Nearly everything about the Yachie lab

Updated on January 6, 2023

Nearly everything about the Yachie lab
By Nozomu Yachie
Welcome to the Yachie lab at the University of British Columbia! Our lab’s missions aredeveloping significant technologies, pioneering new fields, discovering important knowledge
in biology, and making your time together successful. Our lives are only once, so let’s focus
on things that matter for the development of the world and synergize our efforts as a team.
Every member of the lab is supposed to play a professional role. There are diverse rights you
have in the lab. But there are also many rules that you must follow. There are several
expectations from me that you are encouraged to frame to synergize with your career. We arefrom different training backgrounds and cultures. This document explains the ideas I want toshare with you and tries to bring everyone on the same page. Any instruction cannot be perfectand needs to be evolved. Please read this document and ask me or discuss it with people in
the lab if you have any questions. I am not the rulebook. If you have a potential element worth
adding to this document or any question or concern about the existing elements, please
discuss it with me or bring it up to our lab meetings. Let’s evolve the lab culture together.
Please read through this document even for the topics that are not directly relevant to you,understand the ideas behind the whole lab dynamics, sign on the signature form on the last
page, and give it to me.
This is a version shared with the community and contents entirely internal for the Yachie lab
has been omitted from this version.

Quick overview of the Yachie lab
We focus on technology development and scientific discovery and try to benefit our society. We are in
the fields of synthetic biology and systems biology that require the integration of multidisciplinary
knowledge and techniques. Most of the lab projects are new biotechnology development. However,
we also focus on addressing important biological questions by devising new technologies. While ourbiological focus is wide, we try not to spread our technical focus. For example, many of our projects
use genome editing and high-throughput sequencing analysis. We take advantage of the assets wehave in the lab to best succeed.
I believe in people’s potential. Every graduate student or postdoc in the lab is supposed to lead at least
one project and develop skills that are unique to the lab. Everyone is encouraged to help support others’
projects with their expertise (mini collaborations in the lab). They are supposed to lead their first-author
paper projects and contribute to others, thereby also to publish many co-authored papers. The lab has
developed an exceptional collaboration network across the world. We have a strong track record inacquiring competitive funds and publishing papers. Everyone in the lab can access various resources,
tips, and advice to develop their career. I respect people’s different career goals. At the same time, thelab has certain goals. Therefore, I always want to discuss how to align your goal with the lab’s and aim
for the best of our success. Last, everyone in our lab arrives here already with superior education,
skills, knowledge, and other privileges. Science is fun and what can make you enthusiastic. You arehere to enjoy this game. Please always consult with me about any concerns or questions.
School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

If you are new to the lab(Omitted)Your rights, lab rules, general expectations, and advice
There are rights you have in the lab, rules you must follow, and expectations by the lab and me. They
are mainly designed to achieve the high integrity of our science, protect our intellectual properties (IPs),
support your daily life in the lab, and optimize our efforts and performance with the best practice.
Professionalism. You are treated as a professional scientist in the lab. This provides you with the best
training opportunities, but probably also pressure. Nobody is perfect, so there is no need to feelpressure. But please try to develop your professionalism that involves being independent, reliable,setting your own high standards, and showing that you care about every aspect of your job. The
instructions below in this document would help. Making mistakes is ok, but please learn from your own
mistakes and try not to repeat the same mistakes. Please do not hesitate to ask your colleague for
help, advice, and necessary training, but please take notes and try not to ask the same questions morethan once. Please also treat any of our lab members as professional colleagues.
Access to diverse resources. You have access to our state-of-the-art laboratory instruments, highperformance computing infrastructures, and a range of UBC core facilities and services. You canusually pursue your daily research project with sufficient research budgets that I maintain. The Yachie
lab has an exceptional collection of DNA resources and genetic circuits that allow you to quickly
perform DNA engineering and cell and animal experiments (please check our plasmid inventory in the
Google Drive folder). We also have software packages that accelerate our data analyses(https://github.com/yachielab).
Appropriate training and instructions. We have many instruments and materials you can use, butthere are too many. It is impossible for us as a small group to set up a systematic training program for
all the items in the lab. Therefore, we rely on the supervision networks in the lab. Please have a seniorlab member as your supervisor until I tell you that you are good to go by yourself. Please havecomprehensive training for all the items you access and understand appropriate manipulation protocols
and what to do in case of mistakes and incidents. Please try to ask questions when you get training.
You are also encouraged to ask questions to other people surrounding you. Please do not touch items
that you do not know how to manipulate. If you are a senior member of the lab, please try to provide
instructions to your juniors. Please contribute to the protection of the lab environment.
Mentorship. Science is fun, but success in science usually requires your all-around ability in leadership,
followership, management, strategic planning, acquiring funding, establishing networks, andpresenting and writing about your work. You may face struggles related to many of these aspects, butthat is normal. Please consult with me and senior lab members. For example, the lab has many strong
writing and presentation tips that greatly benefit you. Please see the following instructions on deadlinesand get maximum opportunities for your fellowship application, conference presentation, andSchool of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

manuscript preparation. I am also happy to chat and advise you on any aspect of academic life. The
lab also has many great senior lab members, and SBME has many professors who are easy to talk to.
Deadlines. Any materials generated in a lab project must be reviewed by me to obtain a green light
before going outside the lab (even for materials going to department events and committee meetingmembers). Conference abstracts, posters, presentation files, and any other documents shorter than
three pages must be submitted to me two weeks ahead. Other materials, including a fellowship
application package and research report for a committee meeting, require four weeks. This deadline
system is set to protect us from intellectual property (IP) breaches and also to maximize your successwith my support. Reference letter requests must be made four weeks ahead to provide the best one
for you. Please accept any refusal by me caused by not following deadlines.
Work hours and vacations. If you are a student or postdoc, the lab does not set any core working
hours. For example, computational projects can be done anywhere. However, we encourage people
to come to the lab during the daytime to discuss and consult with other members. I simply want every
trainee to manage their progress, life, and career development plans with their own responsibilities.
Only the exceptions are the lab meetings described below that every trainee must attend. When you
cannot attend any of these meetings, you must report it to me in advance. Please also report to me
about your long-term vacation plan where you miss many meetings. If you are a staff member, please
follow the contract and report your work schedule on Workday as soon as you plan them, in addition
to reporting them to me.
Lab meetings. We have two weekly lab meetings: lab progress meetings and journal club meetings.
These are mandatory for all students and postdocs. Every trainee should also join weekly project-basis
meetings relevant to their projects once identified. Please do not be late for the meeting. We usually
have important announcements and discussions on daily lab topics at the beginning of these meetings.
Please let me know on Slack if you be late or absent from the meetings. If you miss any lab businesstopics we have discussed, please follow up on them by asking around.
IP, experimental data, and lab notes. Any data, materials, and documents generated (collectively,
intellectual properties, IPs) as a part of the lab projects are all properties of the lab and the university.
The IPs generated using lab resources and budget do not belong to the scientist individuals who
generated them. You, however, of course, maintain the right to be properly credited for yourachievements. Any IP generated by you should be accessible by the other lab members under mydirection. At the same time, any unpublished data and ideas should not be shared outside of theuniversity without permission or made public through Twitter, Facebook, etc. I am ok that you develop
personal communications and discuss your own projects within the school or university, but pleasetake responsibility that your idea is breached. Please consult with me when you need to discuss yourunpublished IP with somebody outside of the university. IPs are not what always need to be containedin the lab but just what need to be properly managed. Your data and idea can be presented anddiscussed outside the laboratory when they can be managed to meet with our strategic merits. Please
always discuss your specific case with me. Without my permission, you must not talk about somebody
else’s idea of the lab. This is a risky, irreversible act and could lead to huge trouble. If you are uncertain
about your specific case, please always consult me. Based on the ideas of where our IPs belong andhow they should be shared across the lab and the community, we ask you to abide by the following
two ideas for data transparency and reproducibility. First, please deposit all the protocols, program
School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

scripts, raw data, and analyzed data with annotations to your Dropbox folder. Daily program scripts
can be organized in your own GitHub repository but make sure you deposit them all to the lab
repository routinely (any scripts before publication must be maintained as repositories). Large raw
datasets like deep sequencing reads can be stored in one of our high-performance computing servers.
Second, please organize your lab notes daily so other lab members can reproduce your experiments
later. Lab notes must be organized not only for yourself but also for others and you of the future.
Experimental records must be linked to all the data you deposit to the lab Dropbox and the resources
you produce in the lab. Please interpret molecular and cell biology experimental data on the day you
acquire them with necessary annotations and properly leave your discussion on your lab noteregardless of whether you obtain positive or negative results. Some bad habit examples are (1)accumulating raw data with no written interpretations by assuming you can remember yourinterpretations or by planning to record them someday, (2) avoiding recording results with mistakes(for example, taking gel electrophoresis image by using a wrong DNA ladder), and (3) organizing lab
notes with no index that makes it even yourself hard to quickly access specific results you obtained.
Recommended habit examples are (1’) organizing acquired data of the day, making slides, andrecording data interpretations and any thoughts in the lab note before you leave the lab every day, (2’)
recording all data and experimental faults with reflection thoughts, and (3’) making index pages at the
beginning of every lab note or providing systematic experiment codes (index numbers) and using themto organize raw data folders, data slides, and lab notes. (Internal content omitted) Please routinely
have the mycoplasma contamination check of your cell samples and report in the project meetings.
Some journals do not allow us to publish cell culture-based data with no mycoplasma certification.
These are ideas to achieve the high integrity of your research. Please also read the Reproducibility
and Integrity section below.
Write papers and attend conferences. Publish or perish. Let’s write and publish a paper. This is only
the way you can contribute to science and be acknowledged. Projects with no publication are the sameas if they had never happened. The process of writing a paper can greatly polish our idea andphilosophy and truly elevate the value of what we have done. The lab has ideas on what scientificpaper should be, nuts and bolts for writing high-quality papers, and a good track record in publishingpapers. Publishing papers makes you acknowledged by the community and provides you a highchance of winning fellowships and awards and acquiring academic jobs and other opportunities.
Please develop and keep envisioning your path to publish a paper with me. Let’s also aim for highquality works. Please also learn about predatory journals and their equivalents who take advantage of
our wish to publish papers and require high publication fees. They often are observed to publish papers
with flawed scientific procedures and meaningless peer-review processes. I advise you to spend yourprecious time on meaningful works and publishing them. The idea of what is meaningful science work
would come across with the concept of hypothesis testing and HARKing, P-Hacking, and CherryPicking described below. I do not ask you to publish papers in high-profile journals but perform highquality science. While publishing a paper is a long-living contribution to science, presenting at aconference is a short-living contribution. But it is worth doing. Discussing your data with experts outside
the lab often gives new insights. Great talk as a trainee sometimes makes you famous in the community.
You can find collaborators and friends. However, to prevent the IP breach and being scooped, we mustplan the conference presentation strategies, such as patent submission beforehand. Please develop
a conversation with me and solidify your understanding of your project.

School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

Apply to fellowships. Preparing and applying for fellowships both benefits you and the lab. First,
winning a fellowship is a great recognition and provides you with budgetary support. The lab adjusts
your total stipend to be higher than that before having a fellowship. It also saves the lab’s stipend cost.
Second, the process of writing fellowship greatly polishes and improves our research vision andproposal. The lab also has many great tips for preparing competitive applications and a good trackrecord of acquiring research funds. You will learn these through the process of preparing applications
with me. The success rate of each fellowship opportunity is not high, so please be calm and have adefault expectation of not getting it. Some people wait for sufficient data or publication before applying
for a fellowship. Try not to have such a loser’s mindset of feeling fear of denial or wasting your efforts.
Keep trying and developing your skills in preparing a strong application package with a king’s but
humble mindset is the best way to win it.
Collaborations and sharing resources outside the lab. We always think big but often in a way wealso synergize people’s expertise within the lab and with collaborators. We establish many loyal
relationships with other groups across the world. Please be generous to help others, especially byoffering our techniques and equipment to our neighboring labs. We are often asked to provide ourtechniques and share resources (plasmids and cell lines) as a technology lab. However, before youoffer any help to others, you must get my approval to see if I need to step in for any potential concerns
around our IPs and strategic research plans.
Peer-review papers. Critically peer-reviewing papers written by others is one of the best ways tostrengthen your academic writing skill and learn what to expect when you submit a paper. The lab isconstantly requested to peer-review papers by many top-tier journals, including Nature, Science,
Nature Biotechnology, Nature Communications, and many others. I often nominate two trainees fromthe lab to help review papers together upon the editor’s approval. You can list your peer-review
contributions in your CV, like “served as a peer-reviewer for Nature with Dr. Nozomu Yachie.” Please
let me know if you are interested.
Maintain your CV. We recommend you update your CV as you make any scientific contributions andother achievements.
Report. Human errors happen. You should not be blamed for making mistakes or breaking instruments.
However, you must report any incidence, breakage, and equipment malfunction on our Slack channel#labalert_breakagereport for the lab to be aware of common mistakes, near-miss accidents, and any
unavailable reagents and instruments for the planning of others’ experiments. Let’s also appreciate
any reports by people. Being honest also develops your precaution skills.
Consult. You also need to feel confident in your success with the lab, welcomed, trusted and provided
sufficiently by the lab and team members, including me. Any system or intention preventing this must
be removed from our environment. We continue to work hard to maximize our capability to support
your career, but our resources are insufficient. If you have any little concerns about your developmentin the lab, please consult with me or any senior members. Science is fun and allows us to develop
great achievements, and I want to support developing your confidence in your time spent with us.
Please also support each other in general. UBC and SBME have many professors who are easy totalk to. UBC also has student health services and counseling services.

School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

English only. English is chosen to be an official language internationally for science and academia.
You must speak in English with people while you are in our building. We need to create an environment
where people feel free to jump into any scientific discussions. I understand that we sometimes needhome-feeling communications with the first language, but I ask you to please have it outside thebuilding.
Clean after use and lab chores. We share lab benches and instruments, and you will routinely use
these resources. Please keep them clean after use. We also rotate several lab chores and need to relyon that system as a small research group with a limited maintenance capacity. Your understanding
and contribution to these aspects are greatly appreciated.
Stipend support and merit. (Omitted)
Nozomu’s responsibility. I take full responsibility for supervising your development from all theabove-mentioned aspects, managing the lab environment by maintaining sufficient research funds andhigh-quality personnel and leading world-leading research programs. I have been successful in playing
my role as a scientist, conceptor and leader. However, I have a limited bandwidth as a single human.
Please bring up anything when you feel you find a suggestion for the improvement of my management
and leadership.

Expectations for each level of training
The previous section captures most of the common ideas I want you to know. The following provides
more kneaded expectations based on these ideas for lab members in different career stages or withdifferent roles.
Undergraduate students
You are at an entry-level of professional science. Let’s have fun. Please try to learn many from us but
prioritize acquiring solid basic techniques while being a part of our ambitious projects. Please find asenior lab member who agrees to supervise you. You should always be accompanied by them andshould not work alone. Please learn their skills and cultivate their science together. Please also do nothesitate to get help from the other lab members. Please take notes when somebody spends time foryou. Please try not only to be trained but also to help others.
Read papers. Start with papers published in top-tier journals. We are always on the shoulders of giants.
Please find your heroes in science. Please follow their works. Try to steal how their writing and graphics
skills in presenting their works. Try to feel people’s scientific lives through papers. It is fun. Twitter is
one of the good sources to find papers.
You can be more ambitious, have your own project and publish a paper. This option must not be very
hard. Start consulting with senior lab members and bring a new project proposal to a project meeting.
Please try to maximize your benefit by working in one of the areas in which the lab is investing. We areunlikely to approve a project isolated from existing lab projects.

School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

Graduate students
You need to have your independent project. Please find good science mates in the lab and incubate
ideas together. Please try not to work alone and please also try to involve people in your scientificexcitements. Please share your skills with others and cultivate science together. Please develop yourideas on how to swim the daily school and lab life and advice your juniors. Please contribute to thedevelopment of lab science and science in general.
Let’s publish papers. If you are a master’s student, let’s aim to publish at least a small one. If you wantto pursue your academic career, let’s aim to accomplish high-quality work. Please develop multiple
aspects of track records to win a fellowship. Please run at your own pace but know that we sometimes
need to push ourselves a bit for deadlines and other constraints. Any growth requires a load, and it isalways good to be mentally prepared for urgent moments.
Read papers. Please find fields that align your focus and try to be the most expert person in the lab forthe determined fields. Share papers through Slack channel #papers and enjoy discussing intellectual
excitement with the other lab members. Develop skills to critically read papers and understand how
good papers need to be structured. Please try not to cover the field widely and superficially or be a
person who only talks about others’ works. Read papers also to develop your ability to fully write agreat paper. Learn how to critically analyze and interpret different types of data. Do not avoid reading
sections in a paper you think you cannot fully understand. Please care about details and develop yourknowledge, skills, and principles from papers. Please be an actor or a filmmaker but not a movie critic
working for a cheap magazine. Actively survey topics related to your project and implement them into
your project. Keep the focus on your project, and try not to be swamped by trying many exciting new
ideas that dilute your focus and productivity.
Try to articulate what you want to be and consult with me, the lab, and your committee members. I can
openly discuss your career aspiration and help build the best strategic research project, collaboration,and publication and presentation plans. Make the best use of the environment and people in the lab.
Please maintain your CV kept updated. Please lead discussions at lab meetings and develop yourleadership. Please help maintain the good environment of the lab and develop your management skills.
Graduate school life can be stressful, but please enjoy developing your ability for all the above. You
don’t need to be capable of doing them from the beginning. I am always happy to have any type of
conversation for your success.
Postdocs
If you are here as a postdoc, you are probably considering developing your career towards a
professorship or industrial leadership. My expectations and advice are almost the same as those forgraduate students above, but as you have at least one successful experience in running a scientificproject, please explore a different field from your previous ones and widen your view and corecompetency.
Other advice might be to focus on your all-around ability, management skills, and productivity. Science
today is getting more exciting, but it also requires productivity in many ways in return for enjoying it.
You might want to face this fact. This, of course, does not mean you need to merely work hard. Somepeople work hard, and some people work smartly. I would recommend developing the latter first witha little spice of knowing the importance of the former and establishing your career-long, sustainable
School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

workstyle with the confidence that you are moving in the right direction. You might think some PIs of
productive labs are daily working too hard. I cannot lie, and this is true, especially when they are in
their early careers, but also, you can take it easy. We can work hard, likely because we have developed
our all-around ability and management skills to succeed with a fear-less mentality, health, and the
support of our colleagues. Nobody can work like them from the beginning, but knowing the importanceof it and spending time with this idea are important. I am always happy to develop any type of
conversation for your success.
Staff members
We always appreciate our staff members’ support, which is the foundation of our creative and exciting
science and success. I do not have any major items to add to the job description we agreed on upon
your arrival, but please read and understand my advice and expectations for trainees in the lab. It
would be wonderful if you could feel that you are involved in our success and that you are appreciatedby the team. Please also keep in touch with me and consult with me on anything.

Publication and Authorship
Most of your major credits and recognition for doing research in the lab will be translated into yourpeer-reviewed publications. We must consider the questions of authorship on manuscripts seriously.
It is never too early to ask questions about authorship when you embark and help on a project.
In general, we follow the principles outlined by The International Committee of Medical Journal Editors(ICMJE) (http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-roleof-authors-and-contributors.html#two), which is also followed by many journals. The rules of authorshipalso apply to presentations at conferences.
All issues related to authorship will be discussed openly, and you should feel free to bring them up if
you are unsure of your authorship status at any time during the process. However, I will make the final
decision in case of unresolvable conflict.
First authorship. If a student or postdoc takes on a project but subsequently hands it off to anotherstudent or postdoc, they will most likely lose the first authorship unless co-first authorship is appropriate.
This also applies if someone leaves the laboratory without finishing a project or cannot finish it in areasonable amount of time.
Co-authorship. Students and postdocs who help over the course of the project may be added to theauthor list depending on their contribution, and their position in the author list will be discussed with allparties involved in the paper. Contributing important analyses or experiments that finally do not get
involved in the paper does not mean a person will be removed from authorship. Results not included
could still play an important role in how the work was finally done or presented.
Co-first authorship. When two people contribute equally to work, they will be listed as co-first authors
in the paper. The order in which we list the names will be decided through discussion. Very often, two
School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

people have equivalent contributions, but one of them assumes or is assigned leadership on the project.
This person will be listed first.

Reproducibility and Integrity
The Yachie lab is committed to ensuring high research integrity. We will not tolerate intentional
fabrication, falsification, or plagiarism. Read UBC’s policies on academic integrity and actions against
academic misconduct (https://academicintegrity.ubc.ca/). The following conditions must be satisfied forevery experiment of your project. My ideas on “IP, experimental data, and lab notes” in the previous
section would greatly help to achieve them.
Data reproducibility. Your raw data should be reproducible by somebody else. This is critical because
if a third person cannot reproduce your results, it suggests that one (or both) of you has made errors
in the analysis, and the results cannot be trusted. Reproducibility is an essential part of science andan expectation for all projects in the lab.
Complete documentation. Experimental protocols and analysis pipelines must be organized and well
documented so a third person can reproduce your data. All the necessary information required toensure the reproducibility of your experiments must be documented in your lab notes. You should takeextensive notes on each step of your experimental and analysis pipeline. Write down how you
performed every step of experiments in chronological order, from any pre-processing steps of initialmaterials to data analyses and statistical tests.
Replicability. Reproducibility is related to replicability, which refers to whether your results can beobtained again with a different dataset from a replicate experiment performed at a different time. For
an experiment to be convincing to your supervisor/supervisory committee and to be eligible forpublication, the results and conclusions generated from an experiment must be replicated.
Green lights. Initial submissions of manuscript and master’s and PhD theses will be allowed only after
I confirm that all the related files are stored and organized properly for data reproducibility.

Devils in science… Be careful!
Incomplete logics. The most common devils in science whisper to you to accomplish something fast.
Do not listen to these temptations. Rather please enjoy your step-by-step progress and accumulationof solid data with integral research designs. This is the fastest way to succeed in your project. Please
try to observe your experiment objectively and keep asking if your experiment has a single hypothesis
and is designed to logically derive a clear knowledge of each of the hypotheses. I often observe many
experiments executed with vague, subjective expectations (and optimistic hopes that are somewhat
solidified in your brain) end up with obtaining no solidified knowledge or discussion. Please design anexperiment by clarifying what the tests are. Each test should ask for one hypothesis, so it produces
School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

one of the following knowledge types: it supports, denies, or shows its inability to answer the hypothesis.
Incomplete experiments are often designed and performed only by expecting positive results without
sufficient controls. The results from these experiments often cannot fall into any of the above threeknowledge types. Testing two hypotheses in one experiment does not usually work as it is very hard
to set control experiments that perfectly navigate you to a combination of two from the three knowledge
types. Keep in mind that any experiment will not give you an absolute truth. Science is the pursuit ofTruth that you will never reach. We only accumulate supportive evidence for hypotheses that are
combined and built logically to reach closer and closer to Truth. Nobody can always be perfect in allthese aspects. I often design imperfect experiments. But it is important to ensure that you know theseprinciples.
HARKing, P-Hacking, and Cherry-Picking. We are in the era of big data, where multiple hypotheses
can be tested using a single dataset. The following ideas might be hard to understand for some of you
who are new to ideas of the philosophy of science but please at least know that these concepts exist
and try to convince you why they exist through your academic research. The most basic form of scienceis hypothesis testing. Regardless of if your overarching research style is so-called hypothesis-driven
or data-driven, every element of a research project should test a hypothesis. You cannot select ahypothesis after you analyze your data for another hypothesis and pretend it to be set from the
beginning. This is a questionable research practice (QRP) called HARKing (hypothesizing after the
results are known). This may be captured easily by the idea of multiple hypothesis testing. You cantest many hypotheses but cannot select ones showing significant P-values from individual tests andclaim these hypotheses are supported (or their null hypotheses are rejected). This is simply because
objects following the null distributions sometimes appear to be outliers by random chance. In otherwords, if you have one million hypotheses, even when all of their null hypotheses are true, you will get
50 thousand test results (5%) to be positioned in the 5% tail range from the corresponding null
distributions (P-value<0.05, one-sided test). Therefore, selecting hypotheses after testing many
hypotheses and claiming their significance by pretending them to be only the tested hypotheses is
misconduct. In multiple hypothesis testing in data science, hypotheses and statistically significant
results can be screened by testing if these statistical significances from single hypothesis tests arebeyond the expectation that all the null hypotheses are true. Please learn about Bonferroni’s P-value
adjustment, false discovery rate (FDR), and other methods for this concept. Providing another example,
but if you performed one thousand behavioral tests for two genotype groups of mice and claimed
statistical significance of selected tests by not mentioning the other tests, that is misconduct. If you had
only one test but inverted the hypothesis after seeing the result, that’s a QRP called HARKing, which I
would rather define as misconduct. (You can, of course, use your unexpected result against the first
hypothesis to generate the next hypothesis.) Some people repeat replicate experiments until they geta significant P-value after performing an initial test with a defined number of replicates. This is also a
QPR/misconduct called P-Hacking, where dices are kept rolled until an outlier result appears. The last
QPR/misconduct example that I would list here is Cherry-Picking. Some people take many
micrographs for a test and intentionally present only so-called champion images or expected positive
images to manipulate others’ impressions of the test result. As you may see, they are all similar, andthere are more variant forms of QPRs. Please consult with me if you are uncertain about yourexperimental design or data handling process after understanding the existence of these concepts.

School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

Acknowledgment
I thank Christian Landry of Laval University, who shared with me the idea of clarifying lab management
policies and shared their guideline “Landry lab guideline for new members.” Publication and Authorshipand Reproducibility and Integrity sections were largely borrowed from their guideline.

School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org

Nearly everything about the Yachie lab

Updated on January 6, 2023

Signature Form
I confirm that I have read through the document “Nearly everything of the Yachie lab” above. I abideby all the rules defined in this document. I discussed with Nozomu Yachie if some elements were
unclear to me. I will follow any appendices to this document if any. I will also provide my thoughts andcomments on this document to Nozomu, if any.

Print name_____________________________

Signature_____________________________

Date_____________________________

School of Biomedical Engineering, The University of British Columbia
2222 Health Sciences Mall, Vancouver, BC Canada V6T 1Z3
T. 604-822-9512 | E-mail. nozomu.yachie@ubc.ca | Web. https://yachie-lab.org