Animal Behavior virtual conferences for Summer/Fall 2020 that are free (or nearly free)

A silver lining of COVID-19 is that amazing conferences have become far easier and far cheaper to attend. For interdisciplinary researchers, you can now dip your toe into venues that you might not otherwise be able to justify spending the resources on. So it is a great time to branch out!

As an example, there are FOUR virtual Animal Behavior conferences that will be taking place soon this summer or early fall. They are free or nearly free (at least for students), and all of them are still accepting talk/poster abstracts at the time of this posting. If you are doing empirical or theoretical work in animal behavior and would normally present your work at a more methods-based conference, this is a great opportunity to get feedback from the larger behavior community. If you are not currently directly researching behavior, you might really enjoy just hearing reports of great, state-of-the-art research into animal behavior.

My background is in engineering, and I have found that animal behavior conferences to be the most educational and useful in generating bio-inspiration for me. These conferences showcase how animals interact with each other and the world around them in potentially adaptive ways. Plus, it's a great showcase of natural history for those who don't feel like they are naturally naturalists!

So check these out. And this is probably not an exhaustive list!

• ABS 2020 Virtual Meeting [USA animal behavior]
• Nearly free:
• Free registration for student members
• Student membership is $25
• Talk abstracts due: June 17, 2020
• Conference: July 28–30, 2020
• https://www.animalbehaviorsociety.org/2020-virtual/
• Animal Behavior Live [new annual venue; global]
• Free registration
• Talk abstracts due: June 30, 2020
• Conference: 20 & 21 August 2020
• http://animalbehaviour.live/
• ASAB Virtual Conference [British animal behaviour]
• Free registration
• Talk abstracts due: 16th June 2020
• Conference: 16th July 2020
• https://www.asabvirtual.org/
• ASSAB Virtual Conference [Australian animal behaviour]
• Free registration
• [ info coming soon ]
• Conference: 28th September – 1st October, 2020
• https://www.assab.org/

Zoom Virtual Background for Short/Coffee Breaks ("I'll be right back!")

You might know that Zoom has a non-verbal feedback option under the Participants list that includes a "need a break." You could use this to indicate when you have stepped away, but it is intended to indicate to the speaker that you are requesting a break.

So what is an option to indicate to everyone that you have stepped away and aren't just having video problems? One option is to create a virtual background that includes some status signage (or, alternatively, you can make the signage part of your profile picture that shows when your camera is off). Here is an image I put behind me to indicate to others that I've stepped away very briefly and will be back soon.

You can download and use the image above. You can also download the PowerPoint version so you can make edits to it. Here I am with my virtual background behind me. Of course, normally I would only put this up when I was out of the room. :-)

Another option is to print out a tiny version of the image above and hang it in front of your camera. :-)

UPDATE: Another option for this is to combine Zoom with a virtual camera from mmHmm. mmHmm has "Be right back" options that you can quickly switch on and off with far fewer steps than raw Zoom.

Reduce Student Anxiety: Introduce them to "What-If Grades" in Canvas Gradebook

Are your students getting anxious and wondering what their final grades might look like under different “what-if” scenarios related to any assignments yet to be graded? A lot of faculty and students don’t realize that the Canvas gradebook supports “What-If Grades”, which allow a student to click on any grade (even ones not posted) and change it to a hypothetical version to see what the hypothetical effect would be on their final grade.

Check it out:

• Canvas Support: How do I approximate my assignment scores using the What-If Grades feature?

Teaching on Zoom: Fixing Problems with Students Joining Authentication-Only Rooms

To help prevent "#Zoombombing" while still allowing for all of the features that, when not being exploited, provide for productive digital classroom experiences, many universities have recommended that faculty turn on authentication-only Zoom rooms for their classes. For most students, this means that they may have to follow one extra click when joining their classrooms that leads them through the single-sign-on (SSO) process and handoff back to Zoom. Unfortunately, this process is not as simple for some students, especially if they already have their own non-University Zoom accounts.

Here are the instructions (also linked as a PDF or a DOCX) I have been giving to my students to help ensure that they access my authentication-only Zoom classroom using their university account. Of course, there are a few small aspects of these instructions that are customized for ASU, but it would be easy to modify the instructions for your institution.

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Instructions for Accessing Zoom Room as Authenticated ASU Zoom User

To help mitigate problems related to "Zoom-bombing", your course Zoom link may be configured to only allow authenticated ASU users into the room. If you are having trouble connecting to the Zoom class room with your properly authenticated ASU account, you should try following these steps:

1. DO NOT use the normal link to enter the room
2. Instead, go to https://asu.zoom.us/ and then click on the Log In button
3. Once you are logged in to ASU Zoom, click on the "JOIN A MEETING" link in the top right of ASU Zoom
4. Use the Zoom ID: (10-digit code from your instructor; also at the end of course link)
   

These steps are designed to ensure that you are logged in to Zoom with your ASU ID.

If the above steps still do not let you into the room, then you need to open your Zoom app and make sure to "Switch Account" to your ASU account. Follow these steps:

1. Open your Zoom application
2. Click on your profile image, as in the image below, and go to "Switch Account"
   
   
   
3. Select "Sign In with SSO", as shown below:
   
4. Use "asu" as the Company Domain, as shown below:
   
5. Follow the prompts to login to ASU Zoom and return to your application
6. Use your course’s meeting ID (or the normal course link) to connect to the Zoom room
   
   

Those steps should help ensure that you are able to get into the class Zoom room with your authenticated ASU Zoom account.

Teaching on Zoom: Automatic Subtitle Captions on a Whiteboard

In the wake of COVID-19, faculty are looking for ways in which they can extend their original in-class teaching approaches to on-line while maintaining high accessibility.

I recently saw a request by someone using Zoom for whiteboard capability with automatic, real-time captions that have subtitles for the audio. This capability does not currently exist in Zoom's native whiteboard. However, real-time subtitles are available in presentation applications like Microsoft Powerpoint. In addition, Zoom annotations (if enabled) allow a presenter (or anyone in a Zoom room) to annotate any shared screen as if it was a Zoom whiteboard. So I came up with the following solution to the whiteboard-with-subtitltes problem. Note that other variations on this solution exist, but this particular solution was crafted to be the most generalizable and prevent the most conflicts with Zoom and Microsoft competing for access to a single microphone.

Here are a list of steps to make it happen. You can also see the video below if you prefer to see a demo of these steps.

1. Open a Zoom room on a desktop machine that runs PowerPoint 2019 or later (including Office 365 versions of PowerPoint)
• Do not share audio or video
  
2. From the Zoom room, share the desktop that powerpoint will use when it goes into full-screen mode during a presentation
   
3. Start a blank PowerPoint presentation
   
4. Click on the "Toggle Subtitles" button shown in the bottom left corner of the PowerPoint presentation
• You should now see live subtitles being added to your presentation as you speak
  
5. Join your Zoom room from a tablet device
• This time, connect with audio so that your audience listens to you through your tablet presence
• You should see the shared, blank PowerPoint screen on the tablet device
  
6. Use the "Annotations" button in the bottom left of the tablet view to open the annotations
• Note that "Annotations" has to be enabled for your Zoom room
• You can find the setting to enable Annotations in the advanced settings on your Zoom web portal
• When annotations are enabled, anyone can use them, and so make sure you trust your audience
7. Use your tablet (perhaps with stylus) to draw on the white screen provided by PowerPoint as PowerPoint subtitles below your writing
• You can use the eraser and clear (trash can) buttons to get a blank screen
  
8. If you are going to record, I recommend using "Record to Cloud" from the tablet device
• Again, the goal is to take the load off of the desktop machine that is doing the live captioning

Here is a video I put together that demonstrates the above steps:

Woodpeckers can ring and run too

Our Ring Pro video doorbell recently caught this red-headed ding-dong ditcher visiting our front door:

We answered this ring, but we weren't around about an hour later when it returned!

After checking with our neighbors, we found that gila woodpeckers have apparently been terrorizing some other doorbells and surveillance cameras in the area as well. It is pretty adorable... until you have to replace the device.

In this case, hopefully being startled twice by the Ring's chime is enough to encourage it to move on!

Tribute to Mom, Eileen Pavlic (1942–2019)

My mother, Eileen Pavlic, died on Tuesday, August 6, 2019, due to complications from a stroke. She had been battling cancer for a year, and immunotherapy had been working well to reduce the extent of her cancer. She was enthusiastic about the progress of the treatment and had even started to buy new clothes, anticipating at least another year of life. Then, surprisingly and very sadly, she suffered a stroke. We learned that metastatic cancer is a risk factor for stroke, and so this outcome was not a complete surprise to the doctors even though it was devastating to us. She was buried in an outfit that she had recently ordered and had never had the opportunity to wear herself.

We know she was very impressed and encouraged with the immunotherapy she received, and so I hope you will consider donating to the Pelotonia Institute for Immuno-Oncology (PIIO) or another reputable charity advancing the use of immunotherapy for the treatment and possible cure for cancer. 

I shared the comments below during her funeral on August 9, 2019. You can also read her obituary on-line.

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A Son's Tribute to His Mother, Eileen M. Pavlic (September 22, 1942 – August 6, 2019)

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Looking back on your life with someone is less like watching a movie from beginning to end but more like drawing lottery balls from a tumbling urn. There’s one random memory. Then another. Then another. It is only after drawing enough of them that we can look back on them, sort them out, and start seeing hints of a bigger picture. That’s how it was for me when thinking about what to say today, and I only hope this story comes across a little smoother than those lottery balls.

She always wanted me to become a medical doctor, and I was excited to oblige when I was younger. Books and models mom and dad would get me about anatomy and physiology were interesting to me, but ultimately, I think the real source of the appeal was not the content so much as the connection with her. At some point, I pivoted away from medicine toward things like mathematics, computing, and, ultimately, engineering. Even mom might not see how this has anything to do with her, but from my perspective looking back, I remember the young me watching her navigate a DOS prompt, manipulate revealed codes in WordPerfect documents, and designing merge fields for office automation, and she became my model for someone who could learn to use tools around her to do great things. She never viewed herself as a teacher – she would often excuse herself from philosophical discussions that dad and I would have by saying that “she didn’t go to college” – but she was one of my greatest teachers. Today, I teach college students, and I only hope that some of them could be as motivated by me as I was by her. And it’s no surprise to me that biology has shown up in a lot of my engineering research, which sometimes makes me think that the younger version of me is still trying to turn my PhD into an MD to make mom proud.

So, yeah, looking back on life with mom is a little like drawing lottery balls. And by giving me the opportunity to do so, mom’s given me one last lesson – that being her son was winning the jackpot.

Long, non-coding RNA serve an important role in the regulatory pathway controlling human skin wound healing

It seems like there has been a lot of cool wound-healing research results published lately. At the end of March, there was the result that bacteriophages hide their bacterial hosts from being cleared by mammalian immune response. Last week there was the result that aphids soldier nymphs use their own wound-healing proteins to plug gall holes. And now there's this new result on the mechanism underlying the role of long, noncoding RNA (lncRNA) in wound healing of human skin.

So what's long, non-coding RNA? The DNA in the human genome has to be converted to RNA, in much the same way computer code might be converted into assembly language, before it can then be converted into proteins (like assembly language being converted into object code that can actually be executed by the computer). Up until recently, biology has focused entirely on this pipeline -- DNA to RNA to protein. However, there are some bits of DNA that stop at RNA, which are termed "non-coding RNA" because they don't end up producing any proteins. They just float around until they naturally break down. However, there are hints that they are not merely intermediate transitional objects and that they can be functional molecules themselves. One of those hints is that they can be consistently turned on ("up-regulated") in certain situations. However, this doesn't mean that they're actually doing anything. There are technical details that make it useful to distinguish whether these non-coding RNA are short or long. I won't get into those. Just know, for the reset of this post, that "lncRNA" represents "long, non-coding RNA", which is a type of these mysterious molecules. When healthy human skin is wounded, the normal response happens to involve the up-regulation of one of these lncRNA's is consistently generated more than in undamaged tissue, but no one knows why.

In this paper, they show that the molecule actually sequesters other mechanisms within the tissue that would normally turn off the migration of cells important for wound healing. So the lncRNA's are functional -- they get turned on when the skin is wounded, and that sets of a chain reaction that disables other mechanisms that would normally keep wound healing processes turned off. So the lncRNA's are an important step in the regulatory network. That's very cool. It not only helps scientists understand wound healing but also one more way in which lncRNA's can be functional -- not just junk molecules floating around waiting to be broken back down.

Here is the primary source:

"Human skin long noncoding RNA WAKMAR1 regulates wound healing by enhancing keratinocyte migration"
by Li et al.
PNAS (2019), early edition
https://doi.org/10.1073/pnas.1814097116

Significance
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Although constituting the majority of the transcriptional output of the human genome, the functional importance of long noncoding RNAs (lncRNAs) has only recently been recognized. The role of lncRNAs in wound healing is virtually unknown. Our study focused on a skin-specific lncRNA, termed “wound and keratinocyte migration-associated lncRNA 1” (WAKMAR1), which is down-regulated in wound-edge keratinocytes of human chronic nonhealing wounds compared with normal wounds under reepithelialization. We identified WAKMAR1 as being critical for keratinocyte migration and its deficiency as impairing wound reepithelialization. Mechanistically, WAKMAR1 interacts with DNA methyltransferases and interferes with the promoter methylation of the E2F1 gene, which is a key transcription factor controlling a network of migratory genes. This line of evidence demonstrates that lncRNAs play an essential role in human skin wound healing.
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Abstract
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An increasing number of studies reveal the importance of long noncoding RNAs (lncRNAs) in gene expression control underlying many physiological and pathological processes. However, their role in skin wound healing remains poorly understood. Our study focused on a skin-specific lncRNA, LOC105372576, whose expression was increased during physiological wound healing. In human nonhealing wounds, however, its level was significantly lower compared with normal wounds under reepithelialization. We characterized LOC105372576 as a nuclear-localized, RNAPII-transcribed, and polyadenylated lncRNA. In keratinocytes, its expression was induced by TGF-β signaling. Knockdown of LOC105372576 and activation of its endogenous transcription, respectively, reduced and increased the motility of keratinocytes and reepithelialization of human ex vivo skin wounds. Therefore, LOC105372576 was termed “wound and keratinocyte migration-associated lncRNA 1” (WAKMAR1). Further study revealed that WAKMAR1 regulated a network of protein-coding genes important for cell migration, most of which were under the control of transcription factor E2F1. Mechanistically, WAKMAR1 enhanced E2F1 expression by interfering with E2F1 promoter methylation through the sequestration of DNA methyltransferases. Collectively, we have identified a lncRNA important for keratinocyte migration, whose deficiency may be involved in the pathogenesis of chronic wounds.
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Stochastic versus random: The difference is whether you're describing a model or a focal system

It seems like there is a lot of confusion in quantitative modeling circles over the relationship between "randomness" and "stochasticity." This is in large part because the success of stochastic models to make sense of the world around us has led to wide use of stochastic modeling, so much that "stochastic" has become a near synonym for "random." However, the two terms are not identical.

Slide from SOS 212 (Systems, Dynamics, and Sustainability), an introductory modeling course I teach

"Randomness" is a general term representing a special kind of uncertainty where the frequency of possible outcomes can be described using probabilistic methods. Where a photon is going to be at a particular instant of time is fundamentally random; it can only be described using a probability distribution. There are some kinds of uncertainty that cannot be described probabilistically. For example, I might know that an experiment can end in one of three different ways, but exactly how it will end depends upon which participant is performing the experiment. If I need to describe how the experiment can end but do not have any ability to specify a probabilistic weighting of the outcomes, I can describe the system as having a non-deterministic outcome. So something can be fundamentally random or non-deterministic. If it's random, you have some way to describe how one outcome might be more likely than another.

"Stochastic" is a term originating from Greek for "guess" or "conjecture." It describes a modeling technique to simplify a model by assuming (guessing/conjecturing) that the system being modeled is random, even if it is not. In other words, rather than having to account for a wide range of degrees of freedom that might be necessary to specify how a system is going to evolve, you substitute all of that detailed deterministic modeling with a crude approximation of the outcome being "random". The modeling burden then shifts from getting everything right down to high levels of precision to shaping the probability distributions to best match the outcomes that are most likely, regardless of what the underlying mechanism is. So a "stochastic model" is one that describes a system using randomness regardless of whether there is any reason to believe that the randomness is fundamental. It is a modeling trick to add analytically tractability to models that would otherwise be prohibitively complex to be useful.

So you shouldn't refer to phenomena themselves as being "stochastic." It is OK to say that the phenomena is random (if you really believe that). Or it is OK to say you use a stochastic model to describe the system (which implies that you will use randomness in order to omit a large number of degrees of freedom, thus making the model "simpler"). But you shouldn't use "stochastic" as a synonym for "random."

How to write a scientific paper, in four simple steps

Accomplished scientific writers will all have their own tips on how to go about writing a scientific paper. However, when you are first getting started, sometimes it is easier to have a set of steps available. Certainly there are many options available, but I personally have been finding the following set of steps useful when advising students lately.

• Step 1: Write the Introduction (starting with second paragraph)
  The introduction lays out why you bothered to do the study you did. It provides a background from the existing literature, and it points out holes in that literature or opportunities to test answers to questions that have little coverage.
  
  However, the first paragraph of your introduction (in fact, the first few sentences of your paper) are often the hardest ones to write. A colleague points out to her students that a great way to get around this potential writer's block is to simply skip the first paragraph. If you start with the second paragraph, you can immediately start laying out the argument for why your study needs to be done. Once you finish the rest of the introduction, it may be easy to see what the first paragraph needs to be. In other words, once you have 75% of the argument completed, the shape of the puzzle piece that remains will often be clear.
  
• Step 2: Write the Discussion
  If someone is already convinced that your paper has something interesting to say, that person will likely jump straight to the discussion and start reading there. This is where you describe how your data support some story that you want to tell about an inference you have made about the natural world. As you write your discussion, it will become clear exactly which data you need to tell your story. And so that brings us to the next step.
  
• Step 3: Write the Results
  Now that you have crafted a convincing discussion, you know what results are needed to support your argument. Writing the discussion first tells you what to include and what you can exclude. A lot of students make the mistake of starting with all of the possible plots that can be generated and then trying to string together a discussion around them, even if some of those plots really aren't needed. Don't do it that way. Instead, let your discussion guide which results to include.
  
• Step 4: Write the Methods
  Putting this step here is controversial. In many cases where your study has a clear experimental design that tests for something very specific, then it is possible to write your methods first. However, if you are instead working with a very large dataset that might someday result in multiple papers, then your methods might need to wait for you to determine exactly which results you need to make your argument. So once you've written your results, you can then generate methods that explain how all of those results came about.

Those four steps can often soothe writer's block on a scientific paper. You may determine a different flow as you mature in your writing process, but this is just one suggestion of where you might think about starting.

Special Note: Title and Abstract

Of course, two things that are left out of the steps above are the title and abstract. Young writer's often leave these until the end, and they often view them as complementary to the rest of the article. However, with maturity, it should be possible to write them first and view them almost as alternatives (or marketing pieces) for the whole article. Writing them first can also provide structure (similar to an outline) for the rest of the article. So work toward being able to write these two things first, but it's OK if you start by writing them last.

Keep in mind that most readers will only read the title and abstract (and some will only read the title). Consequently, the title should not be clickbait; the title should be an executive summary of the article, giving the punchline as opposed to begging the reader to read further. Interested readers will move on to the abstract. Consequently, your abstract should really have everything an educated reader needs to reconstruct your article; it should have a little bit of all of the sections. Your abstract should concisely say why you did the things you did, how you did them, what the main results were, and why those results are interesting.

Take-away Message: It's About the Reader

People are busy, and they allocate their reading resources accordingly. If you tease them with half statements, they will only get frustrated and move on to the next thing that competes for their time. Instead, give them something interesting and complete in the title. If they want more details, they can read the abstract, which should itself be complete. If they want more details, they'll read the main body (possibly starting with the discussion section). For the reader, it's about sequentially choosing what to read next. When you write, you should always have this in mind as you design the delivery vehicle for the content you hope will be disseminated broadly.