How do cells know what do without intelligence?

#1
I found this article that seems to answer the question. I comes down to chemistry.
Unraveling a mystery in the 'histone code' shows how gene activity is inherited
Every cell in our body has exactly the same DNA, yet every cell is different. A cell's identity is determined by the subset of genes that it activates. But how does a cell know which genes to turn off and which to turn on? While the genetic code carried in our DNA provides instructions for cells to manufacture specific proteins, it is a second code that determines which genes are in fact activated in particular cell types.

Read more at: http://phys.org/news/2014-03-unraveling-mystery-histone-code-gene.html#jCp
 
#3
Lol... it's a little more complicated than that I'm afraid.
The article is brief, but not so complicated that the better explanation is something other than a down to earth explanation. I am sure the study published in the journal Science goes into greater detail.
 
#4
The article is brief, but not so complicated that the better explanation is something other than a down to earth explanation. I am sure the study published in the journal Science goes into greater detail.
Your question is not answered by this study.
 
#5
There is no need for a code in a purely deterministic chemical reaction, why would there be? And evolution would be impossible. Not to mention that the majority of biochemical reactions would take billions of years without enzymes which are defined by information coded within DNA of course. The sequence of which is not defined by chemistry at all!. Saying life is just chemistry is the same as saying your PC works on just electricity. Enzymes can charge molecules for binding but they also can "read" genetic information and even abort charging if an error is detected. Chemistry?

Recently another code was found running opposite direction in DNA to the protein coding genes! So a nucleotide can have multiple functions, a triplet with multiple meanings. Dubbed "Duons". Not only can it encode amino acids but it also can signal binding of transcription factors for gene regulation. Then ontop of these codes we have the histone code which is unafected by the underlaying DNA sequences. So no amount of mutating DNA can explain it.

In addition to the digital code of DNA there is another analog code for gene expression, the same sequence can encode multiple proteins! Then we have the splicing code as well and more, It is codes within codes within codes.

The recent revolution in biology you may have missed in the last couple of decades is the infusion of information science. It is now acceptable to say that biology deals in two mediums one electro chemical the other is information. They are not the same thing.
 

Paul C. Anagnostopoulos

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Member
#6
There is no need for a code in a purely deterministic chemical reaction, why would there be?
The implication of this question is that, with the code, the chemical reactions aren't purely deterministic. Is that what you mean to say?

And evolution would be impossible. Not to mention that the majority of biochemical reactions would take billions of years without enzymes which are defined by information coded within DNA of course. The sequence of which is not defined by chemistry at all!.
It's not defined by chemistry alone, but that does not mean that it is not defined naturalistically.

Saying life is just chemistry is the same as saying your PC works on just electricity. Enzymes can charge molecules for binding but they also can "read" genetic information and even abort charging if an error is detected. Chemistry?
Absolutely. I ask for the tenth time: If these processes are not just chemistry, what else are they?

Recently another code was found running opposite direction in DNA to the protein coding genes! So a nucleotide can have multiple functions, a triplet with multiple meanings. Dubbed "Duons". Not only can it encode amino acids but it also can signal binding of transcription factors for gene regulation. Then ontop of these codes we have the histone code which is unafected by the underlaying DNA sequences. So no amount of mutating DNA can explain it.
I'm not sure where you got the opposite direction thing, but (a) this is not new news, and (b) it's not really a second code.

http://www.geek.com/science/scientists-discover-a-second-genetic-code-except-not-really-1579496/

In addition to the digital code of DNA there is another analog code for gene expression, the same sequence can encode multiple proteins! Then we have the splicing code as well and more, It is codes within codes within codes.
What analog code? The fact that the same sequence can encode multiple proteins is very old news.

http://rspb.royalsocietypublishing.org/content/early/2010/07/03/rspb.2010.1052

~~ Paul
 
#7
Oh boy....

It's not defined by chemistry alone, but that does not mean that it is not defined naturalistically.
Nope, it is not defined by chemistry at all.

Absolutely. I ask for the tenth time: If these processes are not just chemistry, what else are they?
Yawn, god you are obtuse, how many times and how many links does it take? So please explain proof reading for me and provide proof.

For the 1000th time. Information is not chemistry! Sheesh! You have serious issues Paul see a doctor about your memory problem.

There is no direct chemical connection between a codon and it's amino acid. Purely chemical theories have been proposed for the origin of the code as in stereo chemical theories and templating. These are purely chemical and are an attempt to explain the code. Why? because It most certainly is not what life uses, even in the first hyperthetical cell. Can you explain why a purely chemical system is required to explain another purely chemical system? That makes no sense Paul. I am baffled by your inability to recognize this.

I'm not sure where you got the opposite direction thing, but (a) this is not new news, and (b) it's not really a second code.
My mistake I was confusing an RNA antisense code that runs opposite. (Yet more problems for you and yet more code) I have been studying too many papers at once.

The news is that "Duons" are much more prevalent in the protein coding regions than previously thought. Yes the dual use has been known for a while but not to the extent as first thought in exons. As for being a second code that depends on definition.

If we define a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology, then there are multiple genetic codes. Sequences involved in these codes overlap and, thus, both interact with and constrain each other, such as for the triplet code, the intron-splicing code, the code for amphipathic alpha helices, and the chromatin code.
http://www.ncbi.nlm.nih.gov/pubmed/22954214

Also... Actually Trifanov describes at least 12 codes a nucleotide can contribute to.

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013

Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].

What analog code? The fact that the same sequence can encode multiple proteins is very old news.
Never said it was new, in fact I remember explaining it to you once.

What analog code? Glad you asked. It is described as "irreducible organization".
http://link.springer.com/article/10.1007/s00018-013-1394-1

So as far as I can see all your post is really saying is that it is all chemical. Wrong because code and information are not chemistry. Wrong because code has no place in a purely chemical system. Wrong because there is no direct chemical connection between codon and amino acid. Wrong because stereo chemical theories are an attempt to explain codon mapping and is most certainly is not what happens in real biological systems. It also begs the question because enzymes are required that are defined by sequences of DNA that are not determined by chemistry.

The code exploits chemistry. Information, genetic information runs the show. Not chemical reactions, this is basic Paul I am not arguing design here but basic cellular biology. You can't acknowledge the code and claim it is all chemical at the same time! What is not chemical? The code!

Take it or leave it, arguing biology with you is a complete waste of time. Don't expect anymore.
 
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Paul C. Anagnostopoulos

Nap, interrupted.
Member
#8
Oh boy....
Nope, it is not defined by chemistry at all.
If it were not defined by chemistry at all, then DNA would not be restricted to four bases.

Yawn, god you are obtuse, how many times and how many links does it take? So please explain proof reading for me and provide proof.
You've never answered the question. I'm asking which processes are not purely chemical, not whether abstracted DNA sequences are chemical.

For the 1000th time. Information is not chemistry! Sheesh! You have serious issues Paul see a doctor about your memory problem.
You were not talking about pure information. You said:

"Enzymes can charge molecules for binding but they also can "read" genetic information and even abort charging if an error is detected. Chemistry?"

Yes, chemistry. Which part of those three processes are not chemistry? Not the information, the processes.

You're so excited about immaterial information that you can't focus on the processes.

There is no direct chemical connection between a codon and it's amino acid.
Of course there is: translation. Ah, you must be talking about the mapping between codons and amino acids. You appear to be ignoring all the research on the reasons why the genetic code is the way it is.

There is no direct chemical connection between a codon and it's amino acid. Purely chemical theories have been proposed for the origin of the code as in stereo chemical theories and templating. These are purely chemical and are an attempt to explain the code. Why? because It most certainly is not what life uses, even in the first hyperthetical cell. Can you explain why a purely chemical system is required to explain another purely chemical system? That makes no sense Paul. I am baffled by your inability to recognize this.
I don't understand your question. A naturalistic explanation is going to be chemistry all the way down. What exactly doesn't make sense?

The news is that "Duons" are much more prevalent in the protein coding regions than previously thought. Yes the dual use has been known for a while but not to the extent as first thought in exons. As for being a second code that depends on definition.
Sure, their frequency has become known over time. I agree that many things depend on the definition of code. I've been trying to figure out your definition for awhile. Do two choices make a code?

What analog code? Glad you asked. It is described as "irreducible organization".
http://link.springer.com/article/10.1007/s00018-013-1394-1
So everything that specifies the structure and dynamics of a molecule is "analog information"? Sure, why not, but so what?

You can't acknowledge the code and claim it is all chemical at the same time! What is not chemical? The code!
To the extent that a code can be abstracted from its carrier, I agree that the abstracted code is not the carrier or the carrier processes. But you take a giant leap and infer from this abstractability that the code could not evolve naturalistically. And yet you have never explained why you think that inference is legitimate, except by appeal to human code design. Can you define a code and then explain why it cannot evolve?

If mere abstractability is reason to think that something is designed, then everything in nature that humans have abstracted was designed. Do you think this is so?

~~ Paul
 
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#11
If it were not defined by chemistry at all, then DNA would not be restricted to four bases.
Meaningless. Nope, there are no chemical bonds defining the sequence. It did not have to be four bases.

Saying that it is a true code involves the idea that the code is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar phosphate backbone, but there are no bonds along the longitudional axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side the bases can occur in any order, like the letters of a language used to compose words and sentences.
Also...
The amino acid associated with a given triplet of bases does not appear to be chemically determined.
....
The presence of the anticodon on one end of the tRNA does not chemically determine the amino acid attactched to the other end.
http://hyperphysics.phy-astr.gsu.edu/hbase/organic/gencode.html

Just plain wrong I am afraid.

You've never answered the question. I'm asking which processes are not purely chemical, not whether abstracted DNA sequences are chemical.
I did answer. Code and information that writes the machines that do the work! In some cases it appears as an algorithm. Now please explain proof reading and error correction purely chemically.

"Enzymes can charge molecules for binding but they also can "read" genetic information and even abort charging if an error is detected. Chemistry?"

Yes, chemistry. Which part of those three processes are not chemistry? Not the information, the processes.
As above explain how chemicals read and can recognize and correct errors. None of your baseless statements. Citations please.

You're so excited about immaterial information that you can't focus on the processes.
No I am not. I am currently taking a chemistry course in preparation for biochemistry. You are so afraid of information you can't even accept what mainstream science says about it. And you simply do not have a good grasp of the processes, I know this as a fact and can pull up some of your absurd erroneous statements if you like.

Of course there is: translation. Ah, you must be talking about the mapping between codons and amino acids. You appear to be ignoring all the research on the reasons why the genetic code is the way it is.
You got to be kidding. The word translation is taken directly from information science. And no I am not ignoring the most difficult question in biology. You are.

I don't understand your question. A naturalistic explanation is going to be chemistry all the way down. What exactly doesn't make sense?
Purely chemical theories attempt to explain the origin of the code. There is no direct chemical connection between codon and amino acid. That is what the purely chemical models attempt to address because it is not the way it is.

Look, here is a mainstream course stating a naturalistic cause that says exactly that!
http://biology.kenyon.edu/courses/biol114/Chap05/Chapter05.html

The code evolved at random, in that there is no direct chemical connection between, say, GGG and Glycine.

Don't you get tired of being wrong?
And actually there is evidence the selection of amino acids is not random at all.

All the way down you say?

"Chemical based approaches," Walker said, "have stalled at a very early stage of chemical complexity – very far from anything we would consider 'alive.' More seriously they suffer from conceptual shortcomings in that they fail to distinguish between chemistry and biology."
http://www.dailygalaxy.com/my_weblo...e-was-based-on-information-not-chemistry.html

So everything that specifies the structure and dynamics of a molecule is "analog information"? Sure, why not, but so what?
Nope. you asked the question, what analog code? I answered. And as usual you just hand wave..

The rest of your post regards design, which I am not arguing here, only biology. However it does show why you are so unwilling to see what the actual science says. Whenever I post on this you turn up with nonsense and unsupported statements spouted as fact because you seem frustrated not to be able to put a dent in the arguments.
 

Paul C. Anagnostopoulos

Nap, interrupted.
Member
#12
Meaningless. Nope, there are no chemical bonds defining the sequence. It did not have to be four bases.
What? Sure, it could have evolved to be something else. But do you think it could have been anything else? If you think there are no chemical constraints at all, then it could have been four flavors of ice cream. And next Tuesday it could become seven different flavors.

I am afraid.I did answer. Code and information that writes the machines that do the work! In some cases it appears as an algorithm. Now please explain proof reading and error correction purely chemically.
"Writes the machines"? Can you try to be clearer?

Apparently you are not going to agree that any chemical process is "purely chemical" as long as the mechanisms involved are proteins encoded by DNA. This rather begs the question of whether a code can evolve "purely chemically," don't you think?

As above explain how chemicals read and can recognize and correct errors. None of your baseless statements. Citations please.
But now it appears that you are saying that chemicals cannot correct errors, regardless of their origin. Is that what you are saying?

http://en.wikipedia.org/wiki/DNA_repair

No I am not. I am currently taking a chemistry course in preparation for biochemistry. You are so afraid of information you can't even accept what mainstream science says about it. And you simply do not have a good grasp of the processes, I know this as a fact and can pull up some of your absurd erroneous statements if you like.
I have a perfectly good grasp of the processes, but go ahead and waste your time if it makes you feel better.

Note that we are not talking about raw information, but about a code. I have no fear of either. If I was afraid of information, I'd be insisting that there is no information. The question is whether a code can evolve without a guiding hand.

Purely chemical theories attempt to explain the origin of the code. There is no direct chemical connection between codon and amino acid. That is what the purely chemical models attempt to address because it is not the way it is.
The chemical models attempt to address somethng because it is not the way it is. What? Do you think you could be a little clearer?

Look, here is a mainstream course stating a naturalistic cause that says exactly that!
Say exactly what?

The code evolved at random, in that there is no direct chemical connection between, say, GGG and Glycine.
There is a lot of research suggesting that it did not evolve at random. But even if it did, I don't understand why you think that is important.

And actually there is evidence the selection of amino acids is not random at all.
I swear you just contradicted yourself. But perhaps you're hinting that there is a nonrandom non-chemical influence. Tough to tell what you're talking about.

The rest of your post regards design, which I am not arguing here, only biology. However it does show why you are so unwilling to see what the actual science says. Whenever I post on this you turn up with nonsense and unsupported statements spouted as fact because you seem frustrated not to be able to put a dent in the arguments.
I brought up design in an attempt to move past this chemistry versus information argument. Even if you explain clearly what you mean and I agree with you, so what? The fact that the genetic code is some kind of "completely unconstrained pure code" says nothing about its origin. Your claim has been that it must be designed because all human codes are designed, but that does not follow. So what is your point?

I suggest we move past the chemistry versus information issue and address why you think it's interesting that the code is (supposedly) unconstrained.

~~ Paul

P.S. I think you are misreading Davies and Walker. The point, I believe, is that, since it is chemistry all the way down, it is necessary to rely on some higher-level concept to make the demarcation between chemistry and life.

"We believe the transition in the informational architecture of chemical networks is akin to a phase transition ..."

They did not say that there was suddenly something nonchemical going on. It's a change in organization, not a change in physics.

~~ Paul
 
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#13
Pftt... hilarious. You haven't changed, all waffle and no substance. Exactly the response I expected. Your only link does not answer the only question I asked at all. I asked for an explanation not a citation bluff. Wikipedia at that. You failed. Again.

I swear you act stupid just to avoid conceding a point. But maybe it is not acting, who knows. You even ask questions that have just been answered with support from mainstream science!

I provided proof for my statements. Period. You just play word games, quite poorly at that.

My only point in all this is that it cannot be reduced to chemistry. I am not talking about evolution or design. Your insistance to drag it into the argument is obfuscation you even admit it, wanting to change the subject. That is very telling. You have a blind ideology akin to religious fundamentalism.

Btw I am very familiar with Davies work. A phase transition of information flow from bottom up chemistry to top down informational control is nothing but a guess, that is all. It does not solve the issues with code, the symbol matter problem or the sequencing problem. It simply assumes it. And that one line of hand waving imigination is the only solution they give at all! You may as well say "and then some magic happened!"

What it also means is what we have is top down informational control and not a bottom up chemical system that has been used to explain the origin of life. The very point I made earlier.

An unknown law of the universe I suppose Davies would say. Laws immaculately balanced and fine tuned, he would also say. The fact that purely chemical theories have failed is well highlighted in the article. Oh and it supports my only claim here completely. The acknowledgment of top down informational control.

Funny thing is you acknowledge information and claim it is purely chemical in the same breath. You can't tell the difference.

"Information is information not matter or energy." Norbert Weiner founder of cybernetics.
 
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Paul C. Anagnostopoulos

Nap, interrupted.
Member
#15
I swear you act stupid just to avoid conceding a point. But maybe it is not acting, who knows. You even ask questions that have just been answered with support from mainstream science!
I might be happy to concede your point if I knew what it was. We agree there is information in DNA. We agree it's a code, for some definition of the term. Where it goes from there I do not know, since you appear reluctant to address the question of design.

Are you trying to get me to agree to some ideological point, perhaps that information is ontologically different from chemistry?

My only point in all this is that it cannot be reduced to chemistry. I am not talking about evolution or design. Your insistance to drag it into the argument is obfuscation you even admit it, wanting to change the subject. That is very telling. You have a blind ideology akin to religious fundamentalism.
What is "it"? Sometimes you talk about the genetic code, sometimes about the genome, sometimes about the translation process, sometimes about other things. It appears to be a giant jumble in your mind. I certainly agree that the evolution of genomes is not purely chemistry. What else am I supposed to agree with?

Btw I am very familiar with Davies work. A phase transition of information flow from bottom up chemistry to top down informational control is nothing but a guess, that is all. It does not solve the issues with code, the symbol matter problem or the sequencing problem. It simply assumes it. And that one line of hand waving imigination is the only solution they give at all!
Why do you think Davies believes that his idea "solves" the sequencing problem, by which I take you to mean the content of the genome? And why are you even bringing this up when you say you're not talking about evolution versus design?

An unknown law of the universe I suppose Davies would say. Laws immaculately balanced and fine tuned, he would also say.
Why would he say these things? Again, I think you are misinterpreting him.

Funny thing is you acknowledge information and claim it is purely chemical in the same breath. You can't tell the difference.
You keep saying things like this, but then insist that you understand. The storage and manipulation of information is purely chemical. The information itself, when abstracted from the chemistry, is not chemistry, just as with any other abstraction.

The question you refuse to address is this: So what? What is it about abstractable information that makes you to insist that something special is going on? And what is that something special?

I'm willing to take the next step in our conversation, but apparently I first have to swear to some ideological requirement. If this is not the case, then state plainly what assumptions you are making about information versus chemistry. I'll state plainly whether I agree with them or not.

~~ Paul
 
#16
Meaningless. Nope, there are no chemical bonds defining the sequence. It did not have to be four bases.



Also...

http://hyperphysics.phy-astr.gsu.edu/hbase/organic/gencode.html

Just plain wrong I am afraid.



I did answer. Code and information that writes the machines that do the work! In some cases it appears as an algorithm. Now please explain proof reading and error correction purely chemically.



As above explain how chemicals read and can recognize and correct errors. None of your baseless statements. Citations please.



No I am not. I am currently taking a chemistry course in preparation for biochemistry. You are so afraid of information you can't even accept what mainstream science says about it. And you simply do not have a good grasp of the processes, I know this as a fact and can pull up some of your absurd erroneous statements if you like.



You got to be kidding. The word translation is taken


...As I said, your question is not answered by this study.
Though,How is in the title I am not asking a question. But since you think I am, what do you think the question is?
 
#17
You keep saying things like this, but then insist that you understand. The storage and manipulation of information is purely chemical. The information itself, when abstracted from the chemistry, is not chemistry, just as with any other abstraction.
This is pretty much what I have been saying actually. Mostly. The abstraction has meaning/function regardless of our abstractions though, multiple meanings in fact. And many recognition factors are to do with structure and shape btw. The actual chemical process is quite staggering and coordinated through systems controls, and information.processing that is all quite physical. Performed by molecular machines coded by DNA and built by other molecular machines themselves.

You here are speaking of two things. Information and chemistry. Thank you. That is my point. As I said saying it is all chemistry is like saying your computer works through electricity alone. You really get yourself bent out of shape to what I am actually saying.

It uses a chemical code, but the code is not chemistry, the information though mediated through chemistry is not chemistry. For the 1000th time. Information is not the medium that carries it!

I am not arguing design or evolution. Too tedious. Just biology. It is all just the illusion of design remember?
 
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Paul C. Anagnostopoulos

Nap, interrupted.
Member
#18
This is pretty much what I have been saying actually. Mostly. The abstraction has meaning/function regardless of our abstractions though, multiple meanings in fact. And many recognition factors are to do with structure and shape btw. The actual chemical process is quite staggering and coordinated through systems controls, and information.processing that is all quite physical. Performed by molecular machines coded by DNA and built by other molecular machines themselves.
Apparently we have no disagreement here, except possibly if you have loaded the word "meaning" with something nonphysical. But sometimes you sound as if you're saying that the translation process is not entirely chemical. I certainly agree that the processes are stunningly complex.

You here are speaking of two things. Information and chemistry. Thank you. That is my point. As I said saying it is all chemistry is like saying your computer works through electricity alone. You really get yourself bent out of shape to what I am actually saying.
Whether I agree about the computer depends on whether you sound like the word "works" means "operates" or "accomplishes its purpose." The operation is entirely electrical. The programming is not.

It uses a chemical code, but the code is not chemistry, the information though mediated through chemistry is not chemistry. For the 1000th time. Information is not the medium that carries it!
The abstracted code is not chemistry. The storage and translation of the code is chemistry. The evolution of the code is physics/chemistry. I believe you do not agree with that sentence.

I am not arguing design or evolution. Too tedious. Just biology. It is all just the illusion of design remember?
If you are not arguing design versus evolution for the origin of the code, then I have no idea what your point is.

~~ Paul
 

Paul C. Anagnostopoulos

Nap, interrupted.
Member
#20
Yep.
Information is not matter or energy.
And no, before I must repeat, it is not the medium that carries it..
Right, the abstracted information is not the medium, since it can be copied to another medium.

So what is your point? Why are you so jazzed about the distinction between abstracted codes and the chemistry that processes them?

~~ Paul
 
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