Without enzyme, biological reaction essential to life takes 2.3 billion years

November 11, 2008

All biological reactions within human cells depend on enzymes. Their power as catalysts enables biological reactions to occur usually in milliseconds. But how slowly would these reactions proceed spontaneously, in the absence of enzymes – minutes, hours, days? And why even pose the question?

One scientist who studies these issues is Richard Wolfenden, Ph.D., Alumni Distinguished Professor Biochemistry and Biophysics and Chemistry at the University of North Carolina at Chapel Hill. Wolfenden holds posts in both the School of Medicine and in the College of Arts and Sciences and is a member of the National Academy of Sciences.

In 1995, Wolfenden reported that without a particular enzyme, a biological transformation he deemed "absolutely essential" in creating the building blocks of DNA and RNA would take 78 million years.

"Now we've found a reaction that – again, in the absence of an enzyme – is almost 30 times slower than that," Wolfenden said. "Its half-life – the time it takes for half the substance to be consumed – is 2.3 billion years, about half the age of the Earth. Enzymes can make that reaction happen in milliseconds."

With co-author Charles A. Lewis, Ph.D., a postdoctoral scientist in his lab, Wolfenden published a report of their new findings recently in the online early edition of the Proceedings of the National Academy of Science. The study is also due to appear in the Nov. 11 print edition.

The reaction in question is essential for the biosynthesis of hemoglobin and chlorophyll, Wolfenden noted. But when catalyzed by the enzyme uroporphyrinogen decarboxylase, the rate of chlorophyll and hemoglobin production in cells "is increased by a staggering factor, one that's equivalent to the difference between the diameter of a bacterial cell and the distance from the Earth to the sun."

"This enzyme is essential for both plant and animal life on the planet," Wolfenden said. "What we're defining here is what evolution had to overcome, that the enzyme is surmounting a tremendous obstacle, a reaction half-life of 2.3 billion years."

Knowing how long reactions would take without enzymes allows biologists to appreciate their evolution as prolific catalysts, Wolfenden said. It also enables scientists to compare enzymes with artificial catalysts produced in the laboratory.

"Without catalysts, there would be no life at all, from microbes to humans," he said. "It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction."

Experimental methods for observing very slow reactions can also generate important information for rational drug design based on cellular molecular studies.

"Enzymes that do a prodigious job of catalysis are, hands-down, the most sensitive targets for drug development," Wolfenden said. "The enzymes we study are fascinating because they exceed all other known enzymes in their power as catalysts."

Wolfenden has carried out extensive research on enzyme mechanisms and water affinities of biological compound. His work has also influenced rational drug design, and findings from his laboratory helped spur development of ACE inhibitor drugs, now widely used to treat hypertension and stroke. Research on enzymes as proficient catalysts also led to the design of protease inhibitors that are used to treat HIV infection.

"We've only begun to understand how to speed up reactions with chemical catalysts, and no one has even come within shouting distance of producing, or predicting the magnitude of, their catalytic power," Wolfenden said.

Source: University of North Carolina School of Medicine

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mvg
2.1 / 5 (18) Nov 11, 2008
"It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction."

And they would STILL have us believe that it all happened by chance!
Modernmystic
3.9 / 5 (7) Nov 11, 2008
When Darwin wrote his book we thought cells were about as complex as a fishing reel...now in comparison they look like a saturn V.
holmstar
3.6 / 5 (16) Nov 11, 2008
And they would STILL have us believe that it all happened by chance!


Yep. What is so impossible about that?

Alternatively, lets take your position... if God created the universe and everything in it, then what created God? If nothing/nobody created God, then God must have arisen via chance. If some other being created God, then what created that being? Eventually you have to conclude that an incredibly advanced being just popped into existence. That seems a lot more complicated than the possibility that some compounds randomly formed into a self-replicating cell. Note that these first "cells" would be nothing like the cells we see today, they would be orders of magnitude less complicated and elaborate. Simply capable of absorbing compounds and splitting to form two or more cells. Over time things like DNA and organelles could develop, but none of that would be present at the beginning.
acarrilho
3.8 / 5 (12) Nov 11, 2008
holmstar, how dare you apply logic to "God"??!! Don't you know "God" is beyond human logic? That theists presume to understand the motivations of a being beyond human logic is purely coincidental... you heathen!
Nederluv
3.3 / 5 (10) Nov 11, 2008
It's true that we don't know for certain how life started, but it's certain that organic molecules can form from inorganic molecules under the circumstances found on Earth 4 billion years ago (Miller & Urey experiment).
We also that RNA can be a catalyst (enzyme) as well as a molecule that stores information.
So I think that, for as far as the beginning and evolution of life is concerned, God didn´t do a thing.
Modernmystic
2.3 / 5 (12) Nov 11, 2008
It's true that we don't know for certain how life started, but it's certain that organic molecules can form from inorganic molecules under the circumstances found on Earth 4 billion years ago (Miller & Urey experiment).


Which is a looooooooooooooooooooooooong way away from even RNA much less life.

We also that RNA can be a catalyst (enzyme) as well as a molecule that stores information.


How exactly did the RNA get there?

So I think that, for as far as the beginning and evolution of life is concerned, God didn´t do a thing.


I think that's as good a scientific opinion as mine based on our current knowledge/understanding.
Soylent
3.9 / 5 (9) Nov 11, 2008
How exactly did the RNA get there?


Perhaps montmorillonite-clay catalyzed synthesis of RNA oligomers; perhaps one of the many other possible pre-biotic catalyst that haven't been discovered yet.
Modernmystic
2.5 / 5 (11) Nov 11, 2008
How exactly did the RNA get there?


Perhaps montmorillonite-clay catalyzed synthesis of RNA oligomers; perhaps one of the many other possible pre-biotic catalyst that haven't been discovered yet.


IOW you don't know for sure. Actually no one does. Therefore I think it's a tad pretentious to say you know how it DIDN'T happen.
PPihkala
3.2 / 5 (10) Nov 11, 2008
We can not prove or disprove god or other intelligent designer. Because we can not study those, it's pointless to even try. Therefore we should concentrate to things that we can study. And that is how inorganic stuff can become organic stuff. Arguing about ID is just waste of time and is very non-scientific.
Modernmystic
2.2 / 5 (5) Nov 11, 2008
Dude if I want to argue with a young earth creationist I will do so just to learn about them. And if you think learning isnt pointful I will put the point in you dude!


Be my guest, never said you couldn't. I think it's pointless though. I have better things to do with my time than argue about whether or not the Earth is flat, was created in six days, or the sky is blue.

What I would like to do is have an honest debate with the other side on this issue. Unfortunately in the current climate of scientific political correctness that doesn't seem very likely.

Oh and just in case you didn't know it's illegal to threaten someone with bodily harm...whether or not it's in person or over the Internet.
ofidiofile
3.3 / 5 (9) Nov 12, 2008
Do you really KNOW my position? Did I mention "GOD"? I simply insinuated that "chance" appears to be a very unlikely candidate. Do you really understand probability?--or do you always simply close your mind to anything other than what is "the dogma of the day".


i'm afraid this is fallacious; because it most surely not mere chance - it was chance, and the laws of physics. i don't know what religion you practice, if any, but this is really an old chestnut, right there with the mistaken notion that life somehow violates the 2nd law of thermodynamics!
ofidiofile
4.4 / 5 (8) Nov 12, 2008

If you found a watch in the sand you COULD prove there was an intelligent designer. If (as modern biology much to it's own dismay is showing) you can place outside the realm of reasonable possibility that life arose through some random probabilistic unknown "process" then there is only one other alternative.

In fact in the absence of ANY evidence that life did arise sans design there is simply no scientific basis to rule a design/designer out. There is a quasi-religious basis for doing so however.

What's really pointless is trying to argue with someone who says they don't know how something happened, but they know how it didn't happen. It's no different that arguing with a young Earth creationist. THAT is the definition of pointlessness.


wow, what a fantastic load of moonbattery! dear, god, and you so turned the old "evidence of absence" canard on it's head. i'm sure that's not allowed. ;p

as i responded to another, if the origin of life had only the laws of mathematics to count on, it would surely be a different story; as it is, there is mathematics as well as the laws of physics.

living things don't fit together like clockwork, they mesh organically, they GROW together. paley's argument is a poor one, because in using an obvious artifact as examplar he was implicitly assuming his own conclusion by way of his premise. what are prions? are they alive? they don't seem to be much more than little pieces of protein - but they have the ability to "pass on" their shapes, distorting healthy proteins. if you actually did any digging you'd find other examples.

here's another good spot: http://xrl.in/11qj

oh, and i don't know how jimmy hoffa died, but i *do* know how he didn't: he didn't die from Ebola, he didn't die from exposure to vacuum, he didn't step on a stonefish... i could go on, but i think you see the point. it's absurd to think that a scientist has to explore every last possibility to declare anything with certainty. science is about what we know at this moment in time about any particular physical process to the best of our knowledge, given what presently known about the laws of physics and biology, about any particular physical process.
Modernmystic
2 / 5 (7) Nov 12, 2008
oh, and i don't know how jimmy hoffa died, but i *do* know how he didn't: he didn't die from Ebola,


Actually no, if you don't know how he died then you strictly speaking DON'T know he didn't die from Ebola etc...period.

it's absurd to think that a scientist has to explore every last possibility to declare anything with certainty.


Equally absurd to rule out possibilities with no evidence whatsoever.

science is about what we know at this moment in time about any particular physical process to the best of our knowledge, given what presently known about the laws of physics and biology,


Which in this case is NOTHING with any degree of certainty about the origins of life. You certainly can't even come CLOSE (a rather large understatement) to reproducing the process (read experiment). If you don't know, then don't know. Don't be a priest and say you do know because it's what you BELIEVE and hide behind a scientist's mantle.

Why, given the enormity of the problem and the complexities involved couldn't it have been an alien intelligence? Do you know for a fact it wasn't? How? If not then what's the point of even listening to your "argument"?

Nederluv
3.9 / 5 (7) Nov 12, 2008
"I think that's as good a scientific opinion as mine based on our current knowledge/understanding."

No it isn't.

My opinion is an educated guess. We don't know exactly how it happened, but we do have some things to begin with:
We know that organic molecules can form from inorganic molecules & we know that RNA can work as an enzyme AND as a storage molecule.

Your opinion is just a guess. The God hypothesis has no proof at all.
Modernmystic
2 / 5 (10) Nov 12, 2008
Oh and FYI smart guy ebola first appeared in Zaire and Sudan in 1976. Jimmy hoffa disappeared July 30 1975...not such a big stretch.

Are the rest of your facts this well researched and reliable?

:)
mvg
3.5 / 5 (2) Nov 12, 2008
"It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction."

And they would STILL have us believe that it all happened by chance!


Having begun this discussion with the above statement from the author and researcher followed by a simple statement--I am surprised that, given even the author's somewhat tepid endorsement of "natural selection", this conversation has "evolved" as it has.

My intent was to demonstrate that nearly EVERYTHING is more complex than what we at first imagine--that our understanding is incomplete--that scientific "dogma" does not enhance rational discussion--and--that humility is in order.

We can take the discovery (outlined in the above article) of very early and perhaps universal complex processes as a threat to our personal beliefs-or-be willing to, at the very least, be more tolerant of alternative views.
Yes
4 / 5 (4) Nov 13, 2008
I wonder about how long will the half synthesize time be for naturally forming the uroporphyrinogen decarboxylase enzymes that seem to be essential for forming the rest.
Once the enzyme is available the mentioned 3 billion years are reduced to milliseconds.
I fear however that forming the enzymes will also take its eons. (who has ears understands)
And then the hardly formed enzymes have to unite with the right base materials that also take a long time to form I guess.
holmstar
3.8 / 5 (6) Nov 13, 2008
"Yep. What is so impossible about that?
Alternatively, lets take your position..."

Do you really KNOW my position? Did I mention "GOD"? I simply insinuated that "chance" appears to be a very unlikely candidate. Do you really understand probability?--or do you always simply close your mind to anything other than what is "the dogma of the day".


Your position was implied by your argument. It is certainly possible that you were playing "devils advocate".

I was just pointing out that if we did not arise by accident, then something created us on purpose. That something, whatever it was, must have have an origin. Either it arose by chance, or it was created, and so on, and so on. In the end, SOMETHING that would be considered alive ABSOLUTELY MUST have arisen from the basic laws of physics and random chance. There are no other options. Logically it is the only possibility. That is my point.

It is certainly possible that our current understanding of physics is inaccurate, but it is the best that we have thus far based on logic and experimentation. While current physics may not make it clear how life could arise, I have absolute confidence that if we knew all there is to know about physics that it would be clear how life could arise. Though, absent the ability to travel back in time and see, we will NEVER know with absolute certainty the exact way that life arose. Most likely there are many ways.
holmstar
4 / 5 (5) Nov 13, 2008
Oh, and yes, you certainly CAN prove (or at least rule out as ridiculously improbable) that something did not happen in a specific way, while not knowing the exact nature of how it did happen.
mvg
3.6 / 5 (5) Nov 13, 2008
In the end, SOMETHING that would be considered alive ABSOLUTELY MUST have arisen from the basic laws of physics and random chance. There are no other options. Logically it is the only possibility. That is my point.

Yes, I understand your reasoning. Everything we know (or think we know) is enclosed with the confined system of time and space--thus our reasonings most naturally occurr within these bounds as a framework. I've heard it said.(though I can't recall where)--that "the universe is stranger than we know--perhaps it is stranger than we CAN know".

And yes. I agree that "you certainly CAN prove (or at least rule out as ridiculously improbable) that something did not happen in a specific way".--I really believe that this is demonstrated by the article we are commenting on-- and the previous comment recently made by "YES" who said:
I wonder about how long will the half synthesize time be for naturally forming the uroporphyrinogen decarboxylase enzymes that seem to be essential for forming the rest.
Once the enzyme is available the mentioned 3 billion years are reduced to milliseconds.
I fear however that forming the enzymes will also take its eons. (who has ears understands)
And then the hardly formed enzymes have to unite with the right base materials that also take a long time to form I guess.

Thus I consider "chance" to be a "ridiculously improbable" solution.

As to the existence of God--I am not the master of anyone else's faith. You may weigh what facts are available to you and come to your own conclusions. But the scripture does say that "His invisible qualities are clearly seen from the worlds creation onward, even his eternal power and Godship"

I wish you well as we study the world around us.
holmstar
4.7 / 5 (3) Nov 13, 2008
"the universe is stranger than we know--perhaps it is stranger than we CAN know".


I agree, but only insofar as the fact that it is likely that certain aspects of physics are likely to never be within the realm of things that we can test experimentally. Thus, we can only theorize on those aspects. However, I don't believe that physics is so complicated that, if there were a repository of knowledge that explained all aspects of physics, that we wouldn't be able to understand it.

relating to the question of origin... regardless of where original life existed, be it a higher dimension, neighboring universe, or perhaps some higher structure that all of the universe and its dimensions reside within, that life would have had a beginning.

The only possible alternative explanation, and I imagine that some would find this quite comforting, would be that intelligence is a basic property of the cosmos. But at this point we are really more into the realm of philosophy than science.

Note: the fact that we cannot currently disprove the above alternative does not in any way prove that it is true.

To those of you who appear to be threatened by the findings of science, get a grip. Its pretty darn unlikely that science will EVER disprove God.
Modernmystic
2 / 5 (5) Nov 13, 2008
To those of you who appear to be threatened by the findings of science, get a grip. Its pretty darn unlikely that science will EVER disprove God.


Impossible to disprove a negative. The problem I have with some people is their positive assertion that science has done just that...which is about as far from science as you get.
holmstar
3.7 / 5 (3) Nov 13, 2008
Everything we know (or think we know) is enclosed with the confined system of time and space--thus our reasonings most naturally occurr within these bounds as a framework.


If you really want to delve into philosophy and what we truly know...

We (actually I) only know one thing with absolute certainty.

I think, therefore I am.


I exist. That is all. **Everything** else could be an elaborate trick.
holmstar
4.3 / 5 (6) Nov 13, 2008
I'd say there is some strong circumstantial evidence based on complexity alone AND the abject failure of science to explain how such complexity came to be in any "natural" process.


The complexity argument is a non-starter because evolution (which has reams and reams of evidence, and has actually been observed experimentally in the lab) accounts for it.

Lab observed evolution: http://www.pnas.o.../23/7899

In the lab, some bacteria developed a way to metabolize citrate. This is a complex change that requires multiple mutations in order to occur, but they have shown that these mutations do not have to occur all at once.

The very first life form did NOT have to be complicated. It could have been a self-replicating enzyme, or a bubble of organic compounds that tends to grow and split when it gets too large. Over time and many many generations, it would gain complexity until there would be something that we would recognize as alive.
Yes
1.2 / 5 (5) Nov 13, 2008
Cogito Ergo Sum.

I am not impressed by the reasoning.
I am impressed by the conclusion.
holmstar
5 / 5 (6) Nov 13, 2008
Science is always trying to disprove the existence of God and that is impossible because:
Science will prove God!!!!


Ok, great... so why don't you propose an experiment to prove God exits.

Good luck buddy.
holmstar
4.5 / 5 (2) Nov 13, 2008
Cogito Ergo Sum.

I am not impressed by the reasoning.
I am impressed by the conclusion.


so, you are impressed that you exist?
bmcghie
4 / 5 (2) Nov 13, 2008
Yes, except you're all forgetting that the illusion of "I" is merely a construct of the rest of the mind. It has been shown that the conscious regions of the brain are only informed of many decisions AFTER they have been made. For more deliberate thinking, yes we certainly make use of our prefrontal cortex... but for those gut reactions, and other quick decisions, you (the brain) have already made the decision before you ("I") is aware of it.

It's interesting to think about. It also casts that "I think therefore I am" into a whole other light. Are YOU really thinking? Or is it something else telling you what you are thinking?

This is why I prefer to shy away from philosophy, and stick to cell bio and genetics. Much cleaner.
mvg
1 / 5 (2) Nov 13, 2008


I exist. That is all. **Everything** else could be an elaborate trick.


Let us hope that God is not so capricious!
Yes
3.5 / 5 (6) Nov 13, 2008
so, you are impressed that you exist?

Everybody should be!
Yes
1 / 5 (4) Nov 13, 2008
The existence and behaviour of Bose-Einstein condensates implicate that everything is an illusion. Everything is probably 1.
So even 1 plus 1=2 is an illusion.
Within this illusion is me and you.
Me first and then you because as we mentioned I for myself have to convince myself still that there is anything besides me.

What the haeck has this to do with 2.3 billion years of a spontaneous reaction that once was meant to be biological?
holmstar
3.8 / 5 (4) Nov 14, 2008
Yes, except you're all forgetting that the illusion of "I" is merely a construct of the rest of the mind. It has been shown that the conscious regions of the brain are only informed of many decisions AFTER they have been made. For more deliberate thinking, yes we certainly make use of our prefrontal cortex... but for those gut reactions, and other quick decisions, you (the brain) have already made the decision before you ("I") is aware of it.

It's interesting to think about. It also casts that "I think therefore I am" into a whole other light. Are YOU really thinking? Or is it something else telling you what you are thinking?

This is why I prefer to shy away from philosophy, and stick to cell bio and genetics. Much cleaner.


That is all well and good, but you missed the point of the argument, which is that *EVERYTHING* that you observe, even your observations about how neurons function could be an elaborate trick. There is no way for me to know with absolute certainty that anything exists beyond my own consciousness. I am conscious (I think) therefore *I* exist. That is all. For all I know you may be an illusion.
holmstar
4.7 / 5 (3) Nov 14, 2008
The existence and behaviour of Bose-Einstein condensates implicate that everything is an illusion.


I fail to grasp your logic.

This is totally unrelated, but how about this one...

Quantum mechanics describes particles as not being well defined until they are observed. This seems odd, but it is accepted as being true.

The Universe appears to be expanding, which over time causes more and more of the universe to become impossible to view as the space between is expanding faster than light.

Particles can be entangled, such that if one is observed, properties of the other particle, no matter the distance, are instantly defined as well. This seems to violate the speed of light, but we ignore that since no classical information is transmitted. This is odd (or "spooky") also.

Consciousness cannot currently be explained by physics. You can explain how an animal or human machine works, why and how it makes decisions, but there is no explanation to why there is a consciousness that is able to observe all of that. Oh, and don't even try to tell me that consciousness is an illusion.

Here's the thing, all of the above would make sense if we are living in a simulation.

Entangled particles make sense in a simulation because instant changes regardless of location are trivial in a simulation.

Most likely the computer we are running on is not infinitely powerful, thus it would probably stress its resources to be able to run such a simulation in real time, unless they use some tricks in order to simplify the task. One could be to average the effect of individual particles unless they are being directly observed, while also limiting the information that is available when a particle is directly observed. That would explain the Heisenberg uncertainty principle. That would work for a while, but the problem is that as time goes on, the population is rising and more and more people are observing particles. The computer is having trouble rendering all of the detail that is being observed, so it needs to cut processing cycles somewhere else. But they have thought ahead on this by using an expanding universe. As matter passes beyond the horizon of the physical universe the computer no longer needs to simulate it at the detail it once did (it would still need to simulate the effect of gravity on neighboring objects still within the visible galaxy). This frees-up the needed processing power.

So why is it important that the simulation occur in real time? because external creatures take part in it, rather like a holo-deck. Consciousness cannot be explained by our physics because it is a product of different physics, the physics of the real world. We are just observers and players in our universe.

Well, its a bizarre possibility anyway, and a fun thought experiment. Note that this is just as likely as any faith-based explanation for the universe.

Yes
1 / 5 (1) Nov 14, 2008
hahahahahahahaha
I like it when people think, though it is probably nonsense. Thank you for making me laugh a bit.
makotech222
not rated yet Nov 14, 2008
okay wtf... im pretty sure i learned this in AP biology class, why are they researching it further?
Ethelred
3.7 / 5 (3) Nov 15, 2008

Quantum mechanics describes particles as not being well defined until they are observed. This seems odd, but it is accepted as being true.


There is no need for the observation to be done by anything conscious. Any particle will do. Massive or not. At that point the observed and the observer become entangled and remain that way until the entangled system is observed by an outside particle. Iterate to infinity or the edge of the Universe, whichever comes first.
tkjtkj
2 / 5 (4) Nov 15, 2008
"It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction."
And they would STILL have us believe that it all happened by chance!


The author is quite misleading in
his statement about the importance
of knowing the velocity of
non-enzymaticlly accellerated
reaction! It matters
not one bit to the processes of
evolution whether the reaction in
question normally takes one
billion years or 1 hour! Evolution
does not sit down and think " Hey!
This thing that takes so long is
just unacceptable! so lets put
EXTRA energy/thought into the
solution!" Enzymes work by bringing
together the constituents of the
reaction in an efficient way: How
the materials would apprach each
other 'in the wild' matters very
little,if at all! "Slow is Slow".
and "Too Slow is Too Slow". That
randomness can produce some
material that has the ability for
the stuff to get close enough for
a chemical reaction to occur is
generally independent of what
happens without the 'solution',the
evolved 'enzyme'. There is
therefore no need to introduce the
'magic' of religion to explain
an entirely simple process.
Modernmystic
2 / 5 (4) Nov 15, 2008
"It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction."
And they would STILL have us believe that it all happened by chance!


The author is quite misleading in
his statement about the importance
of knowing the velocity of
non-enzymaticlly accellerated
reaction! It matters
not one bit to the processes of
evolution whether the reaction in
question normally takes one
billion years or 1 hour! Evolution
does not sit down and think " Hey!
This thing that takes so long is
just unacceptable! so lets put
EXTRA energy/thought into the
solution!" Enzymes work by bringing
together the constituents of the
reaction in an efficient way: How
the materials would apprach each
other 'in the wild' matters very
little,if at all! "Slow is Slow".
and "Too Slow is Too Slow". That
randomness can produce some
material that has the ability for
the stuff to get close enough for
a chemical reaction to occur is
generally independent of what
happens without the 'solution',the
evolved 'enzyme'. There is
therefore no need to introduce the
'magic' of religion to explain
an entirely simple process.


Time certianly does matter, otherwise it's entirely possible that all the life present on Earth was evolved in 6 days.

Is it REALLY your position that that is a possibility? You can't have it both ways...
superhuman
5 / 5 (2) Nov 15, 2008
This is a bad and misleading article.

The only reason for those billions of years is high activation energy and the fact that our physical models assume that at a given temperature a molecule can have *ANY* energy but the probability drops rapidly as the value moves away from equilibrium (mean thermal energy of molecules). So if you have an activation energy far from equilibrium you can get such numbers, but they are in fact meaningless because the model is really applicable close to equilibrium.

Besides *everything* affects the value given, solvent used, concentrations, pH, ionic strength, temperature, pressure even isotopic ratios and electromagnetic background, so giving just one number and claiming it would take *THAT* much is really silly and clearly aimed at inspiring awe in ignorants.
smiffy
5 / 5 (2) Nov 16, 2008
This seems a really interesting piece of research, but I don't have enough background knowledge to properly appreciate its significance. So here's a stab at it.

It does seem that what the researchers are saying is that this catalyst, uroporphyrinogen decarboxylase or UROD, is vital to some very basic functions of animal and plant life. This would imply that the UROD gene predated the evolution of plants, which means that it would have to have another function even more basic (because earlier) than the two mentioned in the article. I don't know how many base pairs long the DNA sequence must be to code this gene but from a cursory look at a graphic of the enzyme's structure it looks like it could be thousands? - so my guess is that it's not at all a simple gene.

Which begs the questions:
What was its original very basic function?
Has this function since disappeared from the dynamics of living things? (How very curious, if it's so fundamental, that it has.)
superhuman
2 / 5 (1) Nov 16, 2008
It does seem that what the researchers are saying is that this catalyst, uroporphyrinogen decarboxylase or UROD, is vital to some very basic functions of animal and plant life. This would imply that the UROD gene predated the evolution of plants, which means that it would have to have another function even more basic (because earlier) than the two mentioned in the article.

Long before plants appeared the Earth was ruled by their ancestors - cyanobacteria, they were already here 2.8 billion years ago. They had a use for such an enzyme as they photosynthesize.


I don't know how many base pairs long the DNA sequence must be to code this gene but from a cursory look at a graphic of the enzyme's structure it looks like it could be thousands? - so my guess is that it's not at all a simple gene.

That fact that some modern instance of this enzyme (for example from humans) is big doesn't mean that the same enzyme was always big or that the same enzyme is as big in modern algae.
Only a small part of enzyme structure is usually employed for catalysis and there are many places in the remainder of it where evolution can add or remove amino acids without disrupting the overall structure and catalysis efficiency.


Which begs the questions:
What was its original very basic function?
Has this function since disappeared from the dynamics of living things?

During the course of evolution genes are often duplicated so new enzymes can evolve without loosing the functionality provided by their precursors.
ofidiofile
not rated yet Nov 17, 2008
holmstar:


Well, its a bizarre possibility anyway, and a fun thought experiment. Note that this is just as likely as any faith-based explanation for the universe.


interesting idea. have you ever read any of the works of bishop george berkeley, the 18th century irish philosopher? one of my personal faves; and from what you've posted here you'd probably enjoy it too! :)
bmcghie
3 / 5 (2) Nov 18, 2008
Nice posts superhuman. Not so much on your part ModernMystic. I'm really hoping you're not deliberately trying to put words in other people's mouths... It was quite obvious the post was referring the the time required for the reaction to take place, and was not in fact referring to the time required for a catalyst to arise.
Modernmystic
1 / 5 (4) Nov 18, 2008
So how did the catalyst arise and how long did it take?
superhuman
4.3 / 5 (3) Nov 18, 2008
Thanks

So how did the catalyst arise and how long did it take?


It arose by mutations of proteins that predated it.

On the level of whole species DNA is constantly changing, bases get substituted and whole segments get duplicated and deleted. It leads to changes in proteins and form time to time those changes produce new enzymes which then spread throughout the population.

How long did it take depends on what event do you want to measure from and in any case only a very rough estimate is possible. I would say anything between 500 million to 2 billion years since life began on Earth.
Modernmystic
1.7 / 5 (6) Nov 19, 2008
So how did the catalyst arise and how long did it take?

It arose by mutations of proteins that predated it.

Where's your proof of this? Where did the proteins that predated it come from? How complex were they and how long did they take to form? Do you have conclusive proof of how they formed? Has this been reproduced in a lab or are you just assuming and telling your own creation story?

Just wondering because all the information I've seen says we don't know how these processes took place, and have NEVER EVER observed them experimentally. The most we've done is put some CHON in a beaker and run some electricity through it and got some simple amino acids...

On the level of whole species DNA is constantly changing, bases get substituted and whole segments get duplicated and deleted. It leads to changes in proteins and form time to time those changes produce new enzymes which then spread throughout the population.


This is sort of a non-sequitur, because as our esteemed friend bmcghie stated we're only talking about the catalyst here. Not to mention the fact that you're talking about how extant processes behave in an apples and oranges analogy, not exactly what I was asking.

How long did it take depends on what event do you want to measure from and in any case only a very rough estimate is possible. I would say anything between 500 million to 2 billion years since life began on Earth.


Well if it took 2 billion years for the catalyst to form (which to be honest is just a wild guess) then it would have taken life 2 billion years longer to evolve than current thinking suggests. This seems to be out of line with our current understanding that basically as soon as conditions were there life was too.

This kind of bleeds back into my original point. The fact that life requires this enzyme to function on any reasonable time scale points to a conclusion that life was harder to form and function than previously thought.
Ethelred
1 / 5 (1) Nov 20, 2008
This kind of bleeds back into my original point. The fact that life requires this enzyme to function on any reasonable time scale points to a conclusion that life was harder to form and function than previously thought.


It only takes longer IF you didn't take this sort of thing into account. I do.

No we don't know everything. No we can't know everything. This in no way makes Dr. Behe's ideas any more accurate than when he first published them.

ID isn't science. It never has been. Its nothing but a claim that 'We don't know everything, therefor there must be a designer.' And its the ID proponents idea of the designer either explicitly or implied in most cases. It certainly is in Dr. Behe's case.

Science can neither prove nor disprove any sufficiently vaguely defined god. Many Americans and even some ID proponents however, believe in a god that can be proved or disproved. Those that believe in a young earth could easily prove their case or at least show a possibility of their gods existence IF they were right. They are not. The god of Young Earth Creationists does not exist.
superhuman
5 / 5 (2) Nov 20, 2008
Where's your proof of this? Where did the proteins that predated it come from? How complex were they and how long did they take to form? Do you have conclusive proof of how they formed? Has this been reproduced in a lab or are you just assuming and telling your own creation story?


Well, if you are genuinely interested in this subject then read a couple of books on molecular biology and you will soon know answers to your questions.


Just wondering because all the information I've seen says we don't know how these processes took place, and have NEVER EVER observed them experimentally. The most we've done is put some CHON in a beaker and run some electricity through it and got some simple amino acids...


You missed a lot of information it seems.
Here is one example of exactly such event recreated in the lab:

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
http://www.pnas.o...abstract

Abstract:
The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit ) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that %u201Creplayed%u201D evolution from different points in that population's history. We observed no Cit mutants among 8.4 %uFFFD 1012 ancestral cells, nor among 9 %uFFFD 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit , indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.
Ethelred
1 / 5 (2) Nov 20, 2008
Cool post. Thank you.

Dr. Behe got surprised at the Dover hearing by how much evidence there was that covered the situations he called irreducibly complex. ID proponents simply don't want to know about evidence for the evolution of complexity. So they don't look and claim it doesn't exist at all.

When shown evidence they have several ways of responding. I am interested in seeing how Modernmystic responds.

There are NO modern mystics. They just repeat the same things in a modern dress. Well at least its not Theosophy. Thats a philosophy-religion that believes that Harry Houdini did real magic. In Sir Arthur Conan Doyles case even after Harry showed him how it was done.
Excalibur
2.8 / 5 (9) Nov 30, 2008
Impossible to disprove a negative.

DIS-proving a negative is simple; the problem lies in PROVING one.
bmcghie
not rated yet Dec 07, 2008
Modernmystic said: The fact that life requires this enzyme to function on any reasonable time scale points to a conclusion that life was harder to form and function than previously thought.

The key point here is LIFE AS WE KNOW IT. The presence of this enzyme, and the reaction it enables has shaped the evolution of every organism from the point of it's appearance forward. Without the enzyme, you would be seeing different organisms using different mechanisms to overcome this problem.

Also, props to you superhuman for digging that up. I always get pissed when people demand answers to grade 12 biology questions. That's usually when I leave the thread in disgust. :) On campus here, that's not an option. I have lab work to do. The difference is, everyone is aware that the answers we do have fit the situation to the best of our knowledge, and the things we attempt to do WORK using the current models. Try to build an enhanced smallpox vaccine with only "God did it." Nevermind HOW he did it. Just sit in the lab until he does it for you, right? Because it's not like you have any further ideas as to how it'll happen...
Sorry, I got mad again.

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