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Advisor Interview: Exploring the Possibilities of Biology × Computing with Professor Masaki Tateno, Author of 'The Textbook of Trees' ── Toward the Mysteries of Life and Immortality

February 21, 2025

Masaki Tateno, Former Director of the Nikko Botanical Garden, Graduate School of Science, The University of Tokyo

A leading researcher in tree ecology and author of 'The Textbook of Trees (Chikuma Bunko)', Professor Tateno, who serves as an advisor to ThinkX, spoke with us about the challenges in the field of biological research, ThinkX’s VN Machine project that enables original research with advanced custom software without requiring expertise in computing, and Professor Tateno’s future research themes.
Kazuki Otsuka (hereinafter Otsuka) Thank you for today.
Professor Masaki Tateno (hereinafter Tateno) Thank you as well.
Otsuka I took your lectures in 'Introduction to Natural History Biology.' I was deeply drawn to your unique perspective and approach to research, and I really wanted to consult with you, Professor Tateno.
Tateno I understand.
Otsuka Recently, many researchers seem to be using cloud services like AWS to set up computational environments. However, without specialized knowledge, they stumble when it comes to setting up servers, creating databases, or uploading data. So, I’ve been thinking that if there were a system where you could just put data into a dedicated drive and it would automatically create custom software based on your instructions, a lot of people could realize ideas that were previously impossible.
Tateno It would be great if it could be built through dialogue in natural language instead of a programming language.
Otsuka Yes, exactly that kind of thing.
Tateno I think many researchers would use it. In fact, in the field of biology, there are a lot of people who struggle with building mathematical models. Support in that area would be really helpful.
Otsuka For example, what if it could read your past papers and tell you what the software could do next?
Tateno Something like that would help everyone. There are people who can naturally think of using computers, math, or physics to do something, and those who can’t.
Measuring the wind speed that trees can withstand. By attaching 28 strain gauges to the trunk and measuring the relationship between wind speed and strain over several years, it was found that healthy trees don’t break up to a wind speed of 100 meters per second.

Measuring the wind speed that trees can withstand. By attaching 28 strain gauges to the trunk and measuring the relationship between wind speed and strain over several years, it was found that healthy trees don’t break up to a wind speed of 100 meters per second.

Otsuka What’s obvious to computer people might not be to those in another field, and vice versa. Crossing disciplines feels like a significant theme. I’m completely ignorant about biology, so I’d like to hear a lot from you this time.
Tateno Among students, there are many who handle assigned tasks like—excuse the expression—manual laborers, doing routine work every day. That’s not how it is in my lab, though.
Otsuka When I ask graduate students, 'What research are you doing?' many just give me the field name and don’t elaborate.
Tateno In a lab, if you secure, say, 30 million yen, you have to produce results within that budget. That means you need to put students to work. You could hire trained people from a technical school and pay them, but that doesn’t happen often.
Otsuka It seems like it often makes more sense to use them as labor rather than taking the time to guide their research.
Measuring the stress on tree trunks caused by snow in the winter at Mount Kunikoku. Beech trees are quite weak to stress and break on steep slopes in heavy snow areas. Cedar trees, however, don’t break under stress, making them a species adapted to snowy regions.

Measuring the stress on tree trunks caused by snow in the winter at Mount Kunikoku. Beech trees are quite weak to stress and break on steep slopes in heavy snow areas. Cedar trees, however, don’t break under stress, making them a species adapted to snowy regions.

Tateno Some people have ideas about what they really want to do. Especially in the sciences, there’s a tendency for individuals to act like lords of their own castles. Some think they’re smarter than their professors and call them by their first names.
Otsuka (Laughs)
Tateno At places like the Faculty of Science I, students tend to have high motivation for research and their own specific problems. Those people often find it hard to get jobs at big companies and end up continuing research at university.
Otsuka So, rather than professors or labs as a unit, it’s possible that individual members could pioneer research using computing.
Tateno In biology, we used Fortran, then it shifted to C, and recently it’s become the more user-friendly Python. Still, for students who learn it on the side over five years or so, what they can do is limited.
Otsuka I think there’s a big difference in what you can do and the difficulty between a 1,000-line Python program and a system built by professionals at a higher level. For example, in that 'Introduction to Natural History Biology,' there was a task to analyze DNA using a software called MEGA*1. But you’re limited to what that software can do. To pursue a more advanced idea, you’d need to build different software.
Tateno I think there are many cases like that. It’d be especially useful for research in genetic analysis.
Otsuka Could you tell me about the problems you’re tackling next, Professor Tateno?
Tateno There are two themes I feel I can’t die without solving.

The first relates to statistical mechanics, chemical reactions in cells, and the free energy of ATP. When molecules in a living body undergo chemical reactions, sometimes like charges—negative and negative—stick together. For example, what happens at the moment ADP and phosphate combine to form ATP isn’t well explained yet. Sharp students poke at this point. I don’t know, and neither do they. In textbooks, it’s left vague because it’s not understood. Right now, I’m working with a company to build an experimental device for this.

The second is that human chromosomes come in two sets, and if both fail, the cell dies. Plants, however, depending on the species, can have triploid or tetraploid sets—three or more sets of chromosomes. My hypothesis is that this relates to partial 'immortality.' It’s not simply that having more of the same chromosomes means it’s fine if one fails; I think it’s the opposite. Plants keep old cells inside while growing outward, so they could just build the outside with good cells. To identify bad cells, expressing genes from only one of the identical chromosomes could mean that cells with harmful mutations on that chromosome die or can’t proliferate. By leaving those inside, they might be able to select only good cells. I’m currently thinking about ways to test this.
Otsuka Both are incredibly fascinating. Especially the latter feels like a universal problem tied to the very mechanisms of life and death. Thank you so much for today. I look forward to future discussions.
*1 MEGA
Standard software for DNA and protein sequence alignment and phylogenetic analysis
https://www.megasoftware.net/
Masaki Tateno (Tateno Masaki)
Born in 1958. Botanist. Former Director of the Nikko Botanical Garden, Graduate School of Science, The University of Tokyo. A leading figure in ecological research on trees. His main books include "A Botanist’s Walk" (Kanjindō) and "Biology: Focus of Knowledge" (Z-kai).