Science for SciFi: Peer Review

When a research project reaches completion, the investigators often write up their results in a peer-reviewed journal. Once the investigators decide what journal is most appropriate for their research, they submit their paper, if the editor of the journal decides that the research has merit and is a good fit for the journal, they begin the peer review process.

For many scientists, the peer review process can be stressful and drawn out, sometimes for all parties involved. But the peer review process, despite its faults, is vital to ensuring that honest, quality research gets published.

It’s also likely to be a major source of stress for the scientists in your novel.

There are A LOT of memes about Reviewer 2 out there. Source

Article Anatomy

Each publisher and journal will have its own formatting guidelines. These are the essential bits. Sometimes results and discussion will be a single section and not separate.

Abstract – in science we pack the conclusions into the headline. Abstracts vary in length but are normally about a paragraph. An abstract’s job is to convince someone to read the entire article and to help put what follows into context. Writing an abstract is hard, in just a few sentences you need to explain why the research matters, how it was done, and what conclusions were made.

Introduction – this is (for me) the most fun part of the article to write. The introduction explains the basic principles of an article. An introduction should explain the motivations behind the research and what gap the research aims to fill.

Experimental/Materials and Methods – every journal puts this section in a different place within the article. For someone interested in learning the impact of the research this section is fairly boring, for someone who wants to judge how reliable the data is or replicate certain techniques, this section is essential. Experimental contains a list of what tools and materials were used, who manufactured them, and how they were prepared.

Results- this section explains the collected data in excruciating detail. The data is often supplemented by a variety of graphs and other diagrams.

Discussion – here is where the authors get to explain what the data means. This section is filled with explanation and interpretation.

Conclusion – these are short. Almost as short as the abstract. A conclusion should be short and sweet.

References – any claim that is not common knowledge for the audience or data gained from the research needs to be cited. This might include established experimental techniques, general background information, mathematical formulas, computer code, and so on.

How To Read An Article

How you read an article will depend on what you are trying to get from it. If you are trying to discern the salient points you will probably read the abstract to decide if you care about it. Then maybe the introduction, then the discussion and conclusion.

If you want to explain how the authors reached those conclusions you will spend a lot of time reading the experimental and results sections. You will want to know what they did, understand why, and try and see where the project’s weak points are. This can take a good deal of time and may require multiple readings of a single article.

If you want to know the current state of the field, then a single research article just won’t do. You might find many other sources from the reference list at the end of the article, but you’ll quickly find yourself falling down a rabbit hole. If you are new to a field, you will want to find a review article. A review article is meant to summarize the current state of a given field or subfield and will highlight that field’s important developments. These articles may have hundreds of references.

The Review Process

Once the authors submit a paper, the first thing the editor does is decide whether the article is suitable for their publication. Basically, does it fit the focus of the publication and does it have a large enough impact? Some journals are “high-impact” and some are not. But that is a discussion for another day.

If the paper makes it past this stage the article is sent to a set of reviewers. These reviewers are chosen because they are experts in the field. They are the authors’ “peers” and are likely to have the knowledge needed to evaluate the quality of the research.

These experts comment on the experiments, the data, and may suggest changes that need to be made before the paper is ready for publication. This is where many of the Reviewer 2 memes originate. Authors may often feel that a reviewer’s comments are unreasonable, or that they are trying to manipulate the authors for their own benefit. The good news here is that authors can respond to reviewer comments, and if they can convince the editor that the comments have been addressed then the article can be published.

The key thing to remember is that just because an article has gone through peer review does not mean that it is free of mistakes. A research article is the result of the best possible measurements and analyses that were possible at the time. Peer review means that a small group of experts has decided that the research has merit and that it is free of major flaws.

This doesn’t mean that there are no mistakes, that there is not a larger picture, or that better analysis or measurements won’t be done in the future. A single research paper tells just one small part of a larger journey of discovery.

Emotional Costs

The impact of one single paper is likely to be minuscule, but to the authors, it might well be everything. PI’s (principal investigators) are often established, professors. The other authors, however, are likely students. These students spend years working on a project that might result in just a handful of papers. For these students, the process can be very draining. No matter how “small” the project may be in the grand scheme of things, it has, by the time of publication, been a major part of their life.

For many in academia, publishing is everything. Publishing is how graduate students build a resume. And it’s how many professors achieve tenure. Research activity is frequently measured in publications and grants.

Scenarios

There are a lot of ways to write a scientist’s motivations. But based on what we have just talked about above I will provide a few examples. The examples in this list are for creative purposes only. These are WRITING PROMPTS, not recommendations or endorsements.

  • After years of “publish or perish” the character sees their self-worth only in terms of publications. They frequently overwork themselves and lose sleep in order to make progress.
  • Eager to increase their number of publications, the character divides their research into smaller and smaller chunks to get more papers out. This practice is sometimes called “salami slicing.” It’s frowned upon, but they hope that most observers will only see the publication count and not look much deeper.
  • Desperate to publish in a high-profile journal, the character begins to falsify or omit data. After getting away with it multiple times they think they are safe. Then, several years later, they are found out and their career crumbles around them.
  • The rat race of academia is too much. Fed up with the constant publish or perish mentality, the character decides to take a post at a teaching-focused institution. They publish a paper every few years, but what they really care about are the lives of the students they help shape.

Further Reading

I don’t have any book recomendations about the peer review process. However, peer review and publishing play big roles in the lives of scientists. So here are a couple books where you can learn about the history of science and the people who do it.

Science for SciFi: Poisons

This might seem like a bit of a repeat. After all, we just learned about a few natural weapons, right? Sort of. I talked a bit about how snake venom works, but I think it’s worth our time to learn a bit about toxicology. How do poisons work? How are they administered? Can toxicity be quantified? We’ll get to those answers in a minute. But before we start, let’s get two disclaimers out of the way. First, I am not a doctor and nothing you read here should be considered medical advice. Second, some fields distinguish between toxins and poisons. For the sake of simplicity, I will be using them interchangeably.

How do poisons work? Like we saw with snake venom, poisons work by interfering with the natural processes that happen constantly in your body to keep you alive. If you think about it we are really just a leather sack filled with water and chemical reactions. If anything interferes with those systems then we’re in for a bad time.

Measuring Toxicity

Death is in the dosage. Molecules that we need to sustain life can be toxic if we have too much, and molecules known to cause death might not hurt us at all if we have too little. Determining the amount and duration of exposure that results in toxicity can be tricky, but it’s an important consideration.

Two important considerations are acute versus chronic toxicity. Does the poison kill you immediately (acute), or over time with repeated exposure (chronic)? One measure of toxicity is LD50, often denoted in terms of milligrams per kilogram, which is defined as the median dose that kills 50% of the test population. Chronic exposure is something that workers in many industries need to worry about, but the assassins in your crime novel will be more concerned with acute exposure.

But measuring toxicity can be difficult. After all, it’s hard to find willing human subjects. The easiest way to test potential toxins is to see what they do to cells in a petri dish (in vitro). These experiments can reveal a lot, like the mechanism of toxicity (eg. does it block cell receptors or bind to DNA?) but cells in isolation are a poor model for living systems. Sure, maybe a chemical is toxic to liver cells, but if it never leaves the lungs after being inhaled then its effect may be limited. Large multicellular organisms are more than just individual cells, they are complex systems comprised of many cells with many functions. Toxins may then target a specific organ or grouping or organs depending on how the body processes them.

The best way to test toxicity is to use live animal models, but for obvious reasons, not everyone has the time, resources, or inclination to perform those tests.

How Bad Are Heavy Metals?

Mercury and lead are often thought of as extremely toxic, and for good reason, there are a great deal of environmental and health risks that arise from heavy metal pollution. However, just because something contains a heavy metal does not automatically make it dangerous.

The properties of metallic compounds vary greatly depending on their structure, makeup, and reactivity. For example, heavy metal chlorides may be toxic, but heavy metal oxides may be considerably less so.

Water solubility is a big factor here. If a compound cannot dissolve in water it’s going to have a hard time reaching target systems in the human body where it can do the most damage. But factors such as pH and any reactions the metals might undergo once inside the body can also play a role.

Predicting Toxicity

By now it should be clear that toxicity is hard to predict. It’s not just a matter of what a molecule contains, but what reactions that molecule undergoes inside the body which determines how dangerous it is and what kinds of damage it inflicts.

This is a problem for researchers because not all of the chemicals found within a lab will have been fully studied in terms of toxicity. Because of this, it’s easier to assume everything is dangerous and behave accordingly. That said, there are a few things that can be done to predict a molecule’s hazardous effects.

After a few years in the field, most chemists can intuit the reactivity of molecules based on their structure.

  1. Reactions that occur once released into the environment.
  2. Reactions that occur within biological systems.

For these reasons, predicting toxicity is not as straightforward as one might think, although knowledge of structure and reactivity can give us some clues. There have even been attempts to take known reactivity data, feed it into computers, and generate toxicity predictions. These efforts are unfortunately hampered by a general lack of data in many cases and the number of environmental and chemical variables that need to be considered. Even so, progress in this area is being made.

Famous Toxins

Arsenic – a poison that was favored by Agatha Christie, rat catchers, and stylists alike. Arsenic and arsenic-containing compounds have found many uses over the years as rat poisons, pigments, medicines, and more. Because of these many uses arsenic was once easy to come by and could be bought at many pharmacies. The really dangerous form of arsenic is arsenic oxides. Once inside the body, it disrupts the production of ATP, the molecule that our bodies use for fuel. Arsenic (III) oxides are similar in structure to the phosphates that our bodies use to make ATP and so our bodies try to use them instead. Without a regular supply of energy, cell death soon follows.

Capsaicin – do you really need to know why peppers feel hot on our tongues? Do you care? Maybe peppers won’t drop you dead, but the mechanism is fascinating and very useful to science fiction authors. Capsaicin targets neurons, specifically the vanilloid receptor. In practice, they cause the same sensation as heat. So they hurt, but they could hurt more if controlled by a mad scientist. This is actually my favorite toxin here, because in real life it is relatively harmless, but could be used by a writer in a lot of interesting ways. An alien plant for example, could have a much nastier variety of capsaicin for explorers to stumble upon.

Cyanide-cyanide is a classic. No spy would be caught dead without their cyanide capsule. Like arsenic, cyanide disrupts the production of ATP. In this case, however, it functions as an inhibitor that prevents the enzyme cytochrome c oxidase from doing its part in the ATP cycle. It should be noted, that in this case when we say cyanide we actually mean hydrogen cyanide (HCN). Cyano groups (CN) are common in many areas of chemistry, and hydrogen cyanide has many industrial uses.

Sarin – famous as a chemical warfare agent and a neurotoxin. Sarin acts quickly and can strike you dead in under ten minutes. Sarin is not too different from some of the snake venom we looked at a while back. Like our example there, Sarin works by inhibiting signals sent by nerve cells, but the mechanism is different. The key to sarin’s effectiveness is the neurotransmitter acetylcholine. Sarin permanently binds to receptors and prevents muscle cells from correctly interpreting the acetylcholine signal. The victim’s muscles are then unable to process acetylcholine, hindering their movement, and the victim dies from asphyxiation soon after. Sarin is an organophosphorus chemical that evaporates quickly and is incredibly deadly.

Narrative Uses

Agatha Christie was famous for using accurate portrayals of real poisons in her mystery novels, so much so that an entire book was written about it. By doing this she was able to give her readers the chance to deduce the murderer and the means of murder before she revealed it. The clues were all there for anyone who wanted to puzzle it out.

Whatsmore, knowing what a poison is and what its other uses help to build more plausibility into your story. A worker at a chemical plant might have ample access to hydrogen cyanide, just like a pharmacist in Victorian England would have no trouble sourcing arsenic on the down-low. And of course, for you writers of science fiction, knowing about the mechanisms and effects of real-world poisons allow you to ground your fictional toxins in real science.

Sources

A Is For Arsenic: The Poisons of Agatha Christie. Kathryn Harkup.

Measurement and Estimation of Electrophilic Reactivity for Predictive Toxicology. Johannes A. H. Schwobel et al. Chemical Reviews. American Chemical Society. 2011.

Toxicity of Metal Compounds: Knowledge and Myths. Ksenia S. Egorova and Valentine P. Ananikov. Organometallics. American Chemical Society. 2017.

Tips for Surviving Graduate School

This is a weird topic to write about. Here I am starting the third year of my PhD and I still feel like I know nothing. It’s a fun combination of Imposter Syndrome and the Dunning Kruger Effect. Still, I would like to think I’ve learned a few things about surviving grad school at this point.

Now, to be fair to my imposter syndrome, I am in no way an authority on these topics. But as someone who has several labor-intensive hobbies and doesn’t want the degree to consume their entire life, I’ve learned a few tricks that have helped me make time for my hobbies and still make progress towards my degree.

Get Some Sleep

This is one that I am REALLY bad at. I’ve always been a bit of a night owl. Left to my own devices I’ll stay up all night and sleep until noon. It’s hard, especially if you’re like me and a burst of motivation always hits you right before bed time. But it’s worth it to develop good sleep habits. As hard as it is, if you start going to bed earlier you’ll feel more rested and you’ll be able to wake up earlier. This last bit is important because it makes you feel like you have more time in the day and you wont catch yourself staying up late trying to squeeze out a few more drops of productivity. An all-nighter wont make you more productive, it will just make more tired.

Make Time for Other Things

I have a lot of hobbies that work often gets into the way of. Some semesters are going to feel more hectic than others, but you should still make time for your hobbies. Even if it’s just a few minutes before bed you’ll be glad you did. What’s even better is if you try and make time every evening and on the weekends for the things you enjoy. It’s really hard to feel good about your work if it’s consuming your life. Plus the things you work on outside of work can make your work better. Reading and writing as hobbies have made me feel much more prepared for presentations and research papers. But don’t think your hobbies need to also make you better at work.

Be Realistic About How Long Something Will Take

When I first joined the lab I’m in now I constantly felt unproductive. No matter what goals I set for the day I never met all of them and I felt terrible about it. That changed when I realized that it wasn’t that I was doing poorly in lab, it was that I wasn’t blocking out my time effectively. I wasn’t giving myself enough time to complete each task and the result was that I felt like I wasn’t getting anything done.

I fixed this by setting one big goal for each day in the lab and a few of what I like to think of as stretch goals. When I go into lab I normally have one experiment planned. I go in thinking “today I will complete this reaction” or “I will do x number of titrations.” Those are my main objectives for the day and I devote most of my energy to those. If I find myself finishing these early or having to wait for a reaction to finish I work on my stretch goals. These are things that are nice to get to in a given day but don’t need to be done right then. Stretch goals might be cleaning glassware, doing a literature search, or processing data.

Once I started doing this I instantly felt more productive. I was being more honest with myself about how long something would take me to do and I didn’t feel like I needed to do more once I got home. You will also find that you get faster at a lot of these tasks as you gain more experience.

Make Your Laziness Work

Some mornings when I get into the office the last thing I want to do start work in the lab. All I want to do is sit at my desk and sip my coffee. So that’s what I do. I sit down, turn on my computer, sip my coffee, and use that time to see what’s new in the world of science. For me that normally means looking at few American Chemical Society publications. Specifically Inorganic Chemistry, Organometallics, Chemical Reviews, and Accounts of Chemistry Research. I normally have a few keywords I’m looking for in the titles. Anything with the words cobalt, iron, or spin crossover get at least a quick glance. Or a quick download to the folder of files I tell myself I’ll read eventually. I have found a lot of great references that I’ve ended up citing later this way and learned about new fields that I hadn’t heard of before. Not only will doing this help you stay up to date on the latest research, the more time you take to read and review material in your field the more comfortable you’ll feel talking about your own work. It always feels great to whip out a relevant paper in the middle of group meeting that no one else has seen yet.

Listen to Your Undergrads

Universities have tons of social events, clubs, and resources to be taken advantage of. You probably don’t realize a lot of them are there. Talk to and listen to not just your fellow graduate students, but undergrads and staff too. Even if the undergrads in the section you’re a teaching assistant make you pull your hair out its worth listening to them talk. Remember, many of them are on campus 24/7 while you may only be there for a few hours. You can learn a lot about other departments and the resources available on campus if you listen to them while giving them zeros on their lab reports.

Oh yeah, sometimes they have some good research ideas too.

Cultivate Your Social Skills

You don’t need to become a complete extrovert, but it pays to talk to other people around campus. After spending all day on experiments it helps to know a few people down the hall who might want to grab pizza with you. Or they might call you up if they have an extra concert ticket. More practically, it helps to have people you can go to for help whether it’s help studying or getting access to an instrument in their lab. Science is collaborative and in most jobs you’ll have to work together with other people so it pays to get started now.

Remember That You Know More Thank You Think You Know

In graduate school you’re surrounded by competent people. So much so that it’s easy to think that they know more than you or know their project better than you will ever know yours. It’s important to remember that if you are in a graduate program you already have a bachelors. You knew enough to get one degree in your field and now you’re working on another. You know your project better than anyone and you know a lot more in general than you think. The more you talk about your work and your field the more confident you’ll feel. Even if it’s hard at first.