Chantori Blog

Medical Physics / Monte Carlo Simulation / Medical Image Processing

What can a cave tell us about the need to study English?

There is absolutely no necessity to use English in daily life in Japan. However, I strongly believe that more Japanese (indeed, any non-native speakers) should use English and increase their exposure to the world outside of Japan (their own country). This article is about an analogy that I recall every time I encounter people who are not willing to try to use English – the most common language on earth.

   As an example, during my research today, I wanted to learn about the “sigmoid function (シグモイド関数)”. The first thing I did was Google it. I put the phrase within quotation marks “” to search exactly this phrase. The English and Japanese version of Google showed 363,000 and 13,600 hits, respectively. The English Google showed about 30 times more results than the Japanese one. Therefore, it is easy to conclude from this result that “using English provides access to more information”. But, what does this “30 times more information” actually mean? I would like to think about this by using the analogy of a “cave and a flashlight”.

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   Assume that you are walking deep inside a cave. The only thing you have with you is a small flashlight. You can barely see anything, even your own feet. Due to the lack of visual information, you may easily stumble on a stone or not notice dangerous animals waiting for you only a few meters away. As long as we use this small flashlight, we have to accept such dangers because that is how our world is.

   But, what if we have a flashlight that shines with a 30 times broader beam, or 30 times the range of the small one? The improved visibility would undoubtedly help us avoid potential dangers, or at least better prepare for them.

   More importantly, the new flashlight would reveal a variety of information about the cave such as its size, shape, color, pattern, texture etc.; information which we may only vaguely notice when using the small flashlight. We would most likely find that our world was more huge, beautiful, curious and complicated than we had expected. The small flashlight might be enough for us to survive, but the bigger, more powerful flashlight would certainly raise the probability for us to find something that could make our life better.

   In summary, I hope readers might get a new perspective about the use of English in daily life from this analogy. Of course, the main problem is that this article cannot be discovered by the small flashlight...

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Batu caves, Malaysia

Month6: Sweet Caroline

留学も折り返し地点です。米国で過ごす残りの時間に意識が向き、過ごしやすくなってきたボストンの気候に浮かれていられなくなってきました。

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 今月はAAPM(米国医学物理士会)のBoard Examケンタッキー州でありました。日本の医学物理士試験はペーパーテストですが、米国では最後に口述試験があります。米国の制度は、日本と比較するとMedical Physicstになるまでの訓練期間がとても長いようです。PhDを他の分野(加速器、高エネルギー物理、天文学システム開発等)で取得後、ポスドクから医学物理の分野に参入する方も多く、ポスドクでも医学物理士カリキュラムに沿った授業を毎週受けています。日本で医学物理士になる方は遅くても博士課程までには医学物理の分野に入ってくるケースが多いのではないでしょうか。しかし、米国のように博士課程まで別の分野で研究するというのは、分野の裾野を広くすることにつながるので、個人的にはとても良いと思います。そもそも医学物理自体が多分野の融合でできている分野です。

 ボストンで過ごした半年の研究を振り返ると、当初の目論見通りに行かないことは多々ありましたが、成果・スキル・経験のいずれにおいても想定以上の出来でした。このように充実した時間を過ごせた要因を自己分析すると、

  1. 共同研究者の方々が想像以上に協力的であったこと
  2. 研究上の様々なタイミング(抄録提出締切や実験等)が噛み合ったこと

が大きかったと感じています。そして、この半年間で自分が学んだ事の多さを考えると、そういう知識・経験を私よりも長い間積み重ねてきた年長の方々に対し、尊敬せずにはいられません。

 半年間で研究室内外に多くの友人ができ、英語も上達した気がします。これまで英語は日本語と比較して論理的で直線的な”ドライ”な言語だと考えてきましたが、英語にも様々なレベルでの”ぼかし方”があることがわかってきました。そしてインテリは会話の隅々に”丁寧さ(お世辞)”を潜ませるような話し方をしており、私の中での英語の”湿度”が上がってきました。私ももう少しジメジメした会話をできるようになりたいものです。

 幸いにも日本でやり残してきた仕事と、米国で最初に取り掛かった仕事の両方にめどが立ち、次の半年では、いよいよ大きい仕事に取り掛かろうとしています。いつの間にかボスからはお客様扱いをされなくなり、他のポスドク達と同様に指導を受け、成果を求められます。留学当初に胸に抱えていた”ギラギラ感”を思い出し、また再スタートを切りたいと思います。半年後には新しい景色を見ていたいものです。

先月生まれたカナダグースの雛達はすくすく育っています。

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Genomic Analysis of East Asian Male by using 23andMe

I noticed 23andMe shortly after they first launched their gene testing business four years ago, and since then I have been interested in using their product to test my genome. However, if the product is ordered from Japan, several exciting test categories such as “Carrier status” and “Genetic health risk” are not accessible. Therefore, when I knew I would come to the US, I planned to try out 23andMe during my stay. In this post, I review my (pre- and post-) 23andMe gene testing experience.

   I initially became interested in 23andMe for two reasons. First, I wanted to know more about my body and potential genome-related health risks. Moreover, I anticipated that I could utilize this test to change my lifestyle in order to reduce those potential risks. Second, I was particularly interested in the recent enormous developments in the field of genetics. For example, I had come to realize that gene editing techniques such as CRISPR/Cas9* will likely soon start influencing our society in an irreversible way. By using 23andMe, I expected to smell the “scent” of the future governed by emerging technologies in genetics. Thus, I thought it was necessary for me to buy 23andMe in the US instead of Japan.
*CRISPR/Cas9 & Targeted Genome Editing: New Era in Molecular Biology | NEB

   However, I also concerned about the ethical and scientific problems that this technique could stir up inside me. In particular, I was afraid that discovering genetic information that one typically goes through life not knowing might affect my critical decision-making in the future. Therefore, even after my “saliva sampling kit” was delivered, I needed some time to carefully think about the potential personal discomfort that this product could cause before using it. I made several personal rules, such as how I should act in the case that any genetic defects were found, or if my ethnicity was found to be different to what I had expected.

   When I first read through the initial reports I received, the first thing that came to mind was to “cherish myself”. In particular, the “Ancestry” and “Traits” reports were impressive and I felt a sense of pride while reading them. For example, I could see the route that my great, great, …, great-grandmother took to reach east Asia and how my blood was mixed with other races in that region. It was surprising to discover that simply a small portion of saliva could correctly and precisely predict my traits such as cheek dimples, earlobe type, and caffeine consumption. Furthermore, the report also revealed traits that I had never noticed, such as whether or not I can smell the odor of Asparagus. (In fact, I did not even know that this was decided by our genes.)

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   Importantly, the report scientifically explains in detail which part of my DNA causes the specific traits and provides seemingly reliable information about the scientific methods that were used, including the statistical models used to calculate the probability of certain traits, with references.

   Unfortunately, the reports of “Carrier status” and “Genetic health risk” – the categories that I was the most interested in – were not so surprising. Lack of sufficient reference datasets for non-Caucasians is a potential cause of unreliability of the results. I am curious how 23andMe is going to solve this problem since their “signature” test categories are restricted in countries in which non-Caucasians are the majority.

   In summary, trying out 23andMe was an interesting experience and provided me new knowledge about myself. Although there is still room for improvement in terms of the accuracy of 23andMe regarding minority ethnicity groups in the West, I believe this product can give us new insight into who (or what) we are. In conclusion, I feel like I have rediscovered myself and had my first “scent” of the future.

Month5: Poetic

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今月はボストン市内に散らばる、色々な研究施設を訪ねる機会に恵まれました。周りの方々が私の研究に協力してくれ、コラボレーションの範囲が広がっていくのは嬉しいです。今の研究テーマは以前は全く興味がなかった分野ですが、研究が進むほどに、この分野の広さ・深さに魅力を感じます。これまでの環境・条件の制約の中で、自分が”面白い”と思う研究を一生懸命やってきた結果、以前は自分が”イケてない”と判断していた分野(失礼)に行き着くというのは、振り返ってみると面白いなと思います。
 具体的には3D Slicerのあるモジュールの開発に関わっています。3D Slicerは、NIHからの支援のされ方がImageJと似ているので、これからも発展が見込まれます。

 ボストン日本人研究者交流会の「研究者のためのキャリアセミナー」や「ハーバード日本人会懇親会」もありました。
 前者はボストンでPIをされている日本人の先生方のパネルディスカッションでした。特に日本人が海外で研究していく上で英語をimproveしていくことの重要性については、どの先生方も強調されていました。キャリアのそれぞれの段階で、グラントを獲っていくためにも、英語力は重要とのことでした。また、私と同じプログラムで渡米されている方とも話をすることができました。
 後者はSTEM系に限らずハーバードの様々なスクールから日本人が集まり、フランクに懇談する会でした。Undergraduateの方もおり、前者の会よりも年齢層が若い印象でした。私は寿司のbig fanではありませんが、約半年ぶりに普通の寿司を食べた結果、おいしさのあまり気を失いそうになりました。この会で出会ったつながりから、後日、文系の方々と勉強会も行いました。

 日本語を勉強している米国人に、”Japanese is very poetic”と言われたのが、しばらく心に引っかかっています。日本語で厳密な文章を書くには、どうしても「これ」や「それ」といった類の言葉を多用せざるを得ません。なぜ英語ではこれが少なくて済むのか、を理解しないと、英文を書いても日本語らしさが抜けないかもしれません。

A crazy method I used to improve my English skills

 

When I was in junior high and high school, English was my favorite and strongest subject. My English level perhaps owes to my background (I grew up in a multi-lingual environment), however, I distinctly remember studying extremely hard to improve it. This post is about an English studying method that I invented when I was a high school student and my friends called “crazy”.

   In English exams in typical Japanese schools, most questions are about specific articles in the textbooks from which students are taught for several months. At my school, sometimes we were asked to arrange given words in the proper grammatical order, or to fill a blank in a given sentence. The most difficult type of question was to translate a whole Japanese sentence into English.

   To complete all questions in time and get a high score, I figured that the most “straightforward” way was to memorize entire articles in the text book. Therefore, I started by repeatedly reading the textbook aloud until I was able to speak with fluency. Then, I erased several important words in the articles using correction tape and returned to reading out loud. Since some parts of the article were missing (erased by correction tape), it was not easy to read fluently at first. However, as I kept practicing, my brain learnt and it began to feel as if no words were missing. This is the sign that you can erase a few more words. I repeated this process until my textbook finally became totally blank. No words were written in the textbook anymore; they were written in my brain instead (at least on the day of the exam).

   This method might sound like a makeshift solution for only specific types of school exam and not useful for the other exams where we encounter articles that we have never come across before. However, I believe that having hundreds of sentences ingrained in your brain through my method will help you instinctively find the answer. Furthermore, I would like to emphasize that this method was very helpful for me to develop my listening skill that I am very proud of. Do you still think I am crazy?

Introduction

As scientists, we typically write our scientific papers in English for global accessibility. That got me thinking, why not write my blog in English as well? Today, I am posting my first English blog.

   This new challenge has two objectives. First, to improve my English writing skill. Writing is the skill I feel I am lacking the most compared to other communication skills: speaking, reading, and listening. However, besides speaking, I believe writing is the most difficult skill to develop alone. Therefore, my initial drafts of blog posts will be reviewed by a native speaker and I hope to improve my writing skill through this process.

   Second, I am interested in how many readers I can get if I write in English rather than in Japanese. English articles should have more global exposure, however, there will be increased competition from other bloggers, too. My initial hypothesis is that my English posts will have fewer readers than my Japanese posts. However, if I choose the topic carefully, my English posts may become more relevant to specific groups of people and boost my read count.

   A principal aim of my blog is to fill gaps in knowledge. Recently, I have been trying to choose topics (for my Japanese blog) that have never been discussed before and thus are in a greater demand. As a result, some of my recent posts succeeded in getting a greater number of views. This came to make me realize the similarities between writing a blog and a scientific paper: both require “novelty” and “significance”. Therefore, I regard writing this blog as further scientific training.

   As we do in scientific papers, I will write this English blog series formally and professionally. Furthermore, I will endeavor to keep articles simple and short, hopefully ~300 words (approximately equal to that of the abstract of a scientific paper). I do realize that the influence of my blog posts on the world is tiny, but I would like to know exactly how tiny it is.

Week18: Japanese

先週までは、3D slicerで開発途上の、あるモジュールを使った解析にトライしてきました。しかしインターネット上にすら参考になる情報がありません。そこで今週は先週に引き続き、このモジュールの開発者達に付いて回り、使い方を教えてもらいました。自力で解析ができるようになり、やっと研究らしくなってきました。また、医学物理部門の先生方も、これで開発者に聞かなくとも僕に尋ねればモジュールの使い方を学べるということで、喜んでくれました。

今週は年に1回開かれる、Radiation Oncoloy部門全体のDepartment Meetingがありました。医師、医学物理士、Dosimetrist、看護師、事務、その他の研究者などが集合し、支給される朝ごはんを食べながら1年間の総括・次年度の方針などを話し合う会でした。

ボストンマラソン10日後に迫っています。ゴール地点のCopley Squareにはゴールのゲートが組み立てられ始めました。ボストンマラソンは、世界6大マラソンの中で最も歴史の長いマラソンだそうです(1897年~)Excitement is building…

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アメリカでもアップルストアに行くと、大勢の店員さんが丁寧に話しかけてくれます。こちらが断るまで、いつまでもセールストークをしてくれるので、無料の英会話レッスンとして捉えるのもありかもしれません。ちなみにセールストークに乗せられてiPadを買いそうになりました。

そして、今週末はハーバード日本人会懇親会研究者のためのキャリアセミナーが開催されます。僕が参加者として適格なのかは迷う気持ちもありますが、運営の方々のご厚意に甘えて、参加させて頂くことにしました。

 

毎週の出来事を日本語で振り返る、という形式でのブログの運営は、今回で最後となります。今後はこのブログを通して、新しい形で発信していきます。

今週の英語

  1. silver bullet: 特効薬 “there is no silver bullet
  2. staggering: 驚くべき、衝撃的なstaggering amounts of data”
  3. rudimentary: 初歩的な “a rudimentary knowledge of physics”