Bad science, good science – Part 1: The scientific article

April 30, 2011 – 12:00 pm

I see a lot of news announcements with new and extraordinary claims about scientific discoveries, mainly from daily newspapers or websites shown by news feeds. I think it’s time for me to present my point of view about how damaging this process is to correct scientific perception to the public. In addition, I will try to provide you, the reader, with a checklist for protection from such claims.

In this series of three posts, I will explain you how research is performed (and in particular its main result, the scientific article), describe the metrics used to evaluate researchers and journals, and finally raise your awareness about the actual accuracy of any scientific discovery reported by the general media. I will present many different facts and terms, covering a lot of ground, but everything may be boiled down to one simple statement: if you are not into a discipline, correctly understanding the quality and the implications of a scientific result is really, really hard. Be aware of those not qualified to understand it and present it correctly. It takes years in the field to do it.

In this first article, I will present details about the source of information: the scientific article. In the second part, I will talk about the metrics used to evaluate journals, scientists, and individual scientific results. Finally, in the third part, I will put things into perspective so that you can use a critical eye when reading scientific news on traditional media. Hopefully, I will raise awareness on what is the real scientific process of discovery, and what are instead far flung statements made either for sensationalism or simple misunderstanding of the actual scientific finding.

Anatomy of a paper: basic structure

You are a researcher, and you spent the last six months tinkering with an idea you had. You learned something new about it, and it’s time to let the world know what you learned, writing down a “scientific article”, also known as “paper”. After a complex editorial procedure, your article will finally be published on a scientific journal, so that other researchers can learn what you learned and eventually solve a problem they have.

Given this premise, it is clear that the essence of a paper is to report what you evaluated, how you evaluated it, the results you obtained and which conclusions you reached from these results. The structure of this presentation is more or less the same across all the scientific disciplines. Let’s examine this structure in more detail.

Title, authors list and affiliations

The first entry we come across in an article is the title. The title gives a quick excerpt of what the paper is about: by looking at the title, you should be able to understand at a glance what it presents, and what kind of results are obtained.

The author list contains the people who worked on the paper. This means not the pure writing, but the actual science: working in the lab, obtaining the samples, doing the data analysis, checking other similar papers and so on. Any non-trivial work done for a paper normally grants you authorship. Depending on the discipline, the order of the names may have importance or not, but in general, the first name is the main author, the one who did most of the work and may be considered the person who made things happen. The last name, on the other hand, is generally the head of the group, either a professor or a scientific manager. Names in the middle are those who gave support role, such as they did minor things, or they gave directions for the paper to happen. This is the area where Postdoctoral researcher normally fall in when they are supervising a student (which normally is the first author). For some disciplines order is very important; for others, in particular those with strong interdisciplinary nature and lots of collaborators, the order is less important and an alphabetical or arbitrary order may be followed, except maybe for the first author for greater visibility.

Generally, one author is also indicated as the corresponding author: he or she is the one in charge of dealing with the journal editor during the submission process (going from a draft to a published article in the journal) and also answers to any inquire about the research done in the paper, now and in the future. In general, the corresponding author is a relatively stable member of the group, either the professor or some well established postdoc.

The affiliation is the academic institution or company the authors work for. This is not necessarily the entity who gives the money for the research or the salary. This is the entity who hires and provide local services to the author so that he or she can perform its research job.

The Abstract

The abstract is a short excerpt of the article, but longer than the title. It is generally around some tens lines of text, describing in more details the content of the article and the methodology used. It generally does not contain detailed conclusions, just a general description of what has been done. Today, the abstract is also complemented with keywords to make it relevant for specific disciplines, not unlike the internet practice of tagging. This greatly simplifies searching.

The Article Itself

The main body of the article is where the meaty stuff is. In general, the article is divided into subsections: the Introduction gives the current state of the art for the discipline and puts the presented work into perspective; the Method (or Experimental setup) describes the approach used to perform the work, such as the used process, the substances (together with their purity and who sold them), quantities, solvents, timings and temperatures (e.g. for a reaction to occur), plus any relevant caveats and conditions that may be important to reproduce the same procedure, so that any other researcher anywhere else in space or time can redo what was done; the Results presents the obtained data, any additional evaluation performed on these data, and any insight that can be inferred from them; the Conclusions contain a short “take home message”, shrinking the scientific finding into a clear summary report; and finally the Acknowledgements allows the authors to thank people who gave small help for the paper and, most important, the financial agencies who pay the salary. In some cases, it is also customary to disclose any conflict of interest (commercial or otherwise) held by the authors.

The last part of the article anatomy, the citation list, deserves a section alone: it defines its genealogy within the scientific research progress.

Genealogy of a paper: the Citation List

When you perform research, generally you don’t start anew. It’s basically impossible that you do something completely unheard of. Generally, there are other people in your discipline, working on similar topics, or even the same one. Part of being a researcher is having the knowledge of the current up-to-date findings and developments in your main topic, and any collateral topic you may need to do your research. Establishing such knowledge requires a throughout bibliographic search of papers written in the past. Such search takes a lot of time (to download, print, read up to some hundreds of papers and get a sense of what is known, what is not known, where there is space for innovation, etc.), but once you know the bibliography of your field, you have to rebuild it only if you change research field or topic (e.g. different molecule, or different gene). Knowledge of bibliography, and keeping up-to-date with recent developments, is an important but generally very neglected part of the researcher working schedule.

When your paper is conceptually bound to previous publications (either because you compare against their results, use their method or part of it, or point out a different strategy to solve a shared problem) it is important to cite each of them. Every time you call attention to a previous article, a footnote reference is added to the authors, journal name, volume, page number and year of publication of this article. Besides giving recognition to someone’s else work, anyone interested in more details can now fetch the publication, see what they claim, which limitations they had, and eventually compare it with your recent work. This process develops naturally into a tree of connections that brings back to the origin of the discipline or methodology. An example may be the following phrase in an article

"In order to evaluate the molecular energetics, the methodology developed
by Doe and Johnson [1] has been used, corrected with the superduper correction
as detailed by Francis [2]"

[1]: J. Doe and M. Johnson,
     "A new methodology for the evaluation of energies",
     Journal of Fantastic Results, 24, pp. 36-46 (2004)
[2]: M. Francis,
     "Superduper correction: improving the energy in small compounds",
     Journal of Reliable Corrections, 36, pp. 1824-3451 (2005)

The number of times a given article is cited by others may give an idea of how important its content is for other researchers: a paper that gets cited by three or four other articles may be close to irrelevant; a paper that is cited hundreds or thousands of times means that its content started a new technique, or even a new discipline. Cases where the original submission is obscure and forgotten, to be rediscovered tens of years later did certainly happen in the past, but communication and scientific exchange was different back then. Today, it’s less likely to happen. Scientists today make careers on developing new ideas and asking money to further develop these ideas. If a new idea comes by, and appears to be productive, the hunger for grants is so strong that it gets under assault for additional investigation in no time. In addition, the occurrence of sudden breakthroughs that change everything are not as frequent as you may think. Research generally proceeds slowly, one tiny step at a time from different sources, trying to balance scientific rigor, frequency of Eureka moments, human resources, duration and aim of the project, additional tasks (authoring of articles, application of grants, teaching, supervising), synchronization with collaborators, brainstorming and data sharing in meetings and emails, software and hardware problems.

Taxonomy: The different types of scientific paper

There are different types of scientific paper, and depending on their type, different consideration should be done.

A Standard (or Regular) article is a scientific article which presents a new method, procedure or finding. It’s the most common kind of paper, normally between 6 and 20 pages long, and with around some tens of citations towards older papers. They report a new scientific result, pushing the human knowledge a bit forward. Very few of them are groundbreaking. As I said, science proceeds in small steps, and when enough small steps have been collected, someone will have enough high-ground vision to see something new. Standard articles may be cited by others a lot or very little, depending on their impact on the scientific community. We will examine the concept of impact later on.

A Review is a collation of the state of the art in a specific topic. Reviews are normally performed when some topic has been explored for some time and either a reputed scientist or a journal editor is given the task to “clean up and make the point”. Reviews don’t contain new science: they merely sum up the relevant steps forward done by others, integrating different techniques and approaches (for example, laboratory experiments and computer simulations) into a single logical presentation. The size of a review can be from ten pages up to one hundred and more, and the number of older papers cited may well fall close to the thousand or even more, depending how deep is the review and how broad is the analysis.  Reviews tend to attract lots of citations from subsequent papers, being the one-stop resource for acquired knowledge on the topic for researchers with potentially different specialization and research focus. There are scientific journals purely dedicated to reviews.

A Letter is a small article, generally less than four pages long, presenting an interesting result for others to read, as soon as possible. Letters are normally written when there’s a sense of urgency. Publishing a letter generally takes less time, because the article is short and the publishing process is streamlined for a quick release.

A Proceedings is a grouping of scientific contributes provided within the context of an academic conference. Periodically, academics organize conferences to show their latest findings to others, as well as showing off their latest Mac Air, colored laser pointer and enjoying coffee breaks (the best collaboration-builder events). Within the context of the conference setup, an editorial committee may be deployed to collect papers from the conference speakers and contributors. These papers are then evaluated (more on this later) and published as a single booklet, generally under a scientific journal’s special edition. Proceedings articles may be high quality or “low” quality, depending on the conference, the editorial committee and the contributors. It may happen that articles for a Proceedings are not “prime research”, but summarize the latest results of the research group, thus acting as an “internal review” of the group that publishes it, with a sprinkle of original research just to add something new.

Books and patents: these are different communication channels, obeying different rules from the ones above. Books are normally made either as an aggregate of different researchers contributes (e.g. one chapter per contributor) or by a single author or small group to present an aggregation of knowledge deserving a specialized, highly detailed treatment. Patents are mostly business related. For some disciplines involving a lot of money, such as biology, pharmacology and the like, patenting is one way of guaranteeing a potential return of investment, if the patent is used commercially. Small digression on this: although the common mantra you may hear is “those evil pharmas… (rumble) patents… (rumble)” please consider this: a drug takes years to be discovered, developed and tested for safety, thus having very little time to return the expenses before the patent expires and the exclusive rights expire. Drugs don’t invent themselves, and researchers, equipment and clinical tests cost money, a lot of money.

Summing up

To sum up this first part, we discussed:

  • We want to understand the difference between real science and the science as reported by newspapers and tabloids. These two latter entities have very little overlap with formal scientific presentation and a huge tendency towards misinterpretation, exaggeration and oversimplification.
  • We understood the anatomy of a scientific paper, how its structure is organized to presents an argument through an experiment, generally as a small step to answer some obscure question of a larger topic. The presentation must provide details for reproducibility by future scientists. We learned about the authors and the meaning of the naming order.
  • We learned about the bibliography, and in particular the citation system, and how the number of times a paper is cited by others may represent its importance for other researchers.
  • We learned there are different types of articles, and their aim, scope and scientific level may be very different.
By Stefano Borini | Posted in Dissemination | Comments (1)

Eight molecules that changed the rules of the game: CFC

April 15, 2011 – 2:00 pm

Rule changed: made safe and easy refrigeration possible. Raised environmental awareness.

Chlorofluorocarbons (CFC) is a class of compounds, the simplest among them with a structure similar to the one of methane: a tetrahedron. A simple representative is the one pictured below, Dichlorodifluoromethane. It’s a molecule made of one carbon atom (in the center, black), two chlorine atoms (on top, green) and two fluorine atoms (on bottom, pea green).

Dichlorodifluoromethane

Dichlorodifluoromethane, one compound in the CFC class

The class includes slightly more complex molecules, but all of them have one thing in common: they are made of carbon, chlorine and fluorine (and occasionally, hydrogen). In this post, we will briefly examine the history of CFC compounds, why they were so disruptive at the time, why they turned out to be so dangerous, and why their contribute to human knowledge was a strong wake-up call for everybody on this little blue planet.

Why CFCs? A brief history of making cold

Just out of the trees and into the caves, humanity learned how to make heat. Controlling fire was maybe the first important technological advancement of humanity, as it improved quality of food (cooked meat is easier to eat and digest, and cooking kills parasites), safety (dangerous animals don’t like fire) and health by warming the cold, humid cave. It took a very low initial technological level to heat things, for a very valid reason: making heat is easily done because the chemical reaction between organic matter and oxygen (that is, burning) is relatively easy to start, produces a lot of heat, and requires components that are easy to find. The opposite operation, cooling, took much longer and way more advanced knowledge.

Ice manBefore the invention of refrigerators there were basically three techniques to cool down things, typically for preservation purposes. The first technique was storing ice and snow in ice houses during winter. Good insulation and the mass of accumulated snow allowed to keep low temperatures during the warm months. Later in time, services were built around the need for cold, cutting and transporting ice blocks from cold regions to service warm ones. People went around in carts selling ice blocks, typically giving small chunks of ice to children to have fun with. Your parents may recall being among these children. The blocks of ice were put into ice boxes, together with perishables.

Another solution to make cold was mixing common salt and snow, to create a frigorific mixture due to its eutectic properties. With this technique, temperatures as low as -21 degrees Celsius can be obtained with ease. The same property is used to melt snow in winter. Similar to the previous option, it requires to have solid water to begin with.

Finally, a third option was to dissolve in water some very specific salts, such as sodium, potassium or ammonium nitrate. These salts require heat to dissolve, subtracting it from the environment (the dissolution is said to be endothermic, in opposition to exothermic ones which produce heat). This concept is successfully used in instant cold packs you may find at your local sport shop. This option has two advantages, namely that it does not require something already cold to operate, and that the salt can be restored and reused by evaporating the water.

With a better understanding of thermodynamics and the state of matter, at the beginning of the 19th century the knowledge was available to develop better technology for the production of cold. Through a proper strategy of expansions and compression of well-chosen gases, efficient removal of heat was both feasible and practical, first industrially, then at the consumer level. When the first refrigerators arrived on the market, the choices for the exchange gas was limited to ammonia (highly toxic), sulfur dioxide (also toxic if inhaled in large quantities), and chloromethane (toxic and flammable). Needless to say, leaks occurred, people died, and the general public preferred the old “big ice cube in a box” solution, or they kept the refrigerator outside, where an eventual leak would pose no immediate danger. A better solution was needed.

In 1929 Thomas Midgley, Jr. and Charles Franklin Kettering teamed together to tackle the problem, and they found a good solution in CFCs, unaware of the environmental danger of their discovery. Incidentally, from the efforts of these two guys also came out the gasoline additive tetraethyl lead, another very troublesome compound. It appears they had a special sense for stumbling on ecologically devastating stuff.

In addition to refrigeration, CFCs were found useful for other tasks, such as propellants for aerosols, solvents, and fire fighting equipment. Their stable, inert and non-toxic properties were just perfect, or so it appeared.

The ozone cycle

To understand why CFCs are so dangerous, we first need to know the role of ozone in upper atmosphere. In normal conditions, ozone is a gas made of three oxygen atoms, O3.

Ozone

Ozone

In comparison, the “conventional oxygen” we breathe is a molecule made of just two atoms bonded together, O2. Ozone has a characteristic smell we normally call “the smell of electricity”, being generated in appreciable quantities by electrical discharges. At ground level is a dangerous pollutant, because it’s highly reactive and irritant, but in upper atmosphere is our shield against the intense and carcinogenic ultraviolet radiation emitted by the Sun.

Ozone is produced through a very slow process from molecular oxygen. The molecule is smashed into individual atoms by the Sun UV radiations

O2 + UV radiation -> 2 O

and each of these oxygen atoms may attach to other oxygen molecules to form ozone

O2 + O -> O3

a reaction that releases heat via intermediary species. Ozone can now adsorb further UV radiation to split back again

O3 + UV radiation -> O2 + O

and start the cycle again. The net effect is the one of a catalyzer, a substance that eases an interconversion (in this case of dangerous UV radiation into heat) without being depleted, as would be a reactant. Instead, a catalyzer is restored in its active state once the interconversion is over, and it is ready to operate again. Please note: a minimal amount of catalyzer is able to promote a huge amount of interconversions.

Thanks to this chemistry, ozone degrades large quantities of dangerous UV radiations into innocuous heat, in a cycle known as the Ozone-Oxygen cycle.

In normal conditions, there are other two important reactions that can occur. Both destroy ozone and restore molecular oxygen

O3 + O -> 2 O2

2 O -> O2

All the reactions given above (creation, catalysis, and destruction, among many others) constantly happen in upper atmosphere. Their final balance leads to an equilibrium of a relatively stable concentration of ozone, dependent on solar irradiation, which in turn depends on seasons, latitude and solar activity.

How CFC disrupt the ozone cycle

Where do CFC enter in the game? It turns out that the biggest advantage of CFCs, their stability, is also their first major problem. CFCs are heavier than air (and thus tend to sink) but this is not preventing them to reach the upper atmosphere, helped by their long life. Diffusion and winds mix up the atmosphere constantly, creating a relevant concentration of CFCs in upper atmosphere. Once there, the second major problem arises: when hit by UV radiations, CFCs release a chlorine atom:

CCl3F + UV radiation -> CCl2F. + Cl.

The chlorine atom has a lone electron, and in this configuration is highly reactive and combines with ozone, operating as a catalyzer for the ozone distruction. The reactions are complex and numerous (if you want all the gory details, this online book is a start), but the net effect is a reduction of ozone and the creation of molecular oxygen. Remember, a catalyzer emerges unscathed from the reaction it promotes, meaning that a minimal amount of chlorine can promote the destruction of large quantities of ozone, unbalancing the equilibrium previously compensated by the slow reaction of creation O2 + UV -> 2 O. The shielding of UV radiation becomes less and less effective, on par with the decreasing concentration of ozone, and the radiation can now reach the surface.

A swift action is called for: the Montreal protocol

We owe to James Lovelock, Frank Rowland and Mario Molina, among many others if our eyes were open to a dramatic trend. During the 70s, it became clear to the scientific community that CFC were a source of trouble. Confirmation came in the 80s, where incredibly low concentrations of ozone were found over the south polar region, a “ozone hole” of unquestionable evidence.

The Vienna Convention and the Montreal Protocol, enforced on the 1st of January 1989, defined an impressive and immediate worldwide response to the problem, suppressing industrial production and use of CFCs and other ozone-depleting substances. Without this ban, the result would be the one simulated by NASA

Ozone layer simulation by NASA

Total destruction of the ozone layer, with no chance of recovery, before 2060. NASA also released a movie of the simulation, compared side by side with the projected situation we expect with the ban enforced. You can find it at the NASA page for the simulation, or at this YouTube movie. Without ozone layer, the amount of UV radiation reaching the surface would be so high to cause sunburns in minutes, and occurrences of skin cancer would have soared globally. These, of course, would be just the direct effects on humans. The rest of the biosphere would have had an unpleasant situation as well.

CFCs have been banned from almost any application, from refrigeration to pharmaceutical nebulizers. Some temporary, highly scrutinized exceptions have been defined for those applications where no substitute could be found, such as some fire extinction strategies. The general idea is to use compounds which are either degraded before reaching upper atmosphere, or that don’t contain chlorine or bromine atoms, therefore having a reduced impact on the ozone layer.  Common substitutes today are R134a (a fluoroethane, also being phased out) and R600a (isobutane, much safer for the environment but highly flammable). There are also strict regulations in force, concerning maintenance, recovery and recycling of currently existing CFC (see, for example, here at US EPA). Although the dangers have been avoided, the legacy of CFCs usage will linger for at least one hundred years.

The aftermath of a potential catastrophe

The Montreal protocol and the avoided catastrophe of ozone depletion have been a huge wake up call for humanity. We realized that our planet has a fragile ecosystem, whose complexity and interdependency is broad and still to be discovered. As humans, we owe us a big pat on the back, but there are still troubles ahead: global warming, oil depletion, overpopulation. It’s time we stop wasting time, because swift actions are needed again. With Montreal, we demonstrated that humanity can achieve a common goal and solve a common problem. We need strong leaders, iron-clad reason, proper actions and global effort to face the common goals and problems of tomorrow. We have only one planet, this one:

Earth
By Stefano Borini | Posted in Chemistry, Environment | Comments Off

SeisMac and Quake-Catcher Network – turn your mac into a seismograph

March 30, 2011 – 9:00 am

Occasionally, I get to find very interesting scientific apps for the Mac. In light of the recent events, SeisMac is definitely one of those. While not technically useful for the general public, it is a very important application for research.

All Mac laptops include the so-called Sudden Motion Sensor, a Micromechanical system (MEMS) accelerometer. This sensor is a very cheap integrated circuit which can be found in iPhones, iPod touch, the WiiMote, and many others gadgets. In the case of laptops, its main purpose is to park the hard drive head in case of a sudden drop, reducing the chance of damage to hard disk platters due to impact with the reading head. The sensor can however be queried and used for many other applications, from the facetious (like LiquidMac) to the more serious, like SeisMac. The idea is to use the Sudden Motion Sensor to detect earthquakes, effectively converting your laptop in a seismometer. It is interesting to see how sensitive the Sudden Motion Sensor can be. This is a tracking of my laptop with SeisMac

SeisMac image

The nervous, black oscillations you see on the left hand side are produced by a fan on my table, which I then removed. As you can see, these oscillations are uniform on the x, y and z axes. The single spike along the z axis you see in the center it’s me doing a touchpad click to take a screenshot, and the series of strong impulses on the right it’s again me, typing the filename. Don’t be deceived by the stronger than usual gravity. I never calibrated the reading, so the absolute values can be wrong.

SeisMac is great, and you can configure its sensitivity to disregard human-generated events and catch the big deal when the quake strikes, but it does not beat another similar program, with a very interesting distributed project behind it: the Quake Catcher Network. The idea is simple, but very powerful: laptops and desktops volunteering to be part of the network constantly collect seismic data through the Motion Sensor, and alert a central server of any movement. If the laptop is moved, hit, or a local, non-seismic event occurs (such as a truck passing by), the signal will be considered by the central server as spurious due to its locality. However, if multiple unrelated laptops feel the same event, the server will validate it as an actual quake. Knowing the position of each laptop it is possible to obtain the intensity of the quake at each location, the speed of propagation, and the kind of oscillation. All these data provide precious details not only on the quake itself, but also on the terrain and the buildings, a very important dataset to improve prevention and emergency response.

Additional Links

By Stefano Borini | Posted in Earthquakes, MacOSX | Comments Off

Plotting seismic events in Japan in 2D and 3D

March 18, 2011 – 1:15 am

I just saw this very interesting and shocking movie reporting the quakes rattling Japan from 9th to 14th of March.

The amount of events after the big one, at 1:17, is devastating. I wanted to see more, adding the third dimension. I tinkered with wget, bash, gnuplot and ffmpeg to produce this less visually appealing but scientifically important data representation

What you see is the hypocenter (latitude, longitude and depth) of each quake from the 6th to 17th of March. Data were gathered from the Japan Meteorological Agency web pages for the purpose of personal use and research. Red points are surface quakes (from 0 to -20 km), green are medium depth (-30 to -50) and blue are deep quakes (-60 to -80). You can clearly see the very steep subduction zone as a sharp feature digging into the Earth crust. It’s a real tragedy we have to pay such high price associated to these data, but these data from previous events are the ones that allowed many lives to be saved today.

By Stefano Borini | Posted in Earthquakes | Tagged , , | Comments Off

Fusione nucleare e fusione del nucleo. Due cose diverse (In Italian)

March 16, 2011 – 12:22 am

This post is for my Italian readers. There’s no English version because the issue does not exist in English, only in Italian. It is relative to the misunderstanding between the terms “meltdown” and “fusion”, in Italian both translated as “fusione”. I proceed saying that what unfortunately happened in Japan is a reactor core meltdown, not a nuclear fusion, something completely different.

Questo post e’ per i lettori italiani. Non ho scritto una versione inglese dal momento che il problema esiste solo in italiano, ed e’ relativo alla confusione tra due significati diversi di “fusione”. Quello che e’ accaduto in giappone non e’ una fusione nucleare. E’ la fusione (nel senso di liquefazione) del reattore.

Link alla versione italiana.

By Stefano Borini | Posted in Physics | Tagged , , , , | Comments Off

The Japanese quake

March 11, 2011 – 8:56 pm

Yesterday around 14.30 a big quake hit the Sendai area in Japan, followed by a tsunami and a contiguous stream of additional shocks. I immediately contacted friends in Tokyo and they are all fine. Transportation in Tokyo is interrupted, and so is communication. I don’t know any more details. I just have news from a friend.

Plates under Japan. Tokyo is marked with a red dot.

Tokyo and the whole of Japan lays in the so called pacific ring of fire, an area of violent seismic and vulcanic activity due to the pacific tectonic plate subducting with the continental plates on the american and asian sides. The very existence of Japan is due to this subduction, creating the arched set of islands as a consequence of the arising volcanic activity. Tokyo, with a grand total population of 30 millions in the metropolitan area, sits right on a triple trench junction, basically a ticking bomb with an historical average timer of approx. 100 years. Unfortunately this quake is unlikely to reset the timer. The Tokai zone, where this triple junction develops, is further South. Japan as a whole sits on a subduction-powered ticking bomb, and you are reminded often about it. In the year I spent in Tokyo, I experienced a dozen quakes strong enough to be felt.

I could have been there now if I continued my employment at NII. Words fail me. It’s a place I called home for a year, a place I learned to know somehow, and now it has changed completely. Places I visited are now under water, and landmarks I used to see every day are scarred. I am deeply, deeply sad. I know that the people of Japan will shrug this tragedy away with their restless efficiency and poised philosophy, and I wish them all the best.

My final remark wants to remember that it is due to the Japanese productivity and dedication, the advanced planning and organization, the technological level of engineering and the compliance to building regulation that hundred of thousands of lives were saved today. Engineers and builders are the real heroes in this catastrophe, years before it struck. Hands that do are those which make life better.

Edit: Please donate to the Japanese Red Cross today, through google. They need your help. The situation is getting worse and worse.

By Stefano Borini | Posted in Earthquakes | Tagged , | Comments Off

Academia StackExchange reaches Commitment level

March 9, 2011 – 1:41 am

Some time ago, I proposed the foundation of a Question and Answer site for Academia. Now, the Academia StackExchange has reached commitment phase, meaning that the proposal aggregated a consistent number of people who may have an interest in it, and further aggregation of active participant is sought after. You may report your interest in asking or answering at least 10 question as soon as the site enter beta phase by following the link to the Academia StackExchange Commitment.

I really loved some of the comments from early committers, such as

  • “I hope this site will help beginners to initiate their careers in academia, dispel myths to outsiders, and support fellow academics too!” – CesarGon
  • “Should help out those who want to start their scientific research careers, especially for the ones with limited access to quality research education.” – Kit
  • “There is a great opportunity for young and idealistic people who want to change the world to receive good doses of reality checks and inspiration.” – so true user30906, so true

and this one which made me laugh

  • “Whatever Stefano Borini is involved in is probably worth looking into :) ” – Dr_bitz

We will see. The jump start is promising!

By Stefano Borini | Posted in Dissemination, Websites | Tagged | Comments Off

Does chamomile really relax ?

February 25, 2011 – 12:45 am

ChamomileNothing says relax better than a peaceful evening in front of a steamy cup of chamomile. Since thousands of years, humanity uses it as a natural remedy for a large amount of ailments, most notably hypertension, sleeplessness and to ease a flu-dominated night, like in my case recently.

Moved by curiosity, I took some time investigating what is scientifically known about the therapeutic effects of chamomile and their mechanism of action. The results, I must say, are interesting and conflicting. Let’s examine what I was able to gather from around the internet and in a couple of scientific papers.

Chamomile is a class of plants whose main representatives, at least for infuse-making, are Matricaria recutita (German chamomile) and Chamaemelum nobile or Anthemis nobilis (Common Chamomile). It can be found wild or cultivated. Its flower is actually a composite daisy-like sprout. The flowers are the tiny yellow corollae forming the central bulb.

Chrysin

The pleasant fragrance the chamomile flowers produce arises from a large set of compounds (more than 120) including in particular sesquiterpenes such as chamazulene and alpha-bisabolol, flavonoids and flavanoids, like Chrysin, and many others. Most of these compounds are not present in free-form, but are bound to sugars through fragile bonds that can be broken easily, for example by heating.

Some research on the effects of these compounds has been performed. In particular, Chamazulene has been found to have antioxidant properties, together with matricin, alpha-bisabolol, and apigenin. Chrysin appears to show anxiolytic effect in laboratory rats (see also here and here) but nothing has been said for humans yet.

Chamazulene
Chamazulene

Other experiments show that chamomile can have small antibacterial effect on the gut’s bacterial population, both in human and rat. This finding, however, is a mere hypothesis to explain changes in the excreted substances.

So, it appears that chamomile does indeed have relevant activity, and for what concerns anxiolytic effects, some evidence exists. Despite this, The National Institute of Health page for chamomile reports insufficient evidence for most of the claimed therapeutical advantages of chamomile: the report is “C: Unclear scientific evidence for this use”, with only one case (“post-operation sore throat”) where a conclusion has been reached as “D: Fair scientific evidence against this use”. This is a very important example on how evaluation of pharmacological effectiveness is performed. Even when evidence supports presence of therapeutic effect from a given compound or preparation, only a set rigorous tests performed on human subjects allows to finally grant recognition of therapeutic effectiveness (or lack of it). In the case of chamomile, tests have been mainly performed in rats and mice. Even a single successful (or unsuccessful) human test is not enough to grant A (strong positive evidence) or F (strong negative evidence) grades in the Natural Standard grading scale. The grade C refers specifically to

      1. Evidence of benefit from >1 small randomized trials without adequate size, power, statistical significance, or quality of design by objective criteria, OR
      2. conflicting evidence from multiple randomized trials without a clear majority of the properly conducted trials showing evidence of benefit or ineffectiveness, OR
      3. evidence of benefit from >1 cohort/case-control/non-randomized trials AND without supporting evidence in basic science, animal studies, or theory, OR
      4. evidence of efficacy only from basic science, animal studies, or theory.

      Let’s examine the cases one by one.

      The first case occurs when tests result in positive evidence (it works) but the test is not “statistically significant” meaning that it has been performed on too few subjects: for something to be considered working, it must present an effect that occurs with some consistency. If you test a substance Foo on a single sick person, and he recovers, it does not mean that Foo is a cure. That person could have recovered just because he was lucky or strong enough to recover, regardless of Foo. A better test would be: treat 200 sick people with Foo, and take also 200 sick people with no Foo treatment, then compare the recovery rate in the two groups. If in the first group 180 people recover, while in the other only 20 recover, there’s definitely a good point in favour for Foo being effective in curing that sickness. Statistical analysis allows you to decide which numbers of people can be considered strong evidence or not enough evidence for Foo being an effective cure.

      The second case is when two or more tests produce conflicting results. For example if laboratory A sees a recover in its people using Foo, but laboratory B sees no recover. There could be many reasons for this. Improper testing could be one, and even if all tests are performed properly there could be additional factors we don’t know. Example: suppose that people at laboratory A had an unknown strong ease of recovery from that sickness (because they are immune for some biological reason), so the group without Foo medication recovers as well as the group without Foo. The conclusion for the laboratory A is that Foo has no effect, while laboratory B says that Foo has an effect. This is conflicting evidence, and must be resolved by checking more people, until a clear majority allows a unique conclusion to be drawn.

      The third case is when there is evidence for recover, but there’s no evidence from known science, animal studies or theory able to explain the observed phenomenon. This can lead to a scientific breakthrough if a new biological mechanism is found and explained, but until then, it is not possible to say anything about the pharmacological validity. This point also raises the difference from cohort case, control case, randomized or non-randomized trial. It would be an interesting discussion, but it goes a bit outside of my current knowledge, and I am determined to learn more about the details in the future.

      The fourth and last case is when evidence exists only because we infer it should work from what we known today of the human body’s mechanisms, but no actual test has been performed, or tests have been performed only on animals.

      In the case of chamomile, as of today we cannot confirm officially and with strong evidence on humans that a pharmacological effect does exists, because all tests have been performed on animals, with the very few human trials available still insufficient to draw significant conclusions. This does not mean that the effect does not exists.  It could exists, or it could not, and whatever the truth is we cannot put an approval stamp on it yet, because we haven’t tested enough. In agreement to the scientific method, unless something is demonstrated via evidence to hold, it is assumed not to hold. It’s like presumption of innocence in criminal trials: someone is assumed innocent until proven guilty from evidence. The other way around would be disastrous.

      Now, we can probably claim that the pure fact of preparing chamomile and enjoying its pleasant fragrance has a relaxing effect, but that would be a psychological effect triggering internal biochemical actions inside our body, finally leading to a relaxed mood. Mozart could have the same effect. The point is, from the pharmaceutical point of view, the correct answer (as of today) to the question “does chamomile really relax ?” is “some evidence exists that it does, but it’s still not enough to say for sure.”

      Additional Links

      By Stefano Borini | Posted in Biology, Chemistry, Food, Medicine, Natural compounds chemistry | Comments (2)

      Upgraded my mac to SSD == pure bliss

      February 22, 2011 – 12:55 am

      I recently bought this 240 Gigabytes of awesomeness, conveniently packed into a 2.5″ SATA box. It’s an Other World Computing Mercury Extreme Solid State Hard Drive. It has no moving parts, it consumes less battery, and it’s fast. Damn fast. This thing is so fast it opens applications before you lift your finger from the touchpad after the click. It’s also bloody expensive.

      I have a MacBook 13″ unibody, the first model, also known as MacBook5,1. The hard drive is conveniently seriviceable, right under the large battery lid.

      To perform the migration, I needed:

      1. The SSD drive, of course
      2. A small Phillips screwdriver
      3. A small Torx screwdriver (I managed without one)
      4. A USB-to-SATA external drive case.
      5. Carbon Copy Cloner. The software is free but consider making a donation.

      I had two or three options to perform the migration. I don’t have the original OSX install disk here with me (and I don’t want to go through a total reinstall in any case), but I did have the OSX from my iMac, which may be useful as a safety installation if I screw up. As I quickly learned, the iMac install DVD does not work on the MacBook, but it allows, at least, to perform some basic operation, such as disk partitioning.

      My first attempt was based on the assumption that I had to physically copy the partition, low level. I thought this because I wanted to transfer the system while not active (you may have troubles), and I didn’t know how the boot worked, so I assumed I had to copy the partition boot record as well… something I did with Linux once. In addition, moving stuff via USB takes a long time, and trasferring 160 GB would have left me with no laptop for a while. So here was the idea:

      1. Disassemble the original disk, and put it in the external case (yes, Mac can boot from this disk once in USB, just press “C” at boot with the USB drive powered and no DVD disk)
      2. Put the OWC disk in the laptop. Partition in two: one with the original size of my old disk, the other with the remaining space
      3. Install a bare OSX on the remaining space, and start copying low-level from the external drive to the other partition. I thought to do this via “Disk Utility” restore.
      4. When the system is done copying, boot from the first partition, delete the second one (with the bare OSX) and find a way to enlarge the partition including the now-free space.

      This turned out to be not possible, because the OSX DVD I have does not allow me to install. I could, however, still use this process, using Disk Utility from the DVD, which runs. I tried with no luck, as Disk Utility complains about not being able to allocate memory. In addition, I could no longer boot from USB after this event. The reason was not clear. To address this event, I restored the original disk into the laptop, and proceeded with a different strategy, which is the one I did.

      The successful strategy

      1. Preparing the new disk

      I booted my system back with the old disk, and put the OWC SSD in the USB enclosure. It was clear I had to transfer the system while live, so I logged in with a new bare account with admin privileges, instead of my own. This allows not to have active files or mounted FileVaults, which could give trouble.

      I plugged in the SSD in the enclosure, created and formatted a single, whole partition with Disk Utility, exactly in the same format as my system partition. Check in either Disk Utility or from the command line, with the command “diskutil info /dev/disk0s2″. It should be Journaled HFS+, because it’s the one that allows boot. DO NOT enable case-sensitive. You will have a lot of troubles, in particular with File Vault,  (yes, workarounds exist, but I haven’t tried them). I loathe case-preserving/case-insensitive FileSystems, but Mac works this way. Also check to use Partition Type “GUID_partition_scheme” when partitioning.

      2. Copying the system

      Once formatted, I started Carbon Copy Cloner, specified the source as my system disk, the target as the SSD disk, and ticked “backup everything”. The documentation in Carbon Copy Cloner is perfect. Check also the “typical usage cases” shown there, you will find the one you need. Make sure Carbon Copy Cloner tells you the cloned system partition will be bootable.

      3. Swapping the disks

      Carbon Copy Cloner will copy your whole system to the external disk, something that may take many hours. Let it go. When done, I turned off the computer, flipped it, and opened the battery lid. There’s a small Phillips screw keeping the hard drive in place via a simple plastic brace. I unscrewed this brace and took it away, then pivoted the hard drive to lift it and unplugged the SATA cable (gently).

      Now, I disassembled the SSD drive from the external casing. On the sides of the old hard drive there are four small Torx screws that provide support. The plastic brace kept two of these screws pushed down, while the other two allowed for the pivoting on the side of the battery compartment. I had to remove these screws to put them in the SSD drive, but since I didn’t have a Torx screwdriver, I resorted to pliers both for removing them and putting them on. I then plugged in the SATA cable in the SSD, put the disk in the compartment, screwed the brace back and tried to run the laptop with the new setup. Note: conventional wisdom says “first test, then close”, but in this case the assembly/disassembly was so trivial I preferred to put everything back in. Also, the battery does not stay in its place without the lid, so you have to close it anyway, or put the battery aside for a while.

      4. Booting the new disk

      The boot was smooth and uneventful. Not really as fast as I expected, but notably faster. The real difference is in launching applications and logging in. It used to take 10-15 seconds to get to work. Now I have the desktop open in just 2 seconds.

      5. Conclusion

      I now have the old hard drive and an external USB-SATA case. I could format it and use it as an external disk, or keep it as a safety backup system. I decided for the latter.

      By Stefano Borini | Posted in Hardware, MacOSX, Software | Comments (1)

      Tulips!

      February 7, 2011 – 3:03 pm

      As you probably recall, some time ago I proposed to associate scientific dissemination and research to a symbol. I chose this symbol to be the tulip, and I planted some bulbs. As winter will turn into spring soon, they start peeking out of the cold soil

      Tulips

      Satisfying! This year, I decided to donate my royalties to Telethon, as soon as the tulips are ready to be donated as well.

      By Stefano Borini | Posted in Charity, Dissemination, Gardening | Comments Off