rationalskepticism.org

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.