Jani Kotakoski's blog -- RSS Feed science

Disorder in Materials

Thursday, 17th September, 2020

Disorder in Materials

Big news: I started on a tenure track position in Vienna in September 2015!

I was in the very fortunate situation where I ended up being able to select from two excellent offers from exactly the two universities where I most wanted to work. In the end the offers were very similar, and we made a decision as a family to stay in Vienna. It is no suprise to me that Vienna is constantly ranked as one of the best cities to live in. This is a great place.

My research group is called Disorder in Materials. We made the logo of the group together with Toma Susi, who joined my group from the beginning. Now we need to get the offices and lab spaces renovated and start to setup the new equipment in there.

Open Notebook Science

Thursday, 17th September, 2020

Open Notebook Science

I have been horrible with updating the blog recently, and I'm offering no excuses for this. The reason for this update is the Open Notebook which I established on the Wiki of University of Vienna. I will keep the notebook in the spirit of Open Notebook Science for projects where this approach seems suitable. I wish I could do this with all of my projects, and I may indeed start to do this at some point, but for now I will just test the concept. The first project where I'll try this is exfoliation and characterization of 2D crystals, which we are carrying out with a couple of students here at the Uni. We'll start with mechanical exfoliation, and carry out optical microscopy, Raman spectroscopy, atomic force microscopy and transmission electron microscopy on the samples. Let's see how this goes.

The main reason for trying this out is the need of centralized notebook for the project and the appeal of open science. The final push for trying this out came from a presentation by Peter Murray-Rust given yesterday (3.6.2014) in Vienna (organized by the Austrian Science Fund).

Lise Meitner–fellowship 2013–2014

Thursday, 17th September, 2020

Lise Meitner–fellowship 2013–2014

Although I''m still waiting for the official email or letter, the FWF website (you need to click through until the second-to-last page from the links at the bottom, or type in my name here) tells me that my Lise Meitner application "Tailoring of 2D materials beyond graphene" (M1481) has been approved for funding this last Monday (1.10.2012).

As described at the website of the program, Lise Meitner fellowships are targeted at "[h]ighly qualified scientists of any discipline who could contribute to the scientific development of an Austrian research institution by working at it." The fellowship relieves me from teaching duties, gives me a modest salary increase and—more importantly— allows us to hire a new post-doc for the two years for which I will take a leave from my current 6-year University Assistant position at the University of Vienna.

What a nice end for the last couple of weeks of writing somewhat larger applications for three different funding agencies in Vienna, Helsinki and Brussels :)

Tiedejulkaisemisen noidankehää murtamassa

Thursday, 17th September, 2020

Tiedejulkaisemisen noidankehää murtamassa

Tämä kirjoitus julkaistaan Tiedetoimittaja-lehden heinäkuun numerossa 2012.

Jani Kotakoski and Toma Susi

Arabikevään mukaan nimetty akateeminen kevät -protestiliike alkoi matemaatikkojen Elsevier-kustantajaa vastaan suunnattuna protestina. Tutkijat kamppailevat entistä riippumattomamman tieteellisen julkaisemisen puolesta kaupallisten kustantajien ylivaltaa vastaan.

Arabikevään mukaan nimetty akateeminen kevät -protestiliike on jäänyt suomalaisessa mediassa varsin vähälle huomiolle. Muualla maailmassa se on herättänyt kiinnostusta myös ei-akateemisille suunnatuissa julkaisuissa, esimerkiksi aihetta laajasti käsitelleessä englantilaisessa The Guardian -lehdessä. Sosiaalisen median katalysoiman liikkeen saama julkisuus on nopeasti lisännyt kansalaisten ja päättäjien tietoisuutta tieteellisen julkaisemisen ongelmista, mikä näyttäisi johtavan muutoksiin kansainvälisessä tiedepolitiikassa.

Liikkeen tavoite on saattaa tutkimustulokset kaikkien saataville, kun julkaisutoiminta tällä hetkellä keskittyy voittoa tavoitteleville yrityksille. Viimeksi liikettä tukevien tutkijoiden ja kustantajien välit tulehdutti suurimman tieteellisten lehtien kaupallisen kustantajan Elsevierin tuki Yhdysvaltain edustajainhuoneen Research Works Act (RWA) -lakialoitteelle, joka pyrki estämään liittovaltion – eli veronmaksajien – rahoittaman tutkimuksen avoimen julkaisemisen.

Itse protesti sai alkunsa kun Cambridgen professori ja Fields-mitalisti Timothy Gowers toivoi tammikuisessa blogissaan sivustoa, jonka kautta matemaatikot voisivat irtisanoutua työskentelemästä Elsevierin hyväksi. New Yorkin yliopiston tohtoriopiskelija Tyler Neylon toteutti pian Gowersin toiveen, ja vain kaksi päivää myöhemmin thecostofknowledge.com alkoi kerätä tutkijoiden nimiä boikottiin. Nyt kesäkuun alussa sivustolle on kertynyt jo yli 12 000 allekirjoitusta, eikä suinkaan pelkästään matemaatikoilta.

Kustantajat keräävät taloudellisen hyödyn

Tutkijoiden ja kustannusyhtiöiden huonojen välien perimmäinen syy on tutkimusartikkelien päätyminen kustantajien yksityisomistukseen huolimatta siitä, että tieteentekijät tukevat työtä merkittävällä ilmaisella työpanoksella. Tutkijathan paitsi tekevät tutkimukset myös vertaisarvioivat artikkelit ja usein vielä toimittavat julkaisut. Yliopistokirjastot puolestaan joutuvat ostamaan kustantajalta satojen lehtien niputettuja tilauksia, joten lehtiin uppoaa vuosi vuodelta kasvava osuus niiden budjeteista. Suuret kaupalliset kustantamot tahkoavat samaan aikaan ennätyksellisiä tuloksia. Elsevierin viime vuoden 883 miljoonan euron liikevoitto esimerkiksi oli huikeat 37.3 prosenttia liikevaihdosta.

Julkaisijoista nimenomaan Elsevierin maine on tahriintunut myös useissa skandaaleissa. Yrityksen Australian osasto esimerkiksi julkaisi vuosina 2000–2005 lääke- ja kemikaaliyritys Merckin sponsoroimia artikkelikokoelmia vertaisarvioitujen julkaisusarjojen asussa. Elsevierin emoyhtiö puolestaan tuki asekauppaa järjestämällä isoja maanpuolustusnäyttelyitä, kunnes tutkijoiden äänekäs vastustus lopetti tämän toiminnan vuonna 2007. Elsevier on myös toistuvasti julkaissut artikkeleita ilman vertaisarviointia, plagioituja tutkimuksia ja jopa kokonaisia artikkeleita jotka on myöhemmin jouduttu vetämään takaisin.

Urajärjestelmien noidankehä

Tämänvuotinen protesti ei ole ensimmäinen laatuaan. Vuonna 2001 yli 30 000 allekirjoittajaa lupautui olemaan julkaisematta tutkimusartikkeleitaan niiden avointa saatavuutta vastustavien kustantajien lehdissä. Kustantajat eivät kuitenkaan juuri reagoineet protestiin, eikä tutkijoilla tuolloin juuri ollut vaihtoehtoisia julkaisukanavia.

Akateemisen julkaisemisen noidankehän syy on urajärjestelmien luonne: tutkijoiden suoriutumista mitataan tavallisesti laskemalla julkaisuja perinteikkäissä arvostetuissa tutkimuslehdissä, joista kaupalliset julkaisijat omistavat suurimman osan. Avoimen verkkojulkaisemisen merkitys on kuitenkin kasvanut, erityisesti kun yksi edellisen kampanjan johtajista, Berkeleyn yliopiston geneetikko Michael Eisenin, perusti viisi vuotta sitten Public Library of Science (PLoS) -lehtiryppään.

Elsevier nöyrtyi

Elsevier on vastannut tutkijoiden protestiin useilla avoimilla kirjeillä. Alkuun niissä korostettiin julkaisijoiden roolia tutkimuksen tason takeena. Tällaisten väitteiden tueksi ei kuitenkaan ole vahvaa todistusaineistoa, sillä esimerkiksi vertaisarvioitujen lehtien tason mittarina usein käytettävä ns. vaikuttavuuskerroin (impact factor) korreloi huolestuttavalla tavalla takaisin vedettyjen tutkimusten määrän kanssa.

Helmikuun lopussa, mahdollisesti allekirjoitusten määrän ja asian saaman negatiivisen julkisuuden säikäyttämänä, Elsevier veti tukensa RWA-lakialoitteelta, joka muutamaa tuntia myöhemmin kuopattiin kokonaan. Protestin taustavoimat eivät kuitenkaan ole vakuuttuneita kustantajien aidosta halusta muutokseen. He pikemminkin haluavat kokonaan eroon voittoa tavoittelevista kustannusyhtiöistä kehittääkseen julkaisutoiminta aidosti uudelleen.

Tutkimusrahoittajat mukaan

Myös tutkimusrahoittajat ovat nyt ottamassa aiempaa aktiivisemman roolin. Huhtikuussa liikkeen tavoitteiden taakse asettautui maailman toiseksi suurin yksityinen tutkimusrahoittaja Wellcome Trust ja Iso-Britannian yliopisto- ja tiedeministeri David Willets [1]. Pian tämän jälkeen Euroopan komissio ilmoitti, että se asettaa avoimen verkkojulkaisemisen Horizon 2020 -puiteohjelman 80 miljardin euron rahoituksen ehdoksi [2]. Valkoiselle talolle tehtiin samanaikaisesti sosiaalisessa mediassa laajalti levitetty kansalaisvetoomus avoimen verkkosaatavuuden ulottamisesta kaikkeen Yhdysvaltain liittovaltion rahoittamaan tutkimukseen [3]. Vetoomus saavutti vaaditun 25 000 allekirjoituksen rajan 4. kesäkuuta, joten presidentti Obaman hallinnon täytyy vastata siihen virallisesti.

Akateeminen kevät on tehnyt selväksi, että yhä useampi kaupallisten akateemisten kustantajien voittoja ilmaisella työllään ruokkivista tutkijoista tiedostaa nykyisen järjestelmän ongelmat. Näyttää myös, että protestiliikkeen keräämä laaja julkisuus on saanut eri maiden hallitukset kannattamaan liikkeen vaatimuksia, etenkin koska avoimen julkaisemisen odotetaan tuovan merkittäviä säästöjä. Tieteellisen julkaisemisen noidankehä näyttää siis olevan murroksen partaalla – halusivat julkaisijat sitä tai eivät.

Kirjoittajat ovat boikottiin liittyneitä materiaalifysiikan tutkijoita. FT Jani Kotakoski on Helsingin yliopiston dosentti ja Wienin yliopiston yliopistoassistentti. TT Toma Susi on tutkija Aalto-yliopistossa.

On academic publishing, open access & Elsevier

Thursday, 17th September, 2020

On academic publishing, open access & Elsevier

I was recently approached by an editor of a well-known academic journal—published by Elsevier—asking me to review a submitted manuscript. Although I have occasionally published in their journals, reviewed for them, and even participated in conferences organized by them, a recent flow of negative press regarding Elsevier's actions caused me to decline carrying out any free work for them.

Specifically, I cited the following articles published by the Guardian:

"The danger of drugs ... and data" (9 May 2009, by Ben Goldacre)
"Academic publishers have become the enemies of science" (16 January 2012, by Mike Taylor)

For links to discussion on the topic elsewhere, see the end of this post.

Clearly, I'm by far not the only one to have refused to work for Elsevier recently. In fact, already 1441 researchers have signed a pledge at The Cost of Knowledge refusing to publish in, refereeing for, and/or doing editorial work for Elsevier. There is also a pledge called Research Without Walls—at the moment signed by 432 researches—stating that the signatories

"...will assist in the peer review process (as a reviewer, board/committee member, chair, editor, etc.) only for conferences, journals, and other publication venues that make all accepted publications available to the public for free via the web."

Apparently Elsevier is taking this movement relatively seriously since I received a response signed by Rob van Daalen. To provide their view on the topic I quote his reply below in full:

Dear Dr. Kotakoski,

I have been informed that you rejected to review for [an Elsevier journal], which is a very unfortunate. As publisher of the journal I would like to add a shade of meaning to the articles published by the Guardian on which you have based your decision.

1) From 2000 to 2005, our Australia office published a series of sponsored article compilation publications, on behalf of pharmaceutical clients, that were made to look like journals and lacked the proper disclosures. This was an unacceptable practice, and we regret that it took place. This was an isolated practice from a past period in time and it does not reflect the way we operate today. The individuals involved in the project have long since left the company. Our CEO has affirmed our business practices as they relate to what defines a journal and the proper use of disclosure language with our employees to ensure this does not happen again.

We will continue to partner with all scientists and clinical investigators, including those in the pharmaceutical industry, to help communicate the findings of high-quality, peer-reviewed medical research. We have strict disclosure rules in place so that readers are aware of any financial interests behind a specific article or journal, or when entire compilation products are created for pharmaceutical marketing purposes.

2) Our support for the Research Works Act comes down to a question of preferring voluntary partnership with government agencies and other funders to promote access to research works, rather than being subjected to inflexible government mandates like the NIH policy, which don't take into account the needs of different journals.

One of Elsevier's primary missions is to work towards providing universal access to high-quality scientific information in sustainable ways. We support the bipartisan bill, which seeks to prevent US government policies, like the one imposed by the NIH, that mandate the dissemination of journal articles published and funded by the private sector. Elsevier and other publishers have embraced and nurtured a whole range of access options to ensure broad dissemination - author pays journals, delayed access, manuscript posting, and patient access, to name a few. We've worked constructively with a number of government agencies to develop new ways to expand access to journal articles reporting on, analyzing and interpreting agency-funded research. But like other publishers and societies we have always opposed the adoption or extension of the NIH policy, which restricts the author's freedom to choose where to publish and undermines the sustainability of journals published by the private sector. The legislation is an effort to prevent such unsustainable policies.

Elsevier has been continually expanding access to content. In fact, we were the first and largest contributor to PubMed Central as part of the NIH's voluntary posting pilot in 2005. What we're opposed to is the mandate that forces us to contribute our content to PubMed Central, and potentially other platforms, in ways that aren't sustainable to commercial and non-profit publishers. That's why publishers are fighting these government mandates even if it means taking an unpopular stance.

For several years, Elsevier has been a major partner in three information philanthropy initiatives. Health InterNetwork Access to Research Initiative (HINARI), Access to Global Online Research in Agriculture (AGORA) and Online Access to Research in the Environment (OARE) are aimed at those countries that have the least amount of access to information resources. In most advanced countries, access to research is not a pressing problem for researchers, when compared to other issues, such as funding. In the poorest countries, it is a more fundamental barrier. Publishers like Elsevier have been working hard to close down this gap. Together the programs offer scientists in 114 eligible countries free or low-cost access to some 7,500 scientific journals, books and databases.

I hope that this background information will be useful to you and that it may (even slightly) change your opinion on our company.

With kind regards,

Rob van Daalen
Publisher Physical & Theoretical Chemistry
Elsevier - Amsterdam - The Netherlands

Discussion elsewhere

There has been much discussion all over the 'net about Elsevier specifically and the Research Works Act (RWA) specifically. Hence, the list below is necessarily far from complete, and only presents some parts of the complete picture.

"Polymath Journal publishing reform" on http://michaelnielsen.org/
"Open access and academic journals: the publishers respond" on http://theconversation.edu.au published on 11 August 2011 by Sunanda Creagh
"Elsevier = Evil" on http://scienceblogs.com/pharyngula/ published on 16 January 2012 by PZ Myers
"What We Can Do About Science Journals" on http://math.ucr.edu/home/baez/ published 24 January 2011 by John Baez
"Ban Elsevier" on http://johncarlosbaez.wordpress.com/ published on 26 January 2012 by John Baez

Aurora seen from the ISS in Orbit

Thursday, 17th September, 2020

Aurora seen from the ISS in Orbit

A youtube video as taken from the international space station, shared by user isoeph. Beautiful.

Atom-scale modifications in graphene and white graphene

Thursday, 17th September, 2020

Atom-scale modifications in graphene and white graphene

Anticipating leaving University of Helsinki, I will collect here some pieces that have appeared elsewhere. This one appeared as a Division Research Highlight for Division of Materials Physics, University of Helsinki in 2010.

The only known atomically thin two-dimensional materials are graphene and the hexagonal boron-nitride monolayer. They have a similar atomic structure, resembling a honeycomb or a chicken wire, but altogether different chemistry. Graphene is a single layer of the familiar layered carbon material graphite, kept together by the sp2-hybridized covalent bonds between the carbon atoms, and exhibits semi-metallicity (or, in other words, is a zero- band gap semiconductor). Although many properties of graphene had been investigated theoretically as a prototype material for understanding the properties of graphite and carbon nanostructures, e.g., fullerenes and carbon nanotubes, it was a surprise in 2004 when this material was experimentally shown to exist also in reality. Due to this breakthrough discovery, Konstantin Novoselov and Andre Geim received the 2010 Nobel Prize in physics. On the other hand, hexagonal boron nitride monolayer, the insulating counterpart of graphene sometimes called white graphene, is formed due to ionic bonding between the alternating boron and nitrogen atoms.

Discovery of these materials was significantly aided by the recent advances in the high resolution transmission electron microscopy, especially via the introduction of aberration corrected devices, which allowed atomic resolution images at conditions which are not destructive to the targets.

The initial experimental observations displayed, along with the materials themselves, a set of atomic defects which were either intrinsic or caused by the electron beam. Especially in the case of hexagonal boron nitride, the triangular vacancy structures caused much confusion in the field since they seemed to be unexplainable by the existing theories of damage production in this material. Through a collaboration of University of Helsinki and Dr. Suenaga's group from the National Institute of Advanced Industrial Science and Technology (AIST), Japan, we have been able to explain the formation of these defects by primary knock-on events between the electrons and the target atoms. The peculiar triangular shape of the defects is due to easier displacement of boron atoms in the system, which leads to vacancies terminated by nitrogen atoms. For graphene, the observed defects have been much less controversial. However, as we show in our recent review (written in collaboration with Professor Banhart from University of Strasbourg, France), the flexibility of carbon chemistry allows for a breadth of different defect structures to be formed. As a result of collaboration of University of Helsinki and University of Ulm, Germany, we have recently found the lowest energy defect configurations in graphene, which also introduce a band gap into this material. This may prove out to be an important step towards carbon-based electronics of the future. As the limiting case for the growing defect structures, we displayed the first-ever two-dimensional amorphous structure.

References

Kotakoski, J., Jin, C., Lehtinen, O., Suenaga, K. and Krasheninnikov, A.V., 2010. Electron knock-on damage in hexagonal boron nitride monolayers. Phys. Rev. B, 81, 113404 (2010)

Banhart, F., Kotakoski, J. and Krasheninnikov A.V., 2011. Structural defects in graphene. ACS Nano, 5, 26-41 (2011).

Kotakoski, J., Krasheninnikov, A.V., Kaiser, U. and Meyer, J.C., 2011. From point defects in graphene to two-dimensional amorphous carbon. Phys. Rev. Lett. 106, 105505 (2011).

Scientists Are Dicks

Thursday, 17th September, 2020

Scientists Are Dicks

The skeptic community has been discussing vigorously on Phil Plait's (@BadAstronomer) "Don't be a dick" talk at James Randi Educational Foundations's Amazing Meeting 8.

Some people have taken it personally or accused Plait of only relying on anecdotal evidence. In any case, the response in the blogosphere has been fierce.

His point can be put into a single question he posed to the audience during the talk: "How many of you no more believe in those things [UFOs, religion, etc.] because somebody got into your face, screamed at you and called you an idiot?". Some people would answer "Me!" to this question, but not necessarily very many.

Daniel Loxton (@Daniel_Loxton) has been reflecting to this both on twitter and on the Skepticblog (here and here). I posted the following as a comment to the latter blog entry.

Now, getting to the title of this post, what does this all have to do with scientists?

In my opinion, the on-going discussion on the “dickiness” of the skeptics ~~seems to neglect the under-laying reason for it~~ has omitted an interesting parallel to the scientific world. For a scientist, as myself, it seems obvious. We Scientists are trained to tear each other apart. That’s what science is all about.

When we get a manuscript to review from our peers, we do our best to find each and every weakness in it, point it out, and tell the writers to try harder to polish their theory and correct the mistakes, if possible. Sometimes the theories are so bad that they are “Not even wrong!”

Some referee reports are very rude, and sometimes the ‘questions’ after a conference presentation are set to demolish the speaker. Some scientists seem to even try to do this simply to show their power (or to protect their own old theories).

Hence, many of us expect everyone else is (a) ready for similar criticism if they present their own ideas and (b) expecting others to do their best in tearing their arguments apart.

As an anecdote, I should confess that my wife accuses me of doing exactly this when we disagree on something. And that’s with a person I’m deeply in love with. Imagine what happens with people we don’t even like.

As Carl Sagan writes in The Demon-Haunted World (p. 31, paperback): “But there’s one side [in science] that is really striking to the outsider, and that is the gauntlet of criticism considered acceptable or even desirable.”

Randy Olson joins the choir in his recent “Don’t Be Such a Scientist” by noting that (paperback, p. 99): “[W]hen I was a graduate student – we learned to write first drafts of our scientific papers, give them to colleagues, and then eagerly await their comments. The more red ink on the manuscript when it came back, the better. The only thing that would ever cause anger would be someone not covering the manuscript in red ink, suggesting they were just lazy.”

In fact, I know many scientists who have earned their reputations by being the harshest critiques of the work of their students, colleagues and even of themselves.

In my opinion, this indicates where the problem is. Scientists are dicks to each other (for people judging from outside). That’s the way of the scientific mind in the scientific setting. And for many scientists, there is no other setting. They always talk the science talk. Olson felt that the topic was worthy of a book. Judging from the discussion after Phil Plait’s talk, and from other facts like Olson’s book, internet has changed things for the skeptics and for the scientists.

We aren’t any longer simply talking to ourselves. Now we have a broader audience, and it’s time to learn how to communicate with it effectively.

It’s good to have the discussion on. I wish as many scientists as possible will pay attention. This is not just about UFOs and the Bigfoot.