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iSilurian

The Theory Of Evolution

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Guest Jebreil

(bismillah)

Posted this in Thinker's, but didn't get through.

Ah thanks buddy :}, next time we get in a philosophical dispute ill take the benefit of the doubt and give you credence. Which I kind of already try to do anyway (even if i dont admit to it) lol.

It's a vow I've made to myself:

1. If something comes and is clear that it's true, to take it, and if false, to leave it

2. If truths conflict, to cherish them both until they're reconciled - and to prefer knowledge over conjecture

3. To use the same standards of verification for the same kind of claims, and different standards for different kinds of claims

4. To be cautious of taking an absolute stance on things, and to be wary of the "intelligent" feeling that all absolute stances are foolish

5. To trust the way the world normally works, but not too much (or it's inverse rule, always be open to exceptional possibilities, but not too open - exceptions must resist the temptaion of becoming the norm)

Another formulation is: To question received wisdom, but to question its abandoning even more

6. Spinoza's Principle: I have made a ceaseless effort not to ridicule, not to bewail, not to scorn human actions, but to understand them.

which keeps me hesitant from impulsive pre-judgements, and obliges me to extend the most reasonable and charitable reading to another person's beliefs, and preaches patience and prudence until adequate understanding has come - to withhold judgement until knowledge is formed.

7. And Ruskin's Insight: To banish imperfection is to destroy expression, to check exertion, to paralyze vitality. All things are literally better, lovelier, and more beloved for the imperfections which have been divinely appointed, that the law of human life may be Effort, and the law of human judgment, Mercy.

which teaches me to try, but not to expect too much from trying, and to accept the imperfections which jeopardise solid knowledge and strengthen ignorance, but to have faith in trying and have humility in the result. Expressed in a different way, I trust in God that: a human has nothing but his own effort (Qur'an) and that He has mercy over the weakness of my attempts at the truth.

The purpose of this vow is to purify me my way of thinking - from bias, fear and desire - and to be stoic in my quest for knowledge.

The entire vow can be summed up: be sincere to yourself about what you see in reality and in yourself - don't let yourself blind you to reality.

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(bismillah)

The entire vow can be summed up: be sincere to yourself about what you see in reality and in yourself - don't let yourself blind you to reality.

sounds good.

Also, just for shiaben...in case he doesnt respond and everyones like..."oh well maybe Shiaben is correct". From my understanding the moths being on tree stumps has nothing to do with anything. The research is what is important, not how the butterflies are displayed to the public (on tree stumps). Which is why i want to know the name of the butterfly so i can show you why theyre important. And the finches, well quite frankly, i havent looked into the finch research (sorry but i honestly could care less about darwins original research), however if i knew the finches actual classification, i could very easily find out if they have undergone speciation or not. So im waiting on shiaben to provide the butterfly name and the finch name. Either way, whether they have undergone speciation or not really has no bearing on whether or not other animals have. So its really not possible for shiaben to win this discussion (he may not be aware of this yet, but he will find out if he continues to reply here).

Oh also going back on the butterfly thing, i know there is a species of butterfly that actually has evolved the capability of eating banana leaves over in hawaii. The reason this is important is because bananas werent native to this particular hawain island prior to us bringing them there, so it demonstrates observed evolution/speciation in our time phrame. But i dont want to change the subject and start rambling which is why im not going to bother digging up the research on it. But if anyone is interested in the butterfly let me know. And you can read more here >> http://www.ctahr.hawaii.edu/rubinoffd/rubinoff_lab/projects/omiodes_moths/omiodes_moths.htm . But im not a bioloist so dont expect me to go into tangents about butterfly evolution lol. I prefer bones and rocks.

And the fossil record stuff id like to save for later along with the homosexuality and the free will or whatever his last concept was...self awareness. I am a geologist, so i enjoy talking about the fossil record the most, but we need to settle this point by point, so for the sake of winning the argument with less confusion, id like to focus on his first points before moving onto the others.

hence why I am waiting on his response.

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I think you're taking the wrong approach. Even if you find a few things that we can't fully understand using evolution yet it by no means nullifies the theory. The evidence for evolution is overwhelming. It is most definitely a fact. The genetic sequences alone prove this. Not to mention the experiments where we've seen bacteria evolve right in front of our eyes or the evolution of drug resistant TB or HIV. Same with skin colour, if adam and eve were the first two humans, they could only produce a certain range of coloured children, no where near the variation we see today. The evidence is extremely strong. So, when problems like this show up the solution isn't to throw a very correct theory out the window, its to work on how we can find an explanation using evolutionary biology.

I'm happy theres problems because it means we're still making progress and the theory is getting more refined and comprehensive day by day. Its very rare an idea in science does not change or evolve otherwise you have static dogma which is exactly what science isn't. Evolutionary theory has been refined ever since the time of darwin. Darwin realised things evolved but he had no idea how this change was passed on. It was only when gregor mendel (a catholic monk) working on pea plants discovered modern genetics that we could understand how these variations are passed on. There was a problem and we overcame it. This has happened many times.

I always find it bizarre that people don't have problems with any other "theories" like gravity or have any problems when any other ideas have holes, like the higgs bosson in the standard model of physics. We don't yet know if it is or isnt there and yet i dont see anyone here using this to decry the idea or even caring about it or science in general. It's only when theres some percieved conflict against it thats when people start to go on a crusade against it. There are plenty of holes in other theories (https://en.wikipedia...lems_in_physics / https://en.wikipedia...ms_in_chemistry / https://en.wikipedia...ms_in_economics).

Evolution fails to explain homosexuality.

It seems you want to have your cake and eat it too. I often see people around these forums claim homosexuality isn't caused genetically and it is a free choice, so people are morally cupable for it. In case you didn't realise, our genes don't determine our free choices and will for the rest of our lives; If you do believe its purely genetic and subject to evolution, then they aren't morally cupable for being homosexuals. You have to choose one position, you can't argue for both.

Evolution only acts on inherited genetic characteristics. If you lift weights during your life and become very big and strong you don't pass that onto your children because it is an acquired characteristic. Same with someone who decides to be a socialist, its not passed on to your children. If you were born with red hair though or a gene that causes depression that might be passed onto your children.

This is why if according to some homosexuality is indeed a choice, it can't be an inherited characteristic, so, its not subject to evolution.

Either its caused by genetics soley and this causes your supposed problem with evolution but if it isn't their choice you cant hold them account to it, they are not morally culpable then.

OR

It's a free choice and if we have the freedom to make that choice the then it isn't determined by genes and isn't subject to evolution, so, your problem with evolution disappears and they are morally culpable.

So, you either have to pick a fight with evolution but accept homosexuals can't choose their actions or say homosexuals can choose their actions but drop your claim against evolution. I'll hand this one back to you.

So first you need to figure out where you're comming from in regards to that issue.

Edited by kingpomba

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Guest Jebreil

(bismillah)

To Kingpomba

Logically, there is a 3rd option:

Premises:

- If Homosexuality is natural, then Evolution must account for it

- Evolution does not account for Homosexuality

Therefore, either:

- Evolution is wrong + Homosexuality is natural

or

- Evolution is right + Homosexuality is unnatural

or

- Evolution is wrong + Homosexuality is unnatural

but not

- Evolution is right + Homosexuality is natural

Thus, the 3rd option is:

- Evolution is wrong + Homosexuality is unnatural

Which flows consistently from the premises.

-------

Thus, the logical formula is:

Evolution is wrong OR Homosexuality is unnatural

the "or" used is the ordinary logical disjunction, which in "p OR q" means either (p and not-q) or (not-p and q) or (p and q) but not (not-p and not-q).

Just to add: the point is, if you accept these 4 premises:

- If Homosexuality is natural, then Evolution must account for it

- Evolution is an account of nature

- Homosexuality is natural

- Evolution does not account for Homosexuality

then you are being inconsistent. However, to be consistent, you must forsake one of the above.

Either stop believing in Evolution as an account for nature,

or stop beleving in the naturality of Homosexuality.

Of course, you may argue against the 4th premise that "Evolution does not account for Homosexuality", which is Shiaben's challenge.

If you want, you can also reject both Evolution and the naturality of Homosexuality.

Edited by Jebreil

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Well your argument is logically consistent in the sense that your conclusion logically follows from your premises.

So, i'm not rejecting it on that nature.

Obviously (and i'm sure you saw this comming) i am going to object to any premise that states evolution is false. I just dont believe that premise, so, its not like i'm going to buy the conclusion either.

That said i realise you're probably targeting it toward someone who does not believe evolution.

I still reject it though.

It doesnt make sense to me. Just because something is natural does not mean it arises from evolution or is determined by our genetics.

I still stand by what i said.

It comes down to your belief whether or not homosexuality is a choice.

If it is a choice, you can hold them accountable. However, this must mean it isn't genetically determined since we can choose it, thus, you can't use it as an example of a flaw in evolution.

If it isn't a choice and genetically determined, you have an oppertunity to poke holes in evolution but you can no longersay they are accountable for it.

Your argument is very vague though, it is partially based on the idea that "is natural" "is not natural". Could you explain what you mean by this? I mean our thoughts are obviously not determined by our genetics and yet our thoughts are still natural.

I think taking up the premise evolution is wrong is misguided, there is an avalance of evidence in favour of evolution.

I am still really not clear on what you're trying to get at here.

I was kind of going from the angle people who believe homosexuality is a choice or it is caused by a degenerate atheistic western enviroment think it is a choice like political ideology is a choice. No one has socialist genes or libertarian genes for example, its not determined genetically. Its not subject to evolution. Your enviroment also has nothing to do with your genes, its the nurture half of nature vs nurture. So, even then, its still not a problem with evolution. So, if he believe this is the cause of homosexuality, then he can't use it to poke holes in evolution.

I don't think many if any muslims here hold the position homosexuality results from genetics (which we have no control over, so we cant be guilty of that). If they hold this position then by all means they can use it to poke holes in evolution but i dont think many if any do, like i said above.

Edit:

The whole nature thing is throwing me still. Do you just mean to say genetically determined or not genetically determined? Evolution only acts on inhertible, genetic, characteristics.

2nd Edit:

As for "ShiaBen" i provided a comprehensive response (RE - homosexuality and holes in theories) in the thread in thinkers discourse - http://www.shiachat....am/page__st__25 i await your reply.

I must say they're approving things very fast of late...

Also to jebreil, thanks for your position but i was soliciting ShiaBens, your contribution is of course welcome but it is his position i wish to know the most.

Edited by kingpomba

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Guest Jebreil

(bismillah)

By "natural" I mean "behaviour determined by the arrangement in our bodies or the environment" as opposed to "social factors" or "personal choice".

Therefore, since Evolution studies the development, survival and extinction of traits that emerge from an organisms genetic features and ecosystem, then explaining the development of Homosexuality and its continuation poses a question, especially since it contradicts reproduction, which at the moment is the core concept of evolution. Reproduction is the thread which links the earliest cell with the latest human being.

So, the question is, do you hold these 3 as correct? ('Nature' has been defined above)

- Evolution is the correct account of nature (how natural traits develop and continue to survive)

- Homosexuality is natural (is a natural trait that developed and continues to survive)

- Evolution does not account for Homosexuality

If yes, then I would suggest it is inconsistent - because there is one element of nature which the correct account of nature fails to explain.

So, to remain consistent, I would suggest you do one the following:

- reject Evolution as the correct account of nature + affirm the naturality of Homosexuality

or

- reject the naturality of Homosexuality + affirm Evolution as a correct account of nature

or

- reject both

or

- affirm both, but argue against the idea that Evolution does not account for Homosexuality

but you would be inconsistent to hold all 3.

-----

Alternatively, you may argue that Evolution is not a full account of nature, and it only explains the development and survival of some natural traits, while failing to explain the development and survival of other natural traits.

This way, you could retain the belief that Homosexuality is natural.

However, the question would be begged: if these traits did not evolve/survive as taught by Evolutionary theory, then how did they come to be there?

This would mean that there is at least one other way, alternative to Evolution, for a trait to emerge.

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Nobody is taking into account natural occurances that are still subjectively determined. Our body is built by our genetics and it is manipulated by our genetics. A nerd for example can be naturally formed by evolution, but likewise it takes more than just genes alone to make a nerd.

So you can sit and say "evolution cant account for nerds", but i would say, on the contrary, it can, but obviously the nerds environment plays a role as well.

So you can have evolution be true and have it account for homosexuality just fine. Likewise you could argue that homosexuality isnt purely a product of our genetics, and also you could even try making an argument that homosexuality were unnatural, because it gives the appearance of not being purely genetically caused.

And not surprisingly, we find all of these things to be true.

I believe the premises that Jebriel has made in his original response to pomba are false (well not false, but not all of the options), and i pomba should have, if he has not already, clarified that there are other options beyond the 4 originally stated. Or rather, you can interpret them differently.

And i would take this topic further, but im still waiting on Shiaben to respond to my original response. So please dont distract him guys.

And shiaben, i will take notice if you try to avoid me.

with further reading...

"Your argument is very vague though, it is partially based on the idea that "is natural" "is not natural". Could you explain what you mean by this? I mean our thoughts are obviously not determined by our genetics and yet our thoughts are still natural." ~ Pomba

Yes exactly Pomba.

Edited by iDevonian

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(bismillah)

By "natural" I mean "behaviour determined by the arrangement in our bodies or the environment" as opposed to "social factors" or "personal choice".

Social factors and personal choice are arguably still naturally based. I assume you know this is the reply you would recieve.

Therefore, since Evolution studies the development, survival and extinction of traits that emerge from an organisms genetic features and ecosystem, then explaining the development of Homosexuality and its continuation poses a question, especially since it contradicts reproduction, which at the moment is the core concept of evolution. Reproduction is the thread which links the earliest cell with the latest human being.

There is reproduction, and there is sex. Sexual interest is at...well hold on. Reproduction does not link us to the earlier cell (they replicate and consume others, they dont have sex)...but i get your point...Sexual interests are what drive us today in many ways. People play sex games in more ways than we can imagine, and many of which have little or nothing to do with actually making babies (im sure you know what im saying). The question of a man having sex with another man is like, is masturbation natural? It doesnt make babies either. What about all the other sexual acts we perform that dont make babies, are they natural? Sure they are.

There is more to sex than just making babies. Which is why homosexuals can naturally exist.

Alternatively, you may argue that Evolution is not a full account of nature, and it only explains the development and survival of some natural traits, while failing to explain the development and survival of other natural traits.

This way, you could retain the belief that Homosexuality is natural.

evolution obviously isnt going to be the hot topic when discussing why I prefer the delicious taste of buttery pancakes rather than blueberry(even though some people dont), however evolution is obviously behind the development of our ability to make, and our interest in eating pancakes. We do have a choice as to whether or not we will make special meals for dinnner, however that choice is our choice (though its developed and manipulated by evolution, by our brain and taste nerves n such). Evolution does not fail to explain the development and survival of the natural traits that manipulate us to enjoy pancakes. (there are several reasons we like pancakes due to our genes, though some people dont, everyone has their differences in their taste and interests both with pancakes and with sex). I personally am not a fan of blueberry pancakes. Can evolution account for that? Sure, but its a bit difficult to explain every little detail of why im not interested in blueberry pancakes while most other people are. Is it unnatural to prefer one type of pancake over another? No, of course not, does it defy evolution? But i can assure you, when talking about evolution, nobody is going to say "hey evolution cant explain why you like buttery over blueberry". But that doesnt mean that its not responsible for it.

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oh and please pardon my poor grammer lol. sometimes i type while thinking then immediately post without proof reading (actually this happens all the time).

Can evolution account for that? Sure, but its a bit difficult to explain every little detail of why im not interested in blueberry pancakes while most other people are. Is it unnatural to prefer one type of pancake over another? No, of course not, does it defy evolution? But i can assure you, when talking about evolution, nobody is going to say "hey evolution cant explain why you like buttery over blueberry". But that doesnt mean that its not responsible for it.

But we've had this same discussion in the past jebreil. objective genetics combined with subjective choice. Our ability to make choices still being a product of our objective genetics. Its essentially the discussion of evolution and morals.

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Guest Jebreil

(bismillah)

To iSilurian

My response to Kingpomba was double tiered:

1. To show that Shiaben can argue his case on Homosexuality + Evolution without committing to either

2. To show that holding these premises together is inconsistent:

- Evolution is the correct account of nature (how natural traits develop and continue to survive)

- Homosexuality is natural (is a natural trait that developed and continues to survive)

- Evolution does not account for Homosexuality

From your post, I understand that you reject the 3rd premise, and that is why you are able to escape inconsistency. However, Shiaben affirms the 3rd premise and wants to know why you reject it - which is the point of his challenge.

----

On social factors and personal choice, it's important not to leap into conflating it with nature. Yes, ultimately, all things are natural, even unnatural curiosities. All things are normal, even abnormalities. But the essential reason that we should not conflate the two is this:

We have developed a conscience, and conscience is our inner judge of right and wrong. Our conscience does not find fault in how a person was born but finds fault in how a person was raised (society) and how that person conducted itself (personsal choice). Therefore, Homosexuality would be unconscionable (for many, if not most) if it was a product of free human activity, rather than hardwired.

Again, there is no point in wrapping all human activity in the same gift paper and labelling it "natural" because that would seem to propose that there is no "freedom" in our naturality. That somehow, all things are ordained by nature, and personal choice is just a charade. But this is not the case. Nature doesn't ordain one path, but multiple paths - it is much more complex than that:

For example, suicide would be natural, but also holding on. Beating him up would be natural, but so would forgiving and forgetting. These are said to be "chosen", whereas one is not said to "choose" thie favourite colour or flavour. It is the former that may be morally evaluated but the latter escape moral judgement. It is the former that one can use evolution to either continue evolution or break evolution whereas the latter is bound by the dictates of evolution.

Therefore, the latter types are what I called "nature, as opposed to nurture" and the former types are "nurture". In one sense they are all natural/real, but this is not what I intended in the words being used. In one sense evolution has a say in all activities, but some activities have evolved to defy or modify evolution (e.g. to do things which does not follow the principles of evolution).

Therefore, the distinction must be made between things which are dictated by evolution - by which we are generally restrained - and things which are not dictated, but suggested different paths, and which we have learned to distinguish. It would not accurately reflect the world and nature to ignore this distinction.

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(bismillah)

To iSilurian

My response to Kingpomba was double tiered:

1. To show that Shiaben can argue his case on Homosexuality + Evolution without committing to either

2. To show that holding these premises together is inconsistent:

- Evolution is the correct account of nature (how natural traits develop and continue to survive)

- Homosexuality is natural (is a natural trait that developed and continues to survive)

- Evolution does not account for Homosexuality

From your post, I understand that you reject the 3rd premise, and that is why you are able to escape inconsistency. However, Shiaben affirms the 3rd premise and wants to know why you reject it - which is the point of his challenge.

----

On social factors and personal choice, it's important not to leap into conflating it with nature. Yes, ultimately, all things are natural, even unnatural curiosities. All things are normal, even abnormalities. But the essential reason that we should not conflate the two is this:

We have developed a conscience, and conscience is our inner judge of right and wrong. Our conscience does not find fault in how a person was born but finds fault in how a person was raised (society) and how that person conducted itself (personsal choice). Therefore, Homosexuality would be unconscionable (for many, if not most) if it was a product of free human activity, rather than hardwired.

Again, there is no point in wrapping all human activity in the same gift paper and labelling it "natural" because that would seem to propose that there is no "freedom" in our naturality. That somehow, all things are ordained by nature, and personal choice is just a charade. But this is not the case. Nature doesn't ordain one path, but multiple paths - it is much more complex than that:

For example, suicide would be natural, but also holding on. Beating him up would be natural, but so would forgiving and forgetting. These are said to be "chosen", whereas one is not said to "choose" thie favourite colour or flavour. It is the former that may be morally evaluated but the latter escape moral judgement. It is the former that one can use evolution to either continue evolution or break evolution whereas the latter is bound by the dictates of evolution.

Therefore, the latter types are what I called "nature, as opposed to nurture" and the former types are "nurture". In one sense they are all natural/real, but this is not what I intended in the words being used. In one sense evolution has a say in all activities, but some activities have evolved to defy or modify evolution (e.g. to do things which does not follow the principles of evolution).

Therefore, the distinction must be made between things which are dictated by evolution - by which we are generally restrained - and things which are not dictated, but suggested different paths, and which we have learned to distinguish. It would not accurately reflect the world and nature to ignore this distinction.

ya, sure

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Isilurian says I guess, ill make this here. My previous topic on morals condones the theory of evolution, and im sure there are many people here who would automatically reject my concepts just because i use evolution within the topic.

According to you then, the only reason why a human would act moral is if he is inclined by his nature to do so "he feels bad about x",or he fears punishment,can you give any other reason why a person would be moral? Please do so I'm curious to see what you're going to say.

Isilurian says Also before i continue, if anyone here wants to argue against me, or try to refute my statements, i will only accept scientific published peer reviewed research.. Ths means no random youtube videos, no random websites designed by highschool students etc.

Fair enough.

Isilurian says basic

So i would like to present a few things about the theory of evolution that, i imagine people may not be familiar with, just to put some ideas out there. If anyone would like to associate their concepts in faith with it, that would fine as well.

The basic theory of evolution, im sure most people have a general understanding of. It is defined by mutations within our DNA, which are manipulated by natural selection, and evolution occurs in communities.

Evolution is new DNA being introduced VIA mutations which in turn create novel protein parts which bring about a new function or improve on a already existing one,or improve protein parts. Natural selection is nothing more than bad mutations slowing down reproduction causing the mutations to eventually be eliminated from the species' genome or kept at a low level in the population.Yes,yes we have heard of this beautiful master piece of a theory.

From here one does not even have to go on to the evidence he posted to refute what he is saying but we will Insha'Allah.

You're belief rests upon 4 main premises.

1. Mutations can drive evolution.

2. Natural selection can drive evolution.

3. The past shows evolution.

4. Evolution is accepted by most scientists.

1) There has never been a single instance where a novel protein with more than 30-60 amino acids have ever been produced via mutation that you have observed. Average size of proteins are around 300 AA mind you.

According to "talkorigins", the only way a new protein can be generated by mutation is a combination of 2 mutations at same genome location. A copy from an existing protein,and then that copy being frame shifted by a point mutation without it being repaired,and having a new function with keeping the start/stop coding. I won't throw numbers at you but I think you know the probability for that,quite unlikely. It has never been observed.

Evolution according to you works in small steps,lets say the smallest average functional protein is around 40-60 amino acids,lets be generous and say many structures have the same coding,my friend it is still amazingly unlikely...

2) Natural selection was rejected by Aristotle/Plato/the mutakallamun for a number of reasons. And I have heard that even one senior american scientist who helped reformulate natural selection mathematically expressed some concerns.

The problem is quite simple and has yet to be answered by evolutionists.

If natural selection increases the probability of beneficial mutations being passed on to offspring by increasing the number of mates and the life of the mutant,then how? The usual response is that the mutation increases fitness of the organism causing it to better compete with other potential mates,making it live longer,etc. However if evolution works in extremely small steps,then the benefit in turn would be extremely small and thus in turn drastically lower the probability of that particular gene being passed on via improved fitness before the anomaly is removed from genome or caused to be secluded,or never spreading throughout the genome fully but only seen in small fluctuating preponderance.

How do you account for this?

3) I will respond in your age of the earth post,and I will talk about fossils there too.

4) According to you because evolution is accepted by scientists,this acceptance can only be from the truthfulness of the theory and not any other cause for mass acceptance. This however is proven false as most scientists in the past and even in the recent past have all agreed on certain things and then disproved what they all agreed on,thus mass acceptance cannot be used as proof.

If any biologist sincerely disagrees with evolution,they would be out of a job as well. So obviously most scientists would be influenced into accepting evolution,also because they were taught on that curriculum and taught the same arguments over and over.

If a catholic goes to a catholic school and wants to be a theologian,chances are he is going to be a catholic theoligian.

Continued.....

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According to you then, the only reason why a human would act moral is if he is inclined by his nature to do so "he feels bad about x",or he fears punishment,can you give any other reason why a person would be moral? Please do so I'm curious to see what you're going to say.

My statement was relating to people and their bias. But for your question, people act in ways to promote their survival or the survival of others.

1) There has never been a single instance where a novel protein with more than 30-60 amino acids have ever been produced via mutation that you have observed. Average size of proteins are around 300 AA mind you.

New proteins themselves in whole dont need to be produced at all, nor genes. However, there have been observed instances of mutations leading to reorganized reading of far more than "30-60" amino acids within pre existing genes, and other mutations leading to the creation of entirely new genes as well with the changes of the start and stop codons.

Like the one i mentioned in one of my links in the first post. Im not sure if you read it or not.

http://www.ncbi.nlm..../pubmed/6585807

You have a phrame shift mutation leading to hundreds of "new" amino acids. They didnt spring out of thin air, but rather were pre existing and are simply read differently. With alteration of their start codon, you have a new gene in whole.

According to "talkorigins", the only way a new protein can be generated by mutation is a combination of 2 mutations at same genome location. A copy from an existing protein,and then that copy being frame shifted by a point mutation without it being repaired,and having a new function with keeping the start/stop coding. I won't throw numbers at you but I think you know the probability for that,quite unlikely. It has never been observed.

Well again, new proteins do not need to be produced for changes in how they are read.

But on another note, and ill try to find this paper if I can, you may enjoy the read. There was research published not too long ago that basically discussed how mutations in certain areas of the genome can create areas that are more prone to future mutations. Actually, from my understanding this is something that is in todays time commonly known. If you have a mutation of regulatory genes as well, you can have rapid change in genes and everything that is regulated by that gene.

And also ill just add that, modification of theory is common and expected. You shouldnt feel as though any scientist is saying that anyone has the full picture of how evolution occurs.

2) Natural selection was rejected by Aristotle/Plato/the mutakallamun for a number of reasons. And I have heard that even one senior american scientist who helped reformulate natural selection mathematically expressed some concerns.

Many people reject and have concerns for many things.

If natural selection increases the probability of beneficial mutations being passed on to offspring by increasing the number of mates and the life of the mutant,then how? The usual response is that the mutation increases fitness of the organism causing it to better compete with other potential mates,making it live longer,etc. However if evolution works in extremely small steps,then the benefit in turn would be extremely small and thus in turn drastically lower the probability of that particular gene being passed on via improved fitness before the anomaly is removed from genome or caused to be secluded,or never spreading throughout the genome fully but only seen in small fluctuating preponderance.

It depends on the mutation and the benefit. A small change in DNA can lead to a large change in an organisms fitness.

3) I will respond in your age of the earth post,and I will talk about fossils there too.

oh goodie

4) According to you because evolution is accepted by scientists,this acceptance can only be from the truthfulness of the theory and not any other cause for mass acceptance.

I dont think ive ever said that. It demonstrates the fact that its evidence is strong. I wouldnt say that because X Y and Z people believe something, its automatically true.

If any biologist sincerely disagrees with evolution,they would be out of a job as well. So obviously most scientists would be influenced into accepting evolution,also because they were taught on that curriculum and taught the same arguments over and over.

Scientists who reject evolution are...very few in number. At the very least the vast vast majority accept common descent. Even intelligent design advocates in many cases will support some form of common descent. The theory of evolution itself im sure will undergo modification with time, but realistically nobody is walking around saying that there is no relation of organisms over time, nor is anyone saying Adam and Eve sprang out of mud.

Edited by iDevonian

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iDevonian says

My statement was relating to people and their bias. But for your question, people act in ways to promote their survival or the survival of others.

Promoting their own survival falls under of fearing of punishment,why would someone fear punishment? They fear punishment as it hurts them and that I think according to your belief falls under promoting own survival,so they are one in the same.

If these are the only 2 reasons for morality then it is not in reality morality.

iDevonian says

New proteins themselves in whole dont need to be produced at all, nor genes. However, there have been observed instances of mutations leading to reorganized reading of far more than "30-60" amino acids within pre existing genes, and other mutations leading to the creation of entirely new genes as well with the changes of the start and stop codons.

If you have a duplicated gene that has been mutated a slightly then you'll have a duplicate of a prior gene that is a little different. Not in reality a new whole novel protein part with a novel function. What you just mentioned is what I just mentioned before,a duplication of a pre-existing gene and then that pre-existing gene being frame shifted,this has never been observed to create a novel protein part with a new amino acid sequence. I'll explain more in your next quote.

Like the one i mentioned in one of my links in the first post. Im not sure if you read it or not.

http://www.ncbi.nlm..../pubmed/6585807

You have a phrame shift mutation leading to hundreds of "new" amino acids. They didnt spring out of thin air, but rather were pre existing and are simply read differently. With alteration of their start codon, you have a new gene in whole.

This is the common used example the "nylon bacteria mutation",which is why I mentioned the frame shift.

The link you gave me from pubmed does not demonstrate a novel protein part,lets read what you gave.

Pubmed "The mechanism of gene duplication as the means to acquire new genes with previously nonexistent functions is inherently self limiting in that the function possessed by a new protein, in reality,

is but a mere variation of the preexisted theme."

So this isn't a new protein part,but only a slight variation of a prior function that was duplicated and btw is a smaller sequence. What I am talking about is a new protein with a new function. I'll explain why this is necessary at the bottom of the list,it doesn't seem necessary to you.

Pubmed "

392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid linear oligomer hydrolase involved in degradation of nylon oligomers is specified by an alternative open reading frame of the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein."

The old gene used to be 472 AA long,not it is 392 AA long. Something that was stopping the nylon from being used for the bacteria was removed,that is all. Not in reality a new function from a novel protein part.

Idevonian

Well again, new proteins do not need to be produced for changes in how they are read.

But on another note, and ill try to find this paper if I can, you may enjoy the read. There was research published not too long ago that basically discussed how mutations in certain areas of the genome can create areas that are more prone to future mutations. Actually, from my understanding this is something that is in todays time commonly known. If you have a mutation of regulatory genes as well, you can have rapid change in genes and everything that is regulated by that gene.

Thats nice.

Idevonian says And also ill just add that, modification of theory is common and expected. You shouldnt feel as though any scientist is saying that anyone has the full picture of how evolution occurs.

The theory of evolution via NS and RM needs a lot more than mere modifications.

It depends on the mutation and the benefit. A small change in DNA can lead to a large change in an organisms fitness.

I dont think ive ever said that. It demonstrates the fact that its evidence is strong. I wouldnt say that because X Y and Z people believe something, its automatically true.

You don't think you have ever said that,yet you mention the same belief anyways? Mass belief is not evidence for anything,let alone its supporting strengthening of the evidence.

Idevonian says Scientists who reject evolution are...very few in number. At the very least the vast vast majority accept common descent. Even intelligent design advocates in many cases will support some form of common descent. The theory of evolution itself im sure will undergo modification with time, but realistically nobody is walking around saying that there is no relation of organisms over time, nor is anyone saying Adam and Eve sprang out of mud.

The vast majority of scientists accepting evolution was explained already. Adam a.s. and Eve a.s. didn't spring out of the mud but was their ancestors sprung out of h20 with a combination of RNA,and perhaps DNA that was produced without enzymes,yeah you're totally right.

The reason why a new protein with a new function is needed is simple. Without novel proteins the only thing that would occur is mutations changing pre-existing genes,everyone agrees evolutionists,non-evolutionits alike,this can't bring us to where we are today where we have thousands of genes that are interconnected.

So what is needed is a gene duplication as your pudmed said,this mutant gene then is frame shifted into a new protein. What you failed to demonstrate was a new amino acid sequence coding for a novel protein part that assists function or improves it. Your nylon mutation was a point mutation at a part of the bacteria's genome,that actually in a way removed something that was causing the inability of the use of nylon.

The new gene can only come from 2 sources,wholly new mutation (everyone agrees this is impossible).

Or from a duplication,if it comes from a duplication in order for it to be a new part it must be changed/mutated,the more that it is mutated the more loss function is seen in every single case thus limiting the change of the protein and not actually creating any "real new" protein part.

Many famous evolutionists have actually rejected evolution based upon protein science,actually mostly from protein science.....

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Promoting their own survival falls under of fearing of punishment,why would someone fear punishment? They fear punishment as it hurts them and that I think according to your belief falls under promoting own survival,so they are one in the same.

If these are the only 2 reasons for morality then it is not in reality morality.

Yes I agree, its not morality. As a matter of fact I try not to even use that word.

The old gene used to be 472 AA long,not it is 392 AA long. Something that was stopping the nylon from being used for the bacteria was removed,that is all. Not in reality a new function from a novel protein part.

I wouldnt word it like that. It is a new function, that is to say, digesting nylon is a new function of the organism. The nucleotides are the same, but the order in which the DNA is read has been altered, and so the amino acids are sequenced in a different order, and the proteins different as well. They are new.

The vast majority of scientists accepting evolution was explained already. Adam a.s. and Eve a.s. didn't spring out of the mud but was their ancestors sprung out of h20 with a combination of RNA,and perhaps DNA that was produced without enzymes,yeah you're totally right.

good thing nobody believes that adam and eve sprung out of h2o and rna (nobody even really believes in adam and eve to begin with, not in any literal sense anyway). Also, RNA itself can be its own enzyme. Good call on that one. Also, its a good thing we are discussing evolution here and not the origins of life.

The reason why a new protein with a new function is needed is simple. Without novel proteins the only thing that would occur is mutations changing pre-existing genes.

And mutations changing pre existing genes would change the order of amino acids and the proteins. The genes are "new". Yes they are made from pre existing duplicated compounds, but that doesnt somehow stop them from sequencing for new proteins.

So what is needed is a gene duplication as your pudmed said,this mutant gene then is frame shifted into a new protein. What you failed to demonstrate was a new amino acid sequence coding for a novel protein part that assists function or improves it. Your nylon mutation was a point mutation at a part of the bacteria's genome,that actually in a way removed something that was causing the inability of the use of nylon.

I wouldnt word it like that. The new amino acid sequence coding for new proteins is mandated by the original mutation. And I wouldnt use the word "removed". If anything it just manipulated a duplication.

The new gene can only come from 2 sources,wholly new mutation (everyone agrees this is impossible).

Or from a duplication,if it comes from a duplication in order for it to be a new part it must be changed/mutated,the more that it is mutated the more loss function is seen in every single case thus limiting the change of the protein and not actually creating any "real new" protein part.

You have an addition of DNA in the genome, and you have an additional function. Where does the word "loss" come in here? Sure you lost part of your duplicated gene. But the duplicated gene is an overall addition to begin with. So, nothing is being lost here. And then you said "the more that it is mutated the more loss function is seen in every single case thus limiting the change of the protein and not actually creating any "real new" protein part.". But again, you are only losing part of an additional gene. And the gene itself being new is sequencing new protein.

If a mutation occurs that alters the DNA of the bacteria that digests nylon, its going to alter your amino acid sequence, thereby altering your proteins. The DNA mutation, the duplication and point mutation have altered the way in which the entire duplicated gene is read. It essentially has become a new gene. Sure its constituents are the same, but it itself is not the same as the pre-existing gene that was duplicated. With the alteration of the DNA, and the alteration of the insuing RNA transcribes new protein. Thus changing the physical function of the bacteria.

So yes, we have less amino acids than used in the original gene, but the proteins are different none the less because everything is different because its all been mutated.

Edited by iDevonian

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Idevonian says Yes I agree, its not morality. As a matter of fact I try not to even use that word.

So if you agree why are you moral?

Idev says

I wouldnt word it like that. It is a new function, that is to say, digesting nylon is a new function of the organism. The nucleotides are the same, but the order in which the DNA is read has been altered, and so the amino acids are sequenced in a different order, and the proteins different as well. They are new.

If someone comes to me and tells me "I broke my mother legs now she can't get hit by a car",would you consider this an added function? The new function didn't come from a novel sequence,it came from a degradation of one.

Even if it came from a novel sequence,the protein was slightly changed,and if the protein was changed further it would pass a structure threshold and become a completely new fold.

Idev says

good thing nobody believes that adam and eve sprung out of h2o and rna (nobody even really believes in adam and eve to begin with, not in any literal sense anyway). Also, RNA itself can be its own enzyme. Good call on that one. Also, its a good thing we are discussing evolution here and not the origins of life.

I was being sarcastic,the irony is you think that all life came about through an impossible event via h20. RNA can be its own enzyme true,but how? Who and what is activating the nucleotides and causing them to come together to form your enzyme?. This is also admitted by scientists in that field that the current theory violates some principles of entropy. This is another topic though

idev says

And mutations changing pre existing genes would change the order of amino acids and the proteins. The genes are "new". Yes they are made from pre existing duplicated compounds, but that doesnt somehow stop them from sequencing for new proteins.

The sequence isn't truly novel but only a variant and corrupted shadow of the true sequence. This isn't a good example.

I wouldnt word it like that. The new amino acid sequence coding for new proteins is mandated by the original mutation. And I wouldnt use the word "removed". If anything it just manipulated a duplication.

idev says You have an addition of DNA in the genome, and you have an additional function. Where does the word "loss" come in here? Sure you lost part of your duplicated gene. But the duplicated gene is an overall addition to begin with. So, nothing is being lost here. And then you said "the more that it is mutated the more loss function is seen in every single case thus limiting the change of the protein and not actually creating any "real new" protein part.". But again, you are only losing part of an additional gene. And the gene itself being new is sequencing new protein.

The prior sequence that was mutated was more specific in the molecules it accepted,it lost its specificity and became around 350 AA long down from around 450 AA allowing it to accept nylon molecules.

idev says If a mutation occurs that alters the DNA of the bacteria that digests nylon, its going to alter your amino acid sequence, thereby altering your proteins. The DNA mutation, the duplication and point mutation have altered the way in which the entire duplicated gene is read. It essentially has become a new gene. Sure its constituents are the same, but it itself is not the same as the pre-existing gene that was duplicated. With the alteration of the DNA, and the alteration of the insuing RNA transcribes new protein. Thus changing the physical function of the bacteria.

You are making it sound so amazing,but unfortunately all that happened was the cleft of the enzyme was corrupted,there is no "evolution" here.

The sequence that was mutated coded the cleft of the enzyme btw.

idev says So yes, we have less amino acids than used in the original gene, but the proteins are different none the less because everything is different because its all been mutated.

Lets be reasonable and I don't mean that in a condescending or insulting way,

do you really expect frame shift mutations to bring out new protein parts?

How can something that is scrambled become better?

And what is worse is this is the only way a new protein can come about....

For the people reading this thread who aren't to familiar with these terms,Idev wants use to believe that meaning and function can about from scrambling letters.

Also please answer about what I said about natural selection.

Also if you can post your evidences of ERVs,summation,and other genetic proofs we can discuss them here. We can discuss your fossil proofs in the geology thread.

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So if you agree why are you moral?

Because I am trying to survive.

If someone comes to me and tells me "I broke my mother legs now she can't get hit by a car",would you consider this an added function? The new function didn't come from a novel sequence,it came from a degradation of one.

Thats a bad analogy. Its more like, my grandmother had 1 chop stick. I duplicated the chop stick and made her break 10% of the duplicated chop stick off. The duplication is still long enough for her to use, now she has 2 chop sticks and she can eat rice. She couldnt eat rice before with only 1 chop stick. So yes she had to break a piece off of her duplication, but she is still left with a benefit of being able to eat rice now.

I was being sarcastic,the irony is you think that all life came about through an impossible event via h20. RNA can be its own enzyme true,but how? Who and what is activating the nucleotides and causing them to come together to form your enzyme?. This is also admitted by scientists in that field that the current theory violates some principles of entropy. This is another topic though

Um, you dont know how I believe life came about. This is a discussion about evolution, not the origins of life. So dont judge me, ty. If you want to talk about the origins of life, go make an origins of life topic and I will be happy to discuss it there. Also, yes RNA can be its own enzyme, nucleotides dont need "activating", thats what intramolecular forces are for.

And no, none of this violates Entropy. Disorder can be defeated by adding energy to the system being discussed. Its like a baby growing to become an adult. Sure it sounds impossible, and if the baby didnt eat food to add energy to itself, it would in fact decay into nothing. But when you add energy to the system (baby), it allows the baby to grow, thus not defying entropy. The same goes for evolution.

The sequence isn't truly novel but only a variant and corrupted shadow of the true sequence. This isn't a good example.

Its not corrupted if it benefits the organism. Think of it like this. Youre in a pit of lions. Now, you have the option to duplicate a sword(gene) you have. Ok now you have two swords (2 genes). But the catch is, in order to have these two swords, you have to break one of them in half (point mutate it). Well, at the end of the day you still have an additional weapon (half a sword/new gene/new weapon), and your original sword too (original gene). You are not corrupted, you are assisted in survival.

The prior sequence that was mutated was more specific in the molecules it accepted,it lost its specificity and became around 350 AA long down from around 450 AA allowing it to accept nylon molecules.

yes thats true, but the original 450 AA gene still exists as well. So now it has the 450 and the ~350. It didnt sacrifice one for the other, it duplicated the original and changed the duplication into an additional benefit.

You are making it sound so amazing,but unfortunately all that happened was the cleft of the enzyme was corrupted,there is no "evolution" here.

All mutations have some sort of detriment in some way or another in that they sacrifice something to get something more. Its like the human brain, yes we have to sacrifice a lot of energy for it, but its benefits are worth it. So, its not really harmful for the organism, it grants the organism the ability to digest a new form of food, which benefits it.

Lets be reasonable and I don't mean that in a condescending or insulting way,

do you really expect frame shift mutations to bring out new protein parts?

How can something that is scrambled become better?

And what is worse is this is the only way a new protein can come about....

The reason a mutation can lead to new proteins is because its not really "scrambled". Whats important is the order in which the nucleotides are read, not the order of them. So, sure I can shift and "scramble" the DNA. But its still readable DNA and it still sequences for proteins. So its still functional DNA. The original DNA exists and is read too. And even further, that original DNA had already been mutated and "scrambled" a million times before it.

Whats important are the proteins produced, not the order of the nucleotides.

For the people reading this thread who aren't to familiar with these terms,Idev wants use to believe that meaning and function can about from scrambling letters.

For those reading this topic, the order of the DNA is not important. Whats important is what is produced during the reading of the DNA. Your DNA can be "scrambled" a million times over. It doesnt matter, what matters is what is transcribed.

And anyone who knows about transcription and translation knows this.

Ill go ahead and explain.

dna_codes.gif

ok, so lets say we have the gene that is transcribed to ((GTT) (CAA)). And we duplicated the gene, so we have ((GTT) (CAA)) and ((GTT) (CAA)). Then we point mutated the duplication. So now we get ((GTT) (CAA)) and we added a C in between the first G and T. Now we have ((GTT) (CAA)) and ((GCT) (TCA)) + (A), and the duplicated A is removed from the reading. So now we have in total ((GTT) (CAA)) and ((GCT) (TCA)). Mind you, your ((GCT) (TCA)) is from a new gene. Its not from the original gene, it is from the duplicated original, and its order transformed, so it is independent now from the original and is indeed new.

Ok, now lets translate for our proteins. Originally we have the amino acids GTT (valine) and CAA (glutamine),

now after duplicating and point mutating we have GTT (valine) and CAA (glutamine), and we also have have GCT (alanine) and TCA (serine).

Ok so, now yes, our genes arent the same as they were, they are "scrambled", but they are bringing about new operations and proteins (serine and alanine) that benefit the organism. And these proteins were not originally being produced before, they are new to the organism. And this is how "scrambled" DNA can bring new proteins into play.

Also please answer about what I said about natural selection.

I dont know what youre talking about, sorry, re copy and paste it and ill respond.

Also if you can post your evidences of ERVs,summation,and other genetic proofs we can discuss them here. We can discuss your fossil proofs in the geology thread.

sure

Edited by iDevonian

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Hm, something I noticed. For clarity...

Ok so, now yes, our genes arent the same as they were, they are "scrambled", but they are bringing about new operations and proteins (serine and alanine) that benefit the organism. And these proteins were not originally being produced before, they are new to the organism. And this is how "scrambled" DNA can bring new proteins into play.

Your Amino acids (Serine and Alanine) are new, thereby altering the proteins developed. Then, these new proteins developed from the altered amino acids are new to the organism.

And this is how "scrambled" DNA can bring new proteins into play.

And, if anyone has any questions, feel free to ask. Ive basically, in a very simple way just explained how mutations of DNA alter morphological development of organisms.

Obviously in reality the process involves hundreds of amino acids and hundreds more new ones (as opposed to 1 and 2 amino acids like the example I made up off the top of my head). And the new gene comes with the alteration of the stop and start codons (which are also listed in the amino acid chart i posted above).

This is in a simple explanation, how evolution works. Its simple, its observed, its factual.

Edited by iDevonian

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^

(salam) (bismillah)

I think his question was why we have more DNA (number of base pairs) than lets say a bacterium.

The reason, when looking strictly at mutations, is the following:

From what I remember there are many types of mutations, not just one. Sure there may be deletions, nonsense and sense mutations, and other mutations that don't increase the number of base pairs, but there are also mutations that do increase the number of base pairs called insertion mutations.

Long story short, insertion mutations will increase the number of base pairs and result in a gradual increase in the number of genes.

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Idev Because I am trying to survive.

Then by definition you are not moral.

Idev Thats a bad analogy. Its more like, my grandmother had 1 chop stick. I duplicated the chop stick and made her break 10% of the duplicated chop stick off. The duplication is still long enough for her to use, now she has 2 chop sticks and she can eat rice. She couldnt eat rice before with only 1 chop stick. So yes she had to break a piece off of her duplication, but she is still left with a benefit of being able to eat rice now.

You lost specificity,that is the only reason why the enzyme can now use nylon,it was a degradation. If you want we can go into the sequence and the structure of the enzyme and look at before and after pictures.

Can you give us an example of a new protein that that gives off a new function that doesn't involve destruction/degradation?

No I don't think you can. :)

Idev

Um, you dont know how I believe life came about. This is a discussion about evolution, not the origins of life. So dont judge me, ty. If you want to talk about the origins of life, go make an origins of life topic and I will be happy to discuss it there. Also, yes RNA can be its own enzyme, nucleotides dont need "activating", thats what intramolecular forces are for.

Intramolecular forces such as the sun and heat vents cannot in anyway cause enzyme structures to form that is 100 percent non-sense,nor has it ever been produced via experimentation.

When you say nucleotides don't need to be activated via molecular systems then how are they activated? You really think that the sun or other mechanical tools can cause a nucelotide to be activated?

Idev And no, none of this violates Entropy. Disorder can be defeated by adding energy to the system being discussed. Its like a baby growing to become an adult. Sure it sounds impossible, and if the baby didnt eat food to add energy to itself, it would in fact decay into nothing. But when you add energy to the system (baby), it allows the baby to grow, thus not defying entropy. The same goes for evolution.

I'm sorry but it seems you don't understand.

It isn't about adding energy to the system it is about using that energy,for example if you have a car sitting in the sun. The sun can shine on that car for a thousand years the car isn't going to be able to be driven.......

Same problem here,yes we have the sun an abundance of energy supply. But what is causing that energy to be used to activate nucelotides? Its impossible thats why many people have given up on the RNA scenario.

The entire universe is actually a closed system,so nothing can lower entropy on a wide scale only on a local one that in turn increases entropy on the wide scale,this is what enzymes do in reality. They cause complex structures to be formed that would otherwise be impossible because the enzyme is made that way.

When people say evolution goes against entropy,then you may have an argument against them. But when we are talking about free molecules in a soup,to say that they can become structures on their own due to the sun shining on them is non-sense and does violate entropy because the energy is not being used at all....

Idev Its not corrupted if it benefits the organism. Think of it like this. Youre in a pit of lions. Now, you have the option to duplicate a sword(gene) you have. Ok now you have two swords (2 genes). But the catch is, in order to have these two swords, you have to break one of them in half (point mutate it). Well, at the end of the day you still have an additional weapon (half a sword/new gene/new weapon), and your original sword too (original gene). You are not corrupted, you are assisted in survival.

1.The sequence was from a frame shift mutation correct?

2.If it was from a frame [Edited Out] mutation then the DNA sequence is scrambled,correct?

3. If the DNA is scrambled and causes the enzyme to lose specificity allowing it to use other molecules,then I think this is a degradation....

Idev yes thats true, but the original 450 AA gene still exists as well. So now it has the 450 and the ~350. It didnt sacrifice one for the other, it duplicated the original and changed the duplication into an additional benefit.

It doesn't matter it didn't fulfill what is required for evolution and what we see in this,loss of amino acids and loss of specificity means nothing to the topic please use another example.

idev All mutations have some sort of detriment in some way or another in that they sacrifice something to get something more. Its like the human brain, yes we have to sacrifice a lot of energy for it, but its benefits are worth it. So, its not really harmful for the organism, it grants the organism the ability to digest a new form of food, which benefits it.

Every single mutation observed has only been showed to be bad or neutral,even in the examples atheists give. They even have the audacity to call sickle cell a good mutation.

idev The reason a mutation can lead to new proteins is because its not really "scrambled". Whats important is the order in which the nucleotides are read, not the order of them. So, sure I can shift and "scramble" the DNA. But its still readable DNA and it still sequences for proteins. So its still functional DNA. The original DNA exists and is read too. And even further, that original DNA had already been mutated and "scrambled" a million times before it.

What is the point of what you just wrote?

The order of the nucleotides are the order they are read in is that right or wrong? If I change the order of the nucelotides then the order of the codons are going to be changed as well thus changing your protein.

idev Whats important are the proteins produced, not the order of the nucleotides.

Not to be rude but I don't think you know what you're talking about.

Protein structure is determined by DNA,isn't this the dogma of biology?

idev For those reading this topic, the order of the DNA is not important. Whats important is what is produced during the reading of the DNA. Your DNA can be "scrambled" a million times over. It doesnt matter, what matters is what is transcribed.

Sorry the order of the DNA is not important??? What are you talking about? The DNA sequences determines the structure of proteins,you seem to think that DNA can be read the same way if its in a different sequence please tell us why you think this.

What is transcribed is determined by the sequence.

idev And anyone who knows about transcription and translation knows this.

Ill go ahead and explain.

I cut out the chart you gave,you are talking about codons,but what you don't seem to understand is that codons are determined by DNA sequence.

If you change the sequence you change the codons.

and to be honest I think you copy and pasted that text that was colored and below the chart as you are just restating yourself and explaining transcription,but then in your above quotes you completely contradict what is transcription.

What is transcribed is what is sequenced in the DNA,I hope you understand that.

Ok so, now yes, our genes arent the same as they were, they are "scrambled", but they are bringing about new operations and proteins (serine and alanine) that benefit the organism. And these proteins were not originally being produced before, they are new to the organism. And this is how "scrambled" DNA can bring new proteins into play.

If they are scrambled then they are junk its simple,if you take a sentence in English and scramble it you are going to get junk with no meaning.

What you gave us was an example of degradation and loss of amino acids.

idev I dont know what youre talking about, sorry, re copy and paste it and ill respond.

Its simple,natural selection is mathematically/statistically flawed and does not work.

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You lost specificity,that is the only reason why the enzyme can now use nylon,it was a degradation. If you want we can go into the sequence and the structure of the enzyme and look at before and after pictures.

Can you give us an example of a new protein that that gives off a new function that doesn't involve destruction/degradation?

No I don't think you can. :)

The nylonase example is fine, because your original gene is still there perfectly in tact. Also, your enzyme didnt lose specificity, its simply different than the original. its not some broad enzyme that can just act on anything. And ill restate this again, its developed within the duplication. It is an additional gene that develops additional protein which provides an additional function.

Intramolecular forces such as the sun and heat vents cannot in anyway cause enzyme structures to form that is 100 percent non-sense,nor has it ever been produced via experimentation.

I'm sorry but it seems you don't understand.

It isn't about adding energy to the system it is about using that energy,for example if you have a car sitting in the sun. The sun can shine on that car for a thousand years the car isn't going to be able to be driven.......

Same problem here,yes we have the sun an abundance of energy supply. But what is causing that energy to be used to activate nucelotides? Its impossible thats why many people have given up on the RNA scenario.

The entire universe is actually a closed system,so nothing can lower entropy on a wide scale only on a local one that in turn increases entropy on the wide scale,this is what enzymes do in reality. They cause complex structures to be formed that would otherwise be impossible because the enzyme is made that way.

When people say evolution goes against entropy,then you may have an argument against them. But when we are talking about free molecules in a soup,to say that they can become structures on their own due to the sun shining on them is non-sense and does violate entropy because the energy is not being used at all....

Inter* molecular. My mistake. Your electromagnetism in particular is used to bring compounds together. But again, this is for another topic, not here. Go make a new topic and ill be there.

1.The sequence was from a frame shift mutation correct?

2.If it was from a frame [Edited Out] mutation then the DNA sequence is scrambled,correct?

3. If the DNA is scrambled and causes the enzyme to lose specificity allowing it to use other molecules,then I think this is a degradation....

The DNA isnt scrambled. I wouldnt even use that word. Its shifted, thats why they call it phrame shift. Its not a phrame scramble mutation. And the original genes and proteins still exist. The only alteration is performed on the duplicated gene. The new enzymes are specific in digesting nylon. What we have in conclusion is alteration and addition of functions. And you know this.

It doesn't matter it didn't fulfill what is required for evolution and what we see in this,loss of amino acids and loss of specificity means nothing to the topic please use another example.

No, there isnt a loss in amino acids nor is there a loss of specificity. There are an addition of amino acids with different capabilities. The entire gene has been duplicated. You should understand that, that means the gene was doubled. Which means there is an addition. I assume you know what the word duplicate means. And so, your amino acids are doubled as well. Which means we have several hundred more amino acids. And yet you are saying there is a loss of amino acids. The duplicated gene, after being phrame shifted with the point mutation does have...a handful less amino acids than the original gene, but its a completely new gene in addition to the original with completely new amino acids in addition to the original as well. There are over 300 additional amino acids, there has not been a net loss.

quit using the word "scrambled" and quit using the word "loss" or "lost", because nothing is being scrambled and ultimately you have nothing but additional amino acids. Quit saying the protein has lost specificity because nylonase is specific to digesting nylon bonds.

What is the point of what you just wrote?

The order of the nucleotides are the order they are read in is that right or wrong? If I change the order of the nucelotides then the order of the codons are going to be changed as well thus changing your protein.

Its not right or wrong, its just different and in addition to the original. And yes, thats it, like you said, you change your start and stop codons, you change your gene and you change your proteins. And again, ill reiterate, this is an alteration in the duplication.

Not to be rude but I don't think you know what you're talking about.

Protein structure is determined by DNA,isn't this the dogma of biology?

Yes, but it sounds like you are saying that the DNA or amino acids being scrambled degrades the abilities of the organism, which simply isnt true. First off, we need to stop using this "scrambled" word. Its shifted, not scrambled. The importance is in the proteins produced. The proteins produced are controlled by the DNA read, but the DNA being read in a different way isnt what is ultimately significant, which you seem to think that it is. What is ultimately significant is the product. Not the reactants.

The DNA exists, its duplicated. The duplication is shifted and re-read. The organism develops the original proteins of the original gene and new proteins from the new gene. Thats it. When the DNA is shifted, it doesnt just become useless, its used for the new protein. The original gene doesnt just go away either, its still doing what it had been doing.

Sorry the order of the DNA is not important??? What are you talking about? The DNA sequences determines the structure of proteins,you seem to think that DNA can be read the same way if its in a different sequence please tell us why you think this.

What is transcribed is determined by the sequence.

Exactly, and no it cant read the same way if its in a different sequence. But what im saying is, in the case of nylonase, you have your original gene, and you have your new gene. The new gene has a different sequence, which is producing different proteins for the organism. And ultimately, the functions of the organism are whats important, which comes down to its proteins. And so, it doesnt matter if the DNA has been phrame shifted in the additional gene. What matters are the abilities that are coming from it, which are beneficial and in addition to the original gene and its original functions.

I cut out the chart you gave,you are talking about codons,but what you don't seem to understand is that codons are determined by DNA sequence.

If you change the sequence you change the codons.

and to be honest I think you copy and pasted that text that was colored and below the chart as you are just restating yourself and explaining transcription,but then in your above quotes you completely contradict what is transcription.

yea, i know that. Right now it looks to me like it is you who doesnt know what youre talking about. And no i didnt copy and paste anything except the picture itself. It sounds to me like you dont understand what a phrame shift is. You keep using this scrambled word, and then it sounds like you think the organism is weakened by having its DNA shifted. Or you think the gene is useless after having its DNA shifted. But thats not how it works. The DNA is simply re-read and produces an additional capability. I hope you understand that the organism couldnt originally digest nylon. Its an additional function. Additional. Its not replacing anything, its additional. And not only that, but the proteins arent some broad proteins that just react with anything and everything, which you using the word "specific" and "non specific" leads me to think you believe this degraded non specific enzyme can just do whatever it wants. Thats just false if that is what you are saying.

What is transcribed is what is sequenced in the DNA,I hope you understand that.

If they are scrambled then they are junk its simple,if you take a sentence in English and scramble it you are going to get junk with no meaning.

What you gave us was an example of degradation and loss of amino acids.

Thats not how it works. The DNA isnt scrambled, its shifted and re read. I think this is where our conflict is. It sounds to me like you believe that a phrame shift mutation renders the gene utterly useless. Thats just not how it works. And its not degradation, the additional amino acids create proteins which perform functions for the organism that it couldnt originally do in addition to its old functions. They digest nylon, thats what they do. Its not some rediculous enzyme has no specificity that breaks down a multitude of bonds. And no its not a loss of amino acids, the entire gene was duplicated. Overall, your total number of amino acids has almost doubled in the organism, but you still seem to think there has been a loss, which simply isnt true.

Did you understand the example I gave with the colors? It wasnt as complex as what actually happened, but it was a fair example. At the end of my example, we are left with 4 amino acids, and we began with 2. The new amino acids are forming new proteins. This is what happened with nylonase. The new proteins have their own functions that are in the organism now which are additions to the original which still exists as well within the bacteria. Mr. APS o_O

Edited by iDevonian

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Idev saysThe nylonase example is fine, because your original gene is still there perfectly in tact. Also, your enzyme didnt lose specificity, its simply different than the original. its not some broad enzyme that can just act on anything. And ill restate this again, its developed within the duplication. It is an additional gene that develops additional protein which provides an additional function.

This is wrong. The only reason why the enzyme can now use nylon is because the very fact it lost its specificity in choosing molecules.

As the journal of biological chemistry states Journal of Biological Chemistry

280: 39644–39652,

Journal of Molecular Biology

370:142–156 (2 sources).

There was a mutation in

a carboxyesterase gene which caused the cleft to be less specific allowing it to use nylon.

This is far from what we are looking for,this is degradation from a frame shift.

You keep saying "but the genome still has the old sequence". <This my friend is irrelevant as I asked for a new sequence with a new function.

idev says inter* molecular. My mistake. Your electromagnetism in particular is used to bring compounds together. But again, this is for another topic, not here. Go make a new topic and ill be there.

No need to apologize,my grammar sucks anyways. :)

idev says The DNA isnt scrambled. I wouldnt even use that word. Its shifted, thats why they call it phrame shift. Its not a phrame scramble mutation. And the original genes and proteins still exist. The only alteration is performed on the duplicated gene. The new enzymes are specific in digesting nylon. What we have in conclusion is alteration and addition of functions. And you know this.

Call it what you like but to be honest when you think of a frame shift you think of letters being scrambled due to the fact the way the code looks after.

Take this example,this is what happens to a sentence when you frame shift it.

aket hise amplet his isw hath appenst oasentencew heny ouf rames hift it.

I frame shifted every letter to the left similar to what happens when a point mutation causes a frame shift to the way the DNA is read due to the codon triplets being changed.

idev says No, there isnt a loss in amino acids nor is there a loss of specificity. There are an addition of amino acids with different capabilities. The entire gene has been duplicated. You should understand that, that means the gene was doubled. Which means there is an addition. I assume you know what the word duplicate means. And so, your amino acids are doubled as well. Which means we have several hundred more amino acids. And yet you are saying there is a loss of amino acids. The duplicated gene, after being phrame shifted with the point mutation does have...a handful less amino acids than the original gene, but its a completely new gene in addition to the original with completely new amino acids in addition to the original as well. There are over 300 additional amino acids, there has not been a net loss.

Refer to above.

Basically you are saying the genome is now bigger,fine. But the actual new protein is smaller and is indeed frame shifted.

idev says

quit using the word "scrambled" and quit using the word "loss" or "lost", because nothing is being scrambled and ultimately you have nothing but additional amino acids. Quit saying the protein has lost specificity because nylonase is specific to digesting nylon bonds.

If those words bother you I can use other words with the same meaning.

To say that the genome has additional amino acids is meaningless as the new protein has less amino acids.

Yes indeed as many peer reviewed articles has shown that specific folds have a limit of how much change they can get before they become a completely new fold or in most of the time not able to fold at all.

idev says Its not right or wrong, its just different and in addition to the original. And yes, thats it, like you said, you change your start and stop codons, you change your gene and you change your proteins. And again, ill reiterate, this is an alteration in the duplication.

This alteration is a frame shift.

idev says Yes, but it sounds like you are saying that the DNA or amino acids being scrambled degrades the abilities of the organism, which simply isnt true. First off, we need to stop using this "scrambled" word. Its shifted, not scrambled. The importance is in the proteins produced. The proteins produced are controlled by the DNA read, but the DNA being read in a different way isnt what is ultimately significant, which you seem to think that it is. What is ultimately significant is the product. Not the reactants.

Again,the DNA being read determiners the product. If your codon triplets are frame shifted,then your protein is usually junk like in this case.

idev says The DNA exists, its duplicated. The duplication is shifted and re-read. The organism develops the original proteins of the original gene and new proteins from the new gene. Thats it. When the DNA is shifted, it doesnt just become useless, its used for the new protein. The original gene doesnt just go away either, its still doing what it had been doing.

Refer to above.

idev says Exactly, and no it cant read the same way if its in a different sequence. But what im saying is, in the case of nylonase, you have your original gene, and you have your new gene. The new gene has a different sequence, which is producing different proteins for the organism. And ultimately, the functions of the organism are whats important, which comes down to its proteins. And so, it doesnt matter if the DNA has been phrame shifted in the additional gene. What matters are the abilities that are coming from it, which are beneficial and in addition to the original gene and its original functions.

What matters are the abilities that are coming from that protein? But my friend, what determines the ability of the protein? :) The determination of function is from the way the DNA is transcribed,the way the DNA is transcribed is from it's sequence.

So if its frame shifted the protein is going to be affected in a big way,what happend was the enzyme as a whole was slightly mutated due to one of its part being completely mutated,frame shifted,and basically loss its purpose/function which was to specificity what the molecules are used by the enzyme.

idev says yea, i know that. Right now it looks to me like it is you who doesnt know what youre talking about. And no i didnt copy and paste anything except the picture itself. It sounds to me like you dont understand what a phrame shift is. You keep using this scrambled word, and then it sounds like you think the organism is weakened by having its DNA shifted. Or you think the gene is useless after having its DNA shifted. But thats not how it works. The DNA is simply re-read and produces an additional capability. I hope you understand that the organism couldnt originally digest nylon. Its an additional function. Additional. Its not replacing anything, its additional. And not only that, but the proteins arent some broad proteins that just react with anything and everything, which you using the word "specific" and "non specific" leads me to think you believe this degraded non specific enzyme can just do whatever it wants. Thats just false if that is what you are saying.

1. Frame shifts cause deformation of the protein being frame shifted,I think this is pretty clear once you look at what a frame shift is. How could you possibly argue that a frame shift isn't bad when the entire sequenced is changed randomly?

2. The protein is indeed useless when frame shifted,no function comes from the protein.....but rather a loss of function.

This loss of function was specification,that is specifying what molecules are used.

You keep saying "additional function",but this isn't entirely correct.

The additional function only comes from the enzymes inability to act.

For example lets take sickle cell,its a deadly disease because it causes blood cells to become sickle shapped and makes it lose its ability to carry oxygen correctly.

Atheists/evolutionsts come out and say "hey look its a good mutation because now its hard for you to get malaria".

Lol yeah its hard for you to get malaria AND oxygen, AND many other molecules. I wouldn't call this "beneficial". This is like a nazi shooting you in the head for having a scratch and the nazi saying "well at-least you aren't itchy anymore".

The last example was for a comedic effect but I'm sure you get the point.

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This is wrong. The only reason why the enzyme can now use nylon is because the very fact it lost its specificity in choosing molecules.

As the journal of biological chemistry states Journal of Biological Chemistry

280: 39644–39652,

Journal of Molecular Biology

370:142–156 (2 sources).

There was a mutation in

a carboxyesterase gene which caused the cleft to be less specific allowing it to use nylon.

This is far from what we are looking for,this is degradation from a frame shift.

This has no bearing on the value of what it brings to the organism. And the specificity isnt lost, its simply different.

You keep saying "but the genome still has the old sequence". <This my friend is irrelevant as I asked for a new sequence with a new function.

ok, and you got your new sequence (remember, its all been shifted and its read differently now) and you got your new function (the bacteria couldnt originally digest nylon, no such nylonase enzymes existed, its all new).

Call it what you like but to be honest when you think of a frame shift you think of letters being scrambled due to the fact the way the code looks after.

Take this example,this is what happens to a sentence when you frame shift it.

aket hise amplet his isw hath appenst oasentencew heny ouf rames hift it.

I frame shifted every letter to the left similar to what happens when a point mutation causes a frame shift to the way the DNA is read due to the codon triplets being changed.

Thats not really adequate because with DNA, both your prior gene and your product after the shift both can be read.

Basically you are saying the genome is now bigger,fine. But the actual new protein is smaller and is indeed frame shifted.

the additional gene is smaller, yes.

To say that the genome has additional amino acids is meaningless as the new protein has less amino acids.

It doesnt matter. The point is, and clearly you recognize this, we have new protein.

This alteration is a frame shift.

yes

Again,the DNA being read determiners the product. If your codon triplets are frame shifted,then your protein is usually junk like in this case.

Well, in this case, the new protein brings about new functions for the bacteria, so i wouldnt call it junk. Id call it evolution.

What matters are the abilities that are coming from that protein? But my friend, what determines the ability of the protein? :) The determination of function is from the way the DNA is transcribed,the way the DNA is transcribed is from it's sequence.

Yes, and right now we are discussing the value of the proteins developed.

So if its frame shifted the protein is going to be affected in a big way,what happend was the enzyme as a whole was slightly mutated due to one of its part being completely mutated,frame shifted,and basically loss its purpose/function which was to specificity what the molecules are used by the enzyme.

None of this is really significant. What is significant is the new function brought about.

1. Frame shifts cause deformation of the protein being frame shifted,I think this is pretty clear once you look at what a frame shift is. How could you possibly argue that a frame shift isn't bad when the entire sequenced is changed randomly?

Because...first off the original gene still exists, so the organism is functioning just fine. Secondly, the additional gene that has been frame shifted is still being read. This is what ive been trying to tell you, you could shift that DNA a million times over and you would still have various amino acids being produced. The DNA, when mutated doesnt just stop being read. It still operates, which is why what is important is what is being produced, not the order in which the DNA is read. Yes, what is produced depends on the way the DNA is read, but we are discussing the value of proteins that are produced from that DNA, not the DNA itself.

2. The protein is indeed useless when frame shifted,no function comes from the protein.....but rather a loss of function.

This loss of function was specification,that is specifying what molecules are used.

Well obviously you are wrong because the bacteria can now perform a new function that it never could before in addition to functions that it previously could already perform. You're calling it a loss of function but clearly it is not if it can do something more. That is digesting nylon. Also, its original functions still exists as well.

The additional function only comes from the enzymes inability to act.

Look at that, one minute you say "a loss of function" coming from the protein, then right after you say "the additional function". So im going to go ahead and take victory on that one. And its not necisserily an inability to act because the original gene create the proper proteins needed to act. So it doesnt matter if the duplicated gene vanished in thin air, the organism itself wouldnt have any issues continuing to live on.

Obviously the enzyme is still acting and its acting in a way in which no other protein does.

For example lets take sickle cell,its a deadly disease because it causes blood cells to become sickle shapped and makes it lose its ability to carry oxygen correctly.

Atheists/evolutionsts come out and say "hey look its a good mutation because now its hard for you to get malaria".

Lol yeah its hard for you to get malaria AND oxygen, AND many other molecules. I wouldn't call this "beneficial". This is like a nazi shooting you in the head for having a scratch and the nazi saying "well at-least you aren't itchy anymore".

The last example was for a comedic effect but I'm sure you get the point.

The difference between your analogies and nylonase are that the mutation of nylonase benefits the organisms ability to survive moreso than any detriment.

Ok, so lets summarize here. We agree that we have new DNA from the mutation. Its additional DNA to the genome. We agree that the mutated gene is a new gene. We agree that the ensuing amino acids and proteins which are defined by the DNA, are all new. We agree that the new gene provides the bacteria with the function of digesting nylon. We agree that this is a function that couldnt previously be performed, therefore its new.

This is really all there is to it. New DNA, new amino acids, new protein, new function. All are from a duplicated gene and are therefore additional to the genome and the organism.

Thats it. Thats all there is to this, we both agree that these organisms have evolved new functions through mutations that developed new DNA.

Edited by iDevonian

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Also, and this seems to be the only thing left that we are stuck on. (We clearly agree on all of the above). We agree that the organism mutated a new ability. We agree that this new function of digesting nylon mutated into existence. You are saying that the new ability may have mutated into existence, but it only exists...presumably because it lost specificity with its substrates. Now I assume thats what you mean. However, nylonase is an enzyme that breaks down nylon. Thats it, it is specific to breaking down nylon for the bacterias digestion. It breaks down specific bonds within nylon. Thats all it does. And ultimately, and we agree on this, this function is from DNA that had been an overall addition to the genome.

Its new, its additional,it operates, it benefits. And let me just say, we know it benefits the organism because its an additional trait that allows the organism to do more than it originally could and it allowed the bacteria to thrive on new compounds. We both agree on all of these things. Thats it, we agree on evolution.

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It seems like we are going in circles,so I will extract as to what I have collected from you so far and you can agree or disagree and then see if it causes the life we see today.

1. You say that it was a good mutation due to a new gain of function. < Idev

1.1 I interject with the fact that the new function only has arisen due to a loss of specificity and not any actually "good mutation". < Me

1.2 You then say it wasn't a loss of specificity it is only a different new variant code that added a new and different function. < IDev

The problem lies in 1.2,because the function did indeed arise from the loss and corruption of the protein as stated by the people who studied this enzyme.

The statement "There wasn't a loss of specificity" is wrong in every sense of the word.

Atheists, evolutionists,theists, whoever, everyone agrees this function has arisen from the fact that the cleft of the enzyme was corrupted.

So indeed you may say "hey a new function". But this is intellectually honest at best,just like the German soldier solving your mosquito bite itch by shooting you in the head, or sickle cell disease causing you to die but at the same time causing your blood cells from not getting malaria.

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

Another thing Idev,we both agreed it was from a frame shift. This in itself invalidates any claim that it was a good mutation,no one believes that a frame shift mutation could possibly make the protein work better as all of the codon triplets are shifted creating a completely random fold.

The cleft was randomized due to the frame shift,and loss specificity.

I don't think you can honestly disagree with that,not to sound condescending or insulting at all.

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It seems like we are going in circles,so I will extract as to what I have collected from you so far and you can agree or disagree and then see if it causes the life we see today.

1. You say that it was a good mutation due to a new gain of function. < Idev

1.1 I interject with the fact that the new function only has arisen due to a loss of specificity and not any actually "good mutation". < Me

1.2 You then say it wasn't a loss of specificity it is only a different new variant code that added a new and different function. < IDev

The problem lies in 1.2,because the function did indeed arise from the loss and corruption of the protein as stated by the people who studied this enzyme.

The statement "There wasn't a loss of specificity" is wrong in every sense of the word.

Atheists, evolutionists,theists, whoever, everyone agrees this function has arisen from the fact that the cleft of the enzyme was corrupted.

So indeed you may say "hey a new function". But this is intellectually honest at best,just like the German soldier solving your mosquito bite itch by shooting you in the head, or sickle cell disease causing you to die but at the same time causing your blood cells from not getting malaria.

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

A german soldier shooting you in the head to solve a mosquito bite itch would kill you. The nylon digesting bacteria have not been killed, not even harmed. They are better off than they were before because they now have additional capabilities.

Another thing Idev,we both agreed it was from a frame shift. This in itself invalidates any claim that it was a good mutation,no one believes that a frame shift mutation could possibly make the protein work better as all of the codon triplets are shifted creating a completely random fold.

The cleft was randomized due to the frame shift,and loss specificity.

I don't think you can honestly disagree with that,not to sound condescending or insulting at all.

The proteins still have specificity in what they now react with. That is nylon.

And you should agree with both of my responses here as well.

Edited by iDevonian

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Idev says Well obviously you are wrong because the bacteria can now perform a new function that it never could before in addition to functions that it previously could already perform. You're calling it a loss of function but clearly it is not if it can do something more. That is digesting nylon. Also, its original functions still exists as well.

The additional function was from a loss of function,this becomes clear when you understanding the meaning of this statement.

I will give the same clear example so that you and the people reading will understand Insha'Allah.

Sickle cell disease is a disease that causes death due to its inability to carry oxygen in the blood stream due to the "sickle shape" of the cell.

The loss of functon = Ability to carry oxygen properly.

Gain of function = inability to not only carry oxygen,but also malaria.

Added function= resistance from malaria.

I wasn't contradicting myself,so you see nothing really "evolved",I hope this clears this up.

Idev

A german soldier shooting you in the head to solve a mosquito bite itch would kill you. The nylon digesting bacteria have not been killed, not even harmed. They are better off than they were before because they now have additional capabilities.

Notice my analogy has nothing to do with the death of the bacteria,the analogy was to show that your example of the nylon mutation is flawed because the function you see it only an effect of a corruption.

Similarly the stopping of your itch was from the bullet that killed you.

Idev

The proteins still have specificity in what they now react with. That is nylon.

This sentence is essentially meaningless,as they nylon is only used due to the enzymes cleft not being able to block it.

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The additional function was from a loss of function,this becomes clear when you understanding the meaning of this statement.

There has not been a loss in functionality of the bacteria. If you think there is, then tell me what the bacteria can no longer do after having mutated.

.

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Idev says There has not been a loss in functionality of the bacteria. If you think there is, then tell me what the bacteria can no longer do after having mutated.

Sure,the enzyme has lost its ability to block molecules from being used from the corruption of its cleft.

If I have a puzzle that only takes triangles,I then break the hold into a chipped circle and I then say to you "look it can now take squares".

Would you call that evolution?

Not only does the enzyme take nylon,but it takes many other molecules as well due to its loss of specificity.

So you can put a triangle,a pentagon,a square,anything you like now since i broke your puzzle hold that only originally took a triangle.

Also this is actually bad for the protein as it loses energy efficiency because non-specific transporting of the used nylon and other molecules it now takes is degenerative to the enzyme,this is the reason they the cleft was there in the first place.

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Sure,the enzyme has lost its ability to block molecules from being used from the corruption of its cleft.

Not only does the enzyme take nylon,but it takes many other molecules as well due to its loss of specificity.

Also this is actually bad for the protein as it loses energy efficiency because non-specific transporting of the used nylon and other molecules it now takes is degenerative to the enzyme,this is the reason they the cleft was there in the first place.

That particular enzyme sure, because the original enzyme no longer exists in the new gene, or with the new gene rather. But that is not to say the original enzyme isnt still developed by the original gene. Which is why I am asking about the functional capabilities of the organism itself, not the mutated gene. What function has the organism lost? The answer is, none.

And if you think there is, then source it.

Also no, the enzyme doesnt act on a large number of bonds. If you think it does, then source something that says nylonase works with more than just nylon bonds.

Edited by iDevonian

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Idev says

That particular enzyme sure, because the original enzyme no longer exists in the new gene, or with the new gene rather. But that is not to say the original enzyme isnt still developed by the original gene. Which is why I am asking about the functional capabilities of the organism itself, not the mutated gene. What function has the organism lost? The answer is, none.

And if you think there is, then source it.

Also no, the enzyme doesnt act on a large number of bonds. If you think it does, then source something that says nylonase works with more than just nylon bonds.

And if you think there is, then source it.

Also no, the enzyme doesnt act on a large number of bonds. If you think it does, then source something that says nylonase works with more than just nylon bonds.

It seems to me you keep repeating yourself and you keep saying there was no loss of function,when I clearly gave you examples. I already sourced it,it was a loss of specificity because the protein was frame shifted . The enzyme's ability to filter out molecules that cause it to degenerate is now gone.

The enzyme can now use many oligomers including nylon according to the same source I gave you "Journal of Biological Chemistry

You keep saying "but the prior sequence is still there." < This is irrelevant because the cleft is changed and mutated none the less,the duplication caused it to fold differently and lose specificity .

Hope it is clear to you now.

To run away and now jump to the organism is rather silly,as the enzyme directly effects the bacteria's ability to survive. Similarly we digest our food from enzymes,if our enzymes were corrupted in that we digested food in the wrong way or not at all we'd die.

If the enzyme is dysfunctional,the organism is dysfunctional.

Edited by Ibn-Ahmed Aliyy Herz

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It seems to me you keep repeating yourself and you keep saying there was no loss of function,when I clearly gave you examples. I already sourced it,it was a loss of specificity because the protein was frame shifted . The enzyme's ability to filter out molecules that cause it to degenerate is now gone.

You keep referring to the protein functions. Im asking for the organisms functions. The difference is, the organism has the genes to perform its new and original functions. And so there isnt a loss of function in the organism. And im repeating myself because you arent acknowledging this.

To run away and now jump to the organism is rather silly,as the enzyme directly effects the bacteria's ability to survive. Similarly we digest our food from enzymes,if our enzymes were corrupted in that we digested food in the wrong way or not at all we'd die.

Nobody is running away from anything, whats important is the survival of the organism which is why I am talking about it. The functions of these proteins collectively act within the organism. And yes the enzyme does directly effect the bacterias ability to survive, and in this case, it benefits the bacteria. And as you well know, just as we begun this discussion, evolution comes down to survival.

Edited by iDevonian

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The enzyme can now use many oligomers including nylon according to the same source I gave you "Journal of Biological Chemistry

You keep saying "but the prior sequence is still there." < This is irrelevant because the cleft is changed and mutated none the less,the duplication caused it to fold differently and lose specificity .

And your source is discussing oligomers of nylon.

Edited by iDevonian

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