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

[tomascik at novuscom.net]

David, I can take and truly enjoy this type of didactic writing any time 
and I wish we could see more of it.  Your comment about von Kotzube’s 
(1982) accounts of oceanic barrier reefs contrasts with the writings of 
Alfred Russel Wallace (The Malay Archipelago) when he first saw a true 
barrier reef in Indonesia. Darwin’s contemporary, Wallace was well aware 
of Darwin’s work on coral reefs, and here is a quote that I found so 
fascinating:

“This reef is sometimes only marked by a line of breakers when there is 
a little swell on the sea; in their places there is a ridge of dead 
coral above water, which is here and there high enough to support a few 
low bushes. This was the first example I had met with a true barrier 
reef due to subsidence, as has been so clearly shown by Mr. Darwin.” – 
Walace 1869

Wallace was referring to a small barrier reef that surrounds Pulau 
(island) Sago in the Watubella island chain in the eastern Banda Sea 
(east coast of central Sulawesi). I was lucky to visit Pulau Sago and 
actually having read Wallace’s accounts made the visit so much more 
memorable. Anyone who is interested to get more information on the 
extent and the types of barrier reefs in the Indonesian archipelago can 
visit:
  
https://www.researchgate.net/publication/303304936_Tomascik_T_A_J_Mah_A_Nontji_M_K_Moosa_1997_Chapter_Fifteen_Barrier_Reefs_In_The_Ecology_of_the_Indonesia_Seas_Part_II_pp_727-750_Singapore_Periplus_Editions_HK_Ltd

For simple pleasure I would recommend reading “The Malay Archipelago: 
The Land of the Orang-utan, and the Bird of Paradise”.
Tom



On 2020-11-02 06:00, David Blakeway via Coral-List 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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