- For me in this particular episode the emotional parts got in the way of the scientific explanation.
-  questions I would have asked weren't so it didn't sink in 
- principly is measuring acidity for oceans really as easy as reading it in a Can of Coke ?

more info below if someone has time to read

You Said .. "The material in the SS was based on published research - starting with 
the cover story in the journal SCIENCE. We can't help what people 
discover - that's what's going on in nature.

Corals and shellfish are less able to make exoskeletons now (and in 
future) because of acidification of sea water."  
- Thanks, I accept that hypothesis, but feel I wasn't given enough evidence and of future possibility of catastrophe. 

Acidification : The word  acidification was mentioned twice in the script so not it registrying in my brain was half due to my own dullness, but I feel the process was skimmed too quickly.  I see you covered it in detail in 2005, 
- but  this time if questions were asked about the process which should have been, then it would have sunk in.  

What I got was this : There's been a lot of CO2, it's made the oceans acidic, it's killed the coral, if it contines 
like this they'll be all dead by 2050. ...
I'm too tight in money and time to read the AAS Science Magazine article myself, but I imagine it said more than that.
450ppm  blah blah etc 
=========================
Lobster Recovery
You said .. "Up to now lobsters have flourished a) because fish are absent b)
because areas have been well managed to encourage them. But they too will have 
shells affected. .... No contradiction."

CONTRADICTIONS happen, but that doesn't negate the hypothesis in the long run.
- For the last 10 years the evidence of the "CO2 acidification leading to catastrophe hypothesis" in crustaceans stock numbers is contrary.
In fact contradiction in nature is OK as it conforms to full colour rules, not necessarily the black and white rules we would like it to.
, so the hypothesis is certainly possible. If todays trend was that they we declining  it would seem to strengthen the hypothesis and I am sure the presentation would have been even more earnest. 

There is a difference between saying something has happened and saying why.
Yes, the questions asked on the lobster fishery were excellent. He expressed surprise at the rapid increase in lobster, but he wasn't in a position to say why
- " there's still no real firm understanding on why this big increase has happened." 
When pushed he did say it could be lack  of predators, but had no figures , (I guess It  could be other things e.g. that local fisherman unable to catch lobster  have switched to catch more of the predators ) Any theory without numbers isn't worth very much.

=======================
More Notes
I note 
-1. that the podcast has a written introduction mentioning acidification so some listeners were already primed. 
-2. that it has been mentioned it your other programmes and that you didn't mention this as you normally do. 
-3. Some progs like BBC Health Matters have good  1 minute fact-bites to refresh the listener minds, before the main story and they manage this without dumbing down)

The contradiction is in the mind of the listener at home. You've just been told that in the last 10 years corals have dramatically declined and corals and crustaceans are heading for catastrophe. Then you told that today in fact crustaceans are booming.

- As you say you email "that's what's going on in nature". Coral has been dying all around the world you report, wheras lobsters have recently boomed. 

You might be interested in future reports
Call for papers on Ocean Acidification in the Journal 'Coral Reefs'
http://coral.aoml.noaa.gov/pipermail/coral-list/2007-March/004211.html
Although I don't like her un-open minded way of phrasing the invitation, seeming to be only interested in papers that prove the theory.

No SS website link to the article
It would be good, but also promoting a commercial magazine.  http://www.sciencemag.org/cgi/content/summary/318/5857/1712

I notice that BBC report it in their now-typical unsober style : "Acid oceans spell doom for coral"

http://www.sciencemag.org/cgi/data/318/5857/1793b/DC1/1 pdf of AAS Science radio show but drops mention of reefs

http://www.iucn.org/dbtw-wpd/edocs/2006-042.pdf
from pdf year 2006: Consequently, much controversy exists within
the science of coral reefs and climate change,

discussed before http://www.abc.net.au/rn/scienceshow/stories/2006/1644874.htm
660 ppm was the limit then 

http://www.abc.net.au/rn/scienceshow/stories/2005/1406402.htm
does explain the process completely

The idea is that by artificially "fertilising" phytoplankton at the ocean surface, it might be possible to stimulate the take-up of CO2 - locking away some of the extra CO2 in the atmosphere that is believed to be forcing global temperatures to rise.

If increased acidity begins to hinder the natural removal of CO2 from the atmosphere, however, then we may lose one opportunity to reverse any damage induced by human activity. 

in 1997 the same journalist wrote 
ECOLOGY:
Brighter Prospects for the World's Coral Reefs?
Elizabeth Pennisi

Just a few years ago, scientists sounded the alarm that coral reefs around the world were seriously ailing. But now, some coral reef biologists are beginning to suspect that reefs may not be quite as widely imperiled as they once thought. Increasingly, researchers think that the decline may be local or regional rather than global in scope. Although reefs in Southeast Asia and the Caribbean are crumbling, for instance, most in the Pacific and Indian Ocean appear to be in good health.

Read the Full Text

what a surprise just before the international year of the reef

http://www.sciencemag.org/cgi/data/318/5857/1793b/DC1/1 pdf of radio show but drops mention of reefs

from pdf year 2006
http://www.iucn.org/dbtw-wpd/edocs/2006-042.pdf
Consequently, much controversy exists within
the science of coral reefs and climate change,
for example concerning the Adaptive Bleaching
Hypothesis or the effectiveness and necessity
of coral transplantations. Research into issues
such as the mechanisms of adaptation and
acclimatisation of corals, the importance of
connectivity between reefs or the effects of local
water movement on bleaching resistance, has
answered but also created many questions. These
and other scientific gaps in knowledge have been
briefly addressed in this paper. For example,
future opportunities in fields of research such as
coral reef monitoring and economic valuation have
been discussed. Furthermore, a brief overview of
global initiatives working on coral reef resilience to
climate change has been presented.
Overall, it is clear that climate change and coral
reef health are inextricably linked, and that
research should be coherent and co-ordinated
in order to create more efficient solutions to the
complex management challenges that will arise.
There is thus clearly a need for coral reef science
and management to be included in strategies that
deal with the overall adaptation of human society
to predicted climate change. With the increasing
attention coral reef resilience is receiving from the
marine science community, there is hope that this
paradigm will enhance our general knowledge of
ecosystem resilience to climate change, and that
the lessons learnt studying it will be applicable on
broader scales.

from http://www.coralcoe.org.au/news_stories/climatechange.html
10 April 2007
REEF 'AT RISK IN CLIMATE CHANGE'
Temperatures only a degree above the current summer average can cause mass bleaching of corals
A further concern has been the dramatic emergence of coral diseases, some of which have increased in observed area by 500 per cent in the past decade.

- The greatest concern, Prof. Hughes and Hoegh-Guldberg say, is ocean acidification. The oceans have so far absorbed over a third of all the CO2 emitted by human activity into the atmosphere, making the ocean slightly more acidic and significantly reducing the concentration of carbonate ions. 

Palau recovered from damage from a warm summer in 1998