Abiogenesis

[marki]

Originally Posted by avandonk

There is no magical boundary between 'inanimate' matter and 'life' matter it is all the same stuff following the laws of the Universe.


Are self replicating crystals life? Is the PCR of DNA in vitro life? Is a virus alive? Do bacteria have self awareness? Then we have single celled fungi or slime molds that assemble and differentiate to propagate via a fruiting body. You can work your way up the tree of life to us.

We cannot do the experiment as you would have to set up a primordal Earth and wait a a few million or many more years. A simple test tube will not simulate an entire planet.

Bert

Well put Bert, certainly worthy of some thought.

Mark

[Poita (Peter)]

Originally Posted by avandonk

We cannot do the experiment as you would have to set up a primordal Earth and wait a a few million or many more years. A simple test tube will not simulate an entire planet.

Bert

That is kind of my point. If we cannot simplify the process of abiogenesis down into an experiment, or find it in our existing laws, then it needs a new set of laws to explain it happening, or alternatively, it was a total freak event outside the odds.

Usually scientists don't so readily 'believe' in something if they can't formulate something to explain it, or have an experiment to be able to at least recreate a simplified version. We have neither a clear set of rules that we can show lead to life, or an experiment that has had anything close to success in creating it, yet the belief is certainly widespread. (We do have hard science to explain what happen once we get a cell with RNA/DNA and how evolution works from there.) I find it hard to think of another area where scientists are like that. My personal guess it is because they don't want to let the God of the Gaps in, and with good reason, but it is an odd anomaly to me in the way scientists usually treat ideas.

CraigS, I'm not good at paraphrasing, send me your address and I'll send you the P. Davies book, I'm not one of those guys that worries about keeping his books pristine, so I'm happy to lend it out.

[CraigS]

Originally Posted by Poita

That is kind of my point. If we cannot simplify the process of abiogenesis down into an experiment, or find it in our existing laws, then it needs a new set of laws to explain it happening, or alternatively, it was a total freak event outside the odds.

Usually scientists don't so readily 'believe' in something if they can't formulate something to explain it, or have an experiment to be able to at least recreate a simplified version. We have neither a clear set of rules that we can show lead to life, or an experiment that has had anything close to success in creating it, yet the belief is certainly widespread. (We do have hard science to explain what happen once we get a cell with RNA/DNA and how evolution works from there.) I find it hard to think of another area where scientists are like that. My personal guess it is because they don't want to let the God of the Gaps in, and with good reason, but it is an odd anomaly to me in the way scientists usually treat ideas.

CraigS, I'm not good at paraphrasing, send me your address and I'll send you the P. Davies book, I'm not one of those guys that worries about keeping his books pristine, so I'm happy to lend it out.

Peter;
Don't worry about the book .. I'll get my hands on a copy for myself .. thanks for the offer though, much appreciated.

Also, I believe you should take a close to look at Complexity Theory. I really think this is where they have developed the tools which explain, at a systems level, how self assembly of complex structures is the norm arising from a large abundance of components obeying simple rules. Organic chemistry would not be an exception to this.
I also really feel you are making generalised statements about what you perceive there is no scientific discourse on, when there exists quite a lot which describe quite feasible mechanisms to explain the complexity.

Cheers

[avandonk]

Originally Posted by Poita

That is kind of my point. If we cannot simplify the process of abiogenesis down into an experiment, or find it in our existing laws, then it needs a new set of laws to explain it happening, or alternatively, it was a total freak event outside the odds.

Usually scientists don't so readily 'believe' in something if they can't formulate something to explain it, or have an experiment to be able to at least recreate a simplified version. We have neither a clear set of rules that we can show lead to life, or an experiment that has had anything close to success in creating it, yet the belief is certainly widespread. (We do have hard science to explain what happen once we get a cell with RNA/DNA and how evolution works from there.) I find it hard to think of another area where scientists are like that. My personal guess it is because they don't want to let the God of the Gaps in, and with good reason, but it is an odd anomaly to me in the way scientists usually treat ideas.

CraigS, I'm not good at paraphrasing, send me your address and I'll send you the P. Davies book, I'm not one of those guys that worries about keeping his books pristine, so I'm happy to lend it out.

The evidence is there just like archaeology we have to deduce history from the fragments we find.

Bert

[Poita (Peter)]

My thesis was on information theory, which has mutated into complexity theory in recent years. I've read just about every paper I get time to these days, there is plenty of new ground being covered but nothing conclusive yet as far as I have read.
I think this is the arena where a breakthrough will eventually be made, that information will have to be treated as an actual entity, similar to the way it is in quantum physics... the information content of living organisms, even basic ones is huge, it has to come from somewhere. Basic Physics doesn't cover that. Someone in the thread commented that living or dead, there is no difference, that it is just matter following the same laws. The information content of a living vs non-living thing is hugely different, the non-living entity can be easily (relatively) modelled and predicted using standard physics, the living entity cannot. It is an interesting field of study.

Originally Posted by CraigS

Peter;
Don't worry about the book .. I'll get my hands on a copy for myself .. thanks for the offer though, much appreciated.

Also, I believe you should take a close to look at Complexity Theory. I really think this is where they have developed the tools which explain, at a systems level, how self assembly of complex structures is the norm arising from a large abundance of components obeying simple rules. Organic chemistry would not be an exception to this.
I also really feel you are making generalised statements about what you perceive there is no scientific discourse on, when there exists quite a lot which describe quite feasible mechanisms to explain the complexity.

Cheers

[joe_smith]

The evidence is there just like archaeology we have to deduce history from the fragments we find

like this?

[avandonk]

Originally Posted by joe_smith

like this?

That is not deduction it is extrapolation taken to the absurd!

Very funny though.

Bert

[sjastro]

Originally Posted by joe_smith

like this?

Very funny.
Is there a message behind this, namely archaeology isn't a science?

Regards

Steven

[CraigS]

Originally Posted by Poita

My thesis was on information theory, which has mutated into complexity theory in recent years. I've read just about every paper I get time to these days, there is plenty of new ground being covered but nothing conclusive yet as far as I have read.
I think this is the arena where a breakthrough will eventually be made, that information will have to be treated as an actual entity, similar to the way it is in quantum physics... the information content of living organisms, even basic ones is huge, it has to come from somewhere. Basic Physics doesn't cover that. Someone in the thread commented that living or dead, there is no difference, that it is just matter following the same laws. The information content of a living vs non-living thing is hugely different, the non-living entity can be easily (relatively) modelled and predicted using standard physics, the living entity cannot. It is an interesting field of study.

Hmm …
I've always been uncomfortable with viewing DNA as 'information'. Seeing it as 'information', seems to me to imply that its 'sequence' has a purpose.

There are plenty of things we could call 'information' which, when acted upon by a process, result in something other than what it started out as.

I have a feeling 'information' is an illusion we have created in our own minds .. because that's what we do .. acquire 'information' over our lifetimes and then expire.

DNA simply exists .. it has no purpose .. there are no 'huge' or 'tiny' 'amounts' of it. Such comparisons seem like anthropomorphising what simply exists .. for no reason, or purpose.

If one abandons the search for the purpose, then the 'mystery' of how a specific DNA sequence occurred in the first place, also simply disappears.

Cheers

[Poita (Peter)]

I would have to take you to task on that, DNA is a highly evolved, non-periodic, information rich system. I can't think of any other way to explain it, and you would have a hard time finding any scientist that wouldn't consider it information rich I would think (Glad to be shown to be wrong though as always!). Abandoning some imagined purpose does nothing to make the DNA mystery disappear at all, I don't follow your argument here.

I've pretty much exhausted my knowledge on this topic now, I've enjoyed the discussion, but I'll leave you guys to it until I stumble across anything new. The skies are clearing up outside, so I'm off to practice setting up for imaging!

[avandonk]

Here you go then. Check this out.

http://www.sciencedaily.com/releases...1012132651.htm


this is the start of I Robot!

Bert

[CraigS]

Originally Posted by avandonk

Here you go then. Check this out.

http://www.sciencedaily.com/releases...1012132651.htm


this is the start of I Robot!

Bert

Interesting …. and very clever! .. So they’ve achieved self-replication of complex DNA molecules, without the need for an RNA enzyme.

They did however start with a BTX (a bent triple helix molecule containing three DNA double helices), with each BTX molecule composed of 10 DNA strands. For replication, a seed BTX ‘seven-letter word’, is then needed to catalyse ‘multiple generations of identical arrays’.

As I understand it, to-date, replication theories have always required the presence of an RNA enzyme, but no-one has been able to work out how these enzymes arose in the first place .. but this process, doesn’t seem to need one of these. Very clever.

Just summarising, (from this article), with the RNA first hypothesis, the other three traditional problems have been:

i) coming up with a membrane to enclose the replication reactions and to allow passage into and out of the ‘cell’ structure. Szostack seems to have solved this one though, (see my previous post on this) and;

ii) how the first nucleotides got arranged into a long chain RNA molecule, without the presence of enzymes. It seems that activated nucleotides are those with an extra bit tacked on to the phosphate. They worked out some time ago that when these were added to a kind of volcanic clay, RNA molecules up to 55 nucleotides long formed. ‘Ordinary nucleotides’ don’t favour the formation of large RNA molecules (due to a lack of energy), but the activated ones, provide the energy needed to drive the reaction. With this process, RNA molecules, can be seen to form spontaneously. (The only problem which the remains is that the long molecule can break down fairly shortly after it is formed).

iii) how the first nucleotides formed. Two of the four nucleotides in RNA have already been produced in the lab and the hunt for making the other two, is currently underway.

Cheers

[xelasnave]

AND from the same article Craig his comment on membranes........

And membranes were key to the physiology of cells because they protect their contents, concentrate chemicals to promote reactions and isolate successful genes from unsuccessful ones. "It's clear you really need both these elements to get evolution off the ground and running," says Szostak..

As I suggested earlier a simple water drop already has in effect a membrane, and given the alignment of the molecules at the surface maybe this provides a foundation for other molecules to also line up and "evolve" toward a membrane or shell.. a droplet also concentrates chemicals as we know.

It is only my mere opinion but I doubt that isolation of sucessful and unsuccessful genes would be necessary or that would be part of the early membranes job.. it would be probable that certain chemicals were just more stable than others and that was what defined their sucess.

So all we need for a simple cell is a droplet of water maintained at a correct temp and with the correct chemicals to be concentrated in the center... all I am suggesting is the structure of a droplet of water may provide the mechanism for evolvement to a more complex object.

alex

[CraigS]

Here's another drop in the bucket … this study has shown (theoretically) that a thermodynamic state can pass on mutations to chemically replicating 'offspring' ...
Could thermodynamic fluctuations have led to the origins of life?

In his paper, Brogioli looks at replication from a kinetics perspective, in which the kinetic counterpart of the inheritance of mutations is the presence of multiple stationary states, i.e., different lines of mutations can be present simultaneously, and their offspring inherit mutations. He shows that chemical systems that can pass mutations on to offspring can be thought of as systems with multiple stationary states, thus having the property of chemical marginal stability. These systems differ from a simple "self-catalytic" system (e.g., a purely chemical system) that merely produces offspring without transmitting mutations; the kinetic counterpart would be initial states that all lead to only one stationary state.
…
Likewise, spontaneous concentration fluctuations can enable a chemical system to inherit a variety of mutations from its parent system, and any of these mutations can be considered stable.
...
At the moment, the drift has been confirmed only by numerical calculations, and must be regarded as still theoretical. Brogioli notes that most chemical systems that have a replicase do not possess chemical marginal stability, and therefore are not affected by thermodynamic fluctuations. However, his study shows that the existence of a chemical system that is marginally stable and can undergo spontaneous evolution is possible. Investigating this theory further could have extremely important revelations. The demonstration of a marginally stable chemical system in the lab would not only be the first experiment in which a chemical system undergoes spontaneous evolution, but also the first in vitro model of a chemical reaction that leads to life.

Cheers

[CraigS]

And this study has gotten cell membranes to divide into daughter cells which possess completely different functions to the parent cell. All this without involving genes or cellular machinery !

New technique sheds light on the mysterious process of cell division

The team members note that the new modeling technique seems to suggests that simple chemical and physical interactions within cells -- such as self-assembly, phase separation, and partitioning -- can result in seemingly complex behaviors – like asymmetric division -- even when no additional cellular machinery is present. "Since there were no nucleic acids nor enzymes present, we clearly didn't have genes governing how our model cells would behave," Keating said. "So our study supports the hypothesis that structural and organizational 'cues' work in concert with genetic signals to achieve and maintain polarity through successive cell-division cycles."
…
Keating also explained that experimentation on non-living model cells that contain no DNA could help point to clues explaining the mysterious process of abiogenesis.

I don't know whether 'a simple drop of water' is capable of achieving this feat ??

Cheers

[xelasnave]

Craig I think a simple droplet of water is far more complex than we have considered it to be perhaps and maybe capable of providing a basic system from which other complexities evolve... I have little idea really and am looking for the simplest of starting steps.

The reason I dwell upon it is because the more one thinks about it the greater complexity one can suggest and adding simple aspects that may have some effect produces opportunity one possibly overlooked... just with a simple droplet so I am seeing more in it than someone with better things to do I suspect.

I have become preoccupied with this subject and have tried to focus upon only one aspect that being a method of containment... hence the observation of the membrane like characteristic of the skin of water and how such characteristic may offer the initial system for placement of chemicals... would calcium and CO2 etc find a suitable condition to form an egg shell approach and I suspect already the egg did indeed come before the chicken


It would seem that "division" of a simple water droplet is possible from action of temp and or variation in size for example even variation in charge will have consequences making division more or less likely one would think and all I have been trying to consider is if any of these fundamentals offer a course to a development of more complex structures....or put another way ..there must be an initial starting point where the rules of the universe dictate a certain progression will follow...they seem to have things worked out to a large degree with the chemical reactions and I have tried to consider environment aspects.

Anyways great stuff Craig. I have vowed to read and not offer input (opinions) but with this most interesting subject I can not help myself.

alex