Although this has nothing to do with PO, I couldn't resist this:
Scientists crack 40-year-old DNA puzzle and point to ‘hot soup’ at the origin of life
$this->bbcode_second_pass_quote('', 'A')ugust 02, 2005
A new theory that explains why the language of our genes is more complex than it needs to be also suggests that the primordial soup where life began on earth was hot and not cold, as many scientists believe.
In a paper published in the Journal of Molecular Evolution this week, researchers from the University of Bath describe a new theory which they believe could solve a puzzle that has baffled scientists since they first deciphered the language of DNA almost 40 years ago.
As the DNA ‘alphabet’ contains four letters - called bases - there are as many as 64 three-letter words available in the DNA dictionary. This is because it is mathematically possible to produce 64 three-letter words from any combination of four letters.
The new theory builds on an original idea suggested by Francis Crick - one of the discoverers of the structure of DNA - that the three-letter code evolved from a simpler two-letter code, although Crick thought the difference in number was simply an accident “frozen in time”.
The University of Bath researchers suggest that the primordial ‘doublet’ code was read in threes - but with only either the first two ‘prefix’ or last two ‘suffix’ pairs of bases being actively read.
By combining arrangements of these doublet codes together, the scientists can replicate the table of amino acids - explaining why some amino acids can be translated from groups of 2, 4 or 6 codons. They can also show how the groups of water loving (hydrophilic) and water-hating (hydrophobic) amino acids emerge naturally in the table, evolving from overlapping ‘prefix’ and ‘suffix’ codons. “When you evolve our theory for a doublet system into a triplet system, you get an exact match up with the number and range of amino acids we see today,” said Dr van den Elsen, who has worked with Dr Stefan Babgy and Huan-Lin Wu on the theory.
The new theory also highlights two amino acids that can be excluded from the doublet system and are likely to be relatively recent ‘acquisitions’ by the genetic code. As these amino acids - glutamine and asparagine - are unable to hold their shape in high temperatures, this suggests that heat prevented them from being acquired by the code at some point in the past.
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Solved DNA puzzle points to ‘hot soup’ origin of life
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Solved DNA puzzle points to ‘hot soup’ origin of life
by Graeme » Wed 03 Aug 2005, 14:31:34
http://www.physorg.com/news5570.html
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Graeme - Fusion
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by Berkeley » Wed 03 Aug 2005, 20:52:30
That's a really interesting theory. Thanks for pointing it out. It has not appeared on the usual science news sites yet. The idea of DNA itself evolving is mind-blowing. I wonder if there is someway, even theoretically, to date these changes? I was somewhat open to the panspermia theory before this, but if DNA evolves at all then panspermia loses its only good argument.
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Berkeley - Wood
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by linlithgowoil » Thu 04 Aug 2005, 05:54:47
interesting. of course, we're still no closer to explaining why a bunch of dead minerals decided to come to life one day and form one of the most intricate and beautiful molecules known.
maybe the monolith from 2001 space oddesey turned up and gave the hot soup a nice stir?
maybe the monolith from 2001 space oddesey turned up and gave the hot soup a nice stir?
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linlithgowoil - Tar Sands
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by Doly » Thu 04 Aug 2005, 06:06:33
$this->bbcode_second_pass_quote('linlithgowoil', 'o')f course, we're still no closer to explaining why a bunch of dead minerals decided to come to life one day and form one of the most intricate and beautiful molecules known.
Minerals don't take decisions, as far as we know. You can ask how did the process happen exactly, but not about their motives.
You can also ask how is it possible that complexity arises from simpler things, and a few computer simulations may give you a certain understanding of that.
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by EnergySpin » Thu 04 Aug 2005, 10:14:45
$this->bbcode_second_pass_quote('Berkeley', 'T')hat's a really interesting theory. Thanks for pointing it out. It has not appeared on the usual science news sites yet. The idea of DNA itself evolving is mind-blowing. I wonder if there is someway, even theoretically, to date these changes? I was somewhat open to the panspermia theory before this, but if DNA evolves at all then panspermia loses its only good argument.
The genetic code universality is also a matter of degree. There are very ancient (in the evolution sense) bacteria that use a different genetic code (3-4 triplets out of the 64 have a different meaning). In addition the way the mitochondrial DNA is read (we have two sets of genes in our cells, one in the nucleus, the other in the mitochondria) is slightly different from the nuclear DNA. The fact that the genetic code is so stable (despite those differences) is an indication that life originated in a single microenvironment, and latter evolved with differences in the genetic program arising due to the need to explore different ecological niches.. This does not r/o panspermia, nor does it r/i. The most interesting question is what did the pre-cellular life forms look like i.e. there are various theories reviewed in the RNA Word.
$this->bbcode_second_pass_quote('linlithgowoil ', 'o')f course, we're still no closer to explaining why a bunch of dead minerals decided to come to life one day and form one of the most intricate and beautiful molecules known.
There is a scientific consensus today that the conditions that led to the origin of the first life forms will never be known (the geologic history of earth was very different then, no fossil records are available), so that question may never be answered. In addition life cannot be accurately defined so what may consider alive, another person may consider as nonliving (viruses, bacterial spores etc). If one defines life at the physical level (many definitions at different levels of detail are possible), then life is a low temperature non-equilibrium thermodynamic process. A NETP can store retrieve and replicate information (which can be measured in terms of entropy as detailed in the following Wiki page, properties that are shared by other physical systems like crystals. To see a possible (beautiful but unproved theory) of how crystals might have catalyzed the emergence of life out of "dead minerals" check the following page).
A more "mainstream" (mainstream is a matter of degree in biological sciences), focuses on the iron sulfide world, and the nature of the atmosphere - oceans when protolife emerged (Martin Russel Wachterhausen). In that theory metabolic pathways emerged first and everything else is a latter addition (I really like their idea as well as the clay-crystal one ). Short intro from the wikipedia article
$this->bbcode_second_pass_quote('', 'A')ccording to their scenario, the first cellular life forms may have evolved inside so-called black smokers at seafloor spreading zones in the deep sea. These structures consist of microscale caverns that are coated by thin membraneous metal sulfide walls. Therefore, these structures would solve several critical points of the "pure" Wächtershäuser systems at once: (1) the micro-caverns provide a means of concentrating newly synthesised molecules, thereby increasing the chance of forming oligomers; (2) the steep temperature gradients inside a black smoker allow for establishing "optimum zones" of partial reactions in different regions of the black smoker (e.g. monomer synthesis in the hotter, oligomerisation in the colder parts); (3) the flow of hydrothermal water through the structure provides a constant source of building blocks and energy (freshly precipitated metal sulfides); (4) the model allows for a succession of different steps of cellular evolution (prebiotic chemistry, monomer and oligomer synthesis, peptide and protein synthesis, RNA world, ribonucleoprotein assembly and DNA world) in a single structure, facilitating exchange between all developmental stages; (5) synthesis of lipids as a means of "closing" the cells against the environment is not necessary, until basically all cellular functions are developed. This model locates the "last universal common ancestor" (LUCA) inside a black smoker, rather than assuming the existence of a free-living form of LUCA. The last evolutionary step would be the synthesis of a lipid membrane that finally allows the organisms to leave the microcavern system of the black smokers and start their independent lives. This postulated late acquisition of lipids is consistent with the presence of completely different types of membrane lipids in archaebacteria and eubacteria (plus eukaryotes) with highly similar cellular physiology of all life forms in most other aspects.
Common theme to both hypothesis is the pre-existence of a non-living non equilibrium thermodynamic process that ignited or catalyzed life.
However lin is right, we do not have an idea of the events that catalyzed the emergence of life from "dead minerals", even though we know that this is physically ppossible (otherwise we would not be here)
"Nuclear power has long been to the Left what embryonic-stem-cell research is to the Right--irredeemably wrong and a signifier of moral weakness."Esquire Magazine,12/05
The genetic code is commaless and so are my posts.
The genetic code is commaless and so are my posts.
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