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DNA: The Tiny Code That's Toppling Evolution

 
 
patiodog
 
  1  
Reply Sat 7 May, 2005 09:41 pm
Quote:
Still, if you're going to consider the possibility of ET starting life, then you have to figure that the same ET's could have tweaked it, ever so slightly along its way as well.


Well, I'm thinking something more accidental, less deus ex machina. Once you get the yeast started on the wort, there's not much you can do to direct changes in the brew except in the grossest ways -- and the earth is a mightly big brewpot.

Quote:
I like "Cellular Epoch" a lot. May I borrow it? I'll credit you as the author

Does the Cellular Epoch include raw replicative mollecules, or should we also define a larger "Replicative Epoch"?


Hmmm. I'm thinking more, molecular epoch followed by cellular epoch. Perhaps the molecular epoch needs to be broken up into minor replicative and major replicative (or pregenomic) eras. I doubt there could have been a very complex genome before the cell membrane...

Or even if there was a genome before the membrane...
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patiodog
 
  1  
Reply Sat 7 May, 2005 09:43 pm
neologist wrote:
Stay away from ET. If you believe life came about spontaneously or naturally, say so. If you hypothesize another planet, it's just a cop out, right?


All you would do is put the beginning somewhere else, and it would still have to happen somewhere. (Not an idea I favor...)
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rosborne979
 
  1  
Reply Sun 8 May, 2005 06:03 am
patiodog wrote:
neologist wrote:
Stay away from ET. If you believe life came about spontaneously or naturally, say so. If you hypothesize another planet, it's just a cop out, right?


All you would do is put the beginning somewhere else, and it would still have to happen somewhere. (Not an idea I favor...)


I agree. Passing the buck to ET is a useless argument.
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rosborne979
 
  1  
Reply Sun 8 May, 2005 06:07 am
patiodog wrote:
Hmmm. I'm thinking more, molecular epoch followed by cellular epoch. Perhaps the molecular epoch needs to be broken up into minor replicative and major replicative (or pregenomic) eras. I doubt there could have been a very complex genome before the cell membrane...

Or even if there was a genome before the membrane...


I'm not sure about that.

Life probably started with just the merest hint of replication, at which point, Naturally Selective forces would have come into play and accelerated the chemical reactions along lines of sustained replication.

Cell mambranes were still a long way away, hundreds of millions of years, so I would guess there was a pretty well established free growing replicative ecosystem established before cell membranes appeared.
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patiodog
 
  1  
Reply Sun 8 May, 2005 06:53 am
Oh, I agree. By "genome," I'm thinking more along the lines of the modern genes-on-a-chromosome-coding-for-proteins bit. Or if the membrane came up when it was still sloppier than that -- when all was RNA (if such was the case), for instance.
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raprap
 
  1  
Reply Sun 8 May, 2005 07:23 am
Replicating molecules have been discovered that are much simpler than what is conventionally considered RNA/DNA.

This is reported by MIT

Quote:


and Purdue

Quote:
Study breathes new life into question of how life began
WEST LAFAYETTE, Ind. -- A Purdue University study shows that proteins could have played a leading role in the origin of life.
Scientists, looking for clues to how life began at a molecular level, have long considered nucleic acids, such as DNA and RNA, as the star players because of their rare ability to replicate themselves and adapt to changes.

But Purdue University scientist Jean Chmielewski has developed a system made up of four peptides -- the building blocks for proteins -- that can replicate itself and is capable of adapting to changes in the environment. The findings, published in the Dec. 3 issue of the scientific journal Nature, expand the scientific view of how life began.

"This system is the first to show that a peptide-based system has the ability to replicate in novel and adaptive ways," Chmielewski says.

Scientists have long searched for the simplest self-replicating systems as clues to how life may have begun, Chmielewski says.

"The molecules of choice for a long time were molecules like DNA and RNA, because they are known to replicate in living organisms," she says. "The possibility of other self-replicating molecules had also been considered, though until recent years there were no other molecules that were known to be able to reproduce themselves."

In the past 20 years, scientists have found that some other nucleotide-based molecules can replicate themselves. Two years ago, a study published by researchers at Scripps Research Institute showed that some peptides, or pieces of small proteins, also can self replicate.

However, these molecules fell short of DNA and RNA's ability to cross replicate, a feat that allows the nucleic acids to replicate through the use of complementary molecules.

"Self replication would occur if proteins interact with peptide fragments to create an identical copy of themselves," Chmielewski says. "For example, protein AB might interact with peptide A and peptide B and then catalyze to form a new AB protein."

In cross replication, the proteins would interact with complementary peptide fragments, forming a new type of molecule, she says. For example, protein CD might interact with peptide A and peptide B to form an AB protein.

"These cross-replicating molecules are the types of molecules that actually have the potential for building life," Chmielewski says. "It is believed that within a living cell, virtually no substance catalyzes its own formation, so when you talk about a theoretical system that can create life, you want a chemical system in which both self replication and cross replication occurs."

In a recent experiment, the Scripps group developed a system using three peptides that could self replicate and cross replicate through four different chemical reactions. Chmielewski and her group set out to see if they could produce a more complex peptide-based replicating system.

Her group designed a system using four peptides that was capable of carrying out 11 different chemical reactions -- a system almost three times more complex than the Scripps system. Four peptide fragments, called E1, E2, K1 and K2, were used as the feedstock to produce four proteins, namely E1E2, K1K2, E1K2 and K1E2.

The study showed that the four proteins replicated themselves through self replication -- acting as templates for their own formation -- and also used a total of seven cross-replication pathways to produce additional new copies.

"This is the most complex replicating system of its kind to date" Chmielewski says. "This work clearly demonstrates that peptides should be considered in discussions of the nature of the molecular origins of life."

In addition, Chmielewski's group showed that changes to the environment of the reaction had a profound effect on the types of peptides that could be formed.

"If you put the four peptides together, you have the potential to form all of the products, but we can modify the environment of the reaction, such as pH or salt concentration, and only a single molecule can replicate itself and the rest are lost," Chmielewski says.

This ability to survive and reproduce in the face of environmental changes is the basis of Darwinian selection, and it might have allowed for the evolution of early life forms, she adds.

"It is interesting when we imagine that perhaps, in a very early system, only certain molecules were used in the formation of life and others were left behind," Chmielewski says.

Though her study, funded by the National Science Foundation, may help expand the current view of how life formed on Earth, Chmielewski notes that the answers may never be known.

"There is no real way to prove any of this or travel back in time to see how life started," she says. "All we can do is show that various other kinds of molecules are capable of replicating in various ways, and these molecules may have played a role in creating life."

Source: Jean Chmielewski, (765) 494-0135

Writer: Susan Gaidos, (765) 494-2081

Purdue News Service: (765) 494-2096; e-mail, [email protected]


ABSTRACT
Selective Amplification via Auto- and Cross-Catalysis in a Replicating Peptide System
Jean Chmielewski, Shao Yao, Indraneel Ghosh, Reena Zutshi

The successful replication of chemical entities such as DNA and RNA is essential for the transfer of information to succeeding generations. Self replicating chemical systems of nucleotide-based molecules, adenineKemp's triacid conjugates and peptides, have been successfully designed. A living cell, however, is a collective autocatalytic system in which virtually no molecule catalyzes its own production. Therefore, the development of a system in which not only autocatalysis, but also crosscatalysis, can occur is currently a subject of intensive studies. We describe here the first four-component peptide-based system that is capable of both auto- and cross-catalysis. Furthermore, we have selectively amplified one or more of the products by changing the environmental conditions, such as pH or salt concentration, within the reaction.


in the late 90's. Now neither of sources claim to say that this is the same as laboratory life but they indicate that molecular replication occurs at a much more basic level than that of RNA/DNA.

The Purdue study admits the limitation, but it is interesting to note that they noted molecular replication commencing with chains containing as few as 4 peptides This is still a long way from the minimum number of peptides for the most primitive RNA strands.Chembytes

Idea

Rap
0 Replies
 
patiodog
 
  1  
Reply Sun 8 May, 2005 07:52 am
Huh. Hadn't heard of those. Thanks.
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farmerman
 
  1  
Reply Sun 8 May, 2005 07:59 am
Quote:
Technically, the self-replicating compound made by the MIT group is
called an amino adenosine triacid ester (AATE). This molecule was
initially formed by reacting two other molecules. [

When the first self- replicating colloids were synthesized in the mid 90's they were usually interacting in a "real world" substrate. Since these compounds take the form of a complex ester, the hydrolysis wouldhave been actuated by contact with high adsorptive clays. My favorite has always been the volcanic ash clay, bentonite. or the multi functional green clay glauconite. These clays are quick to glom onto to, and promote surface reactions to the base molecules. Thats the evolutionary significance ofchem development in "pre cell membrane world", First the conditions for the chem formation exist, then the planetary environment becomes suitable as oxygen, or highly adsorptive felsdpar clays are deposited in water basins.But as patodog said, nobody believes anything without damn good proof. All this is speculation and, Hoyles pushing of the extra-terrestrial origin of life was at least worthy of consideration because theyve found spectral signatures of at least 2 of the nucleotides and a few proteins in the stars.Weve gotta do something with that data.
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rosborne979
 
  1  
Reply Sun 8 May, 2005 12:10 pm
patiodog wrote:
Huh. Hadn't heard of those. Thanks.


I hadn't either.

It's interesting to think that DNA and RNA may have out-competed simpler self replicators and made them extinct.
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farmerman
 
  1  
Reply Mon 9 May, 2005 09:18 am
Driving back from Maine I was listening to an all night PBS link that was called the world vuiew or something like that.
It was interesting in that the entire 2 hour show was about how China and UK have taken the lead from US on genome and molecular biology in general. The Chinese have spent Zillions setting up large bio research centers since 2000 and have expressed some dismay at how the US, usually a leader in research, has been taken over by a " contrary philosophical position" that does not seem to be supporting such research.
Gotta love the Chinese for their subtle way of saying
"the religious wackos(in the US) are trying to change what science is".

The present national leadership(and its celebration of ignorance) is, IMHO, largely responsible for this very strange trip into the past.
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farmerman
 
  1  
Reply Tue 10 May, 2005 11:08 am
I wonder where the gunga went?
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rosborne979
 
  1  
Reply Tue 10 May, 2005 11:58 am
farmerman wrote:
I wonder where the gunga went?


He's spreading his wisdom in a thread called How to Destroy America, the title of which seems oddly appropriate given his support for Intelligent Design in public science education. Smile
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