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Grammar that!

Brilliant takedown of a grammar jerk in the comments at Ars Technica. User Kikjou writes: "Bacteria is plural of bacterium. Please use is correctly. The same goes for media and medium, which is not in this article but is often misused in scientific writing." To which Ars Centurion Okton responds:

In Latin maybe. And the phrase you are nitpicking is actually "from a bacteria". So if you were anything but pedantic, you would exclaim "that requires the ablative of source! In the singular." Following your logic, the article should read "...from a bacterio". But wait, Latin has no indefinite article, so whether it is "a bacterium" or "a bacterio", the noun phrase is redundant since indefiniteness is presupposed in simple noun forms. But "from bacterio" is neither grammatical English nor comprehensible Latin. And the ablative of source usually employs a preposition, so "from a bacteria" should read "ab bacterio" to be exact.

Problem is: This is not FRICKING Latin. This is a word of Latin origin that has entered into English. Therefore our rules apply. Because if you demand a Latin singular, I demand the proper Latin case, pronunciation, etc. We took the plural form for obvious reasons. Because of the physical size of bacteria, the word became a mass noun and functions as both plural and singular. Same reason for taking "data": it is collective. There are rarely "bacterias". And certainly no "datas". One sheep. Two sheep. Ten sheep. One form, all numbers. It is legal in English - accept it.

I can only assume you are one of those people who thinks the plural of "octopus" is "octopi" as well. Except there is no such word as "octopus" in Latin. The word is "polypus", "Octopus" is from the Greek ὀκτάπους, and the plural of that is ὀκτάποδες. And even if people knew "octopodes" was the true plural, they would say it wrong since the epsilon is not silent. Why? Because it is adapted for usage in the new language. It has no obligations to its old morphology and phonology.

By your inanity, if you ever say the word "cherry" for a single unit, I have every right to chastise you. That word never existed in French. "Cheris(e)" is the singular form that was introduced into English. How dare you impose English conventions of depluralization on it! You will say "Shair-eez" for one piece of fruit, you'll do it in a beret and you'll like it. You doctrinaire dope.

via Ed Yong

Nature acquires open access publisher Frontiers

Nature, the scientific publishing behemoth, has acquired the upstart open-access publisher Frontiers. It will be interesting to see how this will shake out; will Nature publications move towards a more open access model, or will Frontiers shift to a more traditional model?

Scientific publishing is big business. From the Economist article:

Outsell, a consultancy, estimates that open-access journals generated $172m in 2012, up 34% from 2011.

This is still a tiny fraction of the $6 billion or so generated by journal subscriptions. But the traditional subscription-based model is falling out of favour. Academics have long complained that publishers abuse their monopoly-like power. Perusing Tetrahedron, say, is a must for any self-respecting chemist. So they (or rather, their university libraries) grudginly cough up €18,570 ($24,267) for an annual subscription. More than 13,000 scientists are boycotting Elsevier, a big Dutch publisher of thousands of journals, including Tetrahedron, whose 37% margins on $2.1 billion in revenues make it the biggest offender in the eyes of many.

In comparison, $6 billion dollars a year is more revenue the music industry generates from iTunes1 ($5.6 billion), or iOS developers make from the App store2. Scientist must pay significant fees to publish their articles, and then institutions have to pay even larger fees to access the research. Now, with the internet, it is becoming possible to publish in journals or preprint servers that anyone can access. In physics things are already moving this way with the advent of the Arxiv, a free online repository that contains a mix of peer-reviewed and non-peer-reviewed work:

ArXiv is already hosted by Cornell University at a cost of around $830,000 a year. Tacking on an "epijournal", so that referreed papers would sit alongside the original preprints, for instance, should not add too much on top of that.

The idea makes perfect sense. Scientists already do most of the heavy lifting involved in publishing research: they write up and format papers, post them to online servers, sit on journals' editorial boards and review their colleagues' work. One reason for Elsevier's mouth-watering margins is that this work is typically done for no compensation.

With that much money at stake, it will take some time for things to change.

  1. The iTunes Value Structure 
  2. A more complete picture of the iTunes economy 

The Myth of the Well-Rounded Scientist

Adam Ruben writes about the attitude in academia that a moment not spent in the lab is a moment wasted.

My outside interest during grad school—my “Batman job,” as a grad student from Case Western Reserve University called it last month—was stand-up comedy. (I quickly learned that audiences in downtown Baltimore aren’t fans of math puns. Like this one: “I was curious about the alcohol content of my mouthwash, but the label on the bottle didn’t say anything about it. I guess the proof was beyond the text of this Scope!” And that’s why I’m not famous.)

One day, my adviser called me into his office. The campus newspaper had just published a little profile of the stand-up-comedy-performing grad student, and my adviser happened to read it. Over the next 10 minutes, I learned that my hobby was an embarrassment to the department, that there was no way I could properly focus on biology, and that every negative lab result I ever produced was a direct result of telling jokes at night.

My "Batman job" is swing dancing. Many of the best things in my life are a direct result of my being involved in a dance community. I met my wife through dance, I have become a better teacher, and my communications skills have dramatically improved. I remember keeping my physics life and dance life separate at the beginning of grad school after being warned by some well-intentioned individuals that such "poppycock" hobbies would hurt my academic career. Then I realized that dance is a big part of who I am, and I did not want to work at a job where I could not be myself. If my hobbies and passions keep me from getting an academic position, then it isn't a place I want to work. Now my physics and dance lives bleed into one another, and this has led to a number of interesting opportunities for me. My "Batman job" has made me a better physicist.

I would wager there are far more scientists with "Batman jobs" than those without.

Getting your paper rejected may lead to it having a higher scientific impact

Philip Ball reporting for Nature News on a new study about the scientific impact of papers that are initially rejected:

Just had your paper rejected? Don’t worry — that might boost its ultimate citation tally. An excavation of scientific papers' usually hidden prepublication trajectories from journal to journal has found that papers published after having first been rejected elsewhere receive significantly more citations on average than ones accepted on first submission.

The peer-review process is far from perfect, but I feel that every paper I have been involved with has improved as a result of the referee comments. It can be frustrating at times, but the quality of a manuscript can dramatically increase with the (mostly) useful feedback reviewers provide.

Quantum Optics Researchers win 2012 Nobel Prize

Quantum Optics Researchers win 2012 Nobel Prize

David Wineland And Serge Haroche
David Wineland And Serge Haroche

From the Nobel Prize Committee:

The Nobel Prize in Physics 2012 was awarded jointly to Serge Haroche and David J. Wineland "for ground-breaking experimental methods that enable measuring and manipulation of individual quantum systems"

This is exciting news for people, like myself, who work in the field of quantum optics and quantum information. Both David Wineland and Serge Haroche have spent decades carrying out beautiful experiments that further push and refine our ability to manipulate and control quantum systems.

David Wineland's work with trapped ions has led to important improvements in atomic clocks and served as exciting testbed for quantum computing. Serge Haroche's work with cavity quantum electrodynamics is opening up new techniques for controlling the interaction of light and matter.

The Nobel Prize Committee has a nice, but slightly more technical, background of the research that is worth a read:

The behaviour of the individual constituents that make up our world – atoms (matter) and photons (light) – is described by quantum mechanics. These particles are rarely isolated and usually interact strongly with their environment. The behaviour of an ensemble of particles generally differs from isolated ones and can often be described by classical physics. From the beginning of the field of quantum mechanics, physicists used thought experiments to simplify the situation and to predict single quantum particle behaviour.

During the 1980s and 1990s, methods were invented to cool individual ions captured in a trap and to control their state with the help of laser light. Individual ions can now be manipulated and observed in situ by using photons with only minimal interaction with the environment. In another type of experiment, photons can be trapped in a cavity and manipulated. They can be observed without being destroyed through interactions with atoms in cleverly designed experiments. These techniques have led to pioneering studies that test the basis of quantum mechanics and the transition between the microscopic and macroscopic worlds, not only in thought experiments but in reality. They have advanced the field of quantum computing, as well as led to a new generation of high-precision optical clocks.

Here is an interview with David Wineland that IQC conducted earlier this year when he was visiting.

Congratulations to both research groups and everyone involved.

Sheldon may play dice, but scientific publishing cannot be left to chance

Sheldon may play dice, but scientific publishing cannot be left to chance

Sheldon using dice to make his life decisions

This is a guest post written by a fellow physicist, Marco Piani, who loves quantum information and the TV show The Big Bang Theory In a recent episode of the The Big Bang Theory, "The Wiggly Finger Catalyst", Sheldon reverts to taking "minor" decisions by rolling dice. It does not always work perfectly, as Sheldon, for example, ends up eating food he doesn't really want just because the dice have "decided" so.


Nonetheless, Sheldon argues that his mind, not burdened anymore by the consideration of minor issues, can focus better on questions much worthier of Sheldon's attention. He judges his experiment a success, in particular because he is able to publish two papers in "notable peer-reviewed journals" in a short period. The measure of success adopted by Sheldon is actually shared to a good extent by the entire academic system: indeed, one of the main goals of a researcher is that of publishing papers in "good" journals. What does this mean?

A researcher devotes his/her work, for example, to better understand how the world works, to improve the treatment for some disease, or to create some new technology. These results only come with dedication and hard work. When there is enough progress---for example, when a group of astrophysicists have collected enough data about the explosion of a giant star, achieving a better understanding of the life cycle of stars---this progress is reported to the scientific community by means of an article published in a scientific journal---a highly specialized research magazine. Such an article may condense down to few pages years of work.

Roughly speaking, papers constitute the record of the progresses made in science (in all the senses mentioned above, and in many more!) and add to the body of human knowledge. Most importantly, they are used as references---that is, roughly speaking, as the starting point---for the future work of other scientists, as well as for developing applications of scientific knowledge.

It is then quite obvious that published results must be sound: that is, mathematically correct in the case of theory, and supported by the collected data---as well as by the methodology of the data analysis---in the case of experiments. A key issue is that science is divided in so many fields and subfields that only people working on the same or a similar topic can really check that the progresses being reported are, first of all, actually interesting progresses---worth being "archived" and developed in the future---and, most importantly, correct. Hence the notion of "peer-reviewed journals": in order to publish, a researcher has to convince his/her own colleagues that what he/she has done is worth the attention of the scientific community and is correct. Furthermore, the level of "interest" of the results is nowadays often reflected by the journal in which the results are published: "good" journals have a higher bar for what is deemed "interesting".

There are a lot of details and many subtle points that we are leaving out here. For example, the people who have to review a manuscript submitted for publications and to help decide about its acceptance---the "referees"---are often unknown, both to the authors of the manuscripts and to the rest of the community. The idea is that referees can then be less afraid to point out potential issues affecting the submitted paper, while they could restrain themselves from doing it if the persons whose work they are judging today could knowingly end up judging their work in the future.

The principle that whatever new result should be scrutinized by the community of peers is well established; in many ways it is a cornerstone of modern science. On the other hand, the exact process to arrive at the acceptance of new results and to their incorporation into the body of scientific knowledge---as well as the issue of how these results should be made available and disseminated---may change in the near future.

At the moment this process is mainly administered by scientific journals and their editors. It is the editors who receive the request from the authors to publish their manuscript. It is the editors who get in touch with potential referees, asking them to judge the submitted manuscript. It is the editors who, after reading the reviews of the referees, finally choose whether to accept the manuscript for publication. Most importantly, it is often the case that papers appearing in journals---that is, the only papers nowadays "officially" certified as "interesting and correct"---can only be accessed through the payment of a fee.

But exactly in these days many scientists and thinkers (notably Timothy Gowers, a Field medalist 1, and Michael Nielsen, the author of Reinventing discovery, an interesting book about how the Internet will dramatically change the way we do science) are considering how the traditional peer-review process and the scientific publishing industry could be disrupted by new online tools and by the more direct involvement of the community of scientists through these tools.

Sheldon may be happy about letting dice decide about other issues to focus entirely on finding new results, but researchers all around the world are aware that modern science is a very complex and collective enterprise. In particular, new results require both validation and dissemination; while "peer-review journals" have played and still play a primary role in these two processes, things could soon change.

  1. The Field medal is considered the correspondent of the Nobel prize for Mathematics 

We Need More Women in Physics

We Need More Women in Physics

Women in Physics Canada Conferece

This week the Women in Physics Canada conference has been jointly running at the Perimeter Institute and the Institute for Quantum Computing. It has been great to see so many young and enthusiastic physicists around. Only about 20% of physicists are female[1]. Excluding the voices of so many potential physicists has impoverished our field. Left out are the many unique and varied perspectives and novel approaches to solving nature's riddles. (This problem of exclusion also extends beyond gender to the issue of wealth; Africa produces few physicists relative to its population. See this excellent Ted Talk by Neil Turok on attempts to build up a world class African physics community.)

Physics is a man's world, and for a woman to succeed she must play by a man's rules. The situation is similar in many ways to the glass ceiling women have been breaking through in corporate environments. A successful business woman I know once told me that in order to make it, she had to be a better man than her male colleagues. I think a culture shift needs to take place where women can be respected for thinking and acting like women instead of needing to conform (consciously or unconsciously) their behaviour and attitudes to be more male centric. I believe this is directly related to the lack of women role models in physics for both men and women. From my middle school days through to my PhD, the bulk of my science teachers were male. This creates an environment where the opinion and perspectives of men are more highly valued and respected than those of women. The more women that engage and participate in physics, the more these ingrained attitudes will change.

These male centric attitudes arise in different ways—some subtle and some blatant. The manner in which physicists sometimes debate and discuss problems can be brutal and cutting, a testosterone driven combativeness better suited to prize fighting. The long hours and the endless publish or perish treadmill are not conducive to having a family either. A female physicists friend told me that starting a family was nearly career suicide. Taking care of a baby, the lack of sleep, and the dramatic hormonal changes during her maternity leave made it difficult to keep up with the harsh research and publishing demands needed to secure a professorship. The bulk of established male physicists I know have families. Why should it be any different for for a woman?

While a typical physics lab is far from a stereotypical locker room, physicist could do a better job of being aware of how their actions can make others feel. Jennifer Ouellette has an excellent post on Cocktail Physics that outlines some of the challenges women face in the skeptics community. (Before reading any further, I strongly recommend you check out her original article.) Jennifer talks about the harassment and patronizing attitudes herself and others have encountered. What really shocks me is the outrageous and derogatory debate that erupted when people called out this kind of brutish behaviour in the skeptics community. I haven't seen anything nearly this acrimonious happen in physics, but I think many of the things Jennifer points out apply equally to the physics community.

Jennifer proposes a four point Manifesto for Change that I think we would do well to follow in order to shift attitudes. I have paraphrased (and adapted for a physics context) her original points below:

  1. Despite the obstacles and challenges, it is important that women keep participating in physics.
  2. Just because you may not have experienced bias, don't diminish the experience and emotions of others who have.
  3. Those in positions of power and authority need to start changing and shaping institutional culture.
  4. Follow the golden rule (treat others as you would want to be treated). Think about how your words and actions will affect others.

The more women that become physicists, the richer physics will become.

[1] This is true in other disciplines such as engineering, math, computer science, and IT. Feel free to replace the word "physics" or "physicists" with equivalent terms from these other fields. The issues women face are the same.