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InvisibleJoieDeVivre
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Synthetic Biology and Artificial Life
    #17418433 - 12/19/12 06:18 PM (11 years, 3 months ago)

I'm interested in hearing the shroomery's opinion on the use of synthetic biology. If you don't know much about it I'll link to a video discussing genetic engineering tofay and it's uses, which is worth skimming through before voting in the poll.


For some reason this embedding isn't working in the preview so here's a link: http://www.youtube.com/watch?feature=player_embedded&v=rD5uNAMbDaQ.


I want to see the difference in the Shroomery's opinions compared to this 2009 survey done by the New Yorker on public perception of synthetic biology.

The study also found, not included in the image, that 30% responded that “it is morally wrong to create artificial life."




Feel free to discuss below, I'd love to hear about your perception of potential risks and benefits as well as your impression of the "morality" of synthetic life.
What is your impression of the ever increasing use of synthetic biology and it's implications for our society?
You may choose only one
What is your perception of the morality of synthetic biology? (explain your position in the thread)
You may choose only one


Votes accepted from (12/19/12 03:12 PM) to (No end specified)
You must vote before you can view the results of this poll



--------------------
Sapere aude

"We cannot live for ourselves alone. Our lives are connected by a thousand invisible threads, and along these sympathetic fibers, our actions run as causes and return to us as results."


UBUNTU- I am because we are.



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OfflineNullface

Registered: 09/04/11
Posts: 4,734
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Re: Synthetic Biology [Re: JoieDeVivre] * 9
    #17418444 - 12/19/12 06:19 PM (11 years, 3 months ago)

Do you think I'm the kind of man who has time to watch videos, read charts and graphs AND take polls?

:thumbdown:

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Offlineakira_akuma
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Re: Synthetic Biology [Re: Nullface] * 1
    #17418510 - 12/19/12 06:31 PM (11 years, 3 months ago)

that pie chart already shows how dumb the population that took part in the study is... 6% reserving their participation for further review.

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OfflineKremrBigSikter
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Re: Synthetic Biology [Re: Nullface]
    #17418518 - 12/19/12 06:32 PM (11 years, 3 months ago)

I don't think anyone can really foresee what sort of risks could come from this type of thing in the long run, without going into total science fiction holocaust mode. As long as they're doing little projects on e. coli there's probably no problem though, and the applications can probably be very useful and more wide ranging than we can predict now.


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InvisibleAcidic_SlothM
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Re: Synthetic Biology and Artificial Life [Re: JoieDeVivre] * 1
    #17418519 - 12/19/12 06:33 PM (11 years, 3 months ago)

i am hoping to become a synthetic biologist eventually. i have a long way to go to get there though, about a decade of schooling, but it is something i found interesting enough to get me off my ass.


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InvisibleJoieDeVivre
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Re: Synthetic Biology [Re: KremrBigSikter]
    #17418528 - 12/19/12 06:35 PM (11 years, 3 months ago)

I mean, there's risk with any sort of technology we can create when it falls into the wrong hands. :shrug: Bigger projects involving synthetic biology are the types of things that will lead to curing disease, reprogramming cells to be able to fight off infections and protect proper development and being able to create completely organic organs for replacement using the patient's own DNA instead of transplanting organs that may reject.


--------------------
Sapere aude

"We cannot live for ourselves alone. Our lives are connected by a thousand invisible threads, and along these sympathetic fibers, our actions run as causes and return to us as results."


UBUNTU- I am because we are.



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InvisibleSalomon
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Re: Synthetic Biology [Re: akira_akuma]
    #17418540 - 12/19/12 06:37 PM (11 years, 3 months ago)

1.manufacture dna
2.stop aging and disease, engage in hyper reproduction of cells during healing, increase brain efficiency by 300%, etc
3.???
4.world war 4, eugenics, NWO


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EVERYTHING EVENTUALLY BECOMES A DESERT


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Offlineakira_akuma
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Re: Synthetic Biology [Re: Salomon]
    #17418543 - 12/19/12 06:38 PM (11 years, 3 months ago)

or jut over use and eventual degradation of the value of artificial life. :shrug:

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InvisibleAsante
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Re: Synthetic Biology and Artificial Life [Re: JoieDeVivre] * 1
    #17418597 - 12/19/12 06:48 PM (11 years, 3 months ago)

It seems to me that, with computer viruses, we are witnessing the birth of a fifth Eon, the Technozoic Eon.


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Omnicyclion.org
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Offlineteal
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Re: Synthetic Biology [Re: akira_akuma] * 2
    #17418608 - 12/19/12 06:50 PM (11 years, 3 months ago)

Quote:

akira_akuma said:
that pie chart already shows how dumb the population that took part in the study is... 6% reserving their participation for further review.




That's just academia for STAL.

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OfflinePatlal
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Re: Synthetic Biology [Re: teal]
    #17418744 - 12/19/12 07:16 PM (11 years, 3 months ago)

OP's vid is crazy interesting.

I'm proud of humans. As if we got from eating our own shit, to bioengineering...


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InvisibleJoieDeVivre
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Re: Synthetic Biology [Re: Patlal]
    #17418773 - 12/19/12 07:21 PM (11 years, 3 months ago)

Quote:

Patlal said:
OP's vid is crazy interesting.

I'm proud of humans. As if we got from eating our own shit, to bioengineering...



I'm glad you enjoyed it, it's one of my favorite biology videos, closely followed by the inner life of a cell.  :nerd:


--------------------
Sapere aude

"We cannot live for ourselves alone. Our lives are connected by a thousand invisible threads, and along these sympathetic fibers, our actions run as causes and return to us as results."


UBUNTU- I am because we are.



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Offlinempd
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Re: Synthetic Biology [Re: JoieDeVivre]
    #17418853 - 12/19/12 07:35 PM (11 years, 3 months ago)

Joie, I would like to apologize to you for calling you dumb in another thread.  That was an unfortunate choice of words and I regret it.


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There is no truer calling for mankind than that of true conservatism.

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InvisibleJoieDeVivre
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Re: Synthetic Biology [Re: mpd]
    #17418877 - 12/19/12 07:42 PM (11 years, 3 months ago)

Quote:

mpd said:
Joie, I would like to apologize to you for calling you dumb in another thread.  That was an unfortunate choice of words and I regret it.



Apology accepted and appreciated. :hippie:


--------------------
Sapere aude

"We cannot live for ourselves alone. Our lives are connected by a thousand invisible threads, and along these sympathetic fibers, our actions run as causes and return to us as results."


UBUNTU- I am because we are.



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Offlinefloatingwater
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Re: Synthetic Biology [Re: JoieDeVivre]
    #17418964 - 12/19/12 08:02 PM (11 years, 3 months ago)

I hope I'm not getting too metaphorical but I feel like the real question is

Are we comfortable pressing fast-forward on the VCR and actually being aware of it?


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InvisibleJoieDeVivre
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Re: Synthetic Biology [Re: floatingwater]
    #17418973 - 12/19/12 08:05 PM (11 years, 3 months ago)

Interesting question considering we were just recently able to simulate the evolution of the first vertebrate with synthetic biology. (I'm a little iffy on the specifics of this so my wording may be wrong.)


--------------------
Sapere aude

"We cannot live for ourselves alone. Our lives are connected by a thousand invisible threads, and along these sympathetic fibers, our actions run as causes and return to us as results."


UBUNTU- I am because we are.



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Offlinefloatingwater
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Registered: 01/06/09
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Re: Synthetic Biology [Re: JoieDeVivre]
    #17419094 - 12/19/12 08:32 PM (11 years, 3 months ago)

Genetic engineering is pretty neat stuff. A lot of these experiments don't fully address the factor of time though. Sure, we know enough about genes to identify components of the genome that are responsible for x, y, and z, and then we insert our own modifications. The problem is that these properties have been changing ever so slightly (sometimes dramatically) for ages and ages. What we are doing in this day and age will forever alter the future.. Good/bad? tough to say


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InvisibleCaine
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Re: Synthetic Biology [Re: floatingwater]
    #17419139 - 12/19/12 08:43 PM (11 years, 3 months ago)

Quote:

JoieDeVivre said:
Interesting question considering we were just recently able to simulate the evolution of the first vertebrate with synthetic biology. (I'm a little iffy on the specifics of this so my wording may be wrong.)




Some researchers at stanford managed to map the genome of a bacterium and model its life cycle up to the point of cell division. Here's the article if y'all are interested. I'm really not happy about this as an in vitro researcher, pretty soon all chemistry and biology will just be done in silico :lol:

http://news.stanford.edu/news/2012/july/computer-model-organism-071812.html

Quote:

In a breakthrough effort for computational biology, the world's first complete computer model of an organism has been completed, Stanford researchers reported last week in the journal Cell.

A team led by Markus Covert, assistant professor of bioengineering, used data from more than 900 scientific papers to account for every molecular interaction that takes place in the life cycle of Mycoplasma genitalium, the world's smallest free-living bacterium.

By encompassing the entirety of an organism in silico, the paper fulfills a longstanding goal for the field. Not only does the model allow researchers to address questions that aren't practical to examine otherwise, it represents a stepping-stone toward the use of computer-aided design in bioengineering and medicine.

"This achievement demonstrates a transforming approach to answering questions about fundamental biological processes," said James M. Anderson, director of the National Institutes of Health Division of Program Coordination, Planning and Strategic Initiatives. "Comprehensive computer models of entire cells have the potential to advance our understanding of cellular function and, ultimately, to inform new approaches for the diagnosis and treatment of disease."

The research was partially funded by an NIH Director's Pioneer Award from the National Institutes of Health Common Fund.

From information to understanding

Biology over the past two decades has been marked by the rise of high-throughput studies producing enormous troves of cellular information. A lack of experimental data is no longer the primary limiting factor for researchers. Instead, it's how to make sense of what they already know.

Most biological experiments, however, still take a reductionist approach to this vast array of data: knocking out a single gene and seeing what happens.

"Many of the issues we're interested in aren't single-gene problems," said Covert. "They're the complex result of hundreds or thousands of genes interacting."

This situation has resulted in a yawning gap between information and understanding that can only be addressed by "bringing all of that data into one place and seeing how it fits together," according to Stanford bioengineering graduate student and co-first author Jayodita Sanghvi.

Integrative computational models clarify data sets whose sheer size would otherwise place them outside human ken.

"You don't really understand how something works until you can reproduce it yourself," Sanghvi said.

Small is beautiful

Mycoplasma genitalium is a humble parasitic bacterium known mainly for showing up uninvited in human urogenital and respiratory tracts. But the pathogen also has the distinction of containing the smallest genome of any free-living organism – only 525 genes, as opposed to the 4,288 of E. coli, a more traditional laboratory bacterium.

Despite the difficulty of working with this sexually transmitted parasite, the minimalism of its genome has made it the focus of several recent bioengineering efforts. Notably, these include the J. Craig Venter Institute's 2008 synthesis of the first artificial chromosome.

"The goal hasn't only been to understand M. genitalium better," said co-first author and Stanford biophysics graduate student Jonathan Karr. "It's to understand biology generally."

Even at this small scale, the quantity of data that the Stanford researchers incorporated into the virtual cell's code was enormous. The final model made use of more than 1,900 experimentally determined parameters.

To integrate these disparate data points into a unified machine, the researchers modeled individual biological processes as 28 separate "modules," each governed by its own algorithm. These modules then communicated to each other after every time step, making for a unified whole that closely matched M. genitalium's real-world behavior.

Probing the silicon cell

The purely computational cell opens up procedures that would be difficult to perform in an actual organism, as well as opportunities to reexamine experimental data.

In the paper, the model is used to demonstrate a number of these approaches, including detailed investigations of DNA-binding protein dynamics and the identification of new gene functions.

The program also allowed the researchers to address aspects of cell behavior that emerge from vast numbers of interacting factors.

The researchers had noticed, for instance, that the length of individual stages in the cell cycle varied from cell to cell, while the length of the overall cycle was much more consistent. Consulting the model, the researchers hypothesized that the overall cell cycle's lack of variation was the result of a built-in negative feedback mechanism.

Cells that took longer to begin DNA replication had time to amass a large pool of free nucleotides. The actual replication step, which uses these nucleotides to form new DNA strands, then passed relatively quickly. Cells that went through the initial step quicker, on the other hand, had no nucleotide surplus. Replication ended up slowing to the rate of nucleotide production.

These kinds of findings remain hypotheses until they're confirmed by real-world experiments, but they promise to accelerate the process of scientific inquiry.

"If you use a model to guide your experiments, you're going to discover things faster. We've shown that time and time again," said Covert.

Bio-CAD

Much of the model's future promise lies in more applied fields.

CAD – computer-aided design – has revolutionized fields from aeronautics to civil engineering by drastically reducing the trial-and-error involved in design. But our incomplete understanding of even the simplest biological systems has meant that CAD hasn't yet found a place in bioengineering.

Computational models like that of M. genitalium could bring rational design to biology – allowing not only for computer-guided experimental regimes, but also for the wholesale creation of new microorganisms.

Once similar models have been devised for more experimentally tractable organisms, Karr envisions bacteria or yeast specifically designed to mass-produce pharmaceuticals.

Bio-CAD could also lead to enticing medical advances – especially in the field of personalized medicine. But these applications are a long way off, the researchers said.

"This is potentially the new Human Genome Project," Karr said. "It's going to take a really large community effort to get close to a human model."



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InvisibleJoieDeVivre
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Registered: 10/13/11
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Re: Synthetic Biology [Re: floatingwater]
    #17419157 - 12/19/12 08:46 PM (11 years, 3 months ago)

Quote:

floatingwater said:
Genetic engineering is pretty neat stuff. A lot of these experiments don't fully address the factor of time though. Sure, we know enough about genes to identify components of the genome that are responsible for x, y, and z, and then we insert our own modifications. The problem is that these properties have been changing ever so slightly (sometimes dramatically) for ages and ages. What we are doing in this day and age will forever alter the future.. Good/bad? tough to say



Anything we do alters the future because it alters development, behaviors, etc all of which can end up altering our genetics and the genetics of other organisms albeit slowly. If we're only speeding up a natural process can it really be either good or bad bad? I'm inclined to think it will be a combination of both or neutral overall until it is either used for good or bad. :shrug:


--------------------
Sapere aude

"We cannot live for ourselves alone. Our lives are connected by a thousand invisible threads, and along these sympathetic fibers, our actions run as causes and return to us as results."


UBUNTU- I am because we are.



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InvisiblePenelope_Tree
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Re: Synthetic Biology [Re: JoieDeVivre]
    #17419180 - 12/19/12 08:53 PM (11 years, 3 months ago)

Ray Kurzweil banks on this kinda stuff. He believes that GMO's will save the world hunger crisis. I posted a link in PS&P the other day to a successful experiment that was able to genetically alter the way a cell responds to light so that it could interact with a tech interface. It has huge implications for longevity (and what it means to be a homo sapien).



Quote:

Caine said:

pretty soon all chemistry and biology will just be done in silico




Probably not true. Silicon is very fragile. There will be another medium to take its place.


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