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Check this out.

This is from wiki.

"Further study revealed that the three enzymes the bacteria were using to digest the byproducts were significantly different from any other enzymes produced by other Flavobacterium strains (or any other bacteria for that matter), and not effective on any material other than the manmade nylon byproducts."

ino[Edited Out]a, S.; Kageyama, S., Iba, K., Yamada, Y. and Okada, H. (1975). "Utilization of a cyclic dimer and linear oligomers of e-aminocaproic acid by Achromobacter guttatus". Agricultural & Biological Chemistry 39 (6): 1219−23. ISSN 0002-1369

The pages are linked.

Achromobacter guttatus K172, isolated from sludge, was found to utilize ƒأ-caprolactam, ACA, its cyclic dimer, linear dimer, trimer,

tetramer, pentamer, and hexamer of ACA, and dimethylimino ether of the cyclic dimer at various metabolic rates. Fukumura showed1,2), that a strain of Corynebacterium aurantiacum metabolized ACA, ACA2, ACA3, and ACA4, ACA-c-trimer. Another strain, Achromobacter guttatus KF714) could grow on ƒأ-caprolactam but not the cyclic dimer. The cyclic dimer seems to have a stable configuration with strong intramolecular hydrogen bonds and this is a reason to be resistant to biological attack.The crude extract of C. aurantiacum12) had two enzymes which hydrolyzed cyclic and linear oligomers of ACA. Also our recent results showed that one enzyme hydrolyzed ACA-c-dimer to ACA2, and the other ACAlinear- oligomers after extensive purification."' In the experiment on carbobenzoxy derivatives of ACA oligomers, the monomer and the dimer were not utilized but longer oligomers were metabolized slowly. Acrylated ACA monomer and dimer were not utilized.

Now, its a bit of a mouthful but, the organisms are each independent in their own right, breaking down their own nylon compounds. They each have their own specific substrates that they react with, let alone would they be able to react with a wide range of compounds outside of those related to nylon products. That is what they are limitted to, and they do it well.

And ultimately, im going to come back to it again anyway. The organisms new functions are benefitting their survival. And thats ultimately what is most important in this entire discussion. Even if the enzymes lost specificity and reacted with a broad range of substrates (which they dont react with a wide range of substrates and compounds), the organism is still benefiting from the mutation, and the mutation because of this benefit has made its way throughout the entire population and continues to thrive.

New gene, new protein, new function, the function is beneficial to life and propagates throughout the population of bacteria. This is evolution. Thats it.

And that is the bottom line.

And Im reading over your paper as well. Both of our sources are acknowledging this evolution. Both are acknowledging the independent traits of the enzymes produced and their unique specificity.

So, if you follow your own source, you also support evolution. Which leads me to wonder what you are trying to point out here.

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Idev says And your source is discussing oligomers of nylon.

My source is actually a few,I gave you two check them out,that was the link to the website and one of the sources that I used from that website.

None the less the source that I gave you,if you did indeed read through it says very clearly that the enzyme can use much more oligomers than that of nylon,to say otherwise would to be non-sense.

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My source is actually a few,I gave you two check them out,that was the link to the website and one of the sources that I used from that website.

None the less the source that I gave you,if you did indeed read through it says very clearly that the enzyme can use much more oligomers than that of nylon,to say otherwise would to be non-sense.

The link you gave,

http://hwmaint.jbc.o...rt/280/47/39644

Is one article. You even gave the volume and page numbers of the article when you sourced it. If you are referring to the related articles at the bottom, then you should say so.

You should say what article you are referring to and what particular section.

Edited by iDevonian
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Idev says Check this out.

This is from wiki.

"Further study revealed that the three enzymes the bacteria were using to digest the byproducts were significantly different from any other enzymes produced by other Flavobacterium strains (or any other bacteria for that matter), and not effective on any material other than the manmade nylon byproducts."

ino[Edited Out]a, S.; Kageyama, S., Iba, K., Yamada, Y. and Okada, H. (1975). "Utilization of a cyclic dimer and linear oligomers of e-aminocaproic acid by Achromobacter guttatus". Agricultural & Biological Chemistry 39 (6): 1219−23. ISSN 0002-1369

The pages are linked.

Achromobacter guttatus K172, isolated from sludge, was found to utilize ƒأ-caprolactam, ACA, its cyclic dimer, linear dimer, trimer,

tetramer, pentamer, and hexamer of ACA, and dimethylimino ether of the cyclic dimer at various metabolic rates. Fukumura showed1,2), that a strain of Corynebacterium aurantiacum metabolized ACA, ACA2, ACA3, and ACA4, ACA-c-trimer. Another strain, Achromobacter guttatus KF714) could grow on ƒأ-caprolactam but not the cyclic dimer. The cyclic dimer seems to have a stable configuration with strong intramolecular hydrogen bonds and this is a reason to be resistant to biological attack.The crude extract of C. aurantiacum12) had two enzymes which hydrolyzed cyclic and linear oligomers of ACA. Also our recent results showed that one enzyme hydrolyzed ACA-c-dimer to ACA2, and the other ACAlinear- oligomers after extensive purification."' In the experiment on carbobenzoxy derivatives of ACA oligomers, the monomer and the dimer were not utilized but longer oligomers were metabolized slowly. Acrylated ACA monomer and dimer were not utilized.

Now, its a bit of a mouthful but, the organisms are each independent in their own right, breaking down their own nylon compounds. They each have their own specific substrates that they react with, let alone would they be able to react with a wide range of compounds outside of those related to nylon products. That is what they are limitted to, and they do it well.

The information regarding the nylon's ability to only be effective against nylon is not from the article but from the wiki edit I didn't see it in the article. I also showed you from later sources that this mutation was indeed from a loss of specification (this article/source is from 1975).

So you failed by giving me an outdated article that was superseded by later information that I gave you.

Your second blunder is your false interpretation of the information that you have given me

You said that each enzyme was broke down its own oligomer,you either didn't read the article or you are just inputting your interpretation on the article.

Side note : never use Wikipedia when you are debating an issue such as evolution.

The article mentions three enzymes and what they break down

The first enzyme breaks down ACA strains. (shard with enzyme 1,2,and 3)

The second enzyme breaks down ACA, ACA2(shared with enzyme 2 ), ACA3, and ACA4, ACA-c-trimer strains.

The third enzyme breaks down ACA strains, ACA-c-dimer and ACA2

All 3 break down ACA strains,the only difference is the second enzyme breaks down ACA3 and ACA4 which the first enzyme and second enzyme do not.

ACA3 and ACA4 are barely any different from the their brother strands,so to say "they each use their own oligomer" you are trying to create that illusion of lock and key and specificity,when in fact this is far from what the article is saying.

The statement "they each use their own oligomers" is wrong,they all share the same strands except for some exceptions that are barely any different.

Idev says And ultimately, im going to come back to it again anyway. The organisms new functions are benefitting their survival. And thats ultimately what is most important in this entire discussion. Even if the enzymes lost specificity and reacted with a broad range of substrates (which they dont react with a wide range of substrates and compounds), the organism is still benefiting from the mutation, and the mutation because of this benefit has made its way throughout the entire population and continues to thrive.

You keep repeating yourself I already answered this a million times,now I think its best I quote the articles I gave you and comment on them so you can accept what I'm saying.

Idev says New gene, new protein, new function, the function is beneficial to life and propagates throughout the population of bacteria. This is evolution. Thats it.

And that is the bottom line.

And Im reading over your paper as well. Both of our sources are acknowledging this evolution. Both are acknowledging the independent traits of the enzymes produced and their unique specificity.

This is your interpretation,the new sequence is from a corrupted version which lost specificity. Which I will quote for you.

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The information regarding the nylon's ability to only be effective against nylon is not from the article but from the wiki edit I didn't see it in the article. I also showed you from later sources that this mutation was indeed from a loss of specification (this article/source is from 1975).

So you failed by giving me an outdated article that was superseded by later information that I gave you.

Your second blunder is your false interpretation of the information that you have given me

You said that each enzyme was broke down its own oligomer,you either didn't read the article or you are just inputting your interpretation on the article.

The article mentions three enzymes and what they break down

The first enzyme breaks down ACA strains. (shard with enzyme 1,2,and 3)

The second enzyme breaks down ACA, ACA2(shared with enzyme 2 ), ACA3, and ACA4, ACA-c-trimer strains.

The third enzyme breaks down ACA strains, ACA-c-dimer and ACA2

All 3 break down ACA strains,the only difference is the second enzyme breaks down ACA3 and ACA4 which the first enzyme and second enzyme do not.

ACA3 and ACA4 are barely any different from the their brother strands,so to say "they each use their own oligomer" you are trying to create that illusion of lock and key and specificity,when in fact this is far from what the article is saying.

The statement "they each use their own oligomers" is wrong,they all share the same strands except for some exceptions that are barely any different.

fair enough. They have differences in the compounds they act on. And the third* doesnt break down ACA 3 nor ACA4. And your first and 3rd enzymes arent breaking down the same compounds either.

You keep repeating yourself I already answered this a million times,now I think its best I quote the articles I gave you and comment on them so you can accept what I'm saying.

This is your interpretation,the new sequence is from a corrupted version which lost specificity. Which I will quote for you.

sure, and did you answer my statement? You should add that in as well with your commentary.

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( sorry I meant to say that Enzyme 2 breaks down ACA3 and ACA 4,which enzyme 1 and 3 do not break down,makes no difference).

Regarding the specifcity "6-Aminohexanoate-dimer hydrolase (EII), responsible for thedegradation of nylon-6 industry by-products, and its analogousenzyme (EII') that has onlysim.gif0.5% of the specific activity towardthe 6-aminohexanoate-linear dimer, are encoded on plasmid pOAD2ofArthrobacter sp".

Regarding its other functions ". In addition, on the basis of the spatiallocation and role of amino acid residues constituting the activesites of the nylon oligomer hydrolase, carboxylesterase, D-alanyl-D-alanine-peptidase,and beta.gif-lactamases, we conclude that the nylon oligomer hydrolaseutilizes nucleophilic Ser112 as a common active site both fornylon oligomer-hydrolytic and esterolytic activities"

End of quotations.

Both esterolyctic activies (its old function) and break of nylon oligomers are still used,this is possible because both use Ser as a common active site,so any oligomer that can fit past the cleft site that can utilize this common active site which are many that can be quoted from the article I gave you can be used.

I hope you understand now.

1.There was no gain of specificity

2. The enzyme is now degenerative due to its loss of specificity in choosing oligomers. Which I will quote from the article I gave you.

Nature

339:191–195

http://www.nature.co...s/339191a0.html From the intro.

"The substrate specificity of α-lytic protease has been changed dramatically, with a concomitant increase in activity, by replacing an active-site Met with Ala. The substrate specificity of both this mutant and another similar mutant are extraordinarily broad. X-ray crystallographic analysis shows that structural plasticity, a combination of alternate side-chain conformations and binding-site flexibility, allows both large and small substrates to be well accommodated. "

​This states the specificity was lost for a particular enzyme,If you also go into the article the loss of its specificity caused it to be degenerative.

Edited by Ibn-Ahmed Aliyy Herz
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Regarding the specifcity "6-Aminohexanoate-dimer hydrolase (EII), responsible for thedegradation of nylon-6 industry by-products, and its analogousenzyme (EII') that has onlysim.gif0.5% of the specific activity towardthe 6-aminohexanoate-linear dimer, are encoded on plasmid pOAD2ofArthrobacter sp".

Regarding its other functions ". In addition, on the basis of the spatiallocation and role of amino acid residues constituting the activesites of the nylon oligomer hydrolase, carboxylesterase, D-alanyl-D-alanine-peptidase,and beta.gif-lactamases, we conclude that the nylon oligomer hydrolaseutilizes nucleophilic Ser112 as a common active site both fornylon oligomer-hydrolytic and esterolytic activities"

End of quotations.

Both electrolytic activies (its old function) and break of nylon oligomers are still used,this is possible because both use Ser as a common active site,so any oligomer that can fit past the cleft site that can utilize this common active site which are many that can be quoted from the article I gave you can be used.

I hope you understand now.

1.There was no gain of specificity

2. The enzyme is now degenerative due to its loss of specificity in choosing oligomers. Which I will quote from the article I gave you.

Nature

339:191–195

http://www.nature.co...s/339191a0.html From the intro.

"The substrate specificity of α-lytic protease has been changed dramatically, with a concomitant increase in activity, by replacing an active-site Met with Ala. The substrate specificity of both this mutant and another similar mutant are extraordinarily broad. X-ray crystallographic analysis shows that structural plasticity, a combination of alternate side-chain conformations and binding-site flexibility, allows both large and small substrates to be well accommodated. "

​This states the specificity was lost.

If you also go into the article it states that it is also pretty much bad for the bacteria.

If you are subscribed to nature, then quote where it describes the harmfullness to the bacteria and why.

Otherwise, ill accept your statement of decreased specificity of the substrate, however its still highly specific, and let me go back into my source here...one moment.

hm yes.

http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1981.tb05371.x/pdf

"6-Aminohexanoic-acid-oligomerh ydrolase of Flavobacteriurn sp. K172 was purified to homogeneity by

column chromatography three times, and by preparative polyacrylamide gel electrophoresis twice. The purified

enzyme had the following characteristics."

"4. The enzyme was active on 6-aminohexanoic acid oligomers from dimer to hexamer and icosamer but not

on hectamer, and the activity decreased with the increase of the polymerization number of the oligomer. The

oligomers were hydrolyzed so as to remove the 6-aminohexanoic acid residue successively from t he amino

terminus. The enzyme could not hydrolyze other linear amides, cyclic amides, dipeptides, tripeptides or casein."

"The enzyme had no activity on the following compounds :6-aminohexanoic acid cyclic dimer, 6-caparolactam, 5-valerolactam,

2-pyrrolidone, 30 kinds of dipeptides, 8 kinds of tripeptides, tetra-alanine and penta-alanine, casein, 6-N-acetyllysine,

N-acetyltrialanine, N-carbobenzoxyglycylleucinamide, N-acetyltrialanine methyl ether, glutamine and asparagine."

And now Im officially running out of straws. But this appears to be fair. Even if the protein uses a broader ranged active common site for "nylon oligomer-hydrolytic and esterolytic activities", there are still many compounds it doesnt act on, as well as the differences with the other 2 enzymes.

And in the end, you would have to refresh me on your response toward the digestive ability being detrimental to the organism.

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If you are subscribed to nature, then quote where it describes the harmfullness to the bacteria and why.

Otherwise, ill accept your statement of decreased specificity of the substrate, however its still highly specific, and let me go back into my source here...one moment.

If you are subscribed to nature, then quote where it describes the harmfullness to the bacteria and why.

Otherwise, ill accept your statement of decreased specificity of the substrate, however its still highly specific, and let me go back into my source here...one moment.

No one said it wasn't specific,I said it lost specificity.

Obviously it isn't going to take most or all oligomers,I think that is impossible.

If we are done with the idea of beneficial mutations,who can move on to natural selection now.

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No one said it wasn't specific,I said it lost specificity.

Obviously it isn't going to take most or all oligomers,I think that is impossible.

If we are done with the idea of beneficial mutations,who can move on to natural selection now.

alright, good. Thats fair. And hold on, I still dont see why you believe this is detrimental to the organism. Also, im uncertain of if you believe this is evolution or not.

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alright, good. Thats fair. And hold on, I still dont see why you believe this is detrimental to the organism.

alright, good. Thats fair. And hold on, I still dont see why you believe this is detrimental to the organism.

We don't need to go into anything complex or sourced for this as it is basic.

One of the main functions of an enzyme is it's lock and key formation which causes it choose specific molecules.

http://media.photobu...nzymes.jpg?o=14

One of the main reasons for this function is to protect the energy efficiency and the enzyme's ability to transport certain molecules.

So if a bacteria is created by Allah SWT to transport molecule X,and now it lost specificity from it's enzymes and molecule B is now also used,the bacteria is not equipped to transport it.

Edited by Ibn-Ahmed Aliyy Herz
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We don't need to go into anything complex or sourced for this as it is basic.

One of the main functions of an enzyme is it's lock and key formation which causes it choose specific molecules.

http://media.photobu...nzymes.jpg?o=14

One of the main reasons for this function is to protect the energy efficiency and the enzyme's ability to transport certain molecules.

So if a bacteria is created by Allah SWT to transport molecule X,and now it lost specificity from it's enzymes and molecule B is now also used,the bacteria is not equipped to transport it.

Would you be so kind as to quote the nature article for the harmfulness of the mutation? This still sounds like a benefit to me, given that the organism can digest a new product. Or at the very least, it would be a benefit and a detriment.

And thats assuming you are subscribed to them. If you arent, thats fine, perhaps the article is elsewhere. Or, im not even sure if that article is in reference to nylonase.

Either way, if you have something, bring it here, or if you agree with my statement above, thats fine too. If you dont, then just let me know.

And you still havent said whether or not your believe this is evolution. Maybe you want to discuss more before coming to that conclusion. But as of right now it looks like we are on track for it being supportive of my position. Which you may or may not hold as well.

And ill forge ahead now, and if you disagree just let me know. This mutation isnt detrimental to the point it harms the organisms ability to survive to the point it would destroy the organism. Thats apparent in the fact that they prosper with the mutation. And it does benefit the organism in allowing it to digest byproducts of nylon. And I think you should agree with this. And so, I believe that you would agree that it has evolved.

Mind you, evolution isnt a one way beneficial track. Its...whats the phrase. Random walks. Mutations are a medly of pros and cons for all organisms, but what it comes down to is the final product. And in this case, our final product is a prosperous organism that digests nylon with less specific (although still highly specific) enzymes.

Or maybe, when you see something mutate and take on changes in the proteins it develops, and then you watch that organisms trait become the dominant amongst a population...maybe you dont think that is evolution? But thats what I would call it. And I think you know this is all true, considering you essentially just explained it with your own words.

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I think we can conclude after I sum up your remaining points.

1. This type of mutation will lead to life we say today.

2. This type of mutation is not harmful.

You see,the main point of our discussion was for you to give me a reason why random mutations can create novel proteins.

When I say novel proteins I don't mean a corrupted variation that from its essence causes no function and from its inability causes a function.

I'm talking about a protein that is relevant,a protein with actual ability that improves the function of the organism.

Not like the sickle cell example,which this nylon mutation falls under.

Sure sick cell disease is new type of protein,but this isn't what we are looking for at all.

Lets say that the this helped the enzyme 1000%,let say that this nylon eating mutation caused this bacteria to be superior to every single bacteria now in existence.

You still admit that what happened was it just became less specific,can I ask you a question?

How does something becoming less specific lead to the life we see today?

How can an enzyme or anything else being corrupted cause complexity and interlocking and interacting protein machines to form?

Now moving on your the harmfulness of the enzyme,this is irrelevant. I only brought this up as a side issue,but none the less I explained it with my other quote.

I don't have a sub with them anymore but to be honest I don't think you need any type of peer reviewed article as you can find this on simple websites that explain the enzyme lock and key formation and why it is there in the first place.

Edited by Ibn-Ahmed Aliyy Herz
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I think we can conclude after I sum up your remaining points.

1. This type of mutation will lead to life we say today.

2. This type of mutation is not harmful.

You see,the main point of our discussion was for you to give me a reason why random mutations can create novel proteins.

When I say novel proteins I don't mean a corrupted variation that from its essence causes no function and from its inability causes a function.

I'm talking about a protein that is relevant,a protein with actual ability that improves the function of the organism.

Not like the sickle cell example,which this nylon mutation falls under.

Sure sick cell disease is new type of protein,but this isn't what we are looking for at all.

lets take this one step at a time, and I appreciate your honest statements and questions. (and i appreciate your decency with the subject, you have earned my respect).

I would say, your perspective of the mutation is your perspective. You claim it as...harmful, which you could say it is, but you arent recognizing the overriding benefit. Or you are recognizing it, but it sounds like you dont care for it.

The organism, is prospering with its new mutation. The new mutation is granting it a new ability with proteins that are new in its existence. And if you have a number of mutations, the organisms survival is going to come down to the net benefits vs detriments. And, you probably know this, there are many many mutations that occur and many many traits that organisms bring into themselves that harm them in some way. A common one, our brain is massive and we can do great things with it, but it sucks up a lot of our energy, many organisms couldnt use our brain. Or our wrist bones, we can twist our wrists, but in return, they are thin and break easy when we go snowboarding. Clearly its the same thing on a molecular level.

But what it comes down to is survival. If we only mutated purely beneficial functions, we would be Gods and we would be defying reality.

and just out of curiousity, would you be interested in looking into the CCR5 and the LDL receptor protein mutations I have posted in this topic as well? I will look into them, but with you here as well, you could assist me (as you can see, my field isnt biology :P). Also, these other examples may give you what you are looking for. Or not.

Lets say that the this helped the enzyme 1000%,let say that this nylon eating mutation caused this bacteria to be superior to every single bacteria now in existence.

That sounds impossible, or maybe not impossible, but improbable. Organisms do not evolve into greater beings. They evolve into beings more suitable for their environment. Nylon was introduced to the bacterias environment, hence it took on the new trait to benefit in its environment moreso than its predicesors. That doesnt mean no detriment came with the mutation, it simply means the organisms benefits outweight the detriments at this point in time in this particular environment.

Let me know if you agree with that. I think you should.

You still admit that what happened was it just became less specific,can I ask you a question?

How does something becoming less specific lead to the life we see today?

How can an enzyme or anything else being corrupted cause complexity and interlocking and interacting protein machines to form?

Its not about specificity, its about benefits vs detriments. And I wouldnt say its been corrupted. Id say its simply different. You cant say its corrupted if its in part benefitting from the mutation.

Now moving on your the harmfulness of the enzyme,this is irrelevant. I only brought this up as a side issue,but none the less I explained it with my other quote.

I don't have a sub with them anymore but to be honest I don't think you need any type of peer reviewed article as you can find this on simple websites that explain the enzyme lock and key formation and why it is there in the first place.

sure, ill have a look around then.

And in all honesty, i still dont know where you stand on evolution. You seem to understand that the mutation occured and propogated through the population. You also know that evolution is a theory, its always subjected to modification and nowhone would claim it to be the full picture.

But I would call this evolution, none the less. And Im not sure if you are avoiding using the word. But, its ok to call it evolution even if you believe that there is more to it that we dont understand. Because thats what it is, its a theory. Thats what its here for, its here to be criticised while simultaneously explaining things we see, like this whole nylonase concept.

And I think you know all this, but i just dont see you commenting on it. Like you are waiting for a que or something.

The CCR5 and LDL receptor protein mutations are those that lead to HIV immunity and increased bone density in humans. Which to me, again sound like benefits, but perhaps there are detriments that come along side them. You are asking for potentially 1000% beneficial mutations, well perhaps these are purely beneficial, i wouldnt know. As of right now, I would say there is a chance they are, but again, theres also a chance its like nylonase.

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Idev says lets take this one step at a time, and I appreciate your honest statements and questions. (and i appreciate your decency with the subject, you have earned my respect).

I would say, your perspective of the mutation is your perspective. You claim it as...harmful, which you could say it is, but you arent recognizing the overriding benefit. Or you are recognizing it, but it sounds like you dont care for it.

I appreciate your kind statement,thanks. To you as well.

The nylon digesting ability being harmful or not harmful is completely irrelevant,what is relevant to our discussion are those mutations/examples which show how evolution of this life can take place.

Breaking down of specificity isn't an attribute that can cause what we see today,so that's why I rejected your example.

What I didn't see is evolution,because to me evolution is when something becomes better,in this case the bacteria lost in the long run. < But again this is irrelevant to our discussion.

Idev says The organism, is prospering with its new mutation. The new mutation is granting it a new ability with proteins that are new in its existence. And if you have a number of mutations, the organisms survival is going to come down to the net benefits vs detriments. And, you probably know this, there are many many mutations that occur and many many traits that organisms bring into themselves that harm them in some way. A common one, our brain is massive and we can do great things with it, but it sucks up a lot of our energy, many organisms couldnt use our brain. Or our wrist bones, we can twist our wrists, but in return, they are thin and break easy when we go snowboarding. Clearly its the same thing on a molecular level.

To use our brain in this example would fail due to the fact that the energy cost is worth the benefit,thus it is rational to say it is "good". However regarding the nylon bacteria,it poorly transports the new form of energy causing it to degenerate,as with any enzyme using random molecules that bacteria is not familiar with.

Again this is a side issue however.

Idev says But what it comes down to is survival. If we only mutated purely beneficial functions, we would be Gods and we would be defying reality.

Beneficial mutations in the sense of new functional proteins are impossible due to its only way of coming about is via duplication/frame shift.

Idev says and just out of curiousity, would you be interested in looking into the CCR5 and the LDL receptor protein mutations I have posted in this topic as well? I will look into them, but with you here as well, you could assist me (as you can see, my field isnt biology :P). Also, these other examples may give you what you are looking for. Or not.

Sure.

That sounds impossible, or maybe not impossible, but improbable. Organisms do not evolve into greater beings. They evolve into beings more suitable for their environment. Nylon was introduced to the bacterias environment, hence it took on the new trait to benefit in its environment moreso than its predicesors. That doesnt mean no detriment came with the mutation, it simply means the organisms benefits outweight the detriments at this point in time in this particular environment.

Let me know if you agree with that. I think you should.

I said it that way to show you a point not that an organism is going to be the most superior thing in the world or anything like that.

I used an exaggerating statement and number to emphasize rhetorically the greatest benefit you can think of.

I was showing you that even the biggest benefit you can think of is irrelevant to this type of mutation.

Idev says

Its not about specificity, its about benefits vs detriments. And I wouldnt say its been corrupted. Id say its simply different. You cant say its corrupted if its in part benefitting from the mutation.

When speaking about specificity this automatically pushes us out of the realm of biology and puts us in philosophy.

To keep it short and sweet,specificity is basically choosing out of many contingent possibilities.

This also happens to be the foundation of every single argument for the existence of God in Islamic scholastic theology.

So we say.most sequences/protein shapes are random and chaotic with no form or benefit like random playdoe shapes. However within this structure universe there are a few islands of beneficial shapes of protein depending on where I put that shape(I can't put a motor in a carpet).

Likewise with a statue,if it was a block you wouldn't say "this block is specific". If however I detailed a face and a human body,you can then say I specified the shapes on that block according to our understanding of what a human looks like.

Likewise with the shape of that enzyme cleft,that shape was a specific lock and key formation that canceled out non esterlyctic molecules,it lost its specificity and now uses many other oligomers.

If you were to say that mutation formed a shape specifically for nylon molecules I would of agreed you with the very first time you mentioned it to me and I would agree yes this mutation is a good example for what natural selection can preserve.

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The nylon digesting ability being harmful or not harmful is completely irrelevant,what is relevant to our discussion are those mutations/examples which show how evolution of this life can take place.

Breaking down of specificity isn't an attribute that can cause what we see today,so that's why I rejected your example.

My example is what it is, I dont believe I ever claimed it to be "1000% beneficial". I just claimed it to be evolution, which it is.

What I didn't see is evolution,because to me evolution is when something becomes better,in this case the bacteria lost in the long run. < But again this is irrelevant to our discussion.

Ok, well by definition, evolution isnt "something becoming better". So, sorry to dissapoint you.

To use our brain in this example would fail due to the fact that the energy cost is worth the benefit,thus it is rational to say it is "good". However regarding the nylon bacteria,it poorly transports the new form of energy causing it to degenerate,as with any enzyme using random molecules that bacteria is not familiar with.

yup, and digesting nylon is worth the lost specificity for the bacteria. And the reason we know that it is a greater benefit for the bacteria is because it has propogated its way throughout the population of bacteria. Demonstrating its superiority over the detriment. If the detriment were truly as harmful as you believe it were, the organism would die off.

Beneficial mutations in the sense of new functional proteins are impossible due to its only way of coming about is via duplication/frame shift.

Id still say the new function for the nylon digesting bacteria is beneficial.

I said it that way to show you a point not that an organism is going to be the most superior thing in the world or anything like that.

No organism in existence is the most superior in the world. Even humanity is brought to its knees by viruses from time to time. Physically out performed by much of the animal kingdom. Humanity has many detrimental traits. But again, its about net benefits vs net detriments.

I used an exaggerating statement and number to emphasize rhetorically the greatest benefit you can think of.

I was showing you that even the biggest benefit you can think of is irrelevant to this type of mutation.

I dont know if there is such a thing as a perfectly beneficial mutation. Never claimed there was either.

When speaking about specificity this automatically pushes us out of the realm of biology and puts us in philosophy.

To keep it short and sweet,specificity is basically choosing out of many contingent possibilities.

This also happens to be the foundation of every single argument for the existence of God in Islamic scholastic theology.

So we say.most sequences/protein shapes are random and chaotic with no form or benefit like random playdoe shapes. However within this structure universe there are a few islands of beneficial shapes of protein depending on where I put that shape(I can't put a motor in a carpet).

Yea sure.

Likewise with a statue,if it was a block you wouldn't say "this block is specific". If however I detailed a face and a human body,you can then say I specified the shapes on that block according to our understanding of what a human looks like.

Likewise with the shape of that enzyme cleft,that shape was a specific lock and key formation that canceled out non esterlyctic molecules,it lost its specificity and now uses many other oligomers.

If you were to say that mutation formed a shape specifically for nylon molecules I would of agreed you with the very first time you mentioned it to me and I would agree yes this mutation is a good example for what natural selection can preserve.

Yea, sounds fine to me. Are you proposing that the evolution is intelligently guided?

And yet, that sounds strange to me because you are the one who is claiming the mutation was detrimental. If the organism had mutated the perfect shape for nylon molecules then it wouldnt be intelligently guided.

Or are you saying, hypothetically, if the organism did mutate the perfect shape, then you would call it evolution. I dont think id ever make such a claim, but again evolution isnt about evolving into the perfect being. Its not about transforming into Gods. And this is why people say its random, because just as there are benefits, there are detriments, just like what we've just discussed with nylonase.

I think regardless, it is what it is. Its a mutation carried throughout the population. Its evolution.

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Idev says My example is what it is, I dont believe I ever claimed it to be "1000% beneficial". I just claimed it to be evolution, which it is.

I'm not saying you did,I used the 1000 percent statement only to give you an absurd example that is heavily in your favor to show you that it doesn't matter,what matters is what got us here today.

Idev says Ok, well by definition, evolution isnt "something becoming better". So, sorry to dissapoint you.

hmm,I don't think so.

Because when we say "our technology has evolved",what we are saying is that our technology has gotten better.

The very essence of the world "evolve" implies something passing on to a better stage I think everyone can agree to that.

Devolve would be the opposite.

Idev says yup, and digesting nylon is worth the lost specificity for the bacteria. And the reason we know that it is a greater benefit for the bacteria is because it has propogated its way throughout the population of bacteria. Demonstrating its superiority over the detriment. If the detriment were truly as harmful as you believe it were, the organism would die off.

When you say spread through the population of bacteria what are you referring to? Bacteria only reproduces by splitting itself it doesn't spread it genes by finding a partner,etc.

This bacteria belongs to the genus of flavobacterium,under the family of flavobacteriaceae.

Even among its genus of flavobecterium it is considered rare.

The code for this particular strain is Sp. K172 ,also known as the "nylon eating bacteria".

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I'm not saying you did,I used the 1000 percent statement only to give you an absurd example that is heavily in your favor to show you that it doesn't matter,what matters is what got us here today.

ok. yea sure.

hmm,I don't think so.

Because when we say "our technology has evolved",what we are saying is that our technology has gotten better.

The very essence of the world "evolve" implies something passing on to a better stage I think everyone can agree to that.

Devolve would be the opposite.

Well, with the theory of evolution. And this is how I have always learned it. And this is what the evidence shows. Its not a ladder. Its a web that can go in any direction. And there are many evidence for this such as...detrimental mutations. Or mutations that dont have any real clear benefit or detriment. The fossil record, is very non directional.

Im sure you have heard people say evolution is "random". The reason they say this is because organisms dont evolve to become more superior, they just evolve and their traits carry on or die off.

laddervstree.gif

When you say spread through the population of bacteria what are you referring to? Bacteria only reproduces by splitting itself it doesn't spread it genes by finding a partner,etc.

This bacteria belongs to the genus of flavobacterium,under the family of flavobacteriaceae.

Even among its genus of flavobecterium it is considered rare.

What I mean is, the trait/function becomes the dominant feature in a set population of X organism(s).

It could honestly be the worst mutation ever. If the organism lives on and the trait becomes dominant throughout the population of organisms, thats evolution.

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Idev says Well, with the theory of evolution. And this is how I have always learned it. And this is what the evidence shows. Its not a ladder. Its a web that can go in any direction. And there are many evidence for this such as...detrimental mutations. Or mutations that dont have any real clear benefit or detriment. The fossil record, is very non directional.

Im sure you have heard people say evolution is "random". The reason they say this is because organisms dont evolve to become more superior, they just evolve and their traits carry on or die off.

This is variation/speciation,an aspect of the theory of evolution.

When someone says "evolve",then you are saying that X has become better.

There is a logical fallacy among people who try to prove evolution and that is according to them is similarity = common ancestry.

If we put their argument in a syllogism it would look like this.

1. Things which are similar have a common ancestry.

2. Humans and apes are similar.

3. Humans and apes have a common ancestry.

Same thing with summation as well.

The problem is with principle 1 and this fallacy can be explained by analogy,I use a lot of analogy as it is actually one the main tools human use to understand abstract concepts. So don't be put off by it or anything like that,I use it for myself so that I can understand not that I'm trying to assume you or the other people reading this are simple minded.

Lets say that I create life,by logical necessity my creation would have a tree of similarities even though they did not evolve.

Some creations would be more similar to others.

Even with this scenario you can still make a tree,so your ability to make a tree of life is irrelevant to evolution.

All your tree shows is that some species are more similar to other species.

The reason why chimps and humans are similar is simple,we have similar muscular and bone structure,in other words we are shaped the same.

In order for summation and its phylogenetic trees to be valid proof for common ancestry,it would have to be paired with dates.

We are going to speak on that and fossils in your geology post as we said or at least after we are done talking about biology/genetics.

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This is variation/speciation,an aspect of the theory of evolution.

When someone says "evolve",then you are saying that X has become better.

There is a logical fallacy among people who try to prove evolution and that is according to them is similarity = common ancestry.

If we put their argument in a syllogism it would look like this.

1. Things which are similar have a common ancestry.

2. Humans and apes are similar.

3. Humans and apes have a common ancestry.

Same thing with summation as well.

The problem is with principle 1 and this fallacy can be explained by analogy,I use a lot of analogy as it is actually one the main tools human use to understand abstract concepts. So don't be put off by it or anything like that,I use it for myself so that I can understand not that I'm trying to assume you or the other people reading this are simple minded.

Lets say that I create life,by logical necessity my creation would have a tree of similarities even though they did not evolve.

Some creations would be more similar to others.

Even with this scenario you can still make a tree,so your ability to make a tree of life is irrelevant to evolution.

All your tree shows is that some species are more similar to other species.

The reason why chimps and humans are similar is simple,we have similar muscular and bone structure,in other words we are shaped the same.

In order for summation and its phylogenetic trees to be valid proof for common ancestry,it would have to be paired with dates.

We are going to speak on that and fossils in your geology post as we said or at least after we are done talking about biology/genetics.

I dont think anyone claims that simple relatedness in morphology is proof for evolution.

And yes, speciation is one aspect of evolution. Im glad you acknowledge that.

When referring to the theory of evolution, you will rarely hear people refer to evolution as a species becoming "better". Because "better" is a subjective term.

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While you work on your paleo argument, im going to claim victory here in the biology section.

Also, I guess Ill add this in. The tree isnt irrelevant because its a commonly established tree amongst a multitude of fields. It demonstrates true relatedness of organisms.

Though one single tree relating morphology doesnt prove anything.

And actually, if you look at a phylogenetic tree based on DNA relatedness, the tree isnt built on similarities, but rather differences in the DNA. For example, if you had the DNA sequence..

CCA ACT, and CCA GTT and CCA TCT. You would be able to tell that sequence one and 3 are closer related simply because it has the least amount of difference in its DNA structure. And as you know, our DNA structure is changed by mutations. And mutations manipulate function.

Thus, organisms with the most mutations are the least related (or organisms that have evolved the most are the least related). or organisms that are the most morphologically different are the least related. Which is common sense. Know what I mean?

Its not, "the organisms are more similar to eachother, therefore they are closely related", its "these organisms are less different than eachother, therefore they are closely related".

-------------------------------------------------------------------------------------------------

Now it is true, that you demonstrated that the organisms enzyme substrate has decreased specificity on what it acts on. However, the organism itself still has evolved a new function (digestion of nylon). That is to say, there was a mutation that brought about a new beneficial function, and that new function propogated throughout its community.

And you recognize that this is true, but you dont call it evolution because its not 100% beneficial.

However, no biologist or scientist ever claims evolution to be 100% beneficial. Thats why we call it random, because often there are goods and bads, and often you have mutations that are both good and bad.

So even though you are not calling it evolution, everyone else is, because by definition it is.

I almost think you agree with me though. Either way, you understand what happened, and you understand that speciation occurs, and thats a fine start with me.

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Idev says: While you work on your paleo argument, im going to claim victory here in the biology section.

Anyone reading this thread can see that you failed on every single point and your beneficial mutation was nothing but a corruption that lead to the organism being less specific and in the end causing it to be less efficient.

You then agreed to this....

I didn't respond because your last post was this :

I dont think anyone claims that simple relatedness in morphology is proof for evolution.

And yes, speciation is one aspect of evolution. Im glad you acknowledge that.

When referring to the theory of evolution, you will rarely hear people refer to evolution as a species becoming "better". Because "better" is a subjective term.

In response to an entire page of refutations so I took it that you accepted what I said. All you did was agree with me and then try to change the definition of evolution. You had the audacity to try to wiggle your way out of a simple definition that this organism simply did not fill. The definition of evolution is simple,things get better over time. This organism did not fulfill the definition so your point is invalid.

And then days later you make a post saying "I think I'll claim victory". Well you go ahead and claim that but you have failed to convince anyone of your theory.

Notice how he agrees with me

Idev says Now it is true, that you demonstrated that the organisms enzyme substrate has decreased specificity on what it acts on.

And then notice how he repeats himself that it is actually good for it,

Idev says That is to say, there was a mutation that brought about a new beneficial function, and that new function propogated throughout its community.

Even after I showed him it was a logical fallacy, like me breaking my mom's legs so she can't go outside and get hit by a car anymore,no one would call this a "beneficial addition".And I also showed him that loss of specificity in an enzyme was bad for it using another article.

And finally notice how he tries to change the definition of evolution of things improving and becoming better.

Idev says: When referring to the theory of evolution, you will rarely hear people refer to evolution as a species becoming "better". Because "better" is a subjective term.

No my friend,becoming better is not a subjective term at all. It is quite objective and I think everyone here can agree a car is better transportation then a horse. So the concept of "improvement" in a specific environment is objective,this enzyme lost in every single aspect. And I think everyone here can agree that the world "evolve" involves things improving over time.

According to the dictionary the first definition is,

1. A gradual process in which something changes into a different and usually more complex or better form.

To say that becoming better is not intrinsic to the word evolution is wrong.

This can be shown logically.

1. Jessica has become fat and has changed(become different).

2. being diverse or becoming different is evolution.

3. Jessica has evolved.

If you claim change/speciation equals evolution,you claim point 2 and 3 is correct.

Change/speciation/diversity is only an aspect of the word evolution and is not necessary to the word. However becoming better is necessary and intrinsic to the word evolution.

Just because something has changed doesn't mean it has evolved.

Even if biologists,scientists,pope,chupacabra,batman,engineers,anyone who said it,it is wrong.

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Anyone reading this thread can see that you failed on every single point and your beneficial mutation was nothing but a corruption that lead to the organism being less specific and in the end causing it to be less efficient.

You then agreed to this....

Yup, and I also said "Now it is true, that you demonstrated that the organisms enzyme substrate has decreased specificity on what it acts on. However, the organism itself still has evolved a new function (digestion of nylon). That is to say, there was a mutation that brought about a new beneficial function, and that new function propogated throughout its community."

And you have agreed to this. That is to say, you agreed that the enzyme has lost specificity, you have agreed that the population has developed a new function through mutation, and its spread throughout the population. And you agree that it can now digest nylon, which it could not previously do in its nylon rich environment.

And this is how evolution works. You have your mutation, the mutation comes to dominate the population in the coming generations. And the organism is more suitable (it can digest nylon) in its environment (nylon rich environment).

I didn't respond because your last post was this :

In response to an entire page of refutations so I took it that you accepted what I said. All you did was agree with me and then try to change the definition of evolution. You had the audacity to try to wiggle your way out of a simple definition that this organism simply did not fill. The definition of evolution is simple,things get better over time. This organism did not fulfill the definition so your point is invalid.

And then days later you make a post saying "I think I'll claim victory". Well you go ahead and claim that but you have failed to convince anyone of your theory.

The organism did get "better" in the sense that it can now digest nylon in an environment in which theyre is nylon to be digested.

And then notice how he repeats himself that it is actually good for it,

Even after I showed him it was a logical fallacy, like me breaking my mom's legs so she can't go outside and get hit by a car anymore,no one would call this a "beneficial addition".And I also showed him that loss of specificity in an enzyme was bad for it using another article.

And finally notice how he tries to change the definition of evolution of things improving and becoming better.

No my friend,becoming better is not a subjective term at all. It is quite objective and I think everyone here can agree a car is better transportation then a horse. So the concept of "improvement" in a specific environment is objective,this enzyme lost in every single aspect. And I think everyone here can agree that the world "evolve" involves things improving over time.

Ok fine. The organism is clearly not harmed from the lack of specificity of the mutation. Its prospering with the mutation, and the mutation benefits the organism by bringing a new function to it. And when I mentioned that evolution wasnt a ladder. That is to say, a polar bear could evolve in a way in which it was "better" in the arctic, however in a jungle those evolved traits would be a detriment. So organisms evolve to suit their environment, much like the bacteria evolving to digest nylon. Its not necisserily a better organism than its predicessor, but for its particular environment, it benefits from the new function.

According to the dictionary the first definition is,

1. A gradual process in which something changes into a different and usually more complex or better form.

To say that becoming better is not intrinsic to the word evolution is wrong.

Well, in biological terms, it is correct, and this is the way that Ive always been taught about it by a number of PhDs.. And even creationists would agree with me on this one. The complex structures we now hold today, many of which have been around since the cambrian. So its not necisserily organisms becoming "better", its organisms becoming more suitable for their environment.

Perhaps its just semantics we are differing on. Because I can both agree and disagree with you depending on what you mean when you say "better".

Which is another reason I wouldnt use the word.

This can be shown logically.

1. Jessica has become fat and has changed(become different).

2. being diverse or becoming different is evolution.

3. Jessica has evolved.

If you claim change/speciation equals evolution,you claim point 2 and 3 is correct.

point 1 isnt speciation. Point 2 is not evolution either. Becoming fat is not the same as evolving. There is no alteration in your DNA with becoming fat. Also, individuals do not evolve, populations do.

With speciation though, there is an alteration of DNA, which is why speciation is evolution. Change is not the same as speciation. Speciation is evolution. Change is not the same as evolution.

Change/speciation/diversity is only an aspect of the word evolution and is not necessary to the word. However becoming better is necessary and intrinsic to the word evolution.

Not really. We will have to agree to disagree. An example. Bacteria A exists, and this species evolved to digest nylon. The new community of bacteria that can digest nylon isnt necisserily better than the original. Its simply more suitable for its particular environment.

Just because something has changed doesn't mean it has evolved.

Even if biologists,scientists,pope,chupacabra,batman,engineers,anyone who said it,it is wrong.

i never said just because something changes, its evolution. Evolution, lets go get a real definition...

"Evolution (also known as biological, genetic or organic evolution) is the change in the inherited traits of a population of organisms" ~ wiki

"Biological evolution is defined as any genetic change in a population that is inherited over several generations."

"The Definition: Biological evolution, simply put, is descent with modification. " ~ Berkley

"the origin and development of species; the theory that existing organisms are the result of descent with modification from those of past times." thefree dictionary dot com.

"a change in the genetic composition of a population of organisms over time."

ok so, the flavobacterium had a change in the inherited traits (digestion of nylon) of its population of organisms. Ok so by wiki standards its evolution.

The flavobacterium had a genetic change in its population that was inherited over several generations. Ok, so by about.com its evolution as well.

The flavobacterium now able to digest nylon has descended with the modification (a change in an organism caused by environmental factors ) of nylon digestion. Ok so by Berkley standards its evolution.

Again, descent with modification.

The reason we cant say its necisserily simple to complex, is because even in our history, our ancestors have been extraordinarily complex. Now, I guess if you want to compare us to prokaryote ancestors, then sure its simple to complex. But that was billions of years ago.

and again, ill go ahead and claim victory. By each of the definitions above, the concept we have discussed is evolution. The bacteria mutated. The new trait can now be found throughout the population of bacteria. The new trait allows for the digestion of nylon in a environment in which nylon is present, when before it could not.

Now, that doesnt mean that now that it can digest nylon, its a superior organism to its predicessor. It just means its different and more suitable for the environment which it presides.

And yes, the organisms enzyme has lost specificity, but that doesnt mean the organism is corrupted to the point its going to die. As we can see it didnt die, as a matter of fact it prospered and the trait came to prosper throughout its entire population. So clearly the mutation is not as bad as you believe it is. As a matter of fact, the organism can now digest nylon (which at the time was present in its environment), and this is of beneficial use to the organism.

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See. We have the mutation for nylonase. There were no truly unfavorable mutations, being able to digest nylon leaves the flavobacteria with a net benefit. The new trait comes to dominate the population. The next generation of organisms carry on the trait and so forth.

"And yes, the organisms enzyme has lost specificity, but that doesnt mean the organism is corrupted to the point its going to die (see the red X over the white circle). As we can see it didnt die, as a matter of fact it prospered and the trait came to prosper throughout its entire population. So clearly the mutation is not as bad as you believe it is. As a matter of fact, the organism can now digest nylon (which at the time was present in its environment), and this is of beneficial use to the organism."

http://www.duq.edu/s...ution_380px.jpg643px-Explanation_of_Evolution_380px.jpg

remember...

laddervstree.gif

We arent really better than the fish in the fishbowl. We are just different. I bet that fish can swim a lot better than we can, and it can breathe under water a lot better than we can too. So we arent "better" than the fish, even though we evolved from fish. We are just different.

You could say mankind is "better" than fish at breathing air. So in that sense, yes we have evolved into "better" organisms. But still, we arent truly better than fish, because fish are better than us at things as well. And so, we are simply different, and most importantly, more suitable for our own environments.

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Idev says: Yup, and I also said "Now it is true, that you demonstrated that the organisms enzyme substrate has decreased specificity on what it acts on. However, the organism itself still has evolved a new function (digestion of nylon). That is to say, there was a mutation that brought about a new beneficial function, and that new function propogated throughout its community."

And you have agreed to this. That is to say, you agreed that the enzyme has lost specificity, you have agreed that the population has developed a new function through mutation, and its spread throughout the population. And you agree that it can now digest nylon, which it could not previously do in its nylon rich environment.

I cut out your charts as they were irrelevant.

You keep repeating yourself and you keep saying "it has a new function".

Please read this very slowly because you're also making me repeat myself,it is becoming rather pointless you continue talking to you because you simply won't accept the fact that what you have is a false example of beneficial mutations.

This is why it having a new function is irrelevant,because this new function has arisen from a loss of function,I think I made this quite clear. I also believe I made clear why this won't help us get to where we are now.

So I'm going to show you step by step using principles of logic why your position is invalid and false on the issue of nylon,if you still don't get it then responding to a person who keeps repeating him or herself would be fruitless and waste of time and everyone can see my responses anyways.

Your belief of the nylon mutation being a good example of a beneficial mutation are from these premises.

1. The mutation is now apart of the population,hence natural selection thinks its good.

2. The mutation helped the enzyme and gave it a new function,and hence is a good mutation.

3. This type of mutation will lead to life we see today.

(Note: all these premises were already refuted in my earlier posts,which he ignored,I also supplied references.)

Premise 1,

This mutant bacteria is rare,and was found in japan,and only exists in some rare environments where nylon must be used as a energy source.

Premise 2,

All that happened was a loss of specificity due to a corrupting mutation to the cleft of the enzyme which allowed it to act on more substrates.

To say this is "good",would be exactly like the logical fallacy of sickle cell disease being "good",which atheists do use by the way.

Sickle cell disease causes its cells from carrying oxygen eventually killing the infected organism,atheists say this is good due to the fact that the infected person can't carry malaria also.

Anyone with half a brain can see this is simply a logical fallacy and a funny example of atheistic/evolutionist logic. With this analogy,you're nylon mutation becomes invalid as a good example. One reason is because of the analogy given,the second reason due to the fact that no good occured,because now the organims is less efficient. No good has happend to this organism in the long run...

The third reason why its an invalid example is in your third premise.

Premise 3,

This type of mutation will never lead to life and its complex machines we see today do to the simple fact that loss of specificy will never lead to gain the gain of specificity and this is necessarily known.

This is why I said,even if your mutation gave you wings and lets you walk on water,if you mutation is from a loss of specificity it means nothing.

Idev says

And this is how evolution works. You have your mutation, the mutation comes to dominate the population in the coming generations. And the organism is more suitable (it can digest nylon) in its environment (nylon rich environment).

Answered,see above.

Idev says The organism did get "better" in the sense that it can now digest nylon in an environment in which theyre is nylon to be digested.

Answered see above.

idev says

Ok fine. The organism is clearly not harmed from the lack of specificity of the mutation. Its prospering with the mutation, and the mutation benefits the organism by bringing a new function to it. And when I mentioned that evolution wasnt a ladder. That is to say, a polar bear could evolve in a way in which it was "better" in the arctic, however in a jungle those evolved traits would be a detriment. So organisms evolve to suit their environment, much like the bacteria evolving to digest nylon. Its not necisserily a better organism than its predicessor, but for its particular environment, it benefits from the new function.

Irrelevant,and what was barely relevant was answered above.

Idev says

Well, in biological terms, it is correct, and this is the way that Ive always been taught about it by a number of PhDs.. And even creationists would agree with me on this one. The complex structures we now hold today, many of which have been around since the cambrian. So its not necisserily organisms becoming "better", its organisms becoming more suitable for their environment.

Perhaps its just semantics we are differing on. Because I can both agree and disagree with you depending on what you mean when you say "better".

Which is another reason I wouldnt use the word.

An appeal to authority won't help you when we are using clear principles,as it is necessarily known "better" is objective.

Regarding the "Cambrian explosion",I wouldn't mention it as it hurts you more than it helps your case.

idev says point 1 isnt speciation. Point 2 is not evolution either. Becoming fat is not the same as evolving. There is no alteration in your DNA with becoming fat. Also, individuals do not evolve, populations do.

Notice how he agrees that "getting fat" isn't evolution,yet the principles he must necessarily accept forces him to accept the conclusion yet he cannot because he clearly knows its absurd.

Idev says With speciation though, there is an alteration of DNA, which is why speciation is evolution. Change is not the same as speciation. Speciation is evolution. Change is not the same as evolution.

I'm sorry but what you said is absolutely,100 percent completely wrong.

For those who don't know,speciation is when new species come from earlier species.

I.E.,the earlier species were changed and thus becoming new.

The very intrinsic meaning of speciation is change,this is known easily.

How? Tell me one case of speciation that didn't evolve change intrinsically ?

idev says

Not really. We will have to agree to disagree. An example. Bacteria A exists, and this species evolved to digest nylon. The new community of bacteria that can digest nylon isnt necisserily better than the original. Its simply more suitable for its particular environment.

i never said just because something changes, its evolution. Evolution, lets go get a real definition...

"Evolution (also known as biological, genetic or organic evolution) is the change in the inherited traits of a population of organisms" ~ wiki

Using Wikipedia won't help you,due to the fact that change is only an aspect of evolution and not the intrinsic meaning of evolution.

You must accept this,or you think Jessica changing and getting fat is evolution.

Idev says "Biological evolution is defined as any genetic change in a population that is inherited over several generations."

"The Definition: Biological evolution, simply put, is descent with modification. " ~ Berkley

"the origin and development of species; the theory that existing organisms are the result of descent with modification from those of past times." thefree dictionary dot com.

"a change in the genetic composition of a population of organisms over time."

Another appeal to authority,your definition of evolution was already refuted.

He wants us to believe how the atheists define terms,this is simply wrong.

In plain clear English the term "biological evolution" means biological improvement,regardless of what your camp of atheists/evolutionists have to say on the words.

Look its simple,if you think change is the intrinsic meaning of evolution then you must accept this syllogism.

1.Julia got fat.

2.getting fat is change

3. organisms which change evolve.

4. Julia evolved.

There is nothing you can do about the conclusion,if you accept premise 3 (evolution=change of organisms).

My understanding of evolution is simple,things which improve over time.

What you gave me was the definition created by biologists,not the literal meaning.

Idev says ok so, the flavobacterium had a change in the inherited traits (digestion of nylon) of its population of organisms. Ok so by wiki standards its evolution.

The flavobacterium had a genetic change in its population that was inherited over several generations. Ok, so by about.com its evolution as well.

The flavobacterium now able to digest nylon has descended with the modification (a change in an organism caused by environmental factors ) of nylon digestion. Ok so by Berkley standards its evolution.

Again, descent with modification.

The reason we cant say its necisserily simple to complex, is because even in our history, our ancestors have been extraordinarily complex. Now, I guess if you want to compare us to prokaryote ancestors, then sure its simple to complex. But that was billions of years ago.

and again, ill go ahead and claim victory. By each of the definitions above, the concept we have discussed is evolution. The bacteria mutated. The new trait can now be found throughout the population of bacteria. The new trait allows for the digestion of nylon in a environment in which nylon is present, when before it could not.

Now, that doesnt mean that now that it can digest nylon, its a superior organism to its predicessor. It just means its different and more suitable for the environment which it presides.

And yes, the organisms enzyme has lost specificity, but that doesnt mean the organism is corrupted to the point its going to die. As we can see it didnt die, as a matter of fact it prospered and the trait came to prosper throughout its entire population. So clearly the mutation is not as bad as you believe it is. As a matter of fact, the organism can now digest nylon (which at the time was present in its environment), and this is of beneficial use to the organism.

This person relies upon the wiki definition,which was explained why its wrong. The rest of his post relies on that point and thus is also wrong.

His sources are also unreliable,such as Wikipedia and about.com.

His entire argument can be refuted by a simple demonstration.

He claims that the real definition of evolution is," descent with modification".

I'd like everyone here who is reading this to see if we can accept this definition.

A new bacteria arises,the only difference between it and its ancestor species is that it lost its ability to transport itself faster and has morphological differences that causes it harm.

This fulfills descent,and modification.

Did it evolve? I think you can answer that for yourself.

Idev says You could say mankind is "better" than fish at breathing air. So in that sense, yes we have evolved into "better" organisms. But still, we arent truly better than fish, because fish are better than us at things as well. And so, we are simply different, and most importantly, more suitable for our own environments.

To believe that fish are not objectively superior to use would be rather dishonest on your part.

Breathing air leads to warm blooded mammals according to you,and thus humans.

Over all objectively speaking,do you think fish are better than humans in terms of things they can do and accomplish?

Sure they can swim better and breathe water,but over all?

This is another example of wishy washy logic that has no place on Islamic chat rooms.

Even if this was the case,then this isn't evolution,its change.

This is also another example of circular logic.

He is using the conclusion "Men evolved from fish",to prove his argument. No one agrees to that,we don't believe NS plus RM can lead to humans.

Anyways if I don't respond,it is because I already answered your points.

Edited by Ibn-Ahmed Aliyy Herz
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Before my response, I just want to say I think its great that uve taken time to look into these things and i appreciate the discussion. Later in my topic though, i talk a bit more about...conceptually what biological evolution is, and what evolution means as it pertains to biology. It seems a lot of our disagreement is over semantics. We agree on the concepts, but disagree on the words we use.

In all honesty, you dont acknowledge it, but you have already accepted evolution. You just dont call it evolution, because you feel its not the full picture. And its not the full picture. Nylonase evolution is only 1 example of thousands of concepts used in biology and science to define the theory of evolution. but anyway...

This is why it having a new function is irrelevant,because this new function has arisen from a loss of function,I think I made this quite clear. I also believe I made clear why this won't help us get to where we are now.

Ok, so its been an exchange, some good and some bad.

So I'm going to show you step by step using principles of logic why your position is invalid and false on the issue of nylon,if you still don't get it then responding to a person who keeps repeating him or herself would be fruitless and waste of time and everyone can see my responses anyways.

Your belief of the nylon mutation being a good example of a beneficial mutation are from these premises.

1. The mutation is now apart of the population,hence natural selection thinks its good.

2. The mutation helped the enzyme and gave it a new function,and hence is a good mutation.

3. This type of mutation will lead to life we see today.

There are many types of mutations. I never said such a mutation alone would lead to the life we see today.

Premise 1,

This mutant bacteria is rare,and was found in japan,and only exists in some rare environments where nylon must be used as a energy source.

Premise 2,

All that happened was a loss of specificity due to a corrupting mutation to the cleft of the enzyme which allowed it to act on more substrates.

To say this is "good",would be exactly like the logical fallacy of sickle cell disease being "good",which atheists do use by the way.

Sickle cell disease causes its cells from carrying oxygen eventually killing the infected organism,atheists say this is good due to the fact that the infected person can't carry malaria also.

Anyone with half a brain can see this is simply a logical fallacy and a funny example of atheistic/evolutionist logic. With this analogy,you're nylon mutation becomes invalid as a good example. One reason is because of the analogy given,the second reason due to the fact that no good occured,because now the organims is less efficient. No good has happend to this organism in the long run...

The third reason why its an invalid example is in your third premise.

Premise 3,

This type of mutation will never lead to life and its complex machines we see today do to the simple fact that loss of specificy will never lead to gain the gain of specificity and this is necessarily known.

Ok and so, you mentioned that the bacteria is specific to a certain type of environment in a certain place. Ok. thats irrelivant. You mentioned that the mutation would be of no good use in the long run. Well, the organisms are prospering now and its been 30 some odd years. And as for premise 3, its also irrelivant, because never in this topic have I ever said this is the only way evolution can or has occurred.

Well that was easier than I thought it would be.

Notice how he agrees that "getting fat" isn't evolution,yet the principles he must necessarily accept forces him to accept the conclusion yet he cannot because he clearly knows its absurd.

What? What have I ever said that lead you to believe, that i believed growing fat was evolution?

How? Tell me one case of speciation that didn't evolve change intrinsically ?

When speciation occurs, organisms are changing. However, organisms can change without evolving into a new species. And this is why change and speciation are not the same. And Speciation is a form of evolution. And change is not always evolution for the same reason it is not always speciation (it can be adaptation and not necisserily evolution).

Look its simple,if you think change is the intrinsic meaning of evolution then you must accept this syllogism.

1.Julia got fat.

2.getting fat is change

3. organisms which change evolve.

4. Julia evolved.

again, change is not evolution. Change can be adaptation, it can be, changes in allele pronunciation etc. Evolution is change in DNA that propogates throughout a population over time and generations. Which Ive said before.

Im still not quite sure where you got the idea that I believed getting fat was evolution.

What you gave me was the definition created by biologists,not the literal meaning.

Hahaha. Well yea. When we are talking about biological evolution, we are talking about evolution as it pertains to biology. When we discuss biology, we use biological terms and definitions.

Thats like, in biology we also are technically apes. Now, thats by biological definitions. However, by other peoples definitions, we are not apes. But because we are talking about biology, we use biology terms and definitions.

And yes, I understand that the definition you are using for evolution is correct, however, in biology, this is how it is used, this is how it is defined when it pertains to biological evolution.

Evolution as it pertains to biological evolution, defined by biologists...means that organisms do not necisserily become superior than all other organisms. It means they become better suited for their environment, at a set time.

Like I said, we evolved from fish, but that doesnt mean we are superior to fish. Because clearly fish can do many things better than we can. And so, in biological terms, to say that evolution automatically means to become superior through changes, is incorrect.

In laymens terms, sure, if you talk about...the evolution of technology, sure that would mean something more along your definition of becoming superior. But in biology, thats not how its defined.

His sources are also unreliable,such as Wikipedia and about.com.

And berkley U, which is one of the top universities in the world, but its ok to ignore that part of my statement :P

He claims that the real definition of evolution is," descent with modification".

I'd like everyone here who is reading this to see if we can accept this definition.

A new bacteria arises,the only difference between it and its ancestor species is that it lost its ability to transport itself faster and has morphological differences that causes it harm.

Did it evolve? I think you can answer that for yourself.

And it can digest nylon in a nylon rich environment. But again, evolution isnt about becoming superior to all animals in the animal kingdom, its about becoming adapted to your environment at a time. Ie, being able to digest nylon after nylon has been introduced to your environment.

And this definition of descent with modification isnt from wiki, its from berkley U.

To believe that fish are not objectively superior to use would be rather dishonest on your part.

Breathing air leads to warm blooded mammals according to you,and thus humans.

Over all objectively speaking,do you think fish are better than humans in terms of things they can do and accomplish?

When it comes to their environment, Yes, they are. When it comes to our environment, no they arent.

Sure they can swim better and breathe water,but over all?

Well, how about this question. Overall, at this moment in time, are the flavobacteria that can digest nylon over all better in their environment?

The answer is yes.

Sure, you could argue that fish, are not as intelligent as mankind. But fish have a trait that suits them in their environment at this time. If I go swimming, a shark 99.9% of the time will out live me. In its environment, it is the top survivor, and none compete with it.

With the flavobacteria that have mutated the nylon digestion, these bacteria, are the top players in their nylon environment. None compete with them.

So overall, you could argue that humans are better because we are smarter, and you could argue that the original bacteria are better because their enzymes act more specifically.

But at the end of the day, the fish is the best in water, and in water is where they reside. And the nylon digesting bacteria are the best in nylon rich environments, and that is where they reside. And this again is why I say, and why biologists say, evolution is not a ladder. You can evolve without necisserily becoming a superior being.

Remember the picture. The flavobacteria that can digest nylon is not necisserily higher on the ladder than the original bacteria. That is, as you can see in the picture. Wrong. The bacteria that can digest nylon, are more suitable for their environment, they are not necisserily more superior than the original bacteria. Some may even argue that they are worst. Just as some may argue that fish are worst than humans. But at the end of the day, it comes down to what is suitable in what environment at what time.

laddervstree.gif

And this is why everyone calls evolution "random". Its because it doesnt go in one direction. It doesnt transform animals into super animals. It goes up and down, left and right, big and small, round and round. Sharks used to be massive, they dominated the seas like no other. But now, look at how small the great white has become compared to its ancestors. That could be said to be a bad direction for evolution.

However, its not about good or bad, its about what is beneficial in the environment at a time.

And Ive said this multiple times now, and this is how evolution works in biological terms.

Are you familiar with "random walks" in evolution?

Statistically, organisms do not evolve in one direction. And you can see this both in biology and in the fossil record. We never evolve "backwards" per say. Meaning, we dont evolve back into our original DNA state. However, our traits often may go back and forth or may change similarly to a previous state over and over and over again.

What I mean by this is, an organism like a bivalve, may have doubled in size, then shrank, then doubled, then shrank again. Over and over and over.

So the point is, we evolve with our environments. Which may include, but we dont call it this "devolving". We dont call it "devolving" because we dont define evolution as a ladder, but indeed, it does happen. Which is probably why you are so conflicted with me in this discussion.

Heres another example. According to modern evolutionary theory, its possible that we could evolve into a being with a smaller or less efficient brain.

Now, you may think that is "devolving". But no scientist would call it that because thats not how we use the word. We would call it evolving to a more suitable state at a set time in their environment, which may or may not include losing such a powerful brain.

So, the flavobacteria having less specific enzymes, is not "de evolution", its not "devolving". Its evolving, just in a way that to you appears less efficient or beneficial.

But to the organism, that is prospering with the new mutation, it doesnt matter how we define the word, and it doesnt matter what we think of it. At the end of the day, those bacteria are thriving.

And this is why I am calling it evolution and you arent.

Even if this was the case,then this isn't evolution,its change.

Ok, here we go. Now, I want you to tell me, and just try to work with me here. Lets use the biologists definition for evolution. That is mutations, and descent with modification in populations.

Tell me why mankind evolving from fish, is not evolution and is simply change. Or are you referring to the bacteria? Either way, you explain, using biological definition, why it is change, but not evolution.

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Idev says: Before my response, I just want to say I think its great that uve taken time to look into these things and i appreciate the discussion. Later in my topic though, i talk a bit more about...conceptually what biological evolution is, and what evolution means as it pertains to biology. It seems a lot of our disagreement is over semantics. We agree on the concepts, but disagree on the words we use.

You said some new things which is why I will respond,these new things clearly shows you changing your definition of what evolution is which I will show.

It has nothing to do with semantics,you want to believe that I believe in the true meaning of evolution but we disagree on the terms,this is what semantics are,and this does not apply to what we are saying.

Idev says: In all honesty, you dont acknowledge it, but you have already accepted evolution. You just dont call it evolution, because you feel its not the full picture. And its not the full picture. Nylonase evolution is only 1 example of thousands of concepts used in biology and science to define the theory of evolution. but anyway...

I have shown why in my earlier posts have your definition of evolution is wrong.

Idev says Ok, so its been an exchange, some good and some bad.

I don't think you have understood what I wrote.

Idev says

There are many types of mutations. I never said such a mutation alone would lead to the life we see today.

So? This is the only type of mutation that can lead to new proteins,duplication plus frameshift.

If you can't demonstrate how this type of mutation leads to new novel proteins then you have failed in demonstarting how mutations and NS can lead to the complex functionality of life.

Idev says Ok and so, you mentioned that the bacteria is specific to a certain type of environment in a certain place. Ok. thats irrelivant. You mentioned that the mutation would be of no good use in the long run. Well, the organisms are prospering now and its been 30 some odd years. And as for premise 3, its also irrelivant, because never in this topic have I ever said this is the only way evolution can or has occurred.

Well that was easier than I thought it would be.

None of the premises I listed were irrelevant because those premises are essential to your belief,again you have failed to refute or explain the premises.

So I'll claim victory there.

Idev says What? What have I ever said that lead you to believe, that i believed growing fat was evolution?

The problem is,you aren't reading what I'm giving you or you are skimming through it.

I'm not saying you believe getting fat=evolution,i'm show you why you must accept that absurd statement if you think organisms changing= evolution.

Idev says When speciation occurs, organisms are changing. However, organisms can change without evolving into a new species. And this is why change and speciation are not the same. And Speciation is a form of evolution. And change is not always evolution for the same reason it is not always speciation (it can be adaptation and not necisserily evolution).

Your post is full of half truths and contradictions which I'll show.

"Idev says With speciation though, there is an alteration of DNA, which is why speciation is evolution. Change is not the same as speciation"

*claps* good job. You are very convincing.

No one said an organism can change without becoming a new species (irrelevant).

Then he contradicts himself again in the same quote " And this is why change and speciation are not the same. "

This is like you saying fruit and apples aren't the same,yes they are the same,but no one said that all fruits=apples.

Same thing here humans and men are the same,due to the fact that a man fulfills every requirement of a human.

But it does not necessarily follow that all humans=men.

Its simple,all speciation=change. All change =/evolution.

So if all change=/evolution < then logically change is not intrinsic to evolution.

And lastly you say

And Speciation is a form of evolution. And change is not always evolution for the same reason it is not always speciation (it can be adaptation and not necisserily evolution

You have just said that change is not evolution due to the fact that it can be adaption,but isn't adaption change?

Isn't specation change? isn't change change?

Every example you have given is that of change,and I have showed you why change isn't intrinsic to evolution.

again, change is not evolution. Change can be adaptation, it can be, changes in allele pronunciation etc. Evolution is change in DNA that propogates throughout a population over time and generations. Which Ive said before.

Lol this is too funny.

He said in his last paragraph "

idev says And change is not always evolution

Then he says AGAIN in the very same paragraph,changing the definition of evolution to changes in DNA genome.

Evolution is change in DNA that propogates throughout a population over time and generations

Wait what?? I thought change isn't evolution?

He is saying Men are humans,but humans aren't men.

Change isn't evolution,but evolution is change?

Allah yahdeek.

Im still not quite sure where you got the idea that I believed getting fat was evolution.

Hahaha. Well yea. When we are talking about biological evolution, we are talking about evolution as it pertains to biology. When we discuss biology, we use biological terms and definitions.

This is the crux of his problem,he thinks that terms change when talking about different subjects......

Sorry but it doesn't.

When speaking about meanings of words in a debate like this,we do not use SUBJECTIVE criteria.

Idev says Thats like, in biology we also are technically apes. Now, thats by biological definitions. However, by other peoples definitions, we are not apes. But because we are talking about biology, we use biology terms and definitions.

And yes, I understand that the definition you are using for evolution is correct, however, in biology, this is how it is used, this is how it is defined when it pertains to biological evolution.

see above.

Idev saysEvolution as it pertains to biological evolution, defined by biologists...means that organisms do not necisserily become superior than all other organisms. It means they become better suited for their environment, at a set time.

Another contradiction.

He says

they become better suited for their environment

Wait I thought that better does not equal evolution?

Now you're telling us that things becoming better in their environments is evolution?

Like I said, we evolved from fish, but that doesnt mean we are superior to fish. Because clearly fish can do many things better than we can. And so, in biological terms, to say that evolution automatically means to become superior through changes, is incorrect.

In laymens terms, sure, if you talk about...the evolution of technology, sure that would mean something more along your definition of becoming superior. But in biology, thats not how its defined.

And berkley U, which is one of the top universities in the world, but its ok to ignore that part of my statement :P

And it can digest nylon in a nylon rich environment. But again, evolution isnt about becoming superior to all animals in the animal kingdom, its about becoming adapted to your environment at a time. Ie, being able to digest nylon after nylon has been introduced to your environment.

And this definition of descent with modification isnt from wiki, its from berkley U.

When it comes to their environment, Yes, they are. When it comes to our environment, no they arent.

Well, how about this question. Overall, at this moment in time, are the flavobacteria that can digest nylon over all better in their environment?

The answer is yes.

Sure, you could argue that fish, are not as intelligent as mankind. But fish have a trait that suits them in their environment at this time. If I go swimming, a shark 99.9% of the time will out live me. In its environment, it is the top survivor, and none compete with it.

With the flavobacteria that have mutated the nylon digestion, these bacteria, are the top players in their nylon environment. None compete with them.

So overall, you could argue that humans are better because we are smarter, and you could argue that the original bacteria are better because their enzymes act more specifically.

But at the end of the day, the fish is the best in water, and in water is where they reside. And this again is why I say, and why biologists say, evolution is not a ladder. You can evolve without necisserily becoming a superior being.

And this is why everyone calls evolution "random". Its because it doesnt go in one direction. It doesnt transform animals into super animals. It goes up and down, left and right, big and small, round and round. Sharks used to be massive, they dominated the seas like no other. But now, look at how small the great white has become compared to its ancestors. That could be said to be a bad direction for evolution.

However, its not about good or bad, its about what is beneficial in the environment at a time.

And Ive said this multiple times now, and this is how evolution works in biological terms.

Are you familiar with "random walks" in evolution?

Statistically, organisms do not evolve in one direction. And you can see this both in biology and in the fossil record. We never evolve "backwards" per say. Meaning, we dont evolve back into our original DNA state. However, our traits often may go back and forth or may change similarly to a previous state over and over and over again.

What I mean by this is, an organism like a bivalve, may have doubled in size, then shrank, then doubled, then shrank again. Over and over and over.

So the point is, we evolve with our environments. Which may include, but we dont call it this "devolving". We dont call it "devolving" because we dont define evolution as a ladder, but indeed, it does happen. Which is probably why you are so conflicted with me in this discussion.

Heres another example. According to modern evolutionary theory, its possible that we could evolve into a being with a smaller or less efficient brain.

Now, you may think that is "devolving". But no scientist would call it that because thats not how we use the word. We would call it evolving to a more suitable state at a set time in their environment, which may or may not include losing such a powerful brain.

So, the flavobacteria having less specific enzymes, is not "de evolution", its not "devolving". Its evolving, just in a way that to you appears less efficient or beneficial.

But to the organism, that is prospering with the new mutation, it doesnt matter how we define the word, and it doesnt matter what we think of it. At the end of the day, those bacteria are thriving.

And this is why I am calling it evolution and you arent.

Ok, here we go. Now, I want you to tell me, and just try to work with me here. Lets use the biologists definition for evolution. That is mutations, and descent with modification in populations.

All answered in last post and above.

At this point is best to give up when talking to a person like this........

Your first definition of evolution was "modifcation with descent"

I showed you why it is wrong.

Your last definition of evolution was "changes in genome that become prevalent"

So if a bacteria changes for the worse,and it becomes prevalent,then HOW? The only way something can become prevalent according to the theory,is if that change is GOOD,I.E. makes the organism survive better.

I showed you why it doesn't survive better at all,and I showed you why even if it did its 100 percent irrelevant.

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So lets skip to all argumentation and agree on a definition,

evolution is when an organism changes and becomes better for its particular environment.

If the nylon eater becomes better for its particular environment,then how? It can now eat nylon,so what?

The other bacteria that didn't undergo this change still is just as good without it in that environment,the nylon eating bacteria is now less energy efficient. Also another thing that actually disproves you is the fact that the new enzymes are 98 percent less efficient then those without the mutation.

No evolution occurred here on every definition of the word,all that happened was it changed and became worse,if anything it devolved.

And I definitely just proved to you that change=/evolution.

So on what grounds are you calling this evolution?

If indeed it is beneficial then this is an example of microevolution and adapation,something Muslims have accepted since the middle ages.

But it isn't at all.

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Im gonna try to save us some time by consolidating the key points here.

So? This is the only type of mutation that can lead to new proteins,duplication plus frameshift.

A duplication and phrame shift in one organisms obviously isnt going to equate to a duplication in another. And other mutations can alter pre existing proteins braught about through phrame shifts. This is why, this example with nylonase, alone does not define evolutionary mutations in their entirity.

The reason I say this is because, you could theoretically have a mutation that brings about a trait that is more or less beneficial than the one with nylonase, then subsequent mutations can work with the enzyme even further.

The flavobacteria isnt finished evolving. It didnt have one mutation and then just said "ok im done". :P, its going to keep changing, which includes alterations in its new genes or others.

Check this out.

http://ghr.nlm.nih.g...ssiblemutations

"Idev says With speciation though, there is an alteration of DNA, which is why speciation is evolution. Change is not the same as speciation"

*claps* good job. You are very convincing.

Then he contradicts himself again in the same quote " And this is why change and speciation are not the same. "

This is like you saying fruit and apples aren't the same,yes they are the same,but no one said that all fruits=apples.

He is saying Men are humans,but humans aren't men.

Change isn't evolution,but evolution is change?

Thats not a contradiction. Change is not the same as speciation, then I follow by saying change and speciation are not the same. Im saying the same thing.

And fruit and apples are not the same. Some fruits are apples and all apples are fruits, but they are not the same thing. The reason they are not the same thing is because some fruits are oranges. Therefore If i have a sack of oranges, my fruit (oranges) is not the same as apples.

Not all humans are men smart one :P. haha Men are humans, but humans arent necisserily men because some humans can be women.

Alright, im gonna move on now, we both know what apples and oranges and fruit all are. This appears to be just another issue with description.

But it does not necessarily follow that all humans=men.

Its simple,all speciation=change. All change =/evolution.

So if all change=/evolution < then logically change is not intrinsic to evolution.

And lastly you say

You have just said that change is not evolution due to the fact that it can be adaption,but isn't adaption change?

Isn't specation change? isn't change change?

He said in his last paragraph "

Then he says AGAIN in the very same paragraph,changing the definition of evolution to changes in DNA genome.

Wait what?? I thought change isn't evolution?

ohhhh, I see what you are saying. you said "Its simple,all speciation=change. All change =/evolution.

So if all change=/evolution < then logically change is not intrinsic to evolution."

Yes, I see what you are saying. And all speciation is change, but its a specific type of change that involves mutations. All change does not equal evolution because some change does not involve mutation.

That should clarify a lot of our discussion.

I feel like you should already have known this though. But it appears that you didnt. So I will apologize for not being more specific in my descriptions.

well, all evolution is, "Evolution is change in DNA that propogates throughout a population over time and generations" And ill add, obviously we are talking about mutations when we talk about change.

again "again, change is not evolution. Change can be adaptation, it can be, changes in allele pronunciation etc. Evolution is change in DNA that propogates throughout a population over time and generations. Which Ive said before."

And for clarity, by change, im referring to mutations. Which I assume you know.

Speciation is a certain type of change that we would consider evolution. This is because, in order to speciate, you need mutations propogating throughout a population over generations.

Which is what Ive been saying the whole time.

Its not evolution, because as ive said before, not all change is evolution, you can have changes in allele pronunciation for example. So not all change is evolution, however evolution is change in DNA (through mutations, which I assume you know), which becomes dominant in a population over time.

He says

Wait I thought that better does not equal evolution?

Now you're telling us that things becoming better in their environments is evolution?

Thats what Ive been saying the whole time. Let me copy and paste my own words again.

"Evolution as it pertains to biological evolution, defined by biologists...means that organisms do not necisserily become superior than all other organisms. It means they become better suited for their environment, at a set time.

Like I said, we evolved from fish, but that doesnt mean we are superior to fish. Because clearly fish can do many things better than we can. And so, in biological terms, to say that evolution automatically means to become superior through changes, is incorrect."

So, you can say, this organism is "better" in this environment. However, like I said before, a human is not truly better than a fish because fish can do many things better than humans.

So it depends on how you use the word.

Your last definition of evolution was "changes in genome that become prevalent"

So if a bacteria changes for the worse,and it becomes prevalent,then HOW? The only way something can become prevalent according to the theory,is if that change is GOOD,I.E. makes the organism survive better.

I showed you why it doesn't survive better at all,and I showed you why even if it did its 100 percent irrelevant.

Well obviously it does survive "better" or just as good if it now thrives in its new environment.

A lot of our discussion seems to be issues in description. Im sorry if my last definition didnt cover every detail of what evolution is, but you should understand that mutations are a key part of evolution. And so, change without mutations couldnt be evolution. However, evolution is change that involves mutations.

I assumed you already understood that. I apologize for not adding that detail before, but thats...thats a given. You should already know that. But if you didnt, im sorry for not mentioning it myself. I could see that leading to confusion.

So lets skip to all argumentation and agree on a definition,

evolution is when an organism changes and becomes better for its particular environment.

ah, nope. Not quite. Almost. Evolution involves mutation. So put that in your definition, and then run it by me again and lets see if we can agree.

If the nylon eater becomes better for its particular environment,then how? It can now eat nylon,so what?

Its a new trait that exists that has come to dominate in its environment. Thats all. And notice, the new trait came about through mutation, which relates to the statement above.

The other bacteria that didn't undergo this change still is just as good without it in that environment,the nylon eating bacteria is now less energy efficient. Also another thing that actually disproves you is the fact that the new enzymes are 98 percent less efficient then those without the mutation.

ok, and for the sake of moving on. Ill repeat myself.

Well, how about this question. Overall, at this moment in time, are the flavobacteria that can digest nylon over all better in their environment?

The answer is yes.

Sure, you could argue that fish, are not as intelligent as mankind. But fish have a trait that suits them in their environment at this time. If I go swimming, a shark 99.9% of the time will out live me. In its environment, it is the top survivor, and none compete with it.

With the flavobacteria that have mutated the nylon digestion, these bacteria, are the top players in their nylon environment. None compete with them.

So overall, you could argue that humans are better because we are smarter, and you could argue that the original bacteria are better because their enzymes act more specifically.

But at the end of the day, the fish is the best in water, and in water is where they reside. And the nylon digesting bacteria are the best in nylon rich environments, and that is where they reside. And this again is why I say, and why biologists say, evolution is not a ladder. You can evolve without necisserily becoming a superior being.

Remember the picture. The flavobacteria that can digest nylon is not necisserily higher on the ladder than the original bacteria. That is, as you can see in the picture. Wrong. The bacteria that can digest nylon, are more suitable for their environment, they are not necisserily more superior than the original bacteria. Some may even argue that they are worst. Just as some may argue that fish are worst than humans. But at the end of the day, it comes down to what is suitable in what environment at what time.

laddervstree.gif

And this is why everyone calls evolution "random". Its because it doesnt go in one direction. It doesnt transform animals into super animals. It goes up and down, left and right, big and small, round and round. Sharks used to be massive, they dominated the seas like no other. But now, look at how small the great white has become compared to its ancestors. That could be said to be a bad direction for evolution.

However, its not about good or bad, its about what is beneficial in the environment at a time.

And Ive said this multiple times now, and this is how evolution works in biological terms.

Are you familiar with "random walks" in evolution?

Statistically, organisms do not evolve in one direction. And you can see this both in biology and in the fossil record. We never evolve "backwards" per say. Meaning, we dont evolve back into our original DNA state. However, our traits often may go back and forth or may change similarly to a previous state over and over and over again.

What I mean by this is, an organism like a bivalve, may have doubled in size, then shrank, then doubled, then shrank again. Over and over and over.

So the point is, we evolve with our environments. Which may include, but we dont call it this "devolving". We dont call it "devolving" because we dont define evolution as a ladder, but indeed, it does happen. Which is probably why you are so conflicted with me in this discussion.

Heres another example. According to modern evolutionary theory, its possible that we could evolve into a being with a smaller or less efficient brain.

Now, you may think that is "devolving". But no scientist would call it that because thats not how we use the word. We would call it evolving to a more suitable state at a set time in their environment, which may or may not include losing such a powerful brain.

So, the flavobacteria having less specific enzymes, is not "de evolution", its not "devolving". Its evolving, just in a way that to you appears less efficient or beneficial.

But to the organism, that is prospering with the new mutation, it doesnt matter how we define the word, and it doesnt matter what we think of it. At the end of the day, those bacteria are thriving.

And this is why I am calling it evolution and you arent.

No evolution occurred here on every definition of the word,all that happened was it changed and became worse,if anything it devolved.

And I definitely just proved to you that change=/evolution.

So on what grounds are you calling this evolution?

If indeed it is beneficial then this is an example of microevolution and adapation,something Muslims have accepted since the middle ages.

But it isn't at all.

There is a difference between "microevolution" and "adaptation". Im calling it evolution on the grounds that it is change (through mutation), in a way in which a new trait has formed, and has come to dominate its population.

Adaptation doesnt always involve mutation. Which is why adaptation and microevolution are different things.

Edited by iDevonian
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So? This is the only type of mutation that can lead to new proteins,duplication plus frameshift.

Also, you have things like domain shuffling, but im trying to avoid that because its sort of "new school" research. Which again is a demonstration of the development of evolutionary theory.

http://www.ncbi.nlm.nih.gov/pubmed/10570989

Heres, a question for you, and this is a good one.

Often I find creationists who still accept common descent (we came from apes), but they believe in intelligently guided evolution. Like Michael Behe for example. Or Berlinski who is agnostic, but he believes the full picture of how evolution occured is incomplete.

Are you one of those guys? Or are you one of the ones who believes that we all just appeared in full form as is?

Edited by iDevonian
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Idev says:

Im gonna try to save us some time by consolidating the key points here.

Very well I will bring up past quotes to show how you changed your answers :).

Idev says A duplication and phrame shift in one organisms obviously isnt going to equate to a duplication in another. And other mutations can alter pre existing proteins braught about through phrame shifts. This is why, this example with nylonase, alone does not define evolutionary mutations in their entirity.

If you noticed,I did not ask about optimization of pre-existing proteins,I asked about the origination of proteins that must have some function in order to stay with in the genome or be thermodynamically stable.

Optimization of proteins are not unlikely,however large steps of optimization are,this falls in line with microevolution.

Lets go into protein science now,and maybe you can understand more Insha'Allah.

There are discovered around 1000 folds,all proteins fall with in these protein fold families.

So if I have a 200 AA sequence,and I slowly change it,probability states that the more I change it the more exponentially different the protein is going to be. So if I change 30 AA in a sequence of 200,it may just randomly pop into another random shape being completely useless or become unfoldable which most of time occurs.

This is why optimization can only go so far as shown by numerous articles.

The minimum energy compact structures (MECSs), which have protein-like properties, require that the ground states have H residues surrounded by a large number of hydrophobic residues as is topologically allowed. . . There are implications of the spectacular finding that the number of MECSs, which have protein-like characteristics, is very small and does not grow significantly with the size of the polypeptide chain.

The number of possible sequences for a protein with N amino acids is 20N which, for N = 100, is approximately 10130. The number of folds in natural proteins, which are low free energy compact structures, is clearly far less than the number of possible sequences. . .

The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the sequence space. Even though the sequence space grows exponentially with N (the number of amino acid residues [by 20N]) we conjecture that the number of low energy compact structures only scales as lnN [The natural logarithm or the power to which e (2.718 . . . ) would have to be raised to reach N] . . . The number of sequences for which a given fold emerges as a native structure is further reduced by the dual requirements of stability and kinetic accessibility. . . We also suggest that the functional requirement may further reduce the number of sequences that are biologically competent.

Source Thirumalai, D.; Klimov, D. K., Emergence of stable and fast folding protein structures, STOCHASTIC DYNAMICS AND PATTERN FORMATION IN BIOLOGICAL AND COMPLEX SYSTEMS: The APCTP Conference. AIP Conference Proceedings, Volume 501, pp. 95-111 (2000)

So the number of actual folds that can be achieved by the sequence is minimal,the number of folds that can be realized are almost always non-functional as they are random shapes brought out by the frame shift.

The enzyme's cleft was simply frame shifted and lost its ability to be specific causing it harm,this is not an example of how mutations can lead us to where we are now.

You then say this isn't the only type of mutation? Obviously,however this is the only type of mutation that creates new proteins,and unfortunately its completely ineffective.

Idev says: The reason I say this is because, you could theoretically have a mutation that brings about a trait that is more or less beneficial than the one with nylonase, then subsequent mutations can work with the enzyme even further.

The flavobacteria isnt finished evolving. It didnt have one mutation and then just said "ok im done". :P, its going to keep changing, which includes alterations in its new genes or others.

If you claim that optimization on a frameshift mutated sequence can occur,please provide your sources showing an example.

Idev says Thats not a contradiction. Change is not the same as speciation, then I follow by saying change and speciation are not the same. Im saying the same thing.

And fruit and apples are not the same. Some fruits are apples and all apples are fruits, but they are not the same thing. The reason they are not the same thing is because some fruits are oranges. Therefore If i have a sack of oranges, my fruit (oranges) is not the same as apples.

Fruits and apples are the same thing,but not all fruits are apples.

This is a common mistake in logic when dealing with classes (fruits,humans,animals). The reason why they are the same thing is because the word "apple" fulfills every meaning of the word "fruit",so ontologically they are indeed the same. However not all fruits are apples.

Here is an example, a couch that is made of all silk is indeed the same as silk is it not? However it does not logically follow that all silk are couches.

So you did indeed contradict yourself.

Idev says Not all humans are men smart one :P. haha Men are humans, but humans arent necisserily men because some humans can be women.

Please stop skimming through my post and actually read,I never said "All humans are men".

Idev says:

Alright, im gonna move on now, we both know what apples and oranges and fruit all are. This appears to be just another issue with description.

ohhhh, I see what you are saying. you said "Its simple,all speciation=change. All change =/evolution.

So if all change=/evolution &lt; then logically change is not intrinsic to evolution."

Yes, I see what you are saying. And all speciation is change, but its a specific type of change that involves mutations. All change does not equal evolution because some change does not involve mutation.

That should clarify a lot of our discussion.

Look,change without improvement is not evolution,I think we can both agree to that.

Idev says

I feel like you should already have known this though. But it appears that you didnt. So I will apologize for not being more specific in my descriptions.

well, all evolution is, "Evolution is change in DNA that propogates throughout a population over time and generations" And ill add, obviously we are talking about mutations when we talk about change.

Its not about me knowing or not knowing,I am indeed only a human being and all knowledge is given to me by Allah. But it isn't a matter of me not knowing,it is a matter of you not explaining yourself correctly and causing you to contradict yourself.

I know that we were talking about mutations when you said change,however I was showing you that if you claim that all it takes is "change" to be called evolution then I can use the meaning of that word for other absurd things.

Also,you still seem to hold on to the idea that all mutational changes are evolution,sorry but they aren't.

If something devolves and it goes around its genome,it isn't evolution by definition. Evolution means becoming better.

If you want to say "becoming better in a particular setting/time" then I'll have no problem with agreeing with you.

Idev says again "again, change is not evolution. Change can be adaptation, it can be, changes in allele pronunciation etc. Evolution is change in DNA that propogates throughout a population over time and generations. Which Ive said before."

And for clarity, by change, im referring to mutations. Which I assume you know.

Speciation is a certain type of change that we would consider evolution. This is because, in order to speciate, you need mutations propogating throughout a population over generations.

Which is what Ive been saying the whole time.

You consider speciation is evolution,but I have proven to you it isn't.

If we define evolution,and then define speciation,we can see if it is the same.

If something devolves and becomes prevalent,like a disease for example which is common. You would never call this evolution even though it is change in the DNA that is passed on to ancestors,would you?

So something is missing,that is improvement with descent and modification.

If however you stated that speciation included improvement I'd agree with you,however you still seem to be creating your own structure on words that I'm not having,sorry :) .

Idev says Its not evolution, because as ive said before, not all change is evolution, you can have changes in allele pronunciation for example. So not all change is evolution, however evolution is change in DNA (through mutations, which I assume you know), which becomes dominant in a population over time.

Any type of improvement is intrinsically change,obviously. So you are saying something that is already established,what you haven't established in your last posts are the improvement factor.

Idev says

Well obviously it does survive "better" or just as good if it now thrives in its new environment.

A lot of our discussion seems to be issues in description. Im sorry if my last definition didnt cover every detail of what evolution is, but you should understand that mutations are a key part of evolution. And so, change without mutations couldnt be evolution. However, evolution is change that involves mutations.

Its fine next time just be specific in what you say,careful argumentation is key.

I assumed you already understood that. I apologize for not adding that detail before, but thats...thats a given. You should already know that. But if you didnt, im sorry for not mentioning it myself. I could see that leading to confusion.

ah, nope. Not quite. Almost. Evolution involves mutation. So put that in your definition, and then run it by me again and lets see if we can agree.

Lets see if your definition holds up?

Descent with modification without improvement being necessary for the word evolution to be used.

There is a disease that is due to a mutation,that is expressed more in some males,this fulfills the definition of "descent with modification".

Now please answer in your next response,is this disease evolution?

Idev says

Its a new trait that exists that has come to dominate in its environment. Thats all. And notice, the new trait came about through mutation, which relates to the statement above.

Very well I asked you a question in above post,answer that and we can move on.

Idev says There is a difference between "microevolution" and "adaptation". Im calling it evolution on the grounds that it is change (through mutation), in a way in which a new trait has formed, and has come to dominate its population.

Adaptation doesnt always involve mutation. Which is why adaptation and microevolution are different things.

I'm sorry but this is incorrect.

Microevolution is indeed adaption,this is known on clearly rational basis that no sane person who ponders deeply on it can reject.

However i'll spare you the logic chopping,and just quote evolutionists.

From the rationalwiki,anti-theist site.

"When used by scientists, microevolution is the term for the gradual adaptation and evolution by a specieswhich does not result in multiple new species."

If you want some more definitions of microevolution,please ask i'll give you much more. I used rationalwiki because it is extremely anti-theist.

Now lets get to the reason why I even responded to you in the first place.

Can you show us an example of a new functional protein that has resulted from a frame-shift mutation? That is not a degenerated protein that causes loss of function?

If not we can move on to ERVs, and the fusion of human chromosome 2.

I found some evidence for frame shifting food particles randomly becoming a great Christmas dinner.

By a swedish food engineer,this might be evidence.

Edited by Ibn-Ahmed Aliyy Herz
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Regarding exon shuffling,this isn't anything new it has been in mainstream science for over 45 years.

This doesn't explain how new proteins form,only how already existing proteins can come together ,this isn't doesn't explain how new novel protein sequences are formed in the first place.

Exon shuffling is when genes that code for more then one protein exchange domains,coding for new multi-domain proteins.

For example, We have 3 sentences.

1 The dog went to the store.

2 I told him to stay at home.

3 The weather is nice,however.

I can switch the order of these sentences into 2 3 1,or 1 2 3, or 3 2 1,etc.

This doesn't explain where these sentences came about in the first place,the only answer they have is duplication plus frame shift mutation.

Exon shuffling is simple cell functioning and is irrelevant to our conversation.

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You then say this isn't the only type of mutation? Obviously,however this is the only type of mutation that creates new proteins,and unfortunately its completely ineffective.

the development of new functions isnt "ineffective".

Look,change without improvement is not evolution,I think we can both agree to that.

However, there is improvement with the ability to digest nylon.

If you want to say "becoming better in a particular setting/time" then I'll have no problem with agreeing with you.

alright

You consider speciation is evolution,but I have proven to you it isn't.

If we define evolution,and then define speciation,we can see if it is the same.

If something devolves and becomes prevalent,like a disease for example which is common. You would never call this evolution even though it is change in the DNA that is passed on to ancestors,would you?

Yes, you would. It depends on the disease, but something can evolve in a way in which it is more susceptable to harmful diseases or other harmful things. And this would still be evolution.

There is a disease that is due to a mutation,that is expressed more in some males,this fulfills the definition of "descent with modification".

Now please answer in your next response,is this disease evolution?

You'd have to give an example, but people can evolve in harmful ways and it would still be considered evolution given that the trait comes to dominate the population over the coming generations.

Can you show us an example of a new functional protein that has resulted from a frame-shift mutation? That is not a degenerated protein that causes loss of function?

The nylonase mutations have not lead to a loss in function. But if youd like, we can look at some other mutations I am interested in.

Edited by iDevonian
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Regarding exon shuffling,this isn't anything new it has been in mainstream science for over 45 years. This doesn't explain how new proteins form,only how already existing proteins can come together ,this isn't doesn't explain how new novel protein sequences are formed in the first place.

Its how already existing domains can come together, forming new proteins. Research with this material is relatively young.

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Idev says Its how already existing domains can come together, forming new proteins. Research with this material is relatively young.

Who are you trying to kid here? I know for a fact it isn't "new research",the idea of exon shuffling has been around since the 70s.

Also you either repeat what I say,or you repeat what you say.

You also commit a lot of logical fallacies such as saying a loss of specification is good and examples of new function,diseases are evolution,frame shift mutations are good,etc.

What else can a person say to this?

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