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New Genetic Information

Discussion in 'Science' started by UTEOTW, Aug 10, 2005.

  1. UTEOTW

    UTEOTW New Member

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    "While I don't have time to get into this now (just about to leave on vacation)..."

    It will be here when you get back.

    "...I would ask what assumptions have been made here.

    For example, have all the genes been taken into consideration, or just the ones which code for proteins? Since it has been discovered that DNA formerly thought to be junk actually performs functions such as gene activation, this is important.
    "

    I would encourage you to examine the evidence for yourself. If you can find specific mistakes, please point them out. More than likely, we can see where you are going. You will dispute the interpretation of the data. This is where the fun comes in. If you wish to challenge the assumption and the interpretations, then you will need to provide those better YE interpretations that never seem to materialize.

    But there are a number of things which you will need to take into consideration as you formulate your alternative explanations. One of the first things mentioned is how most genes can be categorized into one of a small number of families based on similar sequences. This is an area where two things become important. One is that theoretical studies have shown that there are generally a very large number of potential proteins will be suited for a potential function. Second, while survival of the fittest is the catch phrase, often it is really survival of the barely adequate. Genes that are very similar perform different functions dispite the fact that there is very likely other proteins that could form each function much better. An alternate explanation would need to explain why an intelligently designed organism would use suboptimally designed sequences that are similar to one another rather that properly designing each individual gene for its intended purpose. On a related note, one reference I dug up yesterday but that I did not use (perhaps I'll look it up again later) notes that there are only a very small percentage of the possible protein folding arrangements actually used out of those which are possible. It would seem that an intelligently design organism would use everything available rather than using only a small subset. OTOH, it would be expected based on what we know of evolutionary mechanisms for folding patterns and gene sequences to be highly conserved towards that which has worked before.

    Another aspect you would have to contend with is the evidence for actual duplication. For instance, at least one reference traced a whole series of duplication of the same gene by showing how particular segments in both introns and exons were repeated. In another case, a retroposon was inserted and over tens of millions of years it mutated until it became useful with lineage branches along the way providing means of determining when certain changes to the gene occurred. YOu would need to explain the presence of this particular pattern in the genome.

    As far as your last part, I think that if you read through you will see that both coding and non-coding regions have been used to trace what happened. I'll agree that there have been discoveries in recent years that some parts that were formerly thought of as "junk" have been found to have regulatory purposes if you will acknowledge that much of it really is junk. I have told you several times in the past of methods that can be used to test whether a particular segment actually serves a purpose. Those which are useful will show a diverent pattern of mutation compared to those which are not useful, mainly in the distribution of mutations between the first, second and third positions of each codon. In material that is not useful, the mutations will be equally spread and in those that are useful, the mutations will be much more predominant in the third position. There should also be different rates of muation in selectively conserved sequences and mere junk.

    "Also, the paper noted that some of the genes already contained nitralese genes - how do we know this information isn't ALREADY present?"

    You say "the." Did you read them all? I cannot even find that term when searching my posts on this thread. Could you link to the post that you mean?

    "Next, there is a lot of mention of plasmid DNA rather than nuclear DNA. How do we know these aren't designed to dynamicly adapt under pressure and then disable when the plasmids are de-activated in the abcense of pressure (such as in the case of the nylon eating bacteria)."

    I am not sure what you are reading but I cannot find any mention of plasmid DNA on either page of this thread. Could you link to the post which you are talking about. I can find discusion of specific chromosomes, however.

    But I still do not know why that even matters. DNA that serves a purpose serves a purpose whether it is nuclear or in plasmids. Adaptation is still adaptation. It is confusing why you should try and separate the two. In any case, the evidence for why it is believed that these genes evolved is presented. You are free to present a theory which better explains all aspects of the observations.

    You might also want to explain your nylon bug assertion a bit better. If I remember correctly, it was a frameshift and several point mutations that led to the ability to digest nylon. I am not sure how that fits into whay you are saying.

    Finally, you seem to be willing to accept the idea that plasmid DNA is adaptable, why not the whole genetic code? I personally think, and have posted this in the past, that the arrangement of the three letter codons and the differences that arise from changes to each position seems to indicate that the genetic code itself is optimized to adapt.

    "Seems pretty unsubstantial to me."

    Then you should have no trouble coming up with a better theory. But you did not seem to think the information challenege a few months ago would be very dificult, either, until you actually tried it. You declared victory without ever explaining why any of the examples were not examples of new "information."
     
  2. UTEOTW

    UTEOTW New Member

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    While looking through some of the latest publications, I came across another relevent paper.

    This paper examines the role of duplication and subsequent mutation in the rise of eukaryotes. The entire article, not just an abstract, is online here.

    http://nar.oxfordjournals.org/cgi/content/full/33/14/4626

    Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV, Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell, Nucleic Acids Res. 2005 Aug 16;33(14):4626-38.
     
  3. UTEOTW

    UTEOTW New Member

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    It is amazing how YEers make certain claims but then dissappear when asked to substantiate those claims. I hope to expose a few in this thread. No one really seems to want to take up the challenge. Gup, to his credit, did attempt one post. But he really did not address anything and it does not seem that he even read the thread as he was busy "refuting" things that were not even mentioned.

    I see two main claims being exposed here. The first is the claim that there is no "new information" created through evolution. (With information conveniently never being defined.) This claim can only be made if you ignore the published scientific material. I continue to give examples. And to underscore the point, once a got some examples down, I have just been going to pubmed and searching with a few key words to see what has been published in the very recent past. There are new examples every week. YEers must ignore these ongoing discoveries to make their claims.

    The second claim to be exposed is the one where they claim that YE is a better explanation for the data. When you really dig into the science and start looking at the details, they never have answers. They do have a few stories and vague ideas for some of the most general topics, but you never hear back when you dive into the details of these subjects or when you dive into subjects for which there are no AIG or ICR crib sheets. All I have to do is go straight to the science and I can get an overwheling amount of data. No need for crib sheets, though they can be useful for the common errors or YE. But you will not see a YEer come in here nad offer a better explaination for the data presented no matter how many times they claim to have it.

    And getting back to the action, I have another example where the evolution of genes for making light sensing molecules are traced. The information is interesting and it is also relevant as it shows the role of gene duplications and subsequent mutation in the evolution of these genes.

    Falciatore A, Bowler C, The evolution and function of blue and red light photoreceptors, Curr Top Dev Biol. 2005;68:317-50.

    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16125004&query_hl=2
     
  4. UTEOTW

    UTEOTW New Member

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    I would like to keep hammering home the evidence available to suggest that duplication is an important process in the evolution of organisms providing increased genetic material which can be used to mutate into new genes.

    This paper, to be published tomorrow, shows how analysis of the genomes of several vertebrates shows that there were two distinct duplications of the entire vertebrate genome that aided their evolution. This is similar to the posst above ( http://www.baptistboard.com/ubb/ultimatebb.php/topic/66/104/2.html#000021 ) which demostrates the use of duplication in the rise of eukaryotes.

    Dehal P, Boore JL, Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate, PLoS Biol. 2005 Sep 6;3(10):e314.

    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16128622&query_hl=2
     
  5. UTEOTW

    UTEOTW New Member

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    I will be unable to post for the next few days. I'll be back.

    I thought I would update tghis thread before I go with another of the new papers that just made it to the top of my searches this week. I am hoping that one of the YEers who claim that the data can beeter be explained in their paradigm will come by and tell us why the pattern of a diverse set of genetics looks just like what you would expect if evolution were true and if new genes and metobolic pathways and novel features were largely the result of selection factors on duplication and mutation mechanisms acting upon the genome. I also hope Gup will be back from his vacation soon and pick up where he left off before leaving.

    In any case, here is a study that traces how the family of genes involved in Insulin-Relaxin evolved. It shows how the best explanation is a combination of duplication of parts of the genome and the entire genome, at different points in time, and subsequent mutation of these duplicates.

    Olinski RP, Lundin LG, Hallbook F, Conserved Synteny Between the Ciona Genome and Human Paralogons Identifies Large Duplication Events in the Molecular Evolution of the Insulin-Relaxin Gene Family, Mol Biol Evol. 2005 Aug 31.

    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16135778&query_hl=1
     
  6. UTEOTW

    UTEOTW New Member

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    This abstract provides yet another example of evolution in action.

    Again, the assertion is that most genetic novelty is produced by strings of duplication events and other mutational events. The result is that the genome fits into families or similar sequence but different function. There are even strong indications of how the process takes place in the pattern of repeated introns, division of genes into exons and the location and sequence of pseudogenes.

    So here is another example of finding another gene family that has developed from a gene in a closely related gene family. There is enough detail to trace the phylogenetic relationships between the different genes.

    This, once again, demonstrates that YE assertions about there being no ways to create "new information" are false. There not only are theoretical pathways, but these pathways have been shown operating in the present and the genomes reveal their effects in the past.

    Maier SA, Galellis JR, McDermid HE, Phylogenetic Analysis Reveals a Novel Protein Family Closely Related to Adenosine Deaminase, J Mol Evol. 2005 Oct 20.

    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16245011&query_hl=1
     
  7. UTEOTW

    UTEOTW New Member

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    Silence speaks louder than words.

    The claim has been made that there is no mechanisms for generating novel genetic sequences, or "new information" as it is often called, through evolutionary means. THis thread has shown that such means do exists and that the observations from creation show them to be in used and the the genomes have evidence of them being the method by which the genome was built up. And we still do not have a YE challenge to the actual data.

    One method that we have already discussed for providing new genes is alternative splicing. In this mechanism, exons are combined if various ways to produce new and different genes from the same sequence of DNA. This particular case looks at several different variants that provide various roles by alternative splicing.

    Bayin H, Tamamori-Adachi M, Yang L, Tamura K, Morioka M, Fukuda M, Tanaka Y, Kitajima S., A splice variant of stress response gene ATF3 counteracts NF-kB-dependent anti-apoptosis through inhibiting recruitment of CBP/p300 co-activator, J Biol Chem. 2005 Nov 16.

    http://www.jbc.org/cgi/reprint/M508471200v1

    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16291753&query_hl=1
     
  8. BobRyan

    BobRyan Well-Known Member

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    #1. ALL humans DO share a common ancestor - his name is Noah - and ultimately his name is Adam.

    ALL land animals DO share common ancestors - For clean animals it is the set of Clean animals (by 7's) on the ark and for unclean animals it is the set of unclean animals (by 2's) on the ark.

    Creationists INSIST that all life today can trace itself back to that set of common ancestors for the various "kinds".

    #2. Because we start the lineages with "those base nodes" - Creationism predicts a bushy result with data showing mutation and variation splayed out from each of the ancestral nodes.

    So as we look in the fossile record - Creationism expects us to find "change over time" as mutations splay out from the base nodes.


    #3. Because we start with a trulyl "creative" and "Genius" Creator who presevers many of the land-animal "kinds" in the ark and because sin INTRODUCES extinction, exterminiation, carnage - Creationism expects a larger amount of base nodes, strains at the start with fewer "kinds" surviving in the carnage that follows - down to the present day.

    #4. Because ALL animals are formed from the dust of this earth and because ALL are formed by the same Creator -- Creationism expects to find similarities in the makeup of the "living machinery" God uses to produce each of the pattern archtypes.

    #5. Because The Creator is the one "building" the living systems - Creationism expects to find that those systems are "resilient" and capable of adapting to their environment (with bounds of the kind) and able to self-repair over time.

    #6. Because of the sin principle noted in Romans 8 and 2Cor 5:1-2 - that is breaking down nature iteelf - Creationism expects to find increasing decay and instability in the living biosphere over time.

    In Christ,

    Bob
     
  9. BobRyan

    BobRyan Well-Known Member

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    As with the bogus and debunked evolutionary tales (horse series, piltdown man. Archaeoraptor ) so are all the failed claims of evolutionism following the sme pattern. All these evolutionary-tales have one thing in common. "The Grey fog of new story telling" kept each of them "alive" for a while until "real science" could catch up to the "Story telling" of the psdeudoinece we call "Evolutionism".

    In other words - evolutionism flourishes in the early hours of wild speculation first proposed - only to be choked to death when real science once again exposes the perfidity of the pseudoscience practitioners of evolutionism.

    HENCE the quote - we have "FEWER examples of evolutionary transitions TODAY than we supposedly had in Darwin's day"

    In Christ,

    Bob
     
  10. BobRyan

    BobRyan Well-Known Member

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    Looking for a recent example of the pseudoscience of evolutionism employing “Stories easy enough to make up” that are “not science” when it comes to lizard-to-bird stories? http://www.trueorigin.org/ng_ap01.asp
    In the link above the question is asked
    The pseudoscience authored by the “father of lies” has built into the core of its being “lies and deceit” masked as sincere atheist speculation to service their need for a non-god solution to origins!

    The clear lesson of history is that the myths and fables of evolutionism only survive in the gray fog of uncertainty and speculation where science is not yet able to validate, certify, confirm, test, reproduce, measure facts and separate them from the bogus fiction of that “bad religion” we know as evolutionism.

    But once the data is actually collected and the “full light of day is shining” the result is to erode more and more of the vast territory of speculation staked out by evolutionism’s priesthood.

    David M. Raup, in Field Museum of Natural History Bulletin 50 (1979), p. 29.

    In an article published several years ago in Paleobiology, Stephen Jay Gould of Harvard, and Niles Eldredge of the American Museum of Natural History, wrote concerning Archaeopteryx:
    Notice in the above quote - that what Colin Patterson calls “Stories easy enough to make up – but they are not science” is euphemistically called “thought experiments” by Gould and Eldredge!

    </font>[/QUOTE]
     
  11. UTEOTW

    UTEOTW New Member

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    YOU must "be" very DESPERATE to "obfuscate" the ISSUE here SINCe "none" of your QUOTES has "anything to do" with the "subject" of THE thread.

    THE "subject" is mechanisms used BY evolution TO GENERATE new genes "and" evidence from the GENOMES OF ORGANISMS "that show" these "mechanisms" to have been used BY EVOLUTION.

    I MUST "assume" that you have "no quotes" to provide on EXON SHUFFLING or GENE DUPLICATION and are "instead" trying to "distract" FROM the REAL evidence with "your" our OF context quotes.

    It DOES NOT work.
     
  12. UTEOTW

    UTEOTW New Member

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    Your Patterson quote is completely out of context. Patterson himself said regarding the quote that while it is "is accurate as far as it goes" that "the continuation of the passage shows clearly that your interpretation (at the end of your letter) is correct, and the creationists' is false." That alterante interpreation is that we cannot be 100% sure whether any given fossil is the direct ancestor of any other creature that we know of or whether it is a closely related side branch.

    You might want to examine that Raup quote a little more closely. He is discussing how Darwin expected change to be gradual as we have discovered detailed series, such as the horse, we have found that they are not so gradual and linear but are instead jerky. The horse series was not discarded, it was changed as the details were filled in.

    You have made the same mistake with Gould and Eldredge. They are again pointing out how evolutionary processes are not gradual. They are not saying Archy is not a transitional, they are saying that it fits in better with the idea of jerky evolution as opposed to smooth and gradual.

    Your feather quote is simply too outdated to be useful. We have since discovered featheres in various transitional stages on dinosaurs and have figured out the genetic signaling pathways that lead to feathers.
     
  13. BobRyan

    BobRyan Well-Known Member

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    Shuffling the existing population does not create new genes.

    The population of lab rats never gains the gene for wings. Shuffle all day long please.

    The population of dogs never gain duck bills or grow wings or spin a web or attempt geometry or make a bow and arrow.

    The population of worms never obtain a human eye. Shuffle all day long please.

    "Obviously".

    My point was that in real cases as the quotes show - there is no "Actual" demonstration that one thing changed into another. And THIS was shown USING evolutionist (atheist evolutionist of course) confessions on various "inconvenient facts".

    Facts you "need" to obfuscate, misdirect and gloss over. (As usual).

    In Christ,

    Bob
     
  14. jcrawford

    jcrawford New Member

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    Well, shuffle my genes. With enough genetic engineering I ought to be able to sprout bird feathers on my shoulders and arms and fly with the dino-birds too even though such mythical absurdities may be equated with Greek myths like those of Daedalus and Icarus.
    http://thanasis.com/icarus.htm
     
  15. UTEOTW

    UTEOTW New Member

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    "Shuffling the existing population does not create new genes."

    No it does not.

    But exon shuffling does.

    "The population of lab rats never gains the gene for wings."

    Red herring.

    Why would you expect this?

    "The population of dogs never gain duck bills or grow wings or spin a web or attempt geometry or make a bow and arrow."

    Another red herring.

    Why would you expect this?

    "The population of worms never obtain a human eye."

    Yet another red herring.

    Why would you expect this?

    "Facts you "need" to obfuscate, misdirect and gloss over."

    The information presented on this thread examples of the means evolution uses to create novel genetic material and novel functions. It also shows evidence that the genome as a whole has been built up by such mechanisms.

    That you must propose a string of red herrings instead of dealing with the actual evidence of the thread show who actually is doing the obfuscating.

    "My point was that in real cases as the quotes show - there is no "Actual" demonstration that one thing changed into another. And THIS was shown USING evolutionist (atheist evolutionist of course) confessions on various "inconvenient facts"."

    [YAWN]

    Is this a reference to your dishonest, lying, misrepresenting, mischaracterized and false quotes? Call me when you have quotes whose meaning does not change when put in context.
     
  16. UTEOTW

    UTEOTW New Member

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    "Well, shuffle my genes. With enough genetic engineering I ought to be able to sprout bird feathers on my shoulders and arms and fly with the dino-birds too even though such mythical absurdities may be equated with Greek myths like those of Daedalus and Icarus."

    How many red herrings can we get on one thread?

    Y'all must be real desparate to obfuscate from the OP. It is a good sign that you have nothing factual to say about the issues of the OP.
     
  17. jcrawford

    jcrawford New Member

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    The OP is obfuscating in the first place.

    What do you think we are? Neo-Darwinist race theorists or racial geneticists?
     
  18. BobRyan

    BobRyan Well-Known Member

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    "The population of lab rats never gains the gene for wings."

    That should be your signature line.

    The point remains. NEW genes for new structure is what is "claimed" in the myths of darwinian evolutionism - but never "Seen" to occur nature.

    In fact "after 120 years we have FEWER examples of true transitions than we had to start with". The CLAIMS for the "NEW" Genetic information principle did not pan out with "more discovery" in the fossil record. RATHER even the bogus set that you had to "start with" began to unravel!

    52 cards - shuffle them all day long. You will never get a 53rd card.

    Obviously.

    In Christ,

    Bob
     
  19. BobRyan

    BobRyan Well-Known Member

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