Information and Genetics

Fred,Reply to, http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=5&t=6&m=199#199For those wondering what I'm waffling about, Freds definition of new information is new information = the presence of a new algorithm (coding sequence) in the genome that codes for a new useful feature.I am attempting to show that a mutation in a carbohydrate digesting gene, which produced nylC, a nylon digesting gene, has met the criteria set out by Fred. Namely, a new algorithm (new coding sequence, caused by the addition of a single thymine), has produced a new useful feature (nylon digestion). http://www.nmsr.org/nylon.htm

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Originally posted by Fred Williams:

My point is that after mutation there will now be two gene versions (allele) in the population. I realize I forgot that the context was your porkaryote (one-celled pig ), but it does not at all negate my argument. The population now has two gene versions floating around at that locus. Which one is truly the better version for the population?

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I also notice you, like Percy, avoided an important question. What for you would constitute a loss of information at the genetic level?

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1/ In a pool of predominantly nylon, the nylon gene, obviously. On a biscuit, the carbohydrate gene. They are both useful in their own environments. Or are you suggesting that to be useful, it has to be useful at all times, in all environments?2/ A chromosome loss, that carried expressed genes.

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Originally posted by Fred Williams:

Mark:

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We could go off on an unnecessary paper searching tangent here,

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Fred:

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Unnecessary? The AIG reference shows the information was transferred from another bacteria, so no new information via randomness.

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[QUOTE] [b]
AiG :
"... Finally, Mr Cerutti is out of date about this new nylon digesting ability allegedly from a frame shift. New evidence shows that the ability was due to plasmids /b][/QUOTE]

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Birth of a unique enzyme from an alternative reading frame of the
pre-existed, internally repetitious coding sequence", Susumu Ohno, Proc.
Natl. Acad. Sci. USA, Vol. 81, pp. 2421-2425, April 1984.

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"Analysis of the published base sequence residing in the pOAD2 plasmid of Flavobacterium sp. K172 indicated that the 392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid linear oligomer hydrolase involved in degradation of nylon oligomers is specified by an alternative open reading frame of the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein."

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AiG appears to be happy to wave away the problem as plasmids, their quote doesn’t give specifics at all. Note also that they say, more than one species of bacteria have the ability, & not, more than one species of bacteria possess the nylC gene, which, after all is the salient point. ("A New Nylon Oligomer Degradation Gene (nylC) on Plasmid pOAD2 from a Flavobacterium sp.," Seiji Negoro, Shinji Kakudo, Itaru Urabe, and Hirosuke Okadam Journal of Bacteriology, Dec. 1992, p. 7948-7953..).There is more than one nylon digesting gene, F-nylA, & F-nylB, for example. AiG deftly conflate plasmid, with gene, confusing any potential reader. It is the gene, not the plasmid that is the final arbiter in the argument.The nylC gene is a new nylon digesting gene, unless you can find another gene, common to other bacteria, that codes for the enzyme 6-aminohexanoic acid linear oligomer hydrolase, of course?Regardless, you miss the point, just assume for a moment that you accept my definition of new algorithm, & accept that the ability to digest nylon, in a pool of nylon, is useful. Recall that you are claiming that new information in genetic systems is impossible. In this case a thymine addition in a particular part of the gene sequence fits your definition of new information. A new algorithm produces a new useful feature.The point is not can I demonstrate that it happened that way, but that it is possible for it to happen that way. A gene exists where a single thymine addition would make you & Gitt wrong. We know thymine can be added by mutation, new information is therefore possible.Put another way, we have gene A, that produces a carbohydrate digesting enzyme, & gene B that digests nylon. The only difference is an extra thymine in gene B. This we know. A mutation causing an extra thymine (at the correct position) is possible. The original gene is still extant. We KNOW the functional consequences of that addition.
Ergo, information gain is possible.

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Originally posted by Fred Williams:

but the point surely is, we have the original carbohydrate gene sequence, we have the nylon gene sequence, & the nylon differs by a single thymine addition. Single nucleotide additions are observed, so it is entirely reasonable & plausible to assert that a thymine addition to a gene produces a new function via a new algorithm.

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Originally posted by Fred Williams:
Again, its an altered algorithm, not a new one. That would be like me copying someone’s software, making a single change to one opcode, and calling it new software. More appropriately, it’s a bug fix, or as Percy and I would like to say, enhancement! Regardless, I’ll accept your point for the sake of argument. The same problems still exist for your claim.

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Even though you provisionally accept the point, I’d like to expand on my argument.The only sensible definition of new as far as algorithms in genes is concerned, is that of an algorithm that wasn’t there before, regardless of its origin. This algorithm can be as close or as distant as it likes, it just has to not have been present in the genome.Consider, if ATAGGGGGTTTTCCCCA mutates to ATAGGGGGTCTTCCCCA & it has never existed in the genome, it is a new sequence, therefore a new algorithm. How tiny a variation the mutation makes is irrelevant.Similarly, ATAGGGGGTTTTCCCCA mutates into ACCCCCAAAAGGGGT, this still isn’t a new algorithm by your logic because it’s merely altered, even though only a single nucleotide remains common to both parent & daughter algorithms.Taking the most extreme possibility, there is no requirement for an altered algorithm to share any similarities with the parent, if every single element is altered. As such, altered can mean anything. You can alter any algorithm & come up with any other algorithm. By this logic, there can be no new algorithm, EVER.Let me take the above example again, ATAGGGGGTTTTCCCCA mutates to ACCCCCAAAAGGGGT, a second mutation occurs during the same replication, changing the A to a T, making TCCCCCAAAAGGGGT. Completely different an algorithm than that that started in the parent, that exists at an homologous loci to the unmutated gene. This is a hypothetical scenario, but the daughter algorithm shares nothing in common with the parent. Nevertheless, it's just "altered", & not new, according to you.Therefore, an alteration of an algorithm cannot preclude newness, unless you are actually saying that it is impossible for there to be a new algorithm in any field of information theory?From Genbank:First 60 nucleotides in Mus musculus beta haemoglobin:ccacgcgtcc ggttgtgttg acttgcaacc tcagaaacag acatcatggt gcacctgactFirst 60 nucleotides in Mus musculus cytochrome cgtcttcgagt ccgaacgttc gtggtgttga ccagcccgga acgaattaaa aatgggtgatAs you can see, one algorithm is merely an alteration of another. The question is, would you consider cyt c mutating into haemoglobin a new algorithm, where haemoglobin never previously existed? Remember, we’re not worried about usefulness at this point, just whether it’s a new algorithm, or not.You could alter algorithms that don’t produce sonar, & make them produce sonar, for that matter, & you would have contradicted your own definition of new information. That is, sonar requires new information (so you say), but wait, new information requires new algorithms, but you only have altered algorithms, so even sonar doesn’t require new information! Do you wonder why people tell you your definition of new information isn’t relevant to evolution?In short, you can’t quantify when altered, becomes new, because as far as the genetic information is concerned, they are one & the same.I think I've laboured that point enough!!

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Originally posted by Fred Williams:

To summarize:

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1) plasmid xfer is not generation of new information, it is transfer of already-existing information
2) the new enzyme is no longer specific to its original substrate, which Dr Lee Spetner in ‘Not by Chance’ shows in detail why this type of mutation invariably constitutes a loss of information.

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It brings me back to the question, which gene version is better for the overall population over time? If I get a mutation in my taste buds that makes me crave spam instead of a juicy T-Bone, am I really better off? HECK NO!

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[This message has been edited by Fred Williams, 07-11-2002]

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On a carbohydrate, the carbohydrate gene is better. On nylon, nylon gene is better. In a particular environment nylon digestion is a useful feature. Or perhaps you don’t think the ability to see is a useful feature? It isn’t in a dark room. Or perhaps you don’t think your ability to breath air is a useful feature? It isn’t under water.Taking another tack. Bring a bat up in a room with a moth food supply, then play a loudspeaker at the same frequencies as the bat uses. Voila, sonar/radar is useless. You could do the same to cetaceans in a pool (they prefer fish over moths). Does that mean that sonar isn’t a useful feature? You have claimed that it is, but I can create an environment where it isn’t.Are your eyes useful when you are brought up in the dark?Are your lungs useful 3 hours after falling overboard without a lifejacket?Is the ability to digest nylon useful when you have been transported into a sugarbowl?Are there any useful features? Of course there are, but they aren’t useful in all environments. That they are useful at all qualifies the feature as useful. If they are useful, & never existed before, then they are new useful features.In summary,1/ You either accept that altered algorithms are new, or face the reality that there is no such thing as a new algorithm, even God couldn’t do it after the first one. It’s impossible, it would just be altered.2/ Face the reality that nylon digestion is a useful feature, or accept that your own sonar example isn’t an example of a useful feature.Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 07-15-2002]

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[This message has been edited by mark24, 07-15-2002]

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Originally posted by Fred Williams:
Mark, we are now repeating ourselves which means we are at a dead end. I want serious evidence, not a single change to an algorithm that you claim makes it new. If you get a zit on your face is it a new face, or an altered face? (sorry for the example, I was thinking about the movie Animal House at the moment. )

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A spot on my face isn’t analogous to genetic information, is it? A spot has nothing to do with a coded sequence, can’t you see the difference?new information = the presence of a new algorithm (coding sequence) in the genome that codes for a new useful feature.Tell me Fred, what is a new algorithm re. Genetic information, then? You’ve just defined it in such a way that evolution cannot match. A genetic sequence mutates, meaning it will only ever be altered.So,ATAGGGCCCCAAATMake a new algorithm out of the above, Fred. You can’t, by your very own definition. Doesn’t matter how intelligent you or God are, you cannot make new algorithm out of the above, it will merely be altered. You have attempted to define new in such a way that evolution cannot comply, but in doing so have removed any meaning to the term new algorithm. There can be no new information, at all, ever.

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Originally posted by Fred Williams:

I will also note that you have still failed to give me an example at the genetic level that you would consider a loss of information. Your own view of information by default permits evolution no matter what. Don’t feel bad, it is standard practice of evolutionists to design their arguments to be un-falsifiable.

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I don’t feel bad, Fred, I did exactly as you asked.

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Originally posted by Fred Williams:

You have not made a case showing that nylon digestion is the product of random mutation (the AiG citation shows otherwise - that it is the result of transferred information). Why is it so difficult to cough up with even one solid example? The problem is, there should be a virtually limitless supply if evolution were true.

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The AiG citation shows nothing of the sort. AiG claim that Flavobacterium sp. K172 nylC gene was given to the bacteria on a plasmid, specifically pOAD2. Their quote fails to support this contention. The problem is, Fred, that pOAD2 exists in flavobacterium anyway, so, where did the other pOAD2 plasmid go, there should now be two? ie The one carrying the carbohydrate gene. OMG, ITS MISSING!!! No, it’s still there, the gene just mutated into nylC.Can you produce a scientific paper that says that nylC carrying pOA2 gene is foreign DNA? AiG haven’t cited the relevant part of Kato’s paper, if that’s the case. I, after all, have been able to produce a similar quote that supports my argument.Regardless, a mutation that produces new function is possible, not impossible.If ATAG mutates to GATC, then it isn't a new algorithm. But if GATC appeared out of nowhere, it would be. This is pure semantics. Whether you regard this as a new algorithm is irrelevant anyway. Evolution requires algorithms, that never existed before, that ultimately lead to new traits. They exist.

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Originally posted by Fred Williams:

Mark: In summary,
You either accept that altered algorithms are new, or face the reality that there is no such thing as a new algorithm, even God couldn’t do it after the first one. It’s impossible, it would just be altered.

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Fred:

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Non-sequitur. Sonar programming is so vastly different than say nylon-ingesting that altering one would not lead to the other. They are each products of programming from the ground up. Ooops, that means creation - can’t admit to that!

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Nonsense. Say, God took non-sonar sequence & changed it to a sonar producing sequence, the first that ever existed! God only altered the parent sequence, ergo it’s not a new algorithm, & therefore new information wasn’t required to produce sonar.Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 07-17-2002]

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Originally posted by Fred Williams:
Tell me Fred, what is a new algorithm re. Genetic information, then? You’ve just defined it in such a way that evolution cannot match. A genetic sequence mutates, meaning it will only ever be altered.
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As I have stated several times recently, evolutionists who recognize and try to deal with the information problem attempt to get the information required for NDT to produce new algorithms for new functions via gene duplication, then subsequent modifications to that duplicated gene.

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That doesn’t answer the question. What do YOU think is a new algorithm re. Genetic material.

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Originally posted by Fred Williams:

Mark:
Make a new algorithm out of the above, Fred. You can’t, by your very own definition. Doesn’t matter how intelligent you or God are, you cannot make new algorithm out of the above, it will merely be altered.

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Fred:

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You are putting words in my mouth. I never said an altered program never can become a new program. I said that it is quite unreasonable to view your particular one mutation example (nylon, et al) as a new algorithm. If your boss asked you to report on the enzyme that allows nylon-digesting, which would be more accurate:

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Then I suggest you quantify when an altered algorithm becomes a new algorithm, with citations from info science please.I wasn’t putting words in your mouth, I was making a logical extension.

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Originally posted by Fred Williams:

Mark:
Say, God took non-sonar sequence & changed it to a sonar producing sequence, the first that ever existed! God only altered the parent sequence, ergo it’s not a new algorithm, & therefore new information wasn’t required to produce sonar.

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Fred:

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This is easily refuted. What if the non-sonar parent sequence does not have enough genome space available for the new sonar sequence? Can you take the opcode space available for a simple program like a basic calculator, alter it and produce PowerPoint? Of course not.

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Oh, the genome space increase was a part of the alteration. So God still can alter non-sonar sequence & produce sonar sequence without new information.

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Originally posted by Fred Williams:

Regardless, you continue to miss the primary point. I’ll give it one more try, and this time not even consider the AiG citation that argues it was a transfer of information. In the example you provided, essentially a bit in the program was toggled. In order for it to qualify as an increase in information, we need to know several things.

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A bit wasn’t toggled. IT WAS ADDED!!!!!!

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Originally posted by Fred Williams:

2) Was the mutation random? If so, then from 1) above we can again reasonably conclude that a loss of information occurred. What if the mutation was non-random, that is, environmentally induced? This means there was no net gain or loss of information because the information was already present. I haven’t studied the study you provided in-depth, but from the website you posted my bet is this is a non-random mutation. The author states that it’s been observed more than once. What an un-whitting admission he is making here! Given the odds that this specific mutation would be observable more than once certainly raises eyebrows that this may not be a random event. Another reasonable possibility is that certain portions (hot-spots) of the genome have been pre-programmed for hypermutation during environmental stress to toggle bits in an effort to find a possible combination that improves survival in the degraded environment.

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Hot spots are not pre-programmed. Mutations occur with higher frequency at hot spots regardless of environment.Gene sequence mutation hot spots are nothing new, however, just because there are hot spots doesn’t preclude the rest of the sequence undergoing mutation (as is observed), rendering your argument moot. Furthermore, if you can’t predict where the next mutation is going to occur, then it’s random (in the sense biologists mean it).If you apply a strict statistical definition to random, then all loci must have an equal chance of mutation. This definition doesn’t really restrict evolution, because all sites are subject to potential mutation, it is random in the sense that the next substitution site cannot be predicted. You could say that evolution is non-random mutation culled by natural selection/ drift etc, as long as you’re not going to conflate non-random with pre-programmed. It makes no odds, the biology books would need to be altered, but nothing has physically changed.

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Originally posted by Fred Williams:

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I will also note that you have still failed to give me an example at the genetic level that you would consider a loss of information. Your own view of information by default permits evolution no matter what. Don’t feel bad, it is standard practice of evolutionists to design their arguments to be un-falsifiable.
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I don’t feel bad, Fred, I did exactly as you asked.

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I do not recall you giving me an example that you would consider info loss. Can you or can’t you? I think this is the third time now I’ve asked. The reason I continue to badger you and Percy for this because I think it gets the core of why you version of information is incorrect. The way you have presented your argument throughout this discussion is that any change is new, or increased information.

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You asked for an example of information loss at the genetic level http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=5&t=55&m=5#52/ A chromosome loss, that carried expressed genes.Whole genes being lost, it doesn’t get more genetic than this.

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Originally posted by Fred Williams:

To conclude, your nylon—wearing bacteria example is simply not a valid case of info gain (or new info). If the mutaiton in question is random, then it’s a classic case of information loss. Regardless of how you view Lee Spetner, he is qualified to speak on information science (he taught it for years at John Hopkins). He has a similar example in his book and explains why it is clearly a loss of info. Sorry to be blunt, but I’ve only seen layman reject Spetner’s claim. I have not seen any evolutionists who are involved in info science question this key concept of information. That is why the informed evolutionists try to get info via gene duplication followed by subsequent mutation/selection of the new gene.

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It’s interesting that you can see info loss, but not the gain.1/ Let’s get back to the crux of the argument, does evolution require naturally arising new information in the genome?2/ Does evolution require naturally arising information that never previously existed in the genome?What’s the bloody difference, except for a definitive one? You have tried to say evolution can’t occur because, 1/ can’t occur. If this were actually a physical restraint, you would have a point, but since scenario 2/ CAN be true, evolution is safe from information theory.Mark------------------
Occam's razor is not for shaving with.

Bump.......Fred? Where'd you go?Message 25 please.Mark------------------
Occam's razor is not for shaving with.

dillan, Unfortunately, the ID argument always seems to boil down to the same reasoning - all codes are the result of intelligence, DNA is a code, therefore DNA was intelligently designed. A similar argument is made for complexity. This is a fallacy of composition that renders the argument invalid. It is therefore incumbent on the ID community to be able to test for design in order to sidestep the flaw by providing empirical evidence. As you have pointed out, this is impossible. So what are you left with? An untestable, unfalsifiable, & therefore unknowable fallacy of composition.You can introduce any definition & explanations of information & codes you like, you can introduce as many non-empirically based argumentation you want, you can write books on it if you'd like. But at the end of the day, it will always boil down to the aforementioned logical flaws.All that is required to destroy an argument is to show it is guilty of a logical fallacy, the maker of that argument should then cease to make that argument, right? Why then do ID'ers persist in making the same flaws over & over?Mark------------------
"I can't prove creationism, but they can't prove evolution. It is [also] a religion, so it should not be taught....Christians took over the school board and voted in creationism. That can be done in any school district anywhere, and it ought to be done." Says Kent "consistent" Hovind in "Unmasking the False Religion of Evolution Chapter 6."

Hi all,Would it not be pertinent to define "code"?Mark

Hi Fred, all,Does everyone agree with Fred's definition of code in the above post?Mark------------------
"I can't prove creationism, but they can't prove evolution. It is [also] a religion, so it should not be taught....Christians took over the school board and voted in creationism. That can be done in any school district anywhere, and it ought to be done." Says Kent "consistent" Hovind in "Unmasking the False Religion of Evolution Chapter 6."

Fred, But you can test to see if the rock drops by dropping it. You cannot provide the same test for ID. When I hold pumice under water & let it go, it goes up, not down, so it was lucky I never made the argument you put in my mouth, since it is contradicted by observation! It would in fact be true to say not all rocks "drop" when let go.In other words, the premise in your example is testable, the premise in the ID argument is not, the arguments are qualatitively different, & it is a bad analogy.The point being, in science conclusions are tentative, a theory is only as good as the predictions it makes, so if we do let a rock go & it goes up, not down, we can modify the theory based on empirical evidence. No such testability or falsifiability exists for ID.Mark[This message has been edited by mark24, 09-06-2003]

Fred, But neither are truth statements (depending on definition), I gave you an example of something that rose when it was dropped. And that all codes are the result of ID is an unsupported assertion if you include DNA in the subset "code".Mark------------------
"I can't prove creationism, but they can't prove evolution. It is [also] a religion, so it should not be taught....Christians took over the school board and voted in creationism. That can be done in any school district anywhere, and it ought to be done." Says Kent "consistent" Hovind in "Unmasking the False Religion of Evolution Chapter 6."