Was a triple helix the precursor to RNA in the origin of life?

via http://richarddawkins.net/article,3370,n,n
original article: http://www.sciam.com/article.cfm?id=triple-helix-designing-a-new-molecule

Peptide nucleic acid (gold) readily enters DNA's major groove to form triple-stranded and other structures with DNA, allowing it to modify the activity of genes in new ways.
Jean-Francois Podevin

Origin of Life?
A major goal of these efforts to create life de novo in the laboratory is to better understand how life may have started on earth. Considering the detailed microbiology of contemporary life-forms, it seems very clear that RNA is probably more primordial and central to life than DNA and proteins. This one molecule can carry both the genotype (the genetic sequence information) of an organism and the phenotype (catalytic functions). For this reason as well as other evidence, many scientists now accept the idea that our DNA/RNA/protein world was preceded by an RNA world [see “The Origin of Life on the Earth,” by Leslie E. Orgel; Scientific American, October 1994].

Yet it is very unclear how primitive prebiotic conditions could have produced RNA molecules, in particular the sugar ribose in the RNA backbone. Further, even if RNA molecules were produced, RNA’s very poor chemical stability hardly would have allowed the molecules to survive unprotected long enough to play a central role in the initial chemical evolution of life. Thus, a molecule like PNA appears very attractive as a candidate for a pre-RNA world: it is extremely stable and chemically simple, and it carries sequence information.

In 2000 Stanley L. Miller, famous for his seminal experiments more than 50 years ago showing that amino acids can form under conditions believed to simulate those on the primitive earth, identified precursors of PNA in similar experiments. Researchers have also shown that sequence information in a PNA oligomer can be transferred by “chemical copying” to another PNA oligomer or to an RNA molecule—processes needed for a PNA world and then a following transitional PNA/RNA world. Admittedly, it is a long leap from these scanty observations to building a strong case for a pre-RNA world based on PNA or some very similar molecule, and for the hypothesis to have any legs at all, scientists must uncover PNA molecules possessing catalytic activity.

Much remains to be learned about PNA 15 years after its discovery: Are catalytic PNA molecules possible? What is a good system for delivering therapeutic PNA into cells? Can a totally alien, PNA-based life-form be created in the lab? I am confident these questions and many others will be well answered over the next 15 years.

In addition to fomenting exciting medical research, these amazing molecules have inspired speculations relating to the origin of life on earth. Some scientists have suggested that PNAs or a very similar molecule may have formed the basis of an early kind of life at a time before proteins, DNA and RNA had evolved. Perhaps rather than creating novel life, artificial-life researchers will be re-creating our earliest ancestors.

Yet a genetic replication system is only one component of life, albeit a central one. The essence of life is a network of chemical reactions functioning in a state that is relatively stable yet not in equilibrium and that is open to both inputs and outputs [see “A Simpler Origin for Life,” by Robert Shapiro; Scientific American, June 2007]. A major challenge will therefore be to incorporate the self-replicating molecule in a larger system that carries out other catalytic activity and has a metabolic cycle and to integrate the system with a physical compartment such as a lipid vesicle, forming what some researchers call a “protocell.

From Big Bang to Us - Made Easy

potholer54

A recently completed youtube series on Science and the history of the Universe.

From Big Bang to Us -- Made Easy (Full 11-part series)
http://youtube.com/watch?v=wg1fs6vp9Ok&feature=PlayList&p=DB23537556D7AADB&index=0&playnext=1

(from Potholer54's youtube page:) WE NEED YOU! -- I am looking for people who can "seed" the Made Easy series, either hosting it on their websites, mailing DVDs to schools or to other 'seeds', or spreading through BitTorrents. If you can help spread a bit of science and counter the rolling tide of creationist ignorance, please get in touch. Message me with a description of what you can do. Thanks!

The 'Made Easy' series is designed to explain the evidence that shows how we got here, from the Big bang to human migration out of Africa. A better quality version will soon be available for free download from a website -- details to be announced. I will be happy to send DVDs free of charge to schools after the series is finished.

The 'Made Easy' series of videos can be freely copied and distributed for educational purposes, but cannot be used for commercial gain in whole or in part. They cannot be altered, transformed or added to. If you use repost these videos you must attribute them to 'Potholer54 on YouTube."

Name: Potholer

I've been a journalist for 20 years, 14 years as a science correspondent. My degree is in geology, but while working for a science magazine and several science programs I had to tackle a number of different fields, from quantum physics to microbiology. My particular talent was my ignorance. By not understanding half of what I was assigned to cover, I had to reduce scientific discoveries from the complex to the simple. If I wrote it in a way that I could understand it, then my readers could understand it.

1 -- History of the Universe Made Easy (Part 1)
http://youtube.com/watch?v=wg1fs6vp9Ok
Forget gods and goblins, here is the real story of how we know the extent of our universe in time and space. Throw away all those religious books and look at some hard evidence.

2 -- History of the Universe Made Easy (Part 2)
http://youtube.com/watch?v=KMQk6MveZOE
This concludes the two parts on the history of the universe, showing how our universe, solar system and planet Earth formed through natural and predictable processes.

3 -- The Origin of Life made easy
http://youtube.com/watch?v=ozbFerzjkz4
This video answers two commonly held fundamentalist misconceptions: That scientists believe life popped out of nowhere, and that life cannot come from non-living chemicals. It explains the most commonly accepted hypothesis about the origin of life on Earth. As with all hypotheses, there are things we have yet to understand about the steps that took us from organic chemicals to replicating chemicals -- from non-life to life. If we had all the answers this wouldn't be a hypothesis, it would be a theory. So don't expect a Nobel prize for spotting problems, because solving problems is what research is all about. The video simply shows the various steps to forming primitive cells and challenges fundamentalists to show which one is impossible, and why.

4 -- The Story of the Earth Made Easy
http://youtube.com/watch?v=lN8XXaDrK4A
Is the Earth really 6,500 years old? And was there a global flood 4,000 years ago? The only way to find out is to look at the clues from the past. This video explains the evidence geologists use that shows slow uplift, erosion and sedimentation over hundreds of millions of years. (This video replaces an earlier one which -- horror! -- had audio of Kent Hovind)

5 -- The Age of Our World Made Easy
http://youtube.com/watch?v=w5369-OobM4
Methods of dating easily explained, that clearly prove the age of the Earth and our universe. Part of the "Made Easy" series that explains science in clear and simple terms. A must for people who think the world is just 6,000 years old.

6 -- Natural Selection Made Easy
http://youtube.com/watch?v=R_RXX7pntr8
Explains natural selection in simple terms. A must for anyone who is confused by the Theory of Evolution, and wonders why it's taught in classrooms. This video is part of the 'Made Easy' series that explains the history of our world, from the Big Bang to the human migration out of Africa.

7 -- The Theory of Evolution Made Easy
http://youtube.com/watch?v=7w57_P9DZJ4
Explains the Theory of Evolution in simple terms. A must for anyone who is confused by what the Theory is, what it means, and why it's taught in classrooms. This video is part of the 'Made Easy' series that explains the history of our world, from the Big Bang to the human migration out of Africa.

8 -- Human Evolution Made Easy
http://youtube.com/watch?v=MCayG4IIOEQ
The evidence for human evolution. Part of the "Made Easy" series which traces our origins from the Big Bang to the human migration out of Africa. This video can be copied and distributed fro educational purposes, but not for commercial use. It may not be built upon or transformed. You must attribute this work to "YouTube's Potholer54".

9 -- Human Ancestry Made Easy
http://youtube.com/watch?v=8edyoZFW-Lg
Traces our migration out of Africa and explains, through DNA evidence, how humans colonized the world. Part of the Made Easy series of videos that show the evidence of our origins, from the Big Bang onwards.

10 - The Scientific Method Made Easy
http://youtube.com/watch?v=zcavPAFiG14
The 'Made Easy' series explains the evidence of our origins, from the Big Bang to the human migration out of Africa. This video explains how we acquire this knowledge, and how ideas go from a hunch in a laboratory to accepted theories taught in school.

The video cuts at the end, and the final sentence should read: "In the next video, I'll look at whether belief can be regarded as science."

11 -- Creation 'Science' Made Easy
http://youtube.com/watch?v=xO7IT81h200
Creation Science is fairly simple to understand. The conclusion is laid out for you -- just read Genesis -- so there's nothing to investigate. The question is whether this really is science. Even if it isn't, should it be taght in school as a way of 'opening' young minds?

This is the penultimate video in the 'Made Easy' series, which looks at the evidence showing our origins, from the Big Bang to the human migration out of Africa.

New Way To Think About Earth's First Cells by Science Daily

Thanks to Alberto Sarmento for the link.

http://www.sciencedaily.com/releases/2008/06/080604140959.htm

New Way To Think About Earth's First Cells

ScienceDaily (Jun. 6, 2008) — A team of researchers at Harvard University have modeled in the laboratory a primitive cell, or protocell, that is capable of building, copying and containing DNA.


Above is a three-dimensional view of a model protocell approximately 100 nanometers in diameter. The protocell's fatty acid membrane allows nutrients and DNA building blocks to enter the cell and participate in non-enzymatic copying of the cell's DNA. The newly formed strands of DNA remain in the protocell. (Credit: Janet Iwasa, Szostak Laboratory, Harvard Medical School and Massachusetts General Hospital)

Since there are no physical records of what the first primitive cells on Earth looked like, or how they grew and divided, the research team's protocell project offers a useful way to learn about how Earth's earliest cells may have interacted with their environment approximately 3.5 billion years ago.

The protocell's fatty acid membrane allows chemical compounds, including the building blocks of DNA, to enter into the cell without the assistance of the protein channels and pumps required by today's highly developed cell membranes. Also unlike modern cells, the protocell does not use enzymes for copying its DNA.

Led by Jack W. Szostak of the Harvard Medical School, the research team published its findings in the June 4, 2008, edition of the journal Nature's advance online publication.

"Szostak's group took a creative approach to this research challenge and made a significant contribution to our understanding of small molecule transport through membranes," said Luis Echegoyen, director of the NSF Division of Chemistry.

Some scientists have proposed that ancient hydrothermal vents may have been sites where prebiotic molecules--molecules made before the origin of life, such as fatty acids and amino acids--were formed.

When fatty acids are in an aqueous environment, they spontaneously arrange so that their hydrophilic, or water-loving, "heads" interact with the surrounding water molecules and their hydrophobic, or water-fearing, "tails" are shielded from the water, resulting in the formation of tiny spheres of fatty acids called micelles.

Depending upon chemical concentrations and the pH of their environment, micelles can convert into layered membrane sheets or enclosed vesicles. Researchers commonly use vesicles to model the cellular membranes of protocells.

When the team started its work, the researchers were not sure that the building blocks required for copying the protocell's genetic material would be able to enter the cell.

"By showing that this can happen, and indeed happen quite efficiently, we have come a little closer to our goal of making a functional protocell that, in the right environment, is able to grow and divide on its own," said Szostak.

"We have found that membranes made from fatty acids and related molecules -- the most likely components of primitive cell membranes -- have properties very different from those of the modern cell membrane, which uses specialized pumps, channels or pores to control what gets in and out," says Jack Szostak, PhD, of the MGH Department of Molecular Biology and Center for Computational and Integrative Biology, the report's senior author. "Our report shows that

very primitive cells may have absorbed nutrients from their environment, rather than having to manufacture needed materials internally

, which supports one of two competing theories about fundamental properties of these cells."

Szostak's team carefully analyzed vesicles comprised of different fatty acid molecules and identified particular features that made membranes more or less permeable to potential nutrient molecules. They found that, while large molecules such as strands of DNA or RNA could not pass through fatty acid membranes, the simple sugar molecules and individual nucleotides that make up larger nucleic acids easily crossed the membrane.

To further explore the function of a fatty acid cell membrane, the researchers used activated nucleotides they developed for this study that will copy a DNA template strand without needing the polymerase enzyme usually required for DNA replication. After placing template molecules inside fatty-acid vesicles and adding the activated nucleotides to the external environment, they found that additional DNA was formed within the vesicles, confirming that the nucleotide molecules were passing through the fatty-acid membranes.