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Photosynthesis Protein Synthesised

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Description: A first step to genetically-engineered plants that consume CO2 more efficiently?
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« on: January 19, 2010, 14:32:42 PM »

Scientists in Germany have successfully assembled Rubisco, a protein instrumental for photosynthesis, the process that plants use to produce oxygen and sugars from CO2 and H2O.

If the protein’s efficiency in converting CO2 can be improved, many of the implications would be far-reaching.

News 24 article (what it means).
Insciences article (how it was done).

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« Reply #1 on: January 21, 2010, 09:30:43 AM »

Sounds like an intelligently designed idea? What is wrong with intelligently designing evolution towards a few end points  Evil?

More about chaperones:
http://movingscience.de/en/projects/biology/chaperone_assisted_protein_folding/video.html
They are part of cell's quality control systems.

How do they work? Well, some of them are two-stroke, two-speed, protein machines.

Article:
Setting the chaperonin timer: A two-stroke, two-speed, protein machine
From the article:

Quote
Protein machines and their man-made, macroscopic counterparts share several common attributes, e.g., concerted, coordinated movements, cyclical operation, and energy transduction. These machines are seldom reversible because each cycle generally involves at least one irreversible step, e.g., the consumption of fuel. Often these machines operate at variable speed, a plethora of timing devices adjusting the cycle speed in response to demand.

An exemplary bipartite protein machine is the chaperonin system, typified by GroEL and GroES from Escherichia coli. GroEL is composed of 2 heptameric rings, stacked back to back, which, in the presence of GroES, operate out of phase with one another in the manner of a 2-stroke, reciprocating motor (1, 2). Driven by the hydrolysis of ATP, the chaperonin proteins function as a biological simulated annealing machine (3, 4), optimizing the folding of their substrate proteins (SPs) whose passage to biologically functional conformations is thus assured.

Why these scientists made use of GroEL to make RubiSco  Grin.

Quote
The picture of the chaperonins that emerges from our work is that of a machine equipped with a timer, the trans ring, poised to respond to the appearance of SP [substrate protein inside the cavity] but otherwise idling in a quiescent state. We note that Nature’s design of this 2-speed protein machine minimizes the hydrolysis of ATP in the absence of SP. However, it maximizes the number of turnovers and minimizes the residence time available to the encapsulated SP to reach the native state, design principles well suited to the operation of an iterative annealing device.


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« Reply #2 on: January 21, 2010, 10:57:02 AM »

Sounds like an intelligently designed idea? What is wrong with intelligently designing evolution towards a few end points  Evil?
If one ignores the transparently infantile goading, and the tendentious selectivity of, and emphases within citations in the remainder of your post, then the answer is as follows:  Nothing really, provided it’s done responsibly.  After all, in this case not only do we know the intelligent designers, we have actual, direct, objective, repeatable evidence of them.  That is, there is no need to speculate and conjecture about (a) the existence, (b) the goals, (c) the methods, (d) the nature, or (e) the identity of the intelligent designer.  How cool is that!?

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« Reply #3 on: January 21, 2010, 11:02:36 AM »

Sounds like an intelligently designed idea? What is wrong with intelligently designing evolution towards a few end points  Evil?
If one ignores the transparently infantile goading, and the tendentious selectivity of, and emphases within citations in the remainder of your post, then the answer is as follows:  Nothing really, provided it’s done responsibly.  After all, in this case not only do we know the intelligent designers, we have actual, direct, objective, repeatable evidence of them.  That is, there is no need to speculate and conjecture about (a) the existence, (b) the goals, (c) the methods, (d) the nature, or (e) the identity of the intelligent designer.  How cool is that!?

'Luthon64
Ah well, at least you are able to recognise the existence of design. You unfortunately need to reconcile it with your philosophically materialistic outlook on life. Good luck with the cognitive dissonance there.
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« Reply #4 on: January 21, 2010, 12:54:50 PM »

Please feel free to explain for us slowpokes lagging behind your towering intellect how an ability to recognise intelligent design, given verifiable the verifiable actions of verifiable intelligent designers, is irreconcilable with philosophical materialism.

Can you please do that?  Because it is a supremely important point, perhaps the one cardinal one.

And please do it in baby steps, not by resort to gormless evasion.

Thank you in advance for your no doubt eruditely illuminating reply.  I look forward to it.

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« Reply #5 on: January 21, 2010, 13:15:07 PM »

Please feel free to explain for us slowpokes lagging behind your towering intellect how an ability to recognise intelligent design, given verifiable the verifiable actions of verifiable intelligent designers, is irreconcilable with philosophical materialism.

Can you please do that?  Because it is a supremely important point, perhaps the one cardinal one.

And please do it in baby steps, not by resort to gormless evasion.

Thank you in advance for your no doubt eruditely illuminating reply.  I look forward to it.

'Luthon64
Well now, certain kinds of philosophically materialistic outlooks are plainly incompatible with any kind of design that come from the mental states of engineers, scientists etc. Eliminative materialists for one posit that mental states (such as belief and sensation and goal-directed mental states such as designing something towards a goal) do not actually exist. I am pretty sure you are not an eliminative materialist because you sure believe your mental states do have an effect on the outside world. I guess you need to tell us just what kind of an idiotic philosophical materialist you are though. A type that makes it more compatible with the existence of mental states and your very real ability at goal-directed behaviour.

Do try and explain how you are a philosophical materialist that does not just plainly collapse into eliminative materialism or similar idiotic philosophical outlooks that are just plain self-refuting. Feel free to make a new thread though.

Let's talk more about those chaperone machines and how they are used to design (scientists) new forms of RuBisCo.
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« Reply #6 on: January 21, 2010, 13:50:50 PM »

But you haven’t answered the question that was posed.  You have merely rattled off an irrelevant slew of flat, unsubstantiated and superficially relevant assertions.

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« Reply #7 on: January 21, 2010, 14:09:20 PM »

But you haven’t answered the question that was posed.  You have merely rattled off an irrelevant slew of flat, unsubstantiated and superficially relevant assertions.

'Luthon64
Evade actually defining what kind philosophical materialist you are all you want. If you don't answer that question, I am not able to answer your question as you might actually not be an eliminative materialist or an actual philsophical materialist that does not collapse into EM.
EM is incompatible with the actions of intelligent designers (verifiable or not) because it denies the existence of mental states of intelligent designers in the first. Are you too dumb to actualy get that or just willfully evading defining what kind of philosophical materialist you are that does not collapse into EM?
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« Reply #8 on: January 21, 2010, 14:44:44 PM »

You’re still just dodging.  And flatly asserting, as before.

How is eliminative materialism “incompatible with the actions of intelligent designers (verifiable or not)”?  Where do you get that a denial of “the existence of mental stares [sic] of intelligent designers in the first [sic]” (citation, please!) negates either the actions of designers or intelligence?

You really do make the most remarkable unsubstantiated claims sometimes.  Now answer the original question and the above two, please.

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« Reply #9 on: January 21, 2010, 15:24:03 PM »

Mental states... (fixed)

Damn you must really be that thick:
Here:
1) Eliminative materialism asserts that items that are classified as mental simply do not exist. These include sensations and object-directed mental states such as wanting or desiring something and then acting towards such a goal. Such as wanting to design RuBisCo and then mentally designing a plan and physically carrying it out.
2) Recognising something (such as an intelligent designer) is a sensation.
3) Verifying the actions of an intelligent designer is also a sensation.

EM is irreconcilable with the ability to recognise intelligent design, given verifiable the verifiable actions of verifiable intelligent designers simply because EM states that mental states such as recognising, verifying as well as object-directed states such as wanting and desiring do not exist.

Do you get it? Are you an eliminative materialist? If not, definine what kind of philosophical materialist you are that does not collapse into EM.
If you don't understand EM, go read a book or something.
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« Reply #10 on: January 21, 2010, 15:57:37 PM »

Temporarily accepting your eliminative materialism straw man unreservedly for argument’s sake, how does the illusory existence, variously non-existence of sensations render either the underlying brain states or the stimuli that produced them illusory, variously non-existent?  Before you answer that, though, please give a philosophically satisfactory account of what it means for something “to exist” with particular reference to sensations in general.

So far, that’s five unanswered questions.  Gee, I think you’re right, I must really be that thick!

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« Reply #11 on: January 21, 2010, 20:45:22 PM »

Temporarily accepting your eliminative materialism straw man unreservedly for argument’s sake, how does the illusory existence, variously non-existence of sensations render either the underlying brain states or the stimuli that produced them illusory, variously non-existent?  Before you answer that, though, please give a philosophically satisfactory account of what it means for something “to exist” with particular reference to sensations in general.

So far, that’s five unanswered questions.  Gee, I think you’re right, I must really be that thick!

'Luthon64
Look, I think you need to at least read up on EM before accusing others of straw men. Countless times have I asked others to actually define what they think "philosophical naturalism" and "philosophical materialism" refers to without even a hint of an attempt. You being another prime example. You say you are one but seem to catastrophically fail to go into any remote detail of an understanding of what you think you are (PS, now is a good time to actually describe it). When someone attempts to discuss it, they are accused of straw men by the same interlopers who are incapable of describing it for others and themselves in the first place.

No-one said brain states or the stimuli that are producing them are illusory or variously non present (note, non-existent is not a good way to put it in light of the above definition of "to exist"). EM proposes that beliefs, sensations (such as joy) and other mental states are illusory or variously non present in reality. For example:

You can insist that the sensation of joyfulness is a property of a brain state. This sensation of joyfulness however plays no causal role in bringing about a smile or a tear of joy as the sensation of joyfulness is illusory or variously not present in reality. Only the the physical aspects of the brain state play a causal role in bringing about a smile, or a tear.

What does it mean "to exist"? I don't think there is a general consensus (philosophically speaking) on the meaning of "to exist". If I had to venture a guess, I think for something "to exist" it has to somehow sense reality and be aware of itself, it has to have some sort of consciousness. You might object by saying that "so if there are no conscious beings inside or outside the universe then the universe does not exist?" No, that is not what I am saying, that would just imply that the universe is still present without beings that exist. Difference between presence and existence.

To restate the above post then in light of this definition:
1) Eliminative materialism asserts that items that are classified as mental are simply not present in reality. These include sensations and object-directed mental states such as wanting or desiring something and then acting towards such a goal. Such as wanting to design RuBisCo and then mentally designing a plan and physically carrying it out.
2) Recognising something (such as an intelligent designer) is a sensation.
3) Verifying the actions of an intelligent designer is also a sensation.

EM is irreconcilable with the ability to recognize intelligent design, given verifiable the verifiable actions of verifiable intelligent designers simply because EM states that mental states such as recognizing, verifying as well as object-directed states such as wanting and desiring are not present in reality.




Your turn to actually participate and I think it is a good idea to explain what you mean when you say you are a philosophical materialist.
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« Reply #12 on: January 22, 2010, 19:22:47 PM »

Look, I think you need to at least read up on EM before accusing others of straw men.
Done that already, but you should too, you know.  If your subsequent straw man “refutation” was as simple as you make it out to be, relevant experts of the accomplishments and stature of the Churchlands and Daniel Dennett could reasonably be expected to agree to it because it’s accurate and valid.  But it’s funny – don’t you think? – that they still present a case for EM that many other philosophers deem worth considering even if they disagree with it.  Instead of paying appropriate attention, you present yourself here in this lesser corner of the Internet as a self-styled expert who continually and without respite attempts to sneak in mysticism through the back door after dressing it in the rags and tatters of science shredded by your own amateur hand.



Countless times have I asked others to actually define what they think "philosophical naturalism" and "philosophical materialism" refers to without even a hint of an attempt. You being another prime example.
As usual, that’s a bit of a self-serving distortion.



You say you are one but seem to catastrophically fail to go into any remote detail of an understanding of what you think you are (PS, now is a good time to actually describe it).



Your turn to actually participate and I think it is a good idea to explain what you mean when you say you are a philosophical materialist.
Another self-serving distortion.  I am a philosophical materialist in that I reject any need for non-material, supernatural or mystical accounts of whatsoever phenomena.  Matter and energy in the physicist’s sense are all that ultimately exist, which is not to say that we don’t have different levels and modes of explication appropriate to the particular phenomenon under scrutiny.  Not that I haven’t addressed your questions before and before and before.



When someone attempts to discuss it, they are accused of straw men by the same interlopers who are incapable of describing it for others and themselves in the first place.
Another self-serving distortion.  You’re not attempting to discuss anything.  You’re pushing an agenda and it seems that you wrongly and quite presumptuously think that all others are too dim-witted to see that.  Maybe if you dropped your not-so-clever scheming, more productive discussion will ensue.



EM is irreconcilable with the ability to recognize intelligent design, given verifiable the verifiable actions of verifiable intelligent designers simply because EM states that mental states such as recognizing, verifying as well as object-directed states such as wanting and desiring are not present in reality.
Is that a fact?  Because it looks just like a flat assertion dressed in straw.

And, presently, there remain five unanswered questions.

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« Reply #13 on: January 22, 2010, 22:55:04 PM »

What does it mean "to exist"? I don't think there is a general consensus (philosophically speaking) on the meaning of "to exist".
Exactly. That means your whole argument is up a creek without a paddle.

If I had to venture a guess, I think for something "to exist" it has to somehow sense reality and be aware of itself, it has to have some sort of consciousness. You might object by saying that "so if there are no conscious beings inside or outside the universe then the universe does not exist?" No, that is not what I am saying, that would just imply that the universe is still present without beings that exist. Difference between presence and existence.
Jesus Frikkin' Christ. Back to your bogus semantic tricks, eh?
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« Reply #14 on: January 23, 2010, 18:12:20 PM »

Look, I think you need to at least read up on EM before accusing others of straw men.
Done that already, but you should too, you know.

You haven't got a clue it seems.

If your subsequent straw man “refutation” was as simple as you make it out to be, relevant experts of the accomplishments and stature of the Churchlands and Daniel Dennett could reasonably be expected to agree to it because it’s accurate and valid.

Appealing to authority is not exactly an argument. And appealing to the authority of the Churchlands and Dennett.... you can do better. And do you really think there aren't any good objections from other intelligent philosophers? Really now... Seems you don't know much about the objections to EM or EM in general.

But it’s funny – don’t you think? – that they still present a case for EM that many other philosophers deem worth considering even if they disagree with it.

Again, this argument from authority is not going to get you anywhere if you can't even show a rudimentary understanding of EM. Many other philosophers are of the opinion that panpsychism, information monism, idealism, anti-realism etc. as worthy as well. So what? Want to have a pissing contest or discuss the validity of EM?

Countless times have I asked others to actually define what they think "philosophical naturalism" and "philosophical materialism" refers to without even a hint of an attempt. You being another prime example.
As usual, that’s a bit of a self-serving distortion.

Yeeesss, kinda hypocritical to write that if you ask others to define "to exist". So how about your version there before lecturing others on "self-serving distortions".

You say you are one but seem to catastrophically fail to go into any remote detail of an understanding of what you think you are (PS, now is a good time to actually describe it).



Your turn to actually participate and I think it is a good idea to explain what you mean when you say you are a philosophical materialist.
Another self-serving distortion.  I am a philosophical materialist in that I reject any need for non-material, supernatural or mystical accounts of whatsoever phenomena.  Matter and energy in the physicist’s sense are all that ultimately exist, which is not to say that we don’t have different levels and modes of explication appropriate to the particular phenomenon under scrutiny.

Now is a good time for you to explain what you mean when you say: "Matter and energy in the physicist’s sense are all that ultimately exist"
Define matter and energy in the physicist’s sense. While you are at it, define "to exist" for us before poor Irreverend thinks "your whole argument is up a creek without a paddle". I mean the guy is known for his consistency not?

EM is irreconcilable with the ability to recognize intelligent design, given verifiable the verifiable actions of verifiable intelligent designers simply because EM states that mental states such as recognizing, verifying as well as object-directed states such as wanting and desiring are not present in reality.
Is that a fact?  Because it looks just like a flat assertion dressed in straw.

And, presently, there remain five unanswered questions.

'Luthon64

Gee, perhaps you should start a thread for questions you want answered. I can do the same and then we are all happy little campers...
Let's discuss EM here shall we?
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« Reply #15 on: January 23, 2010, 18:34:09 PM »

So, now we all know how those German scientists assembled Rubisco and what pivotal role it plays in photosynthesis.
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« Reply #16 on: January 23, 2010, 19:46:03 PM »

Here’s something that photosynthesises.  It doesn’t tell lies and it has an attention span, albeit a very short one.


No, let’s not.

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« Reply #17 on: January 24, 2010, 00:39:57 AM »

Appealing to authority is not exactly an argument.
Mecchie me dull lad, every argument is an appeal to authority. It's just a question of which authority.

Want to have a pissing contest or discuss the validity of EM?
With your weak bladder you'll lose either way. I'll put bucks on it.

Yeeesss, kinda hypocritical to write that if you ask others to define "to exist".
So sez Mr Supremo Slick, Esq.

Define matter and energy in the physicist’s sense. While you are at it, define "to exist" for us before poor Irreverend thinks "your whole argument is up a creek without a paddle". I mean the guy is known for his consistency not?
Matter and energy. China, you really suck at this Google thing. Be a cool dear and define, quote, what it means for something "to exist" with particular reference to sensations in general. Go on, stun me by noticing and respecting the "with particular reference to sensations in general".

Gee, perhaps you should start a thread for questions you want answered.
Gee, perhaps you should start a thread with answers to all the questions that have been asked of you. Wait, you'll need an internet all of your own for that.
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« Reply #18 on: January 24, 2010, 20:55:29 PM »

Appealing to authority is not exactly an argument.
Mecchie me dull lad, every argument is an appeal to authority. It's just a question of which authority.

Really, every argument? Wow man, did you come up with all by yourself and want us all to believe it? Try a bit harder.

Define matter and energy in the physicist’s sense. While you are at it, define "to exist" for us before poor Irreverend thinks "your whole argument is up a creek without a paddle". I mean the guy is known for his consistency not?
Matter and energy. China, you really suck at this Google thing. Be a cool dear and define, quote, what it means for something "to exist" with particular reference to sensations in general. Go on, stun me by noticing and respecting the "with particular reference to sensations in general".

Now that you have found the wiki links (pretty deep stuff that must be for you huh) for matter and energy, what can you tell us about it? You can do more than google can't you? Which version of matter do you prefer btw? Common, revised (whatever that is), general, Aristotelian etc? You read it haven't you? Now where is Mefi with her philosophical materialism and her definitions of matter and energy she prefers and what properties she thinks it has?

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« Reply #19 on: January 25, 2010, 08:52:52 AM »

Really, every argument?
Yup, but asking you to think about it is a waste of words.

Which version of matter do you prefer btw?
Not the super-dense kind like inside your head.
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« Reply #20 on: January 25, 2010, 09:40:20 AM »

Which version of matter do you prefer btw?
Not the super-dense kind like inside your head.
Sooo, this is your attempt at an answer? You really shouldn't complain about others that are dodging questions you know.

Which version of matter do you prefer then (waiting for a positive and constructive answer ... Wink )?
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« Reply #21 on: January 25, 2010, 15:44:52 PM »

More about proteins folding other proteins into the correct shape and function:
Chaperonins Prompt Proper Protein Folding -- But How?

Quote
ScienceDaily (Jan. 25, 2010) — In proper society of yesterday, a chaperone ensured that couples maintained appropriate courting rituals. In biology, a group of proteins called chaperonins make sure that proteins are folded properly to carry out their assigned roles in the cells.


Quote
In a new study in archaea (single-celled organisms without nuclei to enclose their genetic information), a consortium of researchers from Baylor College of Medicine and Stanford University in California discovered how the Group II chaperonins close and open folding chambers to initate the folding event and to release the functional protein to the cell. A report of their work appears in the current issue of the journal Nature.

Archaea is one of three major divisions in the classification of living organisms. The other two are bacteria and eukaryotes. Archaea lack a nucleus but have other characteristics that are similar to those of eukaryotes, which include human beings.

"The important thing about the chaperonin molecule is that it is key to folding proteins in the cell -- proteins such as actin, tubulin and tumor suppressors," said Dr. Wah Chiu, professor of biochemistry and molecular biology at BCM and a senior author of the report.

"Previously, people had studied chaperonins in the bacteria Escherichia coli," said Chiu, also director of the National Center for Macromolecular Imaging and of the Nanomedicine Development Center at BCM. "We wanted to look at how chaperonins operated in a new class of organisms, and we chose the archaea."

It turned out that the archaea have a different type of chaperonin dubbed Group II. The structure of this kind of chaperonin is more similar to that of mammals. In essence, both types of chaperonin act as molecular machines, assisting proper protein within the cell. To the surprise of Chiu and his colleagues, the Group II chaperonin worked differently from Group I chaperonins previously studied in E. coli.

"It turns out that this chaperonin -- that we call a molecular nanomachine -- requires ATP (adenosine triphosphate or the major energy currency in cells) to close its chamber," he said.

The group II chaperonins that oversee proper protein folding in this organism have an upper and lower chamber and a built-in lid. ATP adds water to the chaperonin at a critical point. When the water is added, a process called hydrolysis takes place. Without ATP, the chamber is open. When ATP is added, the chamber closes.

"The take home message in this is how the chaperonin opens and closes," said Chiu. The way in which these chaperonins complete a large mechanical motion critical for completing a protein-folding event is different from that of others that have been studied.

Equally important is the tool he and his Stanford colleagues developed to see the complicated structure and dynamic motion of the chaperonin. Combining cryo-electronmicroscopy with intricate computer modeling, they were able to "see" the closed conformation of the single chaperonin particle at a resolution of 4.3 angstroms. (An angstrom is one hundred-millionth of a centimeter. A sheet of paper is approximately 1 million angstroms thick.) The model of the open conformation was resolved down to 8 angstroms.

The models of the open and closed structures reveal how changes in their structure triggered by ATP alter the contacts within the adjacent protein molecules within and across the two chambers, causing a rocking motion that closes the lid of the two chambers of the chaperonin.

"The technique is important in allowing us to see how this nanomachine works," said Chiu. He anticipates that future work with chaperonins in other organisms will reveal even more important structural details.

Others who took part in this work include Junjie Zhang, Matthew L. Baker, Matthew Dougherty, Caroline J. Fu, Joanita Jakana and Dr. Steven J. Ludtke, all of BCM, and Dr. Gunnar F. Schröder, Nicholai R. Douglas, Dr. Stefanie Dr. Reissmann, Dr. Michael Levitt, and Dr. Judith Frydman, all of Stanford University. Zhang was a graduate student in the Program of Structural and Computational Biology and Molecular Biopysics at BCM.

Funding for this work came from the National Institutes of Health Nanomedicine Development Center Roadmap Initiative, the Biomedical Technology Research Center for Structural Biology in the National Center for Research Resources, a Nanobiology Training Fellowship administered by the Keck Center of the Gulf Coast Consortia and the National Science Foundation.


Protein folding machines in all the domains of life... and now we are using it to design our own proteins (see OP).
« Last Edit: January 26, 2010, 09:10:55 AM by Teleological » Logged
rwenzori
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Merda accidit.


« Reply #22 on: January 25, 2010, 18:35:07 PM »

Protein folding machines in all the domains of life... and now we are using it to design our own proteins (see OP).

Oh wow! Ain't Bebeh Jebus so CLEVER!!!
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« Reply #23 on: January 25, 2010, 22:14:32 PM »

Which version of matter do you prefer then (waiting for a positive and constructive answer ... Wink )?
Wait on, MacTellyMecchie. I told you already. If you don't like my answer, that's your, um, cross to bear.

Oh wow! Ain't Bebeh Jebus so CLEVER!!!
Not so CLEVER if he can make a TellyMecchie, should you ask me...
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