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Genome Transplant - (Jun/30/2007 )

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Well, somebody has done it. Now the race is to do it on an artificially constructed genome. (ultimate plasmid transformation - need some really super competant cells aided by membrane fusing agent)

sigh, why am i still a PhD student?

http://www.nature.com/news/2007/070625/full/070625-9.html

QUOTE
By transplanting their genomes, US scientists have converted one species into another.

John Glass and his co-workers at the J. Craig Venter Institute in Rockville, Maryland, have taken DNA from a bacterium called Mycoplasma mycoides and inserted it into cells of the closely related species Mycoplasma capricolum.

They find that the recipient cells with the new genome behave like those of the donor species, making protein molecules characteristic of the donor. It's like re-booting a cell with a new operating system, says Glass.

"The method is very impressive," says biomedical engineer Jim Collins of Boston University. "It's surprising that they could get such a large piece of DNA into the bugs, and even more surprising that they could get the new genome jump-started."

To swap the genomes, the researchers encased M. mycoides cells in a gel and used enzymes to break them apart and destroy their proteins, leaving only their naked DNA.

They mixed this DNA into colonies of M. capricolum and added a chemical that makes cells fuse together. The researchers suspect that some of the recipient cells fused around the naked donor genomes, producing cells with both species' DNA.

When these hybrids divide, one genome ends up in each daughter cell. The donor M. mycoides genome contained a gene conferring resistance to a specific antibiotic, a dose of which was used to kill off all the cells without the donor genome.

The two species' genomes are only about 75% identical. So it wasn't obvious that M. capricolum's machinery for reading and acting on genetic instructions would also work for M. mycoides.

Minimal genome

The work raises the possibility of reprogramming cells with new functions — perhaps even turning cells from other organisms into human stem cells for regenerative medical treatments.

But that is a long way off. Glass's team currently has its sights set on giving a bacterium a completely synthetic genome, made in the laboratory.

This would enable the researchers to design a new species from scratch. It is an ambitious aim, not least because the design rules for an entirely artificial genome are still poorly understood. But the latest work, reported in Science1, shows that a cell's molecular machinery can run on a different genetic operating system.

The bacteria used in the study have very small genomes. Both are pathogens that live in goats, but the team is looking at a related species, Mycoplasma genitalium, a parasite of the human genital tract, as a candidate for making a minimal genome.

The researchers hope to find the smallest set of genes capable of supporting life. They have applied for a patent on a subset of 381 of M. genitalium's 485 genes (see 'The patent threat to designer biology').

Such a minimal genome could be the chassis of a general-purpose cell, to which genes for tailored functions, such as generating pharmaceuticals or biofuels, could be added.

Genome transplants, say the researchers, could make cells that are "platforms for the production of new species using modified natural genomes or manmade genomes". Collins says he expects the team to test their minimal genome by putting it into Mycoplasma. "The question is, can they get it jump-started?" he says
By transplanting their genomes, US scientists have converted one species into another.

John Glass and his co-workers at the J. Craig Venter Institute in Rockville, Maryland, have taken DNA from a bacterium called Mycoplasma mycoides and inserted it into cells of the closely related species Mycoplasma capricolum.

They find that the recipient cells with the new genome behave like those of the donor species, making protein molecules characteristic of the donor. It's like re-booting a cell with a new operating system, says Glass.

"The method is very impressive," says biomedical engineer Jim Collins of Boston University. "It's surprising that they could get such a large piece of DNA into the bugs, and even more surprising that they could get the new genome jump-started."

To swap the genomes, the researchers encased M. mycoides cells in a gel and used enzymes to break them apart and destroy their proteins, leaving only their naked DNA.

They mixed this DNA into colonies of M. capricolum and added a chemical that makes cells fuse together. The researchers suspect that some of the recipient cells fused around the naked donor genomes, producing cells with both species' DNA.

When these hybrids divide, one genome ends up in each daughter cell. The donor M. mycoides genome contained a gene conferring resistance to a specific antibiotic, a dose of which was used to kill off all the cells without the donor genome.

The two species' genomes are only about 75% identical. So it wasn't obvious that M. capricolum's machinery for reading and acting on genetic instructions would also work for M. mycoides.

Minimal genome

The work raises the possibility of reprogramming cells with new functions — perhaps even turning cells from other organisms into human stem cells for regenerative medical treatments.

But that is a long way off. Glass's team currently has its sights set on giving a bacterium a completely synthetic genome, made in the laboratory.

This would enable the researchers to design a new species from scratch. It is an ambitious aim, not least because the design rules for an entirely artificial genome are still poorly understood. But the latest work, reported in Science1, shows that a cell's molecular machinery can run on a different genetic operating system.

The bacteria used in the study have very small genomes. Both are pathogens that live in goats, but the team is looking at a related species, Mycoplasma genitalium, a parasite of the human genital tract, as a candidate for making a minimal genome.

The researchers hope to find the smallest set of genes capable of supporting life. They have applied for a patent on a subset of 381 of M. genitalium's 485 genes (see 'The patent threat to designer biology').

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Such a minimal genome could be the chassis of a general-purpose cell, to which genes for tailored functions, such as generating pharmaceuticals or biofuels, could be added.

Genome transplants, say the researchers, could make cells that are "platforms for the production of new species using modified natural genomes or manmade genomes". Collins says he expects the team to test their minimal genome by putting it into Mycoplasma. "The question is, can they get it jump-started?" he says

-perneseblue-

Now now, dont get over-excited

-mnqcljsm-

Is it the first step towards X-Men ?

-scolix-

QUOTE (perneseblue @ Jun 30 2007, 02:48 AM)
Well, somebody has done it. Now the race is to do it on an artificially constructed genome. (ultimate plasmid transformation - need some really super competant cells aided by membrane fusing agent)

sigh, why am i still a PhD student?



Your excitement is indeed palpable perneseblue (I had to wade through the duplicates of the quoted paragraphs) laugh.gif . And I share your fascination with AL i.e., yours is with the science and mine is with the underlying ethics and metaphysics. Do you think that artificial/synthetic life is inevitable considering man’s (particularly the scientist’s) endless curiosity and tenacity?

Although synthesizing a minimal genome has a lot of practical benefits esp in microbial genetics, would we or could we stop there? With technology that can be harnessed, is man already on the verge of not only controlling and directing but also of creating life?

Have we finally conceded to a reductionist view that life is nothing more than genes and DNA? That we have finally narrowed down our definition of life, its origin and nature, to a mere scientific issue, that could only be poked and prodded with the tools of the natural sciences?

I’m very interested to know if we would somehow undermine the value of ‘natural’ life and the special (almost sacred) status of living things if through man’s sheer genius life can be created, replicated, manipulated…I’m not talking Dr. Moreau’s island here although it’s a cautionary tale.

And now back to a classic metaphysical/philosophical question that will probably be laid to rest very soon (now that the race is on)"what is life?" Or rather “what is the meaning of life?”

-casandra-

QUOTE (casandra @ Jul 3 2007, 09:23 PM)
Although synthesizing a minimal genome has a lot of practical benefits esp in microbial genetics, would we or could we stop there? With technology that can be harnessed, is man already on the verge of not only controlling and directing but also of creating life?

Have we finally conceded to a reductionist view that life is nothing more than genes and DNA? That we have finally narrowed down our definition of life, its origin and nature, to a mere scientific issue, that could only be poked and prodded with the tools of the natural sciences?

I’m very interested to know if we would somehow undermine the value of ‘natural’ life and the special (almost sacred) status of living things if through man’s sheer genius life can be created, replicated, manipulated…I’m not talking Dr. Moreau’s island here although it’s a cautionary tale.

And now back to a classic metaphysical/philosophical question that will probably be laid to rest very soon (now that the race is on)"what is life?" Or rather “what is the meaning of life?”


It could be a possible shortcut to "improved" biological weapons.
But hybridization/introgression/horizontal gene flow are common events in biology, why should we be concerned about meaning of life etc?? And with more complex organisms it is the question if we will become old enough to witness this (except the manipulation that already exists, see GM plants and animals). I don't believe it.
However in my opinion organisms are far evolved machine-like entities and without something like "soul", i.e., automats. I'm a devotee of materialism, and these results support my view.

[attachment=3224:MechaDuck.jpg]

-hobglobin-

At one time it was considered that the chemistry of life, urea, amino acids, fatty acids was somehow different, unique, having a special quality that set it apart from inorganic chemistry. In fact at one time (1800s) it was even believed that organic and inorganic chemistry where set worlds apart, the boarder being the special property of vitalism. BUt that was smashed with the wholy inorganic synthesis of urea, a distinctly organic compound by Friedrich Wöhler.

Of course from where we stand the whole notion of organic chemistry being different from chemistry sounds silly. Chemistry is chemistry. There is nothing different between a molecule derived from a biological source as opposed to a synthetic source.

Similarly in time, I believe the notion of something special or sacred about ‘Natural life’ will fade. Life is life. And natural life is plenty strange enough.

Moreover if you look at it, there is nothing natural about the many plants and animal we take for granted. Look at corn,a plant that cannot even propagate itself without humanity’s help as it seeds are all stuck to the cob and unable to fall off, or dogs – a strangely breed creature that somehow understand human gestures and non-verbal cues better then even chimps. Or farm chickens, cows, or wooly sheep. All these animals have the hand of humans shaping them to such a degree that they can’t thrive without us. Man has long been directing and controlling life. And in direction the flow of genes from one generation to the next has inevitable created life, a multitude of animals and plants that are dependent.

The only worry I have is man’s ability to pervert any technology to the service of war. The biological weapons of tomorrow will be of the nature that only Science Fiction can imagine. What would the iron age of biology bring?

-perneseblue-

QUOTE (hobglobin @ Jul 4 2007, 05:53 AM)
I'm a devotee of materialism, and these results support my view.

Joining the triumvirate retro ranks of Vogt, Buchner and Molleschott, the mid-19th century German “vulgar” or rather scientific materialists? laugh.gif At that time they were quite influential in arguing that all mental and spiritual processes are reducible to the laws of physics (mechanics) and chemistry therefore “the secretion of thought by the brain was analogous to that of urine and bile by the bladder and the kidneys”.

That everything in the universe is explainable in terms of matter and motion or matter and energy. That the only objects that ”exist”, that science can investigate are the “material” hence they’re natural, manipulable, non-mental and perceptible by the senses. They strongly advocated to substitute the dogma of religion with that of physicalism since the only reality for them is the physical (definitely no room for the supernatural, psychical, occult not even for speculative thought).

Whenever I think of reality, I’m always reminded of the parable of the blind men and the elephant. There are several permutations (in hindu and buddhist versions as well) but the famous one is a poem by John Saxe:

“It was six men of Indostan
To learning much inclined,
Who went to see the Elephant
(Though all of them were blind),
That each by observation
Might satisfy his mind…….


The first man touched its stiff side and concluded that the elephant was a wall. The next touched the tusk and said that beast was a spear. The one who touched the trunk said that it was a snake, the next touched a foot and said it was a tree, the ear- a fan and finally the last who touched the tail concluded that it was a rope. Their perception and eventual conclusion depended on where they actually touched the animal. Because of this they were partially correct and all were wrong esp when they reduced the whole animal (reality) into a tiny portion that their sense encountered.

And finally the question: can science (the scientific method, rigours of verification and falsification) give us a complete picture of reality?

casandra

PS
Maybe we should subject your reality to a similar test hobglobin just you know... to satisfy the mind ...ooops the physical senses I mean. Now where can we find 6 blind women? biggrin.gif

-casandra-

QUOTE (perneseblue @ Jul 4 2007, 03:45 PM)
Of course from where we stand the whole notion of organic chemistry being different from chemistry sounds silly. Chemistry is chemistry. There is nothing different between a molecule derived from a biological source as opposed to a synthetic source.

Similarly in time, I believe the notion of something special or sacred about ‘Natural life’ will fade. Life is life. And natural life is plenty strange enough.


The inevitability of synthetic life. Is this what is in store for us? The absolute proof which would debunk the myth of a divine creator once and for all? Or is this a total reductionist approach that "reduces" life to nothing more than molecules and energy? Why are we then mired in social and ethical conflicts involving life issues such as abortion, euthanasia, capital punishment, human cloning etc. I would like to believe that there is so much more than this definition of life.

QUOTE
Moreover if you look at it, there is nothing natural about the many plants and animal we take for granted. Look at corn,a plant that cannot even propagate itself without humanity’s help as it seeds are all stuck to the cob and unable to fall off, or dogs – a strangely breed creature that somehow understand human gestures and non-verbal cues better then even chimps. Or farm chickens, cows, or wooly sheep. All these animals have the hand of humans shaping them to such a degree that they can’t thrive without us. Man has long been directing and controlling life. And in direction the flow of genes from one generation to the next has inevitable created life, a multitude of animals and plants that are dependent.
I stand corrected (graciously acknowledging your much superior knowledge wink.gif) but I think that these plants and animals have existed and survived long before man has ever domesticated them, modifying their qualities to fit his needs. A very good demonstration of man's propensity to control and dominate. He does something because he knows he can.

QUOTE
The only worry I have is man’s ability to pervert any technology to the service of war.


Rightly so. But we shouldn't forget profit which is just as strong a motivator. I think it was B Russell who once said "I've been taught that man is the only rational being on earth. I've spent all my life trying to find proof of this" (probably another botched-up paraphrase) tongue.gif

-casandra-

QUOTE (casandra @ Jul 6 2007, 05:21 PM)
The inevitability of synthetic life. Is this what is in store for us?

The absolute proof which would debunk the myth of a divine creator once and for all? Or is this a total reductionist approach that "reduces" life to nothing more than molecules and energy? Why are we then mired in social and ethical conflicts involving life issues such as abortion, euthanasia, capital punishment, human cloning etc. I would like to believe that there is so much more than this definition of life.


“What is life?”

I see this matter as two wholly different topics framed into the same question.

What is life from a scientific perspective, life is merely a collection of genes, a few proteins, and a bunch of other molecules in a liposome. In due time we will soon learn what this combination is, and in future times perhaps make ‘life’ as a chemical engineer would make a particular compound. Life is hence reduced to ‘chemistry’ of future generations.

And the meaning of life? My mother has already answered that with her astute observation, it is to breed and eat. To which I add my own observation ‘To degrade energy more efficiently and to increase entropy faster then a non living system.‘

But what is life? (From a social perspective.)
Again the same question, but this time a whole different meaning. It is in this perspective that we have religion, politics, war, law, great human endeavours, literature, plays, movies, adventures, discovery, family, failure, victories, grief, happiness and sunsets by the ocean. Life is somewhere in there, an experience that is only ended by death.

The meaning of life? After much thinking, my answer to this question is Purpose.

I believe that much grief and opposition in the world comes from people not being able to perceive the duality of most situations, simply because it is easier to argue black or white, not the many shades of grey which life actually comes in.

-perneseblue-

QUOTE (casandra @ Jul 6 2007, 05:23 PM)
QUOTE (hobglobin @ Jul 4 2007, 05:53 AM)
I'm a devotee of materialism, and these results support my view.

Joining the triumvirate retro ranks of Vogt, Buchner and Molleschott, the mid-19th century German “vulgar” or rather scientific materialists? laugh.gif At that time they were quite influential in arguing that all mental and spiritual processes are reducible to the laws of physics (mechanics) and chemistry therefore “the secretion of thought by the brain was analogous to that of urine and bile by the bladder and the kidneys”.

That everything in the universe is explainable in terms of matter and motion or matter and energy. That the only objects that ”exist”, that science can investigate are the “material” hence they’re natural, manipulable, non-mental and perceptible by the senses. They strongly advocated to substitute the dogma of religion with that of physicalism since the only reality for them is the physical (definitely no room for the supernatural, psychical, occult not even for speculative thought).

Whenever I think of reality, I’m always reminded of the parable of the blind men and the elephant. There are several permutations (in hindu and buddhist versions as well) but the famous one is a poem by John Saxe:

“It was six men of Indostan
To learning much inclined,
Who went to see the Elephant
(Though all of them were blind),
That each by observation
Might satisfy his mind…….


The first man touched its stiff side and concluded that the elephant was a wall. The next touched the tusk and said that beast was a spear. The one who touched the trunk said that it was a snake, the next touched a foot and said it was a tree, the ear- a fan and finally the last who touched the tail concluded that it was a rope. Their perception and eventual conclusion depended on where they actually touched the animal. Because of this they were partially correct and all were wrong esp when they reduced the whole animal (reality) into a tiny portion that their sense encountered.

And finally the question: can science (the scientific method, rigours of verification and falsification) give us a complete picture of reality?

casandra

PS
Maybe we should subject your reality to a similar test hobglobin just you know... to satisfy the mind ...ooops the physical senses I mean. Now where can we find 6 blind women? biggrin.gif


You would be the No 1 tongue.gif
My contribution was meant figuratively. E.g., I cannot see radioactivity, however I'll 'know' it is reality, I can measure it and I take care, if working with it. Human inability not to perceive everything or to perceive it only in a manipulated manner (e.g. wavelengths as colours), won't stop me at least to try to improve the perception e.g. with various measuring equipments and not as you just say: "This is out of human perceptibility and therefore something 'higher', 'metaphysical' stuff etc, and we just should accept it" and this seems your approach. happy.gif
That we cannot detect/investigate/explain everything until now, does not mean that it is divine/magical/ supernatural/occult. We have to develop science (and its equipment, models) further and formulate new hypotheses, even it seems sometimes impossible. Perhaps our view on reality will be never complete and 100% correct, but we can try, and science (using the inductive method) is our armamentarium.
Look at neurosciences, their new insights on brain function, and it has become possible to understand the complex processes that produce the intellectual behaviour, perceiption, emotion etc (at least partly). 10-15 years ago this progress would be unthinkable.

PS:
I would have expected Platos cave allegory here...

Thank you perneseblue for this clear statements on life-definitions. I like them and agree.


"In the Middle Ages people believed that the earth was flat, for
which they at least had the evidence of their senses: we believe it
to be round, not because as many as one percent of us could give
the physical reasons for so quaint a belief, but because modern
science has convinced us that nothing that is obvious is true, and
that everything that is magical, improbable, extraordinary,
gigantic, microscopic, heartless, or outrageous is scientific."

(George Bernard Shaw; Preface to ‘Saint Joan’)

-hobglobin-

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