Friday, December 07, 2007

Marilyn Kozak, professional critic



I think every field needs a solid critic like Marilyn Kozak. We are talking about THE Kozak of the "Kozak consensus sequence fame". She has published a few papers on criticizing the field of internal ribosome entry sites (IRESs). Her lastest is still critical of the existence of viral internal ribosome entry sites which have not only studied for quite some time now but are used as molecular tools for expressing multiple genes from one mRNA. She is persistant. Here is an older response from some scientists in the field to some of her critisisms. Despite being perhaps frustrating to those in the field it is probably good to have such a dedicated (and famous) critic to point out shortcomings in the published data. I wish there was one in my field, at least just for entertainment purposes.


12 comments:

Anonymous said...

I have a very strong feeling she will be gradually vindicated on the "IRES" front over the coming few years - and starting soon.

Bayman said...

Anonymous,

Any particular reason, or just a vision?

I'd like to hear Kozak's reaction to a recent paper that characterizes cellular IRES in yeast. It pretty much seems to beat all the usual anti-IRES arguments.

"The disconcerting absence of shared or similar sequences
among putative IRESs (Baird et al., 2006) is sometimes excused
by postulating that IRESs might instead have a common
secondary structure. Baird et al. (2007) undertook a search for
new IRESs based on that idea. But the search started from a
flawed premise – the hypothetical folded structure proposed for
the XIAP IRES turned out not to be important for function –
and the search uncovered no evidence for a common structure
among cellular IRESs. The absence of structural criteria thus
allows almost anything to be called an IRES (e.g. Dorokhov
et al., 2002; Terenin et al., 2005)."


The newly-discovered yeast IRES consist of polyA tracts that directly bind poly-A binding protein which is known to stimulate translation initiation. Conceptually, this provides a simple mechanism for cap-independent ribosome recruitment, as PABP can bind to eiF4g which in turn can bind the 40S ribosome complex.

"Re-examination of many putative IRESs revealed cryptic
promoters or splice sites which undermine use of the dicistronic
test for internal initiation (Bert et al., 2006; Elango et al., 2006;
Kozak, 2005; Wang et al., 2005)"


The new paper used a cap-deficient, monocistronic reporter containing a 5' stable stem-loop to assay IRES activity. RNA encoding each reporter was directly added to cell-free extracts or live cells, thus promoter activity or splicing was irrelevant.

This was not done in a fraudulent way, of course; it was done by
adopting such weak criteria for recognizing IRES activity that
any sequence of interest could be called “positive.”


Several cellular 5' UTRs failed the IRES test in this paper, as did the reverse complement sequence of every single UTR shown to have IRES activity.

Will this new evidence be enough to convince Kozak?

Anonymous said...

Bayman,

A vision, I suppose, enhanced by some rumblings I have heard. That and the fact that so many IRES papers rely on creaky arguments, particularly the cellular IRES ones. Kozak has laid out those problems, as you know.

I'm not very familiar with the Doudna paper, but on brief glance it looks like pretty strong data. We'll know in time.

Bayman said...

Agreed the IRES and other cap-independent models are not perfect, but it certainly seems that we need more than the scanning model to explain a lot of the observations that have been reported. I'm intrigued if we are on the verge of hearing about a new, more satisfying model...

Bayman said...

My guess - it involves miRNAs and the RISC.

Anonymous Coward said...

Is there anything argonaut doesn't do? It's turning into the next p53...

K.W. Sherrill, Ph.D. said...

Having performed IRES research for years, I agree that Marilyn pointed out a number of legitimate concerns that have been echoed by others. However, after the bar was raised and many new, more stringent controls gave further evidence that IRESes really do exist, she still refused to believe. Mind you, she won't even admit that viruses (such as the picornaviruses) use IRESes, and this has been established for well over 15 years! In our lab, we considered ourselved to have really become "somebody" in the field of IRES research when Kozak comented on our papers in her reviews. In the end, she was reduced to "splitting hairs" because she couldn't find any significant fault in the controls we used. By the way, THERE IS NO HCV IRES. Our lab proved this to be nothing more than a potent splice acceptor (using RT-PCR techniques). See our paper from 2004 in RNA Journal. Holcick has since dropped the whole thing.

By the way, we once got Marylin DQ-ed from a review of my manuscript because her review was mean-sprited, ad homenim, and just plain lacking in coherency. She was so antisocial, she lost her funding and her lab was taken away. Now she's been reduced to writing embittered reviews. I feel bad for her.

Bayman said...

Irrational or not, there's at least something to be said for putting your criticisms out there in the literature with your name on them. A step up from sandbagging other people's ideas behind the shield of reviewer's anonymity. Although - what's better - "irrational" or unfounded criticisms one takes credit for or valid criticisms given anonymously? Is either more useful? I dunno...

K. said...

I was lucky enough to take a class with Marilyn Kozak last year.

I'd known a little bit about IRES's, and in fact had been starting to design uses for them in my own lab work. One of the first things we did in Kozak's class was discuss the evidence for IRES's.

At the end of the end of the discussion, I agreed with her that there is no solid evidence for IRES's. She was not saying that they don't exist, however, the "evidence" for them looks incredibly sloppy. It should look sloppy to anyone who has not convinced themselves that they definitely exist, and won't see anything else.

In terms of Marilyn being "antisocial", she is anything but. How many times have you read an article in a journal, looked at the results, and gone, "they published THIS crap?!" I know I do it on a regular basis, and I don't have half the reasoning capability and background that Marilyn does. Being asked to review papers written by people who should know better making unfounded conclusions from their data would probably frustrate many people.

I think people who don't appreciate Marilyn's criticism are close-minded individuals who shouldn't call themselves scientists. It's one thing to not agree with what she says, but to get annoyed at her for raising any questions or bringing up any criticism is lame. What's the point of peer review except to get feedback and criticism?

And Bayman, was there anything in your comment that was supposed to convince us of the presence of IRES's? The presence of poly A tracts? That's it?

Bayman said...

@K.
And Bayman, was there anything in your comment that was supposed to convince us of the presence of IRES's?

Not really. I pointed out the Doudna paper which used a number of systems to demonstrate IRES-mediated translation of yeast mRNAs, and then went on to give evidence for a molecular mechanism (involving PABP, among others) by which ribosomes could be recruited to IRESs, bypassing the need for a 5' cap. You should read it for yourself and see if you can write off their experiments using the classic Kozak anti-IRES arguments.

Whether you believe the evidence for cellular IRESs or not, it's pretty difficult to deny the existence of viral IRESs. As far as I know Kozak is the only molecular biologist out there still doing this.

C said...

KW Sherrill, Ph.D.,

Marilyn Kozak has been a _tremendous_ benefit to the field of translation, and an indispensible voice of rationality in the IRES field. I suppose some people do not like her personally - or for personal and perhaps petty reasons - but in my view her reviews have been uniformly reasonable, very well-argued, and brave. It's as if we should all just sit back and agree with whatever the "Godfathers" of bioscience, like some of those who have been for years peddling crappy data on cellular "IRES's," tell us. Kozak is a national treasure. Next year, she and Douglas Prasher should get a Nobel.

STGrahamer said...

Hi,
since you wrote a post about her, do you know what has become of Marilyn Kozak?