Category Archives: Writing, for scientists

Frequently confused words

Some words are very frequently confused. Sometimes, this makes the writer’s intent unclear. In other cases, the meaning of the sentence may be clear, but it’s still distracting to those readers who know the difference. So it matters.

This little blog entry focuses on words that commonly appear in scientific writing and that are often confused or misused. There is a longer list of words commonly confused in general writing here: http://writing2.richmond.edu/writing/wweb/conford.html. By all means consult this source in addition to this post.

Principle/principal: “Principle” is a noun that means a fundamental rule, truth or law. It is never an adjective. The adjectival form of this word is “principled“. “Principal” can be either an adjective or a noun. As an adjective, it means “main” or “most important”. So all of you PIs out there are “Principal Investigators”. I hope that you are also “principled investigators”, but “Principle Investigator” would mean someone who carries out research into principles, which I suppose might be applied to ethicists, although it would be unusual to do so. As a noun, “principal” can have one of two meanings: It can mean the main person involved in some affair or transaction, as in “the principal in a lawsuit”, who might be the main plaintiff or defendant, or it can be the title of the leader of an educational institution, e.g. the “Principal of Queen’s University”.

Adapt/adopt: A thing that is adapted is changed to suit some particular purpose. For example, a figure that was adapted from a source was not just copied. Some details of the figure were changed, or else the original was used as a model for a new figure that still retains some resemblance to the original. On the other hand, something that is adopted is just used as is, without modification. You can, for example, adopt the procedure of Smith et al. (1902), which means that you used their procedure exactly as they described it. You can also adapt Smith et al.’s (1902) procedure if you need to change it to use it in a new context, or to work with a different set of instruments, etc.

Affect/effect: This pair can be confusing because both of these words can either be a noun or a verb, but with different meanings. I’m going to focus here on the most common uses of these words in scientific writing. If you’re a psychologist, you’re going to need to do additional reading on this topic because in that discipline, the noun forms of these words have highly technical meanings that you simply have to get right.

Almost always in scientific writing outside of psychology, you’re going to use “affect” as a verb and “effect” as a noun. If you just remember that, you should be in good shape. The verb “affect” means “to produce an effect in”. (Note the use of the nouneffect” in the definition of the verbaffect”.) So, for example, the weather affects the timing of plant flowering. The noun “effect” designates a consequence of some causative event or agent. Late flowering is an effect of cool weather. Similarly, we talk of cause and effect, not cause and affect, unless you’re a psychologist.

Complimentary/complementary: In scientific writing, you want “complementary”. “Complimentary” refers to receiving praise, or being given something free-of-charge, as in “complimentary drinks”. “Complementary” has the sense of one thing completing another. Thus we have complementary angles, complementary base pairs, etc.

Infer/imply: All of the words we have looked at so far had similar spelling. This pair falls into a different category of words that are semantically related. Inferring is a logical deduction made by a person. Note that a person infers something. Lately, I’ve been noticing people using infer when they should be using imply. To imply something is to suggest it. Data can imply a particular conclusion. But only a person can infer that the data implies something. A person infers. Data implies.

Roll/roleRoll has to do with the action of rolling. For example, one can roll dice, or roll across the countryside in a car. A role, on the other hand, is a part that something plays. So mitochondria play a central role in the energy metabolism of a cell, for example.

Refute: This word isn’t a member of a simple pair, but lately I have noticed it being misused quite a lot. “Refute” has exactly one meaning: it is to prove an argument or hypothesis wrong. Note the word “prove”. To refute something is not merely to argue against it, or to provide a counterargument, or to present contradictory data. If you have refuted a hypothesis, it’s dead. It’s a very strong word, and rarely applicable. But good for you if you have managed to refute something. It’s probably a significant achievement. If it’s still at the stage where the thing is debatable, then you need a different word. It’s hard to give specific advice here, because there are many possible nuances, but here are some possible phrases you might use: “argue instead/against”, “provide a counterargument/rebuttal”, “reply”, “respond”, “cite as evidence against”, “deny”, “contradict”, “dissent”, “reject”. The variety of nuance in just these options hopefully suggests one of the problems with misusing “refute”: if it’s clear you don’t actually mean that something was conclusively disproved, what do you in fact mean? If you’re tempted to use “refute”, I would strongly suggest that you think carefully about what you really mean, and then use plain language, which may involve a complete rewriting of your sentence. For example, “Jones and Wang (2001) refuted Amato and Sveshnikov’s (1998) hypothesis”, if it doesn’t actually mean that they disproved the hypothesis, might be rewritten in any of the following ways, among many others, depending on what you’re trying to say: “Amato and Sveshnikov’s (1998) hypothesis was contradicted by Jones and Wang’s (2001) interpretation of the data”; “Jones and Wang (2001) showed that Amato and Sveshnikov’s (1998) hypothesis was more plausibly consistent with…”; Jones and Wang (2001) argued that Amato and Sveshnikov’s (1998) hypothesis was incompatible with…”

Delivery of a clear message requires clear language, and that means using the right words to express a thought.

English words with Latin and Greek-derived plurals

I guess I’m on a language kick… After my recent post about the misuse of “similar to”, I’m going to tackle some Greco-latin plurals that lots of people don’t know how to use.

English is a lovely mongrel of a language, having adopted words and grammar from every invader who ever set foot on the island of Great Britain. The Romans ruled over England and Wales for about 350 years, so naturally, Latin left its mark on English. Some words were also adopted from Greek through the scholarly community. Most Latin and Greek words were eventually anglicized, and English-style pluralization rules applied, but a few retained their Greco-latin plurals. Some of these are heavily (mis)used in scientific writing. I’m going to try to sort out for you some of the ones that are most often used in the texts I read.

If you have a standard for judging something, you have a criterion. That’s right. Criterion. It’s possibly you have never seen this word and would have expected criteria instead, but criteria is the plural of criterion. It’s particularly important to get this right because English has just one definite article, “the”. Thus, “the selection criterion” and “the selection criteria” imply, respectively, one criterion and many. The meaning of the sentence is therefore altered if you use the wrong word. As another example, “a criteria”, which I see a lot, is wrong because “a” is a singular indefinite article, and “criteria” is plural. If you have one rule you use for making a decision, you have a criterion.

Erosion is a natural phenomenon. It’s one of the many geological phenomena that shape our Earth. So again, you would never write “a phenomena”.

Do you grow cells in a medium, or in a media? Hopefully, you would choose the singular “a medium“, media being the plural of medium. We might prepare media (if we are preparing several different media, or possibly several batches of a particular medium), but more commonly we might prepare a medium. It’s surprising how often media is used given how rarely it’s actually the syntactically and grammatically correct choice.

We can search for minima on a potential energy surface, on the assumption that there might be more than one, but when we find one, it’s a minimum. Obviously, the same comment would apply to maximum and its plural maxima, as well as optimum/optima. Incidentally, outside of science, people tend to say minimums and maximums for the plurals of these words—a usage that is sanctioned by modern dictionaries—so perhaps it’s time for us to stop trying to sound learned by using the Latin plurals. Errors in the singular would almost certainly vanish if we did so.

But please, no “criterions”, “phenomenons”, or “mediums”. Unless, in the latter case, you want to get together a group of people who can talk to the dead.

Similar and similarly: are they similar?

As a professor, I see a lot of student writing, some good, some not so good. And I’m one of those people who think that a professor’s job includes teaching writing, regardless of the discipline one belongs to. So here is my first foray into advice on writing.

In the last couple of years, I have noticed that many students use “similar” incorrectly. I often see sentences structured like the following:

Similar to protein A, protein B binds to protein C.

So what’s the problem? To understand that, we have to ask what “Similar to protein A” modifies. What the writer is trying to say is that protein B behaves like protein A in that both bind to protein C. It’s the entire action of protein B modifying protein C that is similar to the action of protein A. Therefore, “Similar to protein A” is modifying the entire principal clause. However, “similar” is an adjective, so it should modify a noun. “Similar” therefore can’t be right.

A modifier of a clause can only be an adverb, so a correct version of the above sentence would be

Similarly to protein A, protein B binds to protein C.

“Similarly” (note the -ly ending) is an adverb, so it can modify an entire clause. Problem solved.

Of course, this isn’t the only solution. It’s always good to have more than one way to say something so you can vary the style of your text a little bit. Sometimes, the simplest way to say something is the best, so one alternative is to replace the adverb by a common preposition:

Like protein A, protein B binds to protein C.

The truth is, though, that neither of the above sentences probably says what the student who wrote it wanted to say. All these sentences really say in the end is that both A and B bind C. However, these constructions often show up in text where a student is actually trying to say that the two proteins bind C in a similar way (using similar contact surfaces, etc.). Why not just say that?

Protein B also binds protein C. B and C make similar contacts as A and C in the respective complexes.

Note that I turned one sentence into two. My meaning is now completely clear and unambiguous. This is another lesson: unless you’re strictly space limited for some reason, sometimes it’s better to use a couple of sentences and a few extra words in order to make your meaning completely clear. Similarity, for example, is a slippery complex. Saying that two things are similar really doesn’t tell us much unless we say in which ways they are similar. Similar comments apply to many other constructions. When writing, ask yourself what you want to say, and then make sure that the words you use convey your meaning without ambiguity.

What exactly do you mean by “stable”?

Stability is a highly context-dependent concept, and so it often leads to confusion among students, and sometimes among professional chemists, too.

If I say that a certain molecule is “stable”, I might mean any of a number of things:

  1. It’s possible to make it, and it won’t spontaneously fall apart.
  2. It’s possible to isolate a pure sample of the substance.
  3. It won’t react with other things. This is often qualified, for example when we say that something is “stable in air”.

The trick is to pick up which one is meant from context. A recent example arose on a test question in my Chemistry 2000 class, where I asked, in a question on molecular orbital (MO) theory, if argon hydride, ArH, is a stable molecule. In this case, the “context” was in fact a lack of context: I simply asked about the stability of this molecule, without any mention of holding it (the isolable substance definition) or of bringing it into contact with anything else. Thus, I was relying on the first definition of stability. Unexpectedly, simple pen-and-paper MO theory predicts that ArH has a bond order of ½, and so is predicted to be stable, although clearly not by much. This ought to be quite a surprise to anyone who has studied chemistry since we normally think of noble gases like argon as being quite unreactive (stable in the third sense), and so unlikely to form compounds. And when we do get compounds of noble gases, they are usually compounds with very electronegative elements such as fluorine. Moreover, ArH would violate the octet rule. Students do run across non-octet compounds from time to time, but the octet rule is deeply ingrained from high school. Finally, ArH would be a radical, and students are often taught to think that radicals are “unstable”, in the sense that they are highly reactive.

As it turns out, the simple MO theory we learned in class is sort of right: excited states of argon hydride are stable enough to be studied spectroscopically—in fact the first such study was carried out at Canada’s National Research Council by JWC Johns1—but the ground electronic state is unstable in the first sense: it dissociates into H and Ar atoms. So our chemical instinct is right about this compound, too. Welcome to the nuances of chemistry.

For the sake of argument, suppose that ArH had a stable ground electronic state, as predicted by simple MO theory. It would fail to be stable in the second sense because the meeting of two ArH molecules would result in the energetically favorable reaction 2 ArH → 2 Ar + H2. And of course, ArH would react with a great many substances. In fact, we could think of this compound as a source of hydrogen atom radicals.

Before we move on from ArH, let’s talk about some of the reflexes that would have led us to predict it to be unstable. The fact that a material is normally unreactive doesn’t mean it won’t form a compound with something else under the right conditions. If I want to make ArH, I won’t try to react argon with hydrogen molecules because the atoms in H2 are held together by a strong bond, so it would be energetically unfavourable to swap that bond for an Ar-H bond. I will need a source of hydrogen atoms. If I do expose argon atoms to hydrogen atoms, the very reactive radical hydrogen atoms may well react with the normally unreactive argon, which is in fact what happens. But none of that is directly relevant to the question of the stability of the ArH molecule. If I ask about that, I just want to know if the thing will hold together assuming it has been made.

The octet rule is deeply embedded into the psyches of anyone who has studied chemistry. It is, indeed, an excellent rule of thumb in many, many cases, especially in organic chemistry. But students are soon exposed to non-octet compounds, so clearly the octet rule is not an absolute. And yet we often hear people talk about an octet as being a “stable electronic configuration”. There’s that word again! But what do people mean when they say that? The answer is, again, highly dependent on context. In s- and p-block atoms, an octet fills a shell, and so the next available atomic orbital is quite high in energy, and it will likely be energetically unfavourable to fill it. In molecules, the octet rule just happens to often result in electronic configurations with an excess of bonding over antibonding character, so they are stable in the first sense. And because eight is an even number, the resulting molecules often have all of their electrons paired, so they are less reactive than they might have been if they had an odd number of electrons. But you may recall that oxygen, on which more below, has two unpaired electrons, even though its Lewis structure satisfies the octet rule. We should always remember then that it’s the octet rule, and not the octet law. Arguing that something is especially stable because it has an octet is just not a very good explanation. Now having said that, the octet rule generally holds for compounds from the second period, largely because trying to add more electrons to these small atoms is energetically unfavourable. But even that is a contingent statement since it depends on where those electrons are coming from and whether they have anywhere else to go. Certainly, you can measure an electron affinity for many molecules with octet-rule structures.

As for the argument that radicals are “unstable” (which you will hear from time to time), it’s not true. Many radicals are very reactive. But a great many radicals are stable in the first and often in the second sense, too. This includes many of the nitrogen oxides, notably nitric oxide, which is stable enough to serve as a neurotransmitter, and can be stored in a gas cylinder, but is conversely reactive enough to be used as part of your body’s immune response. Again we see that stability and reactivity do not necessarily coincide, even though the word “stability” is sometimes used in the sense of “reactivity”.

Of course, ArH is an extreme, and NO is not a terribly familiar compound to most of us, even though our bodies make it. So let’s talk about a more mundane molecule. Oxygen has not one but two unpaired electrons. So despite its Lewis diagram, oxygen is a radical. Nevertheless, oxygen is certainly stable in the first and second senses. There are lots of oxygen molecules in the atmosphere, and they don’t just fall apart on their own. (They do fall apart if supplied with enough energy, for example in the form of an ultraviolet photon, but that is another question altogether.) You can store oxygen in a gas cylinder, so it is certainly isolable. But oxygen is highly reactive, in part because of its unpaired electrons, at least towards some substances and in some circumstances. It’s a fairly strong oxidizing agent for example. Many metals, if left standing in air, will become coated very quickly in a layer of their oxide. And if provided with a little heat, oxygen will react vigorously with many materials. We call these reactions of oxygen “fire”.

The very different meanings of “stable” mean that we have to think when we hear this word. Ideally, we would also banish the third meaning mentioned above in favour of more specific language, such as “reactive towards”. Conflating questions of stability and reactivity just makes it harder to think precisely about what we mean when we say that a molecule or substance is stable.

References:
1J. W. C. Johns (1970) A spectrum of neutral argon hydride. J. Mol. Spectrosc. 36, 488–510.

“Following the treatment of”: How to avoid reinventing the wheel

In my last blog post, I wrote about clean-room writing as a way of avoiding plagiarism. In today’s post, I will talk about how you can avoid charges of plagiarism while providing background information that follows a plan established by someone else.

Here’s a common writing problem: You’re writing background material for a larger work. The background material runs to several paragraphs, and you have found a source (often a book) that explains the issue you need to include in your background material particularly well. In science, we don’t quote long passages. As we discussed earlier, plagiarism is unacceptable, and copying someone’s organization is generally a form of plagiarism. Note the word generally in the last sentence. There’s a small loophole, which you have to use carefully, but which is available to you for cases like this one.

Here’s the loophole: If you explicitly say that you’re presenting something the way it was presented elsewhere, it’s OK. To do this, we often use words like “Following the treatment of…”, or “The organization of the material in this section follows…”. The explicit acknowledgment that you are borrowing someone else’s way of organizing a certain topic (and perhaps their notation and/or terminology) makes this OK. Note that you have to be very clear that you are doing this. A simple citation won’t do here.

Now we have to be clear about something else: Explicit acknowledgment does not provide a blanket exemption from the normal rules of plagiarism.

  • You still have to write your own text, i.e. you can’t just use someone else’s words, even if you have borrowed their organization. I would still write text like this using the clean-room technique described in my previous post. The only difference is that my notes in a case like this might be a little more detailed, laying out the logical sequence of ideas to be covered. I would still avoid writing notes in complete sentences to avoid inadvertent reuse of the original author’s wording.
  • You can only do this for a well-defined portion of your work, e.g. a few paragraphs or, at most, a short section on a specific topic. You can’t compose (for example) entire chapters of a thesis this way.

If you use this loophole, it becomes much more difficult to avoid other forms of plagiarism, and of course there’s always the question of whether you have used too much of someone else’s work in constructing your own. This is therefore something that is to be done with considerable caution, and likely with someone else going through your work to see that it has been done properly. However, it’s often useful to avoid reinventing the wheel by simply acknowledging that it has been done, and then just using the darned thing.

Clean-room writing

How to commit plagiarism

Over the last few years, I have noticed more and more problems with student plagiarism. I’ve spent a lot of time thinking about where these problems come from. I don’t generally think that they are due to deliberate attempts to cheat. Rather, I think that modern tools create situations where plagiarism becomes almost inevitable unless you are both conscious of the issue and careful. In this blog post, I am going to suggest a method for avoiding plagiarism that I think most of us should adopt. It’s not a panacea, but it’s better than what most people are doing right now.

First of all, we should all agree on what plagiarism is. There are lots of sources on plagiarism, of which my favorite was produced by the Office of Research Integrity of the U.S. Department of Health and Human Services. Roughly speaking, I tend to think of plagiarism in terms of a hierarchical classification, which goes from the grossest to the most subtle forms.

The first form involves simply cutting and pasting from a source. Most people would agree that is wrong, although a remarkable number of students appear not to entirely get that. When we think of plagiarism as cheating, this is generally what we are thinking about.

The second form, which has a very similar effect, is using someone else’s words in your text. While this sounds like cutting and pasting, it often happens in a different way, when we write something while we are looking at a source, maybe so we get some details right. People who commit this form of plagiarism are often not even aware they are doing it. The net effect though is text that generally looks an awful lot like the original source, with only a few words changed here and there. If you don’t believe that you are prone to this problem, try reading the Wikipedia’s historical summary of the third law of thermodynamics. (I picked this topic because few people know much about it. Plagiarism becomes all the more likely when writing about topics with which one is not intimately familiar.) Then immediately try to write your own text on this topic. While you are writing, keep the Wikipedia article open and look back at it for details from time to time. Most people find it very difficult to write sentences and paragraphs that differ significantly from the original text under these conditions. This is plagiarism.

If you somehow avoid writing sentences that look like those in the original text, you are likely to at least mimic the structure of the original text, with the same facts presented in the same order. This is the third and most insidious form of plagiarism. It is hard to detect, and people who commit this form of plagiarism will often deny vehemently that they have done anything wrong. However, when you do this, you have not told us what you think about a subject. You have just told us what the writer of, in this case, the Wikipedia article thinks. You may have done it in different words, but you did not organize the facts yourself, which is the key difference between original writing and plagiarism. (There are occasions when it’s appropriate to write something that is organized like someone else’s coverage of a topic. I will come back to this in a later blog post.)

Thinking about the exercise I proposed above, I would suggest that there are at least three distinct issues leading to plagiarism:

  1. Writing while looking at a source, or immediately after reading a source. It is almost impossible to come up with your own words and an original way to organize the facts when you are doing this. The perfectly good words and organization chosen by the original writer become “the obvious way” to write about a topic, and it’s virtually impossible to break out of that.
  2. Excessive reliance on a single source. If you use multiple sources to inform your thinking, the particular way any one author organized his or her writing is much less likely to have a dominant effect on how you write about something.
  3. Not having clearly distinguished research, outline, writing and revision phases in the writing process. This is perhaps the greatest failing of modern students in their approach to writing. If you start by doing some research, taking brief notes as you go, then write an outline as a way of organizing your thoughts, then write text based on your outline, and finally go through several rounds of revisions, it becomes difficult to commit plagiarism because you will really be writing about a topic from your perspective, and not from that of another writer.

How not to commit plagiarism

Having talked about these issues with many students, and given the pervasive nature of information technology, which puts sources at our fingertips almost anywhere, anytime, I have concluded that the best way to fight plagiarism is to adopt what I call clean room writing techniques. Much of what I am going to describe is essentially the research, outline, writing, revision cycle described above. However, I think that we need to go a little farther given how easy it is to unconsciously plagiarize material.

There is a similar problem in the software industry. Let’s say you want to write a piece of software that does the same thing as another existing piece of software. Because software is protected by copyright, you’re not allowed to copy someone else’s software. You may want to peek, but in the end you have to write your own, original implementation. The way this is done is to have people write the software (even if they previously peeked at the other company’s software) in a “clean room”, which is a room where you have everything you need to do your work except the other company’s software. Depending on how paranoid you are, such a room might not have a direct connection to the Internet. Sometimes, the people who peek are different from the people who write the new software. Sometimes, peeking just isn’t allowed.

To avoid plagiarism, you need to write in something like a clean-room environment. What I mean by this is that looking at your sources and writing should not occur at the same time. Your research for whatever you are writing (term paper, thesis introduction, article manuscript, …) should happen at a different time than the actual composition of text. Text should be written from notes which were not generated by simple cutting-and-pasting from a source. Yes, I know, cutting-and-pasting is quick and efficient. The problem, as explained above, is that you’re almost certain to use someone else’s words if you do that. When you take notes, write in your own words what you thought was important or interesting in some particular text you are reading.

Once you have composed a draft of a text, you can of course fact-check against the original sources. Having given the ideas your own form by writing a draft without direct access to the sources, you are much less likely to unintentionally borrow someone’s words during revision.

Note that clean-room writing does not lift the responsibility of citing your sources. Your notes should clearly link content to references, so you should be able to cite your sources as you write. Occasionally, you will need to make a note to yourself to chase down a reference later. You can still add references during the revision stage if you at least note the places in your text that will need to cite sources.

This may seem a bit radical, but I’ve seen too many students get in trouble for plagiarism over the last few years, and I know that many of them did not intend to plagiarize. It just happened, for the reasons I explained in the first part of this blog post. Eventually, you can relax this strict approach a little, but if you’re an inexperienced writer, it’s best to go into the metaphorical clean room anytime you’re writing new text.