Next time your computer hangs, do this!

A few decades ago, you had a computer with 2GB storage space. Your computer would hang after making a ‘kar-kar-kar’ when you tried to open the internet explorer.

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Now things have changed. You now have the best laptop available in the market. You have even better performing desktop computer with you. Your desktop computer has 16GB+ of RAM and 2TB+ of storage space. That is a lot.

However, your computer still hangs. Because you have now much more things to do than before. When you will become old, you will perhaps have a supercomputer with you. But regardless of its capacity and performance, it will still hang. Because ‘hanging’ is the nature of the external world.

Next time your computer hangs, slow down a bit. Your computer is telling you that you are going too fast. It is telling that your mind is out of balance. Your pace is not in harmony with the world you live in.

Life is all about maintaining harmony and balance. If you go too slow, you will fail. But if you go too fast, you will still fail. So find that speed of balance, between the slow and fast one. If you do that, your computer will never hang.

Never compare apples with apples

In scientific community, this phrase is very popular. Wherever you go, people say that you have to “compare apples with apples”. When you make a presentation, someone stands up and says “you are comparing oranges with apples.” When you show some poor results to your professor, your professor says “you should compare apple with apple.”

But, is that the real problem? That you are comparing orange with apple?

No. That is not the real problem. We have always overlooked the real problem.

When you try to compare apple with apple, you are basically accepting that you are a fool. Because why should you compare apple with apple? If you already know that both are apples, what is the point of comparison? Both of them will look round, smell like apple, and taste the same. After all, they are both apples.

When you started, you actually had an orange. You clearly knew how apples look and you were sure that what you have is actually an orange.

However, in the community that you lived, people only had apples. They looked at your stuff and said that you better have an apple. Don’t be an orange guy in this apple community. Everyone is apple here. At least, if you want to live in this community, you should look similar with apple, if not become apple. They said like this.

Your mind then started believing on this during the course of your study. And at some point, may be when it was little dark, you found that both apple and orange look round. So your mind picked this idea and said that both are round and similar. Now you became happy. Obviously people also became happy with you. After all, you had a similar stuff with theirs now.

You completely forgot the reality. You forgot that what you had originally is an orange. You are now only living in your mind, thinking that your orange is an apple.

This is the ugly truth of life. Most of the time, we look at things with our mind. We never see the reality.

So next time you compare your model results with observations, please be aware of this.

Always try to look at things without any presumption. Try to look at things the way they are. If you have to compare, always compare apple with orange. Never compare apple with apple.

 

Why we should stop debating climate change?

Climate has never changed and will never change. It is just as it should be, perfectly following the laws of the nature. It is perfectly responding to the dramatically-increased human activities in the last few hundred years. It is only our mind that is changing.

People on the left side are telling that it is head. Those on the right are telling that it is the tail. In reality, it is just a coin, a whole coin. Neither head, nor tail.

Deep water in the ocean is always calm. There are waves only on the surface. It reality, waves are nothing but water. They rise from the ocean and disappear in the ocean.

Even within us, our heart is silent, like the deep water. The heart is always calm and relaxed. But the mind, it is changing every second. Not just climate, if you look from your mind, everything looks changing. It is your mind that is changing, not your surrounding.

The minds are changing, in both sides. But they have some lag. So they never agree. When the people on the left side think that climate change is happening, those on the right don’t. And when people on the right think it is really changing, people on the left have changed their opinion. It is only the mind that is oscillating.

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We can choose to continue debating. We can continue publishing flamboyant for-and-against peer-reviewed articles on ‘climate change’ and keep fighting. But we have another option too. We can learn to agree and realize how we all are connected, at the level of heart. After all, we all have a common agenda, to save this planet – our home. Do we want to live in a divided world of opinions or in a uniting world of peace, harmony, and love? The question is just this.

Perhaps I will never see him again

We meet, walk together for some time, and then we depart. It happens in trains and public transits noticeably. But even at larger time-scales, it happens in our life all the time. Everyday or every week, we meet new friends, share things with them for some time and again time comes to say good bye. Some of those friends we will see again, some we won’t. Some we want to see again, some we don’t.

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Today, another such friend left a message in my desk and went away.

We not only shared the office, but we shared the air we breathed. I shared his energy and he shared my energy.

We didn’t communicate much as such but communication “happened”. In fact, communication that happens energy-wise is much more powerful and long lasting. He was a person with high energy and positivity. He was a great hiker and more importantly a responsible vegetarian. He was in many ways like a Yogi. I never saw him worried.

I will perhaps never see him again. But I am sure life will remind me of him in different ways at different times in the future.

My best wishes to him too.

 

 

PhD: concluding remarks

When I was a kid, I never dreamed of earning a PhD. All I wanted was to study more and more. So I just followed the course of the river. I didn’t know or care whether the destination is ocean or something else.

When I became an adult, I knew that the society where I was brought up highly revered a PhD. So I had thought that I will also some day do a PhD.

We can plan something but not everything. That is what I have experienced. PhD thought came into my mind when my supervisor at Masdar Institute came to my desk one day. He showed a small ad in an AGU newsletter about a PhD position at UT Austin. I didn’t want to let down my supervisor so I applied. In fact, that was the only place where I applied. Until then, I had only thought of returning back to Nepal and rejoining my low-paid but highly revered ‘engineer’ position. I was not sure about it even after I got the offer. I really didn’t know that UT-Austin was a good ranking Tier 1 university until I posted about this offer in my Facebook page. The comments reflected that UT Austin is a great place. My perceptions got changed. I decided to pursue.

I was about to give up soon after I started my research at UT Austin. I was hit really hard in one of the group meeting. Not only by my supervisor but also by my colleagues. I felt the lowest of my life on that day. But soon I realized that it was because the standard and quality of research was much higher than I expected.

I was very busy taking 3 courses at that time and it was very hard to manage time for research. A few colleagues had already failed in their qualifying exams. So I many times felt that it was a wrong decision to pursue a PhD. My health was also not favoring me; I had been diagnosed with celiac disease (allergic to gluten). I very much regretted for leaving my government job of an Engineer back in Nepal.

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So there were only two options. Do or die. It is the same thing but a different tone is used in research: publish or perish. But as I interacted more and more with my colleagues and knew about research, I realized that we all were on the same boat. So I decided to continue. I worked harder. Time was not a problem for me because I was married single at that time. Weekends and holidays then meant more research. No wonder, my eye power kept on increasing at a rate of 0.25 per year.

Things started getting better. Qualifying exam was a great success.

I was still not comfortable in the world of research. I tried to avoid people who criticized my work. But later I realized that I can’t escape anywhere in research. You can’t escape your peers. You can’t escape your experts in your field. Most importantly you can’t escape the reviewers of you papers. It took little longer for me to realize that such interactions, feedback, comments, etc. are actually good things.

I never thought that I would be able to graduate in three and half years. But it happened. I worked hard and it got reflected. One of the reason for this success is also that I didn’t waste any of my work at UT Austin, not even the class projects. I always kept the main research topic in my mind before I started any class projects. So all of those activities later became part of my dissertation.

My daughter was born in the last year of my PhD. And the degree of ‘father’ means no less than PhD to me. Indeed, graduate study is when many people get engaged, married, or have their first kids.

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With my adviser(to my right), co-adviser(to my left), and examination committee members after the defense on April 15, 2016.

The most important thing that I realized during my PhD study is that learning is a never-ending process. Initially, I really thought that research is or has to be flawless. But I was totally wrong on that. There can be many flaws in your research. That is exactly why we discuss the limitation in the end of a research paper. PhD makes us understand this reality in depth.

I also realized that we can’t be successful in PhD just by gaining knowledge. We have to develop some conscience too. Knowledge without conscience is indeed dangerous.

When I was a child, I believed that if something is written in a text book, it must be true. I believed everything I read in a book. But now, I trust nothing other than my conscience. I now not only buy the conclusions of a research but the wholeness of it, with its limitations and assumptions. After all, a theory is only true until the assumptions are true.

In our research, we try to model the earth system. Modeling the earth system is indeed overwhelmingly complex. Even a grain of sand is very much complex to model, let alone the whole earth. We must simplify many physical processes. We have to make many assumptions. So sometimes it can be frustrating too. But the beauty of research is that we understand little more everyday than yesterday. The beauty of research is in seeking, not in gaining something.

13288124_179159015813437_1353670647_oWith my wife Sirjana and daughter Nova on graduation day, May 21, 2016.

As I look at my Tam hanging on the wall, my heart leaps up with pride realizing that I received the highest degree possible in an academic world. But as I look out of the window and see the wonders of the nature, my heart bows down realizing that there is so much more to explore. I am still not sure how much knowledge I gained during my PhD but I know with certainty that I know very little.

Finally, what does this degree really mean? This degree reflects the knowledge of many people, knowledge that is passed down through generations. I am merely a carrier of this knowledge. It also reflects the aspirations of many people; my family, my teachers, my friends, and many anonymous others. It is an outcome of their good wishes.

 

 

Pilgrimage to AGU Fall Meeting

It was my fourth time. It has always been in San Francisco. About 20,000 scientists and researchers assemble here every year. For many, it could be their first experience. And for a few, it could also be their silver jubilee. I went there for the first time in 2011 when I was doing my Master’s degree in Abu Dhabi. Now I am doing PhD at UT-Austin and still going every year. It is our pilgrimage.

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A view of the poster hall.

It is our Hollywood too. We meet our celebrities here. Our celebrity is not Obama. Not Trump either. Not even Miley Cyrus. Our celebrities are those who have at least a few thousands citations of their paper. Whose papers we often cite. Many of them are known as “AGU Fellows”.

AGU has intruded my life in even more ways. Most of my journal articles published or under review are in AGU Journals: JGR atmosphere, JGR Earth Surface, and GRL. I also get peer-review request from these journals.

For the first time, I was given a poster. For the second time, I was given an oral talk and I was so proud of it. But now I requested for poster when I submitted my abstract. For students, it is more important to get feedback and poster sessions are much better than oral sessions. Oral talks might be better for professionals or late career researchers who need to showcase their works and advertise their labs.

It is customary for us to attend celebrity talks or invited talks that usually happen in oral sessions. The picture that we create in our mind of our celebrities, after reading their numerous papers, often do not match in person. After seeing them more often, we realize that they are common beings who were also graduate students like us at some point.

We can also learn something new in general oral sessions. I knew about Google Earth Engine for the first time in a general oral session. Although Google Earth Engine has not been commonly used until now, it has the potential to become a one-stop shop for satellite data in the future. There are also some interesting talks by highly successful people in the general sessions. This year, Elon Musk gave a featured talk whose company SpaceX successfully landed a re-usable rocket for the first time in history few days ago.

Life of a graduate student is full of free stuff. Many of us go to the conference just to enjoy free beers. In campus, we only get free foods not beers. Every afternoon, some good beers are served during the conference. Many people ask for two glasses at once because the queue is usually serpentine.

Another reason to go to the conference is the free stuff given by the Exhibitors. Some of the stuff such as USB drives, umbrellas, and NASA bags are something we can’t help but pick. I always pick a stress ball although I have never actually used it for its intended purpose.

In the conference we also see many people that we knew by name but never met before. I have seen some people whose paper I had reviewed. I have also met an editor who had edited my paper. One person was asking me critical questions during my poster session and I suspected him to be the reviewer of one of my under-review article. Peer-review is an anonymous process but only one-way. Sometimes, we also meet some arrogant people who believe that they are the only researchers doing good science.

It feels so bad when your poster is visited only by your colleagues. You feel worse when the poster next to you is crowded but you wait for someone to visit your poster. This time I tried to publicize my poster by using my mediocre marketing skills. All I did was I distributed numerous copies of my poster when I visited other posters during earlier sessions. It was a success, more or less.

The conference is a good place for job search especially for those folks who are graduating soon. A random encounter with a Professor or a professional can lead to a job and is sometimes more effective than applying online countless times. And we never know when and in what way a contact that we make today will be useful in the future.

For the first time, I had to wait a few hours to get the registration badge. This time, the wait was less than one minute. The book of abstracts was also given only to those who wanted it. The android application of AGU Fall Meeting was not working this year although it was working fine last year. Technology has certainly made our life easy. We can upload our posters and slides online now. But I hope this conference won’t turn into a virtual conference in the future because of this fast-growing technology.

We also get to see our school buddies there. Last year and this year, I met one of my best college buddy, who has already become an Assistant Professor at Michigan State University. Last time we had met in Nepal, I don’t remember when, but we were both unmarried.

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Me with my best buddy, my college friend Yadu Pokhrel.

AGU is also an excuse for us to travel and have some fun because it happens at the end of the fall semester. I took my wife last year and went to Los Angeles. Driving along the Pacific Coast while going to Los Angeles has been one of my best life experience. Now I already have a plan to take my daughter to the Disney Land in the future.

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Me, my wife, my best buddy and his wife (not in order).

There have been very few unpleasant experiences to me in San Francisco. The hotels are expensive during the time. We had to pay $300 for a two-star hotel this time. The streets are crowded. It is unfortunate to see so many homeless people in the streets of such a thriving city.

No doubt transportation is a pain in San Francisco. But it was surprising to me that there were so many electric buses and trains in San Francisco given some of the largest crude oil and natural gas reserves located in California. California has a plan to obtain at least 33% of electricity from renewable energy sources by 2020.

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Enjoying some crabs and draught beer on Pier-39.

Pier-39 is a must-have experience for some crabs and draught beers. But the chilling winds there can destroy the fun sometimes. The Aquarium located here is also worth watching although a bit expensive for graduate students. The best thing I like about San Francisco is its central location. Both heaven (San Diego) and hell (Las Vegas) are very close from here.

We spend longer time waiting than actually flying in our life. My flight to San Francisco this time was delayed because of bad weather. Traveling has never been a pleasant experience for me except when I flew for the first time in my life and when I got a free Business class pass in Abu Dhabi. This time I was stuck in the last row of a small plane for those four hours. I thought I really needed to practice some Yoga postures for these kind of situations. The only good thing being in the last row was that the restroom was next to it.

I don’t know yet whether this pilgrimage has helped me to experience the god of my research. But I know that I will be going there next year as well.

Understanding publication metrics: impact factor and h-index

I was looking for some papers in Google Scholar yesterday and accidentally clicked on ‘Metrics’ icon located on the right side of the page. In front of me was a list of top 100 journals (of the world) based on their h-index. I was surprised to see that most of the journals in the list were in the field of biological sciences, physics, and chemistry. To my dismay, I didn’t see the journal ‘Nature Geosciences’, the most revered (sorry if you don’t like to say so) journal in the field of Geosciences. But do the above results imply that only the ladies and gentlemen in biology, physics, and chemistry publish good research? Do that mean Geoscientists watch movies all the time?

The answer is certainly “no”.

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So the question is:

Why the journals in biology, physics, and chemistry have the highest impact factor? 

To answer this question, we have to answer another question first:

What exactly is an h-index?

According to Wikipedia, “A scientist has index h if h of his/her Np papers have at least h citations each, and the other (Np − h) papers have no more than h citations each.”

Little confused? Very reasonable! But it is very simple.

If a scientist has an h-index of 12, it means that he/she has published 12 papers that received 12 or more citations.

The h-index was proposed by physicist Jorge E. Hirsh in 2005 aiming to measure both the productivity and citation impact.

So to maintain a high h-index, you have to keep publishing while maintaining the quality of your publications (so that you receive more citations). If you publish a paper that is eventually not cited, you are wasting your time as it won’t contribute to your h-index no matter how many more such papers you publish. The h-index for a journal also means the same thing.

Now we are in a situation to answer the original question. If a journal has a high h-index, it generally means that it has published higher number of papers that received higher number of citations. But what does that really mean? It simply means that there are more people working in that field so that the probability of number of papers being published (and cited) is higher.

Still doesn’t make sense? Lets look at this statistics here about the number of PhDs awarded in 2008 (of course in the US). The number of doctorates awarded in biological sciences is 7,793 while it is 862 for earth, atmospheric, and ocean sciences. So obviously we can expect more publications in biological sciences, and hence more citations, and hence higher h-index, in the journals of that field. This is not surprising considering the fact that the history of research in biological sciences, physics, and chemistry is much longer than that of Geosciences. I hope I answered the original question.

Unfortunately, h-index is not perfect as is this world. For example, if a scientist published only one paper in his life time that received say 2,000 citations, his h-index is 1. Another scientist who published one paper and received only 15 citations, would still have an h-index of 1. Another drawback of these metrics including the h-index is that they do not reflect the difference among different fields. So the h-index of a journal/professor of biology cannot be compared to the h-index of a professor/journal of Geosciences.

In your Google Scholar profile, you will also see another index called i10-index developed by google, which, in fact, is very similar to the h-index. It is just the number of your papers that received at least 10 citations.

Another frequently asked question:

Do you really need to publish in a journal having a very high impact factor to prove yourself?

The answer is “not really”. Have you realized that the impact factor of your paper may be higher or lower than the impact factor of the journal itself?

According to Wikipedia, the impact factor of a journal in any given year is the average number of citations received per paper published in that journal during the two preceding years. So if a journal has a high impact factor, either the journal received higher number of citations or the journal accepted fewer number of articles, or it could be both. For most of the journals, the acceptance ratio would not be too much different. So the major component affecting the impact factor is the number of citations indeed.

Lets take an example of a paper published in 2013. This paper published in April 2013 has received 25 citations until July 2015. That means the impact factor of this paper is 25. Note that the impact factor of the journal Nature in which this paper was published is 41.45 in 2014. So it can be said that this paper is significantly below average for this journal.

Lets take another contrasting example. This paper has received 50 citations in a similar time period, i.e., between May 2013 to July 2015. This means that the impact factor of this paper is 50. Now compare this to the impact factor of the JGR-Atmosphere journal in which it was published, i.e., 3.43. It means that this paper has significantly higher impact than the journal’s average impact.

So it really doesn’t matter in which journal you publish your paper. The only thing that matters is whether you receive citations or not.

One last question:

What is the best way to measure productivity of a researcher?

There will probably be many indices rolling in the future each claiming that it is the best. But, perhaps the best way to evaluate a researcher’s productivity or performance is to simply look at both the number of citations and the number of publications, both of which are shown by Google Scholar and other academic search engines (if made public). In addition, quality of the paper must be evaluated by a researcher in that field. It is that simple. I am not saying that we don’t need those indices. When making comparison among many candidates, those indices are indeed very helpful. And it is always fun to compare your index with that of your peers in Google Scholar. 🙂

Thank you for reading.

P.S.: The original paper about the h-index can be found here.

The author is thankful to Travis Swanson for helpful discussion.

Reject but encourage resubmission

With a dream to be a world-class scientist, you decide to pursue a PhD. One more reason for this decision is that you want to live up to all the expectations of your family and society. After applying to a number of universities, you get admission into a decent university. At the first meeting, your adviser asks you to bring some original idea next day to get started. He tells you that it is our research group’s tradition to have three peer-reviewed publications for a PhD degree and one for a Master’s degree.

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Then you start to think out of the box to get some original ideas. You try everything. You spend longer time in the bathroom. You stay alone hours thinking, with your eyes gazing up. But you get nothing. You are about to give up. But one day you suddenly get an idea while being on the bus and you become excited. You share the idea to your friends and adviser. The next day you find a paper in google scholar and realize that a very similar work was already published last year. Then you start looking for other ideas. You search everything in google scholar and find nothing undiscovered. But you need something to get started otherwise your PhD is in jeopardy. You then made up some problem very similar to a previously published paper and create some vague research questions. You start to work on the problem reluctantly. You use different, better or higher resolution data-set and start playing with the data. You get more and more ideas as you continue working on it. You present your idea again and again in your research group and your colleagues and adviser start to believe it. Your idea then gets established. You enter the world of research.

In the first draft of your first paper, you write everything you learned during the last year. You include all the literature review whether it be relevant or not to the main idea. You write several disconnected thoughts and use unnecessary paragraph breaks and jargon. You write confounding abstract and conclusion. Regardless, you send it to your adviser. You wait for one month for your adviser’s reply. Not getting a reply, you realize that it was badly written. Then you start to revise the paper yourself and work on it for another month or so. You send it again to your adviser. This time you get a reply saying that the paper is badly organized, lacks focus, and is not written well. You don’t see any comment in the paper, however. You feel bad on the day and decide to go for some happy hours. Next day you start to revise it again. After substantial revision, you send it again to your adviser after another month. This time you get a reply within a week with your adviser’s comments in the paper. When you open the paper, you see it all red with tracked changes everywhere. In addition, you also see some comments asking for more figures and explanation. Then you work for another month and send it to the adviser again. This time you get a reply in a few days with some minor comments. You become extremely happy on that day and you embrace some happy hours in the evening.

The next day, you start the process of submitting the paper to a journal. Your adviser picks a high-impact journal even though you already had a journal in your mind with a decent impact factor, typically below two.

You spend about one week to formally submit the article to the journal. After submission, your anxiety level starts to rise linearly. You check the status of your paper everyday. You feel excited to see ‘reviewer assigned’ status. After a month or so, you see the status ‘with editor for decision’. Then your anxiety level tends to reach the peak. That night you don’t sleep well. You don’t eat breakfast well the next morning. After one or two days, you see email from your adviser forwarding the decision letter to you. Before clicking that email, your anxiety reaches the maximum. You open the email and a long list of comments unfold. It says ‘rejected but encouraged to apply’. You don’t understand its meaning and you start to google it.

After reading the comments from the reviewers, you realize that there are three kinds of reviewers. First ones are deliberately negative on your idea from the very beginning. This typically happens either because they didn’t like your idea or because they didn’t see any citation of their papers. It is also possible that the idea presented in your paper undermined their line of thought and the results were against their previous findings. In their comments, they imply that the world is perfect, so your method, data, figures, and everything has to be perfect. Second kind of reviewers always give moderate opinion. They give some comments but they neither agree nor disagree strongly with your idea. Third ones are extremely welcome. They like the paper and they always positively recommend the paper giving only minor comments, mostly on grammars.

You reluctantly tell the fact to your colleagues in the hope to get to know the status of their paper. One of your colleague tells you that her paper was accepted with minor revision. You feel low that day. Next day, you get to know from another colleague that his paper was also rejected recently. Then you feel a bit relieved. You also talk to your friend in another university and your friend tries to comfort you saying his past story. He says that his paper was also rejected but he resubmitted it in the same journal and it was accepted. You also decide to resubmit the paper to the same journal.

You try to incorporate all the comments and work on it. You polish your figures and present them using very high quality graphics. You filter your data and present your result in more complex way possible. You put multiple curves in a single graph and add a few tables. You also add a few pointless extremely vague sentences. While doing this, you remember Einstein’s quote “If you can’t explain it to a six year old, you don’t understand it yourself.” But you ignore it and keep those vague sentences. You also make the ‘tone’ in your paper a bit softer and become careful not to hurt author’s ego when criticizing past works. You also review more relevant papers and add their citations. And you try to be more neutral and balanced in your opinion. You delete those sentences that you wanted to delete from the very beginning, but hadn’t deleted because that would significantly reduce the length of the paper. Finally you submit it to the same journal. This time you get a decision letter indicating ‘accepted with major revisions’.

After a few weeks, you revise your paper giving it a complete new outlook. At this point you realize that criticisms, comments and negative feedback all were actually positive things. You compare your latest paper to your first draft and you realize that the first draft was a piece of ultimate shame. You resubmit the paper and in a few weeks you get an email with a decision ‘accepted’. You find it as one of the happiest moment of you life. Happy hours get extended and become happy days.

With a little perseverance you have now made a history. You will at least be found in google scholar forever, if not cited in the future. Congratulations for being published for the first time.

Happy writing.