Category Archives: Education

Time to restart the LTEE, this virus be damned

The LTEE ran for over 32 years and more than 73,000 generations, without missing a beat. Then this stupid coronavirus came along and made me shut down the lab and stop the experiment. Well, I think it’s high time for everyone to return to the lab and get back to work.

We’ve wasted a hell of a lot of time here.  The LTEE lines were frozen on March 9th.  That’s 23 days ago, for crying out loud.  Do you know how many generations have been lost?  With 100-fold daily dilution and regrowth, that’s ~6.7 generations per day.  So we’ve already lost over 150 generations. And with 12 populations that’s a net loss of more than 1,800 generations.

Another way of looking at it is that each population produces around half a billion new cells each day.  So that’s 23 x 12 x 500,000,000 cells that went missing. You get the picture, that’s a sh*t-load (a technical term for those of us who study E. coli) of baby bacteria that never got born!

I’ve gotten in enough trouble already with a certain crowd for our claim to have observed evolution. If they find out we’ve denied these adorable baby bacteria their existence, there’s no telling what letters they might send me.

Plus, speaking as a scientist, I have this premonition that something really big would have happened during those missing generations. I’ve been expecting them to evolve the ability to produce palladium from citrate. They could then use the palladium for cold fusion, which would surely get some attention. Stupid virus!

Heigh-ho, heigh-ho, it’s back to work I go.  I sure hope you have a nice day at home.

Calendar April

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Do you teach a biology lab that has been disrupted by the coronavirus outbreak?

The following is a guest post written by my colleague, Rob Pennock.

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Do you teach a biology lab that has been disrupted by the coronavirus outbreak?  If so, you may want to consider using the Avida-ED experimental evolution platform as a virtual replacement.

Avida-ED logo

To limit the spread of the coronavirus, many colleages and universities have suspended in-person classes, and instructors have had to scramble to replace them with on-line instruction.  Biology faculty who teach laboratory-based courses find it especially difficult or impossible to do their planned lab exercises.  Avida-ED may provide a valuable substitute for some classes.

Avida-ED is an award-winning educational application developed at Michigan State University for undergraduate biology courses. It is aimed at helping students learn about evolution and the scientific method by allowing them to design and perform actual experiments to test hypotheses about evolutionary mechanisms using evolving digital organisms.  Funded by the NSF, Avida-ED is the educational version of a model system used by researchers to perform evolution experiments–including many that have been published in leading scientific journals (see some examples below).  Avida-ED is not a simulation, but an instantiation of the evolutionary mechanisms and process that allows for real experiments.  Avida-ED produces copious data that can be analyzed within the application or exported for statistical analysis.  Avida-ED has been used in classrooms across the country and around the world for over a decade.

Here are more reasons that Avida-ED may provide a useful, quick replacement for your lab:

  • Avida-ED is free.
  • Avida-ED requires no special registration or configuration.
  • Avida-ED is accessible on-line and runs locally in your web browser.
  • The user-friendly interface requires little technical training to use.
  • It includes ready-to-use exercises to teach a variety of evolutionary concepts.
  • It can also be used for open-ended labs where students design and perform their own experiments.
  • It can be used to teach principles of experimental design and scientific method.

See the Avida-ED web site for:

  • Link to the Avida-ED application launch page.
  • Model exercises (under the Curriculum link).
  • The Avida-ED lab book.
  • Quick start user manual.
  • Background information about digital evolution.
  • Articles about Avida-ED, including effectiveness studies.

The Avida-ED team is working to provide instructional videos for the core exercises from train-the-trainer workshops that we have offered in previous summers, where we teach faculty how to use the software in their own classes.  We can also provide instructor support materials for some exercises offline for certified instructors.  A mirror of the Avida-ED site is available in case the primary site goes down.

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Lenski, R. E., C. Ofria, T. C. Collier, and C. Adami.  1999.  Genome complexity, robustness and genetic interactions in digital organisms.  Nature 400: 661-664.

Wilke, C. O., J. Wang, C. Ofria, R. E. Lenski, and C. Adami.  2001.  Evolution of digital organisms at high mutation rates leads to survival of the flattest.  Nature 412: 331-333.

Lenski, R. E., C. Ofria, R. T. Pennock, and C. Adami.  2003.  The evolutionary origin of complex features.  Nature 423: 139-144.

Ofria, C., and C. O. Wilke.  2004.  Avida: A software platform for research in computational evolutionary biology.  Artificial Life 10: 191-229.

Chow, S. S., C. O. Wilke, C. Ofria, R. E. Lenski, and C. Adami.  2004.  Adaptive radiation from resource competition in digital organisms.  Science 305: 84-86.

Ostrowski, E. A., C. Ofria, and R. E. Lenski.  2007.  Ecological specialization and adaptive decay in digital organisms.  American Naturalist 169: E1-E20.

Clune, J., R. T. Pennock, C. Ofria, and R. E. Lenski.  2012.  Ontogeny tends to recapitulate phylogeny in digital organisms.  American Naturalist 180: E54-E63.

Goldsby, H. J., A. Dornhaus, B. Kerr, and C. Ofria.  Task-switching costs promote the evolution of division of labor and shifts in individuality.  Proceedings of the National Academy of Sciences, USA 109: 13686-13691.

Covert, A. W. III, R. E. Lenski, C. O. Wilke, and C. Ofria.  2013.  Experiments on the role of deleterious mutations as stepping stones in adaptive evolution.  Proceedings of the National Academy of Sciences, USA 110: E3171-E3178.

Goldsby, H. J., D. B. Knoester, C. Ofria, and B. Kerr.  2014.  The evolutionary origin of somatic cells under the dirty work hypothesis.  PLoS Biology 12: e1001858.

Fortuna, M. A., L. Zaman, C. Ofria, and A. Wagner.  2017.  The genotype-phenotype map of an evolving digital organism.  PLoS Computational Biology 13: e1005414.

Canino-Koning, R., M. J. Wiser, and C. Ofria.  2019.  Fluctuating environments select for short-term phenotypic variation leading to long-term exploration.  PLoS Computational Biology 15: e1006445.

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Meetings Large and Small

In this post, I will explain why it is important not only that we cancel large conferences and other events, we should also curtail medium and even small gatherings that are non-essential.

Joshua Weitz has done a great service by explaining how the probability that one or more participants in an event is infected scales with the size of the gathering. In brief, even when the vast majority of people are not infected, the chance that somebody is infected goes up as the number of participants gets larger. I think most people are also now coming to grips with the rapid growth of this outbreak, which means that a meeting with relatively low risk today might be a very bad idea a month from now.

But does this mean that medium-sized and small events can proceed without worry? No. Let me explain why even these events should be reduced to the bare minimum that are essential. Most of my readers are fellow scientists, so what follows is cast in the language of conferences and departmental seminars—but hopefully others can relate these to similarly sized gatherings in their own lives.

Ok, to begin. You’re very pleased to hear that the conference you had planned to attend next month was canceled. With 10,000 attendees, and with infections doubling every week, it was clearly smart to cancel such a large conference. But your departmental research seminar is attended by only 100 people. Surely that can safely continue, right?

If only your department had a seminar, and if it was a one-time event, then sure, why not. However, there are 25 other departments around the country in your field of study alone, and each of the departments has planned 4 weekly talks over the coming month.  Seen in that light, it’s like that large conference of 10,000 — except that its 25 x 4 = 100 events with 100 attendees each. In other words, there are 10,000 potential transmissions of the viral infection.

In general, as event sizes get larger (more participants), the frequency and number of those events becomes smaller.  I don’t have data to back this up (maybe somebody does), but I’d bet that the number of small gatherings increases even faster than the number of participants falls off.  For example, for every conference of 10,000 people, I expect there are even more than 100 meetings of 100 people.

Therefore, reducing non-essential gatherings of all sizes should be part of our individual and collective efforts at social distancing. It’s no fun, I know. But it’s one of the best ways we can ward off this beast of a virus, and thereby protect our colleagues, our friends and families, and our communities.

[This image shows the actor Rowan Atkinson (aka Mr. Bean). It is used here under the doctrine of fair use.]

Mr Bean

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We Interrupt This Experiment

Today I made the decision to close the lab and temporarily suspend our experiments, including the LTEE, in light of the expanding SARS-CoV-2 outbreak.

I started to say it was a difficult decision, but really it was not all that difficult.  Several considerations led me to this decision.

1/ The SARS-CoV-2 outbreak appears to be taking off in many countries, including the USA, despite the substantial containment that has been orchestrated in Wuhan and elsewhere in China.

2/ The absence of evidence of any local cases is not as comforting as it might be, given the near-absence of testing here and in most of the USA.

3/ MSU students just returned from spring break today.  Some of the superb undergrads who work in my lab went to places that have confirmed cases. None of the places they went are among the locations with intense outbreaks, but the confirmed cases in at least one location have grown noticeably in the past week. They also flew on planes to and from their vacations.

4/ As a team, we’re connected not only to one another, but also to people who are health-care workers and others with increased vulnerabilities to infections. (Not to mention that I’m over 60 …) When you think about it, pretty much everyone has those connections.

5/ We’re very lucky because our work is easy to stop and re-start. Our study organisms can be frozen away and revived whenever we see fit.  In the meantime, everyone has classes to take, papers to read and write, data to analyze, etc.  And a little extra time, hopefully, to reflect on and maintain the health and well-being of our friends, families, and selves.  So, we will all be busy, but doing things a bit differently than we had planned.

6/ As we freeze away the long-term lines, the lab notebook will record:  “On this day, the LTEE was temporarily halted and frozen down for the coronavirus pandemic of 2020.”

Hopefully, some future historian of science will look back on today’s entry and say: “What the hell was that all about?”

Freezing LTEE for SARS

[Devin Lake putting the LTEE populations into the ultra-low freezer, where they will stay until they are called back into action … evolution in action.]

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More Words of Wisdom

I assume everyone is familiar with the concept of “going viral” and that you’re paying attention to the SARS-Cov-2 outbreak.  So you understand the importance of social distancing.  When it comes to conferences, they’re not quite what you’d call social distancing, are they?

Well then, Harvard’s Michael Baym puts 2 + 2 together in the way that physicists-turned-biologists seem able to to do with ease and elegance:

“The reason to cancel meetings and seminar visits is the same reason we have them in the first place: by establishing long-distance connections and high-connectivity nodes, we help ideas spread much faster through our social networks. It’s the same for a virus.”

Please see this post for more words of wisdom about pandemics. For suggestions to fellow scientists and lab teams on how to deal with this coronavirus outbreak, here are my thoughts.

 

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Global Dynamics of Coronavirus Spread

Almost a month ago, in my post on expert analysis, I highlighted a model by Richard Neher that looked at the possible global spread of SARS-CoV-2 infections based on numerous seeding events. At that time, many observers were reporting the good news that the rate of increase in the number of infections in Hubei province was declining.

That declining rate of increase was expected given the extreme quarantine measures taken in Wuhan and other cities. However, it was also clear that smaller outbreaks were being seeded elsewhere.

Neher ran simulations to get a handle on this scenario, using his educated guesses for the relevant parameters. He assumed then that many such outbreaks were already underway, and that they were running 2 or 3 months behind the Wuhan outbreak. With increased awareness among the public and health-care workers, he assumed that many of the new outbreaks would grow more slowly than Wuhan’s did and be contained. (As seems to have happened in Singapore.) And even those that grow large would, like Wuhan, slow down once they had become very large due to quarantines and other social distancing. (As seems to be be happening in South Korea.) Nevertheless, Neher found it was possible to envision total global cases in several months that would dwarf those seen in Hubei, even while it looked then as though the rate of increase was declining. I’ve re-posted a screen shot of Neher’s scenario below.

Nerer global scenario 09-Feb-2020

Here, for comparison, is a screenshot of a new graphic produced by CNBC using data from Johns Hopkins University. It’s still too early to say how the numbers will play out over time. Even right now, the total number of infections globally is very uncertain, with many countries (including the USA) lagging in testing for the virus. But qualitatively, at least, Neher’s model prediction is–unfortunately–looking all too real. 

ADDED:  As Richard Neher adds: “I want to point out that the simulations we did 4 weeks ago assumed limited infection control measures and essentially model unchecked growth. China has shown that drastic measures can change the course of a COVID-19 epidemic.”

Coronavirus in and out of China

 

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The Lenski Lab Health Plan for the New Coronavirus Outbreak

The future is unknown, as it always is.  We do know that the SARS-CoV-2 virus is spreading around the globe, but we don’t know how many people will be infected.  Some experts are predicting that something like half of the adult population will be infected, although not all at the same time.  We also know that many cases are relatively mild (like a cold or the usual flu), and some infections may be asymptomatic. However, we also know that some other cases—perhaps 20% or so—are very serious, and some of those are life-threatening.

See MSU’s coronavirus page for University policy, information, and advice.

What can we do, as individuals and a lab group, to protect ourselves, our families, each other, our communities, and our research?  Here are my current thoughts, with an emphasis on activities related to our laboratory and our academic setting.

1/ If you haven’t done so already, get your flu shot. It won’t protect against the coronavirus, and it doesn’t provide perfect protection against the influenza virus, but it will reduce the chance of getting the flu (and save health-care resources for others in need).

2/ Make sure you and your household are prepared for a period of self-isolation or quarantine lasting 2 weeks, or perhaps longer.  This means stocking up on food staples and, importantly, any medicines that you and your household need.  For medicines, I suggest having at least a full month’s supply, maybe longer, in case there are disruptions to availability.  Talk to your doctor about extending prescriptions or any other special needs you might have.

3/ If you develop symptoms of a cold or flu—even mild symptoms—please stay at home and don’t come into the office or the lab.  We don’t want you to spread the infection.  Just email the group list to let us know what’s up, and work from home on your writing and reading if you feel up to it. You won’t impress me, or anyone, by trying to work while you’re sick.

4/ If a member of your household becomes ill, see and follow point 3 above.

5/ Let’s all start practicing more restrained physical interactions, and thus set good examples not only among ourselves but also for our colleagues and friends. That means skipping hugs and handshakes, for the time being.  Instead, you might put your own hands together and bow your head slightly to greet or congratulate someone. Or maybe an elbow bump, if you really must make contact.  Foot bumps are apparently another new thing, too.

6/ Be prepared to stop your lab work on short notice.  In the meantime, I guess March might be a good time to get a week-long or two-week experiment done, before the epidemic grows too large (if it does).  However, I suggest holding off, for the time being, on any plan to start a large and/or long experiment.

7/ Speaking of long experiments, you will recall that we have a certain long-term experiment in our lab.  The LTEE will soon hit 73,500 generations, at which time the samples will be frozen as usual.  After that date, I’d like population samples to be frozen more often, say, every 2 or 3 weeks.  Just freeze away a copy of each population (no need to plate cells)—basically, so we have samples to restart in the event that people get sick, or if the university should at some point curtail certain activities for a while.

8/ Be prepared to cancel your attendance at scientific conferences and other academic or social events as new information arises. Even if an event organizer decides to push ahead, you don’t have to go if you feel it is risky for you personally. As an aside, I recommend delaying purchases of airfares until an event is closer in time, given the current uncertainty.  (Refundable tickets on most airlines are very expensive, and other tickets have restrictions.)  Hotel reservations can usually be cancelled on shorter notice (a day or week, check to be sure), but not if they were booked through a discounter.

9/ And maybe the hardest advice of all is to practice good personal hygiene. Cover your mouth with your forearm or the inside of your elbow when you cough or sneeze unexpectedly.  (If you know you’re sick, then you should have disposable tissues handy. Use those to cover your nose and mouth completely, and dispose of a tissue after one use.) If you find yourself coughing or sneezing repeatedly, see point 3 above. Wash your hands thoroughly [Click that link, with the sound on, and stay for the end!] after you’ve touched shared surfaces, especially before eating. And most difficult of all, avoid touching your own face.  This coronavirus can survive for hours as tiny droplets on surfaces, which we may inadvertently touch (“fomite transmission”). Then, when we touch our mouth, nose, or eyes, we can infect ourselves.

10/ ADDED: Follow the news, and get your news from trustworthy, reliable sources. If it becomes clear that infections are spreading locally, or even if you are just concerned about that possibility, then avoid crowded public venues. (But this does not mean that you should follow the news obsessively, as that can be exhausting. h/t Carl Bergstrom.)

11/ ADDED: If you do isolate yourself, whether because of illness or concern, make sure to maintain frequent social contact with your family, friends, and the lab via phone, email, or whatever works best for you. Don’t let physical isolation and loneliness make you feel miserable. We are all stronger together, even if we might have to be physically apart.

12/ ADDED: Please read these Words of Wisdom, regarding preparedness for infectious disease outbreaks, from Michael Leavitt, a former Secretary of Health and Human Services.

13/ ADDED:  This one is for those of you in science or other relevant scholarly fields.  Do you have data in your lab notebooks and/or on computers accessible only in the lab?  Are the datasets ones that you might need for your analyses and writing if, say, you end up confined at home for a few weeks?  If so, I recommend that you copy it (but only if it’s allowed in the case of certain types of sensitive data!) by scanning it and/or copying it to your personal computer. That way, you can use it while working from home if you decide, or are required, to do so.

Take care everyone.  Please let me know of any errors, omissions, and practical suggestions.

 

 

 

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