Evolution as a fact, not a theory.

[trptamene]

Scripps Research Scientists Automate Molecular Evolution

Results Show Genetic Adaptation to Selective Pressure at Work in Real Time

LA JOLLA, CA, April 8, 2008—Under the control of a computer at The Scripps Research Institute, a population of billions of genes morphed through 500 cycles of forced adaptation to emerge as molecules that could grow faster and faster on a continually dwindling source of chemical fuel—a feat that researchers describe as an example of "Darwinian evolution on a chip."

The super molecules that resulted, a species of RNA enzyme, were produced in about 70 hours using an automated tool that is about the size of a compact disc, according to the study published in the April issue of PLoS Biology. The Scripps Research investigators who designed the device note that the findings provide an example of the Darwinian principle of selective pressure at work, seen in real time.

"This is evolution at the level of molecules as a fact, not a theory," says the study's senior investigator, Gerald Joyce, M.D., Ph.D., Scripps Research professor in the Departments of Chemistry and Molecular Biology. "This is what it looks like when a computer controls conditions that push molecules to adapt in order to thrive—survival of the fittest on the smallest scale possible."

The evolved enzymes that resulted exhibited a new set of 11 mutations that improved their ability to survive under substrate-starvation conditions by 90-fold, compared to the starting molecules.

The study's first author, Brian Paegel, Ph.D., a postdoctoral researcher in Joyce's lab, noted that the study is the first of its kind. In previous research, scientists had managed to force adaptation in the test tube by manually adding and extracting ingredients. However, that technique produced an isolated snapshot rather than a dynamic overview of the evolution process.

"No one has been able to observe what the process looks like until now," Paegel says. "It's like before you could only see little bits of a fine painting. Now, we can step back and watch a complete picture of evolution happening at its most fundamental level, on a molecular scale."

Paegel and Joyce designed and patented the microfluidic device they used in the study. The device is basically a thin glass plate, four inches in diameter, with microscopic channels and valves that a computer can control to add or extract small amounts of material. The cost to construct a device is about $8.

Pushing the Limits of an Artificial Molecule

In this study, the scientists used artificial RNA enzymes based on molecules originally developed by David Bartel and Jack Szostak at Harvard Medical School, which were derived starting from completely random RNA sequences. These molecules had been used before in "test tube" evolution experiments carried out by manual methods. The molecules have the ability to catalyze the joining of other RNA molecules, similar to a large protein known as an RNA polymerase. In the system developed by Paegel and Joyce, an RNA molecule that performed this reaction would automatically be copied to produce molecular "progeny."

In the newly published study, Paegel and Joyce loaded the microfluidic device with billions of RNA enzymes and the RNA copying machinery. They then added the chemical fuel that the RNA enzymes must utilize in order to be copied. The scientists provided progressively lower concentrations of the fuel at set intervals, as a way to direct the evolution of the RNA enzymes. Every time the concentration was reduced, those RNA enzymes whose genetic features allowed them to withstand the more stringent conditions multiplied in greater numbers than RNA enzymes that were not so adapted. Each time the size of the population of molecules reached a predetermined level, the computer isolated 1/10th of the population—which now contained higher numbers of successfully adapted RNA enzymes—and mixed it with a new supply of chemical fuel.

These steps were repeated automatically for 500 iterations of 10-fold growth followed by 10-fold dilution. "The competition between the RNA enzymes to scrape up the few substrates became progressively stiffer, and the variants of RNA enzymes that could bind fastest and tightest to the substrate fuel molecules won out," Paegel says.

"We starved these enzymes, pushing them to become better and faster at forming a bond so they could reproduce themselves," Joyce says. "This is like the evolution of animals that can survive food famines. Only here we can see it happen in 70 hours and we know why the mutations that constitute evolution in these molecules occurred. We witnessed the entire story."

Although RNA molecules are not "alive" in the classic sense, they evolve in the same way that viruses do, Paegel says. But unlike those pathogens, which need protective casings to survive, these molecules are not dangerous, he says, because they degrade quickly outside of the chip.

Besides offering a powerful demonstration of real-time evolution—which could also be used to study adaptation in proteins, viruses, and even cellular organisms—the technology may have a number of practical uses, the scientists say, although it was not designed with these in mind. For example, it may be possible to use the technology to create RNA enzymes that act as super chemical sensors. The technology might also be used to help in the design of new medicines by encouraging molecules to evolve to perform a desired function.

http://www.scripps.edu/news/press/040808.html


The details:

Abstract:
An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other's synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about 1 hour and can be continued indefinitely. Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates, during which recombinant replicators arose and grew to dominate the population. These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system.

Science 27 February 2009:
Vol. 323. no. 5918, pp. 1229 - 1232
DOI: 10.1126/science.1167856

Reputation Comments on this post:

great find

[Ilsa]

great find!!! we've seen this on the cellular level and it's been well-described in the lit, but to see something like this on the molecular level is really cool; RNA's autocatalytic properties were known, but i didn't kinow it was that significant....then again, three years ago we were still using the oxymoronic term junk DNA

[Gradient]

Originally Posted by trptamene

Besides offering a powerful demonstration of real-time evolution—which could also be used to study adaptation in proteins, viruses, and even cellular organisms—the technology may have a number of practical uses, the scientists say, although it was not designed with these in mind. For example, it may be possible to use the technology to create RNA enzymes that act as super chemical sensors. The technology might also be used to help in the design of new medicines by encouraging molecules to evolve to perform a desired function.

Thanks for this! What an exciting prospect; harnessing the very dynamics that lead to our own evolution to fight potential pathogens. Seems like fighting biological fire with fire, a fantastic innovation.

I wonder if similar methods might be applied to pluripotent stem cells to induce neural differentiation? Maybe actually grow some implants for Parkinson's or other neurodegererative disorder patients by restricting the cells development with such great environmental control and regulation of transcription factors?

This has to be one of the brightest prospects to come out of genetics for a while, very cool!

[Slater]

do those cells needed DNA mutations to evolve and the reproduction respected the procents ? did the mutations come up naturaly and only the best one survived against something like 10 milions of other of his specie and reproduced and got to more than 10 mil after ? don't think so.

Reputation Comments on this post:

uninformed and poorly written. does not contribute.

[Nature Boy]

Haha! Anyone who states that evolution is "just a theory" knows nothing about the scientific method. In scientific terms, a theory is a fact only it can be elaborated and improved upon. It's not as if it's some goon in a pub forming a theory about why his pint tastes so bad. Everything established in science is a theory from gravity to thermodynamics. Good post though. Maybe you can email it to Kent Hovind and claim his $250,000 prize for proof of evolution.

[Routemaster Flash]

Evolution is both a fact and a theory.

It is a fact that the assortment of living species on Earth has changed over time, and also that the prevalence of characteristics within a species can change over time.

Darwin's idea of evolution-by-natural-selection is a theory to explain evolution (the phenomenon, or fact). Lamarck's evolution-by-inherited-adaptation is also a theory of evolution. The former is extremely well supported by observational evidence; the latter is not and has been discarded.

So-called intelligent design is not a theory, as theories are based on scientific principles and intelligent design is pseudoscience, or rather mysticism masquerading as science. It is, at best, a hypothesis perhaps.

I've got to run now so I'll pop back tomorrow and have a proper read of that article, it looks interesting.

[coelho]

Well... considering evolution as "just a theory" is almost as absurd as considering gravity "just a theory". Both are well verified, and could be considered as "proven facts".

But, even if evolution is a proven fact, it still doesnt explain the origin of the life. Evolution (the one which is "proven") only shows how living beings can evolve to other living beings (or RNA molecules can evolve to other RNA molecules), but it doesnt explain how a living being (supposedly) appeared from just chemical substances.
So, the question about the origin of the life remains unanswered, despite the evolution.

[Nature Boy]

Originally Posted by coelho

But, even if evolution is a proven fact, it still doesnt explain the origin of the life. Evolution (the one which is "proven") only shows how living beings can evolve to other living beings (or RNA molecules can evolve to other RNA molecules), but it doesnt explain how a living being (supposedly) appeared from just chemical substances.

Well, the Miller-Urey experiment went a long way in explaining that. Of course, there are other ideas and perhaps life on Earth may have emerged through several channels. Panspermia, or more accurately exogenesis, is one of the more interesting ideas but I find the deep sea vent theory to be quite fascinating due to its implication that life in the universe might be far more common than we could have possibly imagined. It evens suggests that there may be life on Europa, Jupiter's watery moon. Whatever sparked life on Earth, it certainly wasn't some beardy deity making men from dust and women from ribs merely 6,000 years ago.

[coelho]

Well... the Miller-Urey experiments actually showed that complex organic molecules could appear from simpler ones, but it still has a flaw: the chance that random collisions of molecules lead to the formation of a living being is very very low.

The genetic code (DNA or RNA) of a living being is a sequence of nucleotides, and there are 4 different nucleotides (A,C,T and G in the DNA and A,C,U and G in RNA) in a given piece of DNA or RNA.

For a DNA sequence with only 1 nucleotide of lenght, there are 4 different possibilities: an A, C, T or G. (the same goes for the RNA). For a DNA with 2 nucleotides of lenght, there are 4 x 4 (16) different possibilities: AA, AC, AT, AG, CA, CC, CT, ... etc.

And so on... for a sequence with N nucleotides of lenght, there are 4^N (4 raised to the N th power) different possibilities, 4^N different DNA sequences with the same lenght.

But this sequences are very sensitive to changes. Take a living cell, or a virus, and change one, only one nucleotide of its sequence. Most changes will cause the living being to die or to have its workings very messed up. Of course some changes may make the organism work better, but they are far rarer than the deleterious changes.

So, for any sequence with a given number of nucleotides, how many of this sequences codify a fully functioning living being, how many codify what could almost be a living being, and how many codify just junk?

Consider the simplest known virus. Its genetic code has more than 3000 nucleotides. How many different sequences of nucleotides can be made with 3000 nucleotides? And how many of them actually codify a working virus?

The total number of sequences is 4^3000, which is about 1.5 x 10^1806, which is the number 15 followed by 1805 zeroes (!).
The number of different sequences that could codify a working virus is not easily estimated. It can be a thousand. Or a million. Or a billion. Or a billion of billions of billions. Or 100 times the square of this. (which is 10^56).
(Im supposing that 10^56 is the number of different sequences with lenght of 3000 that codify a working virus. This number is completly arbitrary, and i only choose it because its a very large number, not that it has any meaning. It could be 10^10 or 10^100, it wouldnt interfer with my reasoning).

But even so, the number of sequences that codify a working virus is tiny in comparsion with the total number of possible sequences. (1 followed by 56 zeroes is nothing compared with 1 followed by 1806 zeroes).

So, the supposition that the genetic code (and all the rest) of living beings appeared by random collisions of organic molecules is not of much use, because the chance that this random collisions made the exact sequence of a working living being is completly negligible.
The chance that it happened would be about 1 in 10^1750 (1806-56).
(If swim were to write this number 10^1750, it would occupy more than 20 lines full of zeroes...)
This number, 10^1750 is enormously larger than any quantity with physical meaning. (Just for comparsion, if the known universe were completly filled with the smallest known subatomic particles, the total number of particles contained into it would be about 10^120, still a tiny number compared with 10^1750).

Even if the sea were completly made of nucleotides, one still would have to wait for a long time, like 10^100 or 10^200 (or some number like this) times longer than universes assumed age until one of the randomly made combinations resulted in the sequence of a working living being.

So, unless the life had some "help", it seems very improbable that it appeared by itself just by chance.

The panspermia is also a interesting idea, but it just moves the problem of the origin of the life to another place, outside the Earth. But even so, the above calculations still apply, and so the probability the life appeared by itself remains too low for being considered.

What lets the question about the origin of the life still open.