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Demon38

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The poster Gup20 continually claims that mutation can not add new information and this proves that evolution can not occur.  Now, he never really defines 'new information', so I guess he's leaving himself a lot of wiggle room.  And he never presents any real evidence to back up his spurious claims.
But I haven't seen my example of nylon eating bacteria discussed.  This strain of bacteria underwent a frame shift mutation that allows it to metabolize nylon in addition to it's normal food.  Since it can now eat nylon IN ADDITION to it's previous diet, this would have to be an example of adding new information to the bacteria.  Since nylon wasn't invented until the 1940's, this ability couldn't have been in the bacteria's genetic makeup before this.  And we know when the bacteria could not have eaten nylon before this mutation, we know when the mutation occurred and where on it's genetic structure it occurred.
I've tried to research Gup20's claim but only creationist sites say that mutations can not add new information.  Whenever I look at any scientific site, where they actually work with genetics, we get a different story.  From here:Mutation

"Mutations are classified as beneficial, harmful or neutral. Harmful mutations will be lost if they reduce the fitness of the individual. If fitness is improved by a mutation, then frequencies of that allele will increase from generation to generation. The mutation could be a change in one allele to resemble one currently in the population, for example from a dominant to a recessive allele. Alternatively, the mutation could generate an entirely new allele."

Wouldn't the generation of an entirely new allele be increasing information?  

Here's another example, from here:MutationII

"In order to make room for new information, there have to be types of mutation which make a genome larger. It turns out that several kinds of mutation do this, notably duplication and polyploidy. "

OK, so the mechanisms do exist for some mutations to increase the size of the genome, they are observed.  

"Gene duplication is a fairly common mutation. Having an extra copy doesn't "cost" much, so a creature with such a mutation isn't at any great disadvantage. Extra copies are actually fairly common in the genetic material of "higher" creatures. And of course a mutation that changes an extra copy is not the same problem as a mutation that changes an only copy."

So where is the barrier that prevents mutation from adding new information?  Gene duplication adds a new duplicate gene and if this new gene mutates, it is new information, the old gene carries out it's original function and the new gene can mutate into something new.

Also from the same site:

"If a bacteria becomes penicillin-resistant, it really does contain new information. We know this because researchers have now got to the point where they have read out (sequenced) every last bit of the DNA in some bacteria. This means that it's possible to do before-and-after measurements."

Aha!  So we have actually seen new information added!  I think this totally demolishes Gup20's claim that mutation can not add new information.




 


Posts: 1664 | Posted: 01:33 AM on April 7, 2004 | IP
Gup20

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Your assertion that adding alleles adds genetic information to a genome is in error.  In fact, you can add as manny alleles as you want through mutation and recombination, and all you get is duplication and corruption of the same information.  No new information is added.

Genetics and evolution have been enemies from the beginning of both concepts. Gregor Mendel, the father of genetics, and Charles Darwin, the father of modern evolution, were contemporaries. At the same time that Darwin was claiming that creatures could change into other creatures, Mendel was showing that even individual characteristics remain constant. While Darwin’s ideas were based on erroneous and untested ideas about inheritance, Mendel’s conclusions were based on careful experimentation. Only by ignoring the total implications of modern genetics has it been possible to maintain the fiction of evolution.

Now, he never really defines 'new information', so I guess he's leaving himself a lot of wiggle room.

Adding of genetic information would be - any trait or genetic coding not already found in the genome.  For example - extra friut fly body parts on a friut fly shows an increase in genetic information, but does NOT show any additional genetic information.  It is simply a higher frequency of the genes the fruit fly aready has.  Additional genetic information would be required for the fruit fly to change into a bird, however, or grow bird body parts.

Mendel's work shows clearly (and it is substanciated in lab after lab today) that naturally it is impossible to add genetic information to a genome.  This, in essence, makes evolution a literal impossibility.  

More to come -


 


Posts: 233 | Posted: 03:55 AM on April 7, 2004 | IP
Gup20

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Environment
This refers to all of the external factors which influence a creature during its lifetime. For example, one person may have darker skin than another simply because she is exposed to more sunshine. Or another may have larger muscles because he exercises more. Such environmentally-caused variations generally have no importance to the history of life, because they cease to exist when their owners die; they are not passed on. In the middle 1800s, some scientists believed that variations caused by the environment could be inherited. Charles Darwin accepted this fallacy, and it no doubt made it easier for him to believe that one creature could change into another. He thus explained the origin of the giraffe’s long neck in part through ‘the inherited effects of the increased use of parts’. In seasons of limited food supply, Darwin reasoned, giraffes would stretch their necks for the high leaves, supposedly resulting in longer necks being passed on to their offspring.

Recombination
This involves shuffling the genes and is the reason that children resemble their parents very closely but are not exactly like either one. The discovery of the principles of recombination was Gregor Mendel’s great contribution to the science of genetics. Mendel showed that while traits might be hidden for a generation they were not usually lost, and when new traits appeared it was because their genetic factors had been there all along. Recombination makes it possible for there to be limited variation within the created kinds. But it is limited because virtually all of the variations are produced by a reshuffling of the genes that are already there.

For example, from 1800, plant breeders sought to increase the sugar content of the sugar beet. And they were very successful. Over some 75 years of selective breeding it was possible to increase the sugar content from 6% to 17%. But there the improvement stopped, and further selection did not increase the sugar content. Why? Because all of the genes for sugar production had been gathered into a single variety and no further increase was possible.

Among the creatures Darwin observed on the Galápagos islands were a group of land birds, the finches. In this single group, we can see wide variation in appearance and in life-style. Darwin provided what I believe to be an essentially correct interpretation of how the finches came to be the way they are. A few individuals were probably blown to the islands from the South American mainland, and today’s finches are descendants of those pioneers. However, while Darwin saw the finches as an example of evolution, we can now recognize them merely as the result of recombination within a single created kind. The pioneer finches brought with them enough genetic variability to be sorted out into the varieties we see today.

Mutation
Now to consider the third source of variation, mutation. Mutations are mistakes in the genetic copying process. Each living cell has intricate molecular machinery designed for accurately copying DNA, the genetic molecule. But as in other copying processes mistakes do occur, although not very often. Once in every 10,000–100,000 copies, a gene will contain a mistake. The cell has machinery for correcting these mistakes, but some mutations still slip through. What kinds of changes are produced by mutations? Some have no effect at all, or produce so small a change that they have no appreciable effect on the creature. But many mutations have a significant effect on their owners.

Based on the creation model, what kind of effect would we expect from random mutations, from genetic mistakes? We would expect virtually all of those which make a difference to be harmful, to make the creatures that possess them less successful than before. And this prediction is borne out most convincingly. Some examples help to illustrate this.

Geneticists began breeding the fruit fly, Drosophila melanogaster, soon after the turn of the century, and since 1910 when the first mutation was reported, some 3,000 mutations have been identified. All of the mutations are harmful or harmless; none of them produce a more successful fruit fly—exactly as predicted by the creation model.

Is there, then, no such thing as a beneficial mutation? Yes, there is. A beneficial mutation is simply one that makes it possible for its possessors to contribute more offspring to future generations than do those creatures that lack the mutation.

Darwin called attention to wingless beetles on the island of Madeira. For a beetle living on a windy island, wings can be a definite disadvantage, because creatures in flight are more likely to be blown into the sea. Mutations producing the loss of flight could be helpful.

The sightless cave fish would be similar. Eyes are quite vulnerable to injury, and a creature that lives in pitch dark would benefit from mutations that would replace the eye with scar-like tissue, reducing that vulnerability. In the world of light, having no eyes would be a terrible handicap, but is no disadvantage in a dark cave. While these mutations produce a drastic and beneficial change, it is important to notice that they always involve loss of information and never gain. One never observes the reverse occurring, namely wings or eyes being produced on creatures which never had the information to produce them.

Natural selection is the obvious fact that some varieties of creatures are going to be more successful than others, and so they will contribute more offspring to future generations. A favourite example of natural section is the peppered moth of England, Biston betularia. As far as anyone knows, this moth has always existed in two basic varieties, speckled and solid black. In pre-industrial England, many of the tree trunks were light in colour. This provided a camouflage for the speckled variety, and the birds tended to prey more heavily on the black variety. Moth collections showed many more speckled than black ones. When the Industrial Age came to England, pollution darkened the tree trunks, so the black variety was hidden, and the speckled variety was conspicuous. Soon there were many more black moths than speckled .

As populations encounter changing environments, such as that described above or as the result of migration into a new area, natural selection favours the combinations of traits which will make the creature more successful in its new environment. This might be considered as the positive role of natural selection. The negative role of natural selection is seen in eliminating or minimizing harmful mutations when they occur.

Creation
The first three sources of variation are woefully inadequate to account for the diversity of life we see on earth today. An essential feature of the creation model is the placement of considerable genetic variety in each created kind at the beginning. Only thus can we explain the possible origin of horses, donkeys, and zebras from the same kind; of lions, tigers, and leopards from the same kind; of some 118 varieties of the domestic dog, as well as jackals, wolves and coyotes from the same kind. As each kind obeyed the Creator’s command to be fruitful and multiply, the chance processes of recombination and the more purposeful process of natural selection caused each kind to subdivide into the vast array we now see.

 


Posts: 233 | Posted: 04:03 AM on April 7, 2004 | IP
Demon38

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Your assertion that adding alleles adds genetic information to a genome is in error.  In fact, you can add as manny alleles as you want through mutation and recombination, and all you get is duplication and corruption of the same information.  No new information is added.

Once again, untrue!  Why don't you comment on the nylon eating bacteria, this is an obvious case of new information being added.  So no, it's not just duplication and corruption.  You asked for an example of an increase in information and I provided on for you, you can't refute it, so your point is disproven.

Genetics and evolution have been enemies from the beginning of both concepts. Gregor Mendel, the father of genetics, and Charles Darwin, the father of modern evolution, were contemporaries. At the same time that Darwin was claiming that creatures could change into other creatures, Mendel was showing that even individual characteristics remain constant. While Darwin’s ideas were based on erroneous and untested ideas about inheritance, Mendel’s conclusions were based on careful experimentation. Only by ignoring the total implications of modern genetics has it been possible to maintain the fiction of evolution.

Again, you make unsubstantiated claims with absolutely no proff to back them up.  You can repeat these lies as often as you like but that won't make them true.  Mendels experiments showed how heredity worked, he filled in a gap
in Darwin's theory.  How does this contradict evolution????  From here:mendel

"The patient monk carefully bred and cross-bred pea plants to see how a few specific traits -- height was one -- were passed down. When Mendel bred a tall plant to a short one, all of the offspring were always tall, never blending to medium size. When he then bred those offspring together, three out of four of their offspring were tall, but one was short.
Mendel knew exactly what this meant. Height was passed down in a particle we now call a gene (though Mendel never used that term himself). A plant was short or tall depending on the random combination of genes it inherited.
So an adaptive mutation could spread slowly through a species and never be blended out. Darwin's theory of natural selection, building on small mutations, could work."

Mendel's work was further evidence that supported the theory of evolution,  every geneticist in the world agrees on it!  You still haven't explained how it disproves it!

Adding of genetic information would be - any trait or genetic coding not already found in the genome.

And the ability to consume nylon is an example of adding genetic information, gaining a resistance to penecilian is adding genetic information.  This has been observed, it is no longer in question, mutations can and do add information!

Mendel's work shows clearly (and it is substanciated in lab after lab today) that naturally it is impossible to add genetic information to a genome.  This, in essence, makes evolution a literal impossibility.

As amply demonstrated above, you are, again, totally wrong.
 


Posts: 1664 | Posted: 04:36 AM on April 7, 2004 | IP
Gup20

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Quote from Demon38 at 04:36 AM on April 7, 2004 :

Once again, untrue!  Why don't you comment on the nylon eating bacteria, this is an obvious case of new information being added.  So no, it's not just duplication and corruption.  You asked for an example of an increase in information and I provided on for you, you can't refute it, so your point is disproven.


You are a little out of date about this "new nylon digesting ability" allegedly from a frame shift. New evidence shows that the ability was due to plasmids [e.g. K. Kato, et al., ‘A plasmid encoding enzymes for nylon oligomer degradation: Nucleotide sequence analysis of pOAD2’, Microbiology (Reading) 141(10):2585–2590, 1995.] In fact, more than one species of bacteria have the ability, residing on plasmids. This suggests that the information already existed, and was just passed between different types of bacteria.

All that would be needed to enable an enzyme to digest nylon is a mutation causing loss of specificity in a proteolytic (protein-degrading) enzyme. This may seem surprising—how would a loss of information create a new ability? Answer: enzymes are usually tuned very precisely to only one type of molecule (the substrate). Loss of information would reduce the effectiveness of its primary function, but would enable it to degrade other substrates, too. Since both nylon and proteins are broken down by breaking amide linkages, a change in a proteolytic enzyme could also allow it to work on nylon. If this process were continued, the result would be a general enzyme with a weakly catalytic effect on the hydrolysis of too many chemicals to be useful where much selectivity is required. To put it into perspective, acids and alkalis also catalyze many hydrolysis reactions, but they also lack specificity. Indeed, an inhibitor of a protein degrading enzyme also inhibits the action of the nylon degrading enzyme.

The principle is explained (for a different example) in the book Not By Chance by Israeli biophysicist Dr Lee Spetner. Yet another example of a ‘defect’ being an advantage, but totally irrelevant to evolution.

Mendel's work was further evidence that supported the theory of evolution,  every geneticist in the world agrees on it!  You still haven't explained how it disproves it!

Only if you choose to ignore the basic principles of Mendel's work, specifically that he showed that genetic information cannot be added.  Once an evolutionist does that... then he can easily incorporate Mendel's work into evolution as "complimentary" to Darwin's theories.  Again, it is the inherent disregard for  "all the facts" that has allowed evolution to come as far as it has today.  They had Mendel's work long ago... they knew that you couldn't naturally add information to DNA long ago (showing the true impossibility of evolution)... but it was the only humanistic theory they could fool people into considering.

And the ability to consume nylon is an example of adding genetic information, gaining a resistance to penecilian is adding genetic information.  This has been observed, it is no longer in question, mutations can and do add information!  

According to Mendel, and any Geneticist worth their salt, this trait was already resident in the DNA of the bacteria.  In this case, it was actually a loss of genetic information resulting in "confused" bacteria.  As stated many times, not all losses are bad, but to call it a gain in genetic information simply because the change resulted in a positive or beneficial  circumstance is foolish.
 


Posts: 233 | Posted: 05:07 AM on April 7, 2004 | IP
Demon38

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Such environmentally-caused variations generally have no importance to the history of life, because they cease to exist when their owners die; they are not passed on. In the middle 1800s, some scientists believed that variations caused by the environment could be inherited. Charles Darwin accepted this fallacy, and it no doubt made it easier for him to believe that one creature could change into another. He thus explained the origin of the giraffe’s long neck in part through ‘the inherited effects of the increased use of parts’. In seasons of limited food supply, Darwin reasoned, giraffes would stretch their necks for the high leaves, supposedly resulting in longer necks being passed on to their offspring.

Wrong again!  This is not what Darwin proposed, this is Lamarckism.  Larmarkism was pretty much washed up by the 1930's, thanks to the study of genetics.  And Darwin himself did not support this theory.  From here:Lamarckism

"Postulated in Philosophie Zoologique at the beginning of the nineteenth century fifty years before Darwin, Lamarckism is the premise of heritable characteristics acquired by the organism in response to the environment - characteristics which are then transmitted to descendants. Lamarck proposed for instance, that the giraffe's neck evolved as a matter of internally-directed adaptation in order to reach the higher leaves. Darwinism says it was a matter of chance mutation which was selected for. "

So Darwin didn't say this, Lamarck did and he was wrong!  Kind of like you are for equating Darwinism with Lamarckism!

Mendel showed that while traits might be hidden for a generation they were not usually lost, and when new traits appeared it was because their genetic factors had been there all along. Recombination makes it possible for there to be limited variation within the created kinds. But it is limited because virtually all of the variations are produced by a reshuffling of the genes that are already there.

Yeah, maybe so, but evolution doesn't depend solely on recombination, so why are you even bringing this up?

However, while Darwin saw the finches as an example of evolution, we can now recognize them merely as the result of recombination within a single created kind. The pioneer finches brought with them enough genetic variability to be sorted out into the varieties we see today.

No this is not how biologists view the Galapagos finches, they are, indeed, examples of evolution.  The original finches did NOT have enough genetic variablity to account for the varieties we see today!  These species are genetically distinct.  From here:finches

"Geographically isolated and without competition from similar species, these finches developed distinctive anatomy (particularly beak size and shape) and behaviors, with each species exploiting a unique feeding niche. The bill is adapted in the different species for different purposes, such as crushing seeds, pecking wood, and probing flowers for nectar. The woodpecker finch, Cactospiza pallida, an insect-eater, holds twigs and cactus spines in its beak to fish out larvae in tree cavities. Darwin proposed that the Galapagos finches evolved on the islands from a single species of finch from mainland South America. Modern methods of DNA (genetic) analysis have confirmed his insight."

So, again, you are wrong...

As populations encounter changing environments, such as that described above or as the result of migration into a new area, natural selection favours the combinations of traits which will make the creature more successful in its new environment. This might be considered as the positive role of natural selection. The negative role of natural selection is seen in eliminating or minimizing harmful mutations when they occur.

Yet you ignore the fact that mutations can add novel new structures to organisms.  I all ready disproved your claim that no mutation can add information, so what's the problem?  From here: mutations

"While some creationists will grudgingly admit that a few mutations can produce beneficial effects, they will almost always fall back on their position that even apparently beneficial mutations lose, not gain, genetic information, thus making large-scale evolution over time impossible. However, modern genetics has again soundly rebutted this point by providing numerous examples of mutations that are both beneficial and increase the information of the genome. The most common class of these are duplication and divergence mutations, in which one gene is duplicated and the copy is then free to undergo mutations that cause it to take on a new function while the original function is preserved. Such mutations have been observed producing resistance in bacteria to antibiotics such as vancomycin; there is also evidence that they are responsible for the development of the vertebrate blood clotting cascade and the antifreeze proteins in the blood of polar fish.
This is evidence for evolution because: As mentioned previously, mutations are a key mechanism of evolution, the method of producing new inheritable traits. The fact that mutations that are both beneficial and increase information have been observed means that, in principle, evolution has the ability to produce great diversity and adaptation over time."

OK, once again, it's a FACT, mutations can and do increase genetic information!

The first three sources of variation are woefully inadequate to account for the diversity of life we see on earth today.

This statement has been shown repeatedly to be untrue.  The theory of evolution accounts for all the variation seen in life on this planet, and it's the only UNFALSIFIED explaination for it, the only scientific explainatin for it.

Only thus can we explain the possible origin of horses, donkeys, and zebras from the same kind; of lions, tigers, and leopards from the same kind; of some 118 varieties of the domestic dog, as well as jackals, wolves and coyotes from the same kind. As each kind obeyed the Creator’s command to be fruitful and multiply, the chance processes of recombination and the more purposeful process of natural selection caused each kind to subdivide into the vast array we now     see.

Since crocodilians are more closely related to birds both physiologically and genetically than they are to other reptiles, are alligators of the 'bird' kind, the 'reptile 'kind or are they their own kind?  But you never gave us a scientific definition for KIND!  And until you do, until all biologists know precisely what you mean by kind, it has no place in a discussion about the TOE!

So far, you've confused Darwinism with Lamarckism, shown that you don't understand evolution, show that you don't understand genetics and mutations, and you refuse to discuss the specific examples I've brought up that counter all your points.  Let's face it, your track record so far sucks!
 


Posts: 1664 | Posted: 05:31 AM on April 7, 2004 | IP
Gup20

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The most common class of these are duplication and divergence mutations, in which one gene is duplicated and the copy is then free to undergo mutations that cause it to take on a new function while the original function is preserved.

So your argument that new information is added is that the current information was duplicated, then the same DNA it already had lost information, a different trait was expressed, therefore the organism has gained genetic information.  

Truely remarkable.  Let me simply that for you with the following analogy - You have a book.  You copy every chapter in the book and add it to the book.  You still have no new information, you just have twice the ammount of same information.  Then you go through remove one of the chapters in the duplicated section of the book.  The result is a thicker book, more capable of being a paper weight, but in fact, no new information has been added.  Volume has been added, certainly, but you get no new information.

Yeah, maybe so, but evolution doesn't depend solely on recombination, so why are you even bringing this up?

Remember those finches?  They already had all the DNA and genetic information when they got there... they made speciated changes caused by isolated breeding and natural selection (in the sense that those born with traits that were most beneficial to the environment survived longer, bred more and became the majority).  

Lets take a clear cut example - Lets say a black person and a white person have a mellatto (spelling?) baby.  That mellato baby grows up and marries another mellato person.  These people then get stranded on an island with very hot sun and few shady areas.  Their offspring would consist of people ranging from white to black as they carry in them the DNA coding for such.  But the more coloration in the skin, the better you deal with sun.. so the darker offspring thrive while the paler offspring have more trouble... with being in the sun... with skin cancers because of burn etc.  After a while, you have a large majority of black people, and few or no white people.  After several generations of this, surprise surprise you can pretty much count on the fact that your baby is going to be born black.  After a while, the peopel there dont' even have the genes for white skin.  Why?  Because natual selection has weeded out those with genes for white skin.

Pretty much the same thing happend with the finches in Gallapagos.

With Dogs - take a mutt that has a trace of an ancestry in him... by selective breeding you can isolate a burbred line usually within 7 generations - why?  The genes are there... you just have to isolate them.  You cannot, however, take a couple pure-bred golden retrievers and expect it to have a cocker-spaniel offspring.  No matter how much the DNA mutates you just gonna keep getting the pure-bread offspring.  No matter how many millions of years it takes for the random mutations to come about... it just isn't going to happen.  That's just common sense.

Yet Evolution depends on this supposition.

So far, you've confused Darwinism with Lamarckism, shown that you don't understand evolution, show that you don't understand genetics and mutations, and you refuse to discuss the specific examples I've brought up that counter all your points.  Let's face it, your track record so far sucks!

I should have researched the Lamarckism/ Darwinism connection more closely.  It would seem from initial investigation that you are right about that distinction.  However, my discussions on mutations and genetics has been dead on, and irrefutable.  So far, your own attepts to refute this data has fallen short.  I have indeed responded to your specific examples (such as the nylon eating bacteria), so can we say that your words, while grandstandingly (hey that's not a word is it?) false, provided at least some entertainment to the evolution mob, eh?

 


Posts: 233 | Posted: 06:30 AM on April 7, 2004 | IP
Demon38

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So your argument that new information is added is that the current information was duplicated, then the same DNA it already had lost information, a different trait was expressed, therefore the organism has gained genetic information.

No, you don't understand!  The current information was duplicated, the new information mutates into something new, you now have the original information and the new information on the formally dupl.icate gene, what's so hard about that?  And as I've said this is an observed phenomenon, it is a fact.

Remember those finches?  They already had all the DNA and genetic information when they got there

No they didn't, their DNA changed, it became different, so they did not have all the DNA information when they got there!

However, my discussions on mutations and genetics has been dead on, and irrefutable.  So far, your own attepts to refute this data has fallen short.  I have indeed responded to your specific examples (such as the nylon eating bacteria),

Where did you explain the nylon eating bacteria???  I didn't see it!  And I showed you where geneticists have disected genomes and shown where new information has been added, where did you refute this??  As I've said time and again, increasing information has been observed!  You have not refuted this!
 


Posts: 1664 | Posted: 06:44 AM on April 7, 2004 | IP
Demon38

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You are a little out of date about this "new nylon digesting ability" allegedly from a frame shift. New evidence shows that the ability was due to plasmids [e.g. K. Kato, et al., ‘A plasmid encoding enzymes for nylon oligomer degradation: Nucleotide sequence analysis of pOAD2’, Microbiology (Reading) 141(10):2585–2590, 1995.] In fact, more than one species of bacteria have the ability, residing on plasmids. This suggests that the information already existed, and was just passed between different types of bacteria.

Sorry, you're the one oput of date, from here:Plasmid

"Sorry, AiG, but just because something is on a plasmid doesn't mean it's always been there! In fact, the plasmid involved in this case is very well known and characterized. Scientists have studied both the original (pre-mutation) plasmid and the novel (post-mutation) plasmid, in great detail. It turns out that the novel plasmid's mutated DNA for production of nylonase is almost identical to a non-coding repetitive DNA sequence on the original plasmid; the difference is the single nucleotide that triggered the Frame Shift. This mutation did not exist 60 years ago. If this gene was always there, whether in a plasmid or not, we can reasonably wonder why a bacteria would have a gene for hydrolysing an artificial polymer that did not exist until just a few decades ago; and why, in the absence of such a substrate, was the gene not mutated to uselessness over the millenia?

Was the plasmid slipped in from another bacterium?  NO!! The plasmid in question, pOAD2, is just one of three plasmids that are harbored by the bacterium under investigation here, Flavobacterium Sp. K172. Here are some citations to back this up:

"Sequence analysis of a cryptic plasmid from Flavobacterium sp. KP1, a psychrophilic bacterium," Makoto Ashiuchi, Mia Md. Zakaria, Yuriko Sakaguchi, Toshiharu Yagi, FEMS (Federation of European Microbiological Societies) Microbiology Letters 170 (1999), 243-249.

"Bacteria of genus Flavobacterium, Gram-negative bacteria, are widely distributed in soil and fresh marine waters. Some of them harbor plasmid(s) involved in metabolism of synthetic organic compounds. Flavobacterium sp. K172 harbors plasmids, pOAD1, pOAD2 and pOAD3; pOAD2 (43.6 kbp) encodes nylon oligomer degradation genes."
"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.

"The EI-encoding gene (F-nylA) and EII-encoding gene (F-nylB) of Flavobacterium sp. K172 are located on plasmid pOAD2 (44 kb), one of the three plasmids harbored in strain K172."
"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.

"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."
It's interesting to note that the precise plasmid of Flavobacterium sp. K172, namely pOAD2, was cited by Susumu Ohno fully eleven years before the publication of the "new evidence" that AiG claims " shows that the ability was due to plasmids..."

The Bottom Line: Just because this mutation wasn't confined to a cell's main chromosomes does not mean it didn't happen. (A plasmid is defined as a replicon - a replicating piece of DNA - that is inherited in an extrachromosomal state.) This case still provides an excellent example of a New Protein that evolved without the assistance of an Intelligent Designer"

so no, you haven't refuted the point, the mutation of the ability to eat nylon IS an increase in information, whether it evolved in a plasmid or not, your wrong again...

Only if you choose to ignore the basic principles of Mendel's work, specifically that he showed that genetic information cannot be added.  

Again, this is just not true!  Mendel did no work on the effects of mutation, this was not his intent and his experiments surely did not prove that genetic information can not be added, you still haven't shown us where Mendel reached these conclusions, please do so or retract your point.  
What he did show was a mechanism for transmitting traits from parents to offspring, heredity.  This was predicted by Darwin and the theory of evolution, so yes, genetics supports the theory of evolution.
 


Posts: 1664 | Posted: 4:14 PM on April 7, 2004 | IP
Gup20

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No, you don't understand!  The current information was duplicated, the new information mutates into something new, you now have the original information and the new information on the formally dupl.icate gene, what's so hard about that?  And as I've said this is an observed phenomenon, it is a fact.


Let me help you to understand this very basic concept.  If I have 1 candy bar, and I duplicate the candy bar, I now have 2 candy bars.  Even if I take the sugar out of the 2nd candy bar, I still only have a candy bar.  Neither candy bar will ever be a cheeseburger.  Why?  Cause it doesn't have the ingredients to be a cheeseburger.  Even if I had 1000 candy bars, I still can't make a cheeseburger.  

In response to your bacteria "update" please view this paragraph

It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins.  The details of just how they do this remains to be elucidated.  The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism.  This mechanism might be analogous to the way that vertebrates rapidly generate novel effective antibodies with hypermutation in B-cell maturation, which does not lend credibility to the grand scheme of neo-Darwinian evolution.11 Further research will, I expect, show that there is a sophisticated, irreducibly complex, molecular system involved in plasmid-based adaptation—the evidence strongly suggests that such a system exists.  This system will once again, as the black box becomes illuminated, speak of intelligent creation, not chance.  Understanding this adaptation system could well lead to a breakthrough in disease control, because specific inhibitors of the adaptation machinery could protect antibiotics from the development of plasmid-based resistance in the target pathogenic microbes.

Plagerized shamelessly from http://www.answersingenesis.org/home/area/magazines/tj/docs/v17n3_nylon.asp

(as are a lot of the evidences in my posts - plagerized from AiG, I mean)

The bottom line here is that the mechanism for adapting to new food sources was already a part of the plasmid's coding.  It is simply doing what it was already designed to do.

Mendel:

The discovery of the principles of recombination was Gregor Mendel’s great contribution to the science of genetics. Mendel showed that while traits might be hidden for a generation they were not usually lost, and when new traits appeared it was because their genetic factors had been there all along. Recombination makes it possible for there to be limited variation within the created kinds. But it is limited because virtually all of the variations are produced by a reshuffling of the genes that are already there.

For example, from 1800, plant breeders sought to increase the sugar content of the sugar beet. And they were very successful. Over some 75 years of selective breeding it was possible to increase the sugar content from 6% to 17%. But there the improvement stopped, and further selection did not increase the sugar content. Why? Because all of the genes for sugar production had been gathered into a single variety and no further increase was possible.

(again plagerized shamelessly from AiG)  http://www.answersingenesis.org/docs/1356.asp

So you see... you still have produced no real evidence that a mutation adds genetic information (in fact it re-arranges and destroys existing).  Also, it was interesting to note the many mis-representations of creationism your link to plasmids had.  They quoted AiG, yet they continue to post quips like "Creationists often say that all mutations are harmful ...".  This is blatently false.  There are many instances where a deletion of a gene causes a benefit for an organism.  But it is still a loss of information, and thereby not a valid mechanism for "neo-Darwinian" evolution.

 Here is a quote from your plasmid link:  "This case still provides an excellent example of a New Protein that evolved without the assistance of an Intelligent Designer."

Unless you count Nylon as having an intelligent designer - oh wait they did -  Here's another quote from your plasmids link:  
"If this gene was always there, whether in a plasmid or not, we can reasonably wonder why a bacteria would have a gene for hydrolysing an artificial polymer that did not exist until just a few decades ago"

But oh no - any evolutionist worth a darn could clearly point out how this is the perfect example of how information is added to a genome in a perfectly natural environment without the assistance of any intelligent design whatsoever.
 


Posts: 233 | Posted: 5:45 PM on April 7, 2004 | IP
TQ

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I still see a lot of huffing and puffing on your part gup, but not much in the way of actual evidence.  A few straw men, very bad analogies, but no evidence.  Demon has provided links to sources who have actually done research in the field of genetics, and you have countered with quotes from a site with poor science and a not-so-hidden agenda.  Hmm, which one is more trustworthy?


-------
"The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka!" (I found it) but 'That's funny...'"
- Isaac Asimov
 


Posts: 234 | Posted: 7:08 PM on April 7, 2004 | IP
Gup20

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Demon has provided links to sources who have actually done research in the field of genetics...

As have I ... in the same exact form as he - again, it's no surprise that you ignored this just as Demon has.

AiG footnotes sources very well.  Simply go there... read the Q&A section.  You will learn a lot.

www.answersingenesis.org

TQ - you do a lot of huffing and puffing, then make claims such as calling AiG "poor science", which are completely unsubstanciated by evidence.  

Your evidence is frequently that it doesn't agree with talkorigins.org website.  Not so  convincing considering what creation scientists think of talkorigins.org - it has bad science with scewed views, weak evidence with multiple interpretations, and partisan, even religious defending of evolutionary dogma.
 


Posts: 233 | Posted: 7:33 PM on April 7, 2004 | IP
TQ

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AiG footnotes their articles very well?  That is quite possibly the funniest thing I have ever heard in my life.  Their "footnotes" are quite possibly the most pathetic attempt at referencing that I've ever seen.

"creation scientists".  Now there's an oxymoron if ever there was one.

it has bad science with scewed views, weak evidence with multiple interpretations, and partisan, even religious defending of evolutionary dogma.

let's see, nope, nope, and nope.  Once again with the "evolution is religion" bluster.  Any actual evidence here?   Nope.


-------
"The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka!" (I found it) but 'That's funny...'"
- Isaac Asimov
 


Posts: 234 | Posted: 10:15 PM on April 7, 2004 | IP
Demon38

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Let me help you to understand this very basic concept.  If I have 1 candy bar, and I duplicate the candy bar, I now have 2 candy bars.  Even if I take the sugar out of the 2nd candy bar, I still only have a candy bar.  Neither candy bar will ever be a cheeseburger.  Why?  Cause it doesn't have the ingredients to be a cheeseburger.  Even if I had 1000 candy bars, I still can't make a cheeseburger.

Your analogies suck!  They don't apply at all to what we are talking about!  Let's restate your stupid candy bar analogy in more evolutionary terms.  You have 1 candy bar, it is duplicated.
Now, say the caramel in the 2nd bar mutates into marshmellow.  Now you have a candy bar with the original ingrediants and one with NEW ingrediants.  Pretty simple, and that's how evolution works, in incremental steps.

It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins.  The details of just how they do this remains to be elucidated.  The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism.

This is not true, show the evidence that the plasmids are designed, once again your wish for it to be true is not evidence.  If you can't show any evidence for intelligent design, admit you are wrong.

The discovery of the principles of recombination was Gregor Mendel’s great contribution to the science of genetics. Mendel showed that while traits might be hidden for a generation they were not usually lost, and when new traits appeared it was because their genetic factors had been there all along. Recombination makes it possible for there to be limited variation within the created kinds. But it is limited because virtually all of the variations are produced by a reshuffling of the genes that are already there.

Again you are spectaculary wrong!  Where does Mendel talk about mutations in his experiments?  One of the problems Darwin had was explaining how traits were passed on from one generation to the next.  Mendel solved this problem, so Mendels work in genetics SUPPORTS evolution.  The combination of Darwins ideas and Mendels research are part of the Modern Synthesis, one of the central theories of biology.  
From here:Modernsyn

"Perhaps the most serious question—one for which Wallace and Darwin had no answer—concerned the inheritance of traits. How exactly were traits passed along to offspring?
Darwin did not know it, but the answer was at hand—although it would not be acknowledged in his lifetime. In the Augustinian monastery at Brünn (now Brno in the Czech Republic), Austrian monk Gregor Mendel experimented with the breeding of garden peas, observing how their traits were passed down through generations. In crossbreeding pea plants to produce different combinations of traits—color, height, smoothness, and other characteristics—Mendel noted that although a given trait might not appear in every generation, the trait did not disappear. Mendel discovered that the expression of traits hinged on whether the traits were dominant or recessive, and on how these dominant and recessive traits combined. He learned that contrary to what most scientists believed at the time, the mixing of traits in sexual reproduction did not result in a random blending. Traits were passed along in discrete units. These units are now known as genes. Mendel performed hundreds of experiments and produced precise statistical models and principles of heredity, now known as Mendel’s Laws, showing how dominant and recessive traits are expressed over generations. However, no one appreciated the significance of Mendel’s work until after his death. But his work ultimately gave birth to the modern field of genetics.
As the science of genetics advanced during the 1920s and 1930s, several key scientists forged a link between Mendel's laws of inheritance and the theory of natural selection proposed by Darwin and Wallace. British mathematician Sir Ronald Fisher, British geneticist J.B.S. Haldane, and American geneticist Sewall Wright pioneered the field of population genetics. By mathematically analyzing the genetic variation in entire populations, these scientists demonstrated that natural selection, and not just mutation, could result in evolutionary change.
Further investigation into population genetics and such fields as paleontology, taxonomy, biogeography, and the biochemistry of genes eventually led to what is called the modern synthesis. This modern view of evolution integrated discoveries and ideas from many different disciplines. In so doing, this view reconciled the many disparate ideas about evolution into the all-encompassing evolutionary science studied today. The modern synthesis was advanced in such books as Genetics and the Origin of Species, published in 1937 by the Russian-born American geneticist Theodosius Dobzhansky; Evolution: The Modern Synthesis (1942) by British biologist Sir Julian Huxley; and Systematics and the Origin of Species (1942) by German-born American evolutionary biologist Ernst Mayr. In 1942, American paleontologist George Gaylord Simpson demonstrated from the fossil record that rates and modes of evolution are correlated: New kinds of organisms arise when their ancestors invade a new niche, and evolve rapidly to best exploit the conditions in the new environment. In the late 1940s American botanist G. Ledyard Stebbins showed that plants display evolutionary patterns similar to those of animals, and especially that plant evolution has demonstrated diverse adaptive responses to environmental pressures and opportunities. "

So as you can plainly see, you are completely wrong in your continued assertion that Mendel somehow disproves evolution.  Mendel's work in genetics and heredity only further strengthens the theory of evolution.

Unless you count Nylon as having an intelligent designer - oh wait they did -  Here's another quote from your plasmids link:  
"If this gene was always there, whether in a plasmid or not, we can reasonably wonder why a bacteria would have a gene for hydrolysing an artificial polymer that did not exist until just a few decades ago"


What??  I swear, you babble on and make no sense.  Are you saying that just because we designed nylon, that we are responsible for the addition of new genetic information in the bacteria???  You really strain to support your myths!  No, you still haven't shown how this is NOT an addition of new information!

From here:Muties

"Mutations are the way new genetic information develops.  The accumulation of mutations time provides the variation in populations upon which natural selection work  with the resulting diversity of living organisms."

Read that first sentance!

Every site that really does the science, really works with genetics says the same thing, new information can be added, novel structures can arise.  All you do is present disproven ideas from dogmatically ignorant religious sites like AIG.  You claimed that Mendels work somehow disproves evolution, when in reality it greatly supports evolution.  I quoted this somewhere else...It's from the Genetics Soceity of America...

"  Science operates first by observation, and then by developing a hypothesis as a preliminary explanation of the data. A theory is a hypothesis that has been subsequently confirmed by abundant, consistent data obtained from tests of the hypothesis. The theory of evolution by natural selection is exactly such a confirmed hypothesis, as developed through the ongoing investigation and understanding of many different areas of biological, chemical, physical and earth science. As such, it is modifiable and constantly refined as new research and information come to light. Without evolutionary theory, we would be forced to completely discard much of what we understand about fields such as genetics, botany, zoology, paleontology, and anthropology."

Now, if Mendel's work, the study of genetics, somehow clashed with the theory of evolution, I'm sure the GENETICS society of America would know about it.  But what we see is that this collection of over 4000 geneticists all agree
that evolution has taken place and still does take place.

Oh and just for fun, let's see what these scientists have to say about creationism....

""Scientific creationism," "intelligent design," and other terms have been offered as alternate explanations for past and present biological processes. However, these represent a collection of beliefs based on a literal interpretation of religious texts, and are thus disguises for religious doctrine, and not scientific theories. They ignore the empirical data around us and fail to provide a testable hypothesis. Consequently, since no testable explanation for biological history has been provided, they cannot be considered scientific theories, and should not be part of school curricula."

 

 


Posts: 1664 | Posted: 10:26 PM on April 7, 2004 | IP
TQ

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an answer to the "information question":

http://home.austarnet.com.au/stear/dawkinschallenge.htm


-------
"The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka!" (I found it) but 'That's funny...'"
- Isaac Asimov
 


Posts: 234 | Posted: 6:02 PM on April 8, 2004 | IP
Gup20

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I like the way Dr Gary Parker says it -

"The two basic ingredients in living things is DNA molecules and protein molecules.    DNA is a long string of repeated units called nucleotides or bases.  A protein molecule is a long string of amino acids.  In all forms of life, the sequence of DNA you inherit tells the cells how to line up amino acids to make each of the proteins responsible for structure and function.  So the cell takes a look at the genetic code and says “ok there are these three beads of DNA over here… I’ll line up one amino acid over here...” and continues checking back and forth.  

Well what about that relationship?  Is that what you would expect by time chance and chemistry?  At first you might say so because after all DNA is a string of bases, protein is a string of amino acids, and nothing is more natural then the reaction between acids and bases.  So the evolutionist says “see – if you just wait long enough, bases will start lining up amino acids and life will begin just by time chance and chemistry, no creator is needed”.  Exactly the opposite [is true].  The problem is that natural relationship between bases and acids is the wrong one as far as living things are concerned.

Bases and acids react alright – but when?  At death!  What is [biological] death anyway?  It is the triumph of chemistry over biology.  As soon as molecules in your body begin doing what they want to chemically, you begin to “return to the dust from which you are taken”.  In DNA the bases stick out along the side of the chain.  IN proteins the acids are part of the chain.  If you let DNA and protein do what come naturally, it actually contributes to the aging process and finally the decomposition and destruction of life.

The living relationship, the one we need for living things, is using a series of bases taking 3 at a time to line up a series of amino acid R groups.  Those groups can be acids… but they can also be base!  Single ring, double ring, short chain, long chain, with or without sulfur – they can be almost anything chemically.  The point is this – there is no natural tendency for a series of bases to line up a series of R groups.  That relationship has to be imposed from the outside.  At this fundamental level, then, we have evidence that life on earth is a product of special creation. "

Dr.  Gary Parker (doctorate in biology)
Author of 5 Biology Textbooks  
Creation Scientist

Taken from his own words in the account "From evolution to Creation" in which he describes his gradual conversion from evolutionist to creationist.

Now, say the caramel in the 2nd bar mutates into marshmellow.

I might accept that, only you can't show me any observational evidence that demonstrates caramel mutating into a marshmallow in nature.  In fact, if I showed you a butterfinger bar, and said I just found it growing somewhere, you wouldn't believe me, would you?  Now, how would you know that it was man-made?  How do you know I didn't find it growing in some pool of sugar and water?  You would take one look at the chocolate peanutbutter bar of sugary yummyness and deduce that it came from intelligent design based on your existing knowledge that you can't find butterfinger bars growing in nature.  The size, shape, color, taste... everything about that butterfinger bar would tell you it was designed by intelligent life - based on what you know about nature.

It's a good example of how "what we already know or think we know" effects our judgements about the evidence we see.

BTW - there is such a thing as the Marshmallow plant.  Although we use sugar and geletin to make marshmallows now, they used to make them out of the marshmallow root hundred years ago.  I would put this challenge to you - if you can observe the marshmallow plant mutating into a butterfinger in a natural environment, I will agree you are correct.  

TQ -

I have seen footage from that video interview with Dawkins.  It is true, he couldn't answer that question.  His answer on the link you gave, however, seems to be logical, but you have to make some pretty big assumptions.  

Dawkins says "Perhaps the main lesson we should learn from Pringle is that the information content of a biological system is another name for its complexity. Therefore the creationist challenge with which we began is tantamount to the standard challenge to explain how biological complexity can evolve from simpler antecedents, one that I have devoted three books to answering (The Blind Watchmaker, River Out of Eden, Climbing Mount Improbable) and I do not propose to repeat their contents here."

Well, I'll repeat their contents here - "We have seen that living things are too improbably and too beautifully 'designed' to have come into existence by chance. "  -Richard Dawkins.  1987.  The Blind Watchmaker.  P. 43

Dawkins says "But it still remains true that natural selection is a narrowing down from an initially wider field of possibilities, including mostly unsuccessful ones, to a narrower field of successful ones."  Then he says "...information is what enables the narrowing down from prior uncertainty to later certainty."  He then states "According to this analogy, natural selection is by definition a process whereby information is fed into the gene pool of the next generation."

Can you guys logically see what he is saying and doing?  He says A is true.  If we re-interpret B to fit with what we believe B should be, and add A and B together then C must be true.  HA!  Proof of evolution!  

Again, this is a prime example of the way an evolutionist thinks and reacts to evidence.  

Carl Sagin, one of evolution's top scientists, is involved in SETI.  Why?  How does he know that the signals they get from space aren't just random background noise?  Organization, and code.  Even Carl knows that organized coding doesnt happen by chance.

Dawkins says "We need only a little poetic licence to say that the information fed into modern genomes by natural selection is actually information about ancient environments in which ancestors survived. "

These are his hardcore "facts" about genetic information - poetic license.  

In one of his talks, Ken Hamm describes it (and I am more or less para-phrasing) this way -

Life is built up on the basis of information in our genes.  These have to have organization in order to mean anything.  You can have sets of DNA and proteins, but they have to be in a particular order to mean anything.  Not only do the DNA have to be in order, but the proteins and amino acids have to be in the right order to interpret them.  You can’t have living things with DNA without the proteins to de-code the DNA, and you can’t have the proteins without the DNA to make the proteins.  

For example.  Lets say a mosquito lands on me.  I reach over and squash it.  It’s now dead.  How did it die?  Well I squashed it didn’t I?  Yeah, but that’s got all the RNA and DNA and everything is all there… that’s the best primordial soup an evolutionist could ever ask for, right?  Do you know why the mosquito died?  Because I disorganized it.

If you take a frog and put it into a blender, chop it up real good… then you can say “here I have a disorganized frog”.  Then leave it sitting around and see if it organizes itself back again.

Matter had to produce the information and code systems for life to start with.  If you believe in evolution, matter had to produce a code system and information and over millions of years millions of times you had to get new bits of code… and new information.  Science has never seen one example where matter gives rise to one bit of new information.  

“There is no known natural law through which matter can give rise to information, neither is any physical process or material phenomenon known that can do this.  “ –Werner Gitt, 1997, In the Beginning Was Information.  CLV, Bielefeld, Germany. P. 64-67, 79, 107

He goes on to say “A code system is always the result of a mental process (it requires an intelligent origin or inventor)… It should be emphasized that matter as such is unable to generate any code.  All experiences indicate that thinking being voluntarily exercising his own free will, cognition, and creativity is required.”
Werner Gitt, 1997.  In the Beginning Was Information.  CLV, Bielefeld, Germany.  P. 64-67

Basically, code systems only come from intelligence, information only comes from information.  Gitt goes on to say there is no known natural law of nature, no known process, no known sequence of events which can cause information to originate by itself in matter.


Perhaps you have a better understanding of "information".  Bacteria loosing the ability to distinguish their food is not an example of genetically gained information.


(Edited by Gup20 4/10/2004 at 2:30 PM).
 


Posts: 233 | Posted: 2:22 PM on April 10, 2004 | IP
Gup20

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Demon - YOu have the link to "muties"

On that page it says -

Mutations are a permanent change in the DNA.  They occur spontaneously but their frequency increases as a result of exposure to mutagenic agents such as radiation, x rays and UV light.

It would be logical to deduce that since the causes of mutations are spontaneous random occurences of exposure to mutagenic agents such as radiation, xrays, and UV light, and mutagenic agenst (ie radiation, xrays, and UV light) cause damage to cells, that a Mutation is synonymous with damage.  It is a loss of existing content.  That's science.  That's logic and observation at work.

When you insert chaos into order, entropy increases.  2nd law of thermodynamics deals with that.  Entropy litterally means loss of information in a code.  Entropy also means inevitable and steady deterioration of a system.  It also means the tendency for all matter and energy in the universe to move toward a state of inert uniformity.  In other words - LOSS!
 


Posts: 233 | Posted: 2:51 PM on April 10, 2004 | IP
Demon38

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Gup20, you still babble on and ignore what the real scientists are saying:

From here:GenInfo

"By any reasonable definition, increases in information have been observed to evolve. We have observed the evolution of:
increased genetic variety in a population [Lenski, 1995; Lenski et al, 1991]
increased genetic material [Brown et al, 1998; Lynch and Conery, 2000; Ohta, 2003; Hughes and Friedman, 2003; Alves et al, 2001]
novel genetic material [Knox et al, 1996; Park et al, 1996]
novel genetically-regulated abilities [Prijambada et al, 1995]
If these don't qualify as information, then nothing about information is relevant to evolution in the first place."

From here:
GenInfoII

"Brown et al. (1998) reported that a population of baker’s yeast grown in a glucose limiting environment for a *few hundred* generations spontaneously produced mutant offspring. The mutant offspring were better able to take up the glucose from the low-glucose environment. The offspring were found to have duplications of two different sugar transport protein genes. Furthermore, NEW GENES WERE FOUND in the offspring which had formed from the combining of the control region of one of the sugar transport genes with the coding region of the other sugar transport gene. Finally, the mutant offspring were able to out-compete individuals of the ancestral population in pair-wise competition experiments."

From here:
GenInfoIII

"Given sufficient time and rates of occurrence, however, mutations can also create useful information.
In other words, random processes lead to useful information with low probability, but not with zero probability.
An altered gene sequence that results in a protein having a novel function would be an example of an increase in information that occurs with low probability."

from here:
GenInfoIV

"Genetic mutations increase genetic diversity and therefore have an important part to play. "

From here:GeninfoV

"There is one other point that needs to be made. In addition to new information being generated by mutation, the capacity for information in living things can be increased by mechanisms that increase the amount of DNA in an organism's cells. Such mechanisms are well documented. For instance, in plants, chromosome number often doubles when plant species hybridize. See Grant(1971) for a cogent discussion of polyploidy in plants. Once polyploidy happens, the amount of genetic material in the cells of the polyploid individuals is dramatically increased and the extra copies of the genes are free to undergo their own mutational history separate from the those on the other chromosome copies. In both plants and animals genes at particular loci can duplicate along the length of the chromosome giving rise to families of related genes that produce related proteins that have different functions, Ohta(1989). The genes related to myoglobin and hemoglobin would seem to be a good example. "

From here:GeninfoVI

"Mutations increase the genetic variability of a population. They are a way to introduce new alleles into a population.
An allele is an alternate form of a gene. Alleles are formed by mutations of pre-existing alleles. For some genes, there may be hundreds of different alleles.
Genetic variability is essential to the survival of a species and even the formation of new species.
Mutations make evolution possible."

All the real science sites say the same thing!  And you ignored the fact that we see novel new structures arise in the fossil record, legs on fish, feathers on dinosaurs, milk producing glands on reptiles, the list goes on and on.  
No, you're argueing against reality and you're losing badly!

When you insert chaos into order, entropy increases.  2nd law of thermodynamics deals with that.  

Where does the 2LOT mention chaos???  You're making this stuff up to support your position!  The 2LOT ONLY deals with heat loss in a closed system, it has nothing to do, says nothing about biological diversity!
 


Posts: 1664 | Posted: 3:58 PM on April 10, 2004 | IP
Gup20

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increased genetic variety in a population

According to Mendel the traits in animals are there from the beginning and passed on to offspring.  The fact that there are more variety is exactly what we would expect to see in animals as creationists.  As animals spread out all over the earth, natural selection and environmental factors started to isolate these existing genetic traits.

Plants on the other hand are not so mobile.  You see the fossil record indicate a much greater variety of plants in the past with greater size and variety.  Logically on can observe they don't really migrate, so their environment would pretty much remain the same - no real chance for specific isolaton of their genes to take place by natural selection.  However we do see a weakening genetically of plants over time as they grow smaller and in less variety.

True to form, Demon, you are puppeting evolution propaganda without thinking critically about it.  You have yet to refute the actual points I made in my post.  Such as how death is the process of chemistry overcoming biology, and why can't you put a frog in a blender, chop it up and leave it sit and eventually have a living frog again?  If evolution were true, this would be observable.  

Did you even read my post?  Does it logically make sense to you that radiation damaging a cell  causes a spontaneous increase in genetic information?  Your point by point analysis of my post ("Gup20, you still babble on and ignore what the real scientists are saying") is not a very compelling argument.  

The random variation which mutations add to populations is the variation which selection acts upon.

Or it could be that it was designed with all the variation possible, and natural selection and the environment isolated the traits the creature needed for the best chance of survival.

natural selection communicates information about the environment to the organism, so that the organism becomes better adapted to it

Again, it is far more likely that the creature has all the genetic information it needs.  When trouble befalls the animal the animals the animals with the dominant genes that give it an advantage are isolated by survival.    Isolation of a particular dominant or recessive gene takes place - speciation and natural selection take place when an existing gene is isolated because of it's survival quality.

This of course is readily observable and does not require you to define, redefine, obscure, blur or otherwise manipulate the meaning of "information" or any other term.

 


Posts: 233 | Posted: 8:34 PM on April 10, 2004 | IP
Gup20

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Basically, 2nd law of thermodynamics deals with matter and energy.  What are all things in the universe made up of - including biological entities?  Matter and energy.  

The 2nd law applies.
 


Posts: 233 | Posted: 8:39 PM on April 10, 2004 | IP
Demon38

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According to Mendel the traits in animals are there from the beginning and passed on to offspring.

Show me where Mendel said this or even tried to prove it.  Mendel did no work with mutations, so you're wrong.  Mendel's work is part of the Modern Synthesis, a cornerstone of biology.  In order to support your point, you'll have to disprove this tenet (and thereby disporve the bulk of modern biology).
Once again, let's look at the modern synthesis:
ModSyn

"The modern evolutionary synthesis (often referred to simply as the modern synthesis) brings together Charles Darwin's theory of the evolution of species by natural selection with Gregor Mendel's theory of genetics as the basis for biological inheritance. Major figures in the development of the modern synthesis include Ronald Fisher, Theodosius Dobzhansky, J.B.S. Haldane, Sewall Wright, Julian Huxley, Ernst Mayr, and George Gaylord Simpson.   According to the modern synthesis as established in the decades of the 1930s and 1940s, genetic variation in populations arises by chance through mutation (this is now known to be due to mistakes in DNA replication) and recombination (crossing over of homologous chromosomes during meiosis). Evolution consists primarily of changes in the frequencies of alleles between one generation and another as a result of genetic drift, gene flow and natural selection. Speciation occurs gradually when populations are reproductively isolated by geographic barriers."

How can the experts in genetics, biology, medecine, in fact, all the life sciences say that Gregor Mendel's work is a part of modern evolutionary theory, while you claim it disproves it???  Either you're right and the rest of biological science is wrong, or you're wrong!  Guess what I go with!

True to form, Demon, you are puppeting evolution propaganda without thinking critically about it.  You have yet to refute the actual points I made in my post.  Such as how death is the process of chemistry overcoming biology, and why can't you put a frog in a blender, chop it up and leave it sit and eventually have a living frog again?  If evolution were true, this would be
observable.


What???!!  Now a frog has to come back to life in order for evolution to be true???  Please show me where the theory of evolution states this????

Did you even read my post?  Does it logically make sense to you that radiation damaging a cell  causes a spontaneous increase in genetic information?

While radiation isn't the only cause of mutation, yes, it makes sense that radiation or cosmic rays could change a DNA sequence, why couldn't it?

Or it could be that it was designed with all the variation possible, and natural selection and the environment isolated the traits the creature needed for the best chance of survival.

Except with gene sequencing techniques we can see where new information has been added, it isn't even debatable anymore, that information is added is a fact.  From here:
Increase

"Tetraploidy in orchids as an increase in "layman's information". Tetraploid orchids carry double the number of chromosomes found in the parent population. They also tend to be larger and have more robust structures. Because the physical appearance of the tetraploid orchid has changed from what the parent looked like, we know that the information which specified its phenotype also has changed. Now, we only need to figure out whether that change corresponds to an increase or a decrease in information. Because the change is accomplished by copies of information, the information can be seen to have increased rather than to have decreased."

And let's look at some of the benefits of examining genonmes:  Genome

"Comparison of the rat genome to those of the human and mouse also opens a new and unique window into mammalian evolution. The rodent lineage, which gave rise to the rat and mouse, and the primate lineage, which gave rise to humans, diverged about 80 million years ago. Humans have 23 pairs of chromosomes, while rats have 21 and mice have 20. However, the new analysis found chromosomes from all three organisms to be related to each other by about 280 large regions of sequence similarity - called "syntenic blocks" - distributed in varying patterns across the organisms' chromosomes."

Aside from the fact that modern genetics still confirms evolution, we see genomes of mice, rats and humans changing, information is being added.

Again, it is far more likely that the creature has all the genetic information it needs

NO it's not far more likely, and it has been shown to be wrong!  You have provided no evidence for this except for your own incedulity!

This of course is readily observable

How is this readily observable????

Basically, 2nd law of thermodynamics deals with matter and energy.  

No it does not, it deals with heat.  From here:
2LOT

"The second law of thermodynamics states that no heat engine can be more efficient than a reversible heat engine working between two fixed temperature limits (Carnot cycle) i.e. the maximum thermal efficiency is equal to the thermal efficiency of the Carnot cycle"

So please explain how this prevents evolution...

 


Posts: 1664 | Posted: 11:30 PM on April 10, 2004 | IP
Young Earth Toad

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From here: New Information

"Evidence against the evolutionary explanation includes:

1. There are five transposable elements on the pOAD2 plasmid.  When activated, transposase enzymes coded therein cause genetic recombination.  Externally imposed stress such as high temperature, exposure to a poison, or starvation can activate transposases.  The presence of the transposases in such numbers on the plasmid suggests that the plasmid is designed to adapt when the bacterium is under stress.

2. All five transposable elements are identical, with 764 base pairs (bp) each.  This comprises over eight percent of the plasmid.  How could random mutations produce three new catalytic/degradative genes (coding for EI, EII and EIII) without at least some changes being made to the transposable elements?  Negoro speculated that the transposable elements must have been a ‘late addition’ to the plasmids to not have changed.  But there is no evidence for this, other than the circular reasoning that supposedly random mutations generated the three enzymes and so they would have changed the transposase genes if they had been in the plasmid all along.  Furthermore, the adaptation to nylon digestion does not take very long (see point 5 below), so the addition of the transposable elements afterwards cannot be seriously entertained.

3. All three types of nylon degrading genes appear on plasmids and only on plasmids.  None appear on the main bacterial chromosomes of either Flavobacterium or Pseudomonas. This does not look like some random origin of these genes—the chance of this happening is low.  If the genome of Flavobacterium is about two million bp,7 and the pOAD2 plasmid comprises 45,519 bp, and if there were say 5 pOAD2 plasmids per cell (~10% of the total chromosomal DNA), then the chance of getting all three of the genes on the pOAD2 plasmid would be about 0.0015.  If we add the probability of the nylon degrading genes of Pseudomonas also only being on plasmids, the probability falls to 2.3 x 10-6.  If the enzymes developed in the independent laboratory-controlled adaptation experiments (see point 5, below) also resulted in enzyme activity on plasmids (almost certainly, but not yet determined), then attributing the development of the adaptive enzymes purely to chance mutations becomes even more implausible.

4. The antisense DNA strand of the four nylon genes investigated in Flavobacterium and Pseudomonas lacks any stop codons.8 This is most remarkable in a total of 1,535 bases.  The probability of this happening by chance in all four antisense sequences is about 1 in 1012.  Furthermore, the EIII gene in Pseudomonas is clearly not phylogenetically related to the EII genes of Flavobacterium, so the lack of stop codons in the antisense strands of all genes cannot be due to any commonality in the genes themselves (or in their ancestry).  Also, the wild-type pOAD2 plasmid is not necessary for the normal growth of Flavobacterium, so functionality in the wild-type parent DNA sequences would appear not to be a factor in keeping the reading frames open in the genes themselves, let alone the antisense strands."

And also, from here: Nylon Feedback

"[Ed. note, 9 April 2004: Research has shown that the correct explanation for the nylon-eating enzyme produced on the plasmids is somewhat different from the previous two paragraphs. It also confirms that the frameshift idea is totally wrong. Rather, there seems to be a special mechanism that recombines parts of the genes in the plasmids in a way that is non-random. This is shown by the absence of stop codons, which would be generated if the variation were random. See The adaptation of bacteria to feeding on nylon waste.]"

Obviously the nylon eating bacteria example is a poor analogy to macroevolution.


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Posts: 50 | Posted: 1:42 PM on April 11, 2004 | IP
Demon38

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There are five transposable elements on the pOAD2 plasmid.  When activated, transposase enzymes coded therein cause genetic recombination.  Externally imposed stress such as high temperature, exposure to a poison, or starvation can activate transposases.  The presence of the transposases in such numbers on the plasmid suggests that the plasmid is designed to adapt when the bacterium is under stress.

How does the presence of transposases suggest the plasmid is designed????

What it comes down to is a new protein evolved still with no evidence of a creator.
From here:  Nylonbug

"UPDATE: Answers In Genesis Dismisses the Nylon Bug as simply due to "Plasmids."

From http://www.answersingenesis.org/home/area/feedback/negative7-24-2000.asp :

"... 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 [e.g. K. Kato, et al., ‘A plasmid encoding enzymes for nylon oligomer degradation: Nucleotide sequence analysis of pOAD2’, Microbiology (Reading) 141(10):2585–2590, 1995. In fact, more than one species of bacteria have the ability, residing on plasmids. This suggests that the information probably already existed, and was just passed between different types of bacteria. ..."

Sorry, AiG, but just because something is on a plasmid doesn't mean it's always been there! In fact, the plasmid involved in this case is very well known and characterized. Scientists have studied both the original (pre-mutation) plasmid and the novel (post-mutation) plasmid, in great detail. It turns out that the novel plasmid's mutated DNA for production of nylonase is almost identical to a non-coding repetitive DNA sequence on the original plasmid; the difference is the single nucleotide that triggered the Frame Shift. This mutation did not exist 60 years ago. If this gene was always there, whether in a plasmid or not, we can reasonably wonder why a bacteria would have a gene for hydrolysing an artificial polymer that did not exist until just a few decades ago; and why, in the absence of such a substrate, was the gene not mutated to uselessness over the millenia?

Was the plasmid slipped in from another bacterium?  NO!! The plasmid in question, pOAD2, is just one of three plasmids that are harbored by the bacterium under investigation here, Flavobacterium Sp. K172. Here are some citations to back this up:

"Sequence analysis of a cryptic plasmid from Flavobacterium sp. KP1, a psychrophilic bacterium," Makoto Ashiuchi, Mia Md. Zakaria, Yuriko Sakaguchi, Toshiharu Yagi, FEMS (Federation of European Microbiological Societies) Microbiology Letters 170 (1999), 243-249.

"Bacteria of genus Flavobacterium, Gram-negative bacteria, are widely distributed in soil and fresh marine waters. Some of them harbor plasmid(s) involved in metabolism of synthetic organic compounds. Flavobacterium sp. K172 harbors plasmids, pOAD1, pOAD2 and pOAD3; pOAD2 (43.6 kbp) encodes nylon oligomer degradation genes."
"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.

"The EI-encoding gene (F-nylA) and EII-encoding gene (F-nylB) of Flavobacterium sp. K172 are located on plasmid pOAD2 (44 kb), one of the three plasmids harbored in strain K172."
"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.

"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."
It's interesting to note that the precise plasmid of Flavobacterium sp. K172, namely pOAD2, was cited by Susumu Ohno fully eleven years before the publication of the "new evidence" that AiG claims " shows that the ability was due to plasmids..."

The Bottom Line: Just because this mutation wasn't confined to a cell's main chromosomes does not mean it didn't happen. (A plasmid is defined as a replicon - a replicating piece of DNA - that is inherited in an extrachromosomal state.) This case still provides an excellent example of a New Protein that evolved without the assistance of an Intelligent Designer."

Better luck next time toad...


 


Posts: 1664 | Posted: 8:18 PM on April 11, 2004 | IP
TQ

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Carl Sagin, one of evolution's top scientists, is involved in SETI.

Carl Sagan was an astronomer, and has been dead for a number of years.  

(Edited by admin 4/12/2004 at 08:47 AM).


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"The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka!" (I found it) but 'That's funny...'"
- Isaac Asimov
 


Posts: 234 | Posted: 10:57 PM on April 11, 2004 | IP
Gup20

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Let me post some of what AiG has said on the issue - this pics up where YEToad's post leaves off -


Some statements by Yomo et al., express their consternation:

‘These results imply that there may be some unknown mechanism behind the evolution of these genes for nylon oligomer-degrading enzymes.

‘The presence of a long NSF (non-stop frame) in the antisense strand seems to be a rare case, but it may be due to the unusual characteristics of the genes or plasmids for nylon oligomer degradation.

‘Accordingly, the actual existence of these NSFs leads us to speculate that some special mechanism exists in the regions of these genes.’

It looks like recombination of codons (base pair triplets), not single base pairs, has occurred between the start and stop codons for each sequence.  This would be about the simplest way that the antisense strand could be protected from stop codon generation. The mechanism for such a recombination is unknown, but it is highly likely that the transposase genes are involved.

Interestingly, Yomo et al. also show that it is highly unlikely that any of these genes arose through a frame shift mutation, because such mutations (forward or reverse) would have generated lots of stop codons.  This nullifies the claim of Thwaites that a functional gene arose from a purely random process (an accident).

The Japanese researchers demonstrated that nylon degrading ability can be obtained de novo in laboratory cultures of Pseudomonas aeruginosa [strain] POA, which initially had no enzymes capable of degrading nylon oligomers.9 This was achieved in a mere nine days!  The rapidity of this adaptation suggests a special mechanism for such adaptation, not something as haphazard as random mutations and selection.

The researchers have not been able to ascertain any putative ancestral gene to the nylon-degrading genes.  They represent a new gene family.  This seems to rule out gene duplications as a source of the raw material for the new genes.8

P. aeruginosa is renowned for its ability to adapt to unusual food sources—such as toluene, naphthalene, camphor, salicylates and alkanes.  These abilities reside on plasmids known as TOL, NAH, CAM, SAL and OCT respectively.2  Significantly, they do not reside on the chromosome (many examples of antibiotic resistance also reside on plasmids).

The chromosome of P. aeruginosa has 6.3 million base pairs, which makes it one of the largest bacterial genomes sequenced.  Being a large genome means that only a relatively low mutation rate can be tolerated within the actual chromosome, otherwise error catastrophe would result.  There is no way that normal mutations in the chromosome could generate a new enzyme in nine days and hypermutation of the chromosome itself would result in non-viable bacteria.  Plasmids seem to be adaptive elements designed to make bacteria capable of adaptation to new situations while maintaining the integrity of the main chromosome.

Stasis in bacteria
P. aeruginosa was first named by Schroeter in 1872.10 It still has the same features that identify it as such.  So, in spite of being so ubiquitous, so prolific and so rapidly adaptable, this bacterium has not evolved into a different type of bacterium.  Note that the number of bacterial generations possible in over 130 years is huge—equivalent to tens of millions of years of human generations, encompassing the origin of the putative common ancestor of ape and man, according to the evolutionary story, indeed perhaps even all primates.  And yet the bacterium shows no evidence of directional change—stasis rules, not progressive evolution.  This alone should cast doubt on the evolutionary paradigm.  Flavobacterium was first named in 1889 and it likewise still has the same characteristics as originally described.

It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins.  The details of just how they do this remains to be elucidated.  The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism.  This mechanism might be analogous to the way that vertebrates rapidly generate novel effective antibodies with hypermutation in B-cell maturation, which does not lend credibility to the grand scheme of neo-Darwinian evolution.11 Further research will, I expect, show that there is a sophisticated, irreducibly complex, molecular system involved in plasmid-based adaptation—the evidence strongly suggests that such a system exists.  This system will once again, as the black box becomes illuminated, speak of intelligent creation, not chance.  Understanding this adaptation system could well lead to a breakthrough in disease control, because specific inhibitors of the adaptation machinery could protect antibiotics from the development of plasmid-based resistance in the target pathogenic microbes.

Additional recommended resources
In the Beginning Was Information
Refuting Evolution
Evolution: A Theory in Crisis
The Biotic Message
References
Kinoshita, S., Kageyama, S., Iba, K., Yamada, Y. and Okada, H., Utilization of a cyclic dimer and linear oligomers of e-aminocapronoic acid by Achromobacter guttatus K172, Agric. Biol. Chem. 39(6):1219–1223, 1975.  Note: A. guttatus K172 syn. Flavobacterium sp. K172. Return to text.
Negoro, S., Biodegradation of nylon oligomers [review], Applied Microbiology and Biotechnology 54:461–466, 2000. Return to text.
A plasmid is an extra-chromosomal loop of DNA in a bacterium.  Such loops of DNA, unlike the chromosomal DNA, can be swapped between different species of bacteria.  An individual bacterium can have several types of plasmid, and multiple copies of each. Return to text.
Thwaites, W.M., New proteins without God’s help, Creation/Evolution 5(2):1–3 (issue XVI), 1985. Return to text.
Ohno, S., Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence, Proceedings of the National Academy of Sciences USA 81:2421–2425, 1984. Return to text.
Truman, R., Protein mutational context dependence: a challenge to neo-Darwinism theory: part 1, TJ 17(1):117–127; Truman, R. and Heisig, M., Protein families: chance or design? TJ 15(3):115–127. Return to text.
As of the date of writing, no Flavobacterium sp. genome has been sequenced. Return to text.
Yomo, T., Urabe, I. and Okada, H., No stop codons in the antisense strands of the genes for nylon oligomer degradation, Proceedings of the National Academy of Sciences USA 89:3780–3784, 1992. Return to text.
Prijambada, I.D., Negoro, S., Yomo, T. and Urabe, I., Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution, Applied and Environmental Microbiology 61(5):2020–2022, 1995. Return to text.
Bacterial Nomenclature Up-to-date, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany. , 18 September 2003. Return to text.
Truman, R., The unsuitability of B-cell maturation as an analogy for neo-Darwinian Theory, March 2002; , 22 August 2003. Return to text.

It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins.

 


Posts: 233 | Posted: 12:44 AM on April 12, 2004 | IP
Demon38

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It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins.  The details of just how they do this remains to be elucidated.  The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism.

How is it clear that plasmids are designed????
Once again, you're making stuff up!
They are evolving to metabolize a new food source, they are increasing their information, no 2 ways about it!  And all the evidence does indicate they came about by mutation, no evidence whatsoever for an intelligently designed system.
 


Posts: 1664 | Posted: 01:33 AM on April 12, 2004 | IP
    
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