Evolution; A challenge.

[porchrat]

You're making the same mistake as many others. Instead of judging the info. you judge the source.

Realistically Conservapedia is an absolute joke.

If you want to talk about questioning the information then just look at the references this source is using to get its information. Newspaper articles, 1 or 2 creationist websites, the website for a campaign in support of evolutionary theories. Not a single journal article. Not a SINGLE reference in the entire introductory section to explain exactly where they got this "evolution syndrome" concept from. No psychology investigations, no nothing. That article is an absolute mess, much like most of the stuff on Conservapedia.

Seriously man if you are relying on Conservapedia to provide information to you then you are an absolute muppet. We all know it is biased. I've seen articles in which it flat out lies (obviously this is easy when you hardly ever reference anything). You only have to read a few articles in it on a topic that you have some knowledge of to see that.

I realise Ekstasis that perhaps as a Christian you might want to consider supporting Conservapedia but trust me you don't want to be associated with idiots like that.

 

[alloytoo]

I had a response to Alloytoo typed out but I'm not even going to bother any more. The fact remains that it's unproven and probably unprovable. Everything that's been found so far have either been made to fit or simply dismissed. Nobody has been able to come up with a test to make it falsifiable.

No one has falsified it. It is not a requirement of falsifiability that something actually be falsified.

Haldene seems to set a very high standard that I'm sure will make even creation falsifiable.

Theistic Creation isn't falsifiable.

A precambrian rabbit oh my.
"In other words, when the assumed evolutionary processes did not match the pattern of fossils that they were supposed to have generated, the pattern was judged to be 'wrong.' A circular argument arises: interpret the fossil record in terms of a particular theory of evolution, inspect the interpretation, and note that it confirms the theory. Well, it would, wouldn't it?" - Tom S. Kemp, "A Fresh Look at the Fossil Record," New Scientist, vol. 108, 1985, p. 66-67

A Quotemine, how surprising.

The fact that the fossil data did not, on the whole, seem to fit this prevailing model of the process of evolution - for example, in the absence of intermediate forms and of gradually changing lineages over millions of years - was readily explained by the notorious incompleteness of the fossil record. In other words, when the assumed evolutionary processes did not match the pattern of fossils that they were supposed to have generated, the pattern was judged to be "wrong". A circular argument arises: interpret the fossil record in terms of a particular theory of evolution, inspect the interpretation, and note that it confirms the theory. Well, it would, wouldn't it?

Spearheaded by this extraordinary journal, palaeontology is now looking at what it actually finds, not what it is told that it is supposed to find. As is now well known, most fossil species appear instantaneously in the record, persist for some millions of years virtually unchanged, only to disappear abruptly - the "punctuated equilibrium" pattern of Eldredge and Gould. Irrespective of one's view of the biological causes of such a pattern (and there continues to be much debate about this), it leads in practice to description of long-term evolution, or macroevolution, in terms of the differential survival, extinction and proliferation of species. The species is the unit of evolution.Tom S. Kemp, "A Fresh Look at the Fossil Record," New Scientist, vol. 108, 1985, p. 66-67

Ooh look another

"Contrary to what most scientists write, the fossil record does not support the Darwinian theory of evolution because it is this theory (there are several) which we use to interpret the fossil record. By doing so we are guilty of circular reasoning if we then say the fossil record supports this theory." - Ronald R. West, "Paleoecology and uniformitarianism". Compass, vol. 45, May 1968, p. 216"

"Boundary conditions are the limits within which the theory is applicable. Thus there does not seem to be any compartmentalization of attitudes as Scott suggests; evolutionary theory deals with biology in the present, and uniformitarianism permits the use of present processes to explain past events. The concept of uniformitarianism does not enter the picture until the attempt is made to use evolutionary theory (biological present) to explain the fossils record (paleobiological past). Contrary to what most scientists write, the fossil record does not support the Darwinian theory of evolution because it is this theory (there are several) which we use to interpret the fossil record. By doing so we are guilty of circular reasoning if we then say the fossil record supports this theory. When an effort is made to explain the fossil record (whether it be taxonomic differences or changes in response to ecological factors) in terms of Darwinian evolution the concept of uniformitarianism is essential, for it allows us to use the present to explain the past. This should be its main purpose, to allow us to reconstruct the past on the basis of a theory or theories founded on nonhistoric events." [Ronald R. West, "Paleoecology and Uniformitarianism", The Compass of Sigma Gamma Epsilon, Vol. 45, No. 4, May 1968, p. 216]

Few people know of archeology's dirty little secret as some have put it. Fossil rocks are dated primarily by what fossils are expected to be found in them. So much for finding that precambrian bunny when you use the bunny to "determine" that it's post-cambrian.

Radiometric dating.

Now I see you take my comment which anybody can see refers to DNA as an admission that the "TOE" is not only falsifiable but proven. Which means you either have bad reading skills or are deliberately twisting my words.

I'm deliberately exposing how silly your position is. Either you don't truely understand falsifiability or you're being deliberately obtuse.

In any event the fact remains that facts still have to be proven as confirmed by your own dictionary definition and that theories should not be taken as facts.

Scientific Facts don't require proving, they require explanation

Theory = explanation of facts.

That wasn't even the issue which was that of a theory (macro evolution) being presented as fact. You have to prove that it can and did happen. I do not have to prove that it can't. Trying to shift the burden of proof onto me disproving it... right, try pulling the other one.

Evolution is a scientific fact. (that requires no proving). "Theory of evolution" explains the scientific fact.

Any alternative explanation needs to explain the facts.

 

[TJ99]

There is no circular reasoning with regards the fossil record. The geological stratum can be dated with radiometric dating. Because the fosil record so accuarrtly follows the radiometric dating is is short hand method for geological dating.

And they don't just use one method of radiometric dating, they use several methods to make sure the results agree.

The OP's view understanding of the subject is irrelevant. Answer the questions if you can. Too cowardly I presume.

See, that's what I thought too. And so did the OP. But, apparently the philosophical interpretation of natural selection is extremely important in answering the question of whether it happens or not. Enough to create pages and pages about. How silly of us.

Resistance to antibiotics IS a an improvement in fitness regardless of what to to blithering idiot at answersingenesis. The fact that many improvement came at the cost of others in no secret.

Oh, you better not call objectively idotic things idiotic. You'll get called out for OMG PURSEKYUSHIN/INSALTS!!!11!!11!1!. (You know, instead of being calmly told why it isn't idiotic like any non-idiot would do) For example, you're not allowed to say anything bad to people who claim to know what a scientific theory is, but then continuously demonstrate a fundamental misunderstanding of the concept. Or people who reference religious sources in a scientific discussion.

If stupid arguments are not pointed out those making stupid argument will never improve.

They probably won't improve, regardless of being pointed out or not. You know, when copacetic started this thread, I thought, "good, maybe we'll finally get some proper answers and find out where the misconceptions are coming from. If we're really lucky people might realise they have no clue what they're attacking in the first place and they might become curious and try to find out". A simple, concise, plain English article explaining how evolution works, with equally simple questions asking why someone disagrees with it. Even unsupported or just plain wrong answers would have at least been something. I'm really impressed by Ekstasis asking questions, honestly. I don't know if he found the answers he was looking for but at least he's thinking about observable things and not bringing religion or mythology into the mix.

 

[Forrest]

Don't think you should quote from conservapedia to prove a point; isn't that a joke site? Its like me quoting from www.hayibo.com to backup a political view.

Perhaps / perhaps not. The reason I quoted it was somewhat satirical but it does fit the behaviour of some individuals here to a tee. They know who they are, if you're not one of them then no need to worry but look at who's going to object most fiercely against it. Most of their stuff is actually just as well referenced as most wikipedia articles are but then wikipedia has been shown to be a joke on some subjects.

Incorrect

And another one that claims it's true but with no proof whatsoever to back this up.

There is no circular reasoning with regards the fossil record. The geological stratum can be dated with radiometric dating. Because the fosil record so accuarrtly follows the radiometric dating is is short hand method for geological dating.

You apparently don't know how few times this is done. That's because archeologists know about inherently difficulties in dating what it is that they are supposed to be dating. I know you will laugh and say but radiometric dating is accurate blah blah blah but consider this: assuming the results are reliable why is there such a hugh interest in developing new dating methods? Because the existing methods can only be reliably applied in a few instances. They are INADEQAUTE!

You can spin it any way you like but fossils are used to date strata and strata are used to date fossils. That IS circular reasoning and if/can/maybe doesn't change that you will likely miss that bunny.

Evolution has been proven to happen. Multiple times.

Nice strawman. Mutation has been proven to happen. The stated premise is still unproven.

Answer the questions if you can. Too cowardly I presume.

I have and so has many others. The problems with the questions have also been pointed out. And why are you allowed to attack me? Please behave or don't take part in a "discussion".

Resistance to antibiotics IS a an improvement in fitness regardless of what to to blithering idiot at answersingenesis. The fact that many improvement came at the cost of others in no secret.

You seem to also be missing the part that it's NOT an overall improvement. Your ad hominems are not winning your argument.

"net-evoltion"? Is this another creationist moronic buzz word?

More ad hominems instead of addressing the issue.

No objections has been laid. Stop lying.

More personal attacks.

If stupid arguments are not pointed out those making stupid argument will never improve.

There is a difference between pointing out the error in an argument you believe is stupid and attacking the person making the argument and calling them names, like YOU are doing.

No one has falsified it. It is not a requirement of falsifiability that something actually be falsified.

Nobody has made that claim. You keep attacking a strawman.

Theistic Creation isn't falsifiable.

Oh yes call it "theistic" creation and then use that to claim it is not falsifiable.

A Quotemine, how surprising.

Ooh look another

How predictable.

I'm deliberately exposing how silly your position is. Either you don't truely understand falsifiability or you're being deliberately obtuse.

You're misrepresenting my comment that referred to DNA and not an "admission" to anything else as you claim it to be.

Scientific Facts don't require proving, they require explanation

Apparently you have never done any experimental science yourself. Neither have I but I know that "facts" are not taken as such just by some Joe's word that they are. They still HAVE to be proven to qualify as facts by multiple people and with careful scrutiny. Even then it is not set in stone they will remain facts as they can still be proven wrong.

Evolution is a scientific fact. (that requires no proving). "Theory of evolution" explains the scientific fact.

You're still attacking the strawman.

Any alternative explanation needs to explain the facts.

If you're implying there has to be an alternative explanation you're wrong. If a theory (or anything else) is wrong then it's wrong regardless if there's anything else to explain it.

See, that's what I thought too. And so did the OP. But, apparently the philosophical interpretation of natural selection is extremely important in answering the question of whether it happens or not. Enough to create pages and pages about. How silly of us.

What a person understands a subject to mean is anything but philosophical. If it happens the way Darwin believed it does then that is regarded as false by most (if not all) in the field. If it doesn't it is still poor support for evolution as Endler explains. Know what, it just dawned on me you're actually right. It doesn't really matter as either way it is unsupportive of the theory of evolution so it doesn't really belong in here. But if we didn't examine it we would not have known this and learned something new. We still don't know what the OP's position is or what he means with the term "evolution" however. Wonder what he learned here. So confusing a "simple" subject like evolution with "easy" answers to "basic" questions.

Oh, you better not call objectively idotic things idiotic. You'll get called out for OMG PURSEKYUSHIN/INSALTS!!!11!!11!1!. (You know, instead of being calmly told why it isn't idiotic like any non-idiot would do)

You mean like any non-idiot would not claim something as idiotic just because they don't agree with it and instead calmly explain in a non-dick manner why they don't agree?

But I'm not going to take part in this manner of discussion. We know what they say about arguing with err... non-idiots.

For example, you're not allowed to say anything bad to people who claim to know what a scientific theory is, but then continuously demonstrate a fundamental misunderstanding of the concept.

You mean those who clearly explained what it is?

Or people who reference religious sources in a scientific discussion.

References please from this thread in context.

 

[alloytoo]

Nobody has made that claim. You keep attacking a strawman.

You keep on implying it, and I'm calling it out for everyone to see.

Oh yes call it "theistic" creation and then use that to claim it is not falsifiable.

Non-Theistic creation is simply a regressive zero sum game.

How predictable.

Some people would be embarrassed at being caught in a lie.

You're misrepresenting my comment that referred to DNA and not an "admission" to anything else as you claim it to be.

Your seem confused about many things.

Apparently you have never done any experimental science yourself. Neither have I but I know that "facts" are not taken as such just by some Joe's word that they are. They still HAVE to be proven to qualify as facts by multiple people and with careful scrutiny. Even then it is not set in stone they will remain facts as they can still be proven wrong.

There were enough facts established in Darwin's day, considerably more today. Facts established by experts in their respective fields, not just some Joe.

If you're implying there has to be an alternative explanation you're wrong. If a theory (or anything else) is wrong then it's wrong regardless if there's anything else to explain it.

Theories explain facts, a falsified theory does not invalidate the facts it sought to explain, the facts remain regardless and will then require an alternative explanation.

 

[Forrest]

@Forrest, you seem to have read up quite a bit on ToE. I've asked the question before and nobody answered me.
Does natural selection (as the term is intended) always improve each generation of a species in it's environment? What is your understanding?

No. And the question should really be if mutations can improve an individual. As the article by Dr. Purdom shows there's no such thing as truely beneficial mutations. Every single mutation witnessed so far is a trade off using available existing information and makes an organism less capable to survive in some other area or in another environment.

Mutations are also not actually so commonplace. Take the tale for example. A single mutation will turn the gene(s) on or off. There have been people born with a rudimentary tail and this is easily interpreted as "evidence" for the ToE by some. But what they ignore is that this is such a rare occurence that it usually only happens once every few generations in one of the largest populations, India. And that's not because it goes unnoticed as these people are usually seen and treated as gods. I don't want to confuse you here but this is important to understand in order to understand natural selection so please bear with me. If a single mutation can take generations to only occur in one individual how long does it take for the thousands of mutations required to make the tail genes to occur and spread in the population?

And remember this, most mutations are harmful. Natural "selection" has an influence here but it weeds out the harmful ones more often than it allows the beneficial ones to propagate. Actually as a matter of fact most of those result in cancer or the collapse of a required biological system. It usually ends up dying not by any outside help from nature but from sickness. Assuming for the sake of argument that nature does "select" against the harmful mutations so the others can propogate it is still far from a perfect system.

The antelope is a good example and this is why Copacetic's source is a poor one. It doesn't really matter if you're slow. As long as you are fast enough to stay with the herd you're okay. It's safety in numbers. The one that strays is usually the one that gets eaten. Does that mean a fast animal will escape and a slow one not? Unless it's a remarkable difference it doesn't make much difference. The lion is a poor example in support of natural selection. Lions are slow animals and stalk their victims through learned behaviour. If an antelope is more than 100 meters away when it detects a lion it can easily escape unless it's the slowest animal in the group.

From these examples it would be correct to conclude that the outskirts of the herd is picked off but in the general population both beneficial (fast) genes and harmful(?) (slow) genes continue to propagate making the herd as a whole weaker than it would otherwise be. Sure there's natural selection going on but in the grand scheme it's more like the credits at the end of a movie. That's why Dr Endler cites it as poor evidence to support evolution.

Dr Endler doesn't say this but most of the "evolution" that occurs upon which natural selection "acts" is actually what we call adaptation. That is a concept that has been well known since antiquity but without an explanation. Each individual inherits one copy of genes from each of its parents of which each parent has two copies. Every base pair can therefor be one of four combinations. In the general population there are different copies of each gene which natural selection can influence.

Take Darwin's finches as an example. He noted their beak sizes increasing with a famine. Indeed their beak sizes do increase but when the famine is over they decrease again as they are either too difficult to maintain or are a hinderance. No evolution was happening here. What is happening is adaptation from already existing genes or information. During famine the larger beak genes become more dominant in the population but when it is over the smaller beak genes become more dominant. Of course this is not recognised as devolving isn't so it's all wrongly presented as forwardly evolving while it's actually lateral back and forth adaptation to the environment without the help of mutation.

There is a nicely detailed critique of the finches here. It also illustrates the religious motives of some evolutionists that would claim they have nothing invested in it yet they can't help but talk about creation. Seems creation science has truelly become a worthy subject of discussion. Also notice the three figures.
#1 is claimed to be the truth of evolution. This is in fact unsupported by the fossil record. Of course you will now likely hear the cries that the fossil record is incomplete and this was a legitimate excuse for Darwin. On ask a biologist however you can find that there are now probably countless billions of complete and incomplete fossils. The number of different kinds of fossils are only a few hundred thousand. That's more than a thousand and possibly tens of thousands of fossils per specie. The fossil record is possibly the largest most complete collection of the past we have. Incompleteness is no longer even an excuse but simply a cop-out.
#2 is the old debunked evolutionist strawman of creation.
#3 is most closely supported by the completeness of the fossil record. It shows the different kinds as they appear suddenly with little to some variation within kinds.

 

[Forrest]

You keep on implying it, and I'm calling it out for everyone to see.

I never implied any such thing. You either keep on seeing into it what you want to see or you are deliberately misrepresenting my comments. For the final time I never said something must be shown to be false for it to be falsifiable. You're attacking a strawman.

Non-Theistic creation is simply a regressive zero sum game.

Whatever that is it's likely irrelevant. I.d. and creation does not require a supernatural Creator. There is a $1,000 prize for anyone that can show otherwise.

There were enough facts established in Darwin's day, considerably more today. Facts established by experts in their respective fields, not just some Joe.

Add to that they all still had to be confirmed independently and you are well on your way to understanding what facts are.

Theories explain facts, a falsified theory does not invalidate the facts it sought to explain, the facts remain regardless and will then require an alternative explanation.

I never said it would. Requiring an alternative explanation also does not mean one will ever exist or that one has to exist before an old proven incorrect one is discarded.

Read John F. McGowan on the falsifiability myth in science.

 

[SanchoP]

People, you're never going to convince him of anything, and even if you did, so what. Just hope that he doesn't inflict this stuff too injuriously on his children.

Rather just go to reddit/r/atheism and we can point fun there at the silly creationists, banging your head against Forrest and the thousands like him will achieve nothing.

EDIT: this, basically:

 

[alloytoo]

No. And the question should really be if mutations can improve an individual.

This question is meaningless. "Improve" implies an absolute scale. The question is whether random mutations can make an species fitter for the environment in which they exist.

As the article by Dr. Purdom shows there's no such thing as truely beneficial mutations. Every single mutation witnessed so far is a trade off using available existing information and makes an organism less capable to survive in some other area or in another environment.

Fitness is relative to environment. Changes in fitness are relative to environment. A change in environment can change fitness.

Finch beaks are an excellent example.

During drought smaller beaks are "fitter" than larger beaks and are more successful causing them to dominate the gene pool. When conditions change larger beaks become fitter and more numerous.

If conditions changed permanently then one characteristic would come to dominate the population permanently and might lead to speciation.

Random mutations occur with every generation, whether they are beneficial, neutral or negative is largely determined by the environment.

Neutral mutations are by far the most numerous, and as they have no effect on fitness are likely to pass to the next generation and accumulate over time.

If conditions change then the accumulated neutral mutations may well become positive.

 

[Forrest]

People, you're never going to convince him of anything, and even if you did, so what. Just hope that he doesn't inflict this stuff too injuriously on his children.

Finch beaks are an excellent example.

During drought smaller beaks are "fitter" than larger beaks and are more successful causing them to dominate the gene pool. When conditions change larger beaks become fitter and more numerous.

I never claimed otherwise. They are indeed an excellent example of creationist variation and adaptation. They are a poor example of evolution that requires the generation of new information and not just swapping old existing information.

If conditions changed permanently then one characteristic would come to dominate the population permanently and might lead to speciation.

You should really be the one to read up on that species problem. Wolphins ftw.

 

[alloytoo]

They are indeed an excellent example of creationist variation and adaptation.

Please explain the mechanisms of "creationist adaptation"

They are a poor example of evolution that requires the generation of new information and not just swapping old existing information.

That's because they're not an example of random mutation generating new information. They're an example of how fitness is defined by environment.

You should really be the one to read up on that species problem. Wolphins ftw.

and we're back to semantics.

 

[porchrat]

Please explain the mechanisms of "creationist adaptation"

When faced with environmental logical pressures such as evidence or simple logic demonstrating that their claims are garbage the creationist shifts it's goalposts in response.

 

[Techne]

Forrest, what do you think of the mutations that caused bacteria to metabolize nylon more efficiently?

One of your claims seems to be that mutations do not improve overall fitness (correct me if I am wrong). But here again we run into problems with definitions. What exactly do you mean by "fitness" and "overall fitness"? Others may shrug this off as mere semantics, but I disagree, a clear understanding of this concept cannot be more relevant and claiming it is just 'semantics" is to me just anti-intellectual.

There are a few views on the concept of fitness and the fitness landscape theories.

 

[Techne]

Forrest, just to show you the importance of the concept of fitness, consider the following article.

Reiss makes the following interesting remark:

The rigor of this approach, however, is lessened because there is as yet no universally agreed upon measure of fitness; fitness is either defined metaphorically, or defined only relative to the particular model or system used. It is fair to say that due to this lack, there is still no real agreement on what exactly the process of natural selection is. This is clearly a problem.

He goes on to argue that implicit in the fitness landscape metaphor is the view that natural selection acts "as a force driving the population toward this improved future state". One can see how Darwin's idea of natural selection as a "force" creeps back again and if evolution is anything close to the metaphor then the process of natural selection is fundamentally teleological.

However, he argues against it and instead "the mean relative fitness of all populations is always 1.0, and never changes as long as the population continues to exist". What this means is that, if we look at the "evolution of colour" example again, each slice of the "color fossil record" will have it that all the populations will have a relative fitness of 1. Meaning, the bacteria 3 billion years ago are no more or less fit than any other group of organisms that live now or have ever lived or are going to live.

So it is important to have clear understanding of the role that fitness plays in evolution and also important to understand that people have different understandings of the concept.

 

[Forrest]

Please explain the mechanisms of "creationist adaptation"

As I understand it is a mechanism itself. I already described how it works.

That's because they're not an example of random mutation generating new information. They're an example of how fitness is defined by environment.

Indeed they are not.

and we're back to semantics.

Say what? You're the one that claimed speciation. Then you have to define what a specie is and that is anything but a certainty. I see you're ignoring the wolphin.

Forrest, what do you think of the mutations that caused bacteria to metabolize nylon more efficiently?

One of your claims seems to be that mutations do not improve overall fitness (correct me if I am wrong). But here again we run into problems with definitions. What exactly do you mean by "fitness" and "overall fitness"? Others may shrug this off as mere semantics, but I disagree, a clear understanding of this concept cannot be more relevant and claiming it is just 'semantics" is to me just anti-intellectual.

There are a few views on the concept of fitness and the fitness landscape theories.

I am not very familiar with the so-called "nylonase" mutation. Information on it also seems to be incomplete and sketchy. First page on google gives a critique of it with a refutation and a refutation on the refutation's ability as a scientist based on his misunderstanding of basic chemistry concepts. Talkorigins seem to be biologists and not chemists.

The assumption seems to be that as nylon is a man made substance it shows new information being inserted into the genome resulting in a new novel function. I think this is false without looking at exactly what was altered. With the lack of a proper critical examination I'll employ my understanding of how the genome works.

I'll start off with it being commonly believed to be a frame shift mutation as the result of a single codon insertion. Negoro et al. (2006) found that this is unlikely but let's assume it is. Note there seems to be a few arguing that some sort of guided mutation occured and information was added. No creationist I know would make such an argument for evolution or basically Darwinism. Ignoring that argument and assuming a frame shift mutation it's still the change of existing information.

I say no novel new information was added and here's why. The "new" mutated gene had to have already been there to evolve. There was no net addition of a gene as one was changed or "overwritten." What that would mean is a loss of an existing protein at the same time. I don't think anybody has tried to find out what that protein does. If it's less efficient or unable to survive in another environment it's another example of a trade-off and not an overall improvement and that is a very likely possibility.

Now, I see you pointing out the problem that there's no measure of fitness and it basically being determined by the environment. So if it can continue to survive it is 100% fit. If it doesn't survive it was less fit. While this works for the purpose of driving evolution there is something lacking. I think everyone that believes in evolution can agree that at some point there must have been an organism incapable of surviving in it's environment. Something must have happened to this organism's descendants so they could survive as life itself.

The basics of all life are genes. The minimum genes for all life would be:
Protein synthesis - to make proteins that can synthesise proteins from DNA.
Nutrient acquisition - to metabolise substances for conversion to amino acids for DNA blueprints and proteins.
Strand separation - to separate DNA strands for replication.
Strand recombination - matching amino acids to specific bases to create new base pairs.
There are likely a lot more but we'll assume these are the minimum. Ignoring the problem of all of them existing by themselves and then combining to form a self replicating organism, if a gene were to mutate and lose one of these functions the organism would be unable to reproduce and become exinct. It's fitness would fall below the minimum fitness level of 1.0.

If it adds another gene without affecting the others in a detrimental way it would add to the fitness level. An example is a gene for creating a protective cell wall. Another would be for a protein to carry nutrients through the cell wall. Now we have 4 essential genes and 2 non-essential. If one of the latter mutated and become non-functioning it would subtract from the overall fitness level and it might not survive in some environments, a harmful mutation. If it didn't change function (neutral mutation) or attained a function like the transport gene becoming another gene for a different food supply the fitness level will remain the same. We can also see that simply splitting any gene into two is not sufficient as a loss of function would also negate the added benefit (if any) and in the case of the 4 essential genes would be detrimental.

A new gene must therefor be created to add to the fitness level. Anything else is not adding information but simply changing existing information. Even if a new gene and information was added it would have to be beneficial or neutral. Any detrimental addition would cause death and so destroy the new information again. Changing a functional gene or copying over one therefor doesn't add to overall fitness. Removing one subtracts from it even if only by removing it's potential to mutate into a functional gene later. Copying genes from one location to another doesn't add to overall fitness as genes are overwritten.

This presents a difficulty that isn't being addressed.

 

[Techne]

Hi Forrest, here is a little background information about the nylon digesting enzymes.

Nylon-6 is produced from caprolactam by ring cleavage polymerization and consists of more than 100 units of 6-aminohexanoate (Ahx). During the polymerization reaction, some molecules fail to polymerize and remain as linear oligomers, while others undergo head-to-tail condensation to form cyclic oligomers (Figure 1). These cyclic and linear oligomers (called nylon oligomers) are the byproducts from nylon factories and can basically become nylon bug food. The P. aeruginosa bacterial strain can obtain the capability within 9 days.

Figure 1​

Three enzymes, 6-aminohexanoate-cyclic dimer hydrolase (EI), 6-aminohexanoate-dimer hydrolase (EII) and endo-type 6-aminohexanoate oligomer hydrolase (EIII) encoded on plasmid pOAD2 (45519 bp) of P. aeruginosa, are found to be responsible for the degradation of the nylon oligomers (Figure 2).

Figure 2​

The end product of the breakdown of the nylon oligomers is 6-aminohexanoate, which is a source (alternate or sole source) of nitrogen and carbon for these bacteria.

So how did it get there? An old study suggests it is as a result of a frame-shift mutation, however there are good reasons to doubt this. The nylonase enzymes are capable of amide hydrolysis (figure 3).

Figure 3​

Amide hydrolysis for other amides present in nature is quite common for example B-lactamases.

EII’ (nylB’) is an enzyme also encoded on plasmid OAD2 of Arthrobacter sp. KI72. The enzyme has B-lactamase folds and is also able to catalyze the breakdown of the 6-aminohexanoate-linear dimer. EII’ is a classical carboxylase with high activity towards carboxylesters with short acyl chains. EII’ is, therefore a pre-existing 6-aminohexanoate-dimer hydrolase with low activity (0.5% that of EII (nylB)) towards the 6-aminohexanoate-dimer that gained an increase in activity towards the 6-aminohexanoate-dimer through amino acid substitutions in the catalytic cleft containing the “Ser-X-X-Lys” motive.

So in essence, a few mutations enhanced an enzyme's capability to degrade one substrate without affecting the original esterase activity.

References:
1. Fukumura T. Hydrolysis of cyclic and linear oligomers of 6-aminocaproic acid by a bacterial cell extract. J Biochem (Tokyo). 1966 Jun;59(6):531-6.
2. Fukumura T. Bacterial breakdown of e-caprolactam and its cyclic oligomers. Plant Cell Physiol 1966;7:93-104
3. Prijambada ID, Negoro S, Yomo T, Urabe I. Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution. Appl Environ Microbiol. 1995 May;61(5):2020-2.
4. Negoro S. Biodegradation of nylon oligomers. Appl Microbiol Biotechnol. 2000 Oct;54(4):461-6.
5. Kato K, Ohtsuki K, Koda Y, Maekawa T, Yomo T. et al. A plasmid encoding enzymes for nylon oligomer degradation: nucleotide sequence and analysis of pOAD2. Microbiology. 1995 Oct;141 ( Pt 10):2585-90.
6. Negoro S, Ohki T, Shibata N, Sasa K, Hayashi H et al. Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase. J Mol Biol. 2007 Jun 29;370(1):142-56.
7. Negoro S, Ohki T, Shibata N, Mizuno N, Wakitani Y et al. X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme. J Biol Chem 2005 Nov 25;280(47):39644-52
8. Ohki T, Wakitani Y, Takeo M, Yasuhira K, Shibata N, Higuchi Y, et al. Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities. FEBS Lett. 2006 Sep 18;580(21):5054-2058.
9. Negoro S, Ohki T, Shibata N, Mizuno N, Wakitani Y et al. X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme. J Biol Chem 2005 Nov 25;280(47):39644-52

 

[Techne]

So one can see how new information was introduced via a few point mutations. This increased the enzyme's capability to degrade nylon without affecting its esterase activity. Sure, you might say it is a change in existing information, but one can argue that any change would result in new information from one moment to another depending of course how one defines information (definitional problem again). Is information constant in the universe, does it change as the universe changes?

 

[alloytoo]

As I understand it is a mechanism itself. I already described how it works.

Random mutation produces characteristics which are filtered by the environment.

Say what? You're the one that claimed speciation. Then you have to define what a specie is and that is anything but a certainty. I see you're ignoring the wolphin.

I said "could lead to speciation". In this context I meant would lead to a separate population which for a variety of reasons wouldn't be able to naturally breed.

This definition is obviously flawed, especially in terms of the TOE. As portions of the populations diverge the inability to breed is based constraints which are not genetic, constraints which are physical or environmental.

Wolphin's by the way do not constitute a species, the two known examples are hybrids.

 

[Chicken Boo]

As I understand it is a mechanism itself. I already described how it works.


Indeed they are not.


Say what? You're the one that claimed speciation. Then you have to define what a specie is and that is anything but a certainty. I see you're ignoring the wolphin.


I am not very familiar with the so-called "nylonase" mutation. Information on it also seems to be incomplete and sketchy. First page on google gives a critique of it with a refutation and a refutation on the refutation's ability as a scientist based on his misunderstanding of basic chemistry concepts. Talkorigins seem to be biologists and not chemists.

The assumption seems to be that as nylon is a man made substance it shows new information being inserted into the genome resulting in a new novel function. I think this is false without looking at exactly what was altered. With the lack of a proper critical examination I'll employ my understanding of how the genome works.

I'll start off with it being commonly believed to be a frame shift mutation as the result of a single codon insertion. Negoro et al. (2006) found that this is unlikely but let's assume it is. Note there seems to be a few arguing that some sort of guided mutation occured and information was added. No creationist I know would make such an argument for evolution or basically Darwinism. Ignoring that argument and assuming a frame shift mutation it's still the change of existing information.

I say no novel new information was added and here's why. The "new" mutated gene had to have already been there to evolve. There was no net addition of a gene as one was changed or "overwritten." What that would mean is a loss of an existing protein at the same time. I don't think anybody has tried to find out what that protein does. If it's less efficient or unable to survive in another environment it's another example of a trade-off and not an overall improvement and that is a very likely possibility.

Now, I see you pointing out the problem that there's no measure of fitness and it basically being determined by the environment. So if it can continue to survive it is 100% fit. If it doesn't survive it was less fit. While this works for the purpose of driving evolution there is something lacking. I think everyone that believes in evolution can agree that at some point there must have been an organism incapable of surviving in it's environment. Something must have happened to this organism's descendants so they could survive as life itself.

The basics of all life are genes. The minimum genes for all life would be:
Protein synthesis - to make proteins that can synthesise proteins from DNA.
Nutrient acquisition - to metabolise substances for conversion to amino acids for DNA blueprints and proteins.
Strand separation - to separate DNA strands for replication.
Strand recombination - matching amino acids to specific bases to create new base pairs.
There are likely a lot more but we'll assume these are the minimum. Ignoring the problem of all of them existing by themselves and then combining to form a self replicating organism, if a gene were to mutate and lose one of these functions the organism would be unable to reproduce and become exinct. It's fitness would fall below the minimum fitness level of 1.0.

If it adds another gene without affecting the others in a detrimental way it would add to the fitness level. An example is a gene for creating a protective cell wall. Another would be for a protein to carry nutrients through the cell wall. Now we have 4 essential genes and 2 non-essential. If one of the latter mutated and become non-functioning it would subtract from the overall fitness level and it might not survive in some environments, a harmful mutation. If it didn't change function (neutral mutation) or attained a function like the transport gene becoming another gene for a different food supply the fitness level will remain the same. We can also see that simply splitting any gene into two is not sufficient as a loss of function would also negate the added benefit (if any) and in the case of the 4 essential genes would be detrimental.

A new gene must therefor be created to add to the fitness level. Anything else is not adding information but simply changing existing information. Even if a new gene and information was added it would have to be beneficial or neutral. Any detrimental addition would cause death and so destroy the new information again. Changing a functional gene or copying over one therefor doesn't add to overall fitness. Removing one subtracts from it even if only by removing it's potential to mutate into a functional gene later. Copying genes from one location to another doesn't add to overall fitness as genes are overwritten.

This presents a difficulty that isn't being addressed.

Interesting post. It suggests to me you actually have a pretty good grasp on this matter, and simply won't admit it is correct (and change a few inconvenient facts to support you - such as the bolded bit).

Regarding that bolded bit, are you suggesting that no genes ever develop along the way? They're all there from the start, and are simply activated or used according to the organism's level of development?

 

[porchrat]

You people are wasting your time. He isn't going to respond to logic or evidence. This is an rza mindset with fancier words.