Information and Genetics

This seems to be a major topic, so I thought I'd
pop a thread up on it.If there already is one, apologies and point me to it I've seen a lot of claims that information theory can be used to refute ToE, and would like to know why.I'm not going to belabour the issue of defining information ...
well not to start with ... but want to question the principle
of applying information theory to genetics.Is there any information content in an organism's genetics ?We use the analogy of a genetic code, but is it actually
a code ?

I considered opening a similar thread and probably should have. I suggest the information theory discussion on the "Give your one best shot - against evolution" thread be moved here. I'll post a note over there.--Percy

I have not delved very deeply into this subject but in communicating with HM Morris he made it certain enough that any discussion of creation and biology or biology and creation that mathematics is seperate, should be seperated and must be from any biology that may appear, to be discussed.In thinking about what he wrote back to me... (title) of Lammert's Journal of Theoretical Biology paper on the seeming inability for translation and transcription to account for the diveristy of information that will be able to cross generations very nearly must too, be a part of this thread. I will work on this as well. My list of to-do-threads seems to be outpacing )my( time devoted to the illusory aspects of this sociological documnetation.

These are replies to Message 220 and Message 221 from SLPx over at the Give your one best shot - against evolution thread.About the Kimura paper, sure, send me a copy if you want: percipient@. But all I'm really seeking is an explanation for how natural selection could create new information. As I said originally, my only guess is that it might involve equating new genetic information with recombining existing alleles permutationally, but it would nice to know what Kimura was actually thinking.About Tom Schneider's assessment of Fred's website, is there a link?--Percy

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]

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. )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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Recall that you are claiming that new information in genetic systems is impossible.

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To be specific, my claim is that new information cannot arise naturalistically, ie without a Sender (intelligence).

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Mark: 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.

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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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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.

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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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[This message has been edited by Fred Williams, 07-16-2002]

Percy, we too are at a dead end. If you insist that a computer is not an intelligent device, or represents intelligence, then what is the point in debating further? Like Mark, you have concocted a version of information that is not falsifiable.Finally, your simulation is fatally flawed. I’ll count the ways:1) GAs cannot generate new information unless intelligence is there to prune it. I have even produced evolutionists who are on the record that GAs are bogus examples of evolution, you only have your opinion to support your claim.
2) Your simulation does not reflect reality. It employs severe truncation selection, yet there is no evidence such selection occurs in nature, and most evolutionists reject such a wild notion.In closing, from Merriam-Webster's Collegiate Dictionary:Main Entry: intelligence
Pronunciation: in-'te-l&-j&n(t)s
Function: noun
Etymology: Middle English, from Middle French, from Latin intelligentia, from intelligent-, intelligens intelligent
Date: 14th century
1 a (1) : the ability to learn or understand or to deal with new or trying situations : REASON; also : the skilled use of reason (2) : the ability to apply knowledge to manipulate one's environment or to think abstractly as measured by objective criteria (as tests) b Christian Science : the basic eternal quality of divine Mind c : mental acuteness : SHREWDNESS
2 a : an intelligent entity; especially : ANGEL b : intelligent minds or mind
3 : the act of understanding : COMPREHENSION
4 a : INFORMATION, NEWS b : information concerning an enemy or possible enemy or an area; also : an agency engaged in obtaining such information
5 : the ability to perform computer functions

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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]

Deleted.Edited by Lewissian, : Outdated.

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Originally posted by Fred Williams:
If you insist that a computer is not an intelligent device, or represents intelligence, then what is the point in debating further? Like Mark, you have concocted a version of information that is not falsifiable.

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Pedantic bit:: A computer is not an intelligent device, it is a
deterministic, electronic 'machine'. Check the definition of
intelligence that you provide if you don't believe me.You assert that a change to an existing 'algorithm' isn't
new information (in the sense that you define info.).What if successive small changes to an algorithm ultimately
produce an algorithm that's function is radically
different from the start-point ? Is that still not new information ?To attempt an analogy using words::If we start with 'cat' and modify one letter to make 'bat'
is the information conveyed by the second word (to an english
speaking individual) new or not ?It's just a modification, but once 'interpreted' to provide
information within the recipient isn't it new information ?

Hi Chase,Now that you are back, maybe you will follow up in this thread: http://www.evcforum.net/cgi-bin/dm.cgi?action=page&f=5&t=3&p=4

It would be quite interesting if we could come to some common understanding of how or if (meaning if how was not...)"natural selection" created new information that we become eventually informed about.I was quite puzzled to see that ICR had permitted some work in (title) with the word "orthogenesis" in it for if there is any possibility of NS getting society some NEW information then it seems most likely to be resovled once and for good the Fisher/Wright so-felt 'tension' where Wright makes refrence to this genesis which Croizat was specific enough to differntiate orthoselection from orthogeneis but not only would natural selection in wild populations first be shown but all these examples could then never contradict the state this new information would be in once it was "extracted".Einstein said that the scientist must first committ the crime before it can be solved. I am not uncertain that nano-ecology may not be this criminality that would obviously set a precendent if true.

"For 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."
--Also in my two replies toward Fred's analysis demonstrates how this is asking what is unlikely to be given. It is however important to note, that the example of nylon digestibility basically does create conflict with assertions on the non-existence of the appearance of a genuinely new algorithm.--There is a point which apparently is biasedly dismissed with an essential lack of discussion or dispute from apparent contradiction with initial beliefs. Creationists must stop scrambling for what they wish were veracious rather than what is. Something which I have realized and I should hope that this realization is swept through the creationist bubble that we need to quite being anti-evolutionary and start being pro-YECist. There is an increasingly vast lack of knowledge and experimentation working within the alternative framework which needs to start being looked over. Rather far too many are piling up on every Science article or quote which displays any suspicion for correction or dispute against an Evolutionary theoretical situation[Not that thats necessarely bad, it's just that most people get carried away on this one]. Believe me, there is more than plenty to be worked on.-WB Chase & Cheers------------------

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

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

Fred writes:

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Percy, we too are at a dead end. If you insist that a computer is not an intelligent device, or represents intelligence, then what is the point in debating further?

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Whether a computer is intelligent or not is a side issue, but there's no point playing musical definitions. Obviously I was using definition 1.You claim that information can only be sent and received by intelligence, but even by your definition 5 it takes no intelligence to send or receive information. The starlight we see is full of information, but it was not sent by intelligence. And you can attach a message to an arrow and shoot it across a battlefield, but the tree it strikes is not intelligent.

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Like Mark, you have concocted a version of information that is not falsifiable.

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If we refer to the Shannon paper you're so fond of referencing, right on page one he says:

Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem.

In other words, the interpretations that intelligence builds around the bits flitting through cyberspace are irrelevant to information theory. And if you look at Figure 1 you'll see that he defines a communication system with an information source, a transmitter, a source of noise, a receiver and a destination. There is no intelligent sender or receiver, and the word intelligence does not appear anywhere in the paper.

Fred writes:

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I have even produced evolutionists who are on the record that GAs are bogus examples of evolution, you only have your opinion to support your claim.

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But this is the fallacy of argument from authority, plus I lead a sheltered life and have never heard of your evolutionists and so have no idea what they have said. Can you reproduce the relevant arguments here?

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Your simulation does not reflect reality. It employs severe truncation selection, yet there is no evidence such selection occurs in nature, and most evolutionists reject such a wild notion.

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My model reflects reality, it's only a matter of degree. The selection criteria can be modified to be whatever you desire, Fred. The model was only intended to falsify your claim that random mutation cannot produce new information, which it does.Let's take a different example, say of a physics equation developed by randomly placing letters into a template, say, a=bc², with the selection criteria being detailed studies of the equation's correspondence with reality. Is it possible that E=mc² could pop out? Of course it is. In fact, given time (mainly for applying the selection criteria, since a computer could arrive at E=mc² in an eyeblink), it's inevitable. Randomness can generate information, and with the right selection criteria it will be appropriate to the task at hand.This is precisely what happens with evolution. The total environment places selection pressures upon organisms. Those that survive to reproduce on average possessed some advantage, and the genes reflecting this advantage are passed on to offspring with modification, both from simple permutational recombination of the haploid egg and sperm chromosomes and from mutation. The offspring are in effect a set of experiments to see which will survive to repeat the process. Mutations that confer an advantage will be selected for. This process is consistent with information theory.--Percy

Deleted.Edited by Lewissian, : Outdated.