Scientists Crack 40-year-old DNA Puzzle And Point To 'Hot Soup' At The Origin Of Life

[Knight-Dragon]

http://www.sciencedaily.com/releases/2005/08/050814170410.htm

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.

In 1968, Marshall Nirenberg, Har Gobind Khorana and Robert Holley received a Nobel Prize for working out how proteins are produced from the genetic code. They discovered that three letter ‘words’ - known as codons - are read from the DNA code and then translated into one of 20 amino acids. These amino acids are then strung together in the order dictated by the DNA code and folded into complex shapes to form a specific protein.

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.

But why there should be 64 words in the DNA dictionary which translate into just 20 amino acids, and why a process that is more complex than it needs to be should have evolved in the first place, has puzzled scientists for the last 40 years.

Dozens of scientists have suggested theories to solve the puzzle, but these have been quickly discounted or failed to explain some of the other quirks in protein synthesis.

“Why there are so many more codons than amino acids has puzzled scientists ever since it was discovered how the genetic code works,” said Dr Jean van den Elsen from the Department of Biology and Biochemistry.

“It meant the genetic code did not have the mathematical brilliance you would expect from something so fundamental to life on earth.”

One of quirks of the genetic code is that there are groups of codons which all translate to the same amino acid. For example, the amino acid leucine can be translated from six different codons whilst some amino acids, which have equally important functions and are translated in the same amount, have just one.

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.

“This simple theory explains many unresolved features of the current genetic code. No one has ever been able to do this before, so we are very excited.”

The theory also explains how the structure of the genetic code maximises error tolerance. For instance, ‘slippage’ in the translation process tends to produce another amino acid with the same characteristics, and explains why the DNA code is so good at maintaining its integrity.

“This is important because these kinds of mistakes can be fatal for an organism,” said Dr van den Elsen. “None of the older theories can explain how this error tolerant structure might have arisen.”

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.

One possible reason for this is that the Last Universal Common Ancestor (LUCA), which evolved into all life on earth, lived in a hot sulphurous pool or thermal vent. As it moved into cooler conditions, it was able to take up these two additional amino acids and evolve into more complex organisms. This provides further evidence for the debate on whether life emerged from a hot or cold primordial soup.

“There are still relics of a very old simple code hidden away in our DNA and in the structures of our cells,” said Dr van den Elsen, who points to several aminoacyl-tRNA synthetases - molecules involved in protein synthesis - which only look at pairs of bases in triplet codons, as well as other physical evidence in support of the theory.

“As the code evolved it has been possible for it to adapt and take on new amino acids. Whether we could eventually reach a full complement of 64 amino acids I don’t know, a compromise between amino acid vocabulary and its error minimising efficiency may have fixed the genetic code in its current format.

 

[Birdjaguar]

Great article! We are one step closer to understanding the beginning of life.

One possible reason for this is that the Last Universal Common Ancestor (LUCA), which evolved into all life on earth, lived in a hot sulphurous pool or thermal vent. As it moved into cooler conditions, it was able to take up these two additional amino acids and evolve into more complex organisms. This provides further evidence for the debate on whether life emerged from a hot or cold primordial soup.

And we have a pretty good guess at where it began, but, it sounds like hell and not eden.

 

[wit>trope]

I think the headlines is obviously a sensational one. The media like to pump up or spice up a story. It's like the headlines for the Slashdot stories.

"It meant the genetic code did not have the mathematical brilliance you would expect from something so fundamental to life on earth"

I think that's the whole problem with science today. We need to go back to Aristotle's idea of final causes and look not only at what caused what but also for what it was caused -- by not looking at this factor we are blinding ourselves to a large chunk of reality and potentially inhibiting the progress of science by a massive amount. Actually I believe we are getting there with some scientists emphasizing the role "beauty" plays in science. We need a principle complementary to Ockam's razor which says: "When given two explanations and one is more beautiful than the other, the more beautiful one is to be preferred, all other things being equal"

I find the idea that we all evolved from a single organism a very silly, almost absurd idea. But it's a fun idea. I look forward to the game Spores

 

[Birdjaguar]

"It meant the genetic code did not have the mathematical brilliance you would expect from something so fundamental to life on earth"

I think that's the whole problem with science today. We need to go back to Aristotle's idea of final causes and look not only at what caused what but also for what it was caused -- by not looking at this factor we are blinding ourselves to a large chunk of reality and potentially inhibiting the progress of science by a massive amount.

I am not a scientist and someone lke Gothmog can better address the points you raise. But such trivial things have never stopped me before...

The questions you raise about final cause and purpose are certainly interesting, but they are not scientific questions. Science needs observable data to work with and we don't have any that pertains to those questions. Science does not apply, religion, cosmology, philosophy all do, but not science. As much as you want to apply scientific methodology to the questions, it cannot be done. You have no data from before creation.

I find the idea that we all evolved from a single organism a very silly, almost absurd idea. But it's a fun idea. I look forward to the game Spores

It is no sillier than Genesis and has more supporting data. As messy as the evolutionary process is (has been), the fundamental rule "survival of the fittest" is very elegant, simple and beautiful.

 

[Yom]

Please, let's not make this into an evo-creation thread.

@XIII: Excellent article as usual. It's very enlightening.

 

[Knight-Dragon]

Moderator Action: This thread won't evolve into a evo-creation thread.

 

[Perfection]

Turning from a 2-codon to 3-coding system seems very strange. I would like to see their proposal for how this mechanism works. The discription here isn't satisfying my curiosity enough.

This thread won't evolve into a evo-creation thread

Heh, the thread creator forbids evolution

 

[Japanrocks12]

I don't think that the 3 codon sequence is anything new.

 

[Birdjaguar]

Heh, the thread creator forbids evolution

Checkmate.

 

[Pontiuth Pilate]

We need a principle complementary to Ockam's razor which says: "When given two explanations and one is more beautiful than the other, the more beautiful one is to be preferred, all other things being equal"

Isn't that just a rather wordy formulation of "wishful thinking"? If we accepted explanations that felt right, the Sun would still be revolving around the Earth.

I don't think that the 3 codon sequence is anything new.

No, a codon is made of three bases, 3 codons is nine bases A code with words of 3 bases with 4 kinds of bases each can produce 64 words (4^3) but they're hypothesizing that the OLD code was made of triplets of which only the first two or last two were read.

 

[Perfection]

I don't think that the 3 codon sequence is anything new.

No but the idea that it evolved from a 2-base pair codon system is

 

[I am the Future]

I know how we really started

But the idea is still interesting.

 

[SonicX]

It makes you wonder if there might be life somewhere out there with more than 4 letters in their genetic alfabet

 

[wit>trope]

Isn't that just a rather wordy formulation of "wishful thinking"? If we accepted explanations that felt right, the Sun would still be revolving around the Earth.

No it doesn't have anything to do with what one wishes. Some people may wish things to be ugly. Those who do probably need some kind of check up for their head, but so do those who wish things to be complicated (which is what the original Ockham's razor is about).

The sun revolving around the earth is not a more beautiful proposition than the earth revolving around the sun. Neither is inherently more beautiful than the other. It's like if you go to a fancy restaurant on top of some kind of tower -- like the Center Point Tower in Sydney for example ... it wouldn't really matter from the perspective of beauty whether the world around the tower is revolving or rotating around the tower or whether the tower (or that portion of it) is just rotating/spinning ... the experience is exactly the same and the view is exactly the same in either case.

In any case there is the "all other things being equal" clause which in economics is known as ceteris paribus ... so if you're going to knock it then you'll have to knock the whole field of economics along with it! So even if one were more beautiful than the other, since all things are not equal since one explanation is more powerful than the other, the more powerful explanation is the one to go with -- this is assuming that the other explanation is even consistent and I don't think it is any longer now that we are able to actually go up into space and observe things from that perspective.

 

[Truronian]

Yes, but how do you measure the beauty of a propotition? Ockham's razor cannot be applied scientifically, in proofs or theories.

 

[wit>trope]

Yes, but how do you measure the beauty of a propotition?

Good question! There are concepts like simplicity (which is covered in Ockham's razor) and elegance and symmetry and proportion ... like the golden proportion or golden ratio which is a mathematical ratio that humans find aesthetically pleasing and has unique mathematical properties. They have already discovered math stuff about the beauty of music so eventually they will discover more and more math stuff about the beauty of visual things. For non-musical and non-visual things, the abstract beauty can still be seen ... that's why mathematicians talk about how a proof is elegant or even beautiful and computer programmers say the same about computer code. Sometimes this more abstract beauty can be represented visually (like in the case of fractals).

 

[Pontiuth Pilate]

Seems like you've deconstructed your entire argument.

Theories (we're talking about real scientific theories here) are constructed based on their ability to explain observations. A new theory would be constructed or formulated only for its ability to explain something an old theory couldn't. A BETTER scientific theory would cover the same things as the old theory and sufficiently explain what was previously unexplained (new or conflicting observations).

Since there is no point in constructing a valid theory that explains EXACTLY as much as another theory (and indeed, that would appear to be nearly impossible) there can never be two theories of equal predictive power, and since you have admitted that predictive power dominates the beauty of the explanation, the beauty of a theory is irrelevant in all cases.

 

[Pontiuth Pilate]

There are concepts like simplicity (which is covered in Ockham's razor) and elegance and symmetry and proportion ... like the golden proportion or golden ratio which is a mathematical ratio that humans find aesthetically pleasing and has unique mathematical properties.

Again, I find it very aesthetically pleasing to believe that the Sun revolves around the Earth once a day. That doesn't make it so. As you yourself have basically admitted, beauty is irrelevant to the truth of a propositon.

 

[wit>trope]

Seems like you've deconstructed your entire argument.

Theories (we're talking about real scientific theories here) are constructed based on their ability to explain observations. A new theory would be constructed or formulated only for its ability to explain something an old theory couldn't. A BETTER scientific theory would cover the same things as the old theory and sufficiently explain what was previously unexplained (new or conflicting observations).

Since there is no point in constructing a valid theory that explains EXACTLY as much as another theory (and indeed, that would appear to be nearly impossible) there can never be two theories of equal predictive power, and since you have admitted that predictive power dominates the beauty of the explanation, the beauty of a theory is irrelevant in all cases.

No there are plenty of theories that fully account for the same data and in these cases the more beautiful theory is to be preferred unless new data causes the less beautiful theory to be preferred on the grounds that it has more explanatory power.

For example, there used to be two theories and both of them fully accounted for the data -- one had the earth revolving around the sun and the other had the sun and other objects in the heavens moving in an extremely mathematically complicated series of orbits (the theory became more and more complicated actually as new data had to be accounted for). Using Ockham's razor one could prefer the simpler theory. You could also use the beauty principle to prefer the more simpler, elegant theory just as a mathematicians prefer simpler, more elegant proofs (for instance if a simpler, elegant proof of Fermat's Last Theorem were possible then that would be much more greatly valued than the complicated proof that is over 100 pages long).

There are examples today like the one above that involve things like black holes and stuff like that.

As you yourself have basically admitted, beauty is irrelevant to the truth of a propositon.

No it's not irrelevant. The more beautiful it is, the more likely it is to be true, ceteris paribus just as the better it accounts for the data the more likely it is to be true. If a theory is just plainly inconsistent with the data then there's no question to be addressed as to whether it or another theory is true -- since theories inconsistent with the data are clearly false. But if two theories are of the same or even very similar explanatory power, which is more beautiful (and this includes which is more simple, elegant, etc.) may tip the balance.

 

[King Alexander]

A good article, Night-Dragon.

It's good to read about advancements; this theory may not be the perfect theory - and a later theory will possibly explain better more things - but it's already a step forward to understand more about ourselves.