Weekly R and R, raves and rants that is.

I’m always happy that Philstar has a sort of weekly dose of science from scientists themselves. Also, Rappler had been busy with some island science for the last couple of days. Here goes my R and R.

Collagen and scurvy

Somehow, I don’t know how to react to this article from Philstar (click here). It’s like attending a lecture class in chemistry. Oh wait! IT was supposed to be a lecture note in chemistry, right?

There are the two things that came to my mind after reading the notes. No, it’s neither about scurvy nor wrinkles.

First. While I have to admit that I can endure reading this kind of article (Have you heard about how wonderfully readable the classical mechanics book of Goldstein is? Yeah, it´s a myth.) and I, most of the time, like to read this kind of article, I wonder what possible engagement does it want from its readers. Is it just FYI or Maám wants to talk to me, personally?

And second. I always encourage my fellow scientists to write, to communicate their science and I laud scientist who tried. However when we write, there is one very basic question we need to answer: Are we possibly alienating more people, not with the science but by the manner with which we communicate it? I have lost a lot of friends by not asking this question to myself by the way. Balance I guess, is the solution.

“Kiko and Stitch”

Rappler gave me my happy island science news for the week (click here). There are three things to emphasize here:

1. “We need not look far for expertise, we just have to believe in our own scientists,” Soriano said. 

2. Pulling expertise from different fields could hasten the pace in which things are done.

“The team included physical oceanographers Dr. Cesar Villanoy and Dr. Laura David from the UP Marine Science Institute; Engr. Roel John Judilla and Engr. Jaylord Jauod from the School of Mechanical Engineering, Mapua Institute of Technology; Dr. Wilfredo Licuanan, Marine Ecologist from DLSU; and Dr. Prospero Naval from UP Dept. of Computer Science.”

Smiles. Courtesy: Rappler.

3. Good science although a local solution, is still good science.

Which brings me to a depressing science story (ies) also courtesy of Rappler (click here and here).

Dishearthening cool science

If I were a kid living in Matnog (Sorsogon), what could be my reaction after reading this article?

“Ang galing naman nya! Sana ako rin nakatira sa Amerika.”

The first sentence is filled with admiration. The second is loaded – maybe a little anger, maybe a bit of sadness but certainly there is hopelessness. Two things: 1) He doesn’t believe that he will prosper in his current situation; and 2) Only people in America can live their dreams. He thinks of getting out of the country so that he can let his kids dream, abandoning his own. (While certainly not really such a bad thing, but that’s a different story.)

Am I the only one with this convoluted thinking? It is a bitter fact that children in the islands are at a disadvantage compared to kids in developed country. (A lot of heroic souls are trying to do something about it.) In writing successful Filipinos abroad who didn’t live the typical Filipino lives of stinking toilets in public schools or of the usual 2 hour trek (or in the case of Matnog, an hour boat ride or swim) to school, what value could these articles have?

I have said it last week: The value of this article for the Philippines, I believe, is that given the right training and stimulus, Filipinos can also be good in science. Nothing more.

Oh yes! These articles are supposed to inspire. Then why am I not inspired? I guess I just feel unattached.

Whatever happened to finding people like the Filipina who proved Einstein right or the Filipina who wants to put ‘chorva’ in Oxford English Dictionary?

How about writing about that guy from Ilocos who is in an international debate about ‘time’, or that guy from Odiongan (Romblon) who is solving complex biology problems with math? Since I don’t want to be accused of being parochial, how about that guy who went to a public high school in Manila and is now dean for Science in NYU or that guy from Cagayan de Oro who is an Astrophysicist working in Trieste, or that lady from Batangas who plays with DNA and RNA in Cornell?

There are many examples whom a kid in Matnog can relate to. Granted that these people have enormous talents, they have even more tremendous determination. The one that makes a mountain a molehill.  Try looking at their tracks and back stories. It is written in the scars of their hearts as P¡nk would say er sing.

Mountains versus mole hills. Which one is which?

We seldom see mainstream media report science and if they do, it is usually side lined.  So I’d like to start a weekly (?) science round up of news or views that had caught my rather short attention span. Be warned most of my comments are rants.

This week it is quite easy. A major broadsheet and two of the largest tv networks carried some sort of science news and views.  These are:

Inqurier asks what’s the value of science

This editorial (click here) has little scientific value. The article has no point.  Ah, I get it! It has multiple points. That’s why I didn’t get the message. The article instead of focusing on the merits of investing on science, made a little detour on the 1) ways to make science learning more enjoyable; 2) the dismal number of science laboratories in public high schools; 3) on the increased budget of the education sector; 4) on the K-12 education change; and 5) on the diaspora of science and technology trained professionals. So where’s the value of science there? I don’t know.

An example of a good op-ed piece on the MONETARY value of science is an editorial in Nature Photonics (click here) which appeared today. It says that for a 47 billion Euro investment a year, the EU27 got 3.4 trillion Euros a year in return in Physics alone. That’s like a 1 peso investment will earn 100 pesos after a year! (Is my math correct? It seems to make no sense.)

But of course, it’s just not about the money. We could go on and on and on on the real value of science.

My point is that the editorial in the Inquirer could have done much much better. Like make an op-ed about the low Research and Development to GDP expenditure of the government,  a measly 0.09% and how it is stifling growth.

If they want to talk about ways to make science learning more enjoyable, shouldn’t they make a feature article instead?

And by the way, visit the article if only for the comments. Really, Teddy Locsin Jr? “…for engineering degree only, just engineering, wag na math, physics, degrees, those can be loopholes;” Loopholes? ¿Cómo?

Jessica Sanchez 2.0 but better

Michael L. Tan in his column Sense and Science talked about a Fil-American who was in TIME’s 100 most influencial because her team “cured” a baby with HIV. (click here.)

I call Dr. Katherine Luzuriaga as Jessica Sanchez 2.0 but better because she speaks Filipino!

Enough of the joke. Honestly speaking, the value of her work should have made headlines everywhere regardless of her ethnicity, and it did by the way at least outside of the Philippines. Imagine that there are only two “cured” HIV patients in the whole world and you’re part of the team that made one possible. That is amazing.

But I was a bit disappointed with how Michael L. Tan approached the article. Three things:

1)  Yes, she has a Filipino blood but she is not from the Philippines. So this sentence, “And yet, despite the groundbreaking impact of her work, she remains largely unacknowledged in her own country,” does not work. She is acknowledged in her country, the USA.

2) And while I agree that there is a gender inequality in science, there is no need to highlight that they are women scientists as “Even more importantly…” What do you mean “even more importantly”?

3) She is not Jessica Sanchez. Go figure.

The value of this article for the Philippines, I believe, is that given the right training and stimulus, Filipinos can also be good in science.  This could have been a better editorial topic for science in the Inquirer.

Which brings me to another Filipina scientist.

Rapid Tubbataha reef assesment

Dr. Maricor Soriano was a guest in ANC’s Headstart with TJ Manotoc. He is sitting in for Karen Davila. They talked about the scientists’ assessment of Tubbataha’s reef in light of the grounding of the Guardian and of a Chinese fishing vessel.

I was lucky to watch the complete interview.  I have to give props to Dr. Soriano for deflecting some questions she has no competence in answering. If I have to give advice to scientists when being interviewed by media is that do not talk about things that you don’t have the capability to answer. In short, do not BS. BS-ing is one way to ruin your hard earned reputation. And besides, it will not look good on video. (Most) Good scientists are bad liars, you know. 

As for TJ Manotoc, why do you have to ask questions that were deflected already? Scientists are not Ernie Barons or Kuya Kims.

I was also waiting for him to ask how the scientists made the assessment fast or maybe it was edited (?). There is nothing more elating to a scientist when you ask her about their work. It also brings more content, a real value.

So what’s the real value of science then?

Palma Hall Pav 3: The Llamas Science Hall. Picture courtesy of Celine Catalan.

This post has been in my queue for a few weeks already. I have written much of the body of this post based on an email interview I did with Dr. Christopher Bernido. I also had some conversations with Dr. Jose Perico Esguerra but I think he is still too young to remember most things during that time. A week ago, I ask some people from the NIP, Dr. Arnel Salvador and Dr. Vince Daria graciously replied. Dr. Salvador remembers the atmosphere, the events, and the excitement. However, I think much more history can still be fleshed out.

The timing of the writing of the history of NIP or of the other institutes is critical. I believe now is the most opportune time – the initial players are still alive and lucid! I like my history from the history makers themselves.

So I’m making this post wikipedia-style but with a strict moderator. Let me crowdsource NIP’s history. How does it work? If you have important history or facts you want to share about the NIP during this time, please leave a comment below or email me, imphscience@gmail.com (for those who are shy). Once verified, I will revise the text below, and put a last revision date in the post. Of course, you will have my never ending thanks. By the way, I am responsible for all editorials that will come out in this post.  

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The 80′s science is headlined by a rare form of disease that afflict mostly gay men [1]. This disease would come to be known as AIDS (Acquired Immune Deficiency Syndrome).  Two decades after, a Nobel Prize in Physiology was awarded to Françoise Barré-Sinoussi and Luc Montagnier “for their discovery of human immunodeficiency virus [2]“, the virus responsible for AIDS (2008). Two more science research from this decade earn Nobel prizes – the ribozymes’ discovery (1982) and the buckyball’s discovery and preparation (1985).

Other science news in the the 80′s include the NASA report about the Ozone hole depletion (1981), the first successful artificial heart implant (1982), the first evidence of a brown draft (1984), and the never confirmed cold fusion experiments (1989). It is also the decade when there was a meltdown in the Chernobyl nuclear power plant (1986) and the explosion of the Challenger (1986) [1].

From on top of up diliman blog.

“In the 1980′s, the University of the Philippines was just a teaching University: there was no real research culture,” says Dr. Christopher Bernido, the National Institute of Physics’ first Director [3].

“In the Physics Department of the UP Diliman, nobody was publishing in international journals except, perhaps, for two new PhD’s who just returned from abroad. There were only 4 or 5 PhDs (holders) in the Department of Physics.”

A year prior to the establishment of the National Institute of Physics, there was no PhD degree program in the whole Philippines. Dr. Roger Posadas proposed a PhD in Physics program as a consortium between the Ateneo de Manila University and the De La Salle University [3,4]. The program incidentally coincided with the Executive Order establishing the National Institute of Physics.

Dr. Emil Javier, then Ministry of Science Secretary, initiated the establishment of the 6 national institutes. “He (Dr. Javier)  should be given credit, ” says Dr. Bernido. Dr. Javier would later become the 17th President of the University of the Philippines.

The creation of the national institutes occur at the same time with major reorganizations in UP – UP Diliman became an autonomous unit and the College of Arts and Sciences were split into three separate colleges: the College of Arts and Letters, the College of Social Science and Philosophy and the College of Science.  According to Dr. Bernido however, these were independent events.

From a Department to an Institute

The transition from a department to an institute was not really felt except for 1) the extra budget which the new institute allotted to research, and 2) the renaming of positions such as Chairman to Director, asst Chairmen to asst. Director.

An NIP Newsletter, a brochure, and a preprint system for research papers were also put up to record the progress of the Institute. Unfortunately, the publication of the newsletter was stopped after Dr. Bernido’s term as Director.

Initial challenges

Dr. Bernido lists three challenges that the new institute encountered. The first is to instill a research culture with publications in international journals as a target since the faculty had always been focused on teaching.

With the aim of developing a research culture, the institute formally identified and set up research groups based on the institutes’ capacity and on global trends. The line of research were chosen based on two modes:

1) If a PhD or a faculty member with expertise is available to carry out and direct research in an area.  This is the case for the Fields and Particles Group.

2) In the absence of a senior faculty member, and in view of the importance of a research area, junior faculty members (non PhD degree holders) were tasked to form a group as in the case of the Laser Physics Group (now, the Photonics Research Laboratory) and the Instrumentation Physics Laboratory.  Visiting professors from the USA, Japan, Wales, and Australia were then invited to beef up the research groups.

Membership in the three original research groups – the Fields and Particles, the Laser and the Instrumentation Physics groups,  were porous as there was no formal application process [6]. There was also an Electronics laboratory which was formed to try to be en sync with developments in the Silicon Valley according to Dr. Vince Daria. It was eventually incorporated to the Instrumentation Physics Lab when its head, Carlos Perez left.

International visitors

“We had many Japanese professors visiting that time and the junior faculty were in charge of  joining them for the field trips , entertaining them with the senior ones – Roger (Posadas), Joey (Magpantay) and Chris (Bernido),” recounts Dr. Arnel Salvador

Dr. Arnel Salvador remembers that there was a professor from Swansea (Wales) who helped in the construction of the first laser in the country. Linda Posadas and Minella Alarcon were sent to Swansea to train in laser physics [5].   

Prof. Shigeo Minami visited the NIP many times as well as Prof. Hajime Ozaki (?) from Japan who talked about amorphous superconductors. Caesar Saloma and Roland Sarmago would later join Prof. Minami and Prof. Ozaki (?) , respectively, as recipient of the sandwich program. More on this later.

A theoretical Physicist from Waseda, Prof. Mikio Namiki also visited the new institute. Namiki ‘s work was on Quantum Mechanics and Stochastic Quantization [6]. 

Dr Gene Stringer, an American professor, also visited NIP as a Fullbright Senior Scholar [5,6]. He taught solid state physics and did some instrumentation work. This probably influenced Caesar to specialize in Instrumentation physics according to Dr. Salvador.

The first Lasers and a “supercomputer” in the NIP

 The Laser group made the first laser in the country, a Nitrogen laser. The team who made the laser is composed of Peter Chua, Sam Peralta, Jerry Dadap and Wilson Garcia. A second laser, a CO2 laser, was also made. Dr. Salvador joined the group with this project [5].

At the Electronics Lab, the group planned to build a supercomputer in the late- 80′s  based on a hypercube geometry.   In the hypercube geometry, microprocessors are arranged such that processing is done “massively parallel”. The final design of NIP’s supercomputer used 16 microprocessors (Inmos T2 Transputers) with programmable serial interconnects and 2 graphics processor units (GPU, Texas Instruments, TI) as interfaces to an IBM XT computer. The construction of the supercomputer was funded by PCASTRD [7].  

“We initially hand-wired the GPU interfaces and programmed the generation of the Mandelbrot set (think Fractals) to demonstrate its performance,” says Dr. Vince Daria.

“In comparison with computing technologies in those days, top of the line computers at that time were only running on Intel 80286 CPU.  Some didn’t have a math co-processor nor a floating point unit and computing of the Fourier Transform (FT) took hours (and even days with 2D FT).  Even with just one GPU interface, the prototype performed way faster than the Intel 80386 CPU when calculating the FTs. Numerical computing using signal and graphics processors were kinda hot during those days. Even when the Intel 80486 CPU came, our prototype was twice faster.”

When Carlos Perez left the institute to pursue graduate studies in the US, Vince Daria (still an undergrad at that time) moved to the Instrumentation Physics Laboratory bringing all the computing resources with him.  Dr. Daria’s first paper with Dr. Saloma and Dr. Munoz made use of their prototype to calculate the FT.

Several research group were formed in the succeeding years – the Plasma Research Laboratory, the Liquid Crystal Laboratory (now, Structure and Dynamics Group) , and the Materials Physics Laboratory (now, Condensed Matter Physics Laboratory).

The publication list of the NIP during its first decade is mostly composed of theoretical papers until 1991. This fact reflects the initial composition of senior researchers of the institute who are mostly theoretical physicists.

The second challenge was recruiting PhD holders who could boost research and advise students in the PhD program. The problem was bypassed according to Dr. Bernido, by a sandwich program where PhD students were matched with foreign professors (mostly from Japan) who could be their thesis advisers. The program was proposed by Dr. Roger Posadas, then the Dean of the College of Science.  Prof. Caesar Saloma, UP Diliman’s current Chancellor is a product of this sandwich program.

The Japanese connection

Dr. Roger Posadas initiated the Japanese tie-ups.  He went to Japan to look for professors who could host some budding talents from the new institute.  He also liked the Japanese model in which the research laboratory was headed by one senior professor with several associate professors as opposed to the American system wherein the laboratory is one-professor-one group system [5].

Linda Posadas was sent to Prof. Suematsu in Tokyo Institute of Technology (TIT) while Jun Yco to Waseda University.   Roland Sarmago joined Prof. Ozaki (?) also in Waseda while Caesar Saloma went to Prof. Minami’s laboratory in Osaka University.  

While in Japan (1990-92), Saloma published papers on applied optics and instrumentation with his mentor (Prof. Shigeo Minami). By 1993, Saloma had fully established the Instrumentation group with 4 ISI publications and maintained research output onwards [7]. As a matter of fact, the Saloma-lead laboratory had the highest publication output in a year (17 publications in 2002) among the research laboratories a decade later. But this is jumping to the third decade. I will write a separate post about the Saloma academic family tree soon.

Until now, there are still a lot of NIP graduates who are pursuing their PhD degree or taking postdoctoral fellowships in Japan.

The solution proved to be a good strategy in raising the research capability of the experimental laboratories. By the end of the institute’s first decade, several experimental groups have started to be productive in terms of publications. The first experimental paper came out from the Instrumentation Physics Laboratory in 1991. Click here (First decade) for a complete list of the first decade’s papers.

Probably, the most difficult challenge for the institute was to give substance and true meaning to the word “national”.  To Dr. Bernido, this would mean that the influence of the NIP should go beyond the UP System.  I’ll reserve a discussion on the influence of the institute on the country in a separate post.

Curriculum change

The undergraduate curriculum was also changed. The most drastic of which was the lengthening of the BS Physics and the BS Applied Physics courses into 5 years in 1984 [6]. This is most probably to accommodate the changes in the curriculum that was revised by Dr. Roger Posadas a few years before.

The then Department of Physics strengthened the program by adding more courses.  During that time, a physics major would only have 1 class each of Quantum Mechanics, Statistical Mechanics, Modern Physics and Electromagnetic Theory according to Dr. Salvador. “Imagine that had we graduated with that program we will only know half of what the current students know (now)”.

The department put 3 Mathematical Physics subjects, 2 Modern Physics courses with 2 Quantum Mechanics courses. They also expanded the treatment of Statistical Mechanics, Classical Mechanics, and the Electromagnetic Theory by adding second courses on these fields.  Experimental Physics and Computational Physics were also added [5]. 

Dr. Salvador thinks that the MS program remained the same but the students are now more prepared because of the changes in the undegraduate curriculum. 

In 1992, the undergraduate curriculum was ripe again for a revision.

The early 1990′s science stories include the launch of the Hubble Space Telescope (1990), the cloning of the human embryo for the first time (1993) and two Nobel prize winning research on the role of the bacteria H. pylori on stomach ulcer (1991) and the detection of the cosmic microwave background (1992) [8].

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I started this post to frame the new National Institute of Physics in terms of research and events happening around the world during its first decade. However by doing so, the new institute appeared to be disconnected, not at par with the rest of the world and was struggling. This is absolutely wrong and unfair. On the contrary, there were a lot of international exchanges and visitors. There were research papers coming out from the institute, albeit trickling, since the new institute was still building research capabilities.  Surely, there are birth pains and it takes decades, centuries even to build a reputable academic name.

In this decade, most of the foundations of the institute were laid thanks to the visionaries (Emil Javier, Roger Posadas, Christopher Bernido, Jose Magpantay) who knew where the institute should be steered. We have seen the results of their hard labor in the institute’s succeeding years.

We also see that there was no dearth of talents either (M.V. Carpio, Caesar Saloma. Arnel Salvador, Roland Sarmago to name a few).  The institute was fortunate that these talents had the willingness to continue what was started. Fast forward in the future, we meet them again as movers not only within the institute but also to the whole Philippine science community as well.

NIP’s first decade was surely exciting.

I will visit the current status of the NIP near the conclusion of this series.

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References
[1] Siegfried, Tom (Ed). “90th Anniversary Issue:1980s.” ScienceNews 9 March 2012. Online.
[2] www.nobelprize.org.
[3] Christopher Bernido, Personal Communication.
[4] The consortium produced graduates who are now in key positions in the academe. It also cemented the close relationship between the three universities’ physics departments. I’ll write more on these in the concluding part of this series.
[5] Arnel Salvador, Personal Communication
[6] Jose Perico Esguerra, Personal Communication
[7] Vince Daria, Personal Communication.
[8] Siegfried, Tom (Ed).”90th Anniversary Issue:1990s.” ScienceNews 9 March 2012. Online.

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Breast cancer is the most common cancer in the Philippines affecting 3 of 100 women. In the country, it has a relatively low 5-year survival rate. This is primarily due to the lack of awareness and of early adequate diagnosis and treatment which lead to the progression of the disease and the subsequent spreading of cancer cells from the breast to other organs. This spreading is the most common form of recurrence of the cancer and is the main cause of death in patients with breast cancer [1].

In a recent paper, researchers from the University of Santo Tomas Hospital were able to identify factors that predict the spreading of breast cancer. They stated that tumour stage, size and lymph node involvement are major predictors of the spreading [1].

The authors however, said that they might have only a small sample set and that they still would like to validate their results with a larger number of patients.

Read more of the abstract of their research here:

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Predictors of early distant metastasis in women with breast cancer

E. Sta. Rosa Mendoza, E. Moreno, P. B. Caguioa
University of Santo Tomas Hospital, Manila, Philippines

Abstract:

Background: Breast cancer is a clinically heterogeneous disease. Approximately 10–15 % of breast cancer patients develop distant metastases within 2 years of diagnosis with a poor 5-year survival rate of 21 %. Little data have been gathered about how some breast cancer metastasizes earlier than expected. The study aimed to identify predictors of distant metastases among breast cancer patients in relation to their clinical and tumour characteristics. The results of the study may have important implications in our understanding of the disease process allowing more aggressive treatment and monitoring of certain subgroups of patients.

Methodology: Retrospective review of 215 patients (54% early stage and 46% locally advanced stage) who fulfilled the specified criteria was performed. Twelve variables were considered. Univariate and multivariate logistic regression analyses were performed to identify independent predictors of developing distant metastasis within 24 months after surgery and adjuvant therapy.

Results Of the 215 patients, 27.9 and 17.7 % developed bone and visceral metastasis, respectively. Bone metastasis was significantly dependent on stage, tumour size, lymph node involvement, lymphovascular invasion, estrogen receptor, progesterone receptor and Her/2-neu pattern (p<0.05). Visceral metastasis was significantly dependent on age, menopausal status, stage, tumour size, lymph node involvement, estrogen receptor, progesterone receptor and Her-2/neu pattern (p<0.05). Among patients with bone and visceral metastases, 67 and 43 % have triple negative pattern, respectively. Logistic regression provided an accurate model for predicting bone but not visceral metastasis.

Conclusion A significant fraction of breast cancer patients experienced early metastasis. Our data suggest that tumour stage, size and lymph node involvement are major predictors of metastasis. Her-2/neu over-expression alone is not a strong predictor of early metastasis but triple negative breast cancers belong to an aggressive subgroup with early metastatic capacity. Young, premenopausal patients may benefit from aggressive surveillance and treatment since they tend to present with early visceral spread.

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Journal Reference:

[1] Rosa Mendoza ES, Moreno E, & Caguioa PB (2013). Predictors of early distant metastasis in women with breast cancer. Journal of cancer research and clinical oncology, 139 (4), 645-52 PMID: 23283528

In 1983, Pres. Ferdinand Marcos established a system of national centers of excellence in the basic sciences. The first institutes to be created were the National Institute of Physics (NIP), the National Institute of Geological Sciences (NIGS), and the Natural Science Research Institute (NSRI) at the University of the Philippines (UP) in Diliman and the Institute of Mathematical Sciences (IMS, now the Institute of Mathematical Sciences and Physics, IMSP), the Institute of Chemistry (IC), and the Institute of Biological Sciences (IBS) at the UP’s Los Baños campus.

In this series of blog posts, I will trace the history of the UP Diliman institutes from the perspective of published research. This post in particular, highlights the most exciting research paper from these institutes in the first decade (1983-1993). In my next post, I will give you a historical sketch of the National Institute of Physics during this decade with the help of  Dr. Chris Bernido, NIP’s first Director.

There were few papers published during this time.  There were only 20 research articles – 17 from the National Institute of Physics, 3 from the Natural Science Research Institute and none from the National Institute of Geological Sciences. I have listed all the papers from this decade here.

Most papers in Physics are from the theoretical Physicists (authors: C. Bernido, M.V. Carpio-Bernido, J. Magpantay, D.M. Yanga); the experimental papers are mostly in optics and signal processing (authors: C. Saloma, V.R. Daria). The NSRI papers are on plant cell tissues (author: S.C. Halos). More on this on my next post.

The most exciting research paper that came out during this decade is a mathematical physics paper by M.V. Carpio-Bernido. The author uses path integration to solve interesting noncentral potentials exactly.

Solutions to noncentral potentials are important in quantum physics and chemistry. For example, the Hartmann potential as well as the Quesne potential are used to model ring-shaped molecules such as benzene. The solutions could also be used in scattering problems that involve nonspherical scatterers.

As new more complex materials are synthesized, or as scattering phenomena have gone beyond symmetric scatterers, this research becomes even more relevant.

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Path integral quantization of certain noncentral systems with dynamic symmetries

M.V. Carpio-Bernido, J of Mathematical Physics 32 1799-1807 (1991). DOI: 10.1063/1.529244

Abstract

Path integral quantization is done for the five classes of potentials appearing in the systematic search for nonrelativistic systems with dynamical symmetries done by Makarov, Smorodinsky, Valiev, and Winternitz [Nuovo Cimento A 52, 1061 (1967)]. By an iterated application of Bateman’s series formula to the polar coordinate path integral, an expansion is obtained on the Feynman kernel or the Green’s function, whichever is possible, in terms of hypergeometric functions of the polar and azimuthal parts and a radial path integral is obtained whose evaluation yields the energy eigenvalues and the normalized wave functions. Special cases include the Hartmann potential and the ring-shaped oscillator.

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Addendum

Another paper of M.V. Carpio-Bernido that is also worth mentioning is about the calculation of the Green function for an axially symmetrical potential field via path integral evaluation (J of Phys A-Mathematical and General 24, 3013-3019 (1991).  DOI: 10.1088/0305-4470/24/13/016). Among the paper published during this decade, this paper had the most number of citations. This paper is also one of the NIP’s most cited paper.

The first paper with an address from the new institutes is from D.M. Yanga and J. Magpantay. In this paper, they derived the Lee-Yang term for velocity-dependent potentials using stochastic quantization (Phys Rev D 32, 516-518 (1985). DOI: 10.1103/PhysRevD.32.516).

Click here for pdf version.

National Institute of Physics

Authors SALOMA, C
Title COMPUTATIONAL-COMPLEXITY AND THE OBSERVATION OF PHYSICAL SIGNALS
Journal JOURNAL OF APPLIED PHYSICS
Volume 74
Issue 9
Beginning page 5314
End page 5319
DOI 10.1063/1.354232
Published Date NOV 1 1993

Abstract The effects of computational complexity on the characteristics of a physical signal that is reconstructed from its representation of sampled data are analyzed. It is found that a more complex algorithm does not only require longer time to implement, but also yields an erroneous reconstruction. The reconstruction suffers from contrast degradation, phase shifts, and attenuation of details relative to the true signal. These unwanted effects are caused by the existence of spurious frequencies in the computed spectrum due to rounding-off errors. The amplitude distribution of the spurious frequencies across the spectral bandwidth strongly depends on the number of data points handled and on the complexity of the particular reconstruction algorithm employed. Since the floating point representation of numbers in a computer is always finite, an upper limit exists in the maximum number of additions or multiplications required to compute a quantity reliably without errors.

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Authors BERNIDO, CC
Title PATH-INTEGRAL TREATMENT OF THE GRAVITATIONAL ANYON IN A UNIFORM MAGNETIC-FIELD
Journal JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL
Volume 26
Issue 20
Beginning page 5461
End page 5471
DOI 10.1088/0305-4470/26/20/029
Published Date OCT 21 1993

Abstract The Green function for a relativistic particle interacting with a gravitational point source and a flux confined at the origin of the (p, phi)-space is evaluated using Feynman’s summation-over-histories. The bound state energy spectrum is calculated when a uniform magnetic field is applied perpendicular to the (p, phi)-space.

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Authors SALOMA, C, XU, XM
Title THE DOIELECTRIC MICROSPHERE IN A SINGLE PLANE POLARIZED GAUSSIAN-BEAM – CHARACTERISTICS OF THE RADOIATION FORCE
Journal OPTIK
Volume 94
Issue 4
Beginning page 173
End page 176
Published Date OCT 1993

Abstract We study the characteristics of the radiation force acting on a dielectric microsphere near the focus of a plane polarized TEM00 Gaussian beam. These characteristics include the magnitude and direction of the force as a function of refractive index relative to the surrounding medium, the dependence of the force magnitude on the wavelength. axial distance and sphere radius corresponding to the two independent states of plane polarization.
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Authors SALOMA, C, DARIA, V,MUNOZ, J
Title FOURIER-TRANSFORM REFRACTOMETRY USING MULTICHANNEL DETECTION
Journal APPLIED OPTICS
Volume 32
Issue 25
Beginning page 4785
End page 4789
Published Date Sep 1 1993

Abstract A versatile refractometer that utilizes multichannel interferometry is developed. The refractive index of a homogeneous sample placed in one arm of the triangular common-path interferometer is computed from the induced shift in the position of the He-Ne probe wavelength. The interferogram is detected by a 2048-element CCD line sensor and Fourier transformed by using a dedicated 32-bit microprocessor. The resolution and accuracy of refractive-index measurements depend on the angle of incidence that the sample makes with the optical axis of the interferometer.

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Authors SALOMA, C, DARIA, VR
Title PERFORMANCE OF A ZERO-CROSSING OPTICAL-SPECTRUM ANALYZER
Journal OPTICS LETTERS
Volume 18
Issue 17
Beginning page 1468
End page 1470
DOI 10.1364/OL.18.001468
Published Date Sep 1 1993

Abstract The performance of a zero-crossing-based optical spectrum analyzer is presented. With the use of only a single comparator, the analyzer circuit detects one zero crossing per Nyquist interval with a location accuracy of 1 part in 256. The dynamic range of sampling is limited only by the supply voltages of the comparator and the noise arising from truncation errors associated with computation. The 512-component spectra of various interferogram inputs are directly computed by Newton’s formula from the measured crossings. The single-channel spectrum analyzer with a preselectable Nyquist sampling interval setting is constructed with discrete transistor-transistor logic and analog components. The ultimate performance characteristics of the analyzer are set by the response capabilities of the electronic components used.
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Authors SALOMA, C, HAEBERLI, P
Title 2-DOIMENSIONAL IMAGE-RECONSTRUCTION FROM FOURIER COEFFICIENTS COMPUTED DOIRECTLY FROM ZERO CROSSINGS
Journal APPLIED OPTICS
Volume 32
Issue 17
Beginning page 3092
End page 3093
Published Date JUN 10 1993

Abstract Two-dimensional image reconstruction using Fourier coefficients that are computed directly from the sampled representation of zero crossings is demonstrated. A two-dimensional image of dimensions N(x) x N(y) is interpreted as a set of N(y) independent x-space lines (in gray-scale format) that are arranged uniquely along they direction. Each line has N(x) elements. Reconstruction is achieved first by computing the entire set of N(y) one-dimensional Fourier transforms from the measured zero crossings using Newton’s formula. Each N(y)th line spectra has N(x) Fourier coefficients. The inverse Fourier transform is then applied to each of the line spectra to obtain a set of N(y) reconstructed x-space lines. The reconstructed image is obtained by arranging the reconstructed lines properly along they direction.

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Authors SALOMA, C, HAEBERLI, P
Title OPTCAL-SPECTRUM ANALYSIS FROM ZERO CROSSINGS
Journal OPTCS LETTERS
Volume 16
Issue 19
Beginning page 1535
End page 1537
DOI 10.1364/OL.16.001535
Published Date OCT 1 1991

Abstract A practical method of computing the spectral components directly from measured zero crossings of interferograms is presented. The method requires the sampling of only one zero crossing per Nyquist interval and yields results with a normalized mean-square error that is better than 10(-6) with respect to the fast Fourier transformation when the zero crossing is located within the Nyquist interval with an accuracy of one part in 10(6). The method is also robust against error frequencies that may arise owing to the finite range in the floating-point representation of numbers in a computer. The error frequencies appear whenever a large number of crossings is processed. This type of error is not related to the accuracy of locating the zero crossings and limits the operational bandwidth of a zero-crossing-based optical spectrum analyzer.
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Authors BASCO, F, BERNIDO, CC, CARPIOBERNIDO, MV
Title ON THE HAMILTONIAN PATH INTEGRAL IN POLAR COORDOINATES FOR NONCENTRAL POTENTIALS
Journal PHYSICS LETTERS A
Volume 157
Issue 8-9
Beginning page 461
End page 464
DOI 10.1016/0375-9601(91)91019-A
Published Date AuthorsG 12 1991

Abstract A new derivation of the Hamiltonian path integral in polar coordinates is presented. This differs from earlier results in that the procedure is applicable to central and noncentral potentials.

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Authors CARPIOBERNIDO, MV
Title GREEN-FUNCTION FOR AN AXIALLY SYMMETRICAL POTENTIAL-FIELD – A PATH INTEGRAL EVALUATION IN POLAR COORDOINATES
Journal JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL
Volume 24
Issue 13
Beginning page 3013
End page 3019
DOI 10.1088/0305-4470/24/13/016
Published Date JUL 7 1991

Abstract An explicit evaluation of the path integral in spherical polar coordinates for the Green function of a particle moving in an axially symmetric potential field is presented. A closed form of the Green function is obtained from which the energy eigenvalues and the normalized eigenfunctions are obtained as the poles and the residues at the poles, respectively.

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Highlighted

Authors CARPIOBERNIDO, MV
Title PATH INTEGRAL QUANTIZATION OF CERTAIN NONCENTRAL SYSTEMS WITH DYNAMIC SYMMETRIES
Journal JOURNAL OF MATHEMATICAL PHYSICS
Volume 32
Issue 7
Beginning page 1799
End page 1807
DOI 10.1063/1.529244
Published Date JUL 1991

Abstract Path integral quantization is done for the five classes of potentials appearing in the systematic search for nonrelativistic systems with dynamical symmetries done by Makarov, Smorodinsky, Valiev, and Winternitz [Nuovo Cimento A 52, 1061 (1967)]. By an iterated application of Bateman’s series formula to the polar coordinate path integral, an expansion is obtained on the Feynman kernel or the Green’s function, whichever is possible, in terms of hypergeometric functions of the polar and azimuthal parts and a radial path integral is obtained whose evaluation yields the energy eigenvalues and the normalized wave functions. Special cases include the Hartmann potential and the ring-shaped oscillator.

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Authors SALOMA, C, DE VERA, AJ
Title PHOTOACOUSTIC DEPTH PROFILING BY CROSS-CORRELATION USING A GAAS LIGHT-EMITTING DOIODE
Journal APPLIED OPTICS
Volume 30
Issue 17
Beginning page 2393
End page 2397
Published Date JUN 10 1991

Abstract We present a new approach to depth profiling optically opaque multilayered samples. The presence of interfaces in a sample is revealed by cross-correlating a randomly generated optical probe beam from a GaAs light emitting diode and its generated photoacoustic signal. The technique attains a throughput advantage over previous profiling methods since it operates without an external optical modulator. Random intensity modulation of the light source is achieved by direct current modulation of the diode. We show the effectiveness of technique by establishing the double-layer structure of a magnetic tape.
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Authors BERNIDO, CC, CARPIO-BERNIDO, MV
Title PATH INTEGRAL QUANTIZATION OF NONRELATIVISTIC SYSTEMS WITH MAGNETIC-CHARGES
Journal JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL
Volume 24
Issue 2
Beginning page 407
End page 413
DOI 10.1088/0305-4470/24/2/014
Published Date JAN 21 1991

Abstract The exact path integration for systems with magnetic charges is presented. The Green function and bound-state energy spectrum of a dyonium are obtained. Unlike earlier works, the exact path integration is done directly in spherical polar coordinates and does not require the use of coordinate transformations such as the non-bijective transformation of Kustaanheimo and Stiefel.
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Authors ALVERO, LM, MAGPANTAY, JA
Title COMPACT SOLUTION TO THE GENERALIZED MASTER EQUATION
Journal PHYSICAL REVIEW A
Volume 41
Issue 6
Beginning page 3369
End page 3371
DOI 10.1103/PhysRevA.41.3369
Published Date MAR 15 1990

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Authors MURIEL, A
Title THE PERIODOICALLY KICKED 2-LEVEL ATOM
Journal PHYSICS LETTERS A
Volume 128
Issue 6-7
Beginning page 367
End page 368
DOI 10.1016/0375-9601(88)90192-2
Published Date APR 11 1988

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Authors MAGPANTAY, JA, YANGA, DM
Title STOCHASTIC QUANTIZATION AND THE TUNNELING PROBLEM
Journal PHYSICAL REVIEW D
Volume 34
Issue 2
Beginning page 557
End page 564
DOI 10.1103/PhysRevD.34.557
Published Date JUL 15 1986

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Authors MAGPANTAY, JA, ROMERO, DB
Title GAUGE-INVARIANT POTENTIALS FROM YANG-MILLS THEORY
Journal ANNALS OF PHYSICS
Volume 161
Issue 2
Beginning page 303
End page 313
DOI 10.1016/0003-4916(85)90082-X
Published Date 1985

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Authors MAGPANTAY, JA, YANGA, DM
Title DERIVATION OF THE LEE-YANG TERM VIA STOCHASTIC QUANTIZATION
Journal PHYSICAL REVIEW D
Volume 32
Issue 2
Beginning page 516
End page 518
DOI 10.1103/PhysRevD.32.516
Published Date 1985

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Natural Science Research Institute

Authors  GO, NE,PEREZOROZCO, GD, HALOS, SC
Title    INVITRO RESPONSE OF EMBRYOS FROM DOIFFERENT PROVENANCES OF PINUS-CARIBAEA VAR HONDURENSIS MORELET
Journal         PLANT CELL TISSUE AND ORGAN CULTURE
Volume         32
Issue 1
Beginning page        1
End page       7
DOI    10.1007/BF00040109
Published Date        JAN 1993

Abstract        The tissue culture response of embryo explants of four fast- and slow-growing provenances of Pinus caribaea var. hondurensis was investigated. Treatments included adventitious bud induction and development with benzyladenine (BA) at different concentrations and exposure periods, root induction with naphthaleneacetic acid (NAA) and indolebutyric acid (IBA) and callus production with combinations of NAA, 2, 4-dichlorophenoxyacetic acid (2, 4-D), BA and kinetin. Fast-growing provenances produced nodules earlier on the cotyledonary surface, developed shoots earlier from induced buds and produced more shoots per surviving embryo at lower BA concentrations tested compared with slow-growing provenances. On the other hand, calluses of the slow-growing provenance, La Mosquitia, grew faster on media supplemented with cytokinins and auxins compared with those grown on media supplemented with auxin only. This reaction was not observed with fast-growing provenances. It is suggested that cytokinins in fast-growing provenances promoted organized development more efficiently than in slow-growing provenances.

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Authors HALOS, SC, GO, NE
Title    MICROPROPAGATUON OF PINUS-CARIBAEA MORELET
Journal         PLANT CELL TISSUE AND ORGAN CULTURE
Volume         32
Issue 1
Beginning page        47
End page       53
DOI    10.1007/BF00040115
Published Date        JAN 1993

Abstract        Adventitious shoot formation was induced in excised mature embryos of Pinus caribaea using a modified Murashige and Skoog medium (MSM) supplemented with 6-benzyladenine. The highest frequency (96%) of adventitious bud production was observed when embryos were exposed to 8.9 muM BA for one week prior to transfer to a growth regulator-free medium. Increased BA concentration and longer exposure to BA significantly reduced survival rates of explants. Dilution of the basal medium to 1/4X and 1/8X decreased shoot formation but 1/2X was just as effective as full-strength. Addition of auxins, glyphosate and coconut water to the rooting medium did not improve rooting success beyond that of spontaneous rooting. Sucrose at 1.5% significantly increased rooting of shoots. Plantlets were successfully transferred to the soil after preincubation in liquid medium.

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Authors PHAM, LJ, HALOS, SC
Title    INTERGENERIC PROTOPLAST FUSION OF TRICHODERMA-REESEI RUT-C-30 AND PENICILLIUM-FUNICULOSUM THOM MG-171 FOR IMPROVED CELLULASE PRODUCTION
Journal         ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
Volume         613
Beginning page        575
End page       581
DOI    10.1111/j.1749-6632.1990.tb18224.x
Published Date        DEC 28 1990

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The first institutes that were created from this EO are the National Institute of Physics (NIP), the National Institute of Geological Sciences (NIGS), and the Natural Science Research Institute (NSRI) at the University of the Philippines (UP) in Diliman and the Institute of Mathematical Sciences (IMS, now the Institute of Mathematical Sciences and Physics, IMSP), the Institute of Chemistry (IC), and the Institute of Biological Sciences (IBS) at the UP’s Los Baños campus.

Initially, each institute received 3M pesos as lumpsum appropriation except for the NSRI which received 5M pesos. In 1983, the exchange rate is more or less 9 pesos to a dollar [2].

These institutes were also “exempted from government limitations in the purchase of scientific and research-related equipment and attendance abroad of appropriate personnel to scientific and technological meetings and conferences upon certification by the Director-General of the National Science and Technology Authority (now DOST).” I wonder if this is still the case.

30 years hence, what are the most exciting research that these institutes have produced?

In this series of blog posts, I will be listing 30 notable research articles from 3 of these 6 institutes. Why only 3? Well, I could not track research articles from the institutes housed at UP Los Baños. They don’t appear on ISI Web of Knowledge.

What is my criteria? Nothing. This is solely based on my own judgement. Perhaps I will factor the number of citations per year. But my decisions will be based more on the over-all “coolness” of the title and the abstract, and the “awesomeness” of the body of the paper. I’ll try to defend by choice. However, if you do not agree with me, then make your own list!

This is a herculean task, mind you. To be able to get only 30 from 403 research articles from 1983 to 2013 would be difficult.  Of course these 403 articles are already filtered such that all articles come solely from the Philippines or are homegrown. This explains the low number of articles published. All papers with collaboration from outside the Philippines are excluded.

Of the 403 articles I will be reviewing (yeah, reviewing), 270 come from the NIP, 73 are from the NSRI, and 60 are from the NIGS. The breadth of topics is as wide as the pacific ocean (probably as deep also) –  from two-photon fluorescence imaging to mineralization potentials of Philippine ophiolite, from a bounded, self-adjoint time operator to Polycyclic aromatic hydrocarbons, from crustal thickening to genotyping. Yeah, goodluck to me.

But more than my ‘fancy’ list, I guess the more important question is how these institutes evolve. What was happening in the Philippines and in the world when these papers were published? What are the “hot topics” in science then? Who are the significant Filipino scientists during those times? I will try to ask a few friends to help me out.

Interestingly, by plotting the publications in years, one could see distinct jumps. What could have caused these? Was there policy changes that could be tied to these?

3 phases are seen when the number of publications is plotted in years for the 3 institutes.

This series will be divided by dates. I’ll start with 1983 to 1993, the first ten years of the institutes. The first years would be relatively easy since there are only a few papers from back then. I still wouldn’t know what to write after that. Stay tuned.

This is my first attempt of narrating Philippine science history from the perspective of published research.

Crossed fingers.

References:

[1] http://www.lawphil.net/executive/execord/eo1983/eo_889_1983.html
[2] http://intl.econ.cuhk.edu.hk/exchange_rate_regime/index.php?cid=1

Gekko coi, Leonard’s Forest Gecko. Courtesy: Brown et al, Herpetologica 67 (2012)

I started posting new articles only on March.  Two new forest lizards: the little one and Leonard’s is a summary of two articles about what else, two new lizards. One is a forest-flap gecko (Luperosaurus angliit) while the other is a forest gecko (Gekko coi).

The next story I wrote was on distinguishing children with mild autism via EEG tracings. It was an interesting research article because the authors used nonlinear time series analysis -  The Lempel-Ziv complexity, covariance complexity and prediction error, to discriminate between normal children, children with mild autism, and children with severe autism. They said that they can differentiate those with mild autism against the normal children and those children with severe autism, with their analyses. However, the normal children and those with severe autism cannot be differentiated.

Prediction error. Points (circles, diamonds, squares) are calculated values from EEG trace of each cohort in the study. Gaussian curves are centered at the mean values of each group, with waists corresponding to twice their respective variances. Big circles are guide to show that there is clustering between values and groups. Data courtesy of L. Co Ting Keh, A. Chupungco, J. Esguerra

I had three consecutive posts about newly discovered animals for my Earth week series: the rare deep water tilefish, Branchiostegus saito, from Laiya, Batangas; the first species of hymenosomatid formally recorded from an anchialine cave and exhibiting true troglomorphic adaptations, Samarplax principe (It’s colorless!); and scientists expanding/ resurrecting 4 previously recognized genera and suggesting 2 new genera to accommodate the diverse species in the Philippines, one is the genus Pinoyscincus.

I was productive in May with 3 very different posts. The first was about an ancient connection between the Philippines and the Marianas seen in pots. It made the editor’s selection of researchblogging.org. The second was on a collaborative study on inorganic elemental contents in white rice of seven Asian countries. And the last was a WHO study about the economic benefits of breastfeeding.

Similar pottery decorations from: 1) Nagsabaran, northern Philippines; 2) Achugao, Saipan, Mariana Islands; 3) Site 13 at Lapita, New Caledonia (2, courtesy of Brian Butler, see Butler 1994; 3, courtesy of Christophe Sand, see Sand 1999: 46). Courtesy: Hung et al, Antiquity, 85 (329), 909-926.

The geological origin of the island of Mindoro was revisited by scientists who are mostly affiliated with the University of the Philippines.  They concluded that the whole island of Mindoro came from mainland Asia. This was my single post in July.

My first science news which came out of a mainstream (vs blog) media organization was on the gene that can increase rice harvest. I wrote it with Neil, a friend who is doing his PhD in Japan. I have to make kulit to Rappler. But it was all worth it. If I have to judge which science news from the islands is the biggest, it would be that news. Unfortunately, it never gained local traction.

The only post in September was about the relationship of fatherhood with Prolactin levels in males, specifically those who are living in Cebu. The study “hints that the function of the hormone may shift as men move through different life history stages.”

I was also able to write a feature article in Rappler – Sketch me a Pinoy Scientists, also in September. The article was about the tumblr site, pinoyscientists.tumblr.com. The site, moderated by Reina, hopes to “help displace outdated and unrealistic stereotypes of scientists.”

The last science-related article I posted this year was the success of Peter Rodrigo in Denmark.  Peter was the recipient of this year’s Danish optics prize. It made headline because it was a wonderful news and also because it got copied by GMAnewsonline.

It was also the year that I explained why I write about science from the Philippines.

Most of the science news that you read in this blog did not make it to mainstream media. Usually, science news are only fillers in a sea of showbiz and political news.

But as I’ve said, “A good research in the Philippines is also an example of the triumph of the Filipino spirit, of its optimism and its strength.”

I hope that I could write more this year.

First, I’d like to stress that I’m very happy that Peter had received the award (He deserves it), and that it was picked up by a media organization with a large readership.  GMANews online is being read by a lot of Filipinos. I hope that a lot of Filipinos will be inspired by his winning.

It is just unfortunate that the real news is being masked by another serious issue, that of plagiarism.

Second, I’d like to thank TJ Dimacali, the Science & Technology Editor of GMA News Online, for giving his apologies. However, I do not agree with him that they “pursued the story independently.” Below is a comparison of the original article I wrote and the article “written” by Shaira F. Panela that originally appeared on their website:

I will probably write a more detailed blog post about this. The updated article still has a lot of flaws. But I still have a deadline to beat on my real job.

Oh by the way, it’s Imprints of Philippine Science and not Imprints of Filipino Science.

Peter was chosen based on his work on wind lidar and his previous research in optical trapping. His different papers on optical trapping have been featured in Optical Society of America’s Optics and Photonics News as one of the most exciting optics research for 2003, 2004, and 2005.

Currently, he is working on semiconductor laser-based wind lidar that can remotely measure wind velocity and direction accurately. The technology developed in their work is now being commercialized by a DTU Fotonik start-up company, Windar Photonics A/S.

Peter received a diploma and cash prize during the DOPS annual meeting and the Northern Optics conference held last 19-21 November 2012 in Snekkersten, Denmark.

Peter obtained his Bachelor’s and Master’s degree from the National Institute of Physics, University of the Philippines Diliman and his Doctor of Philosophy degree from the Niels Bohr Institute, University of Copenhagen.

“The future cannot be predicted, but futures can be invented,“ Peter quotes Dennis Gabor, the inventor of the Holographic technique, on where he finds motivation as an aspiring scientist and inventor.

The Danish Optical Society is the most important professional organization devoted to Denmark’s activities on scientific and technical aspects of optics.

DOPS prize recipient (right) and DOPS chairman Lars René Lindvold (taken from http://www.fotonik.dtu.dk)