Data, Information, and all that....

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How do cells maintain their high degree of order and complexity? This is a VERY SPECIFIC, YET HIGHLY IMPROBABLE state - one that is very much thermodynamically unfavorable.

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Very specific? Yes, assuming a qualitative and subjective view of complexity.

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No, highly specificperiod.Theoretically, how many different ways could the atoms in your body be arranged.? 10^bajillion-gazillion? How many of those ways would make a human. Only an astronomically miniscule fraction. A human is an incredibly specific arrangement of matter. Even the simplest bacterium is in an incredibly specific state: as Richard Dawkins himself has famously said, There are far more ways to be not alive than there are to be alive (paraphrasing).Though this gets off the subject a bit, it makes the current point very strongly. Why haven’t OOL researchers been able to obtain a single, self-replicating RNA molecule? They make the RNA themselves, and they make trillions and trillions of different base sequences of RNA. Gee, could it be because even something as simple as a self-replicating RNA molecule is a very specific arrangement of matter? Yep. And that’s just an RNA molecule: that doesn’t count the proteins, mitochnodria, lysosomes, cells, tissues, organs, and organ systems of a human.So no, you are wrong. A human IS a highly specific state of matter.

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Highly improbable? No, if certain conditions are first met, ie starting from one fertilized human zygote the formation of a multi-cellular human is very probable.

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Are you really that dense?The point is how improbable the arrangement of matter in a human isperiod. Nothing about starting with the DNA, proteins, ribosomes, etc of a zygote.Your argument is kind of like saying that a Pentium 4 3GHz CPU isn't an improbable state of matter. Why? Well, given a chip manufacturing plant, humans/robotics to run the machinery, instructions for making the chip, and so on, it's pretty much certain to occur.Here, let me explain it to you. If you took the individual X number of carbon atoms, Y number of oxygen atoms, Z number of hydrogen atoms, and so on, that make up a human, put them into a container of some sort and supplied undirected energy, how probable is it that the matter would end up being arranged as a living human being? Surely you realize that the probability of that occurring approaches 0.Is this just DNAunion saying that humans (or for that matter, any living thing) are a highly improbable arrangement of matter? No.

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"Have you ever considered how downright improbable you are? What you are contemplating is the thermodynamic improbability that the order of the human body (or any other biological entity) could come into being spontaneously or, for that matter, could be maintained in such a highly ordered state once it had come into being. On the contrary, things in nature usually proceed from an ordered state to a less ordered one, not the other way around." (Wayne M. Becker, Jane B. Reece, & Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p112)

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... [as a human] you are improbable because you are so highly ordered, but you are nonetheless possible because of the information available to you (in the DNA of your cells) and the copious quantities of energy at your disposal (in the bond energies of the food you eat). (Wayne M. Becker, Jane B. Reece, & Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p112)

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"We might, in fact, define life as a continual struggle to maintain a myriad of cellular reactions in positions far from equilibrium because at equilibrium no net reactions are possible, no energy can be released, no work can be done, and the thermodynamically improbable order of the living state cannot be maintained." (Wayne M. Becker, Jane B. Reece, & Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p133)

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How then does it occur? Just as I said (and one of the above quotes alluded to also)...sufficient energy AND sufficient information.

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"However improbable a structure may be because of its order, it can always be generated if sufficient energy and information are available. Energy and information are, in other words, two indispensable prerequisites for the existence of life. Order can be brought about, maintained, and even extended in biological systems provided that adequate information and energy are available. The information is required to specify what form that order should take, and the energy is needed to drive the reactions and processes that lead to the order." (Wayne M. Becker, Jane B. Reece, & Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p112)

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Now how silly do you feel.[This message has been edited by DNAunion, 01-16-2004]

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If take all of a cell's constituents and "jumble them up", you can supply all the undirected energy you want to those "chemicals": put them out in the sun, cook 'em up on the stove, smash them with a hammer, expose them to radiation, ... whatever. You won't get life, even though you've supplied sufficient energy. Mere energy and chemistry alone are not sufficient to make one of our cells...it takes control too, which is where the information comes in.

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Again, if you "jumble-up" the chemistry in any reaction, organic or inorganic, the resultants will be different.

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If you mix NaOH and HCl in solution you will get table salt (NaCl). You can stir the solution all you want, as vigorously as you want, in whatever direction you want, for as long as you want, completely randomizing the arrangement of matter, and you will still end up with salt. If you did the same things with a human cell you’d kill it.

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The cell is no different in this respect than acetic acid vs. ethanol. The information in the cells (DNA) is susceptible to the same thing, information is changed if the chemistry is changed. Changing the DNA sequence is changing it's chemical attributes.

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At the least, you’re missing the forest for the trees: changing base sequences in DNA is changing the information content.In this thought experiment, each nucleotide acts chemically exactly the same after the order of bases was changed as it did before. G still bonds preferentially with C, using 3 hydrogen bonds; and T still bonds with A, using two hydrogen bonds. The polymerase enzymes would still interact chemically the same with each base also - but the polymerase would no longer bind at the right sites, because the order of bases was changed — you know, the information was altered.***********************************
Can't "perfect" this one either - gotta get back to work.[This message has been edited by DNAunion, 01-16-2004]

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I would argue that the maintainence of complexity is a different issue than the origination of complexity. Do you disagree?

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Did you forget that in your response to me you discussed how an adult human would arise?

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Very specific? Yes, assuming a qualitative and subjective view of complexity. Highly improbable? No, if certain conditions are first met, ie starting from one fertilized human zygote the formation of a multi-cellular human is very probable.

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You expanded the topic several ways. You went from it being about maintenance of order and complexity of a cell, to being about how the order and complexity of an adult human being comes about.

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Anyway, again you slip from the maintainence of complexity to the origination of complexity.

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No, YOU did. See my last post just above where I show that you did this.

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So, in what units is complexity measured in? How can you show that a 50-mer of human DNA is any more complex than an arbitrary 50-mer, what units can you use to differentiate? Do the same for a 50-mer amino acid peptide. Which is more complex, an actual small protein in a bacterium or a 50-mer with an arbitrary sequence? This is why I qualified complexity with "qualitative and subjective." Complexity can not be measured but can have explanatory power.

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Algorithmic complexity can be measured by determining the (theoretically) shortest possible list of instructions required to produce what would count as the desired output.As an example, which of these three sequences has the greatest algorithmic complexity.010101010101010101010101010101010101010101010101
010110100101101001011010010110100101101001011010
011100101101010100001010110111101010101000101010It’s the third one.The first sequence has a very short algorithm that can produce it:

Print 01 24 times

The second also has a fairly short algorithm, but it is slightly longer than the previous one.

Print 01011010 6 times

The last sequence has no such shortcut (actually, it might — I just randomly typed out 1s and 0s). So it’s shortest algorithm would (probably) be the sequence itself:

Print 011100101101010100001010110111101010101000101010

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Just to make you feel better, yes the human is complex and humans are highly improbable if they were birthed from a cake on St. Patty's Day, but not improbable within biology in that we understand the mechanisms of internal fertilization and the role of gametes.

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And the zygote already starts with all of the basic information needed to produce a human. Sort of the way a chip manufacturing plant contains all of the basic information needed to make a Pentium 4 3.00GHz CPU. That doesn't make that processor itself any less specific or improbable an arrangement of matter.Here’s another way to look at how much information it takes to make a human from scratch...teleportation.

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To teleport a human would require knowledge of the type and exact position and movement of every atom of the person to be teleported. That is about a hundred thousand million million million million atoms. To send that information down today's fast data transfer systems would take a hundred million times longer than the present age of the Universe (which is about 15 thousand million years). (BBC NEWS | Science/Nature | Q&A: Teleportation)

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Wow, that’s a lot of information.Now ask yourself, would it take that much information to teleport a human-sized salt crystal? Of course not. It's not that the amount of matter needed to be described would be any less, but that the specificity and complexity of the arrangement of matter is much greater for a human than a salt crystal.

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How then does it occur? Just as I said (and one of the above quotes alluded to also)...sufficient energy AND sufficient information.

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I have never seen life occur by giving DNA suffecient energy. Therefore, the information in DNA is not sufficient for life. Where is the remaining information?

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Asking where THE REST OF the information is implies that DNA does contain information: if I could just get everyone here to agree on that much (Peter).I’ve already stated at least twice that proteins contain information — a statement that went completely unchallenged (somewhat by surprise, considering the high resistance Peter has to the simple statement DNA contains information). And a zygote contains proteins, so there is more information than just DNA in a zygote (of course, those inherited proteins were produced in the mother's and father's gametes, from the parents’ DNA base sequences: so even those proteins’ information ultimately comes from DNA). A zygote starts with all the mechanisms needed to operate on that DNA, such as the specific proteins needed for transcription and mRNA editing, as well as ribosomes: a zygote also has things needed to provide energy for the cell, such as mitochondria (which store some of their own information in their own DNA base sequences).The point that was being made is that sufficient energy and mere chemistry is not enough to form a human (or was it a cell - don't feel like looking it up): it takes control too, which is where information comes into play.**********************************************
What some here seem to not get is that information is what humans use to control chemical reactions. If chemistry professor wants his/her students to produce Z, does he just tell them to pick up chemical and random, mix them, then supply what amount of heat they want? No. He/she tells his students to start with P amount reactant X and Q amount of reactant Y, and possibly also to set the pH, temperature, and/or pressure as desired. That's a sort of recipe for making Z: it's a list of instructions used to produce Z. It's information.Cells work similarly (but without consciousness): there is a list of instructions - information - used to produce "Z", such as a specific protein. DNA contains that information (at least as far as producing the correct order of amino acids is concerned, which basically determines the three dimensional conformation the polypeptide will fold up into, and therefore, the resulting protein's ability to perform a certain function).[This message has been edited by DNAunion, 01-17-2004]

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If you mix NaOH and HCl in solution you will get table salt (NaCl). You can stir the solution all you want, as vigorously as you want, in whatever direction you want, for as long as you want, completely randomizing the arrangement of matter, and you will still end up with salt. If you did the same things with a human cell you’d kill it.

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Compartmentalization is as important in cells as it is in chemistry. Try and make a battery work by mixing the anode and cathode solutions together and touch the anode and cathode together in the resulting mixture.

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A battery of the sort you describe is an intelligently designed object that uses chemistry as a means of achieving a desired result. Humans used information — gleaned from experimentation — to arrive at a method of producing batteries. A battery is not mere chemistry: it is at a level above that.Here, let me try to explain it this way. What is the chemical formula for a battery? What is the chemical equation that produces a battery? (And no, I don't mean the chemical equation for the simple chemistry that occurs within a battery, but for the whole enchilada).

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If you change a substrate so that an enzyme no longer recognizes it you have changed the chemistry of the substrate. This goes for RNA polymerases as well as dehydrogenases. Are you going to argue that if I change sucrose to cellulose so that the an enzyme no longer recognizes it that I haven't changed it chemically but only informationally?

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Sucrose to cellulose? You’re comparing apples to oranges.Sucrose is a disaccharide consisting of one glucose linked to one fructose. Cellulose is a polysaccharide consisting of 10,000 or so glucose molecules linked together. One has fructose, the other doesn’t. One consists of just two monosaccharides linked together, the other thousands.What you are discussing is not comparable to what I discussed, which maintained the same QUANTITY and IDENTITY of each component (nucleotide), just changed their ORDER.

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I say that the information in DNA is chemical, and only chemical.

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And that’s where you are wrong. Information is not ONLY chemical, it also exists at a higher level.Do you consider a hand to be ONLY CHEMICAL? Should teachers tell their students, Children, if you have to use the bathroom, just raise your chemicals? Heck, students themselves are only chemicals, aren’t they, so maybe you want teachers to say, Chemicals, if you have to use the bathroom, just raise your chemicals? Well heck, a bathroom is "only chemicals" too, so maybe you want teachers to say, "Chemicals, if you have to use the chemicals, just raise your chemicals"? Sounds like the chemical Smurfs.Not everything that relies upon chemistry at its lowest levels is ONLY chemistry: a person is not ONLY chemistry; a hand is not ONLY chemistry; a tissue is not ONLY chemistry; a cell is not ONLY chemistry. The only people who think that way are die hard reductionists, who miss the forest for the trees. Most rational people allow for more than ONLY a strict reductionist interpretation of everything.I don’t know about the rest of the people out there, but I am not just a bag containing carbon, hydrogen, oxygen, nitrogen, phosphorus, and other atoms undergoing mere chemical reactions. I am a person, composed of organ systems, each of which is composed of organs, each of which is composed of tissues, each of which is composed of different cell types, each of which contains different proteins because different genes are turned on and turned off, and each of those genes is a specific sequence of DNA nucleotides, with each nucleotide consisting of three moieties — deoxyribose, a nitrogenous base, and a phosphate group, each of which is composed of several specific atoms in fixed proportions.In fact, even at the LOWEST levels I discussed things aren’t only chemistry: physics resides at a lower level than chemistry. A hard core reductionist could argue that there's not such thing as chemistry, ONLY physics.At some point moving up the levels I listed, pretty early, in fact, any rational person agrees that things stop being ONLY chemistry. In fact, have you ever heard of a branch of science called biology? It's been around for a while.[This message has been edited by DNAunion, 01-17-2004]

I asked people before why they were a human instead of a cactus or squid or what have you. I ran across this today while preparing notes for one of my tutees.

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"Every individual of a given species has a characteristic number of chromosomes in most nuclei of its body cells. For example, most human body cells have exactly 46 chromosomes.

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Humans are not unique in having 46 chromosomes; some other species of animal and plants also have 46, whereas others have different chromosome number. ...

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Humans are not humans merely because they have 46 chromosomes; in fact, some humans have abnormal karyotypes (chromosomes assortments) with more or fewer than 46. The number of chromosomes is not what makes each species unique but rather the information specified by the genes in the chromosomes." (emphasis in original, Biology: Fifth Edition, Eldra Pearl Solomon, Linda R Berg, & Diana W Martin, Saunders College Publishing, 1999, p199)

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"By providing information needed to carry out one or more specific cellular functions, a gene ultimately affects some characteristic of the organism. For example, we speak of genes controlling eye color in humans, wing length in flies, seed color in peas, and so on." (Biology: Fifth Edition, Eldra Pearl Solomon, Linda R Berg, & Diana W Martin, Saunders College Publishing, 1999, p199)

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[This message has been edited by DNAunion, 03-06-2004]

And another I have not yet posted.

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"In this chapter we consider the nucleic acids, the molecules that (1) contain the information prescribing amino acid sequence in proteins and (2) serve in the several cellular structures that choose, and then link into the correct order, the amino acids of a protein chain. Deoxyribonucleic acid (DNA) is the storehouse, or cellular library, that contains all the information required to build cells and tissues of an organism. The exact duplication of this information in any species from generation to generation assures the genetic continuity of the species. The information is arranged in units identified by classical geneticists from Gregor Mendel through Thomas Hunt Morgan, and known now as genes, hereditary units controlling identifiable traits in organisms. In the process of transcription, the information stored in DNA is copied into ribonucleic acid (RNA) ..." (Harvey Lodish, Arnold Beck, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, Molecular Cell Biology: Fourth Edition, W H Freeman & Co., 2000, p100)

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No definition, just the continual use and explanation of what it is throughout the book, which is all I need to demonstrate my point that DNA contains information.But here's a definition of the term "genetic information" for you that I found very quickly using Google.

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GENETIC INFORMATION
The information encoded (see encoding) in the genetic material with which all living organisms are endowed. The carrier of this information is a complex structure of dna. It represents an organism's biological inheritance and controls that organism's development, reproduction and self-repair. Within an organism, genetic information flows from dna to protein and other products, first, by the transcription of portions of the dna into so-called messenger rna and, second, by the assembly of individual amino acids into polypeptides, including proteins. Thus the growth of an organism is controlled. The absence of a mechanism that could reverse the direction of this flow from proteins to dna is the basis for the fact that the experiences an organism makes during its life time cannot be inherited by biological means (see culture). Changes in the intergenerational communication of genetic information result from mutations (see noise) and are the target of natural selection (see evolution). (Krippendorff) (http://pespmc1.vub.ac.be/ASC/GENETI_INFOR.html)

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[This message has been edited by DNAunion, 03-08-2004]

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So the information involved is purely natural, and the information can change due to natural mechanisms.

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I hope you are not claiming to counter me there. Remember, my point in these threads was never about HOW the information got into DNA, just that it IS there.[This message has been edited by DNAunion, 03-08-2004]

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"Having outlined the principles governing the stepwise assembly of polynucleotides, we now focus briefly on the large-scale arrangement of information in DNA and how this arrangement dictates the requirements for RNA manufacture so that information transfer goes smoothly. The simplest definition of a gene is a "unit of DNA that contains the information to specify synthesis of a single polypeptide chain". The number of genes in cells varies widely, with the simpler non-nucleated prokaryotic cells having far fewer genes than eukaryotic cells. The vast majority of genes carry information to build proteins ..." (Molecular Cell Biology: Fourth Edition, Harvey Lodish, Arnold Beck, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, & James Darnell, W H Freeman & Co., 2000, p114)

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Although DNA stores the information for protein synthesis and RNA carries out the instructions encoded in DNA, most biological activities are carried out by proteins. The accurate synthesis of proteins thus is critical to the proper functioning of cells and organisms. We saw in Chapter 3 that the linear order of amino acids in each protein determines its three-dimensional structure and activity. For this reason, assembly of amino acids in their correct order, as encoded in DNA, is the key to production of functional proteins.

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Three kinds of RNA molecules perform different but cooperative functions in protein synthesis:

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1. Messenger RNA (mRNA) carries the genetic information copied from DNA in the form of a series of thee-base code words, each of which specifies a particular amino acid. (Molecular Cell Biology: Fourth Edition, Harvey Lodish, Arnold Beck, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, W H Freeman & Co., 2000, p116)

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First, y'all, I'm not a Creationist. Even when I was arguing for ID I was offering ETIs, not God.Second, ...

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DNA transmits information from one generation to the next
Humans give birth only to human beings, not to giraffes or rose bushes. In organisms that reproduce sexually, each offspring is a combination of the traits of its parents. In 1953, James Watson and Francis Crick worked out the structure of deoxyribonucleic acid, more simply known as DNA. This chemical substance makes up the genes, the units of hereditary material. The work of Watson and Crick led to the understanding of the genetic code that transmits information from generation to generation. (Biology: Fifth Edition, Eldra Pearl Solomon, Linda R Berg, and Diana W Martin, Saunders College Publishing, 1999, p7)

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Genetic information is stored in DNA molecules and is faithfully replicated and passed on to each new generation of cells during cell division. Information in DNA codes for specific proteins that in turn determine cell structure and function. (Biology: Fifth Edition, Eldra Pearl Solomon, Linda R Berg, and Diana W Martin, Saunders College Publishing, 1999, p73)

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MrHambre: This is the creationism that dares not speak its name.

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Spoken like a true Nazi.(figured as long as you are calling me a name I don’t deserve, I’d return the favor).

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MrHambre: Despite his denials, it's clear that the 'information' he's talking about wouldn't be in DNA unless someone put it there.

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False. But hey, who am I to say what I believeafter all, isn’t it MrHambre who gets to determine what it is I believe?

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MrHambre: Why else would he care what definition of information we accept?

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Uhm, I was the one taking intelligence and consciousness OUT of the definitions and usage of the term information.

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MrHambre: Note he puts the word "random" in scare quotes, like there's any reason to think that point mutations are anything but random.

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Uhm, there are reasons to think that mutations aren’t truly random: for example, genomes can have hotspots where mutations occur at a higher rate. In such genomes, because the mutations are not evenly distributed, technically, they are not random. There are plenty of debates at sites such as this one that are based on what the word random really means and I didn’t want to get bogged down in such.Now, about your real point. I was not saying that intelligence was involved in directing the mutations, and no rational and honest person would interpret my statements otherwise. Here, let me point out several keys things that show your interpretation to be completely unwarranted.

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DNAunion: At this site I’ve not committed to how information got into DNA because HOW has not been my point...just that there IS information in DNA.

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But now I’ll go ahead and state my position: purely natural processes, such as random mutation and natural selection, can increase the information content of DNA. The information needed to produce extant organisms, encoded in DNA base sequences, was produced from natural manipulations of the DNA information needed to produce yesterday’s organisms, which arose in a similar fashion, and so, back through time until reaching a single common ancestor (if we are going to get technical, possibly a single community in the Woese sense). In other words, common descent of all extant life from a universal common ancestor by means of undirected evolution, with the new information entering the collective genome by means of undirected mutation and natural selection.

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Note especially that last emphasized part, which explicitly states UNDIRECTED MUTATION. Gee MrHambre, can you read?

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MrHambre: And I wonder what sort of processes put the information into that proto-DNA, since 'purely natural' ones are supposed to be so inadequate once we get to the common ancestor.

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More distortion. I said exactly that oppositethat purely natural process ARE adequate.

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MrHambre: Again, if undirected mutation and selection is good enough to explain the amazing diversity of life that exists today, I think it could very well explain the origin of life itself.

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Please explain how, since before there was life in the OOL sense, there was no mutation and natural selectionby definition.[This message has been edited by DNAunion, 03-20-2004]

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DNAunion: Remember, my point in these threads was never about HOW the information got into DNA, just that it IS there.

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I think the how question is the one that most people would like to see your position on, and if you could clarify it, maybe it would stop the jumping to conclusions that so riles you

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Uhm, dude, I already made a very clear statement about my position on HOW the information that IS in DNA today got there: common descent by undirected evolution. Can you read?Were you thrown off by MrHambre's horrible response? A moment of stupidity or dishonesty on his part seem to be the best or only explanations for his actions. You shouldn't follow in his footsteps.Now be a good little boy and read my statements again.

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DNAunion: At this site I’ve not committed to how information got into DNA because HOW has not been my point...just that there IS information in DNA.

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But now I’ll go ahead and state my position: purely natural processes, such as random mutation and natural selection, can increase the information content of DNA. The information needed to produce extant organisms, encoded in DNA base sequences, was produced from natural manipulations of the DNA information needed to produce yesterday’s organisms, which arose in a similar fashion, and so, back through time until reaching a single common ancestor (if we are going to get technical, possibly a single community in the Woese sense). In other words, common descent of all extant life from a universal common ancestor by means of undirected evolution, with the new information entering the collective genome by means of undirected mutation and natural selection.

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Come on people...what's so hard to understand about that?[This message has been edited by DNAunion, 03-21-2004]