Archive | science RSS for this section

Predatory or legit? I dunno, but … GBP1500?

Predatory publishers or legit? It’s not always easy to spot. What about this one?

screeenshot of email asking me to contrinute to a book chapter; text extracts below.

Email from InTechOpen asking for a contribution to a book chapter.

Note how the list of institutions is empty!

Dear Dr. Goossens,

Due to your involvement in the field, and the research you published in your paper, “Synchrotron X-ray diffuse scattering from a stable polymorphic material: Terephthalic acid, C8H6O4,” IntechOpen invites you to extend your work and offer a more comprehensive overview of your studies. Contribute a chapter to “Synchrotron Radiation,” an upcoming Open Access book edited by Dr. Name Name.

Work with an internationally recognized peer group and gain increased visibility for your published work. Please visit the book project page to register your interest.

We look forward to hearing from you.

Kind Regards,

Marija Gojevic-Zrnic, from IntechOpen
Author Service Manager

It’s correctly written, their website looks more or less professional, their books do certainly get printed and distributed — I’ve seen them in proper libraries. They’re open about their (high in my opinion) fees — £1500 for a 16 to 20 page chapter. So are they predatory or just expensive? I guess they’re just expensive.

I still would not publish with them.


Something like IUCrJ (fee of USD1300, or about £1000, so quite a bit cheaper) covers similar topics, is also open access, is part of a society publisher of high standing, has a reliable archiving policy and is embedded in all the major search engines and databases. I have no experience with the editorial process at InTech, and it may be very good, I can’t say, but I do know that the IUCr process is superb, with their editors doing more than just farming out the material to review — they genuinely interrogate it themselves.

The issue? IUCrJ might bounce the work! Also, book chapters are often more review-y and may not be publishable as papers.

But … if you are career-conscious, ask; will the book chapter collect citations anyway? Will it fall through the cracks of whatever research metric engine your bosses want to see quoted? Sadly, this is the reality. Monographs and book chapters might be excellent and important, but will they be noticed? I suggest finding a good-looking chapter or two from an InTech or similar volume and then checking its stats in whatever database you use for citation and impact metrics — Web of Science or whatever. Is it there? Are the numbers reasonable? And so on.

In the end, if you want to go open access, there are reputable journals that will take your money, and £1500 is enough to get into some pretty reputable ones. And conventional publication still exists. InTech might be OK, but check it out first and be aware of the options!

It’s all about due diligence.




Physics in Focus for Year 11 second edition

It’s good when a book sells out its first print run then goes to a second edition. I recall someone telling me once that first editions should not be collectors items since every book has one but few go through multiple editions.

Regardless, I’ve seen the cover of the second edition of Physics in Focus for Year 11 , a textbook for high school physics students in New South Wales. It looks a lot like the first edition, but the cover says ‘Updated Feb 2018’ and ‘2nd edition’. The book complies fully with recent changes to the syllabus documents put out by the education authorities in the state. I wrote less of it than any of the other authors, so I cannot claim this is my doing, but it is still nice to see.

Bitmap image of the cover.

Cover of the second edition of Physics in Focus for Year 11, out now from Nelson/Cengage.

I am reliably informed it has just gone to the printers. The website may not even be updated yet.

There are older texts with the same name out there; anything in a different cover no longer reflects the current state of the syllabus, at least in NSW.



Physics in Focus — a new text for Year 11 science

I am now a textbook author! Well, one chapter out of fourteen… it’s a team effort. It’s a new Year 11 physics book for New South Wales, launched now for use in 2018; I have a couple of chapters in the Year 12 book, due out for 2019.

This book is Physics in Focus from Cengage. Here is the link to it:

And sample chapter (pdf).

And here is the cover.

The cover of <I>Physics in Focus</I> for year 11 students. My first textbook!

The cover of Physics in Focus for year 11 students. My first textbook!

There’s a big difference between knowing the physics and writing about it. One of the main things that I had to get used to was the constraints imposed by the curriculum. It is set at a high level and we work against specific dot points, which reduces scope for initiative but provides certainty and structure, and makes sure the book meets the needs to the teachers who are tasked with delivering that curriculum. The other thing was thinking about the language — it has to suit the audience. The kinds of sentences found in a scientific paper just don’t meet the criteria for clarity, simplicity and reading ease.

I’m waiting for my author’s copy to arrive in the post. Maybe I should get together a shelf of stuff instead of putting it in the cardboard box with my handful of other publications.


Modulated molecular crystal structures — well done, Eric!

A new scientific paper. A tribute to the residual momentum of my scientific career, and in particular to Eric Chan, who has built on my work to come up with a way of exploring modulated molecular crystals.

It’s pretty subtle stuff, but basically a crystal structure can show a periodic variation from cell to cell — for example, a displacement or substitution of an atom or molecule. If this variation is periodic, then it can be described using a periodic function. Such a function will have a Fourier transform that requires (relatively) few Fourier terms, and each strong term will give rise to a bright spot in the diffraction pattern. These spots will occur in a motif centred on (some) Bragg peaks, potentially adding many new spots to the diffraction pattern.

So where these bright spots occur tells you about the modulation. However, in something like molecular crystal, the molecular structure factor may be relatively complicated, and so may the nature of the modulation. This may mean that it is not easy to predict where the modulation spots are likely to be intense.

Eric figured out a way to use my program ZMC to generate modulated molecular structures and then calculate their diffraction patterns.

An example of a diffraction pattern calculated using <tt>ZMC</tt> with Eric Chan's modulation wave addon.

An example of a diffraction pattern calculated using ZMC with Eric Chan’s modulation wave addon.

It is pretty heavy and specific stuff, but it also is a capability that I’ve not seen elsewhere. Eric’s webpage is at, and that is the best place to go to have a look for the code.

Other ZMC.

Cambridge Scholars Publishing: Spammers but not dodgy

So I got this email:

Subject: Materials Science Books
From: Helen Edwards

Dear Dr. Goossens,

Firstly, please excuse this unsolicited email. I’m sure that like me you receive too many as it is and so I’ll keep it brief.
I was recently appointed as Commissioning Editor for Cambridge Scholars Publishing with a brief to expand the subject areas in which we publish books. As such I am in the process of developing a collection of books based in the field of Materials Science. As I believe you already have some experience of academic and scientific writing, I wondered whether you would consider us as your publisher should you decide to put ‘pen to paper’ and write a book at some point in the future?
We are also developing Editorial Advisory Groups to help ensure that we only publish high quality texts. If this is something that you would like to become involved in, please do let me know.
As I promised, I have kept this message short, but would be delighted to talk or correspond more if you feel you would like to explore possibilities.
Kind regards,

Helen Edwards
Commissioning Assistant

Social Media: Twitter Facebook LinkedIn Blog

If you experience any difficulty reading this message, please send us an email to

Cambridge Scholars Publishing Ltd is registered in England. Reg. No: 4333775; VAT No: 108280727

Disclaimer: The views and opinions expressed in this message do not necessarily represent those of Cambridge Scholars Publishing Ltd. The contents of this message are intended for the addressee only. They are confidential and may contain private information. Cambridge Scholars Publishing is not responsible for any damages resulting from the unauthorised use, forwarding or disclosure of this message, and will not be held liable for damages or loss caused by any viruses.

About Cambridge Scholars Publishing (

Cambridge Scholars Publishing (CSP) is an independent academic publisher, founded in 2001 by former lecturers and researchers from the University of Cambridge who felt existing publishing companies took too long to publish academic books, monographs, conference proceedings and textbooks.
CSP has its own printing facility, now publishes 750+ titles each year in both electronic and print formats and is committed to providing a forward-thinking publishing service that champions original thinking, whilst ensuring we put our authors at the heart of everything we do. Our back list catalogue contains approximately 7,500 titles.

So I google it ‘cos it looks dodgy and I find this: So it’s not quite clear. They certainly seem to be spammers. But the ‘I’m sure you’re busy’ start is a nice touch.

Now, they’re probably not as dodgy as many on this list; comments on the web are various. Overall impression is that they are not predatory — they do not seem to ask for money up front and in fact promise to pay royalties — but also not terribly highly regarded. But they did solicit work from me using a generic email that looks like it was sent by a robot, albeit a polite one.


March 2018, I got this:

Dear Dr. Goossens,

I am a Commissioning Editor for Cambridge Scholars Publishing (further details below my signature) with a brief to develop the subject areas in which we publish books. As such I am in the process of developing collections based on key areas of Crystallography. As I believe you already have some experience of academic and scientific publication in this field, I wondered whether you would consider publishing a title with us. We are accepting proposals for monographs and edited collections.

We offer a fast, fair and friendly proposal review. Our titles are distributed worldwide via our international network of booksellers including Amazon, Blackwell, Baker & Taylor, YBP and Ingram, in handsome hardback, as well as eBook formats. We offer an escalating royalty payment – the more we sell, the higher the royalty rate. Your book will never be out of stock, with our unique Print on Time global distribution system. And we never charge for publication.

You can download a Book Proposal Form from our website. Alternatively, contact me and I will gladly send one to you and answer any queries you may have.

We are also developing Editorial Advisory Boards across our publishing fields. If this is something that you would like to learn more about, or apply to join, please do let me know. You can see more details on our website.

I look forward to hearing from you.

Kind regards,

Helen Edwards
Commissioning Editor

Social Media: Twitter Facebook LinkedIn Blog

About Cambridge Scholars Publishing ( Cambridge Scholars Publishing (CSP) is an independent academic publisher, founded in 2001 by former lecturers and researchers from the University of Cambridge who felt existing publishing companies took too long to publish academic books, monographs, conference proceedings and textbooks. CSP has its own printing facility, now publishes 750+ titles each year in both electronic and print formats and is committed to providing a forward-thinking publishing service that champions original thinking, whilst ensuring we put our authors at the heart of everything we do. Our back list catalogue contains approximately 7,500 titles.

Click here to Unsubscribe


Cambridge Scholars Publishing – Reg. No: 4333775; VAT No: 108280727
Registered Address: Lady Stephenson Library, Welbeck Road, NE6 2PA

Now, this mentions the royalties in the email, and the text seems a little more precise in addressing me (“I believe you already have some experience of academic and scientific publication in this field“). Having said that, it is still pretty generic.

Conclusion: Still spammers, but not predators. As yet I can’t gauge the quality of the content. A couple of samples I looked at seemed pretty solid, though the production left  a little to be desired — pixelated, oddly positioned equations…


…and a few other style things that look a little amateurish (hyphens rather than en dashes in bullet lists and number ranges, that sort of thing). I suspect they’re doing the best they can with limited resources. Could be quite fine if the author is happy with a slightly low-key publication, but as yet not in the front rank.



Plotly on cygwin; the absolute basics

This has to be about the absolute basics. I don’t know anything else.

Plotly ( is an interactive, online graphing tool. It can be called from JavaScript, Python, whatever. This post is about getting it to work through Python on Cygwin.

This all mostly follows instructions on the Plotly website.

(1) Installed via pip. What’s pip? A Python package manager. I ran the Cygwin setup.exe program and made sure that Puython was installed (in my case it was 2.7) and then installed the matching pip2.7 (Cygwin package python2-pip). So installed that and all its dependencies.

(2) Opened a Cygwin terminal (not an X terminal, just mintty) and typed:

$ pip install plotly

and watched some magic occur.

(3) Went to the Plotly website and created my (free) account. Went to my account settings and selected ‘API keys’. Could not see key — just looked like a row of dots! But hitting ‘Regenerate key’ gave me a new, visible one. Copied that text and noted my username.

(4) In Cygwin, (note, $ is the Cygwin prompt, >>> is the python prompt) typed:

$ python
Python 2.7.13 (default, Mar 13 2017, 20:56:15)
[GCC 5.4.0] on Cygwin

>>> import plotly
>>>'DarrenG2', api_key='<<insert your key here>>')


This set up the info needed for the local Plotly/Python installation to talk to the website where the graph will appear.

(5) Checked that this had worked out. Back at Cygwin prompt, in home directory, typed:

$ cat .plotly/.credentials
    "username": "DarrenG2",
    "stream_ids": [],
    "api_key": "<<your key here>>",
    "proxy_username": "",
    "proxy_password": ""

(6) OK, looked good. Now, tested it by grabbing an example from the Plotly website. Created a file ‘’ and pasted in some text copied from the website:

import plotly.plotly as py	
from plotly.graph_objs import *

trace0 = Scatter(
    x=[1, 2, 3, 4],
    y=[10, 15, 13, 17]
trace1 = Scatter(
    x=[1, 2, 3, 4],
    y=[16, 5, 11, 9]
data = Data([trace0, trace1])

py.plot(data, filename = 'basic-line')

(7) Then saved and ran the script

$ python2.7.exe
High five! You successfuly sent some data to your account on plotly. View your plot in your browser at or inside your account where it is named 'basic-line'

Looked good, though they’ve spelled ‘successfully’ unsuccessfully.

(8) But where was the graph? Well, I was working in a basic terminal window. It sent the graph to the web, but then tried to open it using the default links, the text browser. So all I got was a blank screen (typed ‘q’ to quit links). There are a couple of options to see the graph — one is just to paste the given URL into Edge, Chrome, Firefox. Another is to tell Cygwin to look elsewhere for its browser…

(9) Edited my .bash_profile file in my Cygwin home directory and added these two lines:

$ BROWSER=/cygdrive/c/Users/darren/AppData/Local/Mozilla\ Firefox/firefox.exe
$ export BROWSER

This set up the environment variable BROWSER and pointed it at the firefox.exe file (non-admin install, so in an unusual place). I also ran these two lines in the terminal window to save me closing and reopening it.

(10) Repeated step (7) and — lo and behold! — a Firefox window popped up and the graph was in it!

Plotly graph in Firefox, after running the script in Cygwin.

Plotly graph in Firefox, after running the script in Cygwin.

Now, mastery of Plotly and Python is a much bigger project, but at least this offers the beginnings. Note also that the graph can be edited interactively within the webpage where it appears.


Plots away!


Journal self-archiving policies

One of the most-viewed pages here (it’s all relative; still not very many hits really) is the list of dodgy publishers. It’s a drop in the ocean, but it gets a few hits. Something else I’d like to bring all into one place, even though it’s been done elsewhere, is to summarise self-archiving polices. I’ll focus on the journals I’ve published in, preparatory to putting together a web archive of all my papers that I am allowed to self-archive (on my website and maybe on ResearchGate). It’s really just a resource for me, but I might as well make it public.

Some journals are open access; you don’t need to self-archive those, but usually you can.

Some allow you to archive a proper reprint, processed and edited by the journal — like the IUCr, as shown below.

Some suggest you archive the ‘author’s final version’ but don’t want you to put up anything with the journal’s imprimatur.

Some say ‘mine mine mine’ and don’t let you host it at all. I hope to make this clear.

The page lives at, and so far has exactly one (1) entry, the good old IUCr, which has a very enlightened policy. They allow self-archiving as long as you use the official e-reprint, rather than just the downloaded PDF, and they request that you provide a link to the journal. Seems very reasonable. The official e-reprint is easy to recognise; it has a distinctive front page with some official words on it, something like this (colours may vary):

Front page of IUCr reprint, showing it is dfferent from download from journal.

Note the box with the notice near the bottom of the page.


I think their policy is very reasonable because the IUCr has a very professional publication and editorial team who need to be paid and ought to be paid. Subscriptions are part of the mix, yet they allow authors to house their own work and to distribute copies to colleagues freely. It seems a very sensible mix.

More updates as they come to hand.

The last domino falls: A little bit of science.

This paper and its deposited material explore clustering of 2 × 1 dimers (dominoes) subject to simple interactions and temperature. Much of the work in domino tilings has been statistical, combinatorial and thermodynamic in nature. Instead, here, the domino is used as a simple model of a non-spherical molecule to explore aggregation, rather as if the molecules were interacting in solution. As a result, the work does not look at how many ways there are to tile a plane, but at how the cluster evolves with different parameters in the potential that governs the clustering. These parameters include the rules used to select which of the many possible dominoes will be added to the cluster, and temperature. It is shown that qualitative changes in clustering behaviour occur with temperature, including affects on the shape of the cluster, vacancies and the domain structure.

The paper is on the web, open access, at and It comes with a bundle of software anyone can use to play with the model, modify it, whatever. Please do!

It’s basically a toy model, but it shows some nice behaviour. Apologies to the red/green colour-blind.



T=0. At low temperature, the model gives strongly structured domains.



T=0.16. At intermediate temperatures, the ordering begins to break down, though remains apparent. If temperature continues to increase, vacancies appear.



T=10. Vacancies, no domains, really. Addition of new dominoes is almost random.




This week I started work at Biotext, a company that specialises in writing and editing complex scientific documents. It’s incredibly exciting — it’s the kind of opportunity that does not often come along. There’s a huge amount to learn, but that is part of the enjoyment.

As the name suggests, their focus has often been on biological material, though in the broadest sense — agriculture, environment, and medicine feature strongly. I’m hoping to increase the expertise in the physical sciences.

I looks like a chance to bring together science and writing, and it has come along at a time when I was on the lookout for a new job.

Good luck to me!



Old g95 (for the make use of)

I needed to compile a Windows g95 binary for someone. I have Win 7 in a VM on VirtualBox. I had the g95 install tree from a (quite old) back-up of a previous computer, but not a proper install.

The install tree looks like this:

C:\util>dir /s g95
 Volume in drive C has no label.
 Volume Serial Number is 8440-3CD9

 Directory of C:\util\g95

23/08/2012  09:42 AM              .
23/08/2012  09:42 AM              ..
23/08/2012  09:42 AM              bin
23/08/2012  09:42 AM              doc
23/08/2012  09:42 AM              lib
23/08/2012  09:42 AM            55,782 uninstall-g95.exe
               1 File(s)         55,782 bytes

 Directory of C:\util\g95\bin

23/08/2012  09:42 AM              .
23/08/2012  09:42 AM              ..
26/03/2008  11:49 AM           553,984 ar.exe
26/03/2008  11:49 AM           827,904 as.exe
17/06/2009  09:44 PM           123,046 g95.exe
26/03/2008  11:49 AM           782,848 ld.exe
28/12/2007  12:23 AM            15,964 mingwm10.dll
26/03/2008  11:49 AM           554,496 ranlib.exe
26/03/2008  11:49 AM           685,568 strip.exe
               7 File(s)      3,543,810 bytes

 Directory of C:\util\g95\doc

23/08/2012  09:42 AM              .
23/08/2012  09:42 AM              ..
16/10/2004  09:36 PM            17,015 bg.gif
27/11/2004  03:51 AM            18,007 COPYING.txt
08/12/2005  06:19 AM            22,431 docs.html
23/11/2004  12:00 PM           107,122 g95.bmp
02/01/2007  01:59 AM           170,619 G95Manual.pdf
31/05/2008  06:59 AM            11,858 Readme.html
31/05/2008  07:00 AM             6,687 README.txt
               7 File(s)        353,739 bytes

 Directory of C:\util\g95\lib

23/08/2012  09:42 AM              .
23/08/2012  09:42 AM              ..
28/12/2007  12:23 AM             2,192 crt1.o
28/12/2007  12:23 AM             2,288 crt2.o
28/12/2007  12:23 AM             1,239 dllcrt2.o
23/08/2012  09:42 AM              gcc-lib
22/10/2006  01:27 AM           408,608 libadvapi32.a
30/10/2005  11:13 AM           253,890 libgdi32.a
22/10/2006  01:27 AM           594,018 libkernel32.a
28/12/2007  12:23 AM               458 libm.a
28/12/2007  12:23 AM             7,514 libmingw32.a
28/12/2007  12:23 AM           267,880 libmingwex.a
28/12/2007  12:23 AM            82,558 libmoldname.a
28/12/2007  12:23 AM           503,692 libmsvcrt.a
22/10/2006  01:27 AM           128,262 libshell32.a
22/10/2006  01:27 AM           435,754 libuser32.a
30/10/2005  11:13 AM            82,086 libws2_32.a
              14 File(s)      2,770,439 bytes

 Directory of C:\util\g95\lib\gcc-lib

23/08/2012  09:42 AM              .
23/08/2012  09:42 AM              ..
23/08/2012  09:42 AM              i686-pc-mingw32
               0 File(s)              0 bytes

 Directory of C:\util\g95\lib\gcc-lib\i686-pc-mingw32

23/08/2012  09:42 AM              .
23/08/2012  09:42 AM              ..
23/08/2012  09:42 AM              4.0.4
               0 File(s)              0 bytes

 Directory of C:\util\g95\lib\gcc-lib\i686-pc-mingw32\4.0.4

23/08/2012  09:42 AM              .
23/08/2012  09:42 AM              ..
23/08/2012  09:42 AM             1,022 cc1.lnk
17/06/2009  09:44 PM         5,242,021 f951.exe
17/06/2009  09:44 PM           859,168 libf95.a
17/06/2009  09:44 PM            61,284 libgcc.a
               4 File(s)      6,163,495 bytes

     Total Files Listed:
              33 File(s)     12,887,265 bytes
              20 Dir(s)  42,207,707,136 bytes free

Now, all that is required to make this work is to set some environment variables. (Start → Control Panel → System → Advanced System Settings → Environment Variables).

First, I had to put some directories in the path, so I edit the PATH variable. It works if I have the path to the g95.exe binary and also to the f951.exe file. That is:

PATH=C:\util\g95\bin;c:\util\winvi;c:\util\g95\lib\gcc-lib\i686-pc-mingw32\4.0.4;[[INSERT REST OF PATH HERE]]

I’ve put [[INSERT REST OF PATH HERE]] at the back, but I’ve actually got the g95-related paths at the back (you want the most commonly used bits of the path at the front, not that it matters with modern fast coomputers). Then, I want to create a new variable called LIBRARY_PATH:


Now, I don’t know if I need all three directories in the LIBRARY_PATH, but it works so I am not complaining.

So to compile my tiny little program I can now type:

X:\Downloads\Brill_dir>g95 -o Brill.exe brillouin.f90

And it works. Is it statically linked? Well, on Linux, dynamically linked, compiled with GFortran, it’s about 68 kB. This binary is about 360 kB, so I sure hope it is statically linked!

Caveats: I have not tried anything fancier than this absolutely basic compile. It works. Compiling with the -static flag makes no difference to the size of the binary.