"Binary" Enzyme Created By Scripps Scientists Demonstrates Darwinian Evolution At Its Simplest

Scripps Research Institute / ScienceDaily News ^ | 12/19/2002 | John S. Reader, D.Phil, and Professor Gerald F. Joyce, M.D., Ph.D

[forsnax5]

Two scientists at The Scripps Research Institute (TSRI), Research Associate John S. Reader, D.Phil, and Professor Gerald F. Joyce, M.D., Ph.D., both of the institute's Department of Molecular Biology, have succeeded in creating an enzyme based on a "binary" genetic code--one containing only two different subunits.

This research, described in the latest issue of the journal Nature, demonstrates that Darwinian evolution can occur in a genetic system with only two bases, and it also supports a theory in the field that an early form of life on earth may have been restricted to two bases.

"Nobody will ever top this because binary systems are the most reduced form of information processing," says Joyce. "Two different subunits are the absolute minimum number you need [for Darwinian evolution]."

Where protein enzymes are polymer strings made up of 20 building blocks (the amino acids), and RNA or DNA enzymes are made up of four different building blocks (the nucleotides), the world's first binary enzyme has but two different building blocks, based on the nucleotides A and U.

This enzyme is functionally equivalent to a "polymerase" molecule. Polymerases are ubiquitous in nature as the enzymes tasked with taking a "template" string of DNA or RNA bits and making copies of it.

Reader and Joyce's binary enzyme is able to join pieces of RNA that are composed of the same two nucleotide symbols. In the test tube, the binary string folds into an active three-dimensional structure and uses a portion of this string as a template. On the template, it "ligates," or joins subunits together, copying the template.

Experimental Approaches to the Origins of Life

If the origins of life are a philosopher's dream, then they are also a historian's nightmare. There are no known "sources," no fossils, that show us what the very earliest life on earth looked like. The earliest fossils we have found are stromatolites--large clumps of single-celled bacteria that grew in abundance in the ancient world three and a half billion years ago in what is now western Australia.

But as simple as the bacteria that formed stromatolites are, they were almost certainly not the very first life forms. Since these bacteria were "evolved" enough to have formed metabolic processes, scientists generally assume that they were preceded by some simpler, precursor life form. But between biological nothingness and bacteria, what was there?

Far from being the subject of armchair philosophy or wild speculation, investigating the origins of life is an active area of research and of interest to many scientists who, like Reader and Joyce, approach the questions experimentally.

Since the fossil record may not show us how life began, what scientists can do is to determine, in a general way, how life-like attributes can emerge within complex chemical systems. The goal is not necessarily to answer how life did emerge in our early, chemical world, but to discover how life does emerge in any chemical world--to ask not just what happens in the past, but what happens in general.

The most important questions are: What is feasible? What chemical systems have the capacity to display signs of life? What is the blueprint for making life in the chemical sense?

One of the great advances in the last few decades has been the notion that at one time life was ruled by RNA-based life--an "RNA world" in which RNA enzymes were the chief catalytic molecules and RNA nucleotides were the building blocks that stored genetic information.

"It's pretty clear that there was a time when life was based on RNA," says Joyce, "not just because it's feasible that RNA can be a gene and an enzyme and can evolve, but because we really think it happened historically."

However, RNA is probably not the initial molecule of life, because one of the four RNA bases--"C"--is chemically unstable. It readily degrades into U, and may not have been abundant enough on early Earth for a four-base genetic system to have been feasible.

Odd Base Out

To address this, Nobel Laureate Francis Crick suggested almost 40 years ago that life may have started with two bases instead of four. Now Reader and Joyce have demonstrated that a two-base system is chemically feasible.

Several years ago, Joyce showed that RNA enzymes could be made using only three bases (A, U, and G, but lacking C). The "C minus" enzyme was still able to catalyze reactions, and this work paved the way for creating a two-base enzyme.

In the current study, Reader and Joyce first created a three-base enzyme (A, U, G) and then performed chemical manipulations to convert all the A to D (diaminopurine, a modified form of A) and biochemical manipulations to remove all the G. They were left with an enzyme based on a two-letter code (D and U).

Reader and Joyce insist that their study does not prove life started this way. It does, however, demonstrate that it is possible to have a genetic system of molecules capable of undergoing Darwinian evolution with only two distinct subunits.

The article, "A ribozyme composed of only two different nucleotides," was authored by John S. Reader and Gerald F. Joyce and appears in the December 19, 2002 issue of the journal Nature.

This work was supported by a grant from the National Aeronautics and Space Administration (NASA), the Skaggs Institute for Chemical Biology at The Scripps Research Institute, and through a postdoctoral fellowship from the NASA Specialized Center for Research and Training (NSCORT) in Exobiology.

[PatrickHenry]

101 placemarker.

[AndrewC]

The four base pairs of DNA are a subset of the possible alternatives. Game, set, match.

Bull, again. You are playing with yourself. You'll go blind. You haven't coded anything with snowflakes. We already know that DNA has four bases and codes things. It is repeatable, my point not yours.

[Dimensio]

Wait a minute, aren't we slaves to our cats now?

Yes, but some people don't realise that yet. Those who do accept their lot in life and treat cats with the resepect deserved will ascend to higher beings (cats) in the coming Next Thursday.

[Dimensio]

You're creation theory seems too weak to be taught in the public schools.

I guess you've got a point. It's far more believable that some entity whipped up the universe, the sun, the planet and life on the planet over a period of six days (even though it should have been powerful enough to do it all at once given the definition of the entity in question), that it created everything in some undefined 'perfect' state, that it created two humans and put a tree right within their grasp that, for some reason, it didn't want them touching (why put it there, then?). And, of course, it gave the entire universe the appearance of billions of years of age even though it was brand new at the time.

[MoGalahad]

Patrick, thanks for pinging me on this but I have heard the evolutionary view of things all my life and I find it to be dogmatic and patently unscientific so please drop me from your ping list.

Be good and live free,

MoGalahad

[PatrickHenry]

... please drop me from your ping list.

You were never on my list. Someone else must have pinged you.

[Lessismore]

that it created two humans and put a tree right within their grasp that, for some reason, it didn't want them touching (why put it there, then?).

This has always seemed pretty peculiar to me, also, especially since the entity (being omniscient) certainly knew what would happen -- first the eating of the tree of the knowledge of good and evil, and then the creation of the first fig leaf fashions.

Note that clothing made of skins were later furnished by the entity, which must mean that PETA is at odds with the entity.

[jennyp]

This has always seemed pretty peculiar to me, also, especially since the entity (being omniscient) certainly knew what would happen -- first the eating of the tree of the knowledge of good and evil, and then the creation of the first fig leaf fashions.

In the spirit of the upcoming Lightbulb Day festivities^*, here's an Ayn Rand quote:

What is the nature of the guilt that your teachers call his Original Sin? What are the evils man acquired when he fell from a state they consider perfection? Their myth declares that he ate the fruit of the tree of knowledge - he acquired a mind and became a rational being. It was the knowledge of good and evil - he became a moral being. He was sentenced to earn his bread by his labor - he became a productive being. He was sentenced to experience desire - he acquired the capacity of sexual enjoyment. The evils for which they damn him are reason, morality, creativeness, joy - all the cardinal values of his existence. It is not his vices that their myth of man's fall is designed to explain and condemn, it is not his errors that they hold as his guilt, but the essence of his nature as man. Whatever he was - that robot in the Garden of Eden, who existed without mind, without values, without labor, without love - he was not man.

Man's fall, according to your teachers, was that he gained the virtues required to live. These virtues, by their standard, are his Sin. His evil, they charge, is that he's man. His guilt, they charge, is that he lives.

They call it a morality of mercy and a doctrine of love for Man.
from Galt's speech, in Ayn Rand, Atlas Shrugged

^*Dec. 21, the shortest, darkest, dreariest day of the year; the day we celebrate Man's capacity for reason by going out & looking at all the lights.

[Dimensio]

Note that clothing made of skins were later furnished by the entity, which must mean that PETA is at odds with the entity.

Well, I guess that counts for a few points in this entity's favour.

[jlogajan]

This has always seemed pretty peculiar to me, also, especially since the entity (being omniscient) certainly knew what would happen

Actually, the whole concept of a God with perfect knowledge of past, present and future makes religion a ridiculous concept for just that very reason. God knows all future outcomes, God creates men of "free will" even though he already knows to infinity how each one will behave and whether that person will go to hell or not.

It is all fatalistic -- God already knows the result of his creation -- so what is the point? Is he hoping he suffers from amnesia so that he can be surprised by the results.

Or -- God doesn't know everything and therefore he's not qualified to be passing judgement on anyone else -- in which case he is nothing more than a cheap dictator.

[Stavka2]

Oh, so you can accept micro evolution, because it has already been proven in a thousand year experiment, but macro...well, sorry but we just don't have time for the 300 million year experiment. Kinda like saying: well, I can believe atoms are made of quarks but this whole molecules business is for the dogs.

[Stavka2]

Read up on the Orthodox Christian view of the "Original Sin", you'll be surprised...since it was the Catholics who changed it and the Protestants who kept the new version.

[Stavka2]

Or 3. the future is not written in stone but has many outcomes which God can see all of. There fore, our actions do have an impact on the end result. And as the creator, whether through Evolution or Poof, he has the right to judge his creation...definitly more right then some judge with all the human failings of a mortal who can send you to death row.

[jlogajan]

Or 3. the future is not written in stone but has many outcomes which God can see all of.

So he can see them all, but he knows not which will come to pass? Hmm, once you accept a limit to God's knowledge, you admit he is imperfect, and therefore not fit to judge -- for his judgements may be based in imperfect information, and therefore in error. Imagine condemning someone to eternal hell based upon bad information.

[Doc Savage]

Great! Now about that trick where a rooster turns into a cat?? Can you do that one too??

[laredo44]

but they cannot yet show a case where one species has definitively changed into another, at any level on the food chain

Perhaps not, but then maybe you could provide a definitive explanation on how the horse and ass can mate to produce the mule. Seems to me to be a pretty strong prima facia case of the evolution of two species from one.

[laredo44]

but they cannot yet show a case where one species has definitively changed into another, at any level on the food chain

Perhaps not, but then maybe you could provide a definitive explanation on how the horse and ass can mate to produce the mule. Seems to me to be a pretty strong prima facia case of the evolution of two species from one.

[Stavka2]

Being perfect and having total forsight of the future are two totally seperate things. Sorry, your logic doesn't sit, just sinks. You are linking two seperate things togather. As for judgement, a creator can always judge his creations. As for God, he has more right to judge then a human judge, but yet you submit to a human judge, do you not? And besides, in the end, you really don't get much choice. You can disbelieve Him, but He does't disbelieve you.

[jlogajan]

Being perfect and having total forsight of the future are two totally seperate things.

Only if "perfect" has no meaning. Lacking "total foresight" is a lack of perfect foresight, hence a lack of perfection.

I can walk into a casino, know all the possible outcomes of any game of chance, yet lose every penny I have because I don't know which of the outcomes will come to pass. That's God-like perfection?

So either God is all knowing or he isn't. Which is it?

[Doctor Stochastic]

Does make one wonder how this omniscience doesn't collapse the wave functions for the universe.