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Member (Idle past 1509 days) Posts: 2161 From: Cambridgeshire, UK. Joined: |
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Author | Topic: Data, Information, and all that.... | |||||||||||||||||||||||||||
MrHambre Member (Idle past 1423 days) Posts: 1495 From: Framingham, MA, USA Joined: |
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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Loudmouth Inactive Member |
quote: 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.
quote: 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.-------------------- 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".
quote: 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:---------------------- 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?
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MrHambre Member (Idle past 1423 days) Posts: 1495 From: Framingham, MA, USA Joined: |
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
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crashfrog Member (Idle past 1497 days) Posts: 19762 From: Silver Spring, MD Joined: |
Uhhh ... crash ... if it's "in your head" then may I ask, what IS IT that is "in your head"? 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.
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Peter Member (Idle past 1509 days) Posts: 2161 From: Cambridgeshire, UK. Joined: |
By data in connection to DNA I meant the base
sequence. In that way any change to base sequence represents achange of data. The proteins that are coded for might not be changedby a substitution (for example) and so the information has not changed. The same MAY be true of additions or deletions giventhe right context. If I were seeking intelligence in an assumed design or codeI would expect a single direct traceable mapping -- maybe that's just me.
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Peter Member (Idle past 1509 days) Posts: 2161 From: Cambridgeshire, UK. Joined: |
I cannot read hebrew even without scrambling, just passing on
something that I read here: People Which also suggests that spanish isn't that much of a problem. My thoughts based upon the above page are that recognitionhas 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 alsoprove difficult ... like mhslaatnuger for example.
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Joralex Inactive Member |
"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. 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. As for me : I ain't gots no problema! Joralex
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crashfrog Member (Idle past 1497 days) Posts: 19762 From: Silver Spring, MD Joined: |
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'. 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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Loudmouth Inactive Member |
quote: 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.
quote: 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.
quote: 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]
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NosyNed Member Posts: 9004 From: Canada Joined: |
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?
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Brad McFall Member (Idle past 5063 days) Posts: 3428 From: Ithaca,NY, USA Joined: |
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 unreduction1)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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DNAunion Inactive Member |
quote: 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.html http://www.lecb.ncifcrf.gov/~toms/glossary.html [This message has been edited by DNAunion, 12-12-2003]
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crashfrog Member (Idle past 1497 days) Posts: 19762 From: Silver Spring, MD Joined: |
DNA contains no information????? Surely you're kidding. 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.
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? 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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DNAunion Inactive Member |
quote: quote: quote: 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.
quote: quote: quote: quote: quote: quote: quote: quote: quote: 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.html http://www.lecb.ncifcrf.gov/~toms/glossary.html [This message has been edited by DNAunion, 12-13-2003]
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DNAunion Inactive Member |
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.
quote: quote: quote: [This message has been edited by DNAunion, 12-13-2003]
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