I think the crowd was much entertained and perhaps educated by the whole discussion, but the scientific minutae is hard to decipher for us lay-types.

… which is why no one “piled on” in the discussion.

Reed’s book has some items in addition to the UV issue that I find most interesting. The concept of the “composite” mayfly, and the “maybe” seduction.

I think you’ll like the book on a number of levels – as I did. The UV photography and color plates are most educational. Our sport is often guilty of embracing “new” with too much fervor, rather than waiting for the follow on detail that shows which colors really benefit – or have a markedly different appearance in that spectrum.

I found it a fast, enjoyable read – that didn’t require a PhD to understand many of the concepts Reed was illuminating, UV or otherwise.

Reading it again I find it somewhat disappointing that the thrust of the discussion bogged down in the detailed scientific methodology (neither of us I fear really qualified to criticize) rather than the functional significance of any putative UV ability. My fault for playing catch-up.

I’ve orded the book and when I have read it and received some replies from researchers in the field I’ll have another go at pulling it all together over my way.
many thanks again
Eccles

“I wouldn’t have a problem with the techs used in 2007. Primers is not an issue… What they appear to be doing is using specific probes (riboprobes) to identify the presence (expression) of their target opsins in retinal sections (primers used to amplify cDNA [from mRNA]). Done this before myself (to find the location of microsporidians in tissue sections). The difference between the two papers seems to be that in the 2007 paper the riboprobes were decreased (minimally) in length – they are f**king [MY EDIT - SORRY HE IS A BRIT FROM NORTH LONDON WITH A PARTICULARLY COLOURFUL WAY OF EXPRESSING HIMSELF] long still. I would have like to have seen some sort of diagram showing primer/probe binding sites, but strongly suspect that all is above board: the probes would still be highly specific and therefore the results comparable.”

My colleague does this for a living, has worked on a number of different systems (one of which he refers to) in a number of different labs and has published numerous papers using PCR and rt-PCR. I asked him specifically to compare the Allison et al 2003, 2006 and Cheng & Flamarinque 2007 papers to see if the slight (“minimal” as he puts it) change would make any difference. I also asked him whether if he was reviewing the C&F paper he would have any problem with the methodologies more generally. Clearly he has none. His assessment, the editor handling the paper for JEB and the reviewers for JEB had no problem with it. I would go with these experts then.

You seem to selectively quote the section about labelling and proteinase K. In the next paragraph they amply demonstrate that this is not an issue.

Your detailed comments about microspectrophotometry also require examination which I will have to get to later.

Your suggestion that I think “C&F conclusions must be right, not because of their methods or conclusions, but because no one had bothered to refute those conclusions” is a misrepresentation. I am saying their findings are likely to be right because the methodologies are appropriate (see above for an example)and the conclusions they draw from the results obtained by these methodologies do not seem unreasonable. The editor of JEB and the reviewers of the paper agree else it wouldn’t have been published. The fact that there has been no response (and many journals allow “reply to..” or “comment on …” from the authors who are being critiqued in a paper the journal is about to publish) suggest scientists still studying in this area have little problem with C&F 2007.

Can’t do more now, later.
aye

As displayed above, the world of science, optics, and genetics can be a hideous, contentious and baffling subject.

Reed’s book translates this scientific minutae into plain text that is easily absorbed by the average angler.

Well, that was entertaining and I see that our minds run in parallel — which means they never meet

Once you have taken the time to read the book, do get back to me through my website – http://www.overmywaders.com – with your assessment of my work. Until then, have a very happy holiday.

Warm regards,
Reed

So, according to these Australian researchers, in two studies they performed MSP (microspectrophotometry) which failed to identify the SWS1 cones. MSP is the procedure used by C&F 2007.

In 2001, Hawryshyn, Haimberger and Deutschlander presented a paper on application of MSP using CCD’s rather than visual. ["Microspectrophotometric measurements of vertebrate photoreceptors using CCD-based detection technology" - JEB 2001] so they were aware of the limitations of the MSP when asking C&F to retest differently in 2006.

Indeed as early as 2001, N.S. Hart wrote – “The main drawback of the microspectrophotometric technique is that measurements are made from only a fraction of the total photoreceptor population and it is possible that some photoreceptor types can be overlooked.” (“The Visual Ecology of Avian Photoreceptors” 2001)

and now for something quite new (pub 2009, online dec 2008):

“Microspectrophotometric measurements are notoriously difficult in the UV region of the spectrum (300–400 nm)due to a number of factors, including low UV transmission by most of the microscope objectives used, low UV
content in the measuring beam and because the effects of optical aberrations and scattering by the tissue are more profound at shorter wavelengths. For both the starling and leiothrix, the absorbance spectra of their UVS pigments have poorly defined peaks that would have introduced error when calculating the kmax. The predicted kmax values for these species’ UVS pigments are more similar to
those obtained from other, higher quality UVS visual pigment absorbance spectra (Table 1) and, given the low variation seen in UVS visual pigment kmax in many animals, may well represent the true situation in these bird
species.” from “Assessing the use of genomic DNA as a predictor of the maximum
absorbance wavelength of avian SWS1 opsin visual pigments” by Anders Odeen, Nathan S. Hart, Olle Hastad – J Comp Physiol A (2009)

Eccles, it is not the onus of any one person, or any one team, to challenge the results of a peer-reviewed study. The entire scientific community simply plods forward and speaks quietly, each in their way. Your assumption that Allison et al, should devote their time, money, and energies to disprove C&F 2007 is fallacious. It is the invisible cat fallacy – “There is an invisible cat on that chair.” “I don’t see a cat.” “That proves my point, you can’t see an invisible cat.”

Are we done with this yet? My advice to you remains the same – buy the book, enjoy it, examine all my premises for evolution of UV vision in trout, wander through my theories of vision vs perception, and then tell me what you think.

Warm regards,
Reed