Blog

The MPA backlash has officially begun

Two new essays on the potential downside of MPAs – especially “super-sized MPAs”  - came out this week.

Super-sized MPAs and the marginalization of species conservation – by Nick Dulvy in Aquatic Conservation  download PDF

Environmental cost of conservation victories – by Ray Hilborn in PNAS  download PDF

For full disclosure, I was once a strong supporter of MPAs (and marine reserves in particular) and still am in principle; the problem is they often don’t work (and worse) in the systems I work in (coral reefs mainly in developing countries).

Ray’s piece first. Ray has been a vocal critic of MPAs for a long time.

In the United States, the Papahanaumokuakea Marine National Monument in the NW Hawaiian Islands became the first large-scalereserve closed to fishing in 2006 (1). This reserve is 90% the size of California and was followed by the Pacific Remote Islands Marine National Monument, about half the size of California, in 2009 (2). In total, the United States has established MPAs 19-times the size of California or roughly the area of the Continental United States.

These and other “super-sized MPAs” are widely celebrated as major conservation victories.  But are they? I really don’t think so but for different reasons than Ray, who is mainly concerned that they will simply displace fishing to other place (primarily to poorer nations):

Even if Australia never again caught a single fish, Australians would still be able to eat all they want or can afford. However, most of those fish would come from parts of the world where fisheries are poorly managed or from aquaculture in the developing world, rather than from well managed Australian fisheries.

Jay Stachowicz had this to say about that:

Couldn’t Hilborn’s critique be applied to fishery management too? If we restrict fishing locally with traditional fisheries management that Hilborn frequently advocates, that just means people will go elsewhere to eat fish. Exactly the point of your “Let us eat other peoples fish” response to his NYT op ed.  Maybe he actually internalized some of that critique?

I see Ray’s point.  Yet I can think of several counter arguments to his concerns about the displacement of fishing caused by MPA implementation:

1) Fishing in some of the “super-sized MPAs”, especially the Papahanaumokuakea MNM, was very low before protection.  Although it is possible that in the absence of protection, fishing pressure would have increased.

2) Poaching and poor enforcement is so common in many of the MPAs I work in (mainly in the Caribbean and the Galapagos) I wonder whether they really effectively discourage local fishing.  (Although some clearly do.)  In fact, I suspect many MPAs attract and concentrate fishing pressure.

3) Spillover effects could or would prevent the need for fishery displacement – if by locally closing 20% of an area to fishing the net productivity of the fishery remains constant or is increased, this clearly would not lead to displacement (the key though is the presence of a meaningful degree of spillover).  (And spillover is one reason fishermen seem attracted to fishing near MPAs)

4) The proportion of no-take reserves and highly restrictive MPAs of the whole ocean, is still tiny.

As Jay pointed out, Ray seems to have adopted my related argument about fisheries displacement, which I outlined (ironically) in response to Ray’s NYT op ed “Let us eat fish”, in which he argued American fisheries have recovered from overfishing and thus we Americans should eat more fish.  I disagreed:

By arguing we should eat more fish, what Ray is really saying is that we should be eating more of other people’s fish. In 2009, NOAA reported that 84% of the seafood consumed in the US was imported and this figure is growing.

I am really psyched that Ray seems to have accepted my argument and I share his growing distrust of MPAs. Yet I think his displacement argument is a bit different from mine. Ray is using the displacement theory to argue against local fisheries restrictions where I am arguing that an increase in seafood consumption by rich nations would merely increase fishing (and fish farming) intensity elsewhere.  Also, Ray is focused exclusively on open ocean fisheries management in the US, Canada, and Australia.  My concerns are mainly about overfishing in the impoverished coastal topics.  So to be fair, we have very different perspectives on all of this.

Now on to Nick’s piece.  Nick Dulvy has as much fish and ocean conservation cred as anyone.  He has been working in marine ecology and conservation for decades, he has published some highly influential papers on fisheries and reef conservation (such as this one), and he co-chairs the IUCN shark specialist group.  He takes ocean conservation seriously.

Nick starts by framing the modern marine conservation movement, I think accurately;

Marine species conservation died prematurely early in the new millennium before it had a chance to grow and flourish. The revolution happened; the world turned and moved on to managing higher-order ecological processes and services. The revolutionary conservation and research agenda of the new millennium has at least four interrelated themes: super-sized marine protected areas (MPAs; Wood et al., 2008; Pala, 2013), the ecosystem approach to fisheries management (ICES, 2005), ecosystem services and the economic valuation of nature and the poverty alleviation paradigm (Millennium Ecosystem Assessment, 2005; Sachs et al., 2009; Roe, 2013), plus the outlying game-changer of climate change (Hoegh-Guldberg and Bruno, 2010). These themes all involve higher-level aggregate attributes and values of biodiversity.

Many marine protected areas are not sanctuaries in the sense that the animals inside are safe from fishing (and other damaging activities).

This is another pet peeve of mine: people, e.g., Ray, equating MPAs with marine reserves.  And ignoring for the moment the enforcement issue, some marine reserves do not restrict harvesting and should instead be called marine protected areas.  For example, the Galapagos Islands are in what is called the “Galapagos Marine Reserve” yet legal fishing is widespread and intense there.  The Galapagos is as overfished (legally) as anywhere I’ve ever been (well, except for Jamaica).   The no take reserves are tiny areas of shoreline (none in open water), most are poached intensively, and those that are not are practically inaccessible.  The whole thing is a fraud and everyone (tourists, scientists, conservationists) thinks the marine life in the Galapagos is somehow protected and pristine, just because there are some sea lions, turtles, and iguanas (stuff nobody wants to eat).  The edible and harvested species (such as lobster, pepino or sea cucumbers and “Bacalao” sailfin grouper Mycteroperca olfax) are highly depleted and quite rare at most sites Iv’e been to.

We assume that paper parks have no cost to conservation, is that true?

Is a paper park better than no park? Is a paper park better than using limited resources to tackle other conservation issues? One possible risk is that the paper park alone is perceived to be a conservation success, in terms of protecting species and sustaining fisheries (Rife et al., 2012).  By analogy to the enabling behaviour of ecological restoration, I wonder whether unenforced MPAs may be enabling continued overfishing by precluding fund-raising for effective species management and conservation.

I agree there must be huge costs, e.g.;  1) zillions of dollars and untold effort going into ineffective conservation strategies,  2) the sense of complacency we get when we think a place is “protected” such as the Galapagos: whew, at least somebody took care of that problem…

Nick ends with a section titled “But whatever happened to evidence-based species conservation?” This really is the rub isn’t it. In theory MPAs and marine reserves could do a lot, both for species and “higher-order ecological processes and services”. And there certainly is evidence that they do, but it is mainly from well-funded and managed reserves in the US and Australia – places not exactly representative of most of the ocean world. So why are we so focused on implementing them in places where we know they won’t work?  Or at the least, why don’t the organizations implementing them, do the science to figure out if they are effective, and if not make policy adjustments, etc.

These new essays by Hilborn and Dulvy are just the latests in a growing chorus of concerns and criticisms about the role and realized benefits of MPAs in ocean conservation.  Helen covered a similar piece by Mora and Sale (2011), again arguing that MPAs have been ineffective in preventing or reducing marine biodiversity losses.  There is also the influential piece in PLOS Biology by Cote and Darling (2010), which argues that MPAs could actually make coral reefs more susceptible to global warming.

Yet, marine reserves do not reduce the frequency or intensity of thermally induced coral bleaching [9],[14],[46] or bleaching-induced coral mortality compared to unprotected areas [47][49]. In fact, thermal stress can cause proportionally greater coral mortality of protected than unprotected corals [19],[47][49]. This effect is probably due to the different coral species composition between protected and unprotected sites. Indeed, the higher abundance of thermally sensitive corals, such as Acropora and Montipora, within marine reserves is associated with the increased susceptibility of protected coral assemblages to climate disturbances [19],[47],[48].

I am happy this topic is being discussed, out in the open (finally).  Im curious whether NGOs are listening.

Preprint servers: what are they good for?

Philippe Desjardins-Proulx and colleagues have a nice paper up in PLOS Biology (yes, it is PLOS now and no longer PLoS) The Case for Open Preprints in Biology.  See their Box 1 - Preprint Server Roundup – for an excellent overview of the most popular preprint servers.

Public preprint servers allow authors to make manuscripts publicly available before, or in parallel to, submitting them to journals for traditional peer review. The rationale for preprint servers is fundamentally simple: to make the results of research available to the scientific community as soon as possible, instead of waiting until the peer-review process is fully completed. Sharing manuscripts using preprint servers has numerous advantages, including: 1) rapid dissemination of work-in-progress to a wider audience; 2) immediate visibility of the research output for early-career scientists; 3) improved peer review by encouraging feedback from the entire research community; and 4) a fair and straightforward way to establish precedence.

I applaud the promotion of open preprints for Biology and the life sciences in general.  I think the paper provides a nice overview of the history, benefits, and use of preprint servers.  I agree, a main benefit is to get your work out there quickly, while it bubbles through the long peer review process.

However, another key value of servers like figshare and peerj preprints is as an end point for contributions to the scientific literature.  Most contributions to figshare, arXiv, etc., will never be submitted to “formal” peer review or published elsewhere.  And there is nothing wrong with that.  This is how preprint servers can help free up our clogged peer review system.  For some kinds of articles (e.g., opinion pieces), pre-publication peer review (PrePPR) doesn’t really seem to make sense.  If a preprint server had been available three years ago for a paper we just published at PeerJ Preprints, we would have gone directly there, saving time for everyone, and getting our ideas out much faster.  Another outlet is obviously blogs, like SeaMonster, but preprint servers have the important benefits of being archived (professionally) and citable.

One thing that surprised me about Desjardins-Proulx et al was their views about PrePPR being “formal validation”.  Far to much junk science gets through peer review, even at the top science journals, to call PrePPR “formal validation” with a straight face.  For a sampling of posts about the many problems with peer review go here, herehere, here or here.

“A preprint is simply a document that allows ideas to spread and be discussed, it is not yet formally validated by the peer-review system.”

Validation is a process that begins with the authors themselves, their getting feedback from their colleagues, from reviewers and then readers post-publication.  It isn’t a black and white switch that gets flipped once a paper is accepted by a journal.  So while I agree, a preprint isn’t “formally validated”, nothing in science is.  We don’t use stamps of approval in science.  We dissect, debate, and examine findings and ideas, pretty much forever.

Where greenhouse gases come from

Ecofys released a new, nice graphic depicting where greenhouse gases come from:

emissions chart

It generally seems accurate and they say it is based on 2010 data, although I have not been able to find their methodology.  This chart updates an important, earlier one from WRI here.  In 2000 18.2 % of emissions were attributed to land use change (mainly burning trees).  WRI’s updated 2005 version reduces that to estimate 12.2% which is more in line with current (2011) estimates by the global carbon project of 9%.  At 15%, I think this value in the Ecofys chart is probably too high.  Yet note there are large error bars around these estimates (there is a fair amount of uncertainty).

As the chart below (from Carbon Budget 2012) indicates, the absolute and relative volume of carbon emissions (CO2) from deforestation have been declining, but the relative drop is far more substantial and is due to the massive growth in emissions from other sources.

Screen Shot 2013-05-31 at 5.46.16 PM

How to extract lionfish otoliths

Do you need to know how to get ear bones out of lionfish? Or are you just curious to know what the inside of a lionfish’s head looks like? Either way check out this film shot on location in Abaco, Bahamas featuring the crack lionfish catching team, Serena Hackerott and Katie Dubois.

Otoliths are teeny tiny bones inside fish’s heads that act kind of like a biological version of the accelerometer inside a smart phone or a wii handset – they detect gravity and acceleration, so essentially help the fish figure out where it is and where it’s going.

And you can find out all sorts of cool things from fish otoliths. Like trees, you can count their growth rings and work out how old the fish was. Otoliths can also reveal a whole lot of things about the water that the fish swam through. And they also preserve really well in the fossil record and have been used to figure out what people thousands of years ago were eating.

Read out more about Serena’s work with lionfish  at her guest post for Seamonster. And here too including some awesome footage of her catching lionfish.

Sea level rise in North Carolina

This is a post for my Marine Ecology class.  We covered estuaries yesterday and will get to climate change impacts on the oceans soon.  Sea level rise due to greenhouse gas emissions is one of the main ways climate change is affecting us Tar Heels.  (And yes, this will all be on the final exam)

Read about last years Sea Level Rise saga (AKA the first of many National Embarrassments brought upon us by our state legislators) here.

1) Sea level fluctuates naturally by 10s to 100s of meters but has been relatively stable for the last few thousand years. Changes in sea level are controlled in large part by atmospheric temperature, which in turn controls how much water is locked up on the continents as ice. Cool temperatures = lots of ice and low sea level. When the earth’s temperature increases (by just a few degrees C), water from the melting glaciers drains into the oceans and increases sea level – sometimes very rapidly and by tens of meters.

The graph below depicts global change in sea level since the end of the last “ice age” or “glacial period“. During this 15,000 year period, sea level has increased by a whopping ~125 meters or ~400 feet! You can also see some periods when the earth was transitioning to an interglacial period when sea level rose very rapidly, such as during “Meltwater Pulse 1A” when it appears to increase at least one to two feet per decade. These rapid increases in sea level are – as you might have guessed – caused by the rapid melting of glaciers. So the link is real and far from subtle; the earth warms slightly, the glaciers melt, and sea level rises.

Figure 1. This figure shows sea level rise since the end of the last glacial episode based on data from Fleming et al. 1998, Fleming 2000, & Milne et al. 2005. (Source and details)

During natural glacial cycles global temperature trends are influenced by a number of factors including slight changes in the earth’s obit around the sun and atmospheric composition. However, this time the earth’s warming isn’t due to an increase in heat coming in from the sun, but instead because greenhouse gases are letting less of that heat back out, i.e., the greenhouse effect.

2) Greenhouse gas emissions are causing sea level to rise (Fig. 2) via ”thermal expansion” (warming a liquid increases it’s volume) and by melting mountain glaciers. Until human activities increased the concentration of greenhouse gases in the earth’s atmosphere, global sea level had been relatively stable for several thousand years (which can be seen in Fig. 1 above and with greater detail here).

(more…)

PeerJ Awesomeness

Screen Shot 2013-05-28 at 10.05.08 PM

I’m totally smitten with PeerJ.  A scientific journal.  Yes, I’m am a geek.

But this isn’t just any journal.  It is open access, extremely fast, fair, lets authors retain copyright, publishing costs are low, and the layout of the online and PDF articles and of the submission portal is amazing – elegant, modern, and roomy. Going from the clunky interface used by the evil Elsevier journals is like leaving a PC for Mac.  Dumping your Blackberry for an iphone 5.   Ahhhh.  I finally found science nirvana.

Elegant and Functional: this is what the authors portal looks like.  The editors “dashboard” is even cooler.  It is incredibly easy to find, assign and manage reviewers and make decisions.Screen Shot 2013-05-29 at 6.21.53 AM

Screen Shot 2013-05-29 at 6.23.37 AM

The downloadable manuscript PDFs are also clean and modern (e.g., download Williams et al 2013 here).  Large font.  Single column layout. Pretty color graphics (at no extra charge!).  Nice.

Fast and Efficient: The first paper I handled as an editor, Williams et al. 2013 was submitted on 22 April 2013, accepted on 12 May 2013, and published 28 May 2013.  Five weeks from submission to publication!  Amazing.  The reviewers came in in under two weeks and the authors revised the manuscript and resubmitted it in a day or two.  I remember the first review for my first Ecology paper took nine months!  The whole process took well over two years. And for most journals, this is still not too far off the norm.  I also appreciate the efficiency of minimal email communication with the home office, both as an editor and author.  Even at PLOS One, submitting & publishing a manuscript requires enough email correspondence to fill a book. Very Wasteful.

Open peer review: Open science needs to mean more than simply open access and data sharing.  It must include open peer review.  PeerJ is on board and will share the entire review history of papers, including the reviews, correspondence from and with the editor, rebuttal letters, etc.  This is nothing short of revolutionary in academic science – until now, this was all secret and hidden from view.

Reviewers are encouraged to forgo anonymity – which many seem to be doing.  This changes the whole dynamic.  The reviews I have seen at PeerJ, both as an editor and author, have been objective, friendly, and helpful (which is rarely the case when reviewers are anonymous).

OK. I’m an academic editor for PeerJ, but I actually use the product too!  We published PrePrint #19 here and I just got the reviews back from the second paper I submitted.  I’ll blog about that later today.

It’s time for scientists to tweet

Our new lab post doc @emilysdarling has a great piece in The Conversation about the use of twitter in the life and work of a scientist:

Social media is no longer a new thing. But to scientists it still might be. There are few who are starting to take advantage of social media for professional reasons. What can other scientists learn from such use? What are the benefits and limitations?

To investigate this, three colleagues and I looked at some concrete examples. Among the commonly used social media, the 140-character microblogging service Twitter has been popular. We decided to survey 116 marine scientists that actively tweet to understand the role Twitter plays in the lifetime of a scientific idea – from birth to dissemination.

Here is what we found: Twitter can move conversations from the university lounge to a much larger network of scientists on social media. For example, a scientist’s Twitter following can act as a virtual department to spark and share new ideas. As shown in the graphic below, 55% of the Twitter followers of those surveyed consisted of scientists. Tweeting new ideas to other scientists can push ahead “open science in real time

Scientists can also use Twitter to communicate far beyond the ivory tower of academia. For example, the remaining 45% of the scientists’ followers included people from the media, non-governmental organisations and the general public. Tweeting links to new scientific papers can reach journalists who might cover the story. In fact, using social media to build a network of media followers may be a new public relations strategy for scientists.

Read the rest here

5s7w4kxy-1369490502

The coral reef baselines survey

“The tragedy of recent coral reef decline is that too few people actually know what coral reefs are supposed to be like, and too few of those who now study reefs witnessed what coral reefs used to be like decades ago.” (Peter Sale and Alina Szmant from the Reef Reminiscences Report)

I am fascinated by baselines – what the natural state of a community was, before people came along and starting mucking everything up.   Three colleagues and I recently published a paper about how difficult it is to determine or to estimate baselines (Bruno et al 2013 PeerJ Preprints).  We focused on the basline for coral reef macroalgae, but many of the same points would apply to all kinds of habitats.  You can get a very different answer depending on the approach you take.  

For example, the same has been found for whales and there is a controvery about which method should be used to set the baseline and thus conservation targets and whaling restrictions; molecular genetics, whaling records, fisheries models, etc. One thing we learned during our extended tour of the peer review system (3 years, 6 journals, 9 rejections) was that there is also substantial variability among scientists in what they think is natural.  Although nobody seemed comfortable coming out with a clear value, some seemed to support a very low macroalgal baseline of 0-3% (based on their experience in Jamaica in the late 1970s), while others seemed to lean towards 10 to 20 %.  

I often find it hard to nail down what my colleagues think about a given issue – in part because we are dispersed around the world with little face-to-face interaction.  Venues like the coral-list help fill that void, but like many social forums, it is dominated by a few dozen individuals and many other people are hesitant to share their views on it. To assess the opinions of the coral reef science community (including scientists, managers, students, enthusists, etc) about the baseline values for coral and macroalgal cover on the world’s reefs I set up a SurveyMonkey online survey.  I asked four questions: 

What is the Caribbean baseline for macroalgae? “Macroalgae” includes fleshy and calcareous species (e.g., Halimeda) but not turf or calcareous encrusting algae. What is Caribbean baseline for coral? “Coral” includes stony, scleractinian corals (not soft corals). What is the Indo-Pacific baseline for macroalgae? What is Indo-Pacific baseline for coral?

I was interested in what people think the regional averages were, noting that even in the past, coral and macroalgal cover varied among reefs due to disturbance dynamics and other natural processes.  Therefore, in the pre-human (impact) past, there would be a distribution of state values for coral and macroalgal cover (and other reef characteristics). 

What were the mean values for these baseline distributions? These values likely vary among regions, habitats, depths, etc.  But what general value (if any) would you give managers as an ideal target for conservation or restoration?  Think about what you think “natural” is on shallow (1-15m depth) fore reef environments (not back reefs or reef crests)   

Below are the final results of the survey, which was open for five days (mid-day May 21 – mid-day May 26, 2013).  (Note the summary data can be downloaded as an excel workbook here from FigShare. Contact me for more information about the survey, for more data, about the results, etc.)

Who took the survey?

Screen Shot 2013-05-26 at 1.59.40 PM222 respondents took the survey, 129 of which were scientists.

What is the Caribbean baseline for macroalgae?Macroalgae Caribbean

Most of the respondents thought the Caribbean macroalgal baseline was 5-15% and three times more answered that it was 15-25% than 0-5% .

What is the Indo-Pacific baseline for macroalgae?IP macroalgae

The same was true for the Indo-Pacific where the most common choice was 5-15% for the macroalgal baseline, however, the 0-5% answer was much more common; 24% more respondents thought the macroalgal baseline for the Indo-Pacific was 0-5% (69 of 206) than for the Caribbean (19/200).  To me, this seems to reflect the existing trends in the Pacific, but not historical data (since there is very little pre-mid-1980s survey data for the Indo-Pacific). Macroalgal cover on the outer GBR was roughly 5% that last time I worked with the AIMS GBR survey data (3 or 4 years ago).  Although, there are a lot of very remote and nearly pristine reefs in the central Pacific with substantially higher macroalgal cover (also see this figure from our Baselines PrePrint). Scientists generally answered the same as respondents in the other three categories, e.g., see the summary of answers below from 119 Caribbean scientists compared to the results from all respondents above.  E.g., the percentage of scientists that answered 0-5% for the Caribbean macroalgal baseline was 10.1% vs. 9.5% for everyone (including scientists). caribbean algae only scientists Additionally, the answers from scientists and students for all four main questions were very similar, e.g.; IP macroalgae scientists vs students scientists v students IP coral Just for kicks, I compared the answers of 7 of our most experienced colleagues, scientists like Alina Szmant, Rupert Ormond, Charles Birkeland, and  Clive Wilkinson, to the other 122 scientists.

  • Q3: What is the Caribbean baseline for macroalgae?  Answers: 5-15%, 5-15%, 5-15%, 5-15%, 5-15%
  • Q4: What is Caribbean baseline for coral? Answers: 25-50%, 25-50%, 25-50%, 25-50%, 50-75%
  • Q5: What is the Indo-Pacific baseline for macroalgae? Answers: 0-5%, 5-15%, 0-5%, 0-5%, 5-15%
  • Q6: What is Indo-Pacific baseline for coral?  Answers: 50-75%, 25-50%, 25-50%, 50-75%, 25-50%, 50-75%

Note that like the other respondents, the uber-experienced scientists did not answer every question. All seven answered 5-15% for the Caribbean macroalgae baseline but three of five thought the Indo-Pacific macroalgae baseline was lower (0-5%). At  25-50%, our most experienced colleagues also thought the Caribbean baseline was lower than just over 40% of us (who voted 50-75%).  None voted 10-15% or >75% for baseline coral cover in either region.  And they were split on the coral baseline for the Indo-Pacific with half answering 25-50% and the other half answering 50-75%.

What is the Indo-Pacific baseline for coral?IP coral all

The views in our field about what is “natural” in terms of coral cover is somewhat ambiguous. For the Indo-Pacific, although 50-75% was the most common answer (90/207) a sizable number of people answered 25-50% or >75%.  The same is true for the Caribbean, where both 25-50% and 50-75% were popular choices. In fact, 79% of us think the Caribbean coral cover baseline is between 25 and 75%!  This could be due in part to my choice of answer categories. Perhaps if I had included 40-60% as a choice, our opinions would have appeared less variable.

What is the Caribbean baseline for coral?Caribbean coral all

I agree with the majority of respondents that baseline coral cover is higher in the Indo-Pacific than in the Caribbean, simply due to the morphology of the dominant coral species – the Caribbean lacks the plating Acroporid corals that can dominate Pacific reefs.

Context, Commentary, and Criticism

I received a fair amount of commentary on and criticism of the survey from colleagues via email. Mainly suggestions for how questions could have been worded, etc.

There are a million ways the questions could have been asked.  I kind of regret not asking for specific values instead of supplying a few categorial answers. Then I could have done some cool stats with the results.

Several people wrote to say I should have included a question about age or years diving experience or year of first reef dive.  The idea being that more experienced people would have better insight into what is natural.  I have mixed feelings about this.  On the one hand, the observations of people that were at least working on reefs, and in some cases doing surveys, four or five decades ago are invaluable.  But on the other, I think via a number of venues (e.g., Jackson’s Reefs Since Columbus paper and The Reef Reminiscences Report) these observations have been successfully shared with and absorbed by younger generations of reef scientists (including me), so I wasn’t surprised to see little if any differences in answers between scientists and students and only minor differences between less and more experienced scientists.

Furthermore, ideally, what we each think is “natural” is based on more than simply our own experiences: presumably data, published papers, surveys of near pristine reefs, etc all help form our opinions about coral reef baselines.  In which case, age or experience really shouldn’t matter all that much, assuming the respondent is familiar with the literature, etc.  Additionally, since nobody was diving when humans really began to seriously degrade reefs, it could be argued that observations from the middle part of the last century reflect that period, but not the true baseline.

Regardless, several people wrote to argue the survey was useless since it only collected opinions rather than data.  However, the data is presumably incorporated into our opinions.  And the data comes from too  many sources, using too many approaches, to be combined into a single value.  Finally, as Phil Dustin pointed out (below) we have no perfect data, since we have data from so few quantitative surveys, even in the 1970s and early 1980s.  That said, given how important it is to establish coral reef baselines, I think we need to do the best we can with the data at hand.

The survey certainly has other weaknesses and limitations. It is a bit preposterous to lump the entire Indo-Pacific region (which contains 75% of the worlds reefs) into a single region.  Additionally, since (as we argue here) the natural state of coral reefs certainly varied among sites and regions, asking for a single baseline range could be viewed as foolish.

Below are some of the comments and suggestions I received via email (for which I received permission to reproduce). If you have additional points to make, please do so using the blog comments function (which I have fixed).

Galapagos intertidal

Rachel Gittman took this on Fernandina one foggy morning in February. I love the contrast in colors. P1000322

Are unreasonably harsh reviewers retarding the pace of coral reef science?

I just published my first PeerJ Preprint here

Abstract: Identifying the baseline or natural state of an ecosystem is a critical step in effective conservation and restoration. Like most marine ecosystems, coral reefs are being degraded by human activities: corals and fish have declined in abundance and seaweeds, or macroalgae, have become more prevalent. The challenge for resource managers is to reverse these trends, but by how much? Based on surveys of Caribbean reefs in the 1970s, most reef scientists believe that the average cover of seaweed was very low in the natural state. On the other hand, evidence from remote Pacific reefs, ecological theory, and impacts of over-harvesting in other systems all suggest that, historically, macroalgal biomass may have been higher than assumed. Uncertainties about the natural state of coral reefs illustrate the difficulty of determining the baseline condition of even well-studied systems.

"Preprints" are non-peer reviewed contributions to the scientific literature.  Sort of like a book chapter or an invited review paper at TREE or Science.  Specifically, they do not undergo pre-publication peer review, but there is (or can be) extensive and rigorous post-publication review, which to my mind can be a lot more important.  For one, it isn't (generally) anonymous.  As we all know, many reviewers hide behind the shield of anonymity to trash the work of their peers and competitors or to prevent the publication of science that doesn't agree with their views.    

Screen Shot 2013-05-19 at 1.16.34 PM

Physicists have used pre-peer-reviewed publication via the arXiv server for years decades, to share their ideas, preliminary findings, and draft manuscripts with their colleagues.  Now us biologists have that option.  PeerJ Preprints can be cited, show up on google scholar, are assigned a DOI, and can also be submitted elsewhere simultaneously for publication to most journals. 

In our case, the manuscript has already been submitted and rejected by a number of journals, we think for both valid and invalid reasons.  We decided to share the reviews as a supplement to our preprint.  We masked the identity of the editors, but revealed which journal the reviews came from. 

I think reviews are an important part of the scientific record and conversation.  Having a rapid, open, and respectful back and forth would lead to much better science, better mutual understanding, less wasted time, much faster publication, etc.   I strongly believe in transparency in the publication process and I think reviews of both accepted and rejected manuscripts should be accessible, e.g., on the journal website, in a blog, on FigShare, etc.  The public and the scientific community should be able to see what the reviewers said about a paper, how the editor handled the reviews, and how the authors responded to them.  Doing so would make the whole process more fair, by adding accountability for everyone involved.   

Although a paper is often improved by peer review, the comments are sometimes overly critical, subjective, and far from constructive.  This is especially true at the non-blue chip journals. I rarely get nasty reviews at the most "respectable" or competitive ecological journals, e.g., Ecology and Ecology Letters (although I get plenty of rejections from them).  As an editor at Ecology, the reviews that I see are nearly always respectful and insightful.  It is when I venture into coral reef science and the more specialized marine and conservation journals that the real nastiness and subjectivity comes out.  Why? I don't know.  I don't even know if it is real or just my perception.  And since peer review is a closely guarded secret activity, there is no way to evaluate this objectively.  But A LOT of people I talk to have had similar experiences, especially at the journal Coral Reefs, which took a big nose dive when Rolf Bak took over as editor.

Below is a selection of the more critical comments of our manuscript.  I respond to some to point out the (probably obvious) fallacies in some of the reviewer arguments.  The broader point here is not that our little paper is earth-shattering or even that it should be published, but rather that peer review, at least in this subfield, could be improved.  (I will address how in a later post)

Screen Shot 2013-05-19 at 12.28.57 PM

We did offer solutions in that we concluded with four recommendations.  And the point of the paper was to describe and acknowledge the problem.  In fact, there is no perfect solution.  We will never know exactly what the real baseline is and that is the point.  Since we really don't know exactly what natural is (although we argue in the paper that we know what it isn't) scientists need to tone down their criticisms of managers that don't meet the scientists perceived local baseline, e.g., Pandolfi et al. 2005.  

This comment also illustrates the general tone of editor and reviewer dismissals in coral reef science, especially at the less competitive journals like Marine Policy and Coral Reefs as well as a strong reliance on subjective judgment about "novelty and impact". 

Screen Shot 2013-05-20 at 9.30.07 AM

Screen Shot 2013-05-19 at 12.30.14 PM

We didn't question the competence of elder colleagues. And Bill and Rich are not exactly spring chickens!  Instead, this is an unavoidable consequence of using the two dimensional quantitative survey techniques that are the norm in coral reef science.  Goatley and Bellwood (2011) demonstrated this in an elegant paper recently:

Abstract: Canopies are common among autotrophs, increasing their access to light and thereby increasing competitive abilities. If viewed from above canopies may conceal objects beneath them creating a ‘canopy effect’. Due to complexities in collecting 3-dimensional data, most ecosystem monitoring programmes reduce dimensionality when sampling, resorting to planar views. The resultant ‘canopy effects’ may bias data interpretation, particularly following disturbances. Canopy effects are especially relevant on coral reefs where coral cover is often used to evaluate and communicate ecosystem health. We show that canopies hide benthic components including massive corals and algal turfs, and as planar views are almost ubiquitously used to monitor disturbances, the loss of vulnerable canopy-forming corals may bias findings by presenting pre-existing benthic components as an altered system. Our reliance on planar views in monitoring ecosystems, especially coral cover on reefs, needs to be reassessed if we are to better understand the ecological consequences of ever more frequent disturbances. 

Second, no, we do not think early researchers were dumb. We didn't suggest they ignored macroalgae, we simply point out that when algae and other reef organisms are underneath a canopy-forming or branching coral, their true cover can be under estimated.  Moreover, we didn't argue that that macroalgae cover in the 1970s was 40% and we certainly don't think this is the baseline (it varies from place to place but is likely much lower than this).  Finally, it has been clearly demonstrated that damselfish were historically abundant on reefs and that often high densities are not due to the fishing of their predators. 

Kaufman LS (1977) The threespot damselfish: effects on benthic biota of Caribbean coral reefs. Proc 3rd Intl Coral Reef Symp, Miami 1: 559–564.

Precht WF, Aronson RB, Moody RM, Kaufman L (2010) Changing Patterns of Microhabitat Utilization by the Threespot Damselfish, Stegastes planifrons, on Caribbean Reefs. PLoS ONE 5(5): e10835. doi:10.1371/journal.pone.0010835Screen Shot 2013-05-19 at 11.56.11 AMWe got this argument from several journals, including from Frontiers in Ecology and the Environment (also an ESA journal); i.e., "this idea is dangerous!" – essentially advocating the suppression of data, speech, and ideas that are perceived as threats to reef conservation.  Not professional and definitely not cool. 

Several reviewers also did not care for the contradictory nature of the evidence we presented, which was largely the point of the paper.  This isn't a clean story (as is so often the case in ecology).  The macroalgal baseline is highly dependent on what evidence you consider.  

Screen Shot 2013-05-19 at 12.42.48 PMAs in the comment below and from several other reviewers, this reviewer argued we present selected information (that we cherry picked) without bothering to explain (provide a citation) what is missing.  Why don't editors ask for such references? 

Screen Shot 2013-05-20 at 9.54.56 AMA lot could be said about the subjective nature of the editors comments and of the comments from the second reviewer who thought our paper was "crap".  For one, it seems to me that the editor did in fact receive two reviews.  But the thing that really strikes me is that the main argument is that we are wrong, whereas we heard from many other journals, e.g., Marine Policy, that we are right but everyone already knows this, nobody would disagree, we were not saying anything novel, etc.  For example, here is a comment from MEPS reviewer #3:Screen Shot 2013-05-19 at 11.57.33 AMIt is common to get such contradictory arguments from two reviewers from the same journal, e.g.;

Reviewer 1: This is impossible!  They are clearly wrong!

Reviewer 2: Everyone knows this! The study lacks novelty and impact!

Below are some of the comments from the one complete review from Coral Reefs:

Screen Shot 2013-05-19 at 12.47.36 PMWe did not argue otherwise and wrote "because they can reduce coral recruitment" and included four citations.  It is a perception, however, that seaweeds are harmful invaders and generally bad for corals and reefs.  Moreover, we don't suggest this perception is wrong. This is one of many (willful?) misreadings of our text.   

Screen Shot 2013-05-19 at 12.49.00 PMIt is possible because there are organisms on reefs other than corals and algae, e.g., sponges, gorgonians, etc. Coral cover frequently varies without any response in macroalgae cover.   Here is an example from Belize from Aronson et al 2002 (PDF), where coral cover crashed due to bleaching, urchins held the algae in check, and sponges became the dominant space holder.  

Screen Shot 2013-05-19 at 6.12.11 PM

The same thing has been observed in countless other places, such as on Australia's Great Barrier Reef, where a collapse of coral cover has not been followed by a general increase in macroalgae.

Screen Shot 2013-05-19 at 12.47.08 PM

This is typical of the strange comments from this reviewer.  We didn't suggest otherwise and in fact present a synthesis of the scientific literature. 

Screen Shot 2013-05-19 at 12.48.46 PM

We didn't suggest that Connell used a time machine to survey reefs in the "pre-human past".  This is our sentence: 

Reefs, like all communities, have always been disturbed. Even long ago in the pre-human past, reefs were dynamic, non-equilibrial systems and were not fixed in climax states of coral dominance (Woodley 1992, Connell et al. 1997, Vroom et al. 2006). 

The citation of Connell et al. (and Woodley and Vroom), was for them having made the point that disturbance is natural on reefs.  Is this not obvious?  

The second sentence in the comment above is in response to this sentence from our paper:

In his long-term monitoring study of shallow reefs on the Great Barrier Reef, Connell documented repeated fluctuations of macroalgal cover between 15% and 85% due to natural disturbances and community succession (Connell et al. 2004).

Our intent was to point out that the cover of macroalgae can vary in time as well as in space.  There are countless studies that document this and most of the reviewers argued this was so well-accepted there wasn't any reason in pointing it out.  Yet the Coral Reefs reviewer does not buy it and argues that on the intertidal reef crest, Connell found much lower algal cover.  This is true, but we weren't referring to the barren reef crest.  We indicated we were interested in subtidal reefs here and only referred to Connell's shallow subtidal data.  This is the type of simple misunderstanding that could be clarified in a revised manuscript had we had the chance to do so. 

Screen Shot 2013-05-19 at 12.48.08 PMActually, Cote et al (2006) included 34 studies performed between 1977 and 2001.  But very few (all of which are included in our paper) were from the 1970s or earlier.  

Screen Shot 2013-05-19 at 12.46.50 PMWe got the "why didn't the authors cite the "other" studies that contradict their work" argument from several reviewers and journals.  Reviewers didn't bother to provide a citation, not out of laziness but because they don't exist. This is common in peer review – unscientific criticism of science. 

We did in fact use all available quantitative data for the Caribbean (pre-1980) and on isolated central-Pacific islands (more recent data). We did not cherry pick. We didn't exclude any data.  And we thoroughly searched, especially for old Caribbean data. 

So here we have serious accusations of scientific misconduct, and subsequent rejection of a manuscript, with no request by the editor – effectively the judge – to see some evidence of the crime.  Just a passive acceptance of subjective, emotional criticism. Which is ironic given peer review is a dialogue among scientists about evidence, inference, and hypothesis testing. 

The complete reviews and the responses we sent to the editors can be downloaded here from FigShare. Enjoy!

Peer-Review-Nick-Kim-cartoon3-resize

Fiji fish – Napoleon wrasse

Another coral reef fish I'm hoping to see in Fiji (on my upcoming expedition with Joshua Drew) is the Napoleon wrasse or humphead wrasse (Cheilinus undulatus). They are fish that are especially close to my heart because I spent four years studying them for my PhD.

Here's a splendid male:

HHW Macorig paolo

So I'm biased – clearly – but Napoleons really are brilliant. And these days they are sadly becoming a rare sight.

To study them, I spent months living on a remote atoll in the South China Sea, one of the Sprately Islands called Layang Layang (or Swallow Reef). There's a Navy base and a dive resort on the isand (where we occasionally escaped for a cold beer) but I camped on a patch of rocky ground beside the runway, sleeping under the stars and retreating inside a rusty shipping container when it rained.

I was there to study an incredible natural event: Napoleon wrasse having sex. Because trust me, these fish have spectacular and very organized love lives.

When the moon is new, they gather together in a huge aggregation, each time in the exact same spot on the reef. There was a single, dominant male (he’s huge – up to 6 feet long). He stakes out his territory and jealousy guards it from other males. Then the smaller females show up. Dozens of them. 

HHW Derek Keats

These are normally solitary fish so to see a big shoal of them is truly extraordinary. The females mill around in the mating arena, while the male shows off, looking big and impressive. Then one by one, he leads the females off into the big blue open water. They swim side by side, he rubs against her. And then all of a sudden they rush upwards together. She releases her eggs into the water, he releases a cloud of sperm. As soon as they’ve finished, she scarpers, and he goes right back to the reef to pick up another mate.

Or… he comes back to the reef to find me, hanging around in my scuba kit, in his territory, and he charges right at me, flashing his pointy teeth.

HHW male Stephen n maher

Luckily that time he was just trying to spook me and I had a big underwater camera to hide behind, because what I was doing was filming them. In particular, I was documenting the females’ faces. After months of diving with these amazing fish, and hours analysing my underwater footage, I showed for the first time that the intricate patterns on their faces are unique to each individual, like a fingerprint.

That led me to discover that females in fact return to mate several times each month. And that let me work out accurately how many spawning females there are in the whole population.

If the females survive long enough, they will return to that same spawning site but in a rather different role. In time, they undergo a sex change, and turn into males. They grow big bumps on their head and big rubbery lips. And that’s one of the main reasons why sadly there are now fewer of these fish in the wild than there were a few decades ago.

Because in China, Napoleon wrasse are a delicacy, their lips in particular. They’re worth hundreds of dollars a plate. I wrote a paper in the journal Science, showing how fisheries across the Indian and Pacific Oceans are strip-mining the seas of Napoleon wrasse and other, highly prized coral reef fish.

And in fact, a while after I left that South China Sea island I heard the depressing news that the Napoleon wrasse that I’d studied, each individual that I’d learned to recognize, had been caught and carted off to restaurants.

And I don’t suppose many of the people eating those fish knew what extraordinary lives they’d led.

KONICA MINOLTA DIGITAL CAMERA

Napoleon wrasse are now strictly protected in Fiji under the national Endangered and Protected Species Act. So I'm really hoping I'll get to see some on my trip. It's been a while since I've gazed at the beautiful stripey face of a giant sequential hermaphrodite.

#CUinFiji

Photos by Derek Keats, tezl, Macorig paolo, and Stephen N Maher.

Grad student time budget

phd041913sGrad

The 97% consensus on human-caused climate change

C02_TCP_social_media_image_97

If you believe the climate is changing and that human activties are the cause, then you can probably go back to cleaning your house or whatever you were doing when you took a break to check in with SeaMonster.

But, if you are one of the hundred million or so Americans that still don't believe in this scientific reality, well then you better read on.  

A new survey of over 12,000 peer-reviewed climate science papers by our citizen science team at Skeptical Science has found a 97% consensus in the peer-reviewed literature that humans are causing global warming.

Start here at the new Climate Conensus page.  

Yes, John Skvarla the third, there is indeed a clear, well-establish, well-documented consensus.  

The state of North Carolina's new Secretary of the Department of Environment and Natural Resources is a climate change denier.  In a recent interveiw with Laura Leslie, he argued (wrongly);

"There is a great divergence of opinion on the science of climate. More dialogue is needed.  We must engage the very best minds with diverse opinions to make conclusions on policy that will be driven by fact but simply to say that climate change is settled … science is fluid.”

When Leslie pointed out that 97 percent of qualified scientists agree on the science of climate change, Skvarla said, “I think that’s [the proportion of scientists] misleading. I have studied this every day for 10 years and there is a great divergence of opinion on this. I’m not ready to say which is right or wrong.”

John, it isn't up to you.  Thousands of scientists have already done the work and concluded that climate change is real. Your job is to implement the best policies to mitigate the economic and environmental impacts of climate change on the state.  

Fiji fish – Emperor Angelfish

I'm stoked to be going to Fiji this June with Joshua Drew from Colombia University and his crew of PhDs and masters students. My main role on the expedition is going to be documenting the science and spreading the word to the rest of the world about reefs and conservation and all things fishy (I like to think of myself as the equivalent of Vikram Ray in the Life Aquatic). Here's a bit more from Dr Drew about what we'll be doing.

I was last in Fiji many years ago (I spent a year diving and travelling around the world before starting University) and you have no idea how thrilled I am to have the chance to go back.

I've been flipping through my old dive log book (I'm a total geek when it comes to logging dives. I write them like detailed diary entries describing as much as I can about the dives and also getting nerdily statistical with facts like my accumulated time underwater).

According to my log, the first time I dived in Fiji was my 116th dive (after 62 hours 40 minutes total time underwater). I was diving on the Great Astrolobe Reef that runs past island of Kadavu and it was apparently the first time I'd ever seen an emperor angelfish (Pomacanthus imperator). One of these beauties:

emperor angel Phillipe Guillaume

Isn't it stunning?  I know it's big show off but it is without doubt one of my favourite coral reef fish.

Those blue and yellow stripes are the reason I ride around Cambridge on a blue and yellow bicycle (I have a Pashley Tube Rider in a colour combo no longer available that they called Tropical Fish).

I'm suprised I don't remember that it took me so long to see one. By the time I got to Fiji that first time I'd already spent a long time diving in Belize (okay, no emperors there) and Australia. And when I did finally see it, my log entry went:

I finally saw my EMPEROR ANGELFISH – cool! Beautiful fish - Big for an angelfish. Thank you! I love it.

As juveniles they have a completely different but equally elegant look:

800px-Pomacanthus_imperator_(Emperor_angelfish)_juvenile

One theory about why they undergo such a transformation is that by painting themselves in young 'un colours the juveniles can swim into the adults' territories without getting chased off (they eat different food so aren't competing with grown ups for dinner).

The adults' dark eye band makes them look like a fishy racoon and by hiding their eyes potentially confuses predators who won't know which end is which.

emperor angelfish Derek Keats

Hopefully I'll get to see plenty more emperors this time.

#CUinFiji

Photos by Philippe Guillaume, Derek Keats and Nick Hobgood.

Global warming since 1999

Climate change deniers like to claim there has been “no warming since 1998″ which was an especially warm year due to an intense El Nino.  Well that ain’t true.  Global warming has indeed continued, especially in the deep sea due to the prevalence of several La Nina events recently.

Here is how much the land ocean surface has warmed since 1998 (1999-2012, from NASA):

nmaps

Most the warming is obviously in the Arctic, which is why Arctic sea ice is being lost so rapidly.

nmaps_zonal

Galapagos field site

How about a Galapagos picture break.

This is Lindsey Carr’s field site on Fernandina.  In this bay a crazy diversity of critters coexist, including hermatypic corals and penguins, orcas and white tip sharks, sea lions, marine iguanas and many-a-sea cucumber.  This is one of the few places I’ve been in the Galapagos that is truly protected and not overfished. You can see the northern end of Isabella island in the background.

OLYMPUS DIGITAL CAMERA

5 things everyone should know about ancient oceans

Here’s the first in the series of 5 videos I made with researchers at Cardiff University’s School of Ocean & Earth Sciences.

YouTube Preview Image

Check out all 5 in the playlist here.

Shared office printer instruction manual

phd042413svia PhD comics

Humans are causing more strong hurricanes

The possible effect of global warming on the frequency or severity of cyclonic storms has been debated quite intensely among scientists (not only between scientists and climate change deniers) for over a decade.  Several new studies are helping to clarify (somewhat) whether we are already experiencing (or will soon) more intense storms.  Dana Nuccitelli has a nice summary of two of these new papers, excerpted below (see his full post here).  

The link between human-caused global warming and extreme weather is often difficult to pin down, particularly with regards to hurricanes.  As Kevin Trenberth has discussed, all weather now occurs in a climate that humans have altered.

“it is important to recognize that we have a “new normal,” whereby the environment in which all storms form is simply different than it was just a few decades ago.  Global climate change has contributed to the higher sea surface and sub-surface ocean temperatures, a warmer and moisteratmosphere above the ocean, higher water levels around the globe, and perhaps more precipitation in storms.”

In a new paper, Grinsted et al. (2013) constructed a storm surge index beginning in 1923 from six long tide gauge records in the southeastern USA.  The idea is that surges in sea level recorded at tide gauge stations can tell us about strong hurricane events.  Consistent with their 2012 results, the authors found:

“The strong winds and intense low pressure associated with tropical cyclones generate storm surges. These storm surges are the most harmful aspect of tropical cyclones in the current climate, and wherever tropical cyclones prevail they are the primary cause of storm surges.”

They compared their storm surge index to changes in global surface temperature, to temperatures in the Main Development Region (MDR; a part of the Atlantic Ocean where most hurricanes form), and to MDR warming relative to the tropical mean temperatures (rMDR).  They found that averaged sea surface temperatures over the MDR are the best predictor of Atlantic cyclone activity, followed by global average surface temperature, with MDR warming relative to the tropics being the worst predictor of hurricane activity (Figure 1).

rinsted et al. then used the relationships between hurricane storm surges and global and MDR temperatures to predict how storm surges will change in the future.  They used the Representative Concentrations Pathway (RCP) 4.5 scenario, which represents a future in which we slowly reduce human greenhouse gas emissions such that they peak around the year 2040.  In this scenario, there is approximately 2.4°C global surface warming over the 21st century.  The results are shown in Figure 2.

“The response to a 1°C warming is consistently an increase [in Katrina-levelstorm surges] by a factor of 2–7 … This increase does not include the additional increasing surge threat from sea level rise”

Figure 2: Number of Katrina magnitude surge events per decade (B) hindcast and projected changes in temperatures from climate model BNU-ESM under for RCP4.5 (A).  The thick blue line shows the projection using the full spatial gridded temperatures andconfidence interval (5–16–84–95%); magenta and black show the projections using only Main Development Region (MDR) and global average surface temperature.

Also see a nice summary of Grinsted et al 2012 by Tamino here.

Galapagos flightless cormorant

How about a Galapagos picture break.

OLYMPUS DIGITAL CAMERA