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Old 07-31-2011, 10:59 PM
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Anyone know of some good books on these topics.

Regarding the information aspect I was curious if there is any theories regarding the meaning of information within DNA, specifically, how natural processes create what is seemingly arbitrary meaning regarding the information contained within. Is it deterministic that the meaning of the information within must be as such according to the physical propeties of the arrangment of that information. The information itself is physical is it not? Then would'nt the meaning be determined in some fashion on the arrangement of such information?

Hope this makes sense - I might have confused myself.
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Old 08-01-2011, 04:39 AM
 
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I'm not sure I followed you're train of thought but....why is it necessarily deterministic if the information is physical? (What you said in your last sentence of your post). Also to be clear....the CODING of the information is physical (i.e. sequence of DNA) not the information per se.

Can it not also be physical and random? Darwinian evolution holds that the generation of this information is more/less random, but it is selected for in a non-random way. In that sense you could call it deterministic, but not really.

Hope this makes sense.
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Old 08-01-2011, 06:06 AM
 
Location: Cincinnati near
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The sequence of the DNA does not itself contain all of the information required for life. Much of the information is contained in the environment of the cell, the DNA information is really like a manual that tells the cell how to respond to different environmental stimuli. To use a math analogy, the cell is like a complex differential equation, and the DNA provides the parameters. Obviously the DNA affects the output but a series of parameters without an equation isn't worth much.

In my biochemistry class I teach that the two essential components for life are a barrier to separate an organism from its environment (membrane) and the ability to do work across said barrier. DNA is not essential, it is simply something that has evolved to organize the information into a common language.
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Old 08-01-2011, 07:27 AM
 
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Quote:
Originally Posted by Chemistry_Guy View Post
The sequence of the DNA does not itself contain all of the information required for life. Much of the information is contained in the environment of the cell,
Please elaborate on this. There are exceptions to the rule (RNA viruses for example), but for eukaryotic cells DNA pretty much does contain all information required for life (in this I'm including mitochondrial DNA).

As for the "information contained within the environment of the cell" what are you referring to exactly???

Quote:
Originally Posted by Chemistry_Guy View Post
In my biochemistry class I teach that the two essential components for life are a barrier to separate an organism from its environment (membrane) and the ability to do work across said barrier.
Where does the information come from to encode proteins responsible for creating this barrier as well as generating proton/ion gradients across that barrier? DNA.

Quote:
Originally Posted by Chemistry_Guy View Post
DNA is not essential,


Please provide an example of when a such a barrier is formed and the ability to do work across is done, in the absence of any DNA information.

Lipids can certainly spontaneosly arrange into barriers, but having a barrier with the ability to perform work across it, in the complete absence of DNA information would be a tall feat.
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Old 08-01-2011, 08:38 AM
 
Location: Cincinnati near
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Quote:
Originally Posted by broadbill View Post
Please elaborate on this. There are exceptions to the rule (RNA viruses for example), but for eukaryotic cells DNA pretty much does contain all information required for life (in this I'm including mitochondrial DNA).

As for the "information contained within the environment of the cell" what are you referring to exactly???



Where does the information come from to encode proteins responsible for creating this barrier as well as generating proton/ion gradients across that barrier? DNA.





Please provide an example of when a such a barrier is formed and the ability to do work across is done, in the absence of any DNA information.

Lipids can certainly spontaneosly arrange into barriers, but having a barrier with the ability to perform work across it, in the complete absence of DNA information would be a tall feat.
DNA can't do a thing without a host cell. That's why cloning is such a huge challenge. The DNA only contains the amino acid sequence of the proteins in the organism. Control of transcription is determined by the environment. There is no way of knowing, looking at only the DNA sequence, what the proper intracellular environment is for an organism to develop. In other words, the genome is only a subset of the proteome, and the post-translational modifications and glycosylation of proteins are determined by the cellular environment. Ultimately, the environment could be extended to include the diet and nutritional profile of the organism, as clearly the development of an organism is influenced by diet. For complex organisms like humans, there is a great deal of independence between diet and genome, but that is not the case for all organisms.

Most credible theories for abiogenesis (the topic of the thread) include some form of life predating the development of DNA. My argument is that the threshold for life should not necessarily require DNA or any nucleic acid at all, just the ability to create order (do work across a membrane) using the free energy available in an environment. This is really more philosophy than science, though, as life itself doesn't really care what definition we use to categorize it.
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Old 08-01-2011, 09:16 AM
 
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Quote:
Originally Posted by Chemistry_Guy View Post
DNA can't do a thing without a host cell. That's why cloning is such a huge challenge. The DNA only contains the amino acid sequence of the proteins in the organism. Control of transcription is determined by the environment. There is no way of knowing, looking at only the DNA sequence, what the proper intracellular environment is for an organism to develop. In other words, the genome is only a subset of the proteome, and the post-translational modifications and glycosylation of proteins are determined by the cellular environment. Ultimately, the environment could be extended to include the diet and nutritional profile of the organism, as clearly the development of an organism is influenced by diet. For complex organisms like humans, there is a great deal of independence between diet and genome, but that is not the case for all organisms.

Most credible theories for abiogenesis (the topic of the thread) include some form of life predating the development of DNA. My argument is that the threshold for life should not necessarily require DNA or any nucleic acid at all, just the ability to create order (do work across a membrane) using the free energy available in an environment. This is really more philosophy than science, though, as life itself doesn't really care what definition we use to categorize it.
I think I will give you the benefit of the doubt that you know what you are talking about, but you might want to be careful when you make blanket statements like "DNA is not essential" (it most certainly is for every life-form that is currently known, if you include other "codes" such as RNA, etc), and "The sequence of the DNA does not itself contain all of the information required for life." (it most certainly does).

In the case of abiogenesis, the hard/fast rules do become a bit more "fuzzy" and you run into the "chicken-and-the-egg" argument. What came first...the nucleic acid chemistry with the information to make a cell or did the cell come first which then needed a way to store information?

Either way, the OP should come back and clarify their post a bit. It sounded like they were making the point that because a information code exists (i.e. DNA) there is some sort of deterministic nature behind it. It is a common argument made by creationists and it wrong on multiple levels.
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Old 08-01-2011, 11:08 AM
 
Location: Cincinnati near
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Now that I see where you are coming from your criticism makes a lot more sense. We are in total agreement that DNA contains all of the genomic information by which traits are inherited and species are created and differentiated. I don't have a lot of patience for pseudoscience and I can see how it is easy to be suspicious of everyone in a public place like this where so many have a decidedly unscientific agenda.

Also, we both agree that we don't know exactly what the first life forms looked like or even where the exact threshold between living and nonliving was crossed, just that life on earth evolved a mechanism of genetic inheritance based on nucleic acid sequences.

Where we disagree (I think) is what is considered information. To me, information is any variable in the recipe of life that must be controlled and cannot be left to chance. Some very simple bits of information could be the temperature, pressure, EM flux, gravity, and composition of the air. While these may fall within a common range for many locations on earth, they must be within a certain range for a genetic sequence to translate into life. On a more complex level, the chemical environment must fall within a certain range in order for an organism to sustain life. One example of this is in vitamins: the body is not able to synthesize some molecules itself (such as ascorbate, riboflavin, and beta carotene) so it must obtain them from diet. The practical evidence of this can be seen in microbial ecology, where identical genomes will produce very different organisms in different environments.

A complex organism like a human has more in common with a diverse microbial environment than a monoculture, and because of this microbiologists recognize that the proteome is orders of magnitude more complex than the genome, and the metabolome is more complex than that. Here is a short quote from what I consider to be a very thought provoking article on the topic, from

Trends in Biotechnology
Volume 19, Issue 6, 1 June 2001, Pages 205-210

"Suppose that a certain organism's genome has been completely sequenced. Then suppose that structures and functions of all its gene products have been thoroughly identified. Suppose further that a giant map of the entire metabolic pathways has been drawn flawlessly. Then what? Would we have conquered the cell? The answer is clearly ‘no’ because the overall ‘behavior’ of the cell would still not be understood.To say that we understand the overall behavior of the cell, we must be able to answer questions such as: ‘How would the cell behave if we change the environment, for example, by adding or decreasing a certain substance?’ and ‘What is the result if a certain gene gets knocked out or over-expressed?’ Slightly more sophisticated questions include: ‘What gene needs to be inserted for the cell to behave in such a way’ and ‘What is the ideal culture medium in which to maximize the cell's ability to do such a thing?’"


Anyway, We probably agree on 99% of this, but it is the 1% we don't that is worth discussing.
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Old 08-01-2011, 12:06 PM
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Originally Posted by broadbill View Post
I'm not sure I followed you're train of thought but....why is it necessarily deterministic if the information is physical? (What you said in your last sentence of your post). Also to be clear....the CODING of the information is physical (i.e. sequence of DNA) not the information per se.

Can it not also be physical and random? Darwinian evolution holds that the generation of this information is more/less random, but it is selected for in a non-random way. In that sense you could call it deterministic, but not really.

Hope this makes sense.
OK, Coding would be a better term. The information though has 'meaning' - is the meaning inherent in the way it is coded? In other words is it just arbirtrary that a certain sequence means something or is it determined by the physical properties of the coding?

I actually want to find some good books on why the meaning is physical and random. What is it within the physical properties of the coding that determines it to mean what it does if it is not arbitrary or outside of those physical properties. Why do certain sequences mean this or that - how are they assigned this relationship? As with any other code meaning is arbitrary - there is no inherient meaning in the sequence of letters that I am writing right now - the symbols and sounds could have been assigned a different meaning.

What I am looking for would actually counter any Creationist thinking.

As far as Abiogenisis I was looking for some good books on how the barrier of non-life was crossed over to life, as Chemistry_Guy pointed out.

Did that Help?
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Old 08-01-2011, 02:29 PM
 
Location: Matthews, NC
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According to Chuck, abiogenesis is crap because new life doesn't spring from a jar of peanut butter. Take that, eggheads.


‪Peanut Butter, The Atheist's Nightmare!‬‏ - YouTube
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Old 08-01-2011, 03:42 PM
 
Location: Cincinnati near
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Quote:
Originally Posted by Shiloh1 View Post
OK, Coding would be a better term. The information though has 'meaning' - is the meaning inherent in the way it is coded? In other words is it just arbirtrary that a certain sequence means something or is it determined by the physical properties of the coding?

I actually want to find some good books on why the meaning is physical and random. What is it within the physical properties of the coding that determines it to mean what it does if it is not arbitrary or outside of those physical properties. Why do certain sequences mean this or that - how are they assigned this relationship? As with any other code meaning is arbitrary - there is no inherient meaning in the sequence of letters that I am writing right now - the symbols and sounds could have been assigned a different meaning.

What I am looking for would actually counter any Creationist thinking.

As far as Abiogenisis I was looking for some good books on how the barrier of non-life was crossed over to life, as Chemistry_Guy pointed out.

Did that Help?
The coding is not random at all. The energies of the AT and GC base pairs are extraordinarily critical. Any lower and they would fall apart too easily and any higher and they would not easily replicate. In addition, the codon's representing specific amino acids have been evolutionarily selected based on the stability of the hydrogen bonds between the complementary DNA strands. Evidence of this is the higher percentage of GC (3 H bonds) content in extremophiles living at high temperatures corresponding to the higher annealing temperature of GC vs AT pairs. In other words, not only is the coded message critical, but the paper it is written on is as well. Complex organisms capable of controlling body temperature, freed from this evolutionary constraint, show a much more homogeneous percentage of GC content than simpler species.
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