New evidence for molecular evolution

January 2, 2008

Scientists find missing evolutionary link using tiny fungus crystal

The crystal structure of a molecule from a primitive fungus has served as a time machine to show researchers more about the evolution of life from the simple to the complex.

By studying the three-dimensional version of the fungus protein bound to an RNA molecule, scientists from Purdue University and the University of Texas at Austin have been able to visualize how life progressed from an early self-replicating molecule that also performed chemical reactions to one in which proteins assumed some of the work.

"Now we can see how RNA progressed to share functions with proteins," said Alan Lambowitz, director of the University of Texas Institute for Cellular and Molecular Biology. "This was a critical missing step."

Results of the study were published in Thursday's (Jan. 3) issue of the journal Nature.

news.uns.purdue.edu...

Provides some insight into how a basic replicating molecule might have been able to start interacting with proteins.

...................


ABE: even more rolling back of the fog of ignorance...

New evidence for the evolution of the eye

Fresh Fossil Evidence Of Eye Forerunner Uncovered

ScienceDaily (Jan. 2, 2008) — Ancient armoured fish fossils from Australia present some of the first definite fossil evidence of a forerunner to the human eye, a scientist from The Australian National University says.

www.sciencedaily.com...

Science is excitin' innit? Slowly, slowly catchy monkey...

[edit on 2-1-2008 by melatonin]

Provides some insight into how a basic replicating molecule might have been able to start interacting with proteins.

I like this venture into molecular biology melatonin. I think this is a crucial point at which Deists and Theists will converge to eventually if other Design arguments are confronted by people like yourself.

However, having read the article I thought: 'so what?'. The convention is that DNA is a code for a human being stored in the nucleus or headquarters of all body cells. The DNA codes for proteins through a 'middleman' RNA.

RNA is thought to be the original coding material in evolutionary terms, processing itself and then making protein. DNA was thought to have arrived on the scene later. Right so far?

OK, the article claims to have found protein attached to RNA which fuflils some of its functions. However, we have not gone back far enough in time yet. Where did the small molecules that made RNA come from (the nucleotides)?

Are there natural reactions which make nucleotides without unnatural temeratures and pressure? If so, then the argument becomes more simplified.

Moreover, would you care to comment on the rate of mutation that would have plagued early genetic materials - I would hazard that the rate would be pretty high given the labile nature of genetic material when under attack from environmental mutagens.

ABE: even more rolling back of the fog of ignorance...

New evidence for the evolution of the eye

Fresh Fossil Evidence Of Eye Forerunner Uncovered

ScienceDaily (Jan. 2, 2008) — Ancient armoured fish fossils from Australia present some of the first definite fossil evidence of a forerunner to the human eye, a scientist from The Australian National University says.

www.sciencedaily.com...

Science is excitin' innit? Slowly, slowly catchy monkey...

[edit on 2-1-2008 by melatonin]

This eye one I found interesting. If I am correct then the eye evolved from a photosensitive spot which is thought to have evolved into the modern eye. However, I find it difficult to imagine how that spot would have conferred an advantage on the primitive single cell carrying it unless there are two other mechanisms in play:

1. Regeneration of the pigment. The pigment may have to be broken down and then require an energy cost by the cell to rebuild it so that it would be able to detect more photons.

2. The cell would have to have a mechanism inside it for predator avoidance as soon as the light is interrupted - this seems to require a level of inter-connectedness between light and the motility mechanisms otherwise the natural selection advantage is lost. You are right, of course, science is exciting.

Originally posted by Heronumber0
OK, the article claims to have found protein attached to RNA which fuflils some of its functions. However, we have not gone back far enough in time yet. Where did the small molecules that made RNA come from (the nucleotides)?

Oh, I agree. This is just one possible link in the chain. Much more work to do. But, as I'm sure you know, this is generally how science works, small tentative steps in the right direction. I'm sure we would all like to solve this stuff in one day, not likely to happen though.

I'll answer the eye stuff manana, about to hit the sack. Hope you're well anyway

Originally posted by melatonin

Oh, I agree. This is just one possible link in the chain. Much more work to do. But, as I'm sure you know, this is generally how science works, small tentative steps in the right direction. I'm sure we would all like to solve this stuff in one day, not likely to happen though.

I'll answer the eye stuff manana, about to hit the sack. Hope you're well anyway

I did try to look up nucleotide origin by googling it but came up with very little. It seems to be a bit of a mystery. I knew that simple amino acids, e.g. glycine, were fuond in the ice around stars but could not find a correlation for nucleotides. As for the patient steps, every scientific enquiry seems to end in a big question mark so I don't see this as being any different.

I was snowed under with school work so I could not address this important issue. Hope you are well.

[I listened to the Radiohead Scotch Mist U-Tube sessions - very nice!]

Originally posted by Heronumber0
I did try to look up nucleotide origin by googling it but came up with very little. It seems to be a bit of a mystery. I knew that simple amino acids, e.g. glycine, were fuond in the ice around stars but could not find a correlation for nucleotides.

Amino acids appear to be quite common in space. Some meteorites have been found to contain various (eek, my link died - I'll see if I can fix it later - it was the marchison (sp?) meteorite anyway).

The chances are that the next steps happened on earth. But the basic molecules could have been produced in space. An interesting study a while back showed how homochirality might be due to solar effects.

As for nucleotides, I haven't been keeping up with the literature on this, to be honest - I should do, as it's more interesting than discussing evolution with YECers, heh. I don't think RNA nucleotides are a big problem, I think there's a few steps after nucleotides that are more an issue currently.

Here's a couple of articles that I have myself that a readily available:

RNA-catalysis of nucleotides

Pre-biotic chem and RNA-world

As for the patient steps, every scientific enquiry seems to end in a big question mark so I don't see this as being any different.

heh, too true. I know this only too well from experience, usually several.

[I listened to the Radiohead Scotch Mist U-Tube sessions - very nice!]

Yeah, I'm great. In the calm before the storm period at the moment. Lectures kick off week after next

There was another webcast the other day, a live concert from London. T'was also great stuff. Great album.

[edit on 20-1-2008 by melatonin]

Originally posted by Heronumber0
If I am correct then the eye evolved from a photosensitive spot which is thought to have evolved into the modern eye. However, I find it difficult to imagine how that spot would have conferred an advantage on the primitive single cell carrying it unless there are two other mechanisms in play

I think the first proto-eye in unicellular species would have just aided biochemical processes such as photosynthesis, and led to basic circadian style rhythms.

Originally posted by melatonin
Amino acids appear to be quite common in space. Some meteorites have been found to contain various (eek, my link died - I'll see if I can fix it later - it was the marchison (sp?) meteorite anyway).

The chances are that the next steps happened on earth. But the basic molecules could have been produced in space. An interesting study a while back showed how homochirality might be due to solar effects.

The inevitable conclusion of this survey of nucleotide synthesis
is that there is at present no convincing, prebiotic
total synthesis of any of the nucleotides. Many individual
steps that might have contributed to the formation of nucleotides
on the primitive Earth have been demonstrated,
but few of the reactions give high yields of products, and
those that do tend to produce complex mixtures of products.
It should also be realized that any prebiotic synthesis
of a nucleotide would yield a racemic product, not
the biologically important D-nucleotide.

and

POLYMERIZATION OF ACTIVATED NUCLEOTIDES
The polymerization of nucleotides in aqueous solution is
an uphill reaction and does not occur spontaneously to a
significant extent. Evaporation of acidic solutions of nucleotides
and subsequent heating leads to the formation of
complex mixtures of very short oligonucleotides, in which
2-5-, or 3-5-phosphodiester linkages occur more or less
at random (Moravek, 1967). Consequently, attempts to
polymerize nucleotides from aqueous solution must necessarily
make use of external activating agents. Attempts
along these lines using cyanamide and similar activating
agents or water-soluble carbodiimides have been disappointing,
at best leading to poor yields

Prebiotic Chemistry and the Origin of the RNA World

I tried to read these papers hence the long gap before answering. However, I was eventually forced to 'gut ' the papers and short cut all the findings. However, my original point was that nucleotides do not seem to be found in space and the second part of the study seems to suggest the difficulty in polymerisation of nucleotides in the lab. Of course, you will say: 'wait and see'. But what if the answer is that a clay substrate was needed for the stable formation of nucleotides? What if Adam and Eve were RNA and DNA molecules respectively so that a copy of Adam (RNA) was made into Eve (DNA) and then life multiplied from them? I risk being shot here but I believe that the ethics of the Bible are more important than the science and that the small amount of science in the Bible can be read as metaphor and not as literal fact.

However, scientists also have to be honest and not pretend that they have all the facts at hand or will do so in the future. Science has limits to how far people can hypothesise. I'd love to find out how a stepwise selection would have encouraged predator avoidance in unicellular organisms. Even a general mechanism of the evolution would suffice. Also, a rough idea of how the first photon receptor was able to regenerate itself would be a major step forward in the eye debate.


Hope you are well.

Originally posted by Heronumber0
Of course, you will say: 'wait and see'. But what if the answer is that a clay substrate was needed for the stable formation of nucleotides?

Considering we started pretty much from scratch just a few decades ago with little idea of how these chains were linked, I think we are doing well. Given we don't have all the answers, we are doing better than just making stuff up.

Never underestimate human ingenuity. I'm actually quite sure we'll get there. The Cairns-Smith ideas are interesting, but I'm sure others are yet to be found.

I risk being shot here but I believe that the ethics of the Bible are more important than the science and that the small amount of science in the Bible can be read as metaphor and not as literal fact.

You just need to get that over to a certain type of your fellow christian.

I'd love to find out how a stepwise selection would have encouraged predator avoidance in unicellular organisms. Even a general mechanism of the evolution would suffice. Also, a rough idea of how the first photon receptor was able to regenerate itself would be a major step forward in the eye debate.

And when we do provide reasonable explanations, other gap issues that some find unacceptable will raise their head, and supply more reasons why evolution just can't be correct. In the minds of some, of course.

If you get a chance, listen to the debate between PZ Myers and a DI fellow (Simmons). It's up on PZ's site. It's well worth a laugh, Simmons got skinned alive - I thought he was going to cry at one point.

Hope you are well.

Aye, I am. Hope life's treating you well too.

[edit on 1-2-2008 by melatonin]

reply to post by melatonin


I am a bit disappointed with the reply melatonin. I thought you would have come back with some theory. You must have your opinions and not seek to have every view validated by the opinion of another which is such a common habit in the scientific community. I think the debate on clay as a substrate for life to form would be interesting because it is mentioned in the Bible no?

However I think that this will be an area for future debate because I could not find a source of nucleotides in space matter. This is a mystery that remain unsolved - yes by all means try acid, acid, eutectic freezing but at least copy the hypothetical primordial conditions. Perhaps it will remain unsolved permanently.

However, I think our debate has now ground to a halt.

[What a win for Wales - you must be delighted]

Originally posted by Heronumber0
I am a bit disappointed with the reply melatonin. I thought you would have come back with some theory. You must have your opinions and not seek to have every view validated by the opinion of another which is such a common habit in the scientific community. I think the debate on clay as a substrate for life to form would be interesting because it is mentioned in the Bible no?

Maybe it is, but only by contortion can you make it relevant. In a similar way to the criticism of me, you are just taking a 'square peg' idea in science and ramming it into the 'round hole' of genesis.

I tend to not go for speculation outside of my area of expertise. But I am sorry the reply didn't live up to your expectation. My chemistry knowledge is not as good as it used to be, heh - although I do have a degree in it. There are numerous gaps to be spanned in abiogenesis, but there's not much I can add. Ask me about stuff closer to the neuroscience of social behaviour, and I'll speculate away.

If you wanted me to answer the DNA is adam and RNA is eve, it feels like discussing 'if radiohead were cats and coldplay mice, would Thom still own Chris'. If it makes sense to you, then fair enough.

However I think that this will be an area for future debate because I could not find a source of nucleotides in space matter. This is a mystery that remain unsolved - yes by all means try acid, acid, eutectic freezing but at least copy the hypothetical primordial conditions. Perhaps it will remain unsolved permanently.

I would tend to think nucleotides did first occur on the earth, I think I mentioned that earlier. The issue with this sort of stuff is that we have little insight as to the conditions under which the major events would have occured - it might have been catalysed by other materials, used templates, or even de novo etc etc. The possibilities are somewhat endless, so what can I really add? At this point the answer is 'lots of possibilities, but don't know', or for some 'goddidit'.

From what I gathered from Orgel's article is that polymerisation from preactivated nucleotides is relatively easy, compared to non-activated. Thus, the idea of clays being involved has some possibilities. Indeed, some think we need to look for other less direct pathways to an RNA world, and the Orgel article raises some.

I don't think we can really make any firm insights into the path this research will take. Lots of ideas, lots of problems, lots of time to work on it.

What I don't need to speculate on is that when we do uncover a reasonable explanation, it will be contorted to fit theology by some and misrepresented by others.

[What a win for Wales - you must be delighted]

I actually missed the end, England were winning when I last saw it, my son came in and turned it over...

I have divided loyalties for these games, so I'm usually happy for a good interesting game. Sounds like it was.

Originally posted by melatonin

Maybe it is, but only by contortion can you make it relevant. In a similar way to the criticism of me, you are just taking a 'square peg' idea in science and ramming it into the 'round hole' of genesis.

Not a criticism. Just a comment. You normally come up with something new and interesting. I am not trying to ram Genesis down your throat but it may be relevant that nucleotide formation is accelerated using clay. I am just pointing out that this is how life may have started: clay----RNA + protein-------DNA--------single cell---------mitosis (cell multiplication)-------tissue formation--------selection events---------organ formation by organiser genes--------organ systems----------evolutionary events--------organisms------------------etc... but God kicked it all off by dropping a 'domino'.

I tend to not go for speculation outside of my area of expertise. But I am sorry the reply didn't live up to your expectation. My chemistry knowledge is not as good as it used to be, heh - although I do have a degree in it. There are numerous gaps to be spanned in abiogenesis, but there's not much I can add. Ask me about stuff closer to the neuroscience of social behaviour, and I'll speculate away.

Not a problem. I have NO expertise in anything. My knowledge is a millimetre deep and a mile wide - which is a bit worrying when it comes to debates. I have to do a lot of reading before answering points by respected 'foes'.

If you wanted me to answer the DNA is adam and RNA is eve, it feels like discussing 'if radiohead were cats and coldplay mice, would Thom still own Chris'. If it makes sense to you, then fair enough.

I'm just trying to rationalise and reconcile my faith with the little bit of Science I know.

I would tend to think nucleotides did first occur on the earth, I think I mentioned that earlier. The issue with this sort of stuff is that we have little insight as to the conditions under which the major events would have occured - it might have been catalysed by other materials, used templates, or even de novo etc etc. The possibilities are somewhat endless, so what can I really add? At this point the answer is 'lots of possibilities, but don't know', or for some 'goddidit'.

But you did start off this debate with the RNA makes ribozymes/proteins post so you must have had an idea that this was correct. However, at least you are honest enough to tell us your doubts. I still think Cairns-Smith was on to something.

From what I gathered from Orgel's article is that polymerisation from preactivated nucleotides is relatively easy, compared to non-activated. Thus, the idea of clays being involved has some possibilities. Indeed, some think we need to look for other less direct pathways to an RNA world, and the Orgel article raises some.

Polymerisation is relatively easy from activated nucleotides but the whole process of nucleotide activation and nucleotide formation run counter to favourable free energy conditions, if I read it correctly.

What I don't need to speculate on is that when we do uncover a reasonable explanation, it will be contorted to fit theology by some and misrepresented by others.

I personally am trying to rationalise the part of my faith that can be rationalised with Science and then relying on a Kierkegaardian 'leap of faith' to do the rest. You see a rationalisation as a contortion but I see it as an opportunity to come to grips with faith and to deepen my faith. It's just a different perspective I guess.