Should proteins be interrogated when they conspire?

ABSTRACT

As a follow up to that wildly popular Editor’s Corner, “Look youse guys and gals, dat just ain’t right” published in 2021, I have put together a follow-up guide to some common grammatical mistakes that I encounter in papers submitted to Autophagy. This guide is meant in particular to help non-native English speakers write more clearly but may also be of benefit to other authors who grew up at a time when learning grammar was replaced by autocorrect functions in Word and other programs, or the desire to simplify sentences so that they fit within a tweet, or to ease thumb strain when typing on a smartphone. The guide is also meant to help editors by reducing the number of changes needed to bring papers up to the high standards of clarity that we strive to maintain at Autophagy.

KEYWORDS:

• Autophagy
• grammar
• it’s all about clarity
• meaning what you write
• writing what you mean

To begin, an explanation seems to be in order regarding the title. An interesting verb I have seen used on occasion is “interrogated” as in “We next interrogated the proteins … ” “Interrogated” means “to ask questions of” or “to question formally and systematically” (https://www.merriam-webster.com/dictionary/interrogate) as in, “The police then interrogated the suspects.” Thus, unless these proteins committed a crime, it would be inappropriate to interrogate them. They could, however, be “examined”. Another interesting example is seen with “conspire” as with “These proteins conspire to disrupt … ” “Conspire” means “plot or contrive” (https://www.merriam-webster.com/dictionary/conspire) so suggesting that proteins conspire seems to be a bit of anthropomorphizing (i.e., attributing a human trait to something that is not human). At any rate, no matter how much or how often particular words may conspire, we at Autophagy will not be interrogating or subsequently prosecuting them.

In general, “evidence” as a noun is uncountable (https://www.oxfordlearnersdictionaries.com/us/definition/english/evidence_1?q=evidence) so the use of the plural “evidences” is not correct. “Evidence” or “lines of evidence” can be used as in “The evidence suggests”, which can be either singular or plural or “Various lines of evidence” if you want to emphasize the plural nature of the evidence. A little trickier is “evidencing” or “evidenced” meaning documenting or documented (https://www.merriam-webster.com/thesaurus/evidencing, https://www.merriam-webster.com/thesaurus/evidenced). For example, “ … evidencing the key role” or “ … evidenced the key role” are technically acceptable but “ … demonstrating the key role” or “ … provided evidence for the key role” would be more commonly used. Finally, similar to “evidences”, “literatures” is generally incorrect, and “literature” should be used for both singular and plural forms. This is not to say that there is never a situation when “literatures” is correct, but you will likely not encounter that situation in an Autophagy paper.

“Associated” is an adjective meaning “joined together”, “related” or “connected” (https://www.merriam-webster.com/dictionary/associated). “With” and “to” are both prepositions. When you combine them, you get an adjective prepositional phrase that modifies a noun or verb. “Associated with” means to establish a link/connection between two things. Thus, “associated with autophagy” indicates that something is linked/connected with autophagy. For example, “ULK1 is associated with autophagy”, uses the adjective prepositional phrase “associated with autophagy” to describe the noun “ULK1”. Even though it is another preposition, “to” cannot be used interchangeably; thus, “associated to” as in “ULK1 is associated to autophagy” is generally incorrect. On a related note, I want to briefly consider another example using “to”. “Does not allow to evaluate” may be technically permissible, but native English speakers are much more likely to use “Does not make it possible to evaluate” or “Does not allow one to evaluate”.

While on the topic of native English speakers, here are some additional examples of preferred word usages. 1) “Thrice” vs “Three times”. Although “once” and “twice” are commonly used, “thrice” is pretty much outdated. 2) The word “for” is another preposition that can be used to mean, among various possibilities, “because of” or “having the purpose of” (https://dictionary.cambridge.org/us/dictionary/english/for). There are many good uses of “for” such as “I read a paper in the journal Autophagy for [the purpose of] increasing my knowledge about this process.” In contrast, there are places where “for” does not make sense as in “The cells were cultured for overnight” vs “The cells were cultured overnight”, “The pellets were washed for three times” vs “The pellets were washed three times” or “Placed in an incubator for overnight” includes an unnecessary “for” versus “Placed in an incubator overnight”. 3) Apparently prepositions are quite tricky. Another one that I see used incorrectly is “of”. For example, “ … are responsible of … ” versus “ … are responsible for … ” 4) A frequent problem concerns the use of the verbs “encode” and “code”. “Encoding for core components” is incorrect, whereas either “Encoding core components” or “Coding for core components” are fine. That is, use either “coding for” or “encoding”, but not “encoding for”. 5) Another common mistake is seen with the use of “ … under nutrient starvation”; this should be written as “during nutrient starvation” or “under conditions of nutrient starvation”. 6) A relatively minor infraction is seen with “Overexpression of the C-terminal of … ” versus “Overexpression of the C terminus of … ” and, 7) “Authors show … ” versus “The authors show … ” 8) Finally, sooner or later it was inevitable that we would have to consider “as well as”. “ … has been implicated in many human diseases such as infections, neurodegeneration, autoimmunity, metabolic disorders, cancer, as well as in normal aging” versus “has been implicated in many human diseases such as infections, neurodegeneration, autoimmunity, metabolic disorders, and cancer, as well as in normal aging.” The use of “as well as” indicates that you have reached the end of a list that already has “and” in it (like a last-minute item you remembered to add on, “and don’t forget normal aging”). Another example would be, “involved in the regulation of body weight, feeding behavior, inflammation, as well as glucose and lipid homeostasis” versus “involved in the regulation of body weight, feeding behavior, and inflammation, as well as glucose and lipid homeostasis.”

The incorrect use of commas is a recurring problem and likely an intractable one, but here goes one more attempt. Consider the sentence “The vacuolar protein, Pep4, is involved … ” versus “A vacuolar protein, Pep4, in involved … ” or avoiding the commas altogether, “The vacuolar protein Pep4 is involved … ” This is subtle, but because of the way the commas are used the first sentence suggests that Pep4 is the ONLY vacuolar protein as opposed to a vacuolar protein among other fascinating vacuolar proteins.

Even though many journals are now online only, such that the length of articles is less important than was the case when everything was in print, there is still only so much time in the day. Hence, it is advantageous to eliminate extraneous words (meaning those not forming an essential or vital part [https://www.merriam-webster.com/dictionary/extraneous]) that do not add anything meaningful to a sentence. For example, “It has been shown that rapamycin can … ” versus “Rapamycin can … ” Similarly, “Rapamycin treatment has been shown to increase autophagy” versus “Rapamycin treatment increases autophagy”. Consider the sentences, “These proteins are known to be involved in … ”, “These organelles are able to … ” or “The cells are then washed in order to remove … ” These can be shortened to “These proteins are involved in … ”, “These organelles can … ” and “The cells are then washed to remove … ” without any loss of understanding. Or how about, “Previously published papers demonstrate that rapamycin can inhibit MTOR [1-27].” Considering that you are citing a whole bunch of papers at the end of the sentence, it would not be confusing to just write, “Rapamycin can inhibit MTOR [1-27].” Certainly, this depends on the context, and there are times when you want to make it clear that someone else (i.e., not the current author) provided the evidence for whatever you are citing; however, I edit many papers that use these phrases repeatedly. This is particularly annoying in a review article when just about everything you are writing has been shown previously so there is no need to state (and restate) the obvious. When you remove the extraneous words, the sentence becomes more vibrant, and just downright more enjoyable to read. Once you start to pay attention to these extraneous words you will quickly see what I mean.

Even though this was discussed at some length in the previous article [1], the proper use of “respectively” does not seem to have gotten through. “Respectively” is an adverb that refers to two or more things previously mentioned in a parallel or sequential way (https://www.dictionary.com/browse/respectively) and should only be used if the sentence would be unclear without it. For example, “The strains and plasmids are listed in Tables 1 and 2, respectively.” That is, Table 1 has the strains and Table 2 has the plasmids. Instead, if you wrote, “The strains and plasmids are listed in Table 1, respectively” the use of “respectively” does not add any information to the sentence because both sets of information are in Table 1. Or consider these two examples: First, “The HeLa and PANC-1 cells received 10 µM rapamycin or 5 µM torin 1, respectively.” In this case, the HeLa cells received something different (rapamycin) than the PANC-1 cells (torin 1), and it is necessary to distinguish the precise order by using “respectively”. Without “respectively” this sentence would be interpreted to mean that both cell lines received both chemicals in two separate samples each. Second, “The HeLa cells received 10 µM rapamycin or 5 µM torin 1”. In this sentence, only HeLa cells are being referred to, so there is no need to use “respectively”; again, no further information is provided in this case by including “respectively”.

Another word that apparently requires a refresher is “identify”, which means to perceive or state the identity of (https://www.merriam-webster.com/dictionary/identify) as with “In this paper we identify the cause of Alzheimer as being … ” or “We identify the protein as a target of … ” In contrast, “We identify that this process occurs” or “We identify that the phase is compromised” are incorrect, whereas “We demonstrate that this process occurs” or “We determine that the phase is compromised” are appropriate.

Finally, and it pains me to have to say this, the acronym “ATG” (or even “ATG” in italics) stands for “autophagy related” [2], not “autophagy related genes”. Otherwise, it would be awkward to write “ATG genes” or “ATG proteins,” which when spelled out would mean “autophagy related genes genes” or an equally awkward “autophagy related genes proteins.” Thus, please write “ATG proteins” or “ATG genes”. Autophagy thanks you.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by the National Institute of General Medical Sciences [GM131919].