Data, Information, and all that....

Joralex,I, for one, think Peter overstated the case by saying that the letter-jumbling exercise doesn't work with Hebrew. English has separate vowel letters, but Hebrew uses little marks below the consonant letters to stand for the vowel sounds. In newspapers and such, these marks are omitted entirely, so only readers familiar with the language already would recognize the words. If the consonant letters were jumbled (and the vowel marks missing), it would be much more difficult to reassemble the words. This is a matter of degree and not of kind. I'd say Spanish would be a more difficult language than English in which to play this game, due to the percentage of words that end in -o or -a. That's not to say the exercise wouldn't work.However, linguists have pretty well established the interrelations among modern languages and the ways these derive from previous languages. I'm baffled by the last sentence of your post. Are you saying that languages have not evolved from common ancestors either?------------------
The dark nursery of evolution is very dark indeed.
Brad McFall

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Precisely my point! Tell me, WHAT performs the 'interpretation'? DNA encodes the information for the assembly of proteins (via base sequences) and something has to interpret those base sequences as meaning exactly what the code intends it to mean. But that interpretative act is conducted by a system that is ALSO encoded within the DNA. The mother of all chicken-n-egg?

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I think the word "interpret" with respect to DNA transcription and translation is a bit of a misnomer. It is a chemical reaction, not a decision making process. It is very deterministic, as soon as a few requirements are met a sequence of DNA is transcribed, not read for content like a newspaper. There is no conscious decision at any point in this process.As to the origin of the system, current interdependency does not refute a possibly independent history. Societies dependence on electricity, for example, does not mean that society always had electricity.

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Adding or removing a base changes the data, it may or may not changed the information.

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That is an unsubstantiated assumption. In fact, while the contents in your brain are able to help you retain the information in 'To be, or not be to', changing a base will likely yield an interpretation producing B instead of A. The quantity of information may have remained the same but it is the quality of information that determines life.

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Differences in cytochrome C proteins among organisms seems to indicate that base and amino acid substitutions may not always affect activity or specificity. Human cytC works in E coli just as well as the native protein.Taking this one step further, can random proteins through mutation and selection become intergral parts of a genome? As it turns out, the answer is yes.
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Can an arbitrary sequence evolve towards acquiring a biological function?Hayashi Y, Sakata H, Makino Y, Urabe I, Yomo T.Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, 565-0871, Suita City, Osaka, Japan.To explore the possibility that an arbitrary sequence can evolve towards acquiring functional role when fused with other pre-existing protein modules, we replaced the D2 domain of the fd-tet phage genome with the soluble random polypeptide RP3-42. The replacement yielded an fd-RP defective phage that is six-order magnitude lower infectivity than the wild-type fd-tet phage. The evolvability of RP3-42 was investigated through iterative mutation and selection. Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed. The experimental evolution attested that, from an initial single random sequence, there will be selectable variation in a property of interest and that the property in question was able to improve over several generations. fd-7, the clone with highest infectivity at the end of the experimental evolution, showed a 240-fold increase in infectivity as compared to its origin, fd-RP. Analysis by phage ELISA using anti-M13 antibody and anti-T7 antibody revealed that about 37-fold increase in the infectivity of fd-7 was attributed to the changes in the molecular property of the single polypeptide that replaced the D2 domain of the g3p protein. This study therefore exemplifies the process of a random polypeptide generating a functional role in rejuvenating the infectivity of a defective bacteriophage when fused to some preexisting protein modules, indicating that an arbitrary sequence can evolve toward acquiring a functional role. Overall, this study could herald the conception of new perspective regarding primordial polypeptides in the field of molecular evolution.PMID: 12574862 [PubMed - indexed for MEDLINE]
------------------------Improved infectivity through mutation of a random sequence. This would seem to show that evolution can create meaningful "information" and increase "quality" over time from an increase in "quantity".

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Again, the quantity of information may have remained the same but it is the quality (i.e., the specificity) of information that determines many aspects connected with life.

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I don't think that anyone here will argue that protein specificity is not important. What you are missing is that specificity can arise through naturalistic processes. I think the pubmed citation above attests to that. Another pubmed citation that shows an increase in specificity due a mutation in DNA polymerase:
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Variants of DNA polymerase Beta extend mispaired DNA due to increased affinity for nucleotide substrate.Shah AM, Maitra M, Sweasy JB.Yale University School of Medicine, Departments of Therapeutic Radiology and Genetics, New Haven, Connecticut 06520, USA.DNA polymerase beta offers an attractive system to study the biochemical mechanism of polymerase-dependent mutagenesis. Variants of DNA polymerase beta, Y265F and Y265W, were analyzed for misincorporation efficiency and mispair extension ability, relative to wild-type DNA polymerase beta. Our data show that the fidelity of the mutant polymerases is similar to wild-type enzyme on a one-nucleotide gapped DNA substrate. In contrast, with a six-nucleotide gapped DNA, the mutant proteins are slightly more accurate than the wild-type enzyme. The mutagenic potential of Y265F and Y265W is more pronounced when encountering a mispaired DNA substrate. Here, both variants can extend a G:G mispair quite efficiently, and Y265F can also extend a T:G mispair. The kinetic basis of the increased mispair extension efficiency is due to an improved ability to bind to the incoming nucleotide. Y265W extends the G:G mispair even with an incorrect nucleotide substrate. Overall, our results demonstrate that the Y265 hinge residue is important for stabilizing the architecture of the nucleotide binding pocket of DNA polymerase beta, and that alterations of this residue can have significant impacts upon the fidelity of DNA synthesis.
{emphasis mine}
---------------------So, specificity can be a hallmark of mutation. It would seem that specificity is not a hallmark of ID alone, but can come from mutation. So, why are we to believe that DNA arose from an intelligence when it's properties and plasticity in sequence seem to be natural?

Loudmouth,This is an excellent point. We've said before that Behe and Dembski make a lot out of 'specificity' but the concept is still vague. Usually, they use the analogy of an archer shooting arrows into a target: the specificity comes in the arrow hitting the target, not just shooting an arrow into the wall and painting a target around it.In theory (Peter has argued), there's no way to determine that the target was there before the arrow, so intelligent design creationism loses all hope of empirical relevance. Thanks for giving us a concrete example of this from the very field that Joralex and the IDC crew treat like ready-made creationist propaganda.I wonder what Joralex will make of geneticists documenting 'complex, specified information' coming about through that silly notion of Darwinian evolutionary process.------------------
The dark nursery of evolution is very dark indeed.
Brad McFall

The information. Didn't I make that clear?When we read words, the information isn't in the words. It's in our heads.When we read DNA, the information isn't in the DNA, it's in our heads. Therefore information theory is irrelevant to biology, because DNA contains no information.Apparently you missed the point.

By data in connection to DNA I meant the base
sequence.In that way any change to base sequence represents a
change of data.The proteins that are coded for might not be changed
by a substitution (for example) and so the information
has not changed.The same MAY be true of additions or deletions given
the right context.If I were seeking intelligence in an assumed design or code
I would expect a single direct traceable mapping -- maybe that's
just me.

I cannot read hebrew even without scrambling, just passing on
something that I read here:PeopleWhich also suggests that spanish isn't that much of a problem.My thoughts based upon the above page are that recognition
has more to do with familiarity with the unscrambled word
.
Unusual words (or jargon) are harder to decypher ... different
for everyone 'cause we all have somewhat different backgrounds
and reading habits.Words which are almagamations of more than one word also
prove difficult ... like mhslaatnuger for example.

"Are you saying that languages have not evolved from common ancestors either?" Not at all. The same thing applies to languages as does to organisms, namely, no one (certainly not I) disputes that 'evolution' occurs. 'Evolution' as in 'change'. But evolutionists want to promote that 'because things change, this supports the notion that Earth's entire flora and fauna had a common, single-celled ancestor'. Such a statement has exceeded the realm of science and has entered into the domain of metaphysics. That has been, and continues to be, my position in the matter.

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Likewise, there is no doubt that there has been 'evolution' of languages. Languages change and "new" languages ("new species") have emerged from previous ones, etc ... But the origin of language is as difficult a problem today as is the origin of life. 'Difficult', that is, to the Naturalist.

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As for me : I ain't gots no problema!

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Joralex

Well, not quite right...Evolutionists want to promote that "because we observe new species arising from common decendants, this process is sufficient to account for all species, past and present."I fail to see how that "oversteps the bounds of science" or whatever. Looks like a natural extrapolation from observed trend to me, and what could be more scientific?Now, if you feel that contradicts some metaphysical position, too damn bad. Science overrides metaphysics.

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Not at all. The same thing applies to languages as does to organisms, namely, no one (certainly not I) disputes that 'evolution' occurs. 'Evolution' as in 'change'. But evolutionists want to promote that 'because things change, this supports the notion that Earth's entire flora and fauna had a common, single-celled ancestor'.

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Science does not contend that change alone supports the ToE, but rather the relationships between things that have changed. The fact (according to current methodology) that species fall into nested hierarchies with respect to morphology and genetics speaks to the explanatory power of the theory. Simply citing change ignores a great volume of evidence right from the start.

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Such a statement has exceeded the realm of science and has entered into the domain of metaphysics. That has been, and continues to be, my position in the matter.

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What I contend, and continue to contend, is that not all metaphysical positions are equal with respect to explaining objective truth. Humankind will never be able to rid themselves of bias (at least in my opinion) but what we can do is limit it's effects. Naturalistic methodology seems to be the best system we have right now both in its explanatory power and its predictive power due to its ability to limit personal bias. The very fact you can say that DNA has semantic rules relies upon naturalistic methodologies and assumptions. No one has ever been an eyewitness to a polymerase reaction, if you can understand this statement then you are one step closer to joining the naturalist parade.

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But the origin of language is as difficult a problem today as is the origin of life. 'Difficult', that is, to the Naturalist.

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Origin of life and the evolution of life are two separate theories. The best analogy I can think of is this:Does the manner in which a runner arrives at the starting line affect their position at the finish line?Abiogenesis is how life got to the starting line, evolution is the action after that. Abiogenesis is still a very young field, and in my opinion the word "theory" is used very loosely (hypothesis is more cogent, IMO).However, evolution has been tested to such a point, especially after genetic information became available, that it is a very very strong theory. Evolution is falsifiable by many fields and methodologies, but it still stands as the best explanation we have for species diversity. Creation has no explanatory power, no predictive power, and little to no evidence. So, which metaphysical position is strongest? I think it is the current Theory of Evolution.This is not a demand, but I was wondering if you have a response to the two pubmed citations above (msg 17). Arguments about information in DNA actually interest me more than arguments over metaphysical positions for some strange reason.Added in Edit: Crash, I swear I started typing before your message was posted, and I totally agree with what you wrote. Quetzal and I did the same thing earlier today, I'm starting to feel like someone put a hex on me.[This message has been edited by Loudmouth, 12-09-2003]

Hi, welcome back. You were going to explain complexity and some other terms you introduced weren't you? It's taking a while isn't it?

Sorry Pete,
I had fallen into my own personal aplogetic but for this I am not so sorry nor sore. I was thinking that I NEED a way determine if a given BASE CHANGE could not be EQUIVALENT from the prespective of selection due to recombination vs recombinations that put physical forces in "impossible" arrangements from the current adaptive fitness of the given taxogeny said "changes" are concurrently "within". Yes, I would need to have it understood how Provine thought that Wright's "landscape" IS NOT incomprehensible which I more or less passed over in my mind when posting as I have not had this kind of trouble but I did not or should not have expected you to think the LINE OF FORCE horizontally from and during any base-pair copying or change MUST be different than that along the form of the helix for that may not be true but is something I am generally entertaining as a desire to do with the information in moleuclar biology.You are correct their SHOULD be a single traceable mapping I only maybe have a few more requiements (what is the relation of a polybaramin and programmened cell deaths that may have not so far been attributed to natural selection) than any common whim this trajectory would find a content similar inertia of we both may agree to in some to be made prelimiary simulation of the thing.In addition to this I HAVE been thinking about information flow contrary to the CENTRAL DOGMA. Specifically this came up with MAMMY on methlyation but for me was a little more determinate when I think of guanophore cell physiology as opposed to any old mitoses that may not be age but only the appearence of such in the need to do away with ecology first instead of "ontogeny recapitulates phylogeny" when dealing with any relation of physics to metrics that may be symmetrical ONLY IN 1-D (looks like a difference ONLY of >--->--->--->etc OR ++---++---++---++---.ALL ELSE WOULD BE THE biophysical (not currently scripted metaphysical) "matrix of minor polarites". Gould for one HAS rejected this approach even though I can agree with him that NO amount of addinging information on the CHANGE from an amphibian brain to a reptile IS CORRECT. We both UNDERSTAND THIS PICTURE to be incorrect yet we differ when approaching an issue of perfection (or in Darwinian terms adaptive fitness optimization) as to HOW Wolfram's NEW CLAIM will pan out the golden monster etc. etc. Since Wolfram's holds to both- equivalent sophistication and universality unreduction
1)the metaphysics is still philosophically miswrit
2)the argument from major polarities failed to empircally locate the polarity no matter the duality (which is WHY I am DOING baraminology...)
3)I am incorrect in THEORY about the NODE that arises humanly between psychic and non-psychic in Matchette's rejection of the EASTERN answer.This does not mean my deductions from within panbiogeography are wrong as to the same data nor that I have used inappropirate information only that I give more value to finding said MATIRX in the "TENSION" of WrightvsFisher as say PRICEVSDSTARJORDAN than some other still equally writiable PERVERSION. NOT "Version".SO Wolfram's STILL UP TO DATE NOT****** being able to get much more than 2-D in his "new science" continues to support doing all the rotation and revolution within the 1-D symmetry that would be any new or old kind of base changes.Thanks for the opp to clarify. I dont know if this will help you in any way or not. The issue of good and evil is altogher something else for me but may not be for Gould if he really was a "materialistic nihilist" as Rupert Sheldrake said he was. Of course Gould had a more robust view than Sheldrake continued to maintain. But Gould did not take full advantage of lexic possiblites rather most only grammetological ones. Discovery is not fact finding...true enough.

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Crashfrog: When we read DNA, the information isn't in the DNA, it's in our heads. Therefore information theory is irrelevant to biology, because DNA contains no information.

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DNA contains no information????? Surely you're kidding.Why do you think you are a human instead of a fruit fly, or a cactus, or a sponge? Gee, could it be because of the genetic information stored in your DNA?As far as the validity of applying information theory to DNA, try looking around these pages and their links some:http://www-lmmb.ncifcrf.gov/~toms/sequencelogo.htmlhttp://www.lecb.ncifcrf.gov/~toms/glossary.html[This message has been edited by DNAunion, 12-12-2003]

Nope. Why would I be kidding? Why would something that humans invent and make up - information - be in DNA, a naturally occuring molecule?There's no more information in DNA than there is in a snowflake. The "information stored in my DNA"? Surely you're kidding. The reason I'm not a fruit fly or a cactus is because my DNA is structured differently in such a way that it catalyzes the formation of different protiens.Oh, sure - you can find how much information DNA could store, but in order for me to believe that there is already information in the DNA, you'll have to tell me who put it there.

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Crashfrog: When we read DNA, the information isn't in the DNA, it's in our heads. Therefore information theory is irrelevant to biology, because DNA contains no information.

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DNAunion: DNA contains no information????? Surely you're kidding.

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Crashfrog: Nope. Why would I be kidding?

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Because the alternative is that you are ignorant. I was giving you the benefit of the doubt.But since you now acknowledge that you actually believe DNA does not contain information, read the following and learn.

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In Part I of the text we discussed the presence of genes on chromosomes that control phenotypic traits and the way in which the chromosomes are transmitted through gametes to future offspring. Logically, some form of information must be contained in genes, which, when passed to a new generation, influences the form and characteristics of the offspring; this is called the genetic information. (emphasis added, Concepts of Genetics: Fifth Edition, William S Klug & Michael R Cummings, Prentice Hall, 1997, p262)

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Deoxyribonucleic acid (DNA) is the storehouse, or cellular library, that contains all the information required to build the cells and tissues of an organism. (Molecular Cell Biology: Fourth Edition, Harrvey Lodish, Arnold Beck, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, & James Darnell, W.H Freeman & Co., 2000, p100)

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Nucleic acids are complex substances of high molecular weight that represent a basic manifestation of life. The sequence of nitrogenous bases in these polymeric molecules encodes the genetic information necessary for all aspects of biological inheritance. (Integrated Principles of Zoology: Tenth Edition, Cleveland P Hickman Jr., Larry S. Roberts, & Allan Larson, WCB McGraw-Hill, 1996, p7)

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"Nucleic acids are substituted polymers of the aldopentose ribose that carry an organism's genetic information. A tiny amount of DNA in a fertilized egg cell determines the physical characteristics of the fully developed animal. The difference between a frog and a human being is encoded in a relatively small part of the DNA. Each cell carries a complete set of genetic instructions that determine the type of cell, what its function will be, when it will grow and divide, and how it will synthesize all the proteins, enzymes, carbohydrates, and other substances the cell and the organism need to survive. ... DNA is relatively stable, providing a medium for transmisiion of genetic information from generation to generation." (Organic Chemistry: Fourth Edition, L. G. Wade Jr., Prentice Hall, 1999, p1103)

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A crucial feature of a nucleic acid molecule is the sequence of the four bases along the strand, called the base sequence. The molecules are huge, with molecular masses ranging into the billions for mammalian DNA, so the four bases may be arranged in an essentially infinite number of variations. The specific sequence of the bases along the chain is the information storage system needed to build organisms. (General Chemistry: An Integrated Approach: Second Edition, John W Hill & Ralph H Petrucci, Prentice Hall, 1999, p984)

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Now we know that an organism’s inherited instructions reside in the genetic information of each of its cells as DNA, and we can tell a coherent genetic story starting with this molecules.

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But first let’s step back and use Figure 14-1 to preview how DNA functions as instructional information in cells and, at the same time, how this unit of chapters on information flow in cells is organized. The information carried by DNA flows both between generations of cells and within each individual cell. As Figure 14-1a indicates, the information carried in a eukaryotic cell’s DNA is passed on to daughter cells by the processes of DNA replication and mitosis. Chapter 16 considers the cellular and molecular bases of information flow between generations of sexually reproducing organisms (including Mendel’s work and its chromosomal basis). (The World of the Cell: Third Edition, Wayne M Becker, Jane B Reece, & Martin F Poenie, Benjamin/Cummings Publishing Co., 1996, p408)

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Every organism, even the simplest, contains a massive amount of information in the form of DNA. The major carriers of genetic information in eukaryotes are the chromosomes contained within the cell nucleus. Chromosomes are made up of chromatin, a complex material that consists of fibers containing protein and deoxyribonucleic acid. Each chromosome may contain hundreds or even thousands of genes. As will be evident in succeeding chapters, our concept of the gene has changed considerably since the beginnings of the science of genetics, but our definitions have always centered on the gene as an informational unit. By providing the information needed to carry out one or more specific cellular functions, a gene ultimately affects some characteristics of the organism. For example, we speak of genes controlling eye color in humans, wing length in fruit flies, seed color in peas, and so on. (Biology: Fifth Edition, Eldra Pearl Solomon, Linda R Berg, & Diana W Martin, Saunders College Publishing, 1999, p198-199)

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"The sequence of bases in a DNA or RNA molecule is informational, representing the genetic information necessary to reproduce an identical copy of the oragnism." (Biology of Microorganisms: Sixth Edition, Thomas D Brock & Michael T Madigan, Prentice Hall, 1991, p31)

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Genetics is the science of heredity; it includes the study of what genes are, how they carry information, how they are replicated and passed to subsequent generations of cells or passed between organisms, and how the expression of their information within an organism determines the particular characteristics of that organism. Chromosomes are cellular structures that physically carry hereditary information; the chromosomes contain the genes. Genes are segments of DNA (except in some viruses, in which they are made of RNA) that code for functional products.

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First, the linear sequence of bases provides the actual information. Genetic information is encoded by the sequence of bases along a strand of DNA, in much the same way as our written language uses a linear sequence of letters to form words and sentences. But 1000 of these four bases, the number contained in an average gene, can be arranged in 4^1000 different ways. This astronomically large number explains how genes can be varied enough to provide all the information a cell needs to grow and perform its functions. (Microbiology: And Introduction: Sixth Edition, Gerard J Tortora, Berdell R Funke, & Christine L Case, Benjamin Cummings, 1998, p207-208)

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I could have found dozens of other quotes, but this large batch from multiple college texts should suffice -- at least for any RATIONAL AND HONEST person -- to show that biologists, and even chemists, clearly state that DNA contains information. This is game, set, and match, DNAunion!************************************
Oh, and you didn't address the links I provided that confirmed the validity of applying information theory to DNA. Here they are again, for your convenience.http://www-lmmb.ncifcrf.gov/~toms/sequencelogo.htmlhttp://www.lecb.ncifcrf.gov/~toms/glossary.html[This message has been edited by DNAunion, 12-13-2003]

For good measure, here are more quotes from mainstream (i.e., not ID or Creationist) science books for the general public. Note that these quotes are provided as mere icing on the cake: the cake itself is the many college-text quotes I provided in my previous post.

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For some single-celled organisms whose DNA nucleotide strings have only a fraction of the length of those in our own cells, we can make a crude estimate of the information content. The DNA of an amoeba (a nonsocial one), for example, holds on the order of 10^9 bits. In other words, one billion yes/no instructions are written down in that four-letter script — enough to make another amoeba. This script contains everything an amoeba ever needs to know — how to make its enzymes, how to make its cell membrane, how to slink about, how to digest the foodstuffs, how to react when it gets too dry or too hot, how to reproduce itself. And all of that information is enscrolled into a space so small you would need a good microscope to make it out. If you wanted to give all these instructions in the English language, they would fill some 300 volumes of the size of this book (the information content of an average printed page in English is roughly 10,000 bits). (The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life, Werner R. Loewenstein, Oxford University Press, 1999, p16)

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[Schrodinger’s] book, titled What is Life?, is a classic — still in print, and well worth seeking out — that expounded the idea that the fundamental molecules of life could be understood in terms of the laws of physics. The important molecules to explain in those terms are the genes that carry information about how the body is to be constructed and how it is to operate.

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The order in which different chemical components, called bases, are strung along the DNA spines carries information that the living cell uses to construct the protein molecules that do all the work (In Search of Schrodinger’s Cat: Quantum Physics and Reality, John Gribbin, Bantam Books, 1984, p149)

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All of cellular life is involved in transforming inputs into outputs, the way computers do. Cells are not just little bags of alphabet soup, full of things like ATP and NADH, but are tiny chemical calculators. Compared to even the best of human computers, the living cell is an information processor extraordinaire.

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This is a programming system that’s been around three billion years, Adelman said. I’ll bet it has a lot to tell us aobut how to program....It’s a dazzling display of information processing ability.

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... The DNA in a cell contains enough information not only to make a human body, but to operate one for a lifetime. A gram of dried-out DNA — about the size of two pencil erasers — stores as much information as maybe a trillion CD-ROM disks, Adelman points out. So long before Adelman realized that nature had beaten Alan Turing to the idea of a Turing machine, biologists knew that DNA was the master information storage molecule.

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... Almost from the moment [Watson and Crick] figured out DNA’s design in 1953, it was clear that it stored the information necessary for life to function, reproduce, and evolve. (The Bit and the Pendulum: From Quantum Computing to M Theory — The New Physics of Information, Tom Siegfried, John Wiley & Sons, Inc., 2000, p97)

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[This message has been edited by DNAunion, 12-13-2003]