Designer enzymes

[lee_merrill]

Source: Marcos Eberlin, from the book "Foresight"

¹²

© Copyright Original Source

I think so! Humans ought to be able to improve on bumbling nature, if that is how enzymes came to be.

Blessings,
Lee

1. Referenced here.
2. Referenced here.

[shunyadragon]

Source: Marcos Eberlin, from the book "Foresight"

¹²

© Copyright Original Source

I think so! Humans ought to be able to improve on bumbling nature, if that is how enzymes came to be.

Blessings,
Lee

1. Referenced here.
2. Referenced here.

just by randomly bumbling around

[TheLurch]

I think so! Humans ought to be able to improve on bumbling nature, if that is how enzymes came to be.

[lee_merrill]

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

[TheLurch]

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!

Wait, as written, this says that if design fails to surpass evolution, then it's evidence for design. Is that really what you meant?

[lee_merrill]

Wait, as written, this says that if design fails to surpass evolution, then it's evidence for design. Is that really what you meant?

[TheLurch]

That's the exact opposite of what i said, and the opposite of what you said earlier.

Would you at least pay the rest of us the respect of paying attention to your own arguments?

[shunyadragon]

Well, the "bumbling" quote was from David Baker,

Blessings,
Lee

I most definitely consider you misrepresenting Dr. Baker. You need to cite him more fully and completely.

[shunyadragon]

I most definitely consider you misrepresenting Dr. Baker. You need to cite him more fully and completely.

The 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.

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.

[TheLurch]

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.

[lee_merrill]

The 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.

No, Dr. Baker is saying we should be able to do much better than evolution.

Blessings,
Lee

[shunyadragon]

No, Dr. Baker is saying we should be able to do much better than evolution.

Blessings,
Lee

No, 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.

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.

[lee_merrill]

No, 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.

No one here is arguing that Dr. Baker is a supporter of ID. If however, his prediction fails, that would be some evidence for design.

Part of the problem is the difference in the intent of designing enzymes is different from the natural selection processes of evolution.

Certainly they are different.

Blessings,
Lee

[TheLurch]

No one here is arguing that Dr. Baker is a supporter of ID. If however, his prediction fails, that would be some evidence for design.

His prediction is that we humans can design better enzymes than evolution produced. How, precisely, would the failure of this be evidence for design?

Or are you not paying careful attention to yourself again.

[shunyadragon]

No one here is arguing that Dr. Baker is a supporter of ID. If however, his prediction fails, that would be some evidence for design.

It is only evidence for whether his particular prediction fails or succeeds, and nothing else.

Certainly they are different.

Therefore absolutely no relationship to whether enzymes naturally evolve or not.