Thirty Years of Preprints

Posted in Open Access with tags , , , , on February 21, 2021 by telescoper

I thought I’d share an interesting paper (by Xie, Shen & Wang) that I found on the arXiv with the title Is preprint the future of science? A thirty year journey of online preprint services. The abstract reads:

Preprint is a version of a scientific paper that is publicly distributed preceding formal peer review. Since the launch of arXiv in 1991, preprints have been increasingly distributed over the Internet as opposed to paper copies. It allows open online access to disseminate the original research within a few days, often at a very low operating cost. This work overviews how preprint has been evolving and impacting the research community over the past thirty years alongside the growth of the Web. In this work, we first report that the number of preprints has exponentially increased 63 times in 30 years, although it only accounts for 4% of research articles. Second, we quantify the benefits that preprints bring to authors: preprints reach an audience 14 months earlier on average and associate with five times more citations compared with a non-preprint counterpart. Last, to address the quality concern of preprints, we discover that 41% of preprints are ultimately published at a peer-reviewed destination, and the published venues are as influential as papers without a preprint version. Additionally, we discuss the unprecedented role of preprints in communicating the latest research data during recent public health emergencies. In conclusion, we provide quantitative evidence to unveil the positive impact of preprints on individual researchers and the community. Preprints make scholarly communication more efficient by disseminating scientific discoveries more rapidly and widely with the aid of Web technologies. The measurements we present in this study can help researchers and policymakers make informed decisions about how to effectively use and responsibly embrace a preprint culture.

The paper makes a number of good arguments, backed up with evidence, as to why preprints are a good idea. I recommend reading it.

Here is Figure 1 from the paper:

(Parts of the chart are difficult to read, so see the paper for details).

This shows that about 50% of all preprints are in the areas of physics and mathematics and their distribution mode is predominantly through the arXiv. Other scientific disciplines have much lower prevalence of preprints, e.g. biology. I’ve been putting my papers on arXiv since the early Nineties, i.e. for most of the duration of the period covered by the paper. I don’t know why other fields are so backward.

It’s standard practice in my own field of astrophysics to put preprints of articles on the arXiv but younger readers will probably not realize that preprints were not always produced in the electronic form they are today. We all used to make large numbers of these and post them at great expense to (potentially) interested colleagues before publication in order to get comments. That was extremely useful because a paper could take over a year to be published after being refereed for a journal: that’s too long a timescale when a PhD or PDRA position is only a few years in duration. The first papers I was given to read as a new graduate student in 1985 were all preprints that were not published until well into the following year. In some cases I had more or less figured out what they were about by the time they appeared in a journal!

The practice of circulating preprints persisted well into the 1990s. Usually these were produced by institutions with a distinctive design, logo, etc which gave them a professional look, which made it easier to distinguish `serious’ papers from crank material (which was also in circulation). This also suggested that some internal refereeing inside an institution had taken place before an “official” preprint was produced and this lending it an air of trustworthiness. Smaller institutions couldn’t afford all this, so were somewhat excluded from the preprint business.

With the arrival of the arXiv the practice of circulating hard copies of preprints in astrophysics gradually died out, to be replaced by ever-increasing numbers of electronic articles. The arXiv does have some gatekeeping – in the sense there are some controls on who can deposit a preprint there – but it is definitely far easier to circulate a preprint now than it was.

It is still the case that big institutions and collaborations insist on quite strict internal refereeing before publishing a preprint – and some even insist on waiting for a paper to be accepted by a journal before adding it to the arXiv – but there’s no denying that among the wheat there is quite a lot of chaff, some of which attracts media coverage that it does not deserve. It must be admitted, however, that the same can be said of some papers that have passed peer review and appeared in high-profile journals! No system that is operated by human beings will ever be flawless, and peer review is no different.

Nowadays, in astrophysics, the single most important point of access to scientific literature is through the arXiv, which is why the Open Journal of Astrophysics was set up as an overlay journal to provide a level of rigorous peer review for preprints, not only to provide a sort of quality mark but also to improve the paper through the editorial process.

So is the preprint the future of science? I think that depends on how far ahead you are willing to look. In my opinion we are currently in an era of transition trying to shoehorn old publishing practices into a digital world. At some point in the future people will realize that the scientific paper itself – whether a preprint or not – is an outmoded 18th Century concept and there are far more effective ways of disseminating scientific ideas and information at our fingertips if only we stopped living in the past.

Irish Bingo Lingo

Posted in Education with tags , on February 20, 2021 by telescoper

This week I had my third lunchtime Irish language class during which, among a few other things, we learned about numbers (just 1-10 so far). After some practice in pronunciation, we then had some practice in comprehension by playing Bingo in Irish. Out of interest I’ve put up the Irish numbers along with their counterparts in Welsh for reasons which will become clear:

The first thing to note is the presence of the particle “a” in front of the number in Irish. This is a consequence of something I didn’t know about before taking this course. In Irish there are different ways of using numbers depending on whether you’re using them just as numbers (in which case you put the “a” in front) or if you’re using them to denote a quantity of things or people (in which cases you don’t put the “a” in front but have to use a particular grammatical construction involving the thing being counted). Numbers in Irish are not used simply as adjectives, as in for example English. That’s not how it works in any other language I know. So far we haven’t been taught about these other counting systems so I can’t say any more.

The second thing concerns the similarity of these numbers to those in many other European languages, which is not surprising since they share an Indo-European origin. Integers are such basic things that they are embedded at a very deep level in languages. The Irish numbers resemble those in French particularly strongly. This may be a consequence of modern Irish being influenced by Norman French or may just be evidence of the common root.

Notice the comparison with Welsh, however, which gives very clear evidence of the ancient mutation that led to the distinct language branches of p-Celtic and q-Celtic. Look at the number 4. In Irish, this is a ceathair (which is pronounced “a ka-hir”; the t is weakened by the following h) which resembles the French quatre. There is no q in the standard Irish alphabet but the sound is similar. In Welsh we have pedwar which, apart from the initial letter being a “p”, is structurally similar to the Irish version. A similar change in initial consonant happens with the number five.

Anyway I’m enjoying learning Irish. It’s a very interesting challenge. In the rest of the class we learned how to answer questions like What is your name (Cad is ainm duit?) followed by an exercise in giving names to celebrities shown in photographs. I firmly established my status as the Old Fogey of the class in this part, by being unable to identify a person called Shakira who, I’m told, is a popular vocal artiste of some sort.

The Return to Schools in Ireland – The Facts

Posted in Covid-19, Education, Politics on February 20, 2021 by telescoper

There is some confusion going around about precisely when schools will reopen in the Republic of Ireland. In order to provide a service to the community I therefore thought I would summarize the main points here as clearly, concisely and coherently as possible.

At Primary schools, Junior infants or perhaps Junior and Senior infants and perhaps also including First and Second Class will return either separately or together on either 1st March or possibly 8th March. All other pupils will definitely return on 15th March or possibly a week or two weeks later but definitely by three weeks later than that unless there’s a change of plan.

At Secondary schools, the Junior Cycle will continue as normal apart from not actually happening: the Junior Certificate will be replaced by a voucher to spend on computer games. The Senior Cycle will return at the same time as Primary Schools, or at some different time depending on the circumstances, or perhaps just for the day before the Leaving Certificate examinations. Pupils will be able to choose either to take the examination or to receive a grade based on all the coursework they haven’t done because the schools have been closed or to receive a grade based on how much their parents can afford to pay. Leaving Certificate examinations will take place according to the published timetable unless they’re cancelled at the last minute.

Transition Year students have been completely forgotten but no doubt somebody will think of something when they remember.

I hope this clarifies the situation.

Norma Foley is 51.

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R.I.P. Roger Griffin (1935-2021)

Posted in Film, History, The Universe and Stuff with tags , , , on February 19, 2021 by telescoper

Roger Griffin (picture credit: St John’s College, Cambridge)

Earlier today I heard the sad news of the death at the age of 85 of astronomer Roger Griffin. He passed away on 12th February 2021.

Roger Griffin worked at Cambridge for over six decades, except for one year when he had a post-doctorate position at the Mount Wilson and Palomar Observatories, of the Carnegie Institution of Washington. He was the Assistant Director of Research in Astronomy at the University of Cambridge for nine years before he was promoted to a Readership of Observational Astronomy and later a Professorship. He appeared in the film Starmen alongside Donald Lyndon-Bell, Wal Sargent and Neville “Nick” Woolf.

Roger Griffin worked on astronomical spectroscopy and his main scientific claim to fame was that he invented a method of measuring radial velocities of stars in binary systems described in this classic paper published in 1967:

Over the subsequent years he published many radial velocity curves thus obtained in a long series of papers in the Observatory Magazine and the same method was subsequently used for measuring orbits of black holes and detecting extrasolar planets.

Despite the Cambridge connection I never met Roger Griffin personally but people who did talk about him with great affection and he will be greatly missed.

Rest in peace, Roger Griffin (1935-2021)

Cosmology Talks: Alvaro Pozo on Potential Evidence for Wave Dark Matter

Posted in The Universe and Stuff with tags , , , , , , , , , on February 19, 2021 by telescoper

It’s time I shared another one of those interesting cosmology talks on the Youtube channel curated by Shaun Hotchkiss. This channel features technical talks rather than popular expositions so it won’t be everyone’s cup of tea but for those seriously interested in cosmology at a research level they should prove interesting. This is quite a recent one, from about a week ago.

In the talk, Alvaro Pozo tells us about a recent paper where he an collaborators detect the transition between a core (flat density profile) and halo (power law density profile) in dwarf galaxies. The full core + halo profile matches very closely what is expected in simulations of wave dark matter (sometimes called “fuzzy” dark matter), by which is meant dark matter consisting of a particle so light that its de Broglie wavelength is long enough to be astrophysically relevant. That is, there is a very flat core, which then drops off suddenly and then flattens off to a decaying power-law profile. The core matches the soliton expected in wave dark matter and the halo matches an outer NFW profile expected outside the soliton. They also detect evidence for tidal stripping of the matter in the galaxies. The galaxies closer to the centre of the Milky Way have their transition point between core and halo happen at smaller densities (despite the core density itself not being systematically smaller). The transition also appears to happen closer to the centre of the galaxy, which matches simulations. Of course the core+halo pattern they have clearly observed might be due to something else, but the match between wave dark matter simulations and observations is impressive. An important  caveat is that the mass for the dark matter that they use is very small and in significant tension with Lyman Alpha constraints for wave-like dark matter. This might indicate that the source of this universal core+halo pattern they’re observing comes from something else, or it might indicate that the wave dark matter is more complicated than represented in the simplest models.

P. S. The papers that accompany this talk can be found here.

P.P.S. If you’re interested in wave dark matter there is a nice recent review article by Lam Hui here.

Memories of the Aldwych Bus Bombing

Posted in Biographical, History, LGBT with tags , , , , on February 18, 2021 by telescoper

Twitter just reminded that today is the 25th anniversary of the Aldwych Bus Bombing, which happened while I was living in London. In fact, as it happens, in the late evening of Sunday 18th February 1996, when the bomb went off I was scarily close to it. The bomb went off in Aldwych, near The Strand, while I was standing in a fairly long queue trying to get into a night club near Covent Garden. The explosion was no more than 200 yards away from me.

The reason I was there was a one-nighter called Queer Nation which was on every Sunday in the 90s. I went there quite regularly and provided very nice music and provided an environment that attracted a very interesting crowd of people. Anyway I preferred it to the very big clubs of the more commercial London gay scene of the time, largely because it wasn’t such a big venue as many of the others and you could actually talk to people there without having to shout.

The queue to get in wasn’t too long and I had only been waiting a few minutes when there was a loud bang followed by a tinkling sound caused by pieces of glass falling to the ground. Everyone in the queue including myself instinctively dropped to the ground. The blast sounded very close but we were in a narrow street surrounded by tall buildings and it was hard to figure out from which direction the sound had come from. Shortly afterwards the air was filled with the sound of sirens from police cars and other emergency vehicles. According to Wikipedia the bomb went off at 22:38.

It turned out that an IRA operative had accidentally detonated a bomb on a bus, apparently while en route to plant it somewhere else (probably King’s Cross). The bomb consisted of 2kg of Semtex, which is rather a large amount, hence the enormous blast. The explosion happened on the upper deck of the bus and the only person killed was the person carrying the bomb.

After the people outside the nighclub had stood up and dusted ourselves down, we talked briefly about what to do next. Everyone was rattled. I didn’t feel like going clubbing after what had clearly been a terrorist attack so I said goodnight and left for home.

Getting home turned out to be rather difficult, however. The police quickly threw a cordon around the site of the blast so that several blocks either side were inaccessible. Aldwych is in the West End, but I lived in the East End, on the wrong side of sealed-off area, so I had to find a way around it before heading home. No buses or taxis were to be found so I had to walk all the way. I ended up having to go as far North as the Angel before walking along the City Road towards the East End. I didn’t arrive him until about three o’clock in the morning (though I did stop off for a Bagel in Spitalfields on the way).

So that was 25 years ago. Fortunately since then we’ve had the Good Friday Agreement and such events have virtually disappeared. But how long will that peace last?

New Publication at the Open Journal of Astrophysics

Posted in Open Access, The Universe and Stuff with tags , , , , , on February 18, 2021 by telescoper

Time to announce another publication in the Open Journal of Astrophysics. This one was published yesterday, actually, but I didn’t get time to post about it until just now. It is the second paper in Volume 4 (2021).

The latest publication is entitled Characterizing the Sample Selection for Supernova Cosmology and is written by Alex G. Kim on behalf of the LSST Dark Energy Science Collaboration.  It’s nice to be getting papers from large collaborations like this!

Here is a screen grab of the overlay which includes the abstract:

You can click on the image to make it larger should you wish to do so. You can find the arXiv version of the paper here. This is one for the Cosmology and Nongalactic Astrophysics folder.

Birth of a Galaxy – Max Ernst

Posted in Art, The Universe and Stuff with tags , , on February 17, 2021 by telescoper

by Max Ernst (1891-1976), painted in 1969, 92 x 73 cm, oil on canvas.

Job in Theoretical Physics at Maynooth!

Posted in Maynooth with tags , on February 17, 2021 by telescoper

Just a short post passing on the information that we have a fixed-term job available in the Department of Theoretical Physics at Maynooth University. You can find the details here.

The position is for 10 months, starting in September 2021, and is to provide teaching cover for Professor Jiri Vala who will be on sabbatical next year. He originally intended to take his sabbatical this academic year, starting in September 2020, hence the previous advertisement of this post, but it was postponed for reasons of Covid-19 and the previous position was not filled.

I know it is a relatively short appointment, but it seems to me that it would provide a good opportunity for an early-career academic, perhaps someone straight out of a PhD, to gain some teaching experience.

The deadline for applications is 23.30 on Sunday March 14th, i.e. about 4 weeks away, and you should apply through the jobs portal here.

If you’d like to know any more please feel free to contact me privately.

Oh, and please feel free to pass this on to anyone who may be interested!

Zel’dovich Pancake Day!

Posted in The Universe and Stuff with tags , , , on February 16, 2021 by telescoper

Today it’s Shrove Tuesday but unfortunately I forgot to buy shroves yesterday so will have to make do with pancakes instead, but not the usual kind. I’ve blogged before about the Zel’dovich Approximation (published in Zeldovich, Ya.B. 1970, A&A, 5, 84) but there’s no harm in describing this classic again. Here’s the first page of the original paper:

zeld

In a nutshell, this daringly simple approximation considers the evolution of particles in an expanding Universe from an early near-uniform state into the non-linear regime as a sort of ballistic, or kinematic, process. Imagine the matter particles are initial placed on a uniform grid, where they are labelled by Lagrangian coordinates vec{q}. Their (Eulerian) positions at some later time t are taken to be

vec{r}(vec(q),t) = a(t) vec{x}(vec{q},t) = a(t) left[ vec{q} + b(t) vec{s}(vec{q},t) right].

Here the vec{x} coordinates are comoving, i.e. scaled with the expansion of the Universe using the scale factor a(t). The displacement vec{s}(vec{q},t) between initial and final positions in comoving coordinates is taken to have the form

vec{s}(vec{q},t)= vec{nabla} Phi_0 (vec{q})

where Phi_0 is a kind of velocity potential (which is also in linear Newtonian theory proportional to the gravitational potential).If we’ve got the theory right then the gravitational potential field defined over the initial positions is a Gaussian random field. The function b(t) is the growing mode of density perturbations in the linear theory of gravitational instability.

This all means that the particles just get a small initial kick from the uniform Lagrangian grid and their subsequent motion carries on in the same direction. The approximation predicts the formation of caustics in the final density field when particles from two or more different initial locations arrive at the same final location, a condition known as shell-crossing. The caustics are identified with the main elements we find in large-scale structure. Because the initial collapse is usually along one direction the dominant structures are known as pancakes (or, as Zel’dovich himself might have called them, blini…).

Here’s a picture of a simulation showing these structures from the classic paper of Davis, Efstathiou, Frenk & White (1985):

Despite its simplicity this approximation is known to perform extremely well at reproducing the morphology of the cosmic web, although it breaks down after shell-crossing has occurred. In reality, bound structures are formed whereas the Zel’dovich approximation simply predicts that particles sail straight through the caustic which consequently evaporates.