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

[Douglas Fenner]

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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