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

Tue Nov 3 23:54:18 UTC 2020

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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>>
>>