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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?

"Computational biologist Dannie Durand and colleagues have for the first time tackled the dilemma of how to study the ancestry of multi-domain genes." May 15, 2008

http://www.scienceda...80515205640.htm

just something I was looking at. New research relating to understanding the ancestry of multi domain genes. And this was only 4 years ago.

aside from that...

It is what it is. The flavobacteria is thriving with the new mutation. It has a new ability to digest nylon. Theres not much more to say.

We call this evolution because it is mutation bringing about new functions that in its particular environment, benefits the organism. The organism prospers and its new trait becomes dominant in its population over the following generations.

Thats really all there is to it. And i appreciate your thought provoking critique, its very good for discussion, and it does bring into question various details of how evolution occurs.

If youd like, I personally would like to talk about a couple other examples of evolution. Id like to see what conclusion we can come to with them. They are the increased bone density from mutation of this LDL receptor protein, and HIV immunity with the mutation of CCR5.

Now, im thinking the HIV immunity in this population of people, may be similar to the nylonase mutation in that, the CCR5 protein may have lost specificity that HIV uses to work its way into host cells. Though HIV immunity is a bit more challanging to call "harmful". And the increased bone density in populations of people, I believe they are in northern europe, id be interested to see how that came about.

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You keep bringing back points that I have already answered,so its rather circular and pointless in all honesty.

Idev says

"Computational biologist Dannie Durand and colleagues have for the first time tackled the dilemma of how to study the ancestry of multi-domain genes." May 15, 2008

http://www.scienceda...80515205640.htm

just something I was looking at. New research relating to understanding the ancestry of multi domain genes. And this was only 4 years ago.

This has nothing to do with exon shuffling being new. "Dannie Durand and colleagues have for the first time tackled the dilemma of how to study the ancestry of multi-domain genes"

Walter Gilbert introduced Exon shuffling in 1977.

Also here is an article from 1999 http://www.sciencedirect.com/science/article/pii/S0378111999002280

This means that they are solving how to study exon shuffling,not that exon shuffling is something new as you can see.

Idev says

This is

aside from that...

It is what it is. The flavobacteria is thriving with the new mutation. It has a new ability to digest nylon. Theres not much more to say.

If thats what you believe then thats what you believe,but we both know that your example is a logical fallacy.

Idev says We call this evolution because it is mutation bringing about new functions that in its particular environment, benefits the organism. The organism prospers and its new trait becomes dominant in its population over the following generations.

Thats really all there is to it. And i appreciate your thought provoking critique, its very good for discussion, and it does bring into question various details of how evolution occurs.

Again,already answered. You didn't respond to my points,you just keep repeating "its evolution,its a new function,".

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This has nothing to do with exon shuffling being new. "Dannie Durand and colleagues have for the first time tackled the dilemma of how to study the ancestry of multi-domain genes"

This means that they are solving how to study exon shuffling,not that exon shuffling is something new as you can see.

Well yes, ive been referring to modern research. And even exon shuffling itself isnt that old. 40 years I believe is a number you put on it, thats like...a single generation. The PhDs of today probably didnt even hear about that when they were coming up.

But all this is aside from the topic at hand.

If thats what you believe then thats what you believe,but we both know that your example is a logical fallacy.

Again,already answered. You didn't respond to my points,you just keep repeating "its evolution,its a new function,".

We will have to agree to disagree then.

Well hold on. You remember how you did the thing with, change, speciation and evolution? You showed directly where the logical fallacy was. Can you do that again in a simple way so I can see exactly what you mean?

If you dont mind.

I think I know what you are saying, but I want to single this out so I can be certain.

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Idev says Well yes, ive been referring to modern research. And even exon shuffling itself isnt that old. 40 years I believe is a number you put on it, thats like...a single generation. The PhDs of today probably didnt even hear about that when they were coming up.

So according to you I lied and made up the number?

Lets use simple math,Walter Gilbert introduced exon shuffling theory in 1977,now its 2012,do the math.

Also lets not side track,this is irrelevant.

Can you show us an example of a beneficial mutation via novel protein sequence from a frame shift?

Then we can move on to HIV resistance.

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So according to you I lied and made up the number?

Lets use simple math,Walter Gilbert introduced exon shuffling theory in 1977,now its 2012,do the math.

Also lets not side track,this is irrelevant.

Can you show us an example of a beneficial mutation via novel protein sequence from a frame shift?

Then we can move on to HIV resistance.

I wasnt saying you lied, I was saying, according to your number which is ~40 years..."thats like...a single generation. The PhDs of today probably didnt even hear about that when they were coming up." Well, 35.

Sure, and hopefully this will draw my answer out as well for what you believe my contradiction is. Ill say that the nylonase mutation is beneficial to the organism, which is factual because the organism thrives with the benefit of being able to digest nylon which its exposed to. And the protein, although has decreased specificity, is still highly specific in what it acts on, and is indeed a new protein, that came about from a frame shift of DNA.

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Idev says

I wasnt saying you lied, I was saying, according to your number which is ~40 years..."thats like...a single generation. The PhDs of today probably didnt even hear about that when they were coming up." Well, 35.

Sure, and hopefully this will draw my answer out as well for what you believe my contradiction is. Ill say that the nylonase mutation is beneficial to the organism, which is factual because the organism thrives with the benefit of being able to digest nylon which its exposed to. And the protein, although has decreased specificity, is still highly specific in what it acts on, and is indeed a new protein, that came about from a frame shift of DNA.

Everything which you have just stated has already been refuted,please see above.

Regarding HIV resistance,this is from CCR5 receptors being damaged.

How can something being damaged,something losing specificity,lead to the complex function of life today?

Your examples are logical fallacies,please stop repeating yourself :)

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Everything which you have just stated has already been refuted,please see above.

Well, lets see. Does the organism thrive with the new benefit of being able to digest nylon? Yes it does. Is the protein new? Yes it is. is it still highly specific? Yes it is. Did it come about from a frame shift in DNA? Yes.

ok so what is refuted here?

We can observe the bacteria, so we know the first point is factual. We both have agreed that we have a new protein, and we have both agreed that its highly specific. And we have both agreed that it came about from a frame shift as well.

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Idev says

Well, lets see. Does the organism thrive with the new benefit of being able to digest nylon?

Hmm well,idk lets think about it. The organism is still rare,the organism is now less effective than other bacteria of its class. 50-98 percent less efficient.

hmm Idk,what do you think?

Idev says Yes it does. Is the protein new? Yes it is. is it still highly specific? Yes it is. Did it come about from a frame shift in DNA? Yes.

Is sickle cell disease a new protein? Lets use your logic? Yes? hmmm why isn't it good then? I wonder why?

Are diseases new proteins? Yes they are,you see how you have no argument?

Highly specific? Sorry but I showed you it isn't,it lost specificity and you agreed.

And yes it comes from a frame shift.

Idev says ok so what is refuted here?

Everything

Idev says We can observe the bacteria, so we know the first point is factual. We both have agreed that we have a new protein, and we have both agreed that its highly specific. And we have both agreed that it came about from a frame shift as well.

Answered see above.

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Hmm well,idk lets think about it. The organism is still rare,the organism is now less effective than other bacteria of its class. 50-98 percent less efficient.

But its a thousand times more efficient at digesting nylon, and thats what matters in its environment at this time.

Is sickle cell disease a new protein? Lets use your logic? Yes? hmmm why isn't it good then? I wonder why?

Are diseases new proteins? Yes they are,you see how you have no argument?

Highly specific? Sorry but I showed you it isn't,it lost specificity and you agreed.

Evolution is evolution. The good and the bad.

"No one said it wasn't specific,I said it lost specificity." ~ You earlier in the discussion.

oh, got ya :P. So here you said "no one said it wasnt specific", aka I know it is specific. Then you just said "I showed you it isnt" (specific).

So yes, we agree that it is still highly specific, just not as specific as it was.

Check this out.

http://www.blackwellpublishing.com/ridley/a-z/Sickle_cell_anemia.asp

"

Sickle cell anemia is a nearly lethal condition in humans, responsible for about 100, 000 deaths a year. About 80% of individuals with this condition die before reproducing. Yet despite such apparently strong selection against the gene responsible for sickle cell hemoglobin, it is maintained at frequencies of 10% or even more in some human populations. Why is this?

The answer was first suggested by Haldane and confirmed by Allison. Sickle cell anemia is caused by a genetic variant of a-hemoglobin. If we symbolize the normal hemoglobin allele by A and the sickle cell hemoglobin by S, then people who suffer from sickle cell anemia are SS. Haldane compared a map of the incidence of malaria with a map of the gene frequency: they are strikingly similar. Perhaps hemoglobin S provides some advantage in malarial zones.

It turned out that, although SS is almost lethal, the heterozygote AS is more resistant to malaria than the homozygote AA. AS red blood cells are more difficult for the malarial parasite Plasmodium falciparum to colonize. Therefore, where the malarial parasite is common, AS humans survive better than AA, which suffer from malaria."

Sorry if its long, but notice how its pointing out, advantages in a certain environment, in a certain time for those who have the sickle cell hemoglobin.

Its the least harmful of the two evils for people within malaria prone environments.And if this did evolve through frame shift, it would be an example of evolution. Both the good and the bad.

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Its an enzyme of course its going to be specific,you said it was "highly specific" , like you were implying the mutation caused it to specifically act on nylon.

If it loss specificity then why mention that its still specific?

The examples of Nylon eating,malaria resistance, HIV resistance, all fall in the same category of something being damaged and not working properly.

In the case of nylon eating bacteria and malaria resistance,no good has come out of it.

Regarding HIV resistance,HIV binds to specific receptors,a mutation damaged these receptors making them resistant to the disease.

This isn't an example of a new functional protein forming.

Lol,yet it seems you still have the audacity to call sickle cell disease a good mutation.....

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Its an enzyme of course its going to be specific,you said it was "highly specific" , like you were implying the mutation caused it to specifically act on nylon.

If it loss specificity then why mention that its still specific?

Because, it still being specific allows us to recognize that its still something that is used for benefits. A community can evolve a detriment, and it can prosper with a detriment so long as its outweighed by the benefits.

And this is why something can evolve in a way in which its more prone to something like sickle cell, while still prospering. Because the benefits of having sickle cell, outweigh the detriments in malaria prone environments. So its only beneficial in a certain environment. Otherwise the organism would die.

And I say this with the assumption that the little paragraph from above about malaria and sickle cell anemia is true.

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Idev says Because, it still being specific allows us to recognize that its still something that is used for benefits. An community can evolve a detriment, and it can prosper with a detriment so long as its outweighed by the benefits.

I'm sorry but you aren't going to convince me or anyone else that sickle cell disease,enzymes being damaged,and receptors being damage are proofs for good mutations.

These are pure logical fallacies,

just like you breaking your grandmothers legs and saying "see guys she lives in a busy city environment,now she can't get hit by a car".

idev says And this is why something can evolve in a way in which its more prone to something like sickle cell, while still prospering. Because the benefits of having sickle cell, outweigh the detriments in malaria prone environments. So its only beneficial in a certain environment. Otherwise the organism would die.

Amazing.

"Sickle cell anemia is a nearly lethal condition in humans, responsible for about 100, 000 deaths a year. About 80% of individuals with this condition die before reproducing. "

This benefit of malaria resistance outweighs this?

Who are you trying to kid here?

Sickle cell disease is not a good mutation,why can't you accept this?

How can diseases and dysfunctions be proof for evolution?

I'm sorry but you have made a poor case in all respects and the arguments you are using are abusrd.

I mean honestly,how can you be serious?

What is even more hilarious is that malaria can be cured extremely easily,sickle cell disease outright kills you.

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I'm sorry but you aren't going to convince me or anyone else that sick cell disease,enzymes being damaged,and receptors being damage are proofs for good mutations.

These are pure logical fallacies,

just like you breaking your grandmothers legs and saying "see guys she lives in a busy city environment,now she can't get hit by a car".

How is it a logical fallacy?

Think about it. Lets say grandma has a 99% chance of getting hit by a car if she lives in the city. So she has a 1% chance to live with her legs. But if you break her legs, she has a 80% chance of living.

Grandma would be wise to have her legs broken for her own survival.

hehe, what a cruel example.

But I see what you are saying. And this is a seperate concept.

In one hand, we have the question, is this evolution? I say yes it is.

But you say no, because...the mutation doesnt seem good enough. It still seems too harmful.

Well, we can leave it at that if you want, and look into the CCR5 and LDL receptor mutation if u want. And lets compare the pros and the cons of these mutations.

And remember, grandma with broken legs will live 10 times longer than grandma with legs...but only in the city and only during rush hour.

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Amazing.

"Sickle cell anemia is a nearly lethal condition in humans, responsible for about 100, 000 deaths a year. About 80% of individuals with this condition die before reproducing. "

This benefit of malaria resistance outweighs this?

Who are you trying to kid here?

Sickle cell disease is not a good mutation,why can't you accept this?

How can diseases and dysfunctions be proof for evolution?

I'm sorry but you have made a poor case in all respects and the arguments you are using are abusrd.

I mean honestly,how can you be serious?

What is even more hilarious is that malaria can be cured extremely easily,sickle cell disease outright kills you.

SS is nearly lethal, AS I assume is not. But AS still has the sickle cell Allele. So, think about it this way. If you have AA and I have AS and we are both in a malaria environment, i would live longer than you. But if we both left that environment you would out live me. And if I had a child with another AS and our child was an SS, then our child would most likely die.

but in the mean time, what matters is the environment and the time. And statistically, AS will outlive AA in a malaria rich environment.

it makes perfect sense.

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This is wrong,a person in an environment with malaria is able to be cured of it no problem.

There is no cure for a person with sickle cell disease,and the persons usually dies.

To use this example is absurd,a disease is not an example of a beneficial mutation.

Can you please explain to me how sickle cell disease,damaged receptors,and damaged enzymes can lead to new functional proteins?

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Check this out.

Yes, thats correct. Check it out.

"A gene known as HbS was the center of a medical and evolutionary detective story that began in the middle 1940s in Africa. Doctors noticed that patients who had sickle cell anemia, a serious hereditary blood disease, were more likely to survive malaria, a disease which kills some 1.2 million people every year. What was puzzling was why sickle cell anemia was so prevalent in some African populations.

How could a "bad" gene -- the mutation that causes the sometimes lethal sickle cell disease -- also be beneficial? On the other hand, if it didn't provide some survival advantage, why had the sickle gene persisted in such a high frequency in the populations that had it?

The sickle cell mutation is a like a typographical error in the DNA code of the gene that tells the body how to make a form of hemoglobin (Hb), the oxygen-carrying molecule in our blood. Every person has two copies of the hemoglobin gene. Usually, both genes make a normal hemoglobin protein. When someone inherits two mutant copies of the hemoglobin gene, the abnormal form of the hemoglobin protein causes the red blood cells to lose oxygen and warp into a sickle shape during periods of high activity. These sickled cells become stuck in small blood vessels, causing a "crisis" of pain, fever, swelling, and tissue damage that can lead to death. This is sickle cell anemia.

But it takes two copies of the mutant gene, one from each parent, to give someone the full-blown disease. Many people have just one copy, the other being normal. Those who carry the sickle cell trait do not suffer nearly as severely from the disease.

Researchers found that the sickle cell gene is especially prevalent in areas of Africa hard-hit by malaria. In some regions, as much as 40 percent of the population carries at least one HbS gene.

It turns out that, in these areas, HbS carriers have been naturally selected, because the trait confers some resistance to malaria. Their red blood cells, containing some abnormal hemoglobin, tend to sickle when they are infected by the malaria parasite. Those infected cells flow through the spleen, which culls them out because of their sickle shape -- and the parasite is eliminated along with them."

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Perfect. So yes, People live with the sickle celll Allele within them, and have a much greater chance of survival, especially when compared to malaria prone people in africa (1.2 million a year are killed from it).

The sickle cell Allele/disease only becomes a problem when two people with sickle cell have a child with a double recessive or double dominant or whatever the Allele is.

It is the lesser of two evils.

A person with malaria may be curable, but if 1.2 million people are dying a year, either they arent getting the cure, they cant afford it, or they die before they get it. In comparison to a person with heterozygous alleles, the person with AS has a high probability of never even being effected by the sickle cell disease that they carry. Meanwhile 1.2 million malaria people a year are dying.

If I lived in africa and 1.2 million people a year were dying from malaria, and I was right in the middle of it, I wouldnt necisserily be happy to have the sickle cell gene, but I wouldnt necisserily be dissapointed either, and as long as I didnt have children with another who has sickle cell, the children, my children and progeny would be fine.

And thats another part of evolution right there. propogation of the trait throughout the community. Its perfect. Thank you for bringing this to my attention.

And dont get me wrong, I see what you are saying. Getting sickle cell isnt the greatest thing ever. But, i bet you that disease, which you call detrimental, saved a lot of lives (in the malaria rich environment, at the time in which 1.2 mill a year were dying from malaria). A specific place, a specific environment and time.

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Lets explain why your argument is not sound.

2 million people have sickle cell anemia,out of those 2 million 95 percent of them will die from it.

The disease is hereditary and is commonly given to offspring,this disease also has no cure.

300 million people have malaria,1 million people a year will sadly die from it.

Malaria majority of the time is not fatal,and also has a cure with complete recovery.

People who die from malaria are usually the old or the young.

and also another reason more people die from malaria is because more people have it.

And this is due to social issues in Africa where pest control and disease management are poor.

At the biological level,sickle cell anemia will not only spread faster,but will also kill its victims 95 percent of the time.

If 300 million people had sickle cell anemia,95 percent of them would sadly die.

If 300 million people had malaria, 0.3 percent of them would sadly die off mostly from young or old people.

They are both diseases........ however sickle cell anemia is far more lethal at the biological level and soon the social level.

So if me and you,both healthy men living in Africa and I got malaria and you got sickle cell disease.

Even with no cure ,I'd live on and you'd die.

none the less this is irrelevant to new functional proteins.

and again I ask you, Can you please explain to me how sickle cell disease,damaged receptors,and damaged enzymes can lead to new functional proteins?

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Lets explain why your argument is not sound.

2 million people have sickle cell anemia,out of those 2 million 95 percent of them will die from it.

The disease is hereditary and is commonly given to offspring,this disease also has no cure.

No no, 95% do not die. People who have a heterozygous mix do not. 9% of 2 million will die from it. 91% will live on. 42% will have malaria resistance.

Where did you even get this 95% number? Looks like you just made it up.

300 million people have malaria,1 million people a year will sadly die from it.

Malaria majority of the time is not fatal,and also has a cure with complete recovery.

People who die from malaria are usually the old or the young.

and also another reason more people die from malaria is because more people have it.

And this is due to social issues in Africa where pest control and disease management are poor.

At the biological level,sickle cell anemia will not only spread faster,but will also kill its victims 95 percent of the time.

If 300 million people had sickle cell anemia,95 percent of them would sadly die.

If 300 million people had malaria, 0.3 percent of them would sadly die off mostly from young or old people.

They are both diseases........ however sickle cell anemia is far more lethal at the biological level and soon the social level.

So if me and you,both healthy men living in Africa and I got malaria and you got sickle cell disease.

and again I ask you, Can you please explain to me how sickle cell disease,damaged receptors,and damaged enzymes can lead to new functional proteins?

Annually, 1.5 million people die of malaria (one million in Africa South of Sahara), a child every 30 seconds. About 120 million people died of malaria since 1914,

About 2.5 million African-Americans (1 in 12) are carriers (as) of the sickle cell trait. People who are carriers may not even be aware that they are carrying the S allele!

"n the United States, about 1 in 500 African-Americans develops sickle cell anemia. In Africa, about 1 in 100 individuals develops the disease. Why is the frequency of a potentially fatal disease so much higher in Africa?

The answer is related to another potentially fatal disease, malaria. Malaria is characterized by chills and fever, vomiting, and severe headaches. Anemia and death may result. Malaria is caused by a protozoan parasite (Plasmodium) that is transmitted to humans by the Anopheles mosquito. When malarial parasites invade the bloodstream, the red cells that contain defective hemoglobin become sickled and die, trapping the parasites inside them and reducing infection.

Compared to AS heterozygotes, people with the AA genotype (normal hemoglobin) have a greater risk of dying from malaria. Death of AA homozygotes results in removal of A alleles from the gene pool. Individuals with the AS genotype do not develop sickle cell anemia and have less chance of contracting malaria. They are able to survive and reproduce in malaria-infected regions. Therefore, BOTH the A and S alleles of these people remain in the population. SS homozygotes have sickle cell anemia, which usually results in early death. In this way, S alleles are removed from the gene pool.

In a region where malaria is prevalent, the S allele confers a survival advantage on people who have one copy of the allele, and the otherwise harmful S allele is therefore maintained in the population at a relatively high frequency. This phenomenon will be examined in the Allele Frequencies and Sickle Cell Anemia Lab, which relates the change in allele frequency in a population to evolution."

"The frequency of the S allele in malaria-infected regions of Africa is 16%. The sickle cell allele is also widespread in the Mediterranean and other areas where malaria is or used to be a major threat to life. In contrast, the S allele frequency is only 4%"

http://chroma.gs.was...ickle-back.html

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Ok, so lets go ahead and look at the real danger here.

"Despite mankind's longstanding struggle to control mosquito populations, the World Health Organization currently estimates that each year malaria causes 300 to 500 million infections and over 1 million deaths each year."

"http://malaria.jhsph.edu/about_malaria/"

"Since the homozygous recessive (when the Anaemia is actually expressed) and heterozygous condition do not affect mating probabilities, the allele will naturally remain within the population." ~ http://wiki.answers...._pool_of_the_US

"About 2 million Americans, or 1 in 12 African Americans, carry the sickle cell trait." ~ http://www.ornl.gov/...osome/sca.shtml

Ok, so lets re examine this.

1/12 Africans carry the Allele. Of those 1 in 12, those who have heterozygous frequencies and double recessive are not going to die from sickle cell. Thats, we can round up to 9% for the sake of the statement below.

"Sickle-cell anemia is an interesting genetic disease. Normal homozygous individials (SS) have normal blood cells that are easily infected with the malarial parasite. Thus, many of these individuals become very ill from the parasite and many die. Individuals homozygous for the sickle-cell trait (ss) have red blood cells that readily collapse when deoxygenated. Although malaria cannot grow in these red blood cells, individuals often die because of the genetic defect. However, individuals with the heterozygous condition (Ss) have some sickling of red blood cells, but generally not enough to cause mortality. In addition, malaria cannot survive well within these "partially defective" red blood cells. Thus, heterozygotes tend to survive better than either of the homozygous conditions. If 9% of an African population is born with a severe form of sickle-cell anemia (ss), what percentage of the population will be more resistant to malaria because they are heterozygous (Ss) for the sickle-cell gene? Answer: 9% =.09 = ss = q2. To find q, simply take the square root of 0.09 to get 0.3. Since p = 1 - 0.3, then p must equal 0.7. 2pq = 2 (0.7 x 0.3) = 0.42 = 42% of the population are heterozygotes (carriers). "

~http://www.k-state.edu/parasitology/biology198/answers1.html

ok so, 42% of the population is heterozygous and has immunity to malaria. Thats also 42% who arent dying from sickle cell. Also, homozygous dominant sickle cell holders are going to be passing on the gene as well. 49% are homozygous dominant.

So basically only 9% of these people are dying. The other 91% is going to carry on the gene and probably wont even know it. And of those 42%, 25% of their children will be taking on the double recessive, thats 75% of the 42% that is going to be fine for another generation.

Thats how the gene is spreading. And its perfectly understandable, and you should recognize this.

Sickle cell does kill many people, but it simultaneously is saving them from malaria, and simultaneously is propagating throughout the population of those who carry the gene but arent dying from it.

So what you have is a mutation that brings about this sickle cell anemia, which is in part a detrimental mutation. However, it still benefits the organism in its environment at this particular time.

Which is what we have said time and time again with relation to nylonase. With nylonase, its a new protein, a new function (digestion of nylon), it thrives in its environment and propogates throughout the population.

Sickle cell, which you keep bringing up time and time again is beneficial for those in a particular environment, and it propogates throughout the population because 91% of its carriers arent affected by it. And even further 75% of offspring of the 42% of heterozygous carriers, are not affected by it, and 50% continue to carry it to the next generation.

And this is how disease can be a part of evolution, and how mankind can evolve traits that are more prone to disease. Its because sometimes, the detriments are outweighed by the benefits. This disease not only saved millions of lives, but because it kills off far fewer of its hosts than the number of hosts who carry it, the gene passes on.

And this isnt even an argument, its a statement. This is how it works according to just about any and every source both scientific and non scientific.

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and again I ask you, Can you please explain to me how sickle cell disease,damaged receptors,and damaged enzymes can lead to new functional proteins?

Im still sticking with the nylonase example. The organism benefits from the mutation. Its not like after the mutation somehow the organism is in danger and dying off to become extinct.

On the contrary it is prospering with its new protein and new ability to digest nylon.

Yes the new protein is less specific to the substrates it can act on, however its still highly specific to compounds in nylon byproducts, which is something the organisms proteins could not act on before. So its a specified, new function from a new protein.

So, what you have is a new, functional, beneficial protein. And unlike sickle cell anemia, the organisms arent all dying off from the mutation. (Even though the evolution of Sickle cell Anemia is still an example of evolution none the less).

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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.

Just doing further reading.

6-aminohexanoate-cyclic-dimer hydrolase, cleaves a 2-subunit nylon ring into a 2-subunit linear ring. Your second (6-aminohexanoate-linear-dimer hydrolase) and 3rd (6-aminohexanoate-linear dimer hydrolase) enzymes break down the end and middle sections of your nylon chains.

According to our source from earlier, i believe the number was over 60+ similar compounds were not broken down by these enzymes. So they are very specific in what they do, and the original flavobacterium couldnt do this.

The mutation doesnt appear to harm the organism either. You keep comparing it to sickle cell, but sickle cell kills a number of its host organisms, whereas the nylonase mutation does not.

So Id think of it more along the lines of sickle cell without the fatalities, which would be a benefit in that they would give the organisms the ability to do something better than they originally could, like digest nylon or resist malaria.

and from your source

"X-ray Crystallographic Analysis of 6-Aminohexanoate-Dimer Hydrolase"

"Ser112

The wild-type EII polypeptide includes 26 Ser residues. Previously, we found that EII activity was inhibited by the specific binding of diisopropylfluorophosphate to Ser112 (40). Moreover, site-directedmutagenesis of Ser112 to Ala caused a drastic decrease in the enzyme activity to undetectable levels (40), suggesting the possible involvement of Ser112 in the catalysis. Moreover, the sequence motif common to the EII and EII proteins (i.e. Ser112-Val-Ser-Lys115, is located at the beginning of the 5 helix. This motif is located at the structurally equivalent position in the penicillin-recognizing family of serine-reactive hydrolases (Fig. 5). From these results, we concluded that Ser112 acts as a nucleophile in the catalysis.".

It sounds to me like this is simply a beneficial mutation for the organism. The original enzyme has certain less inhibited substrates, however in response to that, there is the development of essentially a specified combination of new enzymes that almost work as a team to break down nylon. Which is far more impressive than what the original enzyme could do, or in this case, could not do. I dont even think the original enzyme was known to have any particular value to the organism at all.

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Idev says

No no, 95% do not die. People who have a heterozygous mix do not. 9% of 2 million will die from it. 91% will live on. 42% will have malaria resistance.

Where did you even get this 95% number? Looks like you just made it up

You still have yet to answer my question,how can mutations such as frame shifts/loss of specification (nylon) lead to novel protein sequences that are functional?

I read the confidence interval rate and saw 95 percent thinking it was the mortality rate,however the mortality rate is actually worse. You also hardly provide any sources for what you say,anyways.

Here is a source that shows the mortality rate for people with sickle cell anemia.

http://www.plosone.o...al.pone.0014699

http://www.nejm.org/...199406093302303

Lets go into the articles.

"Among children and adults with sickle cell anemia (homozygous for sickle hemoglobin), the median age at death was 42 years for males and 48 years for females."

"The greatest burden of sickle cell anemia (SCA) is in sub-Saharan Africa (SSA), where 75% of the 300,000 global births of affected children live[1], and estimates suggest that 50–80% of these patients will die before adulthood[2]. "

"In this study, adults with sickle cell anemia had a high mortality rate, with few surviving into their 60s."

So according to the study,50-80 perecent will die before adulthood, and those in adulthood dying at around 40. So regarding the death rate,you are refuted there because it is worse. Very few people with sickle cell disease live to to 60 years old.

So thanks for making me re-read I appreciate it.

Also the reason why more people have malaria than sickle cell disease is because those with malaria will survive most of the time,and those with sickle cell disease will die before even reproducing.

Idev says

Annually, 1.5 million people die of malaria (one million in Africa South of Sahara), a child every 30 seconds. About 120 million people died of malaria since 1914,

About 2.5 million African-Americans (1 in 12) are carriers (as) of the sickle cell trait. People who are carriers may not even be aware that they are carrying the S allele!

"n the United States, about 1 in 500 African-Americans develops sickle cell anemia. In Africa, about 1 in 100 individuals develops the disease. Why is the frequency of a potentially fatal disease so much higher in Africa?

The answer is related to another potentially fatal disease, malaria. Malaria is characterized by chills and fever, vomiting, and severe headaches. Anemia and death may result. Malaria is caused by a protozoan parasite (Plasmodium) that is transmitted to humans by the Anopheles mosquito. When malarial parasites invade the bloodstream, the red cells that contain defective hemoglobin become sickled and die, trapping the parasites inside them and reducing infection.

Compared to AS heterozygotes, people with the AA genotype (normal hemoglobin) have a greater risk of dying from malaria. Death of AA homozygotes results in removal of A alleles from the gene pool. Individuals with the AS genotype do not develop sickle cell anemia and have less chance of contracting malaria. They are able to survive and reproduce in malaria-infected regions. Therefore, BOTH the A and S alleles of these people remain in the population. SS homozygotes have sickle cell anemia, which usually results in early death. In this way, S alleles are removed from the gene pool.

In a region where malaria is prevalent, the S allele confers a survival advantage on people who have one copy of the allele, and the otherwise harmful S allele is therefore maintained in the population at a relatively high frequency. This phenomenon will be examined in the Allele Frequencies and Sickle Cell Anemia Lab, which relates the change in allele frequency in a population to evolution."

"The frequency of the S allele in malaria-infected regions of Africa is 16%. The sickle cell allele is also widespread in the Mediterranean and other areas where malaria is or used to be a major threat to life. In contrast, the S allele frequency is only 4%"

http://chroma.gs.was...ickle-back.html

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

First of all,stop giving me random websites and Wikipedia,these are not real sources.

Please stick with medical journals as I am doing,also your article is out of date by 11 years (oops).

It isn't 2.5 million anymore,so the information he gave you is off.

Look its simple,to find the mortality rate we look at age of deaths,number of people with the disease,and the cumulative rate of death.

Anyways The World Health organization says the people who are infected with malaria are 300 million people world wide,out of those 300 million 1 million will die who are mostly children.

http://www.sciencedi...140673600025800

"Estimated malaria specific mortality in under-5s in

hyperendemic to holoendemic areas in Africa 17 is from 20 to 36 per 1000. ."

Compared to 50-80 percent at child hood,there is simply no comparison.

Even if in a magical world sickle cell disease was good for you,then it still only came from a corruption of the cell causing it to fold wrong it isn't an example of a functional novel protein sequence interacting with other protein parts.

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

Idev says

Ok, so lets go ahead and look at the real danger here.

"Despite mankind's longstanding struggle to control mosquito populations, the World Health Organization currently estimates that each year malaria causes 300 to 500 million infections and over 1 million deaths each year."

"http://malaria.jhsph.edu/about_malaria/"

"Since the homozygous recessive (when the Anaemia is actually expressed) and heterozygous condition do not affect mating probabilities, the allele will naturally remain within the population." ~ http://wiki.answers...._pool_of_the_US

"About 2 million Americans, or 1 in 12 African Americans, carry the sickle cell trait." ~ http://www.ornl.gov/...osome/sca.shtml

Ok, so lets re examine this.

1/12 Africans carry the Allele. Of those 1 in 12, those who have heterozygous frequencies and double recessive are not going to die from sickle cell. Thats, we can round up to 9% for the sake of the statement below.

"Sickle-cell anemia is an interesting genetic disease. Normal homozygous individials (SS) have normal blood cells that are easily infected with the malarial parasite. Thus, many of these individuals become very ill from the parasite and many die. Individuals homozygous for the sickle-cell trait (ss) have red blood cells that readily collapse when deoxygenated. Although malaria cannot grow in these red blood cells, individuals often die because of the genetic defect. However, individuals with the heterozygous condition (Ss) have some sickling of red blood cells, but generally not enough to cause mortality. In addition, malaria cannot survive well within these "partially defective" red blood cells. Thus, heterozygotes tend to survive better than either of the homozygous conditions. If 9% of an African population is born with a severe form of sickle-cell anemia (ss), what percentage of the population will be more resistant to malaria because they are heterozygous (Ss) for the sickle-cell gene? Answer: 9% =.09 = ss = q2. To find q, simply take the square root of 0.09 to get 0.3. Since p = 1 - 0.3, then p must equal 0.7. 2pq = 2 (0.7 x 0.3) = 0.42 = 42% of the population are heterozygotes (carriers). "

~http://www.k-state.edu/parasitology/biology198/answers1.html

This is a worksheet for students,you quoted me problem #2.

This is not a real source,however I will accept it.

Lets continue on and then I'll comment on what you are saying.

Idev says ok so, 42% of the population is heterozygous and has immunity to malaria. Thats also 42% who arent dying from sickle cell. Also, homozygous dominant sickle cell holders are going to be passing on the gene as well. 49% are homozygous dominant.

This occurs when one parent carries the allele making the disease mild but still giving off the effects of malaria resistance but not killing the person with the trait. Lets go on. This is not sickle cell disease but sick cell trait.

Idev says Thats how the gene is spreading. And its perfectly understandable, and you should recognize this.

Sickle cell does kill many people, but it simultaneously is saving them from malaria, and simultaneously is propagating throughout the population of those who carry the gene but arent dying from it.

So what you have is a mutation that brings about this sickle cell anemia, which is in part a detrimental mutation. However, it still benefits the organism in its environment at this particular time.

The disease,along with the trait (which is in reality a disease as well) makes the people resistant to malaria.

This is an example of microevolution only,no new functional protein parts have been introduced only the corruption of one. This is the whole point of our conversation.

Lets say malaria is gone,those people with the trait are now less fit with those who aren't, where is the net improvement ?

If there is no net improvement,how does this lead to evolution?

You will probably say "the net improvement is resistance to malaria".

However where is the new genetic content and new functionality?

The resistance to malaria is from and only from the lack of functionality including the trait.

.This isn't going to lead us anywhere.

Idev says

Which is what we have said time and time again with relation to nylonase. With nylonase, its a new protein, a new function (digestion of nylon), it thrives in its environment and propogates throughout the population.

Sickle cell, which you keep bringing up time and time again is beneficial for those in a particular environment, and it propogates throughout the population because 91% of its carriers arent affected by it. And even further 75% of offspring of the 42% of heterozygous carriers, are not affected by it, and 50% continue to carry it to the next generation.

And this is how disease can be a part of evolution, and how mankind can evolve traits that are more prone to disease. Its because sometimes, the detriments are outweighed by the benefits. This disease not only saved millions of lives, but because it kills off far fewer of its hosts than the number of hosts who carry it, the gene passes on.

And this isnt even an argument, its a statement. This is how it works according to just about any and every source both scientific and non scientific

The nylon enzyme does have a new protein,but this protein is again only a corrupted form of its earlier self,so to say its "new" would be wrong.

The "new" protein is also not functional,so this is wrong on your part. The effect you see as good which isn't,only comes from the corruption of the enzyme's cleft,how is this the protein doing a function?

Neither is the sickle cell disease "functional",but only a loss of function..

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Idev says

Just doing further reading. 6-aminohexanoate-cyclic-dimer hydrolase, cleaves a 2-subunit nylon ring into a 2-subunit linear ring. Your second (6-aminohexanoate-linear-dimer hydrolase) and 3rd (6-aminohexanoate-linear dimer hydrolase) enzymes break down the end and middle sections of your nylon chains.

According to our source from earlier, i believe the number was over 60+ similar compounds were not broken down by these enzymes. So they are very specific in what they do, and the original flavobacterium couldnt do this.

The original flavobacterium couldn't do this because its enzymes were more specific and uncorrupted.

You're just repeating yourself now with no new argument :)

Idev says The mutation doesnt appear to harm the organism either.

Sorry but you're wrong,I have shown you medical journals showing the nylon enzyme being much less efficient.

Idev says

You keep comparing it to sickle cell, but sickle cell kills a number of its host organisms, whereas the nylonase mutation does not. So Id think of it more along the lines of sickle cell without the fatalities, which would be a benefit in that they would give the organisms the ability to do something better than they originally could, like digest nylon or resist malaria. and from your source "X-ray Crystallographic Analysis of 6-Aminohexanoate-Dimer Hydrolase" "Ser112 The wild-type EII polypeptide includes 26 Ser residues. Previously, we found that EII activity was inhibited by the specific binding of diisopropylfluorophosphate to Ser112 (40). Moreover, site-directedmutagenesis of Ser112 to Ala caused a drastic decrease in the enzyme activity to undetectable levels (40), suggesting the possible involvement of Ser112 in the catalysis. Moreover, the sequence motif common to the EII and EII proteins (i.e. Ser112-Val-Ser-Lys115, is located at the beginning of the 5 helix. This motif is located at the structurally equivalent position in the penicillin-recognizing family of serine-reactive hydrolases (Fig. 5). From these results, we concluded that Ser112 acts as a nucleophile in the catalysis.".

It sounds to me like this is simply a beneficial mutation for the organism. The original enzyme has certain less inhibited substrates, however in response to that, there is the development of essentially a specified combination of new enzymes that almost work as a team to break down nylon.

Sorry but you either are mistaken or not reading the article correctly.

You think that the new enzyme now has a new active site specifically from the mutation and specifically used for nylon,which causes you to think that the new enzyme has actual new interactive function,this isn't the case ser is already present.

In the same source "we conclude that the nylon oligomer hydrolase utilizes nucleophilic Ser112 as a common active site both for nylon oligomer-hydrolytic and esterolytic activities. "

​break down of electrolytic molecules was the original function of the enzyme,the new nylon uses the exact same active site.

So what changed? A part of the cleft was changed due to a frame shift making it less specific and causing molecules that can use serine as a nucleophile to be used such as nylon.

Anyways,to get to the real point of the conversation.

Can you please show me a novel protein with a new interactive function?

Loss of specificity in an enzyme,corruption of hemoglobin,and damaging of receptors are not examples of this even if they are microevolution.

You act as if any organism improving or becoming better is proof,no it isn't at all.

No one rejects that organisms show mutations and adapt to their environments,what we reject are whole cells and machines coming together via frame shift mutations/natural selection.

So from here I'll have to say,unless you can show me what I asked for you have not proven anything.

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You still have yet to answer my question,how can mutations such as frame shifts/loss of specification (nylon) lead to novel protein sequences that are functional?

This is an example of microevolution only,no new functional protein parts have been introduced only the corruption of one. This is the whole point of our conversation.

Lets say malaria is gone,those people with the trait are now less fit with those who aren't, where is the net improvement ?

If there is no net improvement,how does this lead to evolution?

You will probably say "the net improvement is resistance to malaria".

However where is the new genetic content and new functionality?

The resistance to malaria is from and only from the lack of functionality including the trait.

.This isn't going to lead us anywhere.

The nylon enzyme does have a new protein,but this protein is again only a corrupted form of its earlier self,so to say its "new" would be wrong.

The "new" protein is also not functional,so this is wrong on your part. The effect you see as good which isn't,only comes from the corruption of the enzyme's cleft,how is this the protein doing a function?

Neither is the sickle cell disease "functional",but only a loss of function..

In regards to the sickle cell and malaria topic, i couldnt care less if my sources were from a 2 year old in the 1400's. All sources, professional and lay, old and new all state the same thing. The explanation they give for why sickle cell is around is perfectly reasonable, and if you cant see that, thats not my problem. Thats about all ill bother saying about that.

And the new proteins for nylon digestion are functional. They perform a function that benefits the organism like never before. And its not really "corrupt" or a bad thing if it gives the organism a new nitch in its environment which benefits it. The older generation of the bacteria couldnt capitalize on the nylon in its environment like the newer generations can.

And so, I will stick with the nylonase example, that is to say it is a new function from new proteins that benefit the organism from mutation. Its passed on through the organisms community and is therefore, evolution.

Sorry but you're wrong,I have shown you medical journals showing the nylon enzyme being much less efficient.

Well, clearly they are more efficient at breaking down nylon.

Can you please show me a novel protein with a new interactive function?

You act as if any organism improving or becoming better is proof,no it isn't at all.

No one rejects that organisms show mutations and adapt to their environments,what we reject are whole cells and machines coming together via frame shift mutations/natural selection.

The organism has improved by some means. This is undeniable. You seem to believe the detriment of this enzyme losing specificity outweights its benefits. Also, the organism still has its original gene for development of its original proteins. And im glad you recognize that mutations occur and organisms adapt to their environments using these mutations. That is what we call evolution. And there are a multitude of mutations that can manipulate a gene.

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  • 5 weeks later...

You think that the new enzyme now has a new active site specifically from the mutation and specifically used for nylon,which causes you to think that the new enzyme has actual new interactive function,this isn't the case ser is already present.

Just adding a few things here and there after further reading and talking to some higher level graduates.

First off, nobody can say if the original enzyme did or did not use the ser active site. Because the original structure of that enzyme no longer exists. You cant figure out what something does if it doesnt exist anymore (at least not with molecular biology). The mutation occurred on a separate duplicated gene. So it is a new function to the organism, that is additionally added to the organism as a plasmid, and isnt actually added to the bacterias genome. It's physically an additional process, independent of the original organisms processes. So even if the original enzyme did use the ser site to do something specific, and no longer can be specific toward that operation, its still only occurs in the plasmid and not the bacterial genome itself.

661px-Conjugation.svg.png

Aside from that, Its like, if i were to have...a car. I could drive the car all over and do whatever. But i would risk damaging that car. But if I had another car (duplicated gene/plasmid), I could do 4 by 4 offroading if I wanted, and it wouldnt damage my original car. Even if the additional car wasn't as gas efficient as another secondary car that I could have bought, it would still serve its 4 by 4 offroading capabilities that I could benefit from, along with the benefits of my original car as well.

In the same source "we conclude that the nylon oligomer hydrolase utilizes nucleophilic Ser112 as a common active site both for nylon oligomer-hydrolytic and esterolytic activities. "

​break down of electrolytic molecules was the original function of the enzyme,the new nylon uses the exact same active site.

This, upon closer examination, is simply false. You cannot tell what the original function of the enzyme was. And I have asked not one, but 2 Phds about this now, and they have given the same response.

This person, didnt know what they were talking about.

You dont know if the active site was even active on the original protein, because you dont even know what the structure of the original protein was. And even if hypothetically the ser site was used on the original enzyme, it still wouldnt matter because its independent of the bacterias genome.

And on top of all of this, and Ive said this before...it still grants the organism a new ability, a new nitch in its environment, a new capability that does in fact benefit it with digestion of molecules that it could not originally digest.

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Idev says

First off, nobody can say if the original enzyme did or did not use the ser active site. Because the original structure of that enzyme no longer exists.

I'm not going to insult you,I'm just going to say you are seriously mistaken and are making an absurd claim. :)

The original enzyme is very much still existent ,the original enzyme was a carboxylesterase ,so what are you talking about?

We also have its DNA mapped out with its original AA length,we also know what spot the point mutation was on that caused the frame-shift making the cleft of the enzyme less specific.

So again what are you talking about?

This, upon closer examination, is simply false. You cannot tell what the original function of the enzyme was. And I have asked not one, but 2 Phds about this now, and they have given the same response.

This person, didnt know what they were talking about.

You claim that you spoke to PhD and gradutes and they told you it is impossible to know the original function of the Enzyme before it was mutated?

I find this hard to believe as the original enzyme was a carboxylesterase, its function is breaking down of esterolytic molecules using ser site.

I also showed you that the degenerated enzyme also uses the same site,please refer above to the medical journal I quoted you.

Anyways,your arguments and claims have been answered in my previous posts,if I see something original/new I will try to respond.

Thanks.

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Idev says

I'm not going to insult you,I'm just going to say you are seriously mistaken and are making an absurd claim. :)

The original enzyme is very much still existent ,the original enzyme was a carboxylesterase ,so what are you talking about?

=

We also have its DNA mapped out with its original AA length,we also know what spot the point mutation was on that caused the frame-shift making the cleft of the enzyme less specific.

So again what are you talking about?

You claim that you spoke to PhD and gradutes and they told you it is impossible to know the original function of the Enzyme before it was mutated?

I find this hard to believe as the original enzyme was a carboxylesterase, its function is breaking down of esterolytic molecules using ser site.

Thanks.

Exactly. I have been told that the structure of the enzyme that pre existed EII', is unknown, as is the sequence for that enzyme. And due to the structure being unknown, it cannot be said that the enzyme actually did use ser in that location. If you have a specific question, I can take it to them if you would like.

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Exactly. I have been told that the structure of the enzyme that pre existed EII', is unknown, as is the sequence for that enzyme. And due to the structure being unknown, it cannot be said that the enzyme actually did use ser in that location. If you have a specific question, I can take it to them if you would like.

Exactly. I have been told that the structure of the enzyme that pre existed EII', is unknown, as is the sequence for that enzyme. And due to the structure being unknown, it cannot be said that the enzyme actually did use ser in that location. If you have a specific question, I can take it to them if you would like.

Sorry this is wrong,they know the sequence,they even know the percentage of similarity to the prior

Carboxylesterase.

Medical jounral from pubmed

http://www.ncbi.nlm.nih.gov/pubmed/16949580

Even look at the title of the journal

"Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities.

And the intro to the paper states...

Carboxylesterase (EII') from Arthrobacter sp. KI72 has 88% homology to 6-aminohexanoate-dimer hydrolase (EII) and possesses ca. 0.5% of the level of 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity of EII.

The prior enzyme is a

Carboxylesterase that was around 400 AA long.

So which professor did you ask?

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Sorry this is wrong,they know the sequence,they even know the percentage of similarity to the prior

Carboxylesterase.

Medical jounral from pubmed

http://www.ncbi.nlm....pubmed/16949580

Even look at the title of the journal

"Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities.

Carboxylesterase (EII') from Arthrobacter sp. KI72 has 88% homology to 6-aminohexanoate-dimer hydrolase (EII) and possesses ca. 0.5% of the level of 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity of EII.

The prior enzyme is a

Carboxylesterase that was around 400 AA long.

So which professor did you ask?

In the paper, They are comparing the activity of EII, EII' and their hybrid. Not any precursor enzyme to EII'. The prior sequence and structure of the enzyme predating EII' simply cannot be known because it no longer exists. With the hybrid, they made comparisons of it with other enzymes along with activity with EII. But they never determined the structure or sequence of the enzyme that pre existed EII'. And with that, nobody knows what kind of active site it may or may not have used.

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In the paper, They are comparing the activity of EII, EII' and their hybrid. Not any precursor enzyme to EII'. The prior sequence and structure of the enzyme predating EII' simply cannot be known because it no longer exists. With the hybrid, they made comparisons of it with other enzymes along with activity with EII. But they never determined the structure or sequence of the enzyme that pre existed EII'. And with that, nobody knows what kind of active site it may or may not have used.

In the paper, They are comparing the activity of EII, EII' and their hybrid. Not any precursor enzyme to EII'. The prior sequence and structure of the enzyme predating EII' simply cannot be known because it no longer exists. With the hybrid, they made comparisons of it with other enzymes along with activity with EII. But they never determined the structure or sequence of the enzyme that pre existed EII'. And with that, nobody knows what kind of active site it may or may not have used.

I think you are reading wrong, EII' is not the hybrid,the nylon eating enzyme is EII,EII' is the carboxylesterase. a carboxylesterase hybrid

was introduced later on by the scientists. "

To study relationship between Ald-hydrolytic and esterolytic activities, random mutations were introduced into the gene for Hyb-24 (an EII/EII' hybrid with the majority of the sequence deriving for EII' and possessing an EII'-like level of Ald-hydrolytic activity). "

The paper is analyzing the homology between

carboxylesterase and the nylon eating enzyme,they are also introducing mutations to analyze their similar activity ,which again strongly supports what I have been saying.

"

Carboxylesterase (EII')

from Arthrobacter sp. KI72 has 88% homology to 6-aminohexanoate-dimer hydrolase (EII) and possesses ca. 0.5% of the level of 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity of EII.'

sp. KI72 is the name of the organism,one of its enzyme that assist it in breaking down nylon is

EII.

It has a 88% homology,please refer here for what homology means http://en.wikipedia....ology_(biology)

If they didn't know the sequence how could they know the percentage in homology? "Homology among proteins or DNA is often incorrectly concluded on the basis of sequence similarity. The terms "percent homology" and "sequence similarity" are often used interchangeably. '

Percentages are only taken from numbers,you cannot say that this "tree" is only 88 percent similar to this "tree".

I don't like using silly sources like you by the way ,I only use Wikipedia for definition like it should only be used for.

Anything else?

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I think you are reading wrong, EII' is not the hybrid,the nylon eating enzyme is EII,EII' is the carboxylesterase. a carboxylesterase hybrid was introduced later on by the scientists. "

EII' is not the hybrid created in the experiment. Hyb-24 is. Hence the name.

To study relationship between Ald-hydrolytic and esterolytic activities, random mutations were introduced into the gene for Hyb-24 (an EII/EII' hybrid with the majority of the sequence deriving for EII' and possessing an EII'-like level of Ald-hydrolytic activity). "

yea

The paper is analyzing the homology between

carboxylesterase and the nylon eating enzyme,they are also introducing mutations to analyze their similar activity ,which again strongly supports what I have been saying.

Yes, and neither of these are precursors to EII'.

"

from Arthrobacter sp. KI72 has 88% homology to 6-aminohexanoate-dimer hydrolase (EII) and possesses ca. 0.5% of the level of 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity of EII.'

Carboxylesterase (EII')

sp. KI72 is the name of the organism,one of its enzyme that assist it in breaking down nylon is

EII.

It has a 88% homology,please refer here for what homology means http://en.wikipedia....ology_(biology)

If they didn't know the sequence how could they know the percentage in homology? "Homology among proteins or DNA is often incorrectly concluded on the basis of sequence similarity. The terms "percent homology" and "sequence similarity" are often used interchangeably. '

You can compare two sequences without knowing the prior sequence, just as you can compare two people without knowing what pre existed them. Which is what they are doing in the experiment. They are comparing EII and EII' along with the hybrid.

Percentages are only taken from numbers,you cannot say that this "tree" is only 88 percent similar to this "tree".

I don't like using silly sources like you by the way ,I only use Wikipedia for definition like it should only be used for.

Anything else?

Yes you can. Majority of the time, thats how its done. ABCDE is 80% homologous to to ABCDF. However, what was before ABCDE and ABCDF? Nobody knows. Let alone would they know the structure of that protein. The tree is built off of the homology of sequences. The sequences themselves are related.

Yes, use a consistent font.

Unless there is another paper you have to reference, im sticking with the opinions of the PhDs, that is to say, they dont know what the previous structure of the enzymes was.

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Idev says

EII' is not the hybrid created in the experiment. Hyb-24 is. Hence the name.

I think this is pretty much proof enough you don't know what you're talking about.

The hybrid is EII'/EII

"Hyb-24 (an EII/EII' hybrid with the majority of the sequence deriving for EII' and possessing an EII'-like level of Ald-hydrolytic activity)."

Idev says

Yes, and neither of these are precursors to EII'.

Who mentioned any precursors to EII'? EII' is a carbyoxleterase from the organism,the preceding enzyme of the nylon eating enzyme is carbyoxleterase.

You can compare two sequences without knowing the prior sequence, just as you can compare two people without knowing what pre existed them. Which is what they are doing in the experiment. They are comparing EII and EII' along with the hybrid.

The hybrid isn't EII',EII' is the carbyoxleterase.

Sorry,try again.

Idev says

Yes you can. Majority of the time, thats how its done. ABCDE is 80% homologous to to ABCDF. However, what was before ABCDE and ABCDF? Nobody knows. Let alone would they know the structure of that protein. The tree is built off of the homology of sequences. The sequences themselves are related.

Stupid example,that is comparing a sequence and is mathematical.

Regarding what sequences they were comparing,look above.

Yes, use a consistent font.

Use a consistent argument.

Unless there is another paper you have to reference, im sticking with the opinions of the PhDs, that is to say, they dont know what the previous structure of the enzymes was.

Can you give me the emails of these PhDs and the schools teach at? Thanks.

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Idev says

I think this is pretty much proof enough you don't know what you're talking about.

The hybrid is EII'/EII

You are the one who seems to think EII' is a hybrid. Even though clearly in your very next statement, you quote the paper saying that its not. EII' and EII are 2 of the enzymes. Hyb-24 (hyb for hybrid) is the hybrid.

"Hyb-24 (an EII/EII' hybrid with the majority of the sequence deriving for EII' and possessing an EII'-like level of Ald-hydrolytic activity)."

exactly.... an EII/EII' hybrid. AKA a hydrid of the two. hyb is for hybrid. hyb-24. What do you think hyb-24 is if not the hybrid that they use throughout the paper? They are only using one hybrid. They needed to create the hybrid because they were having issues using EII. So the created the hybrid and used it for comparisons with other enzymes.

Idev says

Who mentioned any precursors to EII'? EII' is a carbyoxleterase from the organism,the preceding enzyme of the nylon eating enzyme is carbyoxleterase.

EII' is the nylon digesting enzyme that mutated from a prior enzyme. EII' is the one with low activity. We dont know where the original protein would even use ser without its structure.

Can you give me the emails of these PhDs and the schools teach at? Thanks.

Ill ask for permission to do so first.

All you have to do now, if you truly believe such a structure exists and does use ser in the particular active site of the EII' or EII enzymes, is find such research that such a thing exists.

Ya know, these guys have enough trouble crystallizing already existing enzymes for studies. I cant imagine how they would be able to determine details about proto enzymes.

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And really, there is no argument here. We've agreed 95% of the time. Here we have gene duplication and subsequent mutation. Passed on and spread throughout a population over generations. By the very definition, what we are discussing here, is evolution. You just dont want to call it that for whatever reason.

You talk about the enzyme having a deficiency with use of its ser active site. But you ignore its enhanced ability to digest nylon, as if it were a fluke or something and that the organism overall was being harmed by the mutation. Even though clearly the benefits of the mutation outweigh any detriments, demonstrated by the plethora of bacteria that now hold the trait.

Beyond that, the bacteria has both EII and EII', so its not like the organism has lost anything. It still has its original traits just as it has its new ones.

Beyond that further, nobody knows the structure of the enzyme pre dating EII'. So its not like we can even determine if the original enzyme even used the current ones ser active site.

So, your argument, to supposedly disprove evolution doesnt hold up. You either agree with me in what happened, or you take a subjective stance and say "oh no, thats not evolution because I say its not", even though everyone else does. You seem to believe that understanding homology mandates recognizing a common ancestor. Which is beyond wrong. Now you seem to think that EII is a hybrid.

The reason my rebuttals do not appear to be consistent is because ive found a multitude of flaws in your arguments. So it leaves fair game for a multitude of rebuttals.

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