Announcement
Collapse
Natural Science 301 Guidelines
This is an open forum area for all members for discussions on all issues of science and origins. This area will and does get volatile at times, but we ask that it be kept to a dull roar, and moderators will intervene to keep the peace if necessary. This means obvious trolling and flaming that becomes a problem will be dealt with, and you might find yourself in the doghouse.
As usual, Tweb rules apply. If you haven't read them now would be a good time.
Forum Rules: Here
As usual, Tweb rules apply. If you haven't read them now would be a good time.
Forum Rules: Here
See more
See less
Designer enzymes
Collapse
X
-
Designer enzymes
"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)Tags: None
-
Problem as usual with the layman misuse of randomness. Nature does not 'randomly bumble around.' What a silly anthropomorphic explanation for science.
Maybe in the future we will have enzymes running around in designer suits.Last edited by shunyadragon; 06-11-2019, 09:08 PM.Glendower: I can call spirits from the vasty deep.
Hotspur: Why, so can I, or so can any man;
But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:
go with the flow the river knows . . .
Frank
I do not know, therefore everything is in pencil.
-
Originally posted by lee_merrill View PostI think so! Humans ought to be able to improve on bumbling nature, if that is how enzymes came to be.
That said, I also see potential here, but of a more limited sort: we have to examine the underlying biology to find useful cases that evolution wouldn't have optimized. This would include things like:
— Enzymes that are on biochemical pathways where some other reaction is limiting, and therefore provide no advantage by operating more efficiently.
— Enzymes that catalyze a reaction under conditions that aren't useful to us could be optimized for operation in conditions that are (different solvent, pH, etc.).
— Enzymes that normally work as part of one pathway, but we'd like to have working as part of a different one.
— Things that the cell normally tightly controls for metabolic balance, but we want operating at full speed all the time.
— Almost certainly others that I can't think of right now.
The unfortunate fact of the matter for Lee is that, if you follow the literature in this field, you'll find that, when faced with wanting to do this, most researchers have simply found it best to stick an enzyme into the context they want it to work in, and put it through multiple rounds of random mutagenesis and evolutionary selection*. There have been cases of intentional design, but they're the minority. In a number of cases, design was tried and failed, forcing researchers to turn to evolutionary approaches.
Where I think design will ultimately matter is when we start doing more with unnatural amino acids. These can have a chemistry that can be quite distinct from anything that existing enzymes have to work with, and therefore probably can't be dropped into an existing enzyme with good results.
*Edited to add: there are reasons for this i can go into if people are interested.Last edited by TheLurch; 06-12-2019, 11:19 AM."Any sufficiently advanced stupidity is indistinguishable from trolling."
Comment
-
Well, the "bumbling" quote was from David Baker, an evolutionist. And if as the Lurch said, intentional design doesn't work very well, then it will be interesting to see when and if this field flourishes and surpasses by far what nature does. If not, then there's evidence for design!
Blessings,
Lee"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)
Comment
-
Originally posted by lee_merrill View PostWell, the "bumbling" quote was from David Baker, an evolutionist. And if as the Lurch said, intentional design doesn't work very well, then it will be interesting to see when and if this field flourishes and surpasses by far what nature does. If not, then there's evidence for design!"Any sufficiently advanced stupidity is indistinguishable from trolling."
Comment
-
Originally posted by TheLurch View PostWait, as written, this says that if design fails to surpass evolution, then it's evidence for design. Is that really what you meant?
Blessings,
Lee"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)
Comment
-
Originally posted by lee_merrill View PostYes, we should be able to beat such a process. "It’s an interesting reverse test of intelligent design, don’t you think?"
Would you at least pay the rest of us the respect of paying attention to your own arguments?"Any sufficiently advanced stupidity is indistinguishable from trolling."
Comment
-
Originally posted by lee_merrill View PostGlendower: I can call spirits from the vasty deep.
Hotspur: Why, so can I, or so can any man;
But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:
go with the flow the river knows . . .
Frank
I do not know, therefore everything is in pencil.
Comment
-
Originally posted by shunyadragon View PostI most definitely consider you misrepresenting Dr. Baker. You need to cite him more fully and completely.
If you read the whole article by Dr. Baker you will find the article is definite scientific perspective of evolution, and than read Marcos Eberlin his work is an 'Intelligent Design' argument in total contradiction of the science of Dr. Baker.
Context, context and context.Glendower: I can call spirits from the vasty deep.
Hotspur: Why, so can I, or so can any man;
But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:
go with the flow the river knows . . .
Frank
I do not know, therefore everything is in pencil.
Comment
-
Got a bit of a break at work, so thought i'd discuss why designing enzymes without using evolution is really, really difficult.
The first issue is the number of problems you've got to solve at once. You may think it's just a matter of chemistry - throw in a positive charge and the reaction should go faster. But there are also structural issues. Maybe the positively charged amino acids are too big to fit into the active site; maybe there are other positive charges nearby that would be repelled by it; etc.
But the big sticking point is that you're also solving a protein-folding problem. Proteins start to fold up as they're being made, which means that any changes you make can potentially start interacting with parts of the protein they'd otherwise be shielded from in a mature protein. So your positive charge might end up sticking to a negative charge somewhere else in the protein that would be inaccessible when the entire protein was intact and folded properly. So, to really understand what changes will be tolerated, we need to fully understand protein folding - a problem researchers have been struggling with for decades.
These aren't impossible barriers, but they mean you generally have to try a number of potential changes in order to be reasonably certain you'll find one that works. And that bumps up against the next problem: it's time consuming to engineer specific changes. You have to manipulate the DNA sequences, get them back into the original gene, get the gene into an organism, check by DNA sequencing that no errors were introduced during the process...
Contrast this with an evolutionary approach. Evolution solves for activity, structural concerns, and folding simultaneously. It tries options we wouldn't necessarily think of. If done for multiple rounds, it provides the possibility of adding mutations that compensate for any problematic effects of the desired changes. A single Petri dish can examine far more changes than can ever reasonably be tested directly. And, given the hassle of engineering changes above, it's possible to do multiple rounds of selection in the same time it would take to engineer and test a single change.
This doesn't mean it's perfect for everything. There's cases where it's hard to set up any kind of selection for a specific activity, which makes it impossible to evolve for better performance of that activity. Outside those cases, however, it's very practical, and far more likely to deliver an improved version of an enzyme."Any sufficiently advanced stupidity is indistinguishable from trolling."
Comment
-
Originally posted by shunyadragon View PostThe problem with the quote from Dr. Baker, when taken into context of the 'whole' article is that it is a frivolous rhetorical devise statement, and when Marcos Eberlin uses the quote he takes it seriously how nature actually works from the scientific perspective.
Blessings,
Lee"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)
Comment
-
Originally posted by lee_merrill View PostNo, Dr. Baker is saying we should be able to do much better than evolution.
Blessings,
Lee
I also believe your ignoring the post by TheLurch addressing this. Part of the problem is the difference in the intent of designing enzymes is different from the natural selection processes of evolution.Last edited by shunyadragon; 06-14-2019, 04:00 PM.Glendower: I can call spirits from the vasty deep.
Hotspur: Why, so can I, or so can any man;
But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:
go with the flow the river knows . . .
Frank
I do not know, therefore everything is in pencil.
Comment
-
Originally posted by shunyadragon View PostNo, not in terms of how you and Marcos Eberlin misrepresent Dr. Baker's article. Marcos Eberlin and your intent is supporting Intelligent Design, and that is not remotely the intent of Dr. Baker.
Part of the problem is the difference in the intent of designing enzymes is different from the natural selection processes of evolution.
Blessings,
Lee"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)
Comment
-
Originally posted by lee_merrill View PostNo one here is arguing that Dr. Baker is a supporter of ID. If however, his prediction fails, that would be some evidence for design.
Or are you not paying careful attention to yourself again."Any sufficiently advanced stupidity is indistinguishable from trolling."
Comment
-
Originally posted by lee_merrill View PostNo one here is arguing that Dr. Baker is a supporter of ID. If however, his prediction fails, that would be some evidence for design.
Certainly they are different.Glendower: I can call spirits from the vasty deep.
Hotspur: Why, so can I, or so can any man;
But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:
go with the flow the river knows . . .
Frank
I do not know, therefore everything is in pencil.
Comment
Comment