* Posts by jjq

3 posts • joined 16 Apr 2010

Chemists bitten by Python scripts: How different OSes produced different results during test number-crunching


same old mistakes

As already noted, the quality of software in the scientific community is generally lamentable; little or no design and poor execution. In this regard, Les Hatton's ``The T Experiments: Errors In Scientific Software'' is worth a read: https://www.leshatton.org/IEEE_CSE_297.html . My own scratchings include https://books.google.com/books?id=OOgBQ97VrpIC&pg=PA3&lpg=PA3 but the text would need to be read to appreciate why I'm not engaging in self promotion.

Last week's Brexit meeting between Johnson and Varadkar, at Thornton Manor, took place five miles from where I watched the moon landing, aged 7. Aged 29, I made it to NASA Langley where Armstrong practiced his moon landings; with a fresh PhD in Aeronautics and a large piece of software I'd written for my thesis. That was 1991. Fast forward to today, with the intervening rise of ``computational science'', the situation for many grad students/post-docs is dire. For they are expected to work with large, legacy codes that are often simply not fit for purpose.

Thus while the present article is to be welcomed, it falls at the superficial end of the spectrum in terms of highlighting computational problems in the research world.

Rid yourself of Adobe: New Firefox 19.0 gets JAVASCRIPT PDF viewer


You see what your knowledge tells you you're seeing

To all those who have posted comments here, I would urge you to view

the opening of James Burke's "The Day the Universe Changed" then ask

yourself how your thoughts will be judged by a computer historian in

the far future, say 2360. The chances are that we will all be thought

moronic for our simplistic, self-centred views.

Note I make this request as someone who has filed a number of PDF

vulnerabilities, as can be verified by a Google search on "James Quirk CVE."

I am not, however, a PDF apologist; nor am I a self-publicist.

My reason for popping up here is to look for volunteers who would be happy to cast

a critical eye over a multi-resolution PDF I am currently constructing. Said PDF ponders

what an electronic document should be to support the propagation of computational expertise

and will be unveiled at a scientific meeting in Seattle, this July.

Sadly, I can't offer any remuneration. But if you have an inquisitive mind,

I can offer material which might stimulate your intellectual juices.

For instance, one experimental PDF has a functioning web-browser embedded

inside a Mandelbrot set, which in turn is buried inside the eye of a duckrabbit

who is under the watchful gaze of a Cheshire Cat. And the Cheshire cat

is buried inside JFK's Moon Speech, and so the madness goes on for a

10^50 variation in length scale; a multi-scale oddysey that is all squeezed

into the dot of an "i" on a PDF page.

Should you wish to learn more, a Google search will throw up my contact details.

Best regards,


Attacks exploit unpatched weakness in Adobe apps


An Alternative Perspective -- Scientific Accountability

I've been following Dan Goodin's articles on PDF vulnerabilities

quite closely for some time now and I would like to offer an

alternative perspective. Specifically, instead of bashing PDF

for its security weaknesses, I believe the format should be

appreciated for the many scientific possibilities it offers, especially

in light of the ongoing climategate scandal.

Before I elaborate on my viewpoint, I should note that I do take

PDF vulnerabilities seriously. For instance, the recent security advisory:


lists me as having identified CVE-2010-0197. And Quirk2003,

http://www.amrita-cfd.org/doc/amr2003, is an example of a PDF

that includes a built-in security FAQ. It does so, because the document

includes /Launch actions, which currently have Stevens in a froth.

However, for added security, its /Launch actions are only active

when the document is viewed using a custom PDF pre-processor.

Therefore, while I would not bill myself as a security expert,

I like to think I have a grasp of the main issues.

My real interest lies with the concept of self-substantiating,

journal articles for injecting rigour into the practical aspects

of computational science. Imagine electronic documents that

preserve the look-and-feel of a traditional scholarly publication,

while containing embedded examples that allow the interested reader

to sample the reported work, first hand, right down to its smallest detail.

Well, Quirk20003 shows that such documents can be prototyped using PDF.

Why bother? Some of you may have read a recent story in The Guardian,

by Darell Ince: ``If you're going to do good science,

release the computer code too'' see:


It is an open secret in scientific computing that programming standards

are extremely poor and desperately need improving.

As luck would have it, I posted the last comment on Ince's article

and so it has its own url,


But the downside to posting the last comment is that I got no feedback.

Undeterred, I contacted Ince directly. Then following an exchange of

e-mails and a phone call, he pointed me in the direction of

``The Fourth Paradigm'' -- scientific discovery

through data intensive processing, see http://www.fourthparadigm.org .

And it was while annotating this Microsoft-sponsored

book that I stumbled upon CVE-2010-0197 .

Now as an undergraduate, I lived in Fitzwilliam St, Cambridge,

directly opposite to where Darwin once lived, and so I'm fully aware

of my own limitations as a scientist. However, given my document

dabblings, it pains me to see the advocacy of a new scientific paradigm,

distributed as a PDF, in which the authors cannot provide the

critical reader with worked examples to show their ``computational thinking.''

The situation is analogous to a mathematician claiming to have a wonderful proof

but only being prepared to discuss the proof in vague generalities.

It jars, because as my annotated version shows:


PDF allows for a much richer dialogue between technical author and

technical reader.

Here I need to make it very clear that my document dabblings are just that,

dabblings, and anyone who downloads jjq-on-4th-paradigm.pdf will soon

see the limitations of my work. The scientific question, however,

is not whether I'm right or wrong. Nor has it anything to do with

format wars, PDF vs XML vs A.N.OTHER. It has to do with accountability,

scholarship, and maintaining standards of critical thinking.

This week the US Library of Congress announced a project to

archive Twitter which, while I have grave misgivings about the target

material, shows that society takes its archiving duties seriously.

For me, a much more exciting initiative is the Federal Research

Public Access Act (FRPAA):


which today, after a number of false starts, was introduced

in the US House of Representatives, not six miles from where

I'm composing this message.

The challenge I would like to leave readers of Dan Goodin's articles

is that the next time you are tempted to bash PDF for having unnecessary

and dangerous features: stop, and imagine a world where taxpayers,

educators, and students could download and try out ``computational classics.''

These are entites that rival literary ones in terms of their cultural significance and

would help inspire generation after generation to the intellectual joys

of computer-based science. Then imagine what document features would be needed

to support said computational classics.

This year, The Royal Society (the world's oldest scientific organization still

in existence) is celebrating its 350th anniversary.

So do your imagining in the year 2360 when the society celebrates

its 700th anniversary. By then, the inherent weaknesses of current

journal papers, for reporting computational work, not withstanding

their strengths, will be apparent to even a kindergarten student.

It is also to be hoped that by then society will have a better

handle on how to deal with computer security.

Yes security is important, but it is also important for document formats

to evolve so as to support rigorous computer-based science.

James J. Quirk

16th April 2010

Alexandria, VA


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