Category: Uncategorized

Deep space biology experiments

Will be carried on Artemis I as described here. This is important because humans will have to traverse deep space to get to Mars (and beyond) and the radiation environment can be extremely challenging. If humans are going to join the robots that are exploring Mars, we are going to have to figure out how to protect them as they transit from Earth. Elon says he wants to die on Mars, preferably not on impact. Well, he to make it there first.

Work Life After the Pandemic

Yesterday, I was in a meeting with work colleagues in the pre-pandemic style: in person. There was coffee. There was the usual round robin introduction segment. There were at least three other NSF alumni besides myself and the subject matter was fairly banal–that is not management of a crisis. So it really felt a bit like my old life running NSF’s biological sciences directorate, even though there were a few masks in the room. To complete the illusion, my current building is about 4 blocks from the old NSF headquarters and so the view out the window was pretty comparable.

But of course, it’s not 2017. Office buildings here in Arlington Virginia are still conspicuously empty of people. The dog days of summer add to the ghost town feeling. Zoom calls are still the normative mechanism for bringing work colleagues together where the phrase “you’re muted” has become the most common utterance no matter the specifics of a particular meeting. Work has changed fundamentally and to my view, probably permanently.

I have colleagues who mostly work remotely–some from overseas–and I’m sure that’s fairly common. This is the case even for running laboratories: checking in on graduate students or postdocs and looking at their latest results does not require occupying the same space. Scientific teams can write proposals and manuscripts collaboratively in the cloud. Coming into the office for the mandatory 8:30AM meeting in the director’s office probably was close to obsolete even before the pandemic hit.

So what comes next? Actually why does anything need to come next? It could be argued that the greatest crisis here is localized to commercial real estate developers and that work life will continue more or less as it is, changed permanently by COVID, but not for the worse. Just different.

Harmful algal blooms…

The background in this Guardian piece here and this Scientific American article here (hat tip NK). I wonder if we could automate this process of water sampling and microscopic analysis? And better yet, might we be able to ecologically predict such occurrences? These are two questions which have significant public health impact and at the same time might be enabled by the appropriate deployment of machine learning.

How to write a review paper…

The first task is to choose a topic that is both interesting and not recently reviewed. This requires some judicious use of Google Scholar. I think it’s also useful to have some demonstrable expertise in the area, although for most senior scientists, they are broad enough in their interests and knowledge to get by with a pretty shallow knowledge base. This first task is arguably the most important since it will drive everything else.

Once the topic is chosen, the next step is to conduct a first cursory review of the most important literature. In other words, you actually have to actively read some papers. This first review of the literature is not meant to be exhaustive. That comes later. Rather, its purpose is to prepare the ground for the next step: the review paper equivalent of a news ‘hook’. This is the notion of an insight that comes from a synthesis of the extant relevant literature. So if we were reviewing explainable AI, the hook might be that biological brains might provide both existence proof and likely explanation. If we were reviewing macrosystems approaches to ecology, the hook might be that robust standardization of measurements at continental-scale is required. The key is that the hook should be non-obvious, but emerges from a rigorous synthesis of the literature.

At this stage, the bibliography construction should begin using appropriate software. I use Zotero, but there are many good choices. The key function we are looking for is the ability to seamlessly grab a citation (and the full pdf) from Google Scholar and store it for later insertion into the manuscript document. This is the most important research stage of writing the review paper and it feeds back onto the prior ‘hook’ step since a full reading of the literature may change the results of the synthesis. That’s fine and is perfectly normal for the proper evolution of an excellent review. When this step is complete manuscript writing can commence.

I tend to write from an outline. This is one method for proceeding. It’s not the only one. If one does use the outline approach, the key is to outline the review so that the hook is never standing alone and obvious as the author’s opinion, but rather naturally emerges from the evidence presented in the paper in the mind of the reader. This is tricky. The reason for this subtlety is that review papers are not hypothesis or position papers.Their proper function is to lay out the evidence in such a way that synthesis emerges organically from the evidence. So the hook has to stay in your ‘mind’s eye’ and hidden from the printed page.

My parents, who were scientists themselves, taught me to use the scientifically formal passive voice for writing. This style was echoed during my training. Both my thesis advisor and post-doc mentor employed such a style. Today, we use a more active voice in our writing–not quite as informal as a blog entry, but certainly using more direct and simple language. Whatever the style, the key is to have citations accompany each claim. In review papers, we usually summarize a set of results in a sentence that contains the relevant paper’s first author as the subject and then the summary of what their scientific RESULTS revealed. So an example would be: “Olds et al (2020) found that soil exposed to fixed nitrogen had reduced bacterial diversity compared to controls.”

For a review paper, I complete the figures after I complete the text (I do the opposite for a regular research publication). Figures for a review paper can be adapted from other figures in the literature with written permission and explicit acknowledgement in the figure legend. The key is to adapt the figure so that it is not identical to the original. I choose figures to assist the reader in their synthesis laid out in the review. Once again, the idea is not to overtly lay out your hook, but rather to schematize the results from the literature in such a way that the reader gleans the hidden gem.

Finally, the bibliography can be built automatically by your software and inserted at the end of the document in the proper format. Congrats, you are ready to submit!

Undergraduate guide to connecting with faculty to advance your career (Blogpost #5)

The scientific training process in graduate school is fundamentally different than the classes and labs at the undergraduate level. A key part of graduate-level training is the active listening that I referred to in Blogpost #4. What this means is a regular spacing of questions (from you) relative to what you’ve just heard from the professor on the other end of the line. A good conversation of this sort can have as many as twenty or so of these talk-question intervals. As you progress in your training, the talk-question intervals regularly reverse: you’ll get the chance eventually to talk with your mentor asking the regular questions. This process works fairly similarly on-line (Zoom or Teams) as it does in person. The key however is that you have to carefully listen to the other person talking in order to ask a question (there is no single correct question) that meets muster.

Undergraduate guide to connecting with faculty to advance your career (Blogpost #4)

So you’ve got yourself a Zoom appointment with a scientist who may be able to help your career. If you are able to, through your college or university (i.e. you can initiate a Zoom call of an hour in length), offer to create the Zoom link yourself. Do be on time (this is critical) and be certain to have a professional appearance for the camera.

As you begin the call, use the words “informational interview” to describe your goal for the conversation. This term conotes that there are no expectations of an offer (job other educational) from the scientist. You will be probably asked to introduce yourself: what this means is to state your name and then to give a short (no longer than 2-3 minute) backgrounder on your undergraduate education to date, your major, what science experiences (including courses and labs) might be relevant. You statement stops with a sentence or two on how you discovered the work of this person (your target) and what papers of hers/his you have read. At this point you get ready to listen.

What is required is active listening. This means engaging visually with the person via the camera. Nodding when appropriate and taking notes so that you can ask intelligent questions. This is really key. The scientist on the other end of the Zoom needs to be able to “feel” your attention. More on this in the next blog post.

Undergraduate guide to connecting with faculty to advance your career (Blogpost #3)

In this blogpost, I describe the most important step: making individual contact with each of your faculty targets. First let me start out with the don’ts:

  • Do not use social media of any kind
  • Do not text
  • Do not even think about using a template

First, use determine the work email of your faculty targets. So this means, the email associated with the place that employs them. For example, in my case, you would want my George Mason University email. I leave it as an exercise on how to get that piece of information, but Google usually works well. Second, you are going to compose a long email to each of your faculty targets in which you will primarily communicate your knowledge of their scholarship/research and your ideas about what you think should be the ‘next experiment’ (Note, for non-bench type professors, this would be the next natural step of scholarly inquiry). Finally, you’ll communicate your interest in carrying out this research while presumably under their guidance as mentor/academic advisor or employer. Also, make clear that you would be overjoyed to do a Zoom informational interview with them at their convenience.

Note, I added nothing about yourself. That’s correct. At this stage, other than a cursory ‘I’m an undergrad at X University majoring in Y’, it’s not about you. Your sole goal in this communication is to convey in the clearest language possible that you are deeply familiar with their research and that you have been thinking about how to add value to their research work flow. When they circle back to you (and if you do this correctly, they surely will), that’s when you can talk about your self and your professional dreams/goals.

In the next blogpost, we’ll talk about your Zoom.