MISHIMA - multiple alignment server

June 11, A.S. 0008 (2008 A.D.)

Dr. Kirill Kryukov, post-doctoral fellow of my lab, recently developed new multiple alignment system MISHIMA, and its webserver is open!

MISHIMA server

He gave oral presentation about MISHIMA at SMBE meeting held at Barcelona on June 8.

MISHIMA is acronym of
"Method for Inferring Sequence History In terms of Multiple Alignment", but of course after Mishima city where our National Institute of Genetics is located. But some people only know Japanese novelist, Mishima Yukio. I am great fan of him, and name of this web server is also homage to him.

We will further update this MISHIMA system, so any comments are welcome! Please email me at saitounr@lab.nig.ac.jp.

Saitou Naruya

I decline to attend ICAES meeting at Kunming 0008

April 1, A.S. 0008

As visitor to Lassa, Tibet last year, i am deeply concerned about current situation there. Because of series of Tibet problems in China in this year, i decided to cancell my attendance to ICAES meeting at Kunming, Yunnan.

Saitou Naruya

C. W. Fox and J. B. Wolf eds. (2006) "Evolutionary Genetics"

I just started to read this book today, January 4, A.S. 0008.
Chapter 1 is about history of evolutionary genetics, written by M. R. Dietrich. Although neutralist-selectionist controversy was covered in one section, its ending is bit strange.
In any case, with many authors, this kind of edited book is not as textbook, but kind of reference book.

Two books with different titles, but...

May 31, A.S. 0007
Last week i was in Cambridge, U.K. to attend DDBJ/EMBL/GenBank International Nucleotide Sequence Database Collaborative meeting held at EBI, Genome Campus south of Cambridge. After this meeting i visited three bookstores in Cambridge and bought various books, as usual. I found book written by Dr. V. S. Ramachandran, titled "The Emerging Mind". Although content seemed quite similar to one i already bought, again in Cambridge 2 years ago, any way i bought it. After returning to Japan, i compared two books.

Book 1) V. S. Ramachandran (2004) A brief tour of human consciousness. Pi Press, New York.
Book 2) V. S. Ramachandran (2003) The emerging mind. Profile Books, London

Although titles are quite different, content was almost same. In Book 1, published one year later than Book2, it was mentioned that it was first published in 2003 from Profile Books. So legally it may be OK. But British and American are almost same language, so readers may be just confused. There were some interesting differences, though. In Book 1, published in USA, index was added. I once heard that in USA, distinction between fiction and non-fiction is whether index exist or not. Because this is non-fiction, American publisher might have thought necessity of adding index. Book cover design is also much more superior in Book 1 than Book 2.

Saitou Naruya

Three phases of Sientific English

Phase 0: Current phase. English used in scientific publication is already slightly different from common English. For example, we rarely or never use inch or pound as unit in scientific publication. There are also some specific Latin words, such as "et al.", in scientific publication. These words are rarely used in common English, at least as far as i know.

Phase 1: I myself already am in this phase when i write emails or abstracts that are not edited by other people. New regulation at this phase is as follows.
A) Exclusive use of international system of units (already realized in Phase 0).
B) Suppression of Latin words such as "etc.", "e. g.", and "et al." These are substituted to "and so on", "for example", and "and others", respectively.
C) Use of American-style spellings. There are some spelling differences between American English and British English, such as neighbor/neighbour. Because American English spellings are generally simpler, we use American-style spellings.
D) Liberal use of articles. "Proper" usage of articles (a, an, the) in writing scientific publication in common English is big hedache for many researchers whose native language is not English. Therefore, use of articles is discouraged.
E) Encouragement of creating new technological jargons using non-English words. There are already many examples, such as "eigen" (originally German) and "tsunami" (originally Japanese). We encourage researchers to coin new terms for more fruitful description of nature.

Points A-E are based on "Use of Scientific English in Anthropological Science" in "Message from the Editor-in-Chief" (Saitou, 1998,; Anthropological Science, vol. 106, No. 1, pp. i-iv).

Phase 2: Spelling will become more closer to real pronunciation. At this phase, "Scientific English" may be spelled as "Saientific English".

Some citations from Sayer's Publications

- "Genome is republic of genes". Saitou (0004)
- New definition of "genome": Largest unit of one self-replicating system. Saitou (0004)
- "All Biology Aspire to Evolution". Saitou (0003)
- Introduction of new calender, "After Science" (AS 0000 = 2000 A.D. This year is AS 0006). Sayer Says (January 10, 0000)
- Proposal of "Scientific English". Saitou (1998)

References
Saitou (1998) Message from the Editor-in-Chief. Anthropological Science, vol. 106, No. 1, pp. i-iv.
Sayer Says (January 10, 0000)
Saitou (0003) When i chaired one session at Gordon Conference, California
Saitou N. (0004) "Genome and Evolution" publsihed by Shinyosha (in Japanese)

"Sayer Says" blog version first time

Hello. This is my first try to set up blog version of "Sayer Says".

"Sayer Says" (in Japanese) can be seen at
http://sayer.lab.nig.ac.jp/~saitou/japanese/sayer-says.html

"Sayer" is my nickname in English.
I myself coined it long time ago, when i was high school student.

When i write something here, i will use either Scientific English (STEP 1) or common Japanese. I also follow new calender called "After Science" or A.S. This year, A.S. 0006, corresponds to 2006 A.D.

Sayer