Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 80 (9005 total)
43 online now:
Aussie, AZPaul3, Diomedes, dwise1, kjsimons, PaulK, xongsmith (7 members, 36 visitors)
Newest Member: kanthesh
Post Volume: Total: 881,113 Year: 12,861/23,288 Month: 586/1,527 Week: 25/240 Day: 6/19 Hour: 1/2

Announcements: Topic abandonment warning (read and/or suffer the consequences)


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Time factor in self assembly calculations?
singularity
Inactive Member


Message 1 of 66 (13985)
07-23-2002 4:26 AM


Apart from their startling naivety of theoretical calculations about the probability of for instance the correct sequence of amino acids coming together to form a protein these calculations seem to lack any consideration of time scales involved.

Sure the chances of a single successful event seem astronomical, but how do the odds look when you factor in that there may be billions of molecules reacting over billions of years?

Do any mathematicians fancy looking over the figures? A more realistic model might be an imaginary self replicating length of RNA- say eight base pairs (four "unnatural" ones) and a unique 200 residue sequence.

Shane


Replies to this message:
 Message 2 by Tranquility Base, posted 07-23-2002 8:22 AM singularity has responded
 Message 13 by peter borger, posted 07-26-2002 12:45 AM singularity has not yet responded
 Message 33 by Brad McFall, posted 07-30-2002 1:33 PM singularity has not yet responded
 Message 39 by blitz77, posted 08-07-2002 8:22 AM singularity has not yet responded

  
Tranquility Base
Inactive Member


Message 2 of 66 (14000)
07-23-2002 8:22 AM
Reply to: Message 1 by singularity
07-23-2002 4:26 AM


^ We have discussed this before - there is little mainstream work on it. A creationist paper published last year (I have the hard copy) suggests that in the (evoltuionary) time available it would be unlikely for a single protein family to appear. I have not critiqued it professionally (due to laziness) but on casual reading it seemed to make sense and was written by German PhDed molecular biologists. I am a mathematical biologist and plan to have a close read sometime. It is linked somewhere in the archives here (to a pdf) and was discussed by myself and SLPx. I think the article talks about cyctochrome c as a specific example. SLPx was not impressed but did not mention specific defects in the arguement or calculations.

This message is a reply to:
 Message 1 by singularity, posted 07-23-2002 4:26 AM singularity has responded

Replies to this message:
 Message 3 by singularity, posted 07-24-2002 11:35 PM Tranquility Base has not yet responded

  
singularity
Inactive Member


Message 3 of 66 (14091)
07-24-2002 11:35 PM
Reply to: Message 2 by Tranquility Base
07-23-2002 8:22 AM


I am not talking about real systems here, merely pointing out what seems to be an obvious flaw in the common creationist arguments for the unlikelihood of molecules self assembling to produce something meaningful. Most of the calculations focus on the unlikelihood of a single event occuring (eg 200 L-amino acids forming a specific sequence of polypeptide, from a pool of random residues). My point was that these estimates don't seem to consider that the reactions could be happening repeatedly potentially over vast samples (primordial ocean soups?) over millions of years.

The separate issue of the evolution of a protein family for instance is undergoing revolutions with the increased understanding of how eukaryotic genomes are arranged in order to undergo deliberate evolution through such mechanisms as functional domain splicing using introns and modifications in gene expression in order to change developmental processes. The former is illustrated with enzyme pathways for polyketide synthesis, the latter with the functional differences between man and chimp despite the similarities in gene sequences. It makes sense that eukaryotic organisms with such a slow turn over of generations need a mechanism to evolve more efficiently than prokaryotes which seem to get by with gene swapping between species and random mutation.

So in summary I was talking about highly theoretical origin of life scenarios- once you start talking about whole organisms and genomes the processes of evolution become anything but random.

Shane


This message is a reply to:
 Message 2 by Tranquility Base, posted 07-23-2002 8:22 AM Tranquility Base has not yet responded

Replies to this message:
 Message 4 by peter borger, posted 07-25-2002 12:57 AM singularity has responded

  
peter borger
Member (Idle past 6291 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 4 of 66 (14100)
07-25-2002 12:57 AM
Reply to: Message 3 by singularity
07-24-2002 11:35 PM


Dear Singularity,
Ever sonicated (lysis through vibration) a culture of bacteria? How long will it take -- according to your scenario -- before a living bacterium will arise from this organic soup? Notably, all required biolecules are present in this soup.
Best wishes,
Peter

This message is a reply to:
 Message 3 by singularity, posted 07-24-2002 11:35 PM singularity has responded

Replies to this message:
 Message 5 by John, posted 07-25-2002 8:59 AM peter borger has not yet responded
 Message 6 by singularity, posted 07-25-2002 8:53 PM peter borger has responded

  
John
Inactive Member


Message 5 of 66 (14130)
07-25-2002 8:59 AM
Reply to: Message 4 by peter borger
07-25-2002 12:57 AM


quote:
Originally posted by peter borger:
Dear Singularity,
Ever sonicated (lysis through vibration) a culture of bacteria? How long will it take -- according to your scenario -- before a living bacterium will arise from this organic soup? Notably, all required biolecules are present in this soup.
Best wishes,
Peter

But that doesn't mean all the conditions are right for abiogenisis.

You are lacking in volume of soup. You are lacking a power supply. And you are lacking the right chemistry as well, as conditions today are much different that 4 billion years ago.

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 4 by peter borger, posted 07-25-2002 12:57 AM peter borger has not yet responded

Replies to this message:
 Message 7 by Tranquility Base, posted 07-25-2002 9:17 PM John has responded

  
singularity
Inactive Member


Message 6 of 66 (14166)
07-25-2002 8:53 PM
Reply to: Message 4 by peter borger
07-25-2002 12:57 AM


Thanks for the interesting question Peter.

Firstly, regarding original abiogenesis, I don't think anyone is seriously proposing that something as complex as a modern bacterium would have formed spontaneously. Incidentally I love how creationists sometimes run thought experiments about eyeballs etc forming spontaneously out of an organic soup- I love the image of a primordial sea of eyeballs

Secondly, on a practical note, in this particular experiment you could never be sure that any emerging life forms are the result of completely disassembled starting bacteria so positive results would be highly tenuous.

Thirdly, and theoretically, the products of a perfectly lysed solution would include lipid vesicles which would contain various cellular components. These vesicles are well known to form spontaneously from lipids. I think it is quite feasable for a functioning bacterium to reform from the soup, given that the ionic composition of the lysate resembles that inside a living bacterium, the extracellular medium is changed (even just diluted with a different cation) after the vesicles form in order to set up a chemical energy gradient across the vesicle membranes and that a large enough sample is used (which would probably need to be far far larger than a beaker). A single functioning cell in this environment would face ideal conditions to rapidly grow by assimilating the soup from which it arose.

This process does rely on the proteins and DNA remaining largely intact, and is exactly the kind of model which should allow funtional bacteria to be made from synthetic genomes, proteins and lipids. If the sonication proceeds as far as reducing proteins to amino acids and DNA to nuclebases you could not expect anything like a bacterium to reform, but self replicating molecules could possibly emerge if an alternate chemical energy source was available. The key to reforming a bacterium is having proteins which can couple ATP generation to a transmembrane potential in order to kick start cellular processes.

An aside thought. One of the key characteristics of living things is the ability to grow and divide. I was just pondering the process of nuclear transplant as used in animal cloning, etc. Surely when a donor egg is stripped of its nucleus it is no longer capable of dividing on its own, therefore it temporarily lacks the prime quality of life and is therefore nonliving. Similarly the nucleus to be inserted into the donor egg is incapable of reproducing itself independently and is also nonliving. Doesnt the implantation of a nucleus into an egg represent the recreation of living matter from non living matter?

Shane


This message is a reply to:
 Message 4 by peter borger, posted 07-25-2002 12:57 AM peter borger has responded

Replies to this message:
 Message 8 by peter borger, posted 07-25-2002 9:40 PM singularity has responded
 Message 11 by peter borger, posted 07-25-2002 9:49 PM singularity has responded

  
Tranquility Base
Inactive Member


Message 7 of 66 (14168)
07-25-2002 9:17 PM
Reply to: Message 5 by John
07-25-2002 8:59 AM


Spoken like a true believer John!.

This message is a reply to:
 Message 5 by John, posted 07-25-2002 8:59 AM John has responded

Replies to this message:
 Message 9 by John, posted 07-25-2002 9:47 PM Tranquility Base has responded

  
peter borger
Member (Idle past 6291 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 8 of 66 (14172)
07-25-2002 9:40 PM
Reply to: Message 6 by singularity
07-25-2002 8:53 PM


You say,
"I was just pondering the process of nuclear transplant as used in animal cloning"

To clone an animal you need viable DNA in a nucleus and bring it into a viable cell. Viable DNA is not simply the plain DNA molecule, it also involves the histons and the histon-code, and the coactivater code of transcription present in the acceptor cell. The recent discovery/inference of these eukaryotic DNA associated codes of transcription prohibits the cloning of the extinct (?) thylacine (and other extinct animals. It is nothing but a waste of money!). Maybe ponder these mechanisms also.

And:
"Doesnt the implantation of a nucleus into an egg represent the recreation of living matter from non living matter?"

No.

Best wishes
Peter


This message is a reply to:
 Message 6 by singularity, posted 07-25-2002 8:53 PM singularity has responded

Replies to this message:
 Message 14 by singularity, posted 07-26-2002 4:05 AM peter borger has responded

  
John
Inactive Member


Message 9 of 66 (14174)
07-25-2002 9:47 PM
Reply to: Message 7 by Tranquility Base
07-25-2002 9:17 PM


quote:
Originally posted by Tranquility Base:
Spoken like a true believer John!.

Not really a statement of belief.... just chemistry. You've got to have the right conditions for a reaction to occur. Not all reactions are reversable.... blah... blah ..... that sort of thing.

Unfortunately the data needed to duplicate those conditions doesn't exist, and might never exist; but I prefer uncertainty to false certainty.

If you can duplicate the appropriate conditions and the experiment still doesn't work, then talk to me about belief. Right now, the only belief I've got is that there is an answer somewhere.

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 7 by Tranquility Base, posted 07-25-2002 9:17 PM Tranquility Base has responded

Replies to this message:
 Message 10 by Tranquility Base, posted 07-25-2002 9:49 PM John has responded
 Message 12 by peter borger, posted 07-25-2002 9:55 PM John has responded

  
Tranquility Base
Inactive Member


Message 10 of 66 (14175)
07-25-2002 9:49 PM
Reply to: Message 9 by John
07-25-2002 9:47 PM


. . . somewhere but not God - right? At least not a God who is at least as conscious as us? Why not?

This message is a reply to:
 Message 9 by John, posted 07-25-2002 9:47 PM John has responded

Replies to this message:
 Message 46 by John, posted 08-07-2002 10:31 PM Tranquility Base has not yet responded

  
peter borger
Member (Idle past 6291 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 11 of 66 (14176)
07-25-2002 9:49 PM
Reply to: Message 6 by singularity
07-25-2002 8:53 PM


dear Shane,

You say:

"I don't think anyone is seriously proposing that something as complex as a modern bacterium would have formed spontaneously."

Problem is that nobody is proposing anything that can hold.
What do you propose?

And:
"synthetic genomes"

Copies of existing genomes? To what benefit?

BW
Peter


This message is a reply to:
 Message 6 by singularity, posted 07-25-2002 8:53 PM singularity has responded

Replies to this message:
 Message 15 by singularity, posted 07-26-2002 4:37 AM peter borger has responded

  
peter borger
Member (Idle past 6291 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 12 of 66 (14177)
07-25-2002 9:55 PM
Reply to: Message 9 by John
07-25-2002 9:47 PM


Dear John,
There are dozens of answers to a question.
It is just a matter of choise.
You are free to choose.
Best Wishes
Peter

This message is a reply to:
 Message 9 by John, posted 07-25-2002 9:47 PM John has responded

Replies to this message:
 Message 18 by John, posted 07-26-2002 10:43 PM peter borger has responded

  
peter borger
Member (Idle past 6291 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 13 of 66 (14182)
07-26-2002 12:45 AM
Reply to: Message 1 by singularity
07-23-2002 4:26 AM


Dear Shane,

You state:
"startling naivety of theoretical calculations about the probability"

It seems that you are a Dawkins disciple. Read "The watchmakers blindness" (chapter 6 (?) Spetner's book Not by Chance). It will pay off to read opposite opinions.

Best Wishes,
Peter


This message is a reply to:
 Message 1 by singularity, posted 07-23-2002 4:26 AM singularity has not yet responded

  
singularity
Inactive Member


Message 14 of 66 (14186)
07-26-2002 4:05 AM
Reply to: Message 8 by peter borger
07-25-2002 9:40 PM


You don't seem to have addressed my point that in the strictest sense neither a naked nucleus nor a denucleated cell constitute living organisms, but putting them together can produce a viable cell. Surely this is a very simple example of destroying and recreating life sensu stricto? In what way is a naked nucleus any more alive than something like a virus? Both need cellular structures in order to replicate themselves. The denucleation case is more interesting though as the cell is also effectively dead without the proper nucleus.

Can anyone else think of other examples where modification of life on a molecular or organelle level causes it to drift across the borderline between life and death?

Shane


This message is a reply to:
 Message 8 by peter borger, posted 07-25-2002 9:40 PM peter borger has responded

Replies to this message:
 Message 16 by peter borger, posted 07-26-2002 4:50 AM singularity has responded

  
singularity
Inactive Member


Message 15 of 66 (14187)
07-26-2002 4:37 AM
Reply to: Message 11 by peter borger
07-25-2002 9:49 PM


Hi Peter

I will readily admit that the theory of abiogenesis is currently much patchier than evolution. But general observations about the capacity for simple molecules to behave in complex ways is leading us to more specific answers- self propagation of prions is a well known example, certainly not evidence of abiogenesis on its own but definitely an indication of how molecules can self replicate under appropriate conditions.

The problem is that any evidence for abiogenesis within extant organisms will be understandably vague or even completely erased by evolution, probably even moreso if life originated earlier in space. The uniformity of the chemical composition of living things is highly suggestive of a common origin, but the development of that starting point has only been theorised around, and I think it is healthy to be highly sceptical of the content of current models.

I would consider the current theories of abiogenesis to be at the same developmental level as emergent Darwinian evolution. In future one of the theories will probably be further substantiated and the others will be viewed with retrospective bemusement (although lamarkian evolution is getting a reevaluation with the discovery of the importance of gene regulation in response to environment). Of some use may be the current efforts of producing bacteria with the minimum essential genes, but I think more work in to the recently discovered nanobes from deep sediments might be more crucial. At this stage they seem to be self propagating chemical reactions- no DNA can be isolated from them, they appear to have mineralised cell walls and their endurance of high temperatures and pressures is unexplained. They seem to fit the bill for early life, even extraterrestrial life, but research has only taken place in this field for a few years by a handfull of scientists. Who knows what else is out there, given we are still discovering new species of monkeys and trees? Surely a lack of crucial evidence should be reason for tentative hypotheses rather than sweeping refutation of any possibilities?

So in summary I would say it is too early to propose a water proof model of abiogenesis. But based on what limited evidence there is it isn't an unreasonable theory. It is closer to being substantiated than to being refuted. It certainly makes more scientific sense than any historical creation story you care to cite. Are there any other alternatives? Raelianism perhaps? I think it is difficult to accuse scientists of being closed minded and dogmatic about their belief structure- sure there is some inertia in changing the status quo, but generally the most controversial new theories come from scientists themselves. Creationists in contrast seem fixated on validation of historical literature.

Shane

PS- I was referring to synthetically produced bacteria as the next step to the production of synthetic polio virus. The purpose of which experiments is that living matter can be carefully created from nonliving matter.


This message is a reply to:
 Message 11 by peter borger, posted 07-25-2002 9:49 PM peter borger has responded

Replies to this message:
 Message 17 by peter borger, posted 07-26-2002 5:03 AM singularity has responded
 Message 26 by peter borger, posted 07-29-2002 10:37 PM singularity has responded

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2020