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

Tue Nov 3 22:26:54 UTC 2020

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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>
>