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JoshCrow
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I was just pondering when this would happen when, lo and behold, it seemingly just has.

Scientists in a lab have effectively combined some ingredients and created a living bacterial organism.
MSNBC link

quote:

It may not quite be "Frankenstein," but for the first time scientists have created an organism controlled by completely human-made DNA.

Using the tools of synthetic biology, scientists from the J. Craig Venter Institute installed a completely artificial genome inside a host cell without DNA. Like the bolt of lightning that awakened Frankenstein, the new genome invigorated the host cell, which began to grow and reproduce, albeit with a few problems.

The research marks a technical milestone in the synthesis and implantation of artificial DNA. Venter expects the research will lead to cheaper drugs, vaccines and biofuels in several years — and dozens of other companies and researchers are working toward the same goal.

Story continues below ↓
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"This is the first synthetic cell that's been made," said Venter. "We call it synthetic because the cell is totally derived from a synthetic chromosome, made with four bottles of chemicals on a chemical synthesizer, starting with information in a computer."

The research, published Thursday by the journal Science, combines two of Venter's past achievements.

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In 2007 Venter transplanted the genome of one Mycoplasma bacterium into another. Venter and his colleagues also synthesized a trimmed down, artificial version of Mycoplasma's DNA, a project known as the Minimal Genome Project. Attempts to implant the synthetic DNA all failed, until now.

In the current research, Venter and his colleagues, who include Nobel laureate Hamilton Smith, first synthesized Mycoplasma's full genome. Then they added hundreds of thousands of additional base pairs to "watermark" the DNA and distinguish it from a natural one.

Venter and his colleagues created a special code, similar to Morse code, to "write" within the DNA itself. Instead of dots and dashes, they used the sequence of four DNA nucleotides, thymine (T), guanine (G), cytosine (C), and adenine (A), as a code for any letter, number or punctuation mark. Using the code, the team included the names of the study co-authors, a website and even several philosophical quotes, complete with punctuation.

The completed DNA sequence was more than 1 million base pairs long. The human genome, by comparison, is more than 3 billion base pairs long.

Cells build up full sequence
No machine can turn out a single piece of DNA anywhere close to that long, however. Instead, Venter and his colleagues started with many relatively small pieces of DNA. Then the scientists transferred DNA pieces back and forth between a yeast cell and E. coli bacteria, turning the many short pieces into fewer but longer DNA segments.

Once the synthetic DNA segment reached the desired length the scientists injected it into a Mycoplasma bacterium that had had its own DNA removed earlier. Needless to say, the process of assembling such a lengthy piece of synthetic DNA was complicated.

"I hope the day comes when making genomes is something everyone can do," said Pamela Silver, a systems biologist at Harvard Medical School.

Some genes suffered glitches
The new, synthetic DNA "booted up" the bacterium, but not without a few problems: Several of the synthesized genes didn't work properly. And the genes that did work didn't do anything particularly useful, at least by human standards.


JCVI
This micrograph shows stained Mycoplasma mycoides cells dividing after transplantation of an artificial genome.
The Mycoplasma bacteria grew and reproduced, but that was about all. Within several years however, Venter and his colleagues hope to create more exciting bacteria that will speed up the production and drive down the costs of biofuels, vaccines and drugs.

Venter has teamed up with a major oil and gas company, and a pharmaceutical company, to help realize these goals.

Venter's work falls into a nascent field of science known as synthetic biology. Synthetic biology builds on the decades-old field of genetic engineering. Unlike genetic engineering, where scientists introduce a handful of new genes into an organism, synthetic biology aims to reprogram entire organisms, including bacteria and viruses.

The creation and insertion of a synthetic genome more than 1 million base pairs is a technical landmark, said Frances Arnold, a synthetic biologist at the California Institute of Technology in Pasadena. He said the feat showcases scientists' ability to precisely manipulate long sections of DNA.

But before consumers see any benefit several significant hurdles have to be solved. One of the biggest problems is that scientists are still searching for the specific genetic code to produce cheap drugs, biofuel and other products.

"We can write anything we want," said Arnold. "The problem is that we don't know what to write."

I tend to greet such news with skepticism (surely I thought this would merit more than just a sidebar article if it were significant!). The premise, however, intrigues me.

If scientists can in fact mix some chemicals and create a living, independent entity... that really does have a lot of religious implications. Not that I think people are likely to be convinced one way or another, but when you think deeply about it, it really seems to suggest that there is nothing particularly special about life.

[ May 20, 2010, 02:41 PM: Message edited by: JoshCrow ]

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JoshCrow
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Here's the Science article:

quote:

Synthetic Genome Brings New Life to Bacterium
Elizabeth Pennisi
For 15 years, J. Craig Venter has chased a dream: to build a genome from scratch and use it to make synthetic life. Now, he and his team at the J. Craig Venter Institute (JCVI) in Rockville, Maryland, and San Diego, California, say they have realized that dream. In this week's Science Express (www.sciencemag.org/cgi/content/abstract/science.1190719), they describe the stepwise creation of a bacterial chromosome and the successful transfer of it into a bacterium, where it replaced the native DNA. Powered by the synthetic genome, that microbial cell began replicating and making a new set of proteins.

This is "a defining moment in the history of biology and biotechnology," says Mark Bedau, a philosopher at Reed College in Portland, Oregon, and editor of the scientific journal Artificial Life. "It represents an important technical milestone in the new field of synthetic genomics," says yeast biologist Jef Boeke of Johns Hopkins University School of Medicine in Baltimore, Maryland.

The synthetic genome created by Venter's team is almost identical to that of a natural bacterium. It was achieved at great expense, an estimated $40 million, and effort, 20 people working for more than a decade. Despite this success, creating heavily customized genomes, such as ones that make fuels or pharmaceuticals, and getting them to "boot" up the same way in a cell is not yet a reality. "There are great challenges ahead before genetic engineers can mix, match, and fully design an organism's genome from scratch," notes Paul Keim, a molecular geneticist at Northern Arizona University in Flagstaff.

The "synthetic" bacteria unveiled this week have their origins in a project headed by Venter and JCVI colleagues Clyde Hutchison III and Hamilton Smith to determine the minimal instructions needed for microbial life and from there add genes that could turn a bacterium into a factory producing compounds useful for humankind. In 1995, a team led by the trio sequenced the 600,000-base chromosome of a bacterium called Mycoplasma genitalium, the smallest genome of a free-living organism. The microbe has about 500 genes, and researchers found they could delete 100 individual genes without ill effect (Science, 14 February 2003, p. 1006).

But confirming the minimal genome suggested by those experiments required synthesizing a full bacterial chromosome and getting it to work in a recipient cell, two steps that have taken years because the technology to make and manipulate whole chromosomes did not exist. In 2007, Venter, Smith, Hutchison, and colleagues finally demonstrated that they could transplant natural chromosomes from one microbial species to another (Science, 3 August 2007, p. 632). By 2008, they showed that they could make an artificial chromosome that matched M. genitalium's but also contained "watermark" DNA sequences that would enable them to tell the synthetic genome from the natural one (Science, 29 February 2008, p. 1215).

But combining those steps became bogged down, in part because M. genitalium grows so slowly that one experiment can take weeks to complete. The team decided to change microbes in midstream, sequencing the 1-million-base genome of the faster-growing M. mycoides and beginning to build a synthetic copy of its chromosome. Last year, they showed they could extract the M. mycoides natural chromosome, place it into yeast, modify the bacterial genome, and then transfer it to M. capricolum, a close microbial relative (Science, 21 August 2009, p. 928; 25 September 2009, p. 1693). The next step was to show that the synthetic copy of the bacterial DNA could be handled the same way.

The researchers started building their synthetic chromosome by going DNA shopping. They bought from a company more than 1000 1080-base sequences that covered the whole M. mycoides genome; to facilitate their assembly in the correct order, the ends of each sequence had 80 bases that overlapped with its neighbors. So that the assembled genome would be recognizable as synthetic, four of the ordered DNA sequences contained strings of bases that, in code, spell out an e-mail address, the names of many of the people involved in the project, and a few famous quotations.

Using yeast to assemble the synthetic DNA in stages, the researchers first stitched together 10,000-base sequences, then 100,000-base sequences, and finally the complete genome. However, when they initially put the synthetic genome into M. capricolum, nothing happened. Like computer programmers debugging faulty software, they systematically transplanted combinations of synthetic and natural DNA, finally homing in on a single-base mistake in the synthetic genome. The error delayed the project 3 months.

After months of unsuccessfully transplanting these various genome combinations, the team's fortune changed about a month ago when the biologists found a blue colony of bacteria had rapidly grown on a lab plate over the weekend. (Blue showed the cells were using the new genome). Project leader Daniel Gibson sent Venter a text message declaring success. "I took my video camera in and filmed [the plate]," says Venter.

They sequenced the DNA in this colony, confirming that the bacteria had the synthetic genome, and checked that the microbes were indeed making proteins characteristic of M. mycoides rather than M capricolum. The colony grew like a typical M. mycoides as well. "We clearly transformed one cell into another," says Venter.

"That's a pretty amazing accomplishment," says Anthony Forster, a molecular biologist at Vanderbilt University in Nashville, Tennessee. Still, he and others emphasize that this work didn't create a truly synthetic life form, because the genome was put into an existing cell.

At the moment, the techniques employed by Venter's team are too difficult to appeal to any potential bioterrorists, researchers stress. Nonetheless, "this experiment will certainly reconfigure the ethical imagination," says Paul Rabinow, an anthropologist at the University of California, Berkeley, who studies synthetic biology. "Over the long term, the approach will be used to synthesize increasingly novel designed genomes," says Kenneth Oye, a social scientist at the Massachusetts Institute of Technology in Cambridge. "Right now, we are shooting in the dark as to what the long-term benefits and long-term risks will be."

As ever more "artificial" life comes into reach, regulatory agencies will need to establish the proper regulations in a timely fashion, adds Oye. "The possibility of misuse unfortunately exists," says Eckard Wimmer of Stony Brook University in New York state, who led a team that in 2002 created the first synthetic virus (Science, 9 August 2002, p. 1016).

Venter says that JCVI has applied for several patents covering the work, assigning them to his company, Synthetic Genomics, which provided much of the funding for the project. A technology watchdog group, ETC Group in Ottawa, has argued that these actions could result in a monopoly on synthesized life (Science, 15 June 2007, p. 1557), but others are not worried. Given the current climate for granting and upholding patents of this type, says Oye, "it is unlikely that Synthetic Genomics will become the Microsoft of synthetic biology."

"One thing is sure," Boeke says. "Interesting creatures will be bubbling out of the Venter Institute's labs."



[ May 20, 2010, 02:36 PM: Message edited by: JoshCrow ]

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Grant
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I would consider it more miraculous if I didn't understand the biology behind it. Seems to me it was simple genetic manipulation of bacteria.

I can already create a living, independent being, by simply combining a sperm cell with an ovum. I don't know about the religious aspects of such combination.

50 to 100 years from now, when they are able to create an entire synthetic human being, I still won't be powerfully impressed, it's simply playing around with what is available. Creating "synthetic" life is no more mysterious then creating "un-synthetic" life the old fashioned way. It's simply science and technology.

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OpsanusTau
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Inaccurate thread title.

Synthetic genome is not a synthetic lifeform. DNA by itself is not life; transcriptional machinery and cellular environment are not inconsequential considerations.

Also, it's not as though the scientists designed ANY of the genes.

Nor was the DNA assembled entirely synthetically - the original sequences were, but already-living cells were required to attach the pieces together.

I don't mean to minimize the accomplishment, it's still really neat. Neatness aside I have my doubts about the utility of such a project, but I could be wrong. And who doesn't like cool things?

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djquag1
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More liberal bias. Obviously only our Lord God can create new lifeforms; there's obviously some fudging of the data going on here.
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Grant
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OT-

Just to clarify for myself. I understand that virus's are not classified as "alive". I did believe that bacteria were classified as being "alive".

While I do not subscribe the concept as miraculous, wouldn't taking two components described as "not alive", and combining them together and forming a component that could be described as "alive", be indeed described as "creating life"?

I understand that DNA by itself is not life, but I assumed that the bacterial shell it was inserted into was also not "alive".

If indeed the cell was already alive, even with it's native DNA removed, as you describe, then you are right, it was not "creating life", but simply genetic manipulation of bacterium.

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JoshCrow
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quote:
Originally posted by Grant:
I would consider it more miraculous if I didn't understand the biology behind it. Seems to me it was simple genetic manipulation of bacteria.

I can already create a living, independent being, by simply combining a sperm cell with an ovum. I don't know about the religious aspects of such combination.

50 to 100 years from now, when they are able to create an entire synthetic human being, I still won't be powerfully impressed, it's simply playing around with what is available. Creating "synthetic" life is no more mysterious then creating "un-synthetic" life the old fashioned way. It's simply science and technology.

In fact it is the very mundane nature of science that demystifies what was once mysterious. You don't think any interesting questions are raised by this avenue of exploration?
If you don't find the religious implications interesting, why post in a thread about it? Just to say "this isn't interesting to me"?

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Gaoics79
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quote:
Venter and his colleagues created a special code, similar to Morse code, to "write" within the DNA itself. Instead of dots and dashes, they used the sequence of four DNA nucleotides, thymine (T), guanine (G), cytosine (C), and adenine (A), as a code for any letter, number or punctuation mark. Using the code, the team included the names of the study co-authors, a website and even several philosophical quotes, complete with punctuation.
This part caught my eye. Is this to say that these scientists are able to encode data in a lifeform that gets passed down to successive generations? Or to put it another way, if they encode the current generation of bacteria with "Hi Mom!" does that mean someone a thousand years from now could catch one of this bacterium's descendants in a test tube and decode "Hi Mom!" from its genetic material?
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JoshCrow
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quote:
Originally posted by jasonr:
quote:
Venter and his colleagues created a special code, similar to Morse code, to "write" within the DNA itself. Instead of dots and dashes, they used the sequence of four DNA nucleotides, thymine (T), guanine (G), cytosine (C), and adenine (A), as a code for any letter, number or punctuation mark. Using the code, the team included the names of the study co-authors, a website and even several philosophical quotes, complete with punctuation.
This part caught my eye. Is this to say that these scientists are able to encode data in a lifeform that gets passed down to successive generations? Or to put it another way, if they encode the current generation of bacteria with "Hi Mom!" does that mean someone a thousand years from now could catch one of this bacterium's descendants in a test tube and decode "Hi Mom!" from its genetic material?
My biological understanding is shaky at best, but I think so, if mutations have not occurred and succeeded in propagating. In this way, they have "watermarked" their creation.
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Jordan
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Josh, Grant is saying that he's doesn't think that the exercise under discussion is particularly interesting, which is a worthwhile counterpoint if someone else is saying that it is. It's not the same as him, personally, not being interested in this thread. [Smile]

Speaking for myself, I do find this interesting, but I agree with Ops and Grant that it will be far more interesting when they manage to create entirely novel, human-designed synthetic genomes. That's sort of what Frances Arnold was saying in the last paragraph of your first post. This is a technology test, which is a step along the road, but the really fascinating stuff is yet to come!

[ May 20, 2010, 03:42 PM: Message edited by: Jordan ]

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MattP
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quote:
if they encode the current generation of bacteria with "Hi Mom!" does that mean someone a thousand years from now could catch one of this bacterium's descendants in a test tube and decode "Hi Mom!" from its genetic material?
If that particular DNA had no beneficial function, then it's likely to not be conserved over such a long period of time, given how rapidly bacteria reproduce and mutate.
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JoshCrow
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quote:
Originally posted by Jordan:
Josh, Grant is saying that he's doesn't think that the exercise under discussion is particularly interesting, which is a worthwhile counterpoint if someone else is saying that it is. It's not the same as him, personally, not being interested in this thread. [Smile]

Heh, not to squelch free speech around here, but for someone to say "It's simply science and technology" and "simply playing around with what is available" is, I think, a worthless contribution to discussion. If someone wanted to start a thread discussing a new law, and someone else chirped up "it's only some legislation, some words on a page somewhere", they have either entered the thread to be obnoxious or to attack the idea of laws themselves, which is a topic for another thread of its own. I could stick my head into every thread and say "meh, it's only so-and-so" - it's my right, but why on earth would I want to do such a thing?

I also think that calling something that took 20 years of hard work to achieve "simple" is just insulting - to the scientists.

In short, I think it's trolling, which is ironic since I defended Grant against the very accusation of trolling in another thread!!

[ May 20, 2010, 03:53 PM: Message edited by: JoshCrow ]

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MattP
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I think Grant was Just indicating that there aren't really religious implications at this point, and I agree. They've used some cool new tech to basically copy an existing biological element. That's not completely novel, just this particular application (DNA) is.

When we can synthesize DNA of our own design to create a novel life form I think then we'll be in the territory of existential pondering but I still think you'll find few people on either side converting. "Yeah, so we created new life, but were only able to do it because God showed us how life works and gave us the basic building blocks to accomplish the feat."

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MattP
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FWIW, I think this is really cool and is a key step on the path to our inevitable ability to basically "print" life.
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Grant
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quote:
Originally posted by MattP:
I think Grant was Just indicating that there aren't really religious implications at this point, and I agree. They've used some cool new tech to basically copy an existing biological element. That's not completely novel, just this particular application (DNA) is.

Thank you Matt, that's what I was trying to say. I wasn't saying that the topic wasn't interesting, just that I didn't see religious connotations in it. Obviously it wasn't simple for those guys, but I bet it will be progressively easier the next time they do it.

I seriously wasn't impugning these people's work. I just don't see it as magic. Genetic manipulation is simply the next step up from cloning, and scientists have been saying that it's right around the corner for awhile now.

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JoshCrow
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quote:
Originally posted by Grant:
quote:
Originally posted by MattP:
I think Grant was Just indicating that there aren't really religious implications at this point, and I agree. They've used some cool new tech to basically copy an existing biological element. That's not completely novel, just this particular application (DNA) is.

Thank you Matt, that's what I was trying to say. I wasn't saying that the topic wasn't interesting, just that I didn't see religious connotations in it. Obviously it wasn't simple for those guys, but I bet it will be progressively easier the next time they do it.

I seriously wasn't impugning these people's work. I just don't see it as magic. Genetic manipulation is simply the next step up from cloning, and scientists have been saying that it's right around the corner for awhile now.

This is a bit more reasonable than your initial comparison to what you can get done "with a sperm and an egg". I never said this was magical, you know, but it IS a milestone in the technology.

And since you don't see any religious implications, I'll spell out what I'm thinking: - if parts can simply be assembled and activated by scientists in a lab, what becomes of the idea of a "soul" to differentiate between a corpse and a living creature? If the parts of a human being can be assembled and "activated" through a technological process, doesn't this potentially cause problems for people who believe certain things about how souls come and go? And what about the implication that this suggests that life on earth could have arisen spontaneously through chemical interaction rather than divine intervention?

There are lots of implications to this. You may not think of these things personally, but I promise you some people do.

[ May 20, 2010, 04:44 PM: Message edited by: JoshCrow ]

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OpsanusTau
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Encoding data in genetic material that is not functional does not seem like a safe way to keep it for a long time. If there's no selection pressure for it to stay, random damage will probably garble or destroy it within a very short time.

The definition of life is difficult to nail down, but it actually doesn't matter that much in this case. The cell into which the new DNA was inserted might or might not have been "alive" at the time of insertion, but it was CERTAINLY alive at some point before that. And when it was alive, it made all of the transcriptional machinery and various background proteins that allowed the new DNA to function when inserted.


quote:
I think this is really cool and is a key step on the path to our inevitable ability to basically "print" life.
I also think that it's neat but disagree that any such ability is inevitable.
And even postulating an eventual future ability to actually make prokaryotes, it is a mind-bogglingly huge step from there even to single-celled eukaryotes - and an even bigger one to multicellular life.

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Grant
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quote:
Originally posted by JoshCrow:
This is a bit more reasonable than your initial comparison to what you can get done "with a sperm and an egg". I never said this was magical, you know, but it IS a milestone in the technology.

And since you don't see any religious implications, I'll spell out what I'm thinking: - if parts can simply be assembled and activated by scientists in a lab, what becomes of the idea of a "soul" to differentiate between a corpse and a living creature? If the parts of a human being can be assembled and "activated" through a technological process, doesn't this potentially cause problems for people who believe certain things about how souls come and go? And what about the implication that this suggests that life on earth could have arisen spontaneously through chemical interaction rather than divine intervention?

There are lots of implications to this. You may not think of these things personally, but I promise you some people do. [/QB]

Ahhh, now that is interesting. But to get to your first point, about the sperm and egg, I think you see what these scientists did as more stupendous then how I see it. All they did was put some DNA into a cell. We've been doing that already with cloning. The hard part was the fact that they artificially constructed the DNA. But I can also put some DNA in another cell, with my sperm. Thus my comparison between the two, and that I did not see the idea as "miraculous." We are simply recreating what biology already does artificially. Maybe "simply" is the wrong word. We are "very difficultly" recreating what biology already does.

But I do understand your implications surrounding the soul now. I do find that very very very interesting. But I think it's a little early to be wondering about that. This was a bacteria, nobody really believed bacteria had souls anyways. A dog is a living being, but according to the monotheist religions, dogs do not possess souls. Same thing for plants. Now when they are able to create an entirely new living human being.......

But OT seems to think this might be impossible. He/she seems to be a little more well read then I am on the subject.

But I will add that something that is seen as impossible today, often is very possible in the future. It's amazing what we can do now that we thought was never possible.

An even more interesting discussion about souls would dwell on Alzheimer's, and what implications it has on the existence of souls.

The ideas of life evolving on earth due to divine intervention and the idea of it arising from chemical combination are actually not opposed to one another. One could simply argue that God controlled the first chemical combination. So the key is not how life came to be, but who was behind it. You can either believe God was behind it, or nobody was behind it. Either way, the how does not matter.

[ May 20, 2010, 05:13 PM: Message edited by: Grant ]

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JoshCrow
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quote:
Originally posted by Grant:

The ideas of life evolving on earth due to divine intervention and the idea of it arising from chemical combination are actually not opposed to one another. One could simply argue that God controlled the first chemical combination. So the key is not how life came to be, but who was behind it. You can either believe God was behind it, or nobody was behind it. Either way, the how does not matter.

One could believe that God was the first "scientist" to do so, but the fact that "mere" humans can also do it may be sees as detracting from the miraculous nature of God doing it.

You could, of course, say God intended for us to learn how to do it all along, and that's an interesting position too (and unfalsifiable, of course).

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Grant
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quote:
Originally posted by JoshCrow:
One could believe that God was the first "scientist" to do so, but the fact that "mere" humans can also do it may be sees as detracting from the miraculous nature of God doing it.

You could, of course, say God intended for us to learn how to do it all along, and that's an interesting position too (and unfalsifiable, of course). [/QB]

Mmmmmmm, yummmy. That would depend on weather the inherent difference between God and Man was power... or knowledge. Of course a wise man would tell you that knowledge WAS power [Big Grin] Heh heh.

One thing that is NOT under debate, is that God, to be God, would possess all knowledge already anyways, regardless of method. Thus, if it were possible for a man or woman to create or destroy, through science, then God already knew how to do it anyways, or in fact that God DESIGNED the universal laws under which science operates. God would not just be the first scientist, he would be the father of science, the creator of science.

The second question is that, once these laws, or system, is created, is God, as the creator, constrained by those rules or not. If God wants to part the Red Sea, can he break the laws of gravity? Or does he have to work within the framework of existance? Certainly no human being can break these laws. In order to fly, man must build a plane, or a balloon, or a jetpack, or something.

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Al Wessex
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There's a really excellent chapter in Kenneth Miller's book "Finding Darwin's God" called "The Road Back Home". Miller is a Professor of Biology at Brown University. He has spent a lot of time over the past few decades doing a thoroughly effective job of shredding the arguments of religion based anti-evolutionists both within and outside of the scientific establishment.

He also is a devout Christian who believes equally strongly in evolution as outlined by Darwin and in the God of his faith. Most of the book is devoted to debunking anti-evolutionist "theories" very effectively, but I have to admit that this chapter also does an outstanding job of explaining why he, as a scientist, also finds plenty of room in nature as science understands it for God's existence. I won't say more than that, but he covers many issues raised in this thread. I highly recommend the book to everyone interested in this debate.

[ May 20, 2010, 09:15 PM: Message edited by: Al Wessex ]

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Gaoics79
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quote:
Encoding data in genetic material that is not functional does not seem like a safe way to keep it for a long time. If there's no selection pressure for it to stay, random damage will probably garble or destroy it within a very short time.
Okay, but that raises the question, does the data last longer than on a flash card or a DVD-R? And most importantly, how many GB can you store on a bacterium? [Smile]
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OpsanusTau
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quote:
Okay, but that raises the question, does the data last longer than on a flash card or a DVD-R? And most importantly, how many GB can you store on a bacterium?
Ha. [Smile]
First question - I doubt it, though I'm not sure. I'd have to poke around and find out what the rate of accumulated mutations in DNA when it's not being selected for.

For the second question again I would have to look, but I bet it's not that many.

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Rallan
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quote:
Originally posted by MattP:
I think Grant was Just indicating that there aren't really religious implications at this point, and I agree.

Ah but it does. It doesn't mean diddly to most folks from most religions, but it will have a (small) impact on Young Earth Creationists because it will involve moving the goalposts yet again and declaring that this is one of those things that they said wasn't a miracle all along and that science will actually have to do something else to impress them.

Because as we all know, the YEC movement defines macroevolution as "anything which hasn't been performed in a lab yet" [Smile]

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LetterRip
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Are you freezing the Bacteria or are you hoping to recover it from the offspring, and how many offspring are you willing to sample?

If you are willing to get a huge sample of the offspring and have a low reproduction rate you might be able to recover the complete data, especially if you have some error correction that you build in. Depends on how many seed bacteria you start with. But generally going with a random offspring in N years, it will have a really high loss rate for unconserved DNA.

Dang I need to correct myself,

replication error rate for DNA is 1 in a billion for bacteria.

http://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/bio%20101/bio%20101%20lectures/dna/dna.htm

So I must have misremembered the error rate. Could have sworn it was far higher.

So perhaps you could get the data back out in a fairly long time and still get it accurate.

http://www.thinkgene.com/how-much-data-is-a-human-genome/

http://en.wikipedia.org/wiki/File:Genome_Sizes.png

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html

(1 bacterium genome) *
(7,000,000 bases / 1 bacterium genome) *
(2 bits / 1 base) *
(1 byte / 8 bits) *
(1 MB / 1,048,576 bytes) = 1.7 MB approximately.

Which is about 1.7 MB uncompressed so .0017 GB.

[ May 20, 2010, 10:58 PM: Message edited by: LetterRip ]

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Gaoics79
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Okay, so how much data can I store in a 6 ounce filet mignon, cooked rare? And will the data be as stable as the meat is tender?
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edgmatt
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Jeez Louise, I read the title of this thread, and then jumped to the end here. Confused is an understatement. Jasonr, do you realize what an incredibly insane question that appears to be from someone who just joined in the conversation? [Confused]
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Grant
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I thought it was funny.
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JWatts
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quote:
Originally posted by jasonr:
Okay, so how much data can I store in a 6 ounce filet mignon, cooked rare? And will the data be as stable as the meat is tender?

Well now, cooking (even rare) is really going to drop your data throughput. You should stick with the sushi.
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OpsanusTau
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Oh LR I hoped you would do some figuring on that one.

But if the error rate during replication is 1 error per billion base pairs -

(1 error/billion base pairs)*
(7,000,000 base pairs/replication of genome)=
(0.007 errors/replication of genome)*
(1 replication of genome/half an hour)=
(0.014 errors/hour)*
(8,760 hours/1 year)=
122.64 errors/year

That is in the absence of any mutagenic stimulus.

I guess it depends on how long you are wanting to store your data, and how clean it needs to be when you get it back.

quote:
Okay, so how much data can I store in a 6 ounce filet mignon, cooked rare?
Well, a lot more!
Because not only are eukaryotic genomes way bigger, we haven't even figured out all the ways eukaryotic cells store information.

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LetterRip
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As I said -

quote:
If you are willing to get a huge sample of the offspring and have a low reproduction rate you might be able to recover the complete data, especially if you have some error correction that you build in. Depends on how many seed bacteria you start with.
For the filet mignon - Only about 430 times more. The reason is that all your filet mignon cells are going to be largely redundant. Actually it would be far less than that since you need the DNA to be functional which means it would have to code for all of its existing proteins etc. So your functional storage might only be slightly more than of the bacteria.
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Mariner
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Letterrip, last time I checked, we still have no idea what introns do, right? If so, I think it's possible that a vertebrate animal like a fish has more "junk" DNA than a bacteria (the bacteria has to code all those proteins, too). Because of all these issues (DNA identical across cells, so you can't store different data in each one; not much empty space), your ability to tinker with the DNA is limited. Basically, imagine what little you'd be able to do if Windows took up 95% of your hard drive.

(Actually, generally genetic manipulations of bacteria don't even bother with the main genome. Instead, they code on plasmids, which are smaller circles of DNA that can be inserted inside the cell. To continue the computer analogy, it would essentially mean running everything you need off a flash drive without putting anything into the hard drive itself)

As for the spiritual/religious implications, I see none. As Ops has already alluded to, the vagueness of what is life and what isn't increases as you go back to simpler organisms. And it becomes a lot less mystical and a lot more focused on the simple chemistry. After all, the spirituality of life is about the awe-inspiring method of the simple, understood physical and chemical laws building up something as complex as intelligent thought. It's not about encoding proteins with DNA. A bacteria can be frozen, inert, and then come back to life. There's a reason computer analogies tend to come up a lot; they seem more a machine than anything else.

And what was done isn't all that impressive. The "synthetic" part doesn't mean it was created from scratch. It means they basically cut and pasted the original data into their own DNA strand (albeit with some specific junk DNA to prove it's theirs). And then put it into an empty cell. While it's an impressive technical feat, it tells us nothing we didn't previously know.

We know how a cell works.
We know what was on the DNA to begin with.
We know how to create synthetic strands of DNA.
We know how to transfer DNA between organisms.

We just have never done something this big before. Basically, it's the difference between the Wright Bros flights and the first transatlantic flight. One revolutionized our knowledge and understanding. The other improved it to a great extent. Sure, it's still great, but there's no reason to be philosophical about it.

In terms of the religious/mystical questions, in my mind there's two big ones: How did life begin, and how does consciousness arise (if it even exists)? This does not get us any closer to understanding either of them.

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Grant
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quote:
Originally posted by Mariner:

In terms of the religious/mystical questions, in my mind there's two big ones: How did life begin, and how does consciousness arise (if it even exists)? This does not get us any closer to understanding either of them.

That's what I initially considered as well. And was why I saw no religious implications as evident. The specific religious questions brought forward by Josh were the implications of consciousness, or the soul. Josh is looking much further ahead then where we are now, when he asks to consider the religious aspects. There may be no religious questions involved with genetically engineering a bacterium, but there certainly would be if you could genetically engineer a human being, say like a Cylon in the latest Battlestar Galactica series, or like a replicant in Bladerunner.

Sorry to make sci-fi references, but when you are looking ahead, it is often the only point of reference available.

I can't speak as to the actually plausibility of such a creation, I think there are better educated individuals here who could do that.

[ May 21, 2010, 03:28 PM: Message edited by: Grant ]

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OpsanusTau
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quote:
Letterrip, last time I checked, we still have no idea what introns do, right?
Well, that's not really true.
We do know some things that they do. One of the most important is that sometimes they are (or parts of them are) exons - it's called alternative splicing, and it's how one gene can code for many different proteins.

But introns are not the same as what's often called "junk DNA". We really don't know what that does. Many people think it doesn't have a function at all; others think we just don't know what it is. That's all the stuff between genes that isn't regulatory sequences.

Still the "junk" makes up most of the genome. So you could still fit a lot more in. 430 times more information is a lot to me!

PLUS there is all the epigenetic information storage, so if we can figure out how to use that, even more storage space is available.

Does it make a difference to the amount of storage available that it's not binary? I suppose it must.

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Grant
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quote:
Originally posted by OpsanusTau:

Does it make a difference to the amount of storage available that it's not binary? I suppose it must.

Yes, it makes a huge difference. You're going to be able to store MUCH more information, even if you only go to a trinary system.

Most of what you are saying is beyond me, but I do know the answer to that.

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Doug64
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quote:
Originally posted by Grant:
That's what I initially considered as well. And was why I saw no religious implications as evident. The specific religious questions brought forward by Josh were the implications of consciousness, or the soul. Josh is looking much further ahead then where we are now, when he asks to consider the religious aspects. There may be no religious questions involved with genetically engineering a bacterium, but there certainly would be if you could genetically engineer a human being, say like a Cylon in the latest Battlestar Galactica series, or like a replicant in Bladerunner.

Sorry to make sci-fi references, but when you are looking ahead, it is often the only point of reference available.

I can't speak as to the actually plausibility of such a creation, I think there are better educated individuals here who could do that.

Personally, I have to agree with your first reaction - it doesn't really have religious implications, mainly because the religious argument isn't that only God can create life, but that life can't spontaneously come into existence. This experiment doesn't touch on that at all. For the question of the existence of souls, I don't think even the possible future existence of replicant-like individuals touches on the question - after all, like you point out, human beings have been creating human beings all along, that's simply a more controlled method for doing so.

Mind, it might have religious significance for the nature of the soul - if we can create brand-new life-forms by mix-and-match genetic manipulation, does God create a soul to match the body, are souls a natural result that matches the body, are they pre-existent "neutral" forms that either are given shape and function by the natural body, or not?

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Grant
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quote:
Originally posted by Doug64:
quote:
Originally posted by Grant:
That's what I initially considered as well. And was why I saw no religious implications as evident. The specific religious questions brought forward by Josh were the implications of consciousness, or the soul. Josh is looking much further ahead then where we are now, when he asks to consider the religious aspects. There may be no religious questions involved with genetically engineering a bacterium, but there certainly would be if you could genetically engineer a human being, say like a Cylon in the latest Battlestar Galactica series, or like a replicant in Bladerunner.

Sorry to make sci-fi references, but when you are looking ahead, it is often the only point of reference available.

I can't speak as to the actually plausibility of such a creation, I think there are better educated individuals here who could do that.

Personally, I have to agree with your first reaction - it doesn't really have religious implications, mainly because the religious argument isn't that only God can create life, but that life can't spontaneously come into existence. This experiment doesn't touch on that at all. For the question of the existence of souls, I don't think even the possible future existence of replicant-like individuals touches on the question - after all, like you point out, human beings have been creating human beings all along, that's simply a more controlled method for doing so.

Mind, it might have religious significance for the nature of the soul - if we can create brand-new life-forms by mix-and-match genetic manipulation, does God create a soul to match the body, are souls a natural result that matches the body, are they pre-existent "neutral" forms that either are given shape and function by the natural body, or not?

I agree 100%, Doug.
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Hannibal
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Am I the only one who thinks that this is going to lead into a zombie epidemic?
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Brian
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My question is:
Where did they stick the DNA used as the 'watermark'?
How would the existance of 30% more DNA affect the normal transcription?
What happens if a chunk of that watermark gets spliced into the working DNA of the cell?

I know that the watermark says 'name, name, quote, knowwhatimean?' in their special Morse code, but what does it say in the cellular code?
Is it possible to construct a series of base pairs that the cellular machinery will fail to recognize and so just skip it?

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JWatts
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quote:
Originally posted by Hannibal:
Am I the only one who thinks that this is going to lead into a zombie epidemic?

Perhaps, it's time I stocked up on ammo. [Big Grin]

And I should retrieve my copy of The Zombie Survival Guide.

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