"Photons stimulating visual cortex within sight sense alone do not account for the blind and…"
The mixing of religious and non-religious beliefs in an individual.
Evolvability: A Good Design Principle
By Katie Galloway
[Katie Galloway is an RTB volunteer apologist. She is completing her PhD at Caltech in Chemical Engineering with an emphasis in biological systems.]
Your computer's newest antivirus probably comes with live updates so it can arm itself against the latest trojan-phishing-spyware attack. It may not stop you from doing silly things like sending your bank information to that lovely man from the British lottery that just happens to want to give you a million dollars, but hopefully it will neutralize other less obvious threats. The antivirus protection works well because teams of people constantly update the database with signatures of the latest threats so your software is prepared. Internet threats adapt very fast so good antivirus software must evolve as quickly or your computer system might not survive. The same principle applies to biological systems and their survival programs.
In Earth's highly dynamic environment, survival requires that biological systems swiftly yield solutions to new threats. Enzymes, known as biology's workhorses, perform a variety of cellular functions such as harvesting energy, degrading toxins, and assembling new proteins. Organisms like bacteria can live in highly variable settings that offer ever-changing challenges, including the introduction of a new predator, toxin, or energy source. To survive and compete in such surroundings, organisms require highly flexible enzymes that can quickly adapt (which is the intended use of "evolve" throughout this article) to take advantage of environmental variation. Evolving latent, promiscuous (or secondary) functions allows biological systems to rapidly respond to environmental fluctuations.
Promiscuous functions permit enzymes to perform catalysis on more than one type of molecule. Usually, enzymes are specified for certain molecules or types of molecules called substrates. When scientists discover an enzyme that catalyzes reactions with unexpected molecules, the enzyme is said to have promiscuous catalytic activity.
As an example of this activity, consider using a shoe as a hammer. Even though the shoe is clearly meant and designed for a different purpose it can still be semi-useful in a bind. Similarly, biological systems appropriate their enzymes for unusual tasks. Sometimes these functions eventually become necessary for the survival of an organism. In these cases, the enzyme can undergo molecular evolution to become dedicated and specialized to its promiscuous function. One notable example is the organophosphate hydrolases (OPH).
Organophosphates are man-made esters (a large class of organic compounds often used in fragrances) of phosphoric acid introduced into the environment as insecticides and nerve gases within the last few decades. Yet scientists have already discovered an enzyme in bacteria called phosphotriesterase (PTE) that hydrolyzes (breaks down) the organophosphate paraoxon with great efficiency. The fact that PTE exists to breakdown a recently introduced and previously completely foreign type of molecule is unexpected. One hypothesis that explains this is the existence of promiscuous activity in existing natural enzymes.
Researchers suspect that this rapid adaptation can be accounted for by the existence of promiscuous functions in enzymes called esterases. Esterases hydrolyze their unique type of esters; in other words, they specifically break particular esters apart with the help of water. The activity of these esterases on new substrates is initially weak, but scientists theorize that the advantage conferred by rare beneficial mutations accelerates the spread of the mutation throughout the population and allows the enzyme to increase its ability to hydrolyze the novel substrate.
Through in vitro evolution laboratory techniques, researchers simulated the evolution of an esterase into an efficient OPH.1 Starting with an esterase that demonstrated slight promiscuous activity as an OPH, researchers mutated the sequence into a library of variants and screened for those with increased ability to hydrolyze the organophosphate paraoxon. Through multiple rounds of in vitro evolution, the OPH activity was increased 10- to150-fold over the native enzyme. Additionally, researchers demonstrated that activity for non-native substrates can increase without destroying activity for the native substrate. Theoretically, this allows the cell to benefit from the new function while retaining the old.
Just like smart engineers who create software that can evolve to the changing demands of users, God has built proteins to be evolvable to satisfy the changing conditions of life. Evolvability is a good design principle because it affords biological systems the robustness and flexibility to adapt to new challenges while maintaining essential cellular processes.
Additionally, by allowing organisms such as bacteria the latitude to evolve new functions from existing proteins, bacteria can maintain smaller, more efficient genomes while responding to novel situations. Furthermore, development of these new functions creates the potential for remedying man-made ecological disasters such as the spread of organophosphates into drinking water.
A good engineer chooses the appropriate materials to fulfill his purposes. In a similar way, this scientific research points to a Creator who has demonstrated purposefulness by choosing to build life out of highly evolvable materials.
A. Aharoni et al., “The ‘evolvability’ of promiscuous protein functions,” Nature Genetics 37, no. 1 (2005): 73-6.
http://www.reasons.org/Evolvability-AGoodDesignPrinciple
[Katie Galloway is an RTB volunteer apologist. She is completing her PhD at Caltech in Chemical Engineering with an emphasis in biological systems.]
Your computer's newest antivirus probably comes with live updates so it can arm itself against the latest trojan-phishing-spyware attack. It may not stop you from doing silly things like sending your bank information to that lovely man from the British lottery that just happens to want to give you a million dollars, but hopefully it will neutralize other less obvious threats. The antivirus protection works well because teams of people constantly update the database with signatures of the latest threats so your software is prepared. Internet threats adapt very fast so good antivirus software must evolve as quickly or your computer system might not survive. The same principle applies to biological systems and their survival programs.
In Earth's highly dynamic environment, survival requires that biological systems swiftly yield solutions to new threats. Enzymes, known as biology's workhorses, perform a variety of cellular functions such as harvesting energy, degrading toxins, and assembling new proteins. Organisms like bacteria can live in highly variable settings that offer ever-changing challenges, including the introduction of a new predator, toxin, or energy source. To survive and compete in such surroundings, organisms require highly flexible enzymes that can quickly adapt (which is the intended use of "evolve" throughout this article) to take advantage of environmental variation. Evolving latent, promiscuous (or secondary) functions allows biological systems to rapidly respond to environmental fluctuations.
Promiscuous functions permit enzymes to perform catalysis on more than one type of molecule. Usually, enzymes are specified for certain molecules or types of molecules called substrates. When scientists discover an enzyme that catalyzes reactions with unexpected molecules, the enzyme is said to have promiscuous catalytic activity.
As an example of this activity, consider using a shoe as a hammer. Even though the shoe is clearly meant and designed for a different purpose it can still be semi-useful in a bind. Similarly, biological systems appropriate their enzymes for unusual tasks. Sometimes these functions eventually become necessary for the survival of an organism. In these cases, the enzyme can undergo molecular evolution to become dedicated and specialized to its promiscuous function. One notable example is the organophosphate hydrolases (OPH).
Organophosphates are man-made esters (a large class of organic compounds often used in fragrances) of phosphoric acid introduced into the environment as insecticides and nerve gases within the last few decades. Yet scientists have already discovered an enzyme in bacteria called phosphotriesterase (PTE) that hydrolyzes (breaks down) the organophosphate paraoxon with great efficiency. The fact that PTE exists to breakdown a recently introduced and previously completely foreign type of molecule is unexpected. One hypothesis that explains this is the existence of promiscuous activity in existing natural enzymes.
Researchers suspect that this rapid adaptation can be accounted for by the existence of promiscuous functions in enzymes called esterases. Esterases hydrolyze their unique type of esters; in other words, they specifically break particular esters apart with the help of water. The activity of these esterases on new substrates is initially weak, but scientists theorize that the advantage conferred by rare beneficial mutations accelerates the spread of the mutation throughout the population and allows the enzyme to increase its ability to hydrolyze the novel substrate.
Through in vitro evolution laboratory techniques, researchers simulated the evolution of an esterase into an efficient OPH.1 Starting with an esterase that demonstrated slight promiscuous activity as an OPH, researchers mutated the sequence into a library of variants and screened for those with increased ability to hydrolyze the organophosphate paraoxon. Through multiple rounds of in vitro evolution, the OPH activity was increased 10- to150-fold over the native enzyme. Additionally, researchers demonstrated that activity for non-native substrates can increase without destroying activity for the native substrate. Theoretically, this allows the cell to benefit from the new function while retaining the old.
Just like smart engineers who create software that can evolve to the changing demands of users, God has built proteins to be evolvable to satisfy the changing conditions of life. Evolvability is a good design principle because it affords biological systems the robustness and flexibility to adapt to new challenges while maintaining essential cellular processes.
Additionally, by allowing organisms such as bacteria the latitude to evolve new functions from existing proteins, bacteria can maintain smaller, more efficient genomes while responding to novel situations. Furthermore, development of these new functions creates the potential for remedying man-made ecological disasters such as the spread of organophosphates into drinking water.
A good engineer chooses the appropriate materials to fulfill his purposes. In a similar way, this scientific research points to a Creator who has demonstrated purposefulness by choosing to build life out of highly evolvable materials.
A. Aharoni et al., “The ‘evolvability’ of promiscuous protein functions,” Nature Genetics 37, no. 1 (2005): 73-6.
http://www.reasons.org/Evolvability-AGoodDesignPrinciple
Views: 0
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Comment by Dane on April 26, 2009 at 6:18pm -
"Just like smart engineers who create software that can evolve to the changing demands of users, God has built proteins to be evolvable to satisfy the changing conditions of life. Evolvability is a good design principle because it affords biological systems the robustness and flexibility to adapt to new challenges while maintaining essential cellular processes.
Additionally, by allowing organisms such as bacteria the latitude to evolve new functions from existing proteins, bacteria can maintain smaller, more efficient genomes while responding to novel situations. Furthermore, development of these new functions creates the potential for remedying man-made ecological disasters such as the spread of organophosphates into drinking water.
A good engineer chooses the appropriate materials to fulfill his purposes. In a similar way, this scientific research points to a Creator who has demonstrated purposefulness by choosing to build life out of highly evolvable materials."
I must say, everything was going swimmingly until these last three paragraphs. Suddenly...god is responsible. We'll agree that evolution occurs, but now say that god is responsible for it. You're one step closer...
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Comment by James S Saint on April 26, 2009 at 6:36pm -
"I must say, everything was going swimmingly until these last three paragraphs. Suddenly...god is responsible. We'll agree that evolution occurs, but now say that god is responsible for it."
lol
They call that being "non-sequitor" and I have to agree.
The sad thing is that she is actually correct, but simply doesn't know enough about God to draw the relationship.
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Comment by Jeff H on April 26, 2009 at 7:37pm -
The point is that the design is to sophisticated to have come by accident. This mesh of attributes fall in to the catagory of irreducible complexity. They aren't something that would evolve piecemeal. Your right my friend, the article is well thought out, logical and scientifically viable. You are truly one step closer. :-)
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Comment by Dane on April 26, 2009 at 8:08pm
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Irreducible complexity is a marketing term for I.D., and as far as I've seen isn't a concept that has legs. The idea that scientists think evolution or anything else in biology or chemistry has happened by 'accident' is a big misconception. I agree, these things did not happen by accident. I look at currently persistent life forms as a distillation of genes. The parts that don't work are removed. The ones that do work well remain. All life forms are chemical factories, I like to call the cell 'a walking stomach'. On a biological level, we all live to satisfy our stomachs, and spawn new walking stomachs. Human beings have the unique advantage of a relatively speaking highly developed brain that allows us to change our surroundings to better suit ourselves, instead of necessarily having to adapt ourselves that much better to our environment. In this case, the environment is usually the eventual loser, or succumbs to our needs. The bacteria aren't much different on a lesser level - they still have 'stomachs' that need to be satisfied and reproduce themselves. The big advantage that that bacteria have is not a brain or opposable thumb, but extreme resiliency through a relatively simple structure that is very adaptive. Which one is better or more successful? In terms of numbers and biometric mass, bacteria beat us by a landslide. But doubt they 'enjoy' life, which we fortunately have the privilege to do.
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Comment by Jeff H on April 26, 2009 at 8:08pm
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James... You posted "The sad thing is that she is actually correct, but simply doesn't know enough about God to draw the relationship. " Could you explain what you mean, please?
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Comment by Jeff H on April 26, 2009 at 8:16pm
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Irreducible complexity just makes sense. There are some systems that had to happen... as you might put it... "Tah Da!" just because if any facet weren't there from the start, none of the pieces would work. Kind of like a watch, but on a biochemical level of course.
Cheers!
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Comment by Jeff H on April 26, 2009 at 8:56pm
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Time doesn't fix the fact that the have to happen simultaneously. You might also re-consider the blog... The Perfect Pool Shot.
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Comment by James S Saint on April 26, 2009 at 10:07pm
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"'The sad thing is that she is actually correct, but simply doesn't know enough about God to draw the relationship. ' Could you explain what you mean, please?"
When Sid, and IF Sid, ever gets around to getting back to actually redefining God. And IF I have any say in the matter, the resolved definition will be able to used to show exactly how and why all of creation works in the way that it does - including the adaptive process being called "evolution". And further, it will be able to be shown that there actually is no other choice (although that takes some far more serious metaphysical cognition).
A small part of that discussion took place a short while ago on the comments for a picture, but I can't seem to find out how to locate such things once a little activity comes about.
The comments I am referring to (in part), I will repost here;
================================================================================
The short answer, assuming that you wanted a comment, is that God has assigned the dealing of evil to Man.
The Scriptures point out methods, but if no one goes to the trouble of understanding them, then they must deal with evil through their own chosen method.
Maybe if we merely declare that it doesn't exist, it will go away. Maybe we can do the same with hurricanes, floods, diseases, and politicians.
:))
----------- posted by MUwaM;
You miss the point. If God is omniscient and all powerful then He or She is responsible for hurricanes, floods and death. Why have a God if the God you worship allows Evil to Exist? Or why call him God if He or She is powerless against the forces of Evil?
It may be that God created the universe and left to do other activities or that the God is the Universe and incorporates both Good and Evil. I don't know. I do know that the God of the Old Testament is one of the more unlikely candidates for being a real God.
--------------------
Well, I DID say that it was the short answer, but if you want to get into more detail;
If you were God himself and created an entire universe, only to have some tiny minuscule creature within it tell you what is just and right and what is your responsibility and blame (which could only be determined by that same universe), what would you think?
Even I can see that God uses what you call "evil" so as to get to the eventual result of its absence. Of course, you might ask, "Then why didn't he create it that way to begin with?" I would reply, "He IS."
In the midst of creating anything, there is a time between when it is done and when it started. If you want a cake baked, why don't you just instantaneously cause it to be baked? You use an oven and SLOWLY bake it??? How cruel of you.
No matter how quickly God causes the universe to come to its final destination, being a tiny bit of the making of it will yield the appearance of it taking forever. The tiny molecules in the cake might ask, "Why are you taking so long if you merely want the result?" You might reply, "I am doing it in the way that makes sense to ME. YOUR job is before you as a molecule. BE a molecule and stop trying to tell me how to be a man baking a cake."
From the "GOD perspective", the time in which evil exists is but a tiny fraction quickly resolved by the humans placed in the mix. That is why they are there. They are one of the ingredients. Their complaint that they want to be God and not suffer as Man is a bit silly, but such is to be expected from such tiny little creatures.
Enzymes within your own body might be tempted to ask the same silly question to you. If you want something digested, why don't you just cause that result. I would expect you to reply;
"I AM".
This is no way comes even close to the final logic and rationale that we can achieve once a proper definition is agreed upon. But making such an agreement happens to involve God himself, believe it or not. It requires CREATING something in a similar manner as GOD creates all things. Ahdam was made after the pattern of GOD for a reason - it is the pattern of progress. {{and NO, I didn't say "religion", but GOD}}.
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Comment by James S Saint on April 26, 2009 at 10:15pm
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