specific energy source only really provided in the lab, it will die. They set them up with a 'suicide' gene to make this happen in the event that it does escape. I'm not sure how high-security is around the labs but I think they would be more worried about others getting into their data then about the organisms getting out and about.

 

[rhody]

Indeed, however I'm pretty sure that they implement a 'kill-switch' into their organisms. There are many ways to make this work but I believe the 'popular' one is to make the organism somehow environment dependent. If it leaves the specific environment conditions of the lab, it will die. Or if it runs out of a specific energy source only really provided in the lab, it will die. They set them up with a 'suicide' gene to make this happen in the event that it does escape. I'm not sure how high-security is around the labs but I think they would be more worried about others getting into their data then about the organisms getting out and about.

zomgwtf,

Wow, watermarking, kill-switches, environment survival factors... sounds like science fiction, I will take your word that it is science fact. This http://blogs.sciencemag.org/origins/2009/03/fast-mutating-viroids-hold-clu.html" gives me pause, however, something called: "Raw RNA".

While plant scientists try to figure out how to cure crops of viroids, other biologists are fascinated by them because they strip the processes of life down so far to the bone. Recently, Rafael Sanjuán of the University of Valencia in Spain and his colleagues decided to see how much viroids mutate. Humans, chrysanthemums, and other multicellular organisms have many ways of lowering their mutation rate. They can proofread their DNA as it is copied and correct errors. Bacteria are not quite so careful, but they can still repair a lot of DNA damage. Many viruses are decidedly sloppier. What's intriguing about this pattern is the size of the genomes involved: The higher the mutation rate, the smaller the genome.

Viroids offered a fresh opportunity to test this relationship, because they are hundreds of times smaller than viruses, the smallest genomes for which mutation rates had been estimated. Sanjuán and his colleagues infected chrysanthemums with viroids and then let them breed. The researchers then harvested the new viroids and scanned their genomes for mutations. In particular, they looked for mutations that would keep the viroids from replicating, because these must have been new. (They couldn't be carried down from earlier generations, because they keep the viroids from replicating.) To make sure these really were lethal mutations, the scientists engineered viroids with these mutations and injected the mutant viroids into plants. The plants didn't get sick.

and

If early RNA-based life forms had genomes on par with those of viroids, they would have had a gigantic mutation rate. We could not survive with such a high mutation rate because we have such a big genome, with so many vulnerable spots where mutations could deal lethal blows. With a much smaller genome, viruses can survive at a higher mutation rate. And viroids, smaller still, afford mutations an even smaller target.

But the reverse is also true: Without a way to lower their mutation rate, viroids are trapped below a so-called error threshold. The evolution of very accurate gene replication was thus probably a crucial stage in the emergence of more complex life. If life had stayed sloppy, we'd all still be little more than viroids.

The upside of this is that without a stable core of the genome as I understand it, life could not have evolved, a good thing. On the flip side, the fast mutation rate of small genomes is of concern, producing unpredictable results in a "mutated copy", even with all the safeguards built in as mentioned above.

Rhody...

 

[zomgwtf]

Hey, sorry I didn't see your response before I had left or I probably could have responded back while you were still around . Oh well.

zomgwtf,

Wow, watermarking, kill-switches, environment survival factors... sounds like science fiction, I will take your word that it is science fact.

I completely understand your skepticism to do with this. It does seem like a pretty far-fetched idea. So just to make sure you can see I'm not making things up I went looking for this specific technique being used by the Institute.

You can see here:

researchers will be able to engineer synthetic bacterial cells so they cannot live outside of the lab or other production environments. This is done by, for example, ensuring that these organisms have built in dependencies for certain nutrients without which they cannot survive. They can also be engineered with so called “suicide genes” that kick into prevent the organism from living outside of the lab or environment in which they were grown.

http://www.jcvi.org/cms/research/projects/first-self-replicating-synthetic-bacterial-cell/faq/#q8
That it discusses what I was talking about. I remembered reading about it that's why I posted it. So for when they create synthetic organisms they will be able to implement this feature.

The upside of this is that without a stable core of the genome as I understand it, life could not have evolved, a good thing. On the flip side, the fast mutation rate of small genomes is of concern, producing unpredictable results in a "mutated copy", even with all the safeguards built in as mentioned above.

Rhody...

Hmm. When I had first read your post and Andy's response I thought it was dealing with only genetically engineered bacterial organisms (I don't even know why I didn't read further into the part about viruses lol).
If it is only regarding genetically engineered organisms then yes: Viruses that are engineered can still be extremely dangerous, I believe even if their virulent genes are deleted or 'deactivated'. Exactly for the reason you posted, they can rapidly evolve especially when it comes to the ability to infect a greater amount of hosts. So if we engineer a virus specifically to target some other organism, I don't think there is any gurantee that it will not infect a nontarget host. I think this is what you're getting at correct?

Hmm... I can only assume that work done with a virus is done under strict biological confinement(which the above mentioned technique is a part of), and the virulent part of the DNA is deleted and deactivated and its generation time would be increased. I'm not so sure if this is related to the OP though because viruses and fungi are quite different from bacterial cells.
Here's a book from 2004 on the subject:
http://www.nap.edu/openbook.php?record_id=10880&page=169
(They also go into Suicide genes on page 173, if you're further interested in reading about it. But as I mentioned above it doesn't really work the same way on viruses)

I'll leave the rest of the answer for yggg, cause I'm not 100% sure of the safety concerns related to viruses on fungi at this institute

Sorry for the confusion.

 

[Ygggdrasil]

i was hoping for something that was actually expository. the popular write ups aren't detailed enough and gibsons paper assumes too much. the problem is that I'm not trained as a biologist and while i can look up the words and understand them i don't know why he's using the techniques that he is. for example i don't understand why he gets the cassettes synthesized then puts them into a BAC vector plasmid then cuts them out again with a type 2 restriction exonuclease.

Unfortunately, I don't think you'd be able to find an article like this. Your best bet would be to read up a molecular biology textbook to get an idea of how the general techniques work.

It would seem that research (this question applies to the US) is well underway with work on "artificial life", a large number of Google hits confirm this. Do either of you know if said research is being done in the strictest of environments ?

I mean Biohazard Level IV (Doubly sealed, negative pressure buildings buried deep underground) Highly Secured Containment Facilities, and if so with oversight from official US agencies, NIST, DOE. One would hope so...

Venter's work on the M. mycoides was not done in a BL4 lab and would not need to be done in any lab with anything more than the standard safety practices of a microbiology lab. The NIH publishes a set of guidelines for work on recombinant DNA (http://oba.od.nih.gov/rdna/nih_guidelines_oba.html ) that all biology labs follow. In addition, as zomgwtf mentioned, the bacteria we work with is non-pathogenic and has been bred/engineered to not be able to survive outside of the lab. Since Venter's synthetic bacterium is essentially the same as a normal M. mycoides, they pose no more risk to us or the environment as the mycoplasma species that ubiquitously inhabit our world.

The general field of synthetic biology, however, does pose some risks. For example, Venter has said that scientists could use his technology to create flu viruses for vaccine development. This work, and any work involving the synthesis of pathogens, would certainly have to be done in the appropriate facilities and follow existing guidelines for handling these agents. Synthetic biology could, in theory, allow people to obtain controlled pathogens (e.g. smallpox) for nefarious purposes. However, most gene synthesis companies screen customers' orders for sequences from known pathogens (http://www.genesynthesisconsortium.org/Gene_Synthesis_Consortium/Harmonized_Screening_Protocol.html) to help minimize this risk. In terms of what happens when the first completely new species is created using synthetic biology, I'm not sure what the safety requirements would be. Since Venter is interested in creating a bacterium with the smallest possible genome, it seems unlikely that this type of bacterium would pose a threat to anything as it would be unable to survive outside of very specific laboratory conditions.

Scientists have been modifying the genomes of bacteria and other species since the 1970s, when the first recombinant DNA technologies were being developed. Following some fairly common-sense guidelines (such as only working with potentially pathogenic species or sequences in controlled environments and using species that can only survive in laboratory conditions) has kept scientists and others safe from any unintended consequences of their work. The techniques developed by Venter and others certainly open up new possibilities in the realm of genome engineering, but Venter has pushed the bioethics of synthetic biology along with this work (for example, by recruiting bioethicists to review the field of synthetic biology and make suggestions both to his scientists as well as policy makers). I think that the existing regulatory frameworks that oversee research in biology as well as the standard safety practices used by biologists will be sufficient to deal with the potential dangers posed by synthetic biology.

 

[rhody]

As if you didn't need any new evidence on the sheer amount of data available on the internet, consider this: http://fastflip.googlelabs.com/view?q=view%3Apopular&a=0kbs3jlPJS8ieM&source=news&type=embed"

excerpt:

281 Exabytes of Online Data in 2009

In her presentation at PARC, intriguingly entitled 'The Physics of Data,' Marissa Mayer noted that there have been 3 big changes to Internet data in recent times:

1. Speed (real-time data);
2. Scale ("unprecedented processing power");
3. Sensors ("new kinds of data").

Mayer went on to say that there were 5 exabytes of data online in 2002, which had risen to 281 exabytes in 2009. That's a growth rate of 56x over 7 years. Partly, she said, this has been the result of people uploading more data. Mayer said that the average person uploads 15 times more data today (in 2009) than they did just 3 years ago.

and

Exascale Web

HP sees its role as providing the computing platform required to deal with this massive influx of data and the complexity of processing it in real-time. Google clearly sees itself as a provider of exascale web services.

We don't know yet which computing or Internet companies will be most successful over the next 5-10 years, but one thing is for sure. They'll have to know how to process and make sense of massive quantities of data flowing through the Web - and do it in real-time.

Rhody...

 

[alxm]

Hmm, maybe I'm pooping the party a bit.. But really, I haven't been able to see the huge scientific breakthrough here. Now I'm not a biochemist (even if I do some work on biochemical systems), but my girlfriend is, as are many of my friends and colleagues. And most of them seem to be of about the same opinion as me: Venter is very good at PR, and has been for quite some time, and that the amount of attention this got is somewhat disproportionate.

Sequencing DNA isn't new, nor is synthesizing a given sequence of DNA. Personally I don't really regard the genome as being 'chemically synthesized' from 'four bottles of chemicals' when they're in fact assembling the DNA using the same enzymes that do this in vivo. To me, synthesizing 'chemically' would be to use organic chemistry methods, not to use cells to do the job for you.

E.g. say you modify E. Coli or S. Cerevisae to express some protein for you, and purify it. (This is a routine task, almost doable by biochem undergrads these days) I've never heard such a protein being referred to as 'artificial', or 'chemically synthesized'. And if so - what meaning would these terms have?

Leaving some replication errors in (after finding by trial-and-error to that they were biologically insignificant), and then calling it a 'watermark' is a bit silly (but good PR). And then there's of course the whole question of whether replacing the genome of an pre-existing cell counts as "artificially synthesizing". I don't begrudge Venter his success, but I think it needs to be clear here that most of the work here was done using standard (commercialized, even) methods used all around the world every day.

It's certainly a milestone - but basically I'm saying it's an engineering milestone. They didn't do anything people hadn't done before, they just did it on a bigger scale. And made it sound like a lot more than it is.

It's akin to taking some prefabricated parts and assembling them into an engine, according to a given blueprint, and then mounting this engine into a pre-existing chassis/transmission/etc. You could say you built a car, but it'd be more correct to say you built an engine. And it would certainly be stretching it beyond credibility to say you built 'a car from scratch'.

 

[alxm]

Plus there's research on the actual nasties themselves: ebola, anthrax, prions, etc., also not in highly secure labs.

Saywhat? Handling Ebola requires a BSL-4 facility (the highest level) and anthrax is BSL-3 (except for antibiotics-resistant anthracis which is BSL-4, too).

Prions aren't that dangerous to handle. I don't know why you'd worry about them.

(BTW, Rhody: AFAIK BSL-4 buildings aren't required to be underground. The ones I've seen haven't been.)

 

[JRDunassigned]

You folks may enjoy the video of him announcing it:
http://goo.gl/6isZ

My ears are not those of a trained scientist - if you're in the same boat, jump to the last two minutes.

 

[rhody]

Prions aren't that dangerous to handle. I don't know why you'd worry about them.

(BTW, Rhody: AFAIK BSL-4 buildings aren't required to be underground. The ones I've seen haven't been.)

alxm,

One quick off topic question: http://en.wikipedia.org/wiki/Prion" . 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.

A prion (pronounced /ˈpriː.ɒn/ ( listen)[1]) is an infectious agent that is composed primarily of protein.[2] To date, all such agents have been discovered to propagate by transmitting a mis-folded protein state; as with viruses the protein itself does not self-replicate, rather it induces existing polypeptides in the host organism to take on the rogue form.[3] The misfolded form of the prion protein has been implicated in a number of diseases in a variety of mammals, including bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in cattle and Creutzfeldt–Jakob disease (CJD) in humans.

Rhody...

 

[rhody]

On Topic question for Andy, Yggg, zomgwtf, alxm,

With all of Venter's data/methods available for public scrutiny, will any other genetics Lab take on the task or reproducing their results ? Or would the feat simply take too long and cost too much money in order to do so ?

Rhody...

 

[alxm]

One quick off topic question: http://en.wikipedia.org/wiki/Prion" . 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'm no expert but it does sound plausible, if unlikely.
IF it had prions from mad-cow animals, if they're inhaled, if they can then get into your digestive tract, if they manage to survive your digestive tract without geting digested, if they then get into your blood, if they then get into your brain, if they can start 'replicating' there before being destroyed, and if your immune system can't stop the process. - It's got to be at least an order-of-magnitude or so less likely than getting CJD from eating a mad cow, which isn't terribly likely to begin with.

Personally I wouldn't worry, although you can always wear a paper respirator and bring that risk down yet another order of magnitude. Main point was, of course, not that prions are safe - but that there's a vast difference between 'safe to eat', 'safe to handle' and 'safe to handle in a lab'.

I'd rate purified prions as safe to handle in an ordinary chemical lab. They can't replicate on their own, they can't be absorbed through the skin, much less gloves, or inhaled as vapor (if they're in solution). They photo- and biodegrade, so they're not persistent, etc.

Now I went and looked it up, yes, purified prions are typically BSL-2, which is comparable to how hazardous chemicals are treated in a chem lab. Although I just realized this 'explanation' probably doesn't say much to everyone who doesn't have lab experience, but.. Basically I'm talking "be careful, use common sense, know what you're doing and what the risky actions are" level of safety and not "use extreme caution, think twice before every action" level.

 

[alxm]

My ears are not those of a trained scientist - if you're in the same boat, jump to the last two minutes.

Well, his ending there kind of illustrates my point - A good salesman.
It's all good and true. But he naturally leaves out the fact that these are things that very, very, many other people are working on (and that they're not neccesarily at the forefront of it). And that most of what he mentions (better vaccines, synthetic fuels, etc) are (at best) only tangentially related to the work he was announcing.
I'm prepared to give him the benefit of the doubt, but I can't really see any connection at all; i.e. why their 'synthetic' version of this bacteria be better for these purposes than the wild-type. Or indeed, why this species of bacteria would be useful at all. After all, they chose to reproduce this particular bacteria because it had a small genome (i.e. the least amount of work). There's no reason to assume it's the best choice for any other purpose.

With all of Venter's data/methods available for public scrutiny, will any other genetics Lab take on the task or reproducing their results? Or would the feat simply take too long and cost too much money in order to do so ?

Well, AFAIK (and I'm not in the field at all) Venter & Co were the only ones even attempting this to begin with. And again, I consider it more an engineering feat than a scientific one - a nice display of what can be done with current technology, but not something that pushed the boundaries of the technology itself much. So it sounds harsh but scientifically, I'm not sure there's much value in reproducing their result - because I'm not sure there's so much scientific value to begin with. I don't think anyone doubts they did it, and I don't think very many doubted it was possible with today's technology.

On the other hand it'll certainly be repeated eventually. But I think when they do, they'll have a specific reason for doing so. We've gone from 'we believe we can do it' to 'we know we can do it'. So now I think it's mostly a solution waiting for a problem. I know Venter has a project to try to pare down a bacteria to its bare minimum, to create a simple and well-understood organism. A 'vanilla' bacteria if you like. It might be that in that context, they'll want to re-synthesize the DNA 'from scratch' - in which case this is useful. If they're successful I think that'll end up having much more utility.

 

[ViewsofMars]

Thanks to the OP (Gokul43201)for starting this topic. Mention of the article from Science was noted on Eurekalert. http://www.eurekalert.org/pub_releases/2010-05/aaft-su051710.php

Discussion about J. Craig Venter Ph.D. roused my interest. He seems to be involved with quite a few organizations and their projects. He is Chairman of Scientific Advisory Board, U.S. Genomics, Inc.
http://investing.businessweek.com/research/stocks/private/person.asp?personId=401200

U.S. Genomics, Inc. is a very interesting!

U.S. Genomics, Inc. Presents at 13th Annual Software Design for Medical Devices Conference, May-24-2010
04/26/2010
U.S. Genomics, Inc. Presents at 13th Annual Software Design for Medical Devices Conference, May-24-2010 . Venue: Westgate Hotel, San Diego, California, United States. Speakers: Paul Fernandes, Director, Software Development.

U.S. Genomics Inc. Signs Agreement with Becton, Dickinson and Company to Develop Infectious Disease Diagnostic Platform
09/23/2008
U.S. Genomics Inc. has entered into a strategic collaboration with Becton, Dickinson and Company to develop a novel infectious disease diagnostic platform. The collaboration would focus on application of U.S. Genomics' DirectLinear Analysis technology for the detection of infectious organisms in a single molecular diagnostic test.

U.S. Genomics Wins $9.1 Million Contract for Development of Advanced Biosensor by the U.S. Department of Homeland Security
07/16/2008
U.S. Genomics Inc. announced the award of a $9.1 million contract by the U.S. Department of Homeland Security (DHS) Science and Technology Directorate. The Phase IIIX contract under the Bioagent Autonomous Networked Detectors (BAND) program will enable U.S. Genomics to continue development, testing and optimization of the company's sophisticated biological sensor for the detection of airborne pathogens using single molecule DNA mapping technology. U.S. Genomics' unique DNA mapping technology allows extremely precise broadband detection of bacterial pathogens, toxins and viruses in a biological sample. The technology's readings are sensitive to the single-molecule level and yield extremely low false positive rates. Using a universal reagent set that can detect and identify pathogens, the technology produces a genetic signature unique to each DNA fragment in the sample, and also identifies the organism from which the DNA originates.
[Please read on . . .]
http://investing.businessweek.com/research/stocks/private/snapshot.asp?privcapId=96009

 

[Andy Resnick]

It's akin to taking some prefabricated parts and assembling them into an engine, according to a given blueprint, and then mounting this engine into a pre-existing chassis/transmission/etc. You could say you built a car, but it'd be more correct to say you built an engine. And it would certainly be stretching it beyond credibility to say you built 'a car from scratch'.

But this paper is not the endpoint- going on with your analogy, once you've gotten experience building a kit car, the next step is to modify the kit.

 

[Andy Resnick]

On Topic question for Andy, Yggg, zomgwtf, alxm,

With all of Venter's data/methods available for public scrutiny, will any other genetics Lab take on the task or reproducing their results ? Or would the feat simply take too long and cost too much money in order to do so ?

Rhody...

From what I understand (and it's not much), the real value to others is publication of the 'recipe' (or 'technique', if you prefer). It's not obvious to me that anyone will try and duplicate the exact work, but I can guarantee there are other labs trying the same technique using their own cells right now.

 

[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...