[Coral-List] For graduate and undergraduate coral reef scientists

[David Blakeway]

I’d like to follow up on our discussion about the value of historic
literature by providing some examples. Actually, I haven’t found any
examples of historic literature generating new research, but this is
telling because there are plenty that should have. One topic already
mentioned by Tomas is coral colonisation and reef development in turbid
muddy habitats. It is now known, through research in North Queensland and
elsewhere over the last three decades, that coral reefs are growing
spectacularly well in such habitats, refuting the clear-water coral reef
paradigm. However, in publications through 1890-1931, the Dutch researchers
de Sluiter, Umbgrove and Verwey had already completely described the
phenomenon, including the inference that corals may be obtaining nutrition
from the turbid water.

Another example is the recent discovery of coral reef hypoxia and tropical
dead zones by Altieri et al. (2017). This is a great piece of work that has
sparked multiple research programs. But the field *should* have begun with
Verwey (again!, 1931) whose comprehensive reef surveys and lab experiments
showed that, in his words: “…*the oxygen consumption of a reef can be so
considerable that the water around it may become deprived of a large part
of its oxygen.*” and “…*the quantity of oxygen, present in the water, must
often be the limiting factor in reef growth*.”

I will emphasise here that, although I obviously have an interest in
historic coral reef literature, I’ve only read a fraction of it, and
nothing in other languages. The obvious inference is that there are many
more ground-breaking ideas to be rediscovered and that, at least in older
fields such as ecology, *the best way forward is to look back*. There are
also clear implications for newer fields; an important one being the
recognition that some of today’s ideas will be tomorrow’s undiscovered
gems. How do great ideas slip away undetected? No doubt there are several
reasons, but I’m pretty sure the present H-index-driven blizzard of
publications isn’t helping.

For students reading this, especially those interested in reef ecology, I
have an agenda in presenting the two examples above and it’s this: in both
cases the phenomenon is expressed in reef geomorphology. In the turbid
muddy reefs example, these reefs often colonise the seaward edges of
sedimentary structures such as delta lobes (see India’s Gulf of Kachchh for
some awesome specimens). Deltas are, obviously, turbid muddy environments,
and it’s extremely unlikely there’s any hard substrate beneath the reefs
because deltas are built of sediment. So straight away, from geomorphology
alone, you can deduce that coral reefs are thriving (or at least existing)
in turbid water, and that they have colonised unconsolidated sediment, not
rock.

The hypoxia example is more complex because in this case the reef doesn’t
adopt the underlying morphology, it builds the morphology itself. At least
that is what I think. You can see my reasoning in this preprint:
https://peerj.com/preprints/26794/ (critical feedback appreciated). This
self-constructing aspect of reefs is interesting because it potentially
allows you to derive aspects of local-scale ecology from large-scale reef
geomorphology—reef geomorphology becomes a symbolic language, conveying
ecological information. I would love to see young ecologists start decoding
this information! If you’re interested, but concerned that you don’t know
enough geology, don’t worry. Geological text can be dry and dense, with
lots of jargon (like ecology), but conceptually it is not difficult. In
fact, perhaps there’s no such thing as coral reef geology, it’s just
ecology plus time (just trying to get a bite here :)

Altieri AH, Harrison SB, Seemann J, Collin R, Diaz RJ, Knowlton N. 2017.
Tropical dead zones and mass mortalities on coral reefs. Proceedings of the
National Academy of Sciences. 114:3660–3665.
https://doi.org/10.1073/pnas.1621517114

*Verwey*, J, *1931*. *Coral reef* studies. II. The *depth* of *coral reefs* in
relation to their *oxygen*. consumption and the penetration of light in
water. Treubia, 13(2): 169-198

On Wed, Nov 4, 2020 at 7:54 AM Douglas Fenner <douglasfennertassi at gmail.com>
wrote:

> I agree.  Nearly all our research is publicly funded by taxpayers, and
> publishing is a hugely profitable enterprise.  They nearly strangle
> libraries, which again are usually publicly funded, even private
> universities are nor-for-profit.
> Cheers, Doug
>
> On Tue, Nov 3, 2020 at 11:28 AM David Blakeway <
> fathom5marineresearch at gmail.com> wrote:
>
>> Doug, you are right a lot of it (by no means virtually everything) can be
>> obtained by alternative methods. I just don't think those workarounds
>> should be necessary. And I believe many in the publishing game would shut
>> down the workarounds if they could. Perhaps I am misrepresenting them. But
>> the dissemination of (largely taxpayer-funded) knowledge should NOT be a
>> for-profit exercise.
>> Requests to authors have been a little hit or miss for me, 20-30% of them
>> don't respond. And a couple have said "let me know if you have any
>> questions" then haven't answered my questions. Maybe you have a nicer email
>> manner :)
>> Yep there seem to be plenty of low-quality journals, but they are easy to
>> avoid. PeerJ has been alright for me so far. An interesting aspect is that
>> they publish the drafts and reviews alongside the article - it's not
>> compulsory but most authors do it. It probably results in more thorough
>> reviews. Reviewers can still remain anonymous if they wish.
>>
>> Tomas, thanks for your research links. I have downloaded them all (some I
>> had already). Wallace and Wallacea were and are exceptional.
>>
>> Vassil - Hello and thank you!
>>
>> On Tue, Nov 3, 2020 at 4:50 AM Douglas Fenner <
>> douglasfennertassi at gmail.com> wrote:
>>
>>> Thank you for this David!
>>>      Reading older literature and digging things out is called good
>>> scholarship, and it used to be valued.
>>>      I have long not had institutional access to any journals, and the
>>> nearest big university library is thousands of miles away.  But I can get
>>> almost everything.  I subscribe to Coral Reefs, the only journal that
>>> exclusively has coral reef articles, I subscribe to online only, I can
>>> download any article they have ever published, I subscribe for 3 years at a
>>> time to get a discount, and I am in an developing country so I get a
>>> discount.  It is very cheap per article, and it gets me membership in the
>>> society and a discount on ICRS.  What's not to like???  For other articles,
>>> I start with Google Scholar, where I can get a lot, but not everything.  If
>>> I can't get it that way, I go to the journal website, find the article, and
>>> look for an author's email, then write them, asking for a pdf copy.  They
>>> always send me one.  Anyone who wants to can do the same thing.  You can
>>> get virtually everything.
>>>      One danger with open-access journals is the predatory journals,
>>> which are thriving because it costs almost nothing to produce a paper
>>> online, while print versions cost real money.  Any journal charging more
>>> than a pittance for online only is pocketing the rest.  But be careful that
>>> the journal you use actually does peer review.
>>> Cheers, Doug
>>>
>>> On Mon, Nov 2, 2020 at 3:10 AM David Blakeway via Coral-List <
>>> coral-list at coral.aoml.noaa.gov> wrote:
>>>
>>>> For graduate and undergraduate coral reef scientists
>>>>
>>>> The recent ‘Darwin was wrong’ thread elicited many comments and
>>>> perspectives that I feel are important for young scientists to be aware
>>>> of,
>>>> and which I have tried to collate below. I hope it does not sound
>>>> didactic.
>>>> I am open to feedback of course if any of it seems incorrect or out of
>>>> line. I have arranged them in three topics:
>>>>
>>>>  *1.       **Accept uncertainty*
>>>>
>>>> If you have what seems to be a good idea, it’s easy to develop the
>>>> conviction that it is right. But in fact, history shows that it will
>>>> not be
>>>> right; the best you can hope for is that it will be incomplete. If it’s
>>>> a
>>>> bad idea it will be quickly rejected (in theory). If it’s a good idea it
>>>> might gain hold for a while, but experiment and observation will
>>>> gradually
>>>> reveal anomalies. Then someone will develop a new idea that explains
>>>> everything the original idea did, plus the anomalies. Eventually people
>>>> will find anomalies in the new idea, and so on. Recognising this
>>>> pattern,
>>>> it is important that you search for evidence inconsistent with your
>>>> ideas
>>>> and include that evidence in your articles. That might help you develop
>>>> the
>>>> next idea! Or someone else. Either way it’s progress.
>>>>
>>>> Charles Darwin is a great example here because he spent so much time
>>>> trying
>>>> to disprove his own ideas. The article by Droxler & Jorry discussed in
>>>> the
>>>> ‘Darwin was wrong’ thread is a bad example because they do not even
>>>> mention
>>>> previous research contrary to their ideas.
>>>>
>>>>  *2.       **Explore historic research*
>>>>
>>>> I recall, in an older coral list post, a frustrated graduate student
>>>> recounting her institution’s policy of not citing publications more
>>>> than 15
>>>> years old, presumably because they didn’t want to appear outdated. This
>>>> policy is ill-informed and counterproductive. Reading and citing
>>>> historic
>>>> research is valuable for at least three reasons. Firstly, to acknowledge
>>>> and credit those who’ve built our foundation. Most are dead by now of
>>>> course, and no longer need the kudos. Still, respect the legacy! (and
>>>> bear
>>>> in mind that our own period will be history soon enough). Secondly,
>>>> reading
>>>> the original papers will ensure you don’t mis-cite them. For example,
>>>> with
>>>> respect to the Droxler & Jorry article, the reality is that although
>>>> Darwin
>>>> believed his fringing-barrier-atoll model explained most atolls (and it
>>>> probably really does), he knew it did not explain them all, because he
>>>> had
>>>> explored the anomalies. Droxler & Jorry are in fact arguing against a
>>>> deeply ingrained *interpretation* of Darwin. Thirdly, and most
>>>> importantly,
>>>> the historic literature contains many great ideas that have either been
>>>> forgotten or were not understood at the time. The best of these, if they
>>>> come to light, will be revolutionary and will generate entire new
>>>> fields of
>>>> research. Nineteenth-century literature is particularly rich, because
>>>> naturalists of the time were very broadly educated, and really got out
>>>> there (Darwin’s Beagle voyage lasted nearly five years, as did von
>>>> Humboldt’s exploration of the Americas). And some of this literature is
>>>> great reading! You will be holding your breath at von Kotzebue’s (1821)
>>>> account of sounding barrier reef fronts in the South Seas - extremely
>>>> dangerous work, all for science! (one wonders what the crew were
>>>> thinking).
>>>>
>>>>  *3.       **Understand (distortions in) the publication and citation
>>>> system*
>>>>
>>>> If you are a student within an academic institution you likely have
>>>> unlimited access to scientific publications, because your institution is
>>>> paying large annual subscriptions to the publishers. Once you leave
>>>> academia, or get a job in less wealthy academia, you will find that most
>>>> publications become inaccessible unless you can pay 20-30 $/€ per
>>>> article.
>>>> It’s difficult to do effective research in these circumstances, and it’s
>>>> very frustrating knowing the information is there but held to ransom.
>>>> This
>>>> situation has arisen because a small group of companies control the
>>>> extremely profitable business of academic publishing. They have
>>>> manoeuvred
>>>> into the incredible position of being able to charge their workforce
>>>> (us)
>>>> to provide goods (hard won knowledge in the form of articles) that they
>>>> can
>>>> sell an unlimited number of times until copyright expires! Which I think
>>>> might be never! (copyright for individuals normally expires 70 years
>>>> after
>>>> death but I don’t believe that applies once you’ve signed over
>>>> copyright to
>>>> a company). These companies are understandably protective of their
>>>> business
>>>> model and will attempt to crush, through legal action, anyone trying to
>>>> circumvent their system by providing universal free access to the
>>>> knowledge
>>>> (e.g. Aaron Swartz, Alexandra Elbakyan). Of course, publishing
>>>> companies do
>>>> have costs; Nature apparently claims production costs are $20-30,000 per
>>>> article. This sounds improbably high. If it’s true it indicates inflated
>>>> salaries at Nature, most likely among the executive not the troops.
>>>>
>>>> I don’t know enough about the publishing system to guess how it will
>>>> evolve, or how individual researchers can best act to make it more
>>>> equitable. Personally, I won’t submit my research to paywalled journals,
>>>> but you might find that approach difficult if your supervisors
>>>> disagree. I
>>>> like open access journals, especially PeerJ. But even they have
>>>> disappointed recently, by significantly raising fees and discontinuing
>>>> their preprint service. Maybe bioRxiv? Maybe Coral Reefs can leave
>>>> Springer
>>>> and self-publish under some archived creative commons arrangement?? I
>>>> don’t
>>>> know, I just hope things change.
>>>>
>>>> Regarding citation metrics: Evaluating the quality and future
>>>> significance
>>>> of scientific work is difficult. This has led to the rise of citation
>>>> metrics, such as the H-index, as a proxy for the quality of articles,
>>>> researchers and journals. The main reason these metrics have become so
>>>> prevalent is that they are easy to calculate, and calculation can be
>>>> automated. As a proxy for quality they are inherently unreliable,
>>>> especially once they become influential in job prospects and funding
>>>> allocations. The problem is best expressed by Strathern (1997): “*When a
>>>> measure becomes a target, it ceases to be a good measure*”. This is
>>>> exactly
>>>> what’s happened in science, to the extent that your viability as a
>>>> scientist depends on hitting the target. In fact, somebody else will hit
>>>> the target, so you’d better exceed it. This obligation is probably the
>>>> reason why relatively few early and mid-career scientists are active on
>>>> Coral-List; they simply don’t have the time. Some scientists do better
>>>> on
>>>> the treadmill than others, but I believe almost all would produce more
>>>> meaningful work if they had more time to explore and reflect. Citation
>>>> metrics are perhaps even more insidious and entrenched than paywalls,
>>>> and I
>>>> don’t have any good solutions here either. Just be aware that they, like
>>>> the paywalls, are impeding science (in my opinion).
>>>>
>>>> One other aspect related to the pursuit of citations and publicity:
>>>> sensationalist headlines can easily be misappropriated. Rupert’s
>>>> prediction
>>>> about Droxler & Jorry article inciting fundamentalists is already borne
>>>> out
>>>> in this link (same as the one Doug showed):
>>>>
>>>> https://crev.info/2020/10/darwin-coral-atolls/
>>>>
>>>> It is interesting that the link was provided by the author André
>>>> Droxler.
>>>> If I were him I would be backpedalling fast from this one. I can only
>>>> presume more hits on this page generates more hits on the Rice
>>>> University
>>>> page and more hits on the Annual Reviews page and everyone’s happy!
>>>>
>>>>
>>>> Anyway Dear Student,
>>>>
>>>> Coral reefs are still there (for now) and the privilege of experiencing
>>>> and
>>>> (partially) understanding the reef will always outweigh the obstacles
>>>> you
>>>> might face. Good luck and please do read some of those early books,
>>>> ideally
>>>> in original cloth-bound hardback. They feel good and smell right! Most
>>>> were
>>>> reprinted several times and the later editions are not costly. A great
>>>> one
>>>> to start with is:
>>>>
>>>> Darwin, C.R. 1842. The Structure and Distribution of Coral Reefs
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>>>
>>>