Genesis - getting closer

black wolf · 04-04-07, 01:31 AM

If it's done, will creationists call it a lie again, as they call evolution a lie? Or will they concede the defeat of 'creation science'?

from: Primordial Soup's On: Scientists Repeat Evolution's Most Famous Experiment: Scientific American
"In Focus
March 28, 2007
Primordial Soup's On: Scientists Repeat Evolution's Most Famous Experiment
Their results could change the way we imagine life arose on early Earth
By Douglas Fox

A Frankensteinesque contraption of glass bulbs and crackling electrodes has produced yet another revelation about the origin of life.

The results suggest that Earth's early atmosphere could have produced chemicals necessary for life—contradicting the view that life's building blocks had to come from comets and meteors. "Maybe we're over-optimistic, but I think this is a paradigm shift," says chemist Jeffrey Bada, whose team performed the experiment at the Scripps Institution of Oceanography in La Jolla, Calif.

Bada was revisiting the famous experiment first done by his mentor, chemist Stanley Miller, at the University of Chicago in 1953. Miller, along with his colleague Harold Urey, used a sparking device to mimic a lightning storm on early Earth. Their experiment produced a brown broth rich in amino acids, the building blocks of proteins. The disclosure made the pages of national magazines and showed that theories about the origin of life could actually be tested in the laboratory.

But the Miller-Urey results were later questioned: It turns out that the gases he used (a reactive mixture of methane and ammonia) did not exist in large amounts on early Earth. Scientists now believe the primeval atmosphere contained an inert mix of carbon dioxide and nitrogen—a change that made a world of difference.

When Miller repeated the experiment using the correct combo in 1983, the brown broth failed to materialize. Instead, the mix created a colorless brew, containing few amino acids. It seemed to refute a long-cherished icon of evolution—and creationists quickly seized on it as supposed evidence of evolution's wobbly foundations.

But Bada's repeat of the experiment—armed with a new insight—seems likely to turn the tables once again.

Bada discovered that the reactions were producing chemicals called nitrites, which destroy amino acids as quickly as they form. They were also turning the water acidic—which prevents amino acids from forming. Yet primitive Earth would have contained iron and carbonate minerals that neutralized nitrites and acids. So Bada added chemicals to the experiment to duplicate these functions. When he reran it, he still got the same watery liquid as Miller did in 1983, but this time it was chock-full of amino acids. Bada presented his results this week at the American Chemical Society annual meeting in Chicago.

"It's important work," says Christopher McKay, a planetary scientist at NASA Ames Research Center in Moffett Field, Calif. "This is a move toward more realism in terms of what the conditions were on early Earth."

Most researchers believe that the origin of life depended heavily on chemicals delivered to Earth by comets and meteorites. But if the new work holds up, it could tilt that equation, says Christopher Chyba, an astrobiologist at Princeton University. "That would be a terrific result for understanding the origin of life," he says, "and for understanding the prospects for life elsewhere."

But James Ferris, a prebiotic chemist at Rensselaer Polytechnic Institute in Troy, N.Y., doubts that atmospheric electricity could have been the only source of organic molecules. "You get a fair amount of amino acids," he says. "What you don't get are things like building blocks of nucleic acids." Meteors, comets or primordial ponds of hydrogen cyanide would still need to provide those molecules.

Bada's experiment could also have implications for life on Mars, because the Red Planet may have been swaddled in nitrogen and carbon dioxide early in its life. Bada intends to test this extrapolation by doing experiments with lower-pressure mixes of those gases.

Chyba is cautious: "We don't know," he says, "whether Mars really ever had that atmosphere." That's because Mars today has carbon dioxide, but hardly any nitrogen—which is also needed for making amino acids. Some scientists suspect that nitrogen gas existed on Mars, but was blasted away by asteroid impacts billions of years ago."

Thinker · 04-04-07, 02:54 AM

I suspect we shall create a self-replicating molecule of sufficient complexity to
allow variation (i.e., life, and hence evolution) within the next 100 years. That's
not exactly "soon", but I don't think it will only happen in the "far distant" future.

I don't think it will be done by generating random chemicals, as that will probably
take far too long. More likely, a specific molecule will be designed and
synthesised.

tecoyah · 04-04-07, 07:42 AM

Soon....very soon:

"BERKELEY, Calif. - They're called "synthetic biologists" and they boldly claim the ability to make never-before-seen living things, one genetic molecule at a time.

They're mixing, matching and stacking DNA's chemical components like microscopic Lego blocks in an effort to make biologically based computers, medicines and alternative energy sources. The rapidly expanding field is confounding the taxonomists' centuries-old system of classifying species and raising concerns about the new technology's potential for misuse.

Though scientists have been combining the genetic material of two species for 30 years now, their work has remained relatively simplistic."

Researchers creating life from scratch - Science - MSNBC.com

Monk-Eye · 04-04-07, 09:55 AM

"Winter Solstice 2012"

Quote:

Originally Posted by Thnker

I suspect we shall create a self-replicating molecule of sufficient complexity to allow variation (i.e., life, and hence evolution) within the next 100 years. That's not exactly "soon", but I don't think it will only happen in the "far distant" future.
I don't think it will be done by generating random chemicals, as that will probably take far too long. More likely, a specific molecule will be designed and
synthesised.

A self-replicating molecule like Virus RNA?

The principle point is to establish a natural pathos for abiogenesis.
A manner of pursuit is to replicate earth conditions because it is a supposed example of success.

Scientist can and do generate oligonucleotides to specification.
Genetic engineers could create their own Island of Doctor Mar-rue (Moreau)
mar - Make imperfect
rue - Sorrow; repetance

YHVH built a garden east of Eden.
When the Grigori/Anunnaki show up, what will you say?

Lachean · 04-04-07, 11:21 AM

This isnt a hurdle for the creationists. For theirs is the fallacy of an infinite regression. Now they will step back and question the "apparantly fine tuned" physical constants that allow for the conditions of a self-replicating molecule.

Since we cannot prove that this universe may not be alone, the idea that this universe is the only, and that it is so perfectly tuned for randomly varying complexity, will be used to support the idea that it must have been "intelligently designed."

ashurbanipal · 04-04-07, 12:15 PM

I don't think this really answers anything. A couple questions:

1) Self-replicating molecules deserve the moniker, but how do they "self-replicate?" This has never been sufficiently answered, and if you reflect on it, it does seem a little odd that a molecule would in essence deconstruct other molecules, or coopt them, to create replicas of itself. Amino acids aren't the only molecules that do it--but this still doesn't answer the question.

2) There's also no really clear path for how we go from that to actual organisms. Clearly, something else is needed aside from self-replication, or else we'd just have a bunch of amino acids. There's no a priori reason amino acids wouldn't be perfectly happy just staying as amino acids.

Monk-Eye · 04-04-07, 01:27 PM

"Hops, Skips, And Jumps"

There is a gap between raw amino acids and RNA and, between RNA and DNA.

Quote:

Originally Posted by ashurbanipal

I don't think this really answers anything. A couple questions:
1) Self-replicating molecules deserve the moniker, but how do they "self-replicate?" This has never been sufficiently answered,

RNA World Hypothesis

RNA self splicing

Quote:

Ribosomes
A ribozyme (from ribonucleic acid enzyme, also called RNA enzyme or catalytic RNA) is an RNA molecule that catalyzes a chemical reaction. Many natural ribozymes catalyze either their own cleavage or the cleavage of other RNAs, but they have also been found to catalyze the aminotransferase activity of the ribosome. Investigators studying the origin of life have produced ribozymes in the laboratory that are capable of catalyzing their own synthesis under very specific conditions, such as an RNA polymerase ribozyme.[1] More work needs to be done in this area though, as the polymerase ribozyme does not have enough catalytic prowess: it is able to add up to 14 nucleotides to a primer template in 24 hours until it is decomposed by hydrolysis of the phosphodiester bonds.

Quote:

Originally Posted by ashurbanipal

2) There's also no really clear path for how we go from that to actual organisms. Clearly, something else is needed aside from self-replication, or else we'd just have a bunch of amino acids. There's no a priori reason amino acids wouldn't be perfectly happy just staying as amino acids.

Quote:

RNA Virus
Mutation rates
RNA viruses generally have very high mutation rates as they lack DNA polymerases which can find and fix mistakes, and are therefore unable to conduct DNA repair of damaged genetic material. DNA viruses have considerably lower mutation rates due to the proof-reading ability of DNA polymerases within the host cell. Retroviruses integrate a DNA intermediate of their RNA genome into the host genome, and therefore have a higher chance of correcting any mistakes in their genome thanks to the action of proof-reading DNA polymerases belonging to the host cell.

Although RNA usually mutates rapidly, recent work found that the SARS virus and related RNA viruses contain a gene that mutates very slowly.[2] The gene in question has a complex three-dimensional structure which is hypothesized to provide a chemical function necessary for viral propagation, perhaps as a ribozyme. If so, most mutations would render it unfit for that purpose and would not propagate.

ashurbanipal · 04-04-07, 02:58 PM

Monk-eye,

Interesting articles, but they still don't offer explanations. Quite often, that we observe many similar actions is offered as an explanation for why any particular action exists. But it's no explanation.

Consider a completely unrelated analogy--serial murderers. Suppose we want to know what motivates someone to murder over and over. Is it any explanation to point out that it's somewhat common across cultures, that many other people do the same thing?

Similarly, we observe that RNA does some interesting stuff. But the questions are why and how it does those things. We've managed to show that ribozymes can form under certain conditions thought to be prevalent on this planet about 3 billion years ago. We still haven't answered why they do what they do, and how.

This is stuff I've spent a lot of time thinking about, and the more I ponder it, the more I think it may boil down to trying to understand how energy and matter interact. If you think about it, it's kind of something we take for granted, but there's still no really good explanation, even for everyday occurrences. When one billiard ball strikes another, causing the second to move, what exactly is happening? We don't really know. We have terms that describe the process and allow us to predict certain important results from initial conditions, but that doesn't mean we really understand the process.

Similarly, as any self-replicating molecule bumps up against the building blocks of itself, it tends to fold those other molecules around it's frame until there's a replicant. But how, exactly, that occurs, and why some molecules do it and others don't, remains a mystery.

Thinker · 04-04-07, 03:03 PM

Quote:

Originally Posted by Monk-Eye

"Winter Solstice 2012"

A self-replicating molecule like Virus RNA?

No. That's far, far too complicated as a starting point.

Thinker · 04-04-07, 03:16 PM

Quote:

Originally Posted by ashurbanipal

1) Self-replicating molecules deserve the moniker, but how do they "self-replicate?"

By acting as catalysts for their own creation.

Quote:

This has never been sufficiently answered, and if you reflect on it, it does seem a little odd that a molecule would in essence deconstruct other molecules, or coopt them, to create replicas of itself.

Why odd? One mechanism could be that the molecule has sites into which
other, simpler molecules "fit". When the molecule is in an environment with the
necessary simpler molecules, it starts to gather them. Once all the necessary
molecules have attached, they combine and break away, leaving a copy of
the original.

Quote:

2) There's also no really clear path for how we go from that to actual organisms. Clearly, something else is needed aside from self-replication, or else we'd just have a bunch of amino acids.

You are assuming amino acids were the starting point.

You are right in that something else is needed, and that is variation. The
molecules need to be able to make mistakes in replicating. This could be
putting the "wrong" molecule in one position, or getting two copies of itself to
join together to make a longer self-replicating molecule. Once you have such
variation, natural selection can take place and you have evolution.