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Wednesday, November 02, 2011

Alternative Splicing and Why IDiots Don't Understand How Science Works

One of the characteristics of creationists is their inability to understand how science works. For example, in biology, our knowledge of how living things work advances in fits and starts with many hypotheses being tested and rejected before we arrive at a consensus.

At any given point in time there are a number of "works in progress" where scientists have not settled on a definitive model. Many papers will be published and a good number of them will turn out to be wrong. Creationists exploit genuine scientific controversies in two ways: (1) they use them to discredit science, and (2) they selectively quote from those on one side of an issue without mentioning that many other scientists disagree. (Most creationists use both tactics, sometimes in the same paragraph.)

We saw how Jonathan Wells did this in The Myth of Junk DNA. He picked papers that question junk DNA and used them to try and show that the issue has not been settled in spite of what some leading scientists say. This is a valid point, but he goes on to conclude that junk DNA is a myth when the proper conclusion is that scientists haven't reached a consensus but the majority favor junk DNA.

He also selected specific papers that showed evidence of function for some part of the genome without mentioning that this evidence is often disputed. In many cases it isn't clear whether this "evidence" is correct. He ignores controversy when it suits him and exploits it when it's to his benefit.

Some papers have claimed that most of the human genome is transcribed. Wells takes this as evidence that the transcribed DNA is not junk. In this particular case, the objections to this interpretation couldn't be ignored so he spends a page or so dismissing the idea that the data might be wrong and that the conclusion might be wrong. He forgets to mention that the consensus among molecular biologists is that most of the transcript are junk RNA due to accidental transcription. The DNA being transcribed is still junk.

Jonathan M makes a similar mistake in his latest posting [Why the "Onion Test" Fails as an Argument for "Junk DNA"]. The issue is alternative splicing. There are many scientists who think that alternative splicing is widespread in the human genome. Some claim that the vast majority of human genes (>90%) make two or more biologically functional alternative transcripts. This is usually offered as one "explanation" for why humans don't have as many genes as our egos demand [The Deflated Ego Problem]. Fact is, most of us never thought this was a problem in the first place so no "solution" is required.

Here's how Jonathan M describes alternative splicing ....
Alternative Splicing and Genome Size

A second point I made was that the phenomena of alternative splicing and alternative polyadenylation may have some explanatory power when it comes to accounting for the C-value enigma. Alternative splicing allows a single form of a pre-mRNA transcript to be spliced into a number of different forms by skipping exons or by recognizing alternative splice sites. I stated that the level of alternative splicing exhibited in humans (more than 90%, with an average of 2 or 3 transcripts per gene) is much higher than that for C. elegans (about 22%, with less than 2 transcripts per gene), and argued that this may, in part, explain why humans have only marginally more genes than C. elegans, which is otherwise seemingly paradoxical given the complexity of humans as compared to the roundworm.
I don't really understand the connection between alternative splicing and the C-value paradox. How does it explain why closely related species of onion have very different genome sizes?

But that's not the point I want to make. When Jonathan M raised this issue before, I replied, "I don't agree with the facts. I don't think it's true that most human genes produce multiple functional copies of mRNA by alternative splicing."

That prompted the following response ...
On this point, Moran is not just in disagreement with me, he is also out-of-date with the literature by about ten years! As this 2008 article from Science Daily reports,
Nearly all human genes, about 94 percent, generate more than one form of their protein products, the team reports in the Nov. 2 online edition of Nature. Scientists' previous estimates ranged from a few percent 10 years ago to 50-plus percent more recently.

"A decade ago, alternative splicing of a gene was considered unusual, exotic ... but it turns out that's not true at all -- it's a nearly universal feature of human genes," said Christopher Burge, senior author of the paper and the Whitehead Career Development Associate Professor of Biology and Biological Engineering at MIT.
Wang et al. (2008), moreover, report in Nature,
Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing, ~86% with a minor isoform frequency of 15% or more.
I've written about IDiots and alternative splicing before, especially their inability to understand what they're talking about [Jonathan Wells Weighs in on Alternative Splicing]. But the issue here is somewhat different. It's whether the idea that most human genes are alternatively spliced is a scientific fact or whether it's controversial. Like most IDiots, Jonathan M doesn't understand the subject well enough to know the difference.

Just because there are some papers making truly outlandish claims about alternative splicing doesn't mean they are correct—no matter where those papers are published. In order to understand science you have to dig deeper than that and decide whether the claims have been accepted.

The claim of abundant alternative splicing (i.e. the vast majority of human genes have two or more functional transcripts) has not been accepted. It's a scientific controversy. Hardly any molecular biologist believes that >90% of our genes produce functional alternative transcripts in spite what Jonathan M might believe.

In some cases it's a matter of definition. My colleague, Ben Blencowe, for example, has played a prominent role in promoting the idea that >90% of human genes are alternatively spliced (Pan et al, 2008) but he tells me that this does not mean that all alternative transcripts are functional. He concedes that many of the these transcripts could be due to splicing errors but they still qualify as alternative splicing events.

I don't agree with that definition. Many of us began teaching alternative splicing back in 1980 and putting in textbooks a few years later. "Alternative splicing" always meant "functional" alternatives. It means that the gene produced more that one biologically functional product. The definition changed in the past decade or so, but most people still interpret abundant alternative splicing to mean abundant functional products.

No reasonable molecular biologist could look at the database of spliced transcripts and conclude that most of them have a biological function. (See Two Examples of "Alternative Splicing" to see if you agree.) Most of those transcripts are clearly due to splicing errors just as most of the minor genome transcripts are due to transcription errors. There's just as much junk splicing as there is junk RNA.

Anyone familiar with the subject of alternative transcription knows that the conclusions are controversial. They know that many scientists are skeptical of the claims for massive amounts of functional alternative splicing. They know that those extraordinary claims don't make sense in the light of evolution and are probably wrong. (See A Challenge to Fans of Alternative Splicing.)

Here are some papers from well-known labs attempting to deal with the controversy.
Zhang et al. (2009)

Nonsense-mediated decay is a mechanism that degrades mRNAs with a premature termination codon. That some exons have premature termination codons at fixation is paradoxical: why make a transcript if it is only to be destroyed? One model supposes that splicing is inherently noisy and spurious transcripts are common. The evolution of a premature termination codon in a regularly made unwanted transcript can be a means to prevent costly translation. Alternatively, nonsense-mediated decay can be regulated under certain conditions so the presence of a premature termination codon can be a means to up-regulate transcripts needed when nonsense-mediated decay is suppressed....

We conclude that for recently evolved exons the noisy splicing model is the better explanation of their properties, while for ancient exons the nonsense-mediated decay regulated gene expression is a viable explanation.
Tress et al. (2007)

Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological function of the expressed protein and even to create new protein functions. Alternative splicing has been suggested as one explanation for the discrepancy between the number of human genes and functional complexity. Here, we carry out a detailed study of the alternatively spliced gene products annotated in the ENCODE pilot project. We find that alternative splicing in human genes is more frequent than has commonly been suggested, and we demonstrate that many of the potential alternative gene products will have markedly different structure and function from their constitutively spliced counterparts. For the vast majority of these alternative isoforms, little evidence exists to suggest they have a role as functional proteins, and it seems unlikely that the spectrum of conventional enzymatic or structural functions can be substantially extended through alternative splicing.
Melamud and Moult (2009)

The number of known alternative human isoforms has been increasing steadily with the amount of available transcription data. To date, over 100 000 isoforms have been detected in EST libraries, and at least 75% of human genes have at least one alternative isoform. In this paper, we propose that most alternative splicing events are the result of noise in the splicing process. We show that the number of isoforms and their abundance can be predicted by a simple stochastic noise model that takes into account two factors: the number of introns in a gene and the expression level of a gene. The results strongly support the hypothesis that most alternative splicing is a consequence of stochastic noise in the splicing machinery, and has no functional significance. The results are also consistent with error rates tuned to ensure that an adequate level of functional product is produced and to reduce the toxic effect of accumulation of misfolding proteins. Based on simulation of sampling of virtual cDNA libraries, we estimate that error rates range from 1 to 10% depending on the number of introns and the expression level of a gene.
This is a controversial topic. Some of us believe that alternative splicing in human genes is not particularly widespread and most of the data can be explained as errors in splicing. Others believe that the data is real and most human genes produce multiple transcripts with different biological functions.

It doesn't matter so much which side you pick. What matters is that you understand science well enough to know that the data and the conclusions are disputed. What this means is that you cannot just assume that >90% of human genes are alternatively spliced and use this "fact" to bolster your case for Intelligent Design Creationism.

I'm tempted to say that Jonathan M is "... out-of-date with the literature by about ten years!" but that would be unkind.

Melamud, E. and Moult, J. (2009) Stochastic noise in splicing machinery. Nucleic Acids Res. 37:4873-4886. [doi: 10.1093/nar/gkp471]

Pan, Q., Shai, O., Lee, L.J., Frey, B.J., and Blencowe, B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008 Dec;40(12):1413-5. Epub 2008 Nov 2. [doi:10.1038/ng.259]

Tress, M.L., Martelli, P.L., Frankish, A., Reeves, G.A., Wesselink, J.J,, Yeats, C., Olason, P.I., Albrecht, M., Hegyi, H., Giorgetti, A., Raimondo, D., Lagarde, J., Laskowski, R.A., López, G., Sadowski, M.I., Watsonk J.D., Fariselli, P., Rossi, I., Nagy, A., Kai, W., Størling, Z., Orsini, M., Assenov, Y., Blankenburg, H., Huthmacher, C., Ramírez, F., Schlicker, A., Denoeud, F., Jones, P., Kerrien, S., Orchard, S., Antonarakis, S.E., Reymond, A., Birney, E., Brunak, S., Casadio, R., Guigo, R., Harrow, J., Hermjakob, H., Jones, D.T., Lengauer, T., Orengo, C.A., Patthy, L., Thornton, J.M., Tramontano, A., and Valencia, A. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc. Natl. Acad. Sci. USA 104:5495-5500. [doi: 10.1073/pnas.0700800104]

Zhang, Z., Xin, D., Wang, P., Zhou, L., Hu, L., Kong, X., and Hurst, L.D. (2009) Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay. BMC Biol. 7:23-36. [doi:10.1186/1741-7007-7-23]


Anonymous said...

It's off topic but are you aware of the fact the the IDiots of the DI will present their new movie in Toronto next Saturday with Paul Nelson talking about "“Intelligent Design: the Beauty and Design of Butterflies”? Additional talks will be:
"The Assumptions of Atheism” by Bruno Cordovado

“Are Humans Just Like Animals?” by Geoff Francis

“The Human Genome – Evolution’s Achille’s Heel (Ascent or Descent?)” by Richard J. Van Seters

“Be Ready to Give Answers” by Christine Williams

“The Universe: By Design or By Chance” by Don Wallar

The DI's announcement:


Anonymous said...

...most of the transcript are junk RNA due to accidental transcription...

'Stochastic' would be a more accurate description of this transcription than 'accidental'. The opposite of 'by accident' is 'by design', so when you use the term 'accidental' you are speaking your opponents' language. It is only a partial win if you convince the audience that instead of all of the genome being intelligently designed, only some of it (the non-accidental part) is.

Larry Moran said...

anonymous asks,

It's off topic but are you aware of the fact the the IDiots of the DI will present their new movie in Toronto next Saturday with Paul Nelson ...

Yes. I'd go but I have more important things to do next Saturday, like attend a wedding.

Larry Moran said...

anonymous says,

The opposite of 'by accident' is 'by design', so when you use the term 'accidental' you are speaking your opponents' language.

The opposite of "by accident" is "regulated" or "controlled."

Anonymous said...

Most of the useless DNA is not in introns. Still, how does that explain why some onions need so much more alternative splicing? Worse. if we could have >90% alternatively spliced genes, why would some onions need >500% alternatively spliced genes?

Anonymous said...

The opposite of "by accident" is "regulated" or "controlled."

No, it isn't. The opposite of "by accident" is "on purpose". Anthropomorphizing the biology with terms like "by accident" is inconsistent with the broader point you are trying to make (with which I agree), namely that there is no designer and no purpose, but rather impersonal physics, chemistry, and the natural laws (like evolution) that follow from these axioms.

M. Dionis said...

Anonymous wrote: No, it isn't. The opposite of "by accident" is "on purpose". Anthropomorphizing the biology with terms like "by accident" is inconsistent

Actually no. The only rigorous opposite of "by accident" is "not by accident". "On purpose" is definitely not the opposite of "by accident" because it does not cover a broad class of facts and phenomena which do not occur "by accident". Consider for instance the equality of Moon's rotation and revolution periods: it occurred not "by accident" but as a result of complex tidal interactions in the gravitationally coupled Earth/Moon system (the same holds for Mercury, BTW); most certainly, the stabilizing effect has nothing to do with any "purpose". Or you might notice that the Atlantic contours of African and South-American continental plates are basically mirroring each other: this is of course neither an "accident", nor someone's "purpose", but the result of a split which happened tens of MYA and whose trace is quite visible in the middle of the ocean. The falling rain water has the natural tendency to accumulate and flow in the valleys, on the steepest descent available not by accident/purpose but because of natural laws.
The very idea to insert a "purpose" in any scientific discourse about nature is an unsupported teleology and a very bad method to cope with natural facts.
As for another expression meaning the opposite of "by accident", I can't think at any simple accurate label out of the simple negation since it would require lots of additional explanations, it is still better to correctly assimilate the concept than assigning it a label.

Anonymous said...

Consider for instance the equality of Moon's rotation and revolution periods: it occurred not "by accident" but as a result of complex tidal interactions in the gravitationally coupled Earth/Moon system

Yes, but by this description, the "accidental" transcription under discussion is no accident either: it is the result of non-sequence-specific RNA polymerase binding, the thermodynamics of melting the DNA duplex in the relative absence of accessory proteins and the initiation of new RNA synthesis, etc, all of which are presumably 'deterministic' rather than 'accidental'. That is why I prefer the term 'stochastic' to describe this aspect of the behavior of RNA pol.

M. Dionis said...

Anonymous wrote: Yes, but by this description, the "accidental" transcription under discussion is no accident either: it is the result of non-sequence-specific RNA polymerase binding, the thermodynamics of melting the DNA duplex in the relative absence of accessory proteins and the initiation of new RNA synthesis, etc, all of which are presumably 'deterministic' rather than 'accidental'.

The word 'deterministic' is not really a good description of anything implying near equilibrium quantum mechanics (-> chemistry) at finite temperatures. One would rather use terms of probability (also "stochasticity" sounds fair enough).
Think about defects in crystals: at any non-zero temperature they have to exist (thermodynamics says that, their existence is "deterministic") but their characteristics as precise location and type are of course "accidental". My (hopefully educated) guess is that Dr. Moran used the word "accidental" to characterize the still transcribed junk DNA, while its very existence remains determined by natural laws at finite temperature.
Anyway, my primary aim was to point out that "accidental" & "on purpose" do not form a complete cover of the reality phenomena, so they cannot be used as opposite terms.