Science shows that evolution can't create new genes

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Re: Science shows that evolution can't create new genes

#221  Postby TopCat » Feb 08, 2015 10:39 pm

I spose when he's typing that stuff he isn't doing damage anywhere else, so we should be glad of that. I needed the eyebrow exercise anyway, so I'm good.
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Re: Science shows that evolution can't create new genes

#222  Postby hackenslash » Feb 08, 2015 10:41 pm

TopCat wrote:I needed the eyebrow exercise anyway, so I'm good.


This wins the internet. :rofl:
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Strawman Re: Science shows that evolution can't create new genes

#223  Postby Greyman » Feb 08, 2015 10:41 pm

The gun-to-head analogy is obviously flawed. That's a single all-or-nothing trial with one-true-solution.

Evolution clearly operates when there are many parallel trials taking place within each generation, the travails are not guaranteed lethal (or at least don't target one-hundred percent of the population), and when the random answers are inherited traits for use with variation by each subsequent generation.
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Re: Strawman Re: Science shows that evolution can't create new genes

#224  Postby hackenslash » Feb 08, 2015 10:43 pm

Greyman wrote:The gun-to-head analogy is obviously flawed. That's a single all-or-nothing trial with one-true-solution.


Depends what QM ontology you subscribe to...

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Re: Science shows that evolution can't create new genes

#225  Postby Rumraket » Feb 08, 2015 11:01 pm

That is probably the shittiest analogy of the process of evolution I have so far seen in my life.

MarioNovak wrote:We know that if cells get introns inserted into a genes, cells will eventually die out.

No we don't.

We know that if a cells get an introns inserted into a certain genes, in a specific location, that cells will eventually die out.

Fixed.

See, introns arise as a type of mutation that inserts itself a random place in the genome. But there's a whole population of cells, trillions of them, but only some of them get this "proto-intron" mutation. Of those that get this mutation, not all of them die, because not all of the "proto-introns" are lethal(because they happen in places where their effect is small, so the cells only have somewhat lower fitness), and some are even facultatively(aka situationally) neutral(because they happen in genes that are only used under certain conditions).

Does this mean that all cells ever will die out if some cells manage to evolve introns? No. At worst, only the cells that actually evolve introns but cannot get rid of them would die out, leaving only cells without introns. Makes sense.

But of course, introns exist, and cells have ways to get rid of them before mRNA is translated, so what gives?

Same shit all over again as in my previous post on this. Among the population of cells that now carry facultatively neutral, or slightly deleterious "proto introns", additional mutations will happen in the genomes as they make copies of themselves.

MarioNovak wrote:Now consider the following analogy: someone holds a gun up to you and threatens to kill you if you don't know the answer to a random question he asks. So, your life will be spared if you provide the right combination of letters and words, just like cell's life will be "spared" if evolution provides the right combination of molecules. Now we are at a crucial point, and we will put ourselves in evolution shoes.

What an utterly, utterly terrible analogy.

Let me fix it.

Instead of just a single person, how about a huge population of about 80 trillion people instead (there's about 1030 cells on Earth so I'm being extremely generous here). The analogy here is that there isn't just a single cell in the population with an outright lethal intron.

And there isn't one guy for every one of those people, because introns didn't suddenly pop into existence fully formed, simultaneously in every cell on the planet. Some few cells in the population had mutations that produced introns.
So we modify your analogy further: There's maybe 1000 guys with guns. Just as the "solution" to introns had to arise gradually, so did introns themselves.

Also, not all introns would be outright lethal. Many of them would be neutral because they would only be happening in facultatively useful genes, others are slightly deleterious because they happen in genes with high copy numbers(meaning the copies without introns compensate for the loss of the copy WITH introns in it), and others still are deleterious because they happen in areas of the protein coding sequence which are not terribly important for protein function(which means it might only weakly impact the solubility of the protein in question, for example). So we modify your analogy further: The guys with guns miss their shots 90% of the time.

Now the process starts. The 1000 guys start asking random questions, and even the people who guess wrong still often survive because the shooters miss their targets. That means most of the people who have been asked a question and answered wrongly still get to live and remember that their answer was wrong, so the next time they run into a shooter they get to "mutate" their previous answer.

But it also turns out that biochemistry is not all-or-nothing. Protein or RNA sequences don't have to be EXACT and UNIQUE to be weakly functional. So as an analogy to this, some times an approximately correct sentence is still readable, even if there is spelling and grammatical errors. So when the people who are asked questions get sufficiently close in words and letters (50% ?), their answers start "working" and now the shooter will occasionally elect not to shoot at all when an "approximately correct" answer is given. So they obviously still get to keep their previous, now even better working answers and mutate it further should they run into the shooters again.

There, analogy fixed. I'm willing to run this experiment. Are you?
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Re: Strawman Re: Science shows that evolution can't create new genes

#226  Postby Rumraket » Feb 08, 2015 11:02 pm

Greyman wrote:The gun-to-head analogy is obviously flawed. That's a single all-or-nothing trial with one-true-solution.

Evolution clearly operates when there are many parallel trials taking place within each generation, the travails are not guaranteed lethal (or at least don't target one-hundred percent of the population), and when the random answers are inherited traits for use with variation by each subsequent generation.

Heh, I fixed his analogy above.
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Re: Strawman Re: Science shows that evolution can't create new genes

#227  Postby Rumraket » Feb 08, 2015 11:02 pm

hackenslash wrote:
Greyman wrote:The gun-to-head analogy is obviously flawed. That's a single all-or-nothing trial with one-true-solution.


Depends what QM ontology you subscribe to...

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Re: Science shows that evolution can't create new genes

#228  Postby Rumraket » Feb 08, 2015 11:09 pm

hackenslash wrote:That about covers it.

What a load of ignorant fucking drivel. Anybody who thinks we operate on the assumption that evolution has foresight has failed dismally to understand evolutionary theory, which is quite a special achievement, since it's simple enough to be understood by anybody with two or more functioning neurons. That anybody could hold that position and still be able to turn on a computer to expose such a failure to the world at large seems somewhat paradoxical.

What makes this doubly amazing is that he continues to hold this misconceptions after having had this explained to him in exquisite detail multiple times.
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Re: Science shows that evolution can't create new genes

#229  Postby Rumraket » Feb 08, 2015 11:11 pm

Bleh, I crossed the 10.000 post mark earlier today and didn't even notice. Time to go to bed.
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Re: Science shows that evolution can't create new genes

#230  Postby MarioNovak » Feb 09, 2015 11:23 am

Rumraket wrote:
See, introns arise as a type of mutation that inserts itself a random place in the genome. But there's a whole population of cells, trillions of them, but only some of them get this "proto-intron" mutation. Of those that get this mutation, not all of them die, because not all of the "proto-introns" are lethal(because they happen in places where their effect is small, so the cells only have somewhat lower fitness), and some are even facultatively(aka situationally) neutral(because they happen in genes that are only used under certain conditions).

Does this mean that all cells ever will die out if some cells manage to evolve introns? No. At worst, only the cells that actually evolve introns but cannot get rid of them would die out, leaving only cells without introns. Makes sense.

But of course, introns exist, and cells have ways to get rid of them before mRNA is translated, so what gives?

Same shit all over again as in my previous post on this. Among the population of cells that now carry facultatively neutral, or slightly deleterious "proto introns", additional mutations will happen in the genomes as they make copies of themselves.
So you deny that accumulation of intronic insertions into a functional protein coding genes, without solution in the form of the right combination of molecules*, will cause cells to eventually die out?

* http://www.ncbi.nlm.nih.gov/pubmed/12887888
What's in a spliceosome? More than we ever imagined, according to recent reports employing proteomics techniques to analyze this multi-megadalton machine. As of 1999, around 100 splicing factors were identified (Burge et al., 1999); however, that number has now nearly doubled due primarily to improved purification of spliceosomes coupled with advances in mass spectrometry analyses of complex mixtures. Gratifyingly, most of the previously identified splicing factors were found in the recent mass spec studies. Nonetheless, the number of new proteins emerging with no prior connection to splicing was surprising.
SmB/B, SmD1, SmD2, SmD3, SmE1, SmF1, SmG1, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, U1-70kD, U1-A, U1-C, U2-A, U2-B, SF3a60, SF3a66, SF3a120, SF3b49, SF3b145, SF3b130, SF3b155, p14, PRP8, U5-200kD, U5-116kD, U5-102kD, U5-100kD, U5-40kD, U5-15kD, HPRP3, HPRP4, RY-1, USA-Cyp, 15.5 tri-snRNP, U2AF65, SF1, CBP20, CBP80, U2AF35, ASF/SF2, UAP56, PRP5, Tat-SF1, PTB, PRP19, PRP31, DDX16, PRP16, PRP17, SLU7, PRP18, PRP22, EWS, PRP43, PRP24, DDX3, CDC5, ISY1, SYF1, CRN, GCIP-IP, PRL1, BCAS2, SKIP, ECM2, SART1, p68, SPF45, SPF30, PSF, FLJ31121, SAD1, LUC7, SRm300, SRm160, SC35, SRp40, SRp55, SRp75, SRp30c, 9G8, SRp54, SFRS10, SRp20, REF, RNPS1, Y14, MAGOH, hTHO2, hHPR1, HsKin17, ASR2B, KIAA0983, C21orf66, PAB2, CF I-68kD, CF I-25kD, CPSF 160K, HDB/DICE1, Abstrakt, eIF4a3, DDX35, DDX9, KIAA0052, p72, CypE, KIAA0073, Cyp60, PPIL3b, PPIL1, SDCCAG10, KIAA1604, TIP39, G10, FLJ10374, MGC13125, ZNF183, FLJ10634, SF3b14b, SPF31, CHERP, F23858, CA150, SF3b10, SR140, RBM5, E1B-AP5, FLJ10805, MFAP1, KIAA0560, RED protein, Pinin, NOSIP, FLJ10206, PUF60, DGSI, Cactin, FRG1, PMSCL2, RBP 7, MGC23918, SNP70, OTT, IMP3, PRP4 kinase, AcinusL, RNPC2, FLJ90157, NuMA, hnRNP A1, hnRNPA2/B2, hnRNP A3, hnRNP C, hnRNP D, hnRNP F, hnRNP G, hnRNP H1, hnRNP K, hnRNP L, hnRNP M, hnRNPR, hnRNP U, hnRNP RALY, Ku70, PTB, Gry-Rbp, hUR, NF45, NF90, MAT3, YB-1, TLS ip, HSP70-2, HSP71, FUS.

Let me fix it.

Instead of just a single person, how about a huge population of about 80 trillion people instead (there's about 1030 cells on Earth so I'm being extremely generous here). The analogy here is that there isn't just a single cell in the population with an outright lethal intron.

No problem. We can assume population of about 10^80 people(this is the estimated number of atoms in the observable universe) Ok?

And there isn't one guy for every one of those people, because introns didn't suddenly pop into existence fully formed, simultaneously in every cell on the planet. Some few cells in the population had mutations that produced introns.
So we modify your analogy further: There's maybe 1000 guys with guns. Just as the "solution" to introns had to arise gradually, so did introns themselves.

I agree with your modification. And btw, this was already assumed in my analogy when I said this: You can combine existing letters, words and sentences that exist in books, newspapers, magazines, ...or in your mind. You can use pre-adaptation, exaptation, co-option, you can create new information that is not present in existing literature. You can do whatever you want in creating new combinations of linguistic elements.

So, I did not say you have only one attempt.

Also, not all introns would be outright lethal. Many of them would be neutral because they would only be happening in facultatively useful genes, others are slightly deleterious because they happen in genes with high copy numbers(meaning the copies without introns compensate for the loss of the copy WITH introns in it), and others still are deleterious because they happen in areas of the protein coding sequence which are not terribly important for protein function(which means it might only weakly impact the solubility of the protein in question, for example). So we modify your analogy further: The guys with guns miss their shots 90% of the time.

Again, I agree, and again this was assumed in my analogy. I didn't say that you will be killed after one failed attempt.

Now the process starts. The 1000 guys start asking random questions, and even the people who guess wrong still often survive because the shooters miss their targets. That means most of the people who have been asked a question and answered wrongly still get to live and remember that their answer was wrong, so the next time they run into a shooter they get to "mutate" their previous answer.

I agree.

But it also turns out that biochemistry is not all-or-nothing. Protein or RNA sequences don't have to be EXACT and UNIQUE to be weakly functional. So as an analogy to this, some times an approximately correct sentence is still readable, even if there is spelling and grammatical errors.

I agree. Let us suppose that a question is this: What did 1998 CBS News poll showed Americans believed about assassination of John F. Kennedy?

Answer is this: A 1998 CBS News poll showed that 76% of Americans believed the President had been killed as the result of a conspiracy.

Now, just as in biochemistry this answer is not all-or-nothing. Answer or question don't have to be EXACT and UNIQUE to be functional.

This one is also correct answer: poll showed 76% of people believed the Kennedy had been killed as the result of a conspiracy.

This one is also O.K: survey of public opinion showed 76% of people believed the John had been killed as the result of a inside job.

And this: surveyyyy offff public opinion showwed 76% of peopleaaa believed the John had been killed as the result of a inside job.

See, answer don't have to be exact.

So when the people who are asked questions get sufficiently close in words and letters (50% ?), their answers start "working" and now the shooter will occasionally elect not to shoot at all when an "approximately correct" answer is given. So they obviously still get to keep their previous, now even better working answers and mutate it further should they run into the shooters again.

There, analogy fixed. I'm willing to run this experiment. Are you?


Wrong, you are presupposing communication which is an intelligent activity. Communication is a purposeful activity of exchanging information and meaning across space and time, and we know evolution have no intelligence, no purpose, no vision, no mind, no foresight... and therefore no knowledge of what is the percentage of correct molecules(30%, 50%, 80%). If we assume existance of fully functional and correct RNA splicing helper proteins that assembly at the intron-exon borders to guide small nuclear ribo proteins to form a splicing machine, this partial correctness of splicing process won't cause introns to magically disappear without a splicing machine. This partial correctness won't cause random, blind and intelligent process to put aside these helper proteins because they're good for the future splicing function. Evolution has no long term goal. There is no long distance target to serve as a criterion for selection. See, you are constantly presupposing knowledge and intelligence in explaining how a particular evolutionary result was achieved, but in the same time you deny traces of intelligence in biology.
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Re: Science shows that evolution can't create new genes

#231  Postby Shrunk » Feb 09, 2015 11:43 am

Do I need to translate the acronym in my last post for you?
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Re: Science shows that evolution can't create new genes

#232  Postby hackenslash » Feb 09, 2015 11:43 am

You can't do that without communicating.

Checkmate, atheists!
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Re: Science shows that evolution can't create new genes

#233  Postby Sendraks » Feb 09, 2015 11:44 am

MarioNovak wrote:So you deny that accumulation of intronic insertions into a functional protein coding genes, without solution in the form of the right combination of molecules*, will cause cells to eventually die out?


Did you not read what Rumraket posted? That's a rhetorical question, I realise that the other half of the conversation is being constructed entirely in your imagination.
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Re: Science shows that evolution can't create new genes

#234  Postby Rumraket » Feb 09, 2015 1:05 pm

:picard:
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Re: Science shows that evolution can't create new genes

#235  Postby Rumraket » Feb 09, 2015 1:24 pm

MarioNovak wrote:
Rumraket wrote:
See, introns arise as a type of mutation that inserts itself a random place in the genome. But there's a whole population of cells, trillions of them, but only some of them get this "proto-intron" mutation. Of those that get this mutation, not all of them die, because not all of the "proto-introns" are lethal(because they happen in places where their effect is small, so the cells only have somewhat lower fitness), and some are even facultatively(aka situationally) neutral(because they happen in genes that are only used under certain conditions).

Does this mean that all cells ever will die out if some cells manage to evolve introns? No. At worst, only the cells that actually evolve introns but cannot get rid of them would die out, leaving only cells without introns. Makes sense.

But of course, introns exist, and cells have ways to get rid of them before mRNA is translated, so what gives?

Same shit all over again as in my previous post on this. Among the population of cells that now carry facultatively neutral, or slightly deleterious "proto introns", additional mutations will happen in the genomes as they make copies of themselves.
So you deny that accumulation of intronic insertions into a functional protein coding genes, without solution in the form of the right combination of molecules*, will cause cells to eventually die out?

This is idiotic.

Dude, how do introns acquire the ability to insert themselves all over the genome to begin with? They have to evolve this ability too. Which means there's a long period of selection to get rid of them before they become too numerous and hit critical gene regions.

So to begin with, there's really no "accumulation" of them. A few cells in the population of cells will evolve one here and there, and that "proto-intron" will only manage to copy and insert itself in a new location very rarely.

If the intron kills the cell in question, the intron longer exists. So introns that evolve to kill their host MAKE THEMSELVES GO EXTINCT. Such introns are instantly outcompeted by cells with introns that DON'T kill their host. :o

It is a piece of selfish DNA that is under selection to evolve a method of propagating itself without killing the host, because if the host dies, there no more introns of that type either.

So there are two simultaneous seletion processes in effect on the mutations that happen in the cells and in the introns themselves: One for the cell to find a way of cutting out their introns and another for the intron itself to find a way of cutting itself out.

Weirdly and mysteriously, now today 2 billion years later, those very two types of introns still exist. Self-splicing introns that cut themselves out and introns that need the help of the spliceosome to get cut out.

Get it?

Guess which one evolved due to which selection pressure and win a cookie. :ask:
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Re: Science shows that evolution can't create new genes

#236  Postby Rumraket » Feb 09, 2015 1:27 pm

MarioNovak wrote:
Rumraket wrote:But it also turns out that biochemistry is not all-or-nothing. Protein or RNA sequences don't have to be EXACT and UNIQUE to be weakly functional. So as an analogy to this, some times an approximately correct sentence is still readable, even if there is spelling and grammatical errors.

I agree. Let us suppose that a question is this: What did 1998 CBS News poll showed Americans believed about assassination of John F. Kennedy?

Answer is this: A 1998 CBS News poll showed that 76% of Americans believed the President had been killed as the result of a conspiracy.

Now, just as in biochemistry this answer is not all-or-nothing. Answer or question don't have to be EXACT and UNIQUE to be functional.

This one is also correct answer: poll showed 76% of people believed the Kennedy had been killed as the result of a conspiracy.

This one is also O.K: survey of public opinion showed 76% of people believed the John had been killed as the result of a inside job.

And this: surveyyyy offff public opinion showwed 76% of peopleaaa believed the John had been killed as the result of a inside job.

See, answer don't have to be exact.

Rumraket wrote:So when the people who are asked questions get sufficiently close in words and letters (50% ?), their answers start "working" and now the shooter will occasionally elect not to shoot at all when an "approximately correct" answer is given. So they obviously still get to keep their previous, now even better working answers and mutate it further should they run into the shooters again.

There, analogy fixed. I'm willing to run this experiment. Are you?


Wrong, you are presupposing communication which is an intelligent activity.

:picard:

:picard:

First you agree to my fixing of your analogy every step of the way, and then when it's time to try and see ho this affects your "simulation" you suddenly protest a step you agreed to immediately beforehand.

I'm afraid that in your case, communication isn't particularly intelligent.
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Re: Science shows that evolution can't create new genes

#237  Postby Shrunk » Feb 09, 2015 2:24 pm

Rumraket wrote:Bleh, I crossed the 10.000 post mark earlier today and didn't even notice. Time to go to bed.



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Re: Science shows that evolution can't create new genes

#238  Postby MarioNovak » Feb 10, 2015 8:51 am

Rumraket wrote:
This is idiotic.

Dude, how do introns acquire the ability to insert themselves all over the genome to begin with? They have to evolve this ability too. Which means there's a long period of selection to get rid of them before they become too numerous and hit critical gene regions.

So to begin with, there's really no "accumulation" of them. A few cells in the population of cells will evolve one here and there, and that "proto-intron" will only manage to copy and insert itself in a new location very rarely.

If the intron kills the cell in question, the intron longer exists. So introns that evolve to kill their host MAKE THEMSELVES GO EXTINCT. Such introns are instantly outcompeted by cells with introns that DON'T kill their host. :o

It is a piece of selfish DNA that is under selection to evolve a method of propagating itself without killing the host, because if the host dies, there no more introns of that type either.

So there are two simultaneous seletion processes in effect on the mutations that happen in the cells and in the introns themselves: One for the cell to find a way of cutting out their introns and another for the intron itself to find a way of cutting itself out.

Weirdly and mysteriously, now today 2 billion years later, those very two types of introns still exist. Self-splicing introns that cut themselves out and introns that need the help of the spliceosome to get cut out.

Get it?

Guess which one evolved due to which selection pressure and win a cookie. :ask:

Whatever, I can agree with that to. You won't get killed, people won't get killed, whatever. So, we will replace life threatening situation with the threat of bodily harm. When you find the right answer threat will cease to exist.

Now that we've agreed that intronic insertions won't cause cells to eventually die out, we can finally focus, through the lens of reductio ad absurdum argument, on the real question: how will cell "find a way" of cutting out their introns, using evolutionary mechanisms of random variation and natural selection?

As I have already said, life is the ability to do something. Ability to do something comes from the right combination of molecules. In the same way, RNA splicing process which takes place in the nucleus of eukaryotes, is the ability to capture, cut, rearrange, join and release mRNA molecule and it comes from the right combination of amino acids, nucleotides, proteins and small nuclear RNAs.

Since RNA splicing molecular components are completely useless in splicing job until all five of its subprocesses(capture, cut, rearrange, join and release) are present, the potential of the evolutionary random DNA rearrangement to generate fully functional RNA splicing process is the same as the potential to generate molecular machinery that spells your name and surname together with your address, using multiprotein complexes. Due to this reason I am really interested in how you'll transform the magic phrase - "find a way of cutting", into a reasonable scientific explanation on how did evolution created complex RNA splicing process through accumulations of small changes.

I am waiting.
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Re: Science shows that evolution can't create new genes

#239  Postby Thomas Eshuis » Feb 10, 2015 9:16 am

:facepalm:
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Re: Science shows that evolution can't create new genes

#240  Postby Rumraket » Feb 10, 2015 9:45 am

MarioNovak wrote:
Rumraket wrote:
This is idiotic.

Dude, how do introns acquire the ability to insert themselves all over the genome to begin with? They have to evolve this ability too. Which means there's a long period of selection to get rid of them before they become too numerous and hit critical gene regions.

So to begin with, there's really no "accumulation" of them. A few cells in the population of cells will evolve one here and there, and that "proto-intron" will only manage to copy and insert itself in a new location very rarely.

If the intron kills the cell in question, the intron longer exists. So introns that evolve to kill their host MAKE THEMSELVES GO EXTINCT. Such introns are instantly outcompeted by cells with introns that DON'T kill their host. :o

It is a piece of selfish DNA that is under selection to evolve a method of propagating itself without killing the host, because if the host dies, there no more introns of that type either.

So there are two simultaneous seletion processes in effect on the mutations that happen in the cells and in the introns themselves: One for the cell to find a way of cutting out their introns and another for the intron itself to find a way of cutting itself out.

Weirdly and mysteriously, now today 2 billion years later, those very two types of introns still exist. Self-splicing introns that cut themselves out and introns that need the help of the spliceosome to get cut out.

Get it?

Guess which one evolved due to which selection pressure and win a cookie. :ask:

Whatever, I can agree with that to. You won't get killed, people won't get killed, whatever. So, we will replace life threatening situation with the threat of bodily harm. When you find the right answer threat will cease to exist.

Now that we've agreed that intronic insertions won't cause cells to eventually die out, we can finally focus, through the lens of reductio ad absurdum argument, on the real question: how will cell "find a way" of cutting out their introns, using evolutionary mechanisms of random variation and natural selection?

As I have already said, life is the ability to do something. Ability to do something comes from the right combination of molecules. In the same way, RNA splicing process which takes place in the nucleus of eukaryotes, is the ability to capture, cut, rearrange, join and release mRNA molecule and it comes from the right combination of amino acids, nucleotides, proteins and small nuclear RNAs.

Since RNA splicing molecular components are completely useless in splicing job until all five of its subprocesses(capture, cut, rearrange, join and release) are present, the potential of the evolutionary random DNA rearrangement to generate fully functional RNA splicing process is the same as the potential to generate molecular machinery that spells your name and surname together with your address, using multiprotein complexes. Due to this reason I am really interested in how you'll transform the magic phrase - "find a way of cutting", into a reasonable scientific explanation on how did evolution created complex RNA splicing process through accumulations of small changes.

I am waiting.

The introns cut themselves out using metal ions as cofactors, sort of like small "spot welders". Such introns exist today, we call them self-splicint introns. They belong to http://en.wikipedia.org/wiki/Group_I_catalytic_intron and http://en.wikipedia.org/wiki/Group_II_intron.

RNA can do that. The RNA backbone is negatively charged (it just is, the phosphate group is negatively charged, this doesn't have to evolve), so it binds a positively charged metal cofactor such as Mg2+.

All RNA folds into some structure, some of them stably, some of them not. So it folds back on itself and when the metal cofactor comes into contact with the phosphodiester backbone, it breaks the bonds.

There, that's it. No reason for me to sit here and spell it all out. You can just read this:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756803/
Structural Insights into RNA Splicing
Navtej Toor,Kevin S. Keating, and Anna Marie Pyle
Summary of recent advances
Intron splicing is a fundamental biological process whereby non-coding sequences are removed from precursor RNAs. Recent work has provided new insights into the structural features and reaction mechanisms of two introns that catalyze their own splicing from precursor RNA: the group I and II introns. In addition, there is an increasing amount of structural information on the spliceosome, which is a ribonucleoprotein machine that catalyzes nuclear pre-mRNA splicing in eukaryotes. Here, we compare structures and catalytic mechanisms of self-splicing RNAs and we discuss the possible implications for spliceosomal reaction mechanisms.


You will note how there are introns that don't depend on proteins to help them excise themselves. So all that is required to make introns cut themselves out to begin with is that mutations change the first introns insertions such that they bind metal cofactors and fold themselves into the right position.

Here's some basics:
Half-Life 3 - I want to believe
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