Ready When Made

Yes, you are right, of course, thanks for the correction.It's early.

quote:

---

Whoops. We're at crosspurposes here. I completely agree with everything balyons said, except that no mutation can be beneficial. Mutations can be beneficial - depending on what criteria you're using - but they can't add information. This ties in nicely with Loudmouth's argument concerning nylon-digesting bacteria. Although that may have looked like new genetic information, or macroevolution, at first, it's more likely to have been a loss of information in that the enzyme catalysis processes became less specific. By a loss of information, the enzymes would be less effective but more general in what they digested, allowing the enzymes to remove any inbuilt inhibition they may have had against chewing up nylon. Proteins and nylon are digested in a very similar manner (which is why nylon is the first substance you'd notice being catalysed if these mutations began). Degeneration again - beneficial for the moment, mind you, depending on whether nylon is good for bacteria, but such losses of information would eventually create an enzyme that is permitted to digest a wide range of substances but is not good at it. Such bacteria would not survive when pitted against bacteria with substrate-specific very efficient enzymes.
But new evidence actually suggests plasmids may be responsible for the nylon digestion. Other bacteria have the same property and could have passed this information to the flavobacteria. See e.g. K. Kato, et al., A plasmid encoding enzymes for nylon oligomer degradation: Nucleotide sequence analysis of pOAD2, Microbiology (Reading) 141(10):25852590, 1995.

---

Defender, nylon didn't exist until modern times. So, quite obviously, something evolved the ability to digest it, whether it was flavobacteria or other. By adding the ability to digest it, it now has a brand new niche that it can fill, much the same as how if a non-photosynthetic bacteria in the early earth became able to harness energy from light - even weakly - it would spread to fill the Earth.Virtually everything is give and take (although there was essentially no "give" in the link I presented above); however, replication + mutation means that the original ability is retained, and a new ability is added; replication + mutation occurs all the time, and in fact, the copy tends to mutate at a different rate than the parent.------------------
"Illuminant light,
illuminate me."

Nylon may not have existed until modern times, but remember it's a man-made compound composed of natural substances which did exist a long time ago. Enzymes, as far as my limited knowledge tells me, are specific in what they digest. As I said above, a degeneration in the gene pool could have reduced their inhibition towards digesting the particular composition of natural materials that makes up the polymers of nylon. Nylon and protein digestion processes are very similar.
Before this mutation, the enzyme has a precise design of what it will digest. Afterwards, its plan is incomplete and it will digest a similar substrate that is also composed of organic substances and also involves destroying amide linkages. This is a loss in information, and since it also involves the enzyme becoming less specific, is probably not in the long run beneficial.

Dear schrafinator:If, say, the bears can't survive without a coat length of at least 10 cm, all bears with anything less than that will die. Thus the genes for anything longer than 10 cm will survive, and above that number there will be variation. Genes will be unlikely to survive for hair beneath 10 cm. If the following heat wave kills bears with a coat length of more than 8 cm, since all genetic information for such hair is gone - the DNA has lost the ability to create it - the bears will become extinct. Variation can only occur if the information for hair less than 8 cm exists.
To gain such hair by a gain in mutation would be macroevolution. Such gains have not been observed, but even if they did happen the bears could not afford to wait until one came along.

First, you haven't addressed the points I raised previously that demonstrate your analogy is false. Second, you've succeeded in erecting and then defeating a strawman, since what you're claiming for evolution has no bearing on nor is it a prediction of evolution. Finally, congratulations - you've successfully falsified Intelligent Design with your analogy. Teleological evolution is one of the tenets held by some ID proponents (i.e., the bears develop long hair because they have to due to environmental change). When the bears don't develop the capability in response to the environment, it effectively falsifies Mikes "goddidit" ID and the anthropic principle all in one go. Well done... [This message has been edited by Quetzal, 10-22-2003]

(Emphasis mine)But this simply doesn't happen, not over very short periods of time anyway. A bear with 9.5cm of hair will have a lower probability of survival than one with 10.0 cm of hair (or 9.6 cm of hair), but they won't all die. As well, there'll be areas of land where 9.3cm of hair is sufficent; the environment isn't homogenous. Genetics tends not to work in such a clear cut fashion, it would take a long time to remove all short-hair genes from the gene pool, particularly if some are recessive. A bear with 9.5cm would be more likely to survive than one with 11cm; this wouldn't happen overnight, and more likely the long-haired bear population would simply migrate into colder climbs (along with all the other flora and fauna that likes the colder conditions). Hardly, changes in hair length are non macro events, probably they can be achieved by relative simply genetic mutations, or even the simple recombination of existing genes. Note how almost every form of domesticated animal has long-haired varieties, and most have a fairly continous spread of hair lengths across different breeds.

quote:

---

Nylon may not have existed until modern times, but remember it's a man-made compound composed of natural substances which did exist a long time ago.

---

Doesn't change the fact that these bacteria, according to all the evidence, are the result of a mutation that formed a new species. If you're disputing any other facts with this statement, maybe you could clarify what those are.

quote:

---

Enzymes, as far as my limited knowledge tells me, are specific in what they digest. As I said above, a degeneration in the gene pool could have reduced their inhibition towards digesting the particular composition of natural materials that makes up the polymers of nylon. Nylon and protein digestion processes are very similar.

---

What makes this a degeneration? Enzymes don't have "inhibitions" toward digesting anything. They react according to the laws of chemistry with whatever substance they meet. Your value judgments and loaded terminology don't follow from the facts.

quote:

---

Before this mutation, the enzyme has a precise design of what it will digest.

---

No. The enzyme's structure, which is governed by the laws of chemistry, is efficient in the breakdown of a particular substance which releases energy inside a bacterium. Design is not obvious or supported by evidence.

quote:

---

Afterwards, its plan is incomplete and it will digest a similar substrate that is also composed of organic substances and also involves destroying amide linkages.

---

What is incomplete about it? The bacteria now digest a different food! You can throw as many negative words in the direction of the facts as you want, but this is what happens in real life: they now perform the same function on a new food source. As it happens, the source is unexploited and they have no competition for food.

quote:

---

This is a loss in information, and since it also involves the enzyme becoming less specific, is probably not in the long run beneficial.

---

HAHAHAHA!!! Probability is not an issue. A species that didn't exist before now thrives, free of competition, on a food source that we create as waste. This bacterium has probably got it better than its ancestors ever did! And you have the gall to insist that the mutation is harmful?What prevents this view from being hilarious in my mind is that there are those who would propose that my future children be forced to learn it.

quote:

---

Nylon may not have existed until modern times, but remember it's a man-made compound composed of natural substances which did exist a long time ago. Enzymes, as far as my limited knowledge tells me, are specific in what they digest. As I said above, a degeneration in the gene pool could have reduced their inhibition towards digesting the particular composition of natural materials that makes up the polymers of nylon.

---

1) That's not at all how things work. Polymers have different properties than their component materials.2) That would be an *improvement* in the organism, to be able to handle a wider variety of food sources.

quote:

---

Nylon and protein digestion processes are very similar.

---

In what manner? Nylon is polyamide - that is, a long chain of subunits of:H O
| |
N --- C --- (CH2)5Proteins are long chains of amino acids.Not at all related, except that they use carbon to make long chains.

quote:

---

This is a loss in information, and since it also involves the enzyme becoming less specific, is probably not in the long run beneficial.

---

Please explain how having a brand new food source is "not in the long run beneficial". If humans in a 3rd-world country suddenly became able to eat dirt, would that somehow be "not in the long run beneficial"?The enzyme that breaks down nylon doesn't just attack random things. It breaks down nylon, and gets energy from it, which it gives to the cell.------------------
"Illuminant light,
illuminate me."

quote:

---

Such gains have not been observed, but even if they did happen the bears could not afford to wait until one came along.

---

Wow, if you think something as simple as gaining and losing hair are "macroevolution", what do you think of these pigeons (and yes, they are real): There's plenty more where these came from... by putting selective breeding forces on pigeons, people have created the most bizarre forms imaginable. Now, even though humans use a 100% selection criteria, as I demonstrate in this thread, it need not be even close to 100%.------------------
"Illuminant light,
illuminate me."

Explain how a new open reading frame whose product digests material only around since the early part of this century is not new information. You are switching from one gene product to a "catalysis process". The old catalysis process, a complete glycolysis pathway, has been turned off due to lack of carbohydrates. The genes for the glycolytic pathway are still there. What has been produced, by a single mutation, is a novel pathway that supplies energy to the cell from a substrate that was up until this time unused.Also, explain how the flavobacterium was inhibited in its ability to digest nylon. You seem to be suggesting that the bacteria had the ability to digest nylon before but another protein/chemical was preventing this. Is there another example of a protein digesting enzyme that also digests nylon? I haven't heard of any, but I could be wrong. Could you please cite any examples. Explain how taking advantage of an unused niche is bad for a bacterium. Also explain how further mutation will cause the enzyme to be less specific, citing examples of other mutations to nylonase genes. Explain how digesting nylon is bad on principle alone. In a solution of nylon, the new flavobacterium will kick the butt of any other bacteria out there. If you don't think so, cite another bacterium that can survive on nylon alone. Also, cite any other nylonase genes that are more nylon specific than that found in the flavobacterium. The nylC gene on the plasmid has been known from the start. What you are missing is that the identical plasmid, minus the frameshift mutation, is present in the wild-type carbohydrate only flavobacterium. Horizontal gene transfer may have contributed the plasmid in the past, but gene mutation that occurred could have been in the chromosomal genome as easily as in the plasmid. Frameshift mutations can occur in the chromosome as easily as in the plasmids.
If you think there is a disctinction, please explain how mutation to extrachromosomal DNA does not count as being beneficial or an increase in information.In general, could you also explain what new information, in a genetic sense, would look like? Before you can explain away a negative, I think it would only be fair to define a positive as well. To simply say new information can not arise through mutation is a priori dismissing it without first defining what new information would look like.

Defender, there are two possibilities here:1) The concept of information increase and decrease you are talking about here is one of your own invention. In this case you need to explain rather fully what you are talking about. In particular you need to define the terms you are using. The word "information" without adornment in particular is a problem since many will presume you mean the definition of information that Claude Shannon put forward and is used in information theory a lot.2) You took this idea form someone else. I have read a number of sources that attempt to use this agruement. In none of them is the term defined. If you took it from elsewhere it is possible that your source is deliberately misleading you since the flaws in the arguement have been pointed out over and over again.Perhaps you could clarify which case it is? And, then, in any case, you could back up a bit and define your terms.(a short note on your nickname, you are in no way defending your faith if you attempt to use spurious already refuted arguments to attack science. If fact to the majority of individuals, including Christians, you are doing your faith harm.)

Both proteins and nylon are polyamides - each has a carbon with a double-bonded oxygen, a nitrogen, and a carbon attached. The big difference, and the one that I would think makes nylon oligomers relatively indigestible, is that in all proteins the "carbon attached" is itself attached to another nitrogen in the polymer chain. In nylon, it is seperated from that next nitrogen by several carbons (and perhaps some other groups - it depends on which sort of nylon.) Like this, but without a blackboard to make it clear:
Protein: -N-C-C-N-C-C-.......
Nylon 6-6: -N-C-C-C-C-C-C-N-C-C-C-C-C-C-N-.......[This message has been edited by Coragyps, 10-22-2003]

Ah, my bad, thanks. Chains of amino acids are polyamides.------------------
"Illuminant light,
illuminate me."