A very open final exam

This year I wanted my final exam for Molecular Cell Physiology (UNBC BIOL 312) to be as open as possible, so I’m posting it here online.

Students who take BIOL 312 at UNBC have already taken basic cell biology. BIOL 312 integrates the details of basic cell biology into larger concepts. We spent a lot of time this (online) semester studying developmental biology, including a book club discussion on Neil Shubin’s Your Inner Fish.

The final exam for this course is intended to allow the students to showcase everything that they have learned over the course of the past two semesters, and to use their detailed knowledge to assess big ideas in evolutionary developmental biology.

This is the final exam, below. I’d love to hear your ideas for improvement in future years.

Also feel free to use/modify/etc. this exam or concept for your own courses.

BIOL 312 Final Exam (2021 Winter semester) 

Each of these papers below, listed in chronological order of publication, is either a classic scholarly work in the field of evolutionary developmental biology or is a relatively new paper of potential long-term importance to the field.

The PDFs of these works are available in the final exam folder on Blackboard. They are also available via the UNBC library.

Lewis, E. B. (1978) A gene complex controlling segmentation in Drosophila. Nature 276:565-570. https://doi.org/10.1038/276565a0 Scholarly works that cite this paper. 

Nüsslein-Volhard, C. & Wieschaus, E. (1980) Mutations affecting segment number and polarity in Drosophila. Nature 287:795-801. https://doi.org/10.1038/287795a0 Scholarly works that cite this paper.

Daeschler, E. B., Shubin, N. H. & Jenkins, F. A. (2006) A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. https://doi.org/10.1038/nature04639 Nature 440:757-763. Scholarly works that cite this paper.

Tan, T., Wu, J., Si, C., Dai, S., Zhang, Y., Sun, N., … & Belmonte, J. C. I. (2021) Chimeric contribution of human extended pluripotent stem cells to monkey embryos ex vivo. Cell 184:2020-2032. https://doi.org/10.1016/j.cell.2021.03.020 Scholarly works that cite this paper.

Please pick one paper from the papers listed above as your exam topic.

Along with each citation above, I have included a Google Scholar link to scholarly works that cite the paper in question. In the case of the older works, those will give you some idea of the novel research that the paper you’re interested in has stimulated over the years.

This exam is, obviously, open book. You may use course materials or any other resources you wish. You may also discuss your work with others. However individual writing must be unique. I.e., don’t simply cut and paste from others’ work – write in your own words.

Please write a four-page (maximum), double-spaced, short paper describing the contents of the article that you have chosen. Please see below for the required outline. I will not mark beyond four pages. You must adhere to these formatting stipulations or you will lose marks.

  • Use 12-point font.
  • Use 2 cm margins all around.
  • The four pages must be double-spaced.
  • Use Times New Roman or Helvetica Neue font.

You should also include a short citation section at the end – the citation section does not count toward your page limit. The citation format is up to you, just be consistent.

Use concepts and terms we have discussed over the course of the semester.

Discuss one other scholarly work the article you have chosen has influenced or the work it will likely influence (for the newer article). The links to citations may be useful here, but you may also find other papers that relate to the concepts in your chosen article and to the concepts you will discuss in your exam paper. Be sure to properly cite this scholarly work.

Work to integrate many of the cell physiological (etc.) concepts that we have covered in BIOL 312 and in your introductory cell biology course (e.g. UNBC BIOL 311). In particular, discuss concepts related to evolutionary developmental biology. Think all the way from the scale of the genome to the cell to tissues, organs, and organisms… and then think about the evolution of genomes and organisms across deep time. Be creative and think broadly. Do not simply restate facts. Think and write around, above, below, and beyond the topic.

This exam must be handed in via the link provided in Blackboard. I will not accept or mark emailed submissions.

The exam is due at our scheduled exam date and end time: 1200h (noon) on Thursday 29-APR-2021 Pacific Daylight Time.

You are allowed one hand-in attempt at at time. If you hand something in to Blackboard in error, let me know and I will erase your attempt so that you can make another. Papers should be handed in as Blackboard-compatible file formats – so generally use DOCX or PDF files (although other files types may work).

This is the outline that you must follow:

  • ~0.75 pages: Discuss what the author(s) did. Write about hypotheses and concepts more than you write about techniques. Technology changes, but it can only be used effectively in the context of incisive questions and clear thinking. (5 points)
  • ~0.75 pages: Why is this paper important in the context of evolutionary developmental biology? (5 points)
  • ~1 page: Describe the influence of your chosen scholarly work on one subsequent scholarly work or on anticipated scholarly work, as described above. (5 points)
  • ~0.5 pages: Conclude/summarize. (5 points)
  • Include citations in any format you would like to use (does not count toward page limit).

I will be using this outline as the marking rubric, so please adhere to it.


April is designated as National Poetry Month. I assume that designation is for the United States, but I figure that it might as well be for everywhere else as well. Poetry does not reside in one country. Arguably poetry does not reside in one month either, so…

Part of National Poetry Month is National Poetry Writing Month, or #NaPoWriMo. Poets are encouraged to write a poem each day of April. I have taken part in this during a number of recent Aprils, and you can see the (variable) results here. I write poems at other times too, but life gets in the way and, if nothing else, April forces me to pay attention to the world around me a bit more than normal.

This year, as everyone in the world knows, North America pretty much shut down in the middle of March due to COVID-19. One Friday in mid-March I was delivering an invertebrate zoology lab on insects (absolutely my wheelhouse) to about 50 undergraduates, and by the following Monday I was trying to figure out how to deliver the rest of the semester remotely. It was jarring for me as an instructor, and likely doubly so for my long-suffering students who then graciously put up with my attempts at online lecturing.

(Aside: Thank you all of my undergraduate and graduate students. I can’t ever fully express how much I appreciate you. I feel like crying as I type this.)

During some less fraught #NaPoWriMo Aprils, I have written whatever strikes my fancy on any given day. However this April was wall-to-wall COVID-19. April Fool’s Day was anything but fun foolery this year. Most– all! – of us were more concerned with not getting infected, and not getting our friends and family infected. We were indoors all day other than an afternoon walk. Those of us lucky enough to still have paying jobs were trying to navigate a new normal (I hate that overused term). Everyone was navigating a new normal (I still hate that overused term, but I’ll use it anyway). Going out for groceries took a level of planning that one might normally associate with  prepping for a military patrol in a hostile sector. We spent our mornings and afternoons listening to politicians and their associates – some more reputable (and ultimately more successful and curbing the effects of this pandemic) than others. No one knew what was next. To be honest, we still don’t.

So April 2020 presented a perfect foil for my #NaPoWriMo musings. During that month I put together a poem for each day, plus some photographs, that documented what was coming at me and my family. I don’t expect that my experiences were solitary. I’ve experienced quite a bit of craziness up to now in my middle-aged life, but nothing compares with this. Nothing has ever been as comprehensively global. Nothing has left me feeling that I could have similar discussions with someone in my local grocery store (socially distanced, of course) or a market in, say, Tanzania. Nothing has left me completely not knowing what’s next.

COVID-19 has added a level of stochasticity to our lives that juxtaposes with grinding monotony. That means that we often can’t tell one day from another even though each day feels completely whacked. In an attempt to emulate that uncertainty in verse, I used an app called Word Swag that takes short passages and randomizes the line structure. Most people use Word Swag to produce funky invitations and posters and the like. I used it to input my short COVID-19 poems and let it delineate line breaks for me. That resulted in internal rhyming, unexpected rhythms, and a sense of unpredictability imposed upon my short verses.

I have taken those #NaPoWriMo poems, along with a few of the photographs that I took during that early period of the pandemic, and have turned them into a chapbook.

I will mail you the chapbook for free, but in return I simply ask that you either:

1) donate any amount to a conservation-based charity of your choice, or

2) spend some time in natural area near to where you live – and that could, of course, range from some distant backcountry to an urban greenbelt a few hundred meters from your front door to your own pesticide-free lawn and garden. I’m not picky!

If you donate, please simply send me a PDF copy or screenshot of your donation receipt. If you spend time appreciating your local environment, just send me a photograph of your time spent.

You can DM me your photo or receipt or whatever at @docdez on Twitter or at huber@unbc.ca. Please send your name and snail 🐌 mail address as well so that I can send a copy.  

I will print a first edition of 25 chapbooks. If there’s more interest than that, I’ll print up editions in batches 25 or so after that. I will mail this to you wherever in the world you happen to be.

This pandemic, like virtually every human pandemic prior to this, was brought on due to conservation and food supply malpractice. Right now our valiant health care professionals are treating the acute symptoms that are devastating individuals and families. But we, as a global society, need to confront the direct causes so that this doesn’t happen again. Specifically, we need to stand against the pervasive materialist consumerism that has us encroaching upon nature, consuming beyond the planet’s capacity, and exploiting and degrading ecosystem services. Combine that with climate change, and the existential crisis that we now confront is beyond that ever faced by humanity. Our current generations – young, and old, and in-between – need to deal with this, or there will be no future generations to appreciate the beauty of our pale blue dot. Don’t let anyone fool you, this work will not be easy or short term. The current pandemic pales in comparison to dealing with the root causes.

At this moment, people are dying because of your and my and our ancestors’ selfish choices. This needs to end. It needs to end today. It should have ended yesterday, but today is better than tomorrow.

Your donations to conservation-based charities, and your time spent in nature make a true difference. Personal actions like these are the only way to treat the cause of the current pandemic, and others like it that are sure to follow in its morbid wake if nothing changes.

Writing these poems and letting an algorithm decide on the form was both a form of mourning and a catharsis for me. I hope that these poems and photographs can be of some use to you too.

Join the lab!

A PDF of this ad can be downloaded here.

We are seeking highly motivated students at graduate (M.Sc. and Ph.D.) and undergraduate levels to join our lab group as we begin NSERC-funded research into changes in arthropod biodiversity and community assemblages following massive disturbances in western Canadian forests.

British Columbia land area affected by mountain pine beetle, spruce beetle, and fire.

Background: British Columbia has recently been affected by insect infestations and fire. Mountain pine beetle infestations are currently declining in British Columbia due to depletion of the insect’s suitable hosts, but the beetles have now moved into novel hosts – hybrid and jack pines – in Alberta. They now threaten the remainder of Canada’s boreal forest. Spruce beetle infestations have increased substantially in recent years, particularly in the central interior of BC. The summers of 2017 and 2018 saw record-breaking fire activity in British Columbia, along with massive, catastrophic fires in other parts of western North America.

Research objectives: Bark beetle infestations and fire interact with each other, and with anthropogenic landscape modifications and climate change. This has caused major perturbations in forested ecosystems in the interior of British Columbia and in Alberta. The main objective of this research is to determine the effect of massive disturbance events on arthropod assemblages, their related ecological services, and resilience under a shifting climate regime. Other objectives include: (a) identifying indicator species that can be used by silvicultural managers to monitor future forest health and recovery; (b) creating species lists, along with vouchered specimens and data, as baseline natural history data in an under-surveyed region of Canada; and (c) detection and investigation of species of conservation concern, cryptic species, etc. Specifically, available projects include:

  • arthropod assemblages following mountain pine beetle infestation and during early recovery in British Columbia lodgepole pine forests.
  • shifts in arthropod assemblages following mountain pine beetle infestation in Alberta forests.
  • arthropod assemblages following spruce beetle infestation and early recovery in central British Columbia.
  • shifts in arthropod assemblages following recent massive fires in British Columbia’s central interior.

About UNBC: UNBC is a small, research-intensive university in the central interior of British Columbia. It is consistently recognized as one of the top small universities in Canada. The geographic location of the main campus, as well as the several regional campuses across northern and northwestern British Columbia, offer ample field research opportunities. UNBC also administers two research forests within close driving distance to the main campus, and a nearby research station on the Quesnel River.

UNBC maintains extensive, modern laboratory facilities including a molecular biology core facility and an environmental analytical lab. Researchers also have access to high-performance computing as well as comprehensive GIS infrastructure. Our insect ecology lab at UNBC, is accessible and well-supplied with field equipment, research vehicles, microscopes, and molecular biology equipment. A list of publications from our research group can be found here.

Prince George is the largest city in British Columbia’s central interior (population ~80,000) and supports the surrounding area with services ranging from education to comprehensive health care to shopping and other commercial activities. The city has active outdoor recreational, sporting, and cultural communities and there are always opportunities to get involved and meet others. For more information about things to do in and near the city, please see the Tourism Prince George website.

Study and stipend details: Undergraduate students interested in this work should be enrolled at UNBC in a relevant degree program. Most undergraduates will work as field assistants for graduate students. In some cases (honours thesis, undergraduate thesis, NSERC USRA), students will also work on their own project.

Graduate student degrees (Ph.D. and M.Sc.) will be run within the Natural Resources and Environmental Studies Institute at UNBC. More information about the NRESI and its graduate programs can be found here. 

Graduate students without external funding will be provided with stipends related to current NSERC graduate-level stipends. Direct funding will be provided for an average of six months each year, and students will usually be required to work as teaching assistants or find external funding beyond that. There are generally sufficient teaching assistant opportunities available in our department to ensure full yearly stipends. In addition, UNBC and the Province of British Columbia offer a variety of graduate scholarships to eligible students, and all Ph.D. students receive an automatic 100% tuition rebate for up to four years. Students who arrive with or bring in external funding will have their external stipends topped-up via available internal research funds.

Requirements: Successful graduate candidates must have an appropriate prior degree from a recognized university for admittance. Top candidates will be able to demonstrate a keen and continuing interest in insect ecology, biodiversity, and community ecology – previous research experience in these fields will be considered advantageous. Applicants should have prior field and lab research experience, as well as strong statistical/analytical capabilities. Applicants must be independent thinkers and must also demonstrate a solid grasp of the English language.

Ph.D. applicants will preferably have published (or recently submitted) one or more research papers in peer reviewed journals. Publishing experience will be considered an asset for M.Sc. applicants, but is not necessary.

Undergraduate applicants should have a strong interest in entomology and/or ecology, and a willingness to learn.

We encourage Indigenous people, visible minorities, diversely-abled people, women, and people from the LGBTQ2S+ communities to apply.

Initial application process: Graduate candidates should send the following application package to Dr. Dezene Huber at huber@unbc.ca:

  • a cover letter explaining background, skills, and interest in the project.
  • a CV listing items such as education, publications, science communication, professional presentations, and service work. Please include details about external scholarship funding that has been received or applied for.
  • contact details for two or three research scientists (academic, government, NGO, industrial/consulting, or otherwise) who would be willing to provide a reference.

Undergraduates should contact me via email and they do not need to submit a cover letter or CV.

The review of applications will be ongoing until candidates are found, but applying earlier is better for access to potential graduate scholarships, and to teaching assistantships.

Successful preliminary applicants will be invited to formally apply to UNBC.

Other useful links:

An Opportunity for gratitude

Being an entomologist means that my scientific point-of-view is literally down-to-earth much of the time. But like just about every scientist whom I know, I am completely fascinated by space exploration.

This morning, I read that Opportunity, one of NASA’s Mars rovers, has likely completed its mission. This is a big deal for a number of reasons, and in particular because the mission was only expected to last a few month but has gone on for 15 years. That, in itself, is a major engineering accomplishment. Add onto it all of the amazing research that has been done in that time, and you can see why this NASA mission was a roaring success.

I have, in the past, measured the temporal run of my scientific career in comparison to space missions. Voyager took me through my grade school years and is still going. The Mars Rovers have taken me through most of my postdoctoral and tenure track years. Opportunity launched in July of 2003, right as I was completing my first postdoctoral stint at UBC and was planning on moving to California for my second. Since then I have completed that second postdoc, landed a position at UNBC, and moved through the various professorial ranks.

But Opportunity, like all other space missions, and indeed all other science, is a great reminder that this entire endeavour of discovery is a massive team effort. And for me, hearing the news of Opportunity’s demise this morning (its last message was along the lines of “I’m running out of battery power and the darkness is closing in”) was a reminder for me of all those who I have to thank for helping to get me this far, and for working alongside me in the past and present.

I know that a list like this will never be complete, but I’m going to attempt it because fear of missing someone shouldn’t stop me from thanking these people. Please know that if I missed you, it was not intentional.

Of course some of my biggest thanks go to my mom and dad who encouraged my love of biology from a young age and who have been constantly there through the ups and downs of graduate school, uncertainty about ever landing a job, stress about the tenure track, and the various ups and downs that continue each year. I love you guys and I’m glad that you’re only a phone call or a reasonably short drive away.

Thanks to Dr. Gerrit Voordouw at the University of Calgary who took me into his lab for a couple of summers during my undergraduate zoology degree. That research experience, including my first publication, helped me to make my choice to work towards a career in the business of discovery. What an amazing opportunity!

Thanks to all of my undergraduate professors, and to a few in particular. Dr. Robert Barclay taught me how to integrate basic information into complex ideas in an animal behaviour course and whose lecturing chalk skills are phenomenal. Dr. Robert Longair and Dr. Ralph Cartar showed me the world of invertebrates and stamped my heart with a desire to learn more about them. Dr. Elisabeth Dixon told us about chemical ecology as a bit of an aside in her organic chemistry course one day, and at that moment sparked my lifetime fascination.

Thanks to Dr. John Borden, my Ph.D. advisor. John took a chance on an untested student straight out of his undergraduate degree. He told me that a Ph.D. is as much a process of maturation as it is of discovery. He provided guidance and funds and a continual stream of great ideas. He taught me how to be organized, how to prioritize multiple tasks, how to give an effective presentation, how to write a publication-worthy paper (depleting many red pens in the process), and how to approach the scientific endeavour with a continual smile. John, I truly appreciate your continued mentorship after all of these years.

Thanks, also, to a bunch of other academic mentors from my time as a Ph.D. student at Simon Fraser University, whether as graduate course instructors, or as instructors in courses that I TA-ed, or in other contexts. These individuals include Dr. Gerhard Gries, Ms. Regine Gries, Ms. Tammy McMullan, Dr. Mark Winston, Dr. Larry Dill, Dr. Bernie Crespi, Dr. Elizabeth Elle, and Dr. John Webster. You each taught me important things about natural history, about surviving in academia, about the practice of teaching, and about professionalism.

Thanks to Dr. Jörg Bohlmann for getting me involved in great projects that truly stretched my thinking and my technical capabilities during my postdoctoral time in his lab at UBC. Thanks also for all of our many past and ongoing collaborations, for our friendship, and for teaching me about approaching both basic and applied science with vigor, passion, professionalism, and kindness.

—We pause here for Opportunity’s launch, 7 July 2003.—

Thanks to Dr. Steve Seybold who gave me the opportunity to experience science in another country and to see how things operate outside of academia. Thanks also to Steve for demonstrating a deep commitment to getting the details correct and for exemplifying a love of forest natural history. Thanks to Dr. Chris Fettig who kept me going in non-host volatile work, who is an example of professionalism, and who continues to be a supportive colleague. Thanks to both Steve and Chris for their ongoing, valuable interactions that help to stretch my thinking and for their friendship.

Thanks to Dr. Staffan Lindgren who noticed my talk at a WFIWC meeting in San Diego and suggested that I apply for an open position at UNBC. Thanks, also, to Staffan for the years of mentorship that continue to this day even though he has retired to somewhat warmer climes. I miss you being here at UNBC, Staffan, but I’m glad that we get to see each other on occasion.

Thanks to UNBC for hiring me and for the many opportunities that I’ve had here over the past 13 years. Thanks to Dr. Keith Egger who was the Program Chair when I arrived and helped me to get my feet on the ground. Thanks to Dr. Kathy Lewis who has been the Program Chair for the majority of my time here at UNBC and who has been an amazing example of gracious, kind, and fair leadership. And thanks to my many colleagues at UNBC who have been great mentors and friends through the inevitable ups and downs (mostly ups!) of institutional life.

Thanks to my colleagues beyond the walls of UNBC who have encouraged me, collaborated with me, written proposals with me, published papers with me, organized symposia with me, tweeted with me, and had a beer or two with me. While not without faults (let’s work on those!) our community of entomologists and ecologists is something special.

And some of my biggest thanks to the many students, postdocs, and technicians whom I’ve worked with over the years. Some of you influenced my thinking (and continue to do so!) during my undergraduate, graduate, and postdoctoral years. Many of you have worked in my program or in the programs of close colleagues. Most advances in science happen because of hard work by those in the trenches, and I’m thankful to each of you with whom I’ve interacted with in various ways – as a peer, as a mentor, as an examiner…

And finally my definite biggest thanks to my wife, Joyel. We were married about a month after the launch of Opportunity, and we moved from BC to California almost immediately thereafter. I know that it’s not always easy being the spouse of an academic with the uncertainty about the next job, the moves to who-knows-where for said jobs, and generally weird (but thankfully generally flexible) schedules. There’s no way I could do the work that I do without your support.

I am certain that I’ve missed some people here, and this blog post will likely grow with edits over the years.

While Opportunity is now cold on Mars, my heart was warmed today thinking of all of you who have influenced me during its time of exploration.

Tragedy of the Climate Commons

Nobel-Laureate economist, Paul Romer, provides one of the best encapsulations of the Tragedy of the Commons that I’ve ever heard:

“We know that the market system doesn’t guide people in the right direction when their actions impose costs on others.”

In other words, the free market is great, except when it isn’t.

The “free” use of air and water to dispose of waste is not actually free. Pollution – like any other use of a common resource – imposes costs. But those costs are rarely exclusively placed on the polluter. Instead the cost is divided up among many who rely on that resource for one reason or another, most of whom don’t reap a profit.

The polluter – not owning the air or water – has no incentive to steward it. But the polluter does have a massive incentive to a free-riding profit if they are permitted to take that free ride.

When governments allow free riding, they are not allowing the free market to work – even if they say that they believe in free markets – because permitting the imposition of costs on others by the polluter is a subsidy to the polluter.

There are four ways to deal with a Tragedy of the Commons when privatization is not possible:

  1. Ignore the problem: but eventually the Commons is destroyed.
  2. Regulate it: this can work, but this is highly susceptible to intentional rigging in favor of some against others.
  3. Impose a cost on use of the Commons, since the Commons cannot be privatized. In a climate context, put a price on carbon emissions.
  4. Some combination of the above three options.

Option 3 is not without it’s potential issues, but has been proven to work over and over again in a variety of Commons contexts. This is basic economics, and basic game theory.

But option 3 also takes political will to implement. Our politicians know all of this, but it seems that many of them would rather play games with our future for the sake of realizing their short-term goals of power.

But wait a minute,” some say, “all we need to do is wait for carbon-removing technology to become efficient and usable, then polluters can pollute all they want and the scrubbers can just remove that plus past atmospheric carbon inputs. So let’s just get working on those technologies.

Yes, indeed, let’s do that. But this does not change the economic argument because at some point someone is going to have to pay for the R&D to create the technology, the materials and expertise to build it, and the expertise and energy to run it.

Even in this (rather hopeful) scenario, someone still has to pay, and not insisting that polluters pay is a subsidy to polluters.

(And, in this scenario, there is one more question: who pays to clean up carbon already added to the atmosphere by past polluters?)