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Author Topic:   Abiogenisis by the Numbers
Loudmouth
Inactive Member


Message 136 of 206 (159815)
11-15-2004 3:40 PM
Reply to: Message 133 by Brad McFall
11-15-2004 3:31 PM


quote:
My guess is that if someone thinks there is NO MORE DECODING but only molecular biology left, to do, then one might think like Watson who said on Charlie Rose, "if I only had Bill Gates' $, I would solve all diseases in a couple of decades
By "NO MORE DECODING" I think you hit it on the head. The information conveyed by DNA is no different than the information conveyed by oxygen when combing with two hydrogens. What information we extract from DNA is through abstraction, assigning somewhat anthropic characteristics onto a chemical reaction. For instance, instead of displaying the physical characteristics of nucleotides, we describe them as a string of letters (eg TAACCGTTGGC). Instead of describing proteins as an active participant in chemical reactions, we describe proteins as a string of letters (eg MQDRKSKT). Through refinement, information is created but true form is lost.
This message has been edited by Loudmouth, 11-15-2004 03:40 PM

This message is a reply to:
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dshortt
Inactive Member


Message 137 of 206 (159825)
11-15-2004 3:56 PM
Reply to: Message 134 by Loudmouth
11-15-2004 3:34 PM


Tree rings are not "instructing" the tree or me when I look at them to move, build, repair, etc. I think we just disagree on this "layer of abstraction". Clearly the cellular machinery is motivated to action, as opposed to a star spectrum which produces no such phenomena. The layer of abstraction may not be as thick or heavy as your use of the word "colloquial" perhaps, but the medium (the ink if you will) appears to produce definite actions in the receivers (the microbiological machinery in the cell).

This message is a reply to:
 Message 134 by Loudmouth, posted 11-15-2004 3:34 PM Loudmouth has replied

Replies to this message:
 Message 138 by Loudmouth, posted 11-15-2004 4:32 PM dshortt has replied

  
Loudmouth
Inactive Member


Message 138 of 206 (159839)
11-15-2004 4:32 PM
Reply to: Message 137 by dshortt
11-15-2004 3:56 PM


We are swiftly moving off-topic, so this will be my last post in this vein. If you want to continue this discussion perhaps we should open a new thread?
quote:
but the medium (the ink if you will) appears to produce definite actions in the receivers (the microbiological machinery in the cell).
The same could be said for the chain reaction in nuclear devices, all chemical reactions, etc. There is nothing different at a chemical level in cell or in a reaction vial in chemistry class. If DNA carries a certain type of information, then that same information is carried by every single atom in the universe.
Feel free to reply, but we should try and tie in the probability of abiogenesis at some point in this discussion.

This message is a reply to:
 Message 137 by dshortt, posted 11-15-2004 3:56 PM dshortt has replied

Replies to this message:
 Message 139 by dshortt, posted 11-15-2004 4:52 PM Loudmouth has replied
 Message 140 by Percy, posted 11-15-2004 5:02 PM Loudmouth has replied

  
dshortt
Inactive Member


Message 139 of 206 (159848)
11-15-2004 4:52 PM
Reply to: Message 138 by Loudmouth
11-15-2004 4:32 PM


Loudmouth's reply: "The same could be said for the chain reaction in nuclear devices, all chemical reactions, etc. There is nothing different at a chemical level in cell or in a reaction vial in chemistry class. If DNA carries a certain type of information, then that same information is carried by every single atom in the universe."
Yes, I agree at a chemical level. The problem, and this is where the abiogenisis tie in occurs, is that when H2 bonds with O we get nothing more extraordinary than water (which don't get me wrong I find fascinating in itself). But introduce DNA into a cell and suddenly that cell is replicating, combining with other cells to form organs, and doing such marvelous things as writing this reply to you. So in order for life to form spontaneously, I think we have to factor in this information, which some of us would contend contains a layer of abstraction beyond any information we could decode from any other set of atoms in the universe.

This message is a reply to:
 Message 138 by Loudmouth, posted 11-15-2004 4:32 PM Loudmouth has replied

Replies to this message:
 Message 146 by Brad McFall, posted 11-16-2004 9:21 AM dshortt has not replied
 Message 148 by Loudmouth, posted 11-16-2004 11:35 AM dshortt has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 140 of 206 (159859)
11-15-2004 5:02 PM
Reply to: Message 138 by Loudmouth
11-15-2004 4:32 PM


Just guessing, but dshortt may have in mind the question of where the information in DNA came from if it arose by a natural processes. If he believes that information can only be created by an intelligence, then he may be making the point that a natural origin for DNA is not possible.
I have a different take on the information aspect of the discussion. It seems perfectly valid to me to view DNA encodings as Shannon information. The letters/ink analogy has relevance, but I don't think it should be used to sidestep consideration of the DNA code as Shannon information.
It works better for me to draw a distinction between information and meaning. As Shannon says right on page one of his landmark paper, "Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem."
Once you've established that Shannon information is independent of meaning, then it is easy to consider DNA as containing information. In fact, such an obvious code of course contains information. How could it not? The human interpretive structure you mentioned before is the meaning that is irrelevant to Shannon information. All voice phone calls are now translated into binary streams. The information carrying capacity of the telephone network is measured by bits, and it does not change if the discussion turns from gossip to nuclear physics. The bits that carry the information know nothing about meaning.
And neither does DNA know anything about meaning. It's just an encoding that results in a biological representation that interacts with an environment in a process that governs whether the DNA (some of it, with sexual reproduction) survives into the next generation.
But could the information in DNA arise naturally? Now, there lies a discussion!
--Percy

This message is a reply to:
 Message 138 by Loudmouth, posted 11-15-2004 4:32 PM Loudmouth has replied

Replies to this message:
 Message 147 by Loudmouth, posted 11-16-2004 11:29 AM Percy has not replied

  
JESUS freak
Inactive Member


Message 141 of 206 (159862)
11-15-2004 5:08 PM
Reply to: Message 126 by Coragyps
11-15-2004 2:10 PM


Re: Calculations
So your saying that all cobos but 3 or so failed?
This message has been edited by JESUS freak, 11-15-2004 05:13 PM

This message is a reply to:
 Message 126 by Coragyps, posted 11-15-2004 2:10 PM Coragyps has replied

Replies to this message:
 Message 145 by Coragyps, posted 11-15-2004 6:39 PM JESUS freak has not replied

  
JESUS freak
Inactive Member


Message 142 of 206 (159863)
11-15-2004 5:08 PM
Reply to: Message 126 by Coragyps
11-15-2004 2:10 PM


Re: Calculations
But even if there are few other combos, the odds are still Trillions of trillions to one.
This message has been edited by JESUS freak, 11-15-2004 05:12 PM

This message is a reply to:
 Message 126 by Coragyps, posted 11-15-2004 2:10 PM Coragyps has not replied

Replies to this message:
 Message 143 by coffee_addict, posted 11-15-2004 5:13 PM JESUS freak has not replied
 Message 144 by pink sasquatch, posted 11-15-2004 5:20 PM JESUS freak has not replied
 Message 149 by Loudmouth, posted 11-16-2004 11:46 AM JESUS freak has not replied

  
coffee_addict
Member (Idle past 477 days)
Posts: 3645
From: Indianapolis, IN
Joined: 03-29-2004


Message 143 of 206 (159865)
11-15-2004 5:13 PM
Reply to: Message 142 by JESUS freak
11-15-2004 5:08 PM


Re: Calculations
Hey JF, could you please read this thread by Adminmoose?
Also, if you want to add a thought after you've submitted your reply, you can edit it with the edit button.
Thanks.

This message is a reply to:
 Message 142 by JESUS freak, posted 11-15-2004 5:08 PM JESUS freak has not replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 144 of 206 (159876)
11-15-2004 5:20 PM
Reply to: Message 142 by JESUS freak
11-15-2004 5:08 PM


Re: Calculations
the odds are still Trillions of trillions to one.
Do you actually have conditions and calculations for how this probability was derived? No ID proponent in this thread has provided any yet.

This message is a reply to:
 Message 142 by JESUS freak, posted 11-15-2004 5:08 PM JESUS freak has not replied

  
Coragyps
Member (Idle past 735 days)
Posts: 5553
From: Snyder, Texas, USA
Joined: 11-12-2002


Message 145 of 206 (159911)
11-15-2004 6:39 PM
Reply to: Message 141 by JESUS freak
11-15-2004 5:08 PM


Re: Calculations
So your saying that all cobos but 3 or so failed?
That's possible, I'm sure. One would have been enough, neh?

This message is a reply to:
 Message 141 by JESUS freak, posted 11-15-2004 5:08 PM JESUS freak has not replied

  
Brad McFall
Member (Idle past 5033 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 146 of 206 (160058)
11-16-2004 9:21 AM
Reply to: Message 139 by dshortt
11-15-2004 4:52 PM


I am not completely confident but all discussions I have been having here at EvC have been leading me to surmise that macromolecular aggreations display DIFFERENT categories of ELECTRON FAMILIES but can only be associated with biological function when many molecules are associated in vivo. The difficulty for me is to think how compute which electrons to classify and which to not but to have a means of correlating it objectively subsequently. Gladyshev's macrothermodynamics gives some index that might suggest an approach biophysically but I dont have the physics sophistication to follow through. Provided this be recieved, THEN becomes thinkable that DNA differences (coded) might reflect differences of that determination.
Loudmouth writes across two problems here. One is what order of magnitude the information would not be available in but could nonetheless be exposed to natural selection and the other is any motivation to think that additional information might evetually be squeezed from the material itself. As Percy quoted...since Niche Constructors speak of "semantic information transfer" for abiotic information describable genetically, it becomes trasferable from the Shannon release of semantic necessity to biological increases of cross generational adaptive semantic instantiation but if some electron families DO NOT RELY on CODED INFORMATION it becomes incumbent to descript what identifiable molecular aggreagtes ARE involved. I have some ideas on how to approach this experimentally with electrolytic redox reactions but I have little notion of how generally this occurrs should it be natural as Percy indicated. My ability to think of these biochemical things has been made possible by cognitive excurisions beyond the purely nontranscendental however you divide the effect of creationist inductions on my thought which goes beyond that of Bertrand Russell if for only my ability to NOT RELY on French Philosophy of the Calculus and transitive readins of Kant's Critique of Reason but rather to afford the marginal scriblings of Cantor a bit more value than Russell received subtracted in Great Britain delievered, as to any continuity the electrons would likely correlations maintaining (if) naturally or artifically (matters not as to the purpose) photonically across some, if existant, supramoleuclar volume or mass.
When I think of this fundamentally, I often cosider that DNA torque is involved but I havent been able to extrapolate any class of this kind of angular momentum to side chain categories in proteins. That I would think would be a first step in resovling the existence of any such "abstraction" between levels of organization and levels of selection that biologist might desire to dispute without knowing how to toss teleology into its own teleomatic mix or instructed mixture, I think you quite pointed re-cognized.

This message is a reply to:
 Message 139 by dshortt, posted 11-15-2004 4:52 PM dshortt has not replied

  
Loudmouth
Inactive Member


Message 147 of 206 (160080)
11-16-2004 11:29 AM
Reply to: Message 140 by Percy
11-15-2004 5:02 PM


quote:
I have a different take on the information aspect of the discussion. It seems perfectly valid to me to view DNA encodings as Shannon information. The letters/ink analogy has relevance, but I don't think it should be used to sidestep consideration of the DNA code as Shannon information.
Schneider argues that genetic systems can be modeled using Shannon information and entropy. However, acording to Schneider, just because you can model genetic systems with Shannon information it doesn't mean that information was intended nor an integral part of the system.
quote:
It works better for me to draw a distinction between information and meaning. As Shannon says right on page one of his landmark paper, "Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem."
OK, you got me on that one. Information does not necessarily need to have a semantic meaning, nor a layer of abstraction. This still doesn't separate simple chemical reactions from the more complex chemical reactions occuring in cells nor the chemistry hypothesized for abiogenesis.
quote:
But could the information in DNA arise naturally? Now, there lies a discussion!
I think you answered that question with this quote "It's just an encoding that results in a biological representation that interacts with an environment in a process that governs whether the DNA (some of it, with sexual reproduction) survives into the next generation." The information in DNA is dependent on the environment. Information is created in DNA through differential reproductive success. The minimum amount of information, or the "spark of life", needed to start this cycle is hypothetically attainable through abiogenesis, as has been shown by catalytic RNA and other experiments. All you need is an imperfect self replicator that passes one round of selection. Once a replicator is able to "live" in one small environment, mutation and selection will ensure the spread of this replicator into new environments.

This message is a reply to:
 Message 140 by Percy, posted 11-15-2004 5:02 PM Percy has not replied

  
Loudmouth
Inactive Member


Message 148 of 206 (160083)
11-16-2004 11:35 AM
Reply to: Message 139 by dshortt
11-15-2004 4:52 PM


quote:
Yes, I agree at a chemical level. The problem, and this is where the abiogenisis tie in occurs, is that when H2 bonds with O we get nothing more extraordinary than water (which don't get me wrong I find fascinating in itself).
Yes, and the combustion of molecular hydrogen in the presence of molecular oxygen ALWAYS results in water, with a few exceptions. This repeatability is also seen in genetic systems, where certain codons ALWAYS result in a specific amino acid, where certain amino acid chains always fold into a specific enzyme, where certain bases are complimented with another base. The information for this repeatability is a characteristic of the atoms that make up larger molecules. The information needed to create a self replicating system is present in atoms, not in a nebulous metaphysical creation process.
quote:
But introduce DNA into a cell and suddenly that cell is replicating, combining with other cells to form organs, and doing such marvelous things as writing this reply to you.
And where in this process is physics and chemistry not involved? Where in this process is any natural law broken? Nowhere. The same laws that govern the combustion of hydrogen govern the chemistry of life. Also, put water in a gas tank and what happens? Nothing. Specificity of reactions applies to non-life as well as life.
quote:
So in order for life to form spontaneously, I think we have to factor in this information, which some of us would contend contains a layer of abstraction beyond any information we could decode from any other set of atoms in the universe.
I say that it is already factored in, in the form of chemical bonds and the specificity of reactions governed by atomic theory.

This message is a reply to:
 Message 139 by dshortt, posted 11-15-2004 4:52 PM dshortt has replied

Replies to this message:
 Message 153 by dshortt, posted 11-16-2004 3:10 PM Loudmouth has not replied

  
Loudmouth
Inactive Member


Message 149 of 206 (160084)
11-16-2004 11:46 AM
Reply to: Message 142 by JESUS freak
11-15-2004 5:08 PM


Re: Calculations
quote:
But even if there are few other combos, the odds are still Trillions of trillions to one.
Alright, let's go with a trillion trillion to one. A trillion is 10^24 (one trillion is 10^12). A 300 amino acid protein has an approximate molecular weight of 25,000 g/mol. There are 6.02 X 10^23 molecules per mole. So, to ensure that this trillion trillion to one molecule forms we need approximately 250 kg of protein formed over a 500 million year period on earth. This means that only 250 mg of protein needs to be produced per year in areas that could sustain this type of life. It isn't that difficult to produce 250 mg in such a large area.
Secondly, we also need to factor in all possible planets that could sustain life. If only 1 planet in 1 billion could sustain life, this still leaves us with 1 billion planets (approx 1 billion galaxies with 1 billion stars each). So, we only need 250 picograms of protein produced per year on each of these planets to ensure that life occurs on at least one of these planets.
Needless to say, even at 1 in a trillion trillion, the chances of this occuring are quite high.

This message is a reply to:
 Message 142 by JESUS freak, posted 11-15-2004 5:08 PM JESUS freak has not replied

Replies to this message:
 Message 150 by dshortt, posted 11-16-2004 2:47 PM Loudmouth has replied

  
dshortt
Inactive Member


Message 150 of 206 (160136)
11-16-2004 2:47 PM
Reply to: Message 149 by Loudmouth
11-16-2004 11:46 AM


Re: Calculations
First off, it is highly doubtful that there are a billion planets that could support life. Next, all you end up with is protein. This protein would have to be in close proximaty (highly unlikely), and then of course comes the leap from non-life to life which is the basis of this discussion.
It also occurs to me that, in accordance with an earlier post, there are a ton of "conditions" that must be met for this life synthesis to even be possible. Wouldn't it make sense to calculate the odds of finding those conditions in the first place before the odds of that first little creature forming could be calculated?

This message is a reply to:
 Message 149 by Loudmouth, posted 11-16-2004 11:46 AM Loudmouth has replied

Replies to this message:
 Message 151 by Loudmouth, posted 11-16-2004 3:02 PM dshortt has replied
 Message 152 by Coragyps, posted 11-16-2004 3:02 PM dshortt has not replied

  
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