In this next module, I'm going to edit for you a student's essay from a previous course. This person responded to a prompt on essay assignment one to describe a hot paper in their field. What I want you to do now, is to pause the video, read through the essay at least once or twice, and then restart the video, and I'll walk you through it. I've also provided a text file if you'd rather read the essay there. And if you have time, you might even try editing it on your own. So this paper is on a biological topic. It describes a key paper that found a new role for reactive oxygen species. The essay has a lot of strengths. It has some nice language. The author also did a great job of getting across the main point very quickly in the essay. So in this first paragraph, last sentence, "In a landmark study, published in the journal Plant Cell, Tanaka and colleagues recently uncovered an additional role for ROS as regulators of symbiosis. So that's a beautiful summary of exactly what this essay is about, and the reader is told very early on what this paper is going to be about. The essay is also very well organized. It flows nicely and logically. We start with an overview, then we get some background, then the experiments, then the results, then the questions coming out of those results. So I'm not going to do any rearranging of sentences or paragraphs in this essay, I'm mostly going to focus on a little nip and tuck, kind of few spots where we can take out some unnecessary details and trim some extra words. So starting with the first paragraph here. First sentence, "Reactive oxygen species (ROS) are highly reactive chemicals often associated with escalating warfare between pathogens and their host." That's a really nice, vivid sentence. It draws the reader in. I'm going to leave it exactly as it is. "Most people today have probably heard about reactive oxygen species. They're widely talked about in the popular media. Most people know they're bad players." And that's a nice metaphor we can work with here. I'm going to make one little change to the second sentence. So that sentence reads fine, except at the very end we get this, "To ward off microbial infections." That's just kind of hanging there. It's just did a little bit awkward. Instead there's an easy fix though. All we have to do, is add some dashes. We're going to set off the examples of the biological defenses with dashes here. So I can say, put those examples right in dashes here. And then, we get at the end another dash. So for example, "ROS are integral to biological defenses such as example, example, and then, we have to change the "to" to a "that". "That ward off microbial infections." Setting it off in dashes just makes that whole thing easier to read. Makes the connection between the beginning and the end of the sentence more clear. I'm going to also change "to ward off microbial infections" to "microbial invaders". It's just a slightly stronger word there, and it goes along with this theme of warfare. One tiny change I'm going to make in the last sentence "in a landmark study". The author uses the term "recently". It's not exactly a recent study. If you look at the reference, it's a 2006 study. It's not totally recent, so I'm going to say "in a landmark 2006 study". Let's just specify the date rather than saying "recently". Moving onto the second paragraph. The second paragraph gives some background. The author goes into a little bit of technical detail about words to describe the fungus. In the context of this essay, I don't think that those are necessary because remember, this essay is about the reactive oxygen species. It's not really about the fungus, so I'm going to delete some of the technical terms here. For example, in the first sentence, we get that the grass and the fungus, "the fungus lives endophytically i. e. inside the grass". Let's just say that the fungus lives inside the grass. We don't need that technical word there. Then, we don't really need to hear about the mycelium of the fungus. Let's just say, "the fungus". Again, it's not important to give the technical term in this particular context. So "the fungus", and then we can get rid of this "composed of cells called hyphae". Again, I don't think we need to know the technical term for the cells, it's not really important for this particular essay. And then, the second sentence, was a little bit long. And the most important point is really at the end. "The fungus grows in perfect synchrony with the leaves of its plant." So I'm actually going to rearrange this sentence just slightly by moving up that last thought to the beginning of the sentence. "The fungus grows in perfect synchrony with the plant", and I'm even going to delete "the leaves". "The leaves" will come next, "with the plant", so we get right away the idea of this symbiosis. "It grows in perfect synchrony with the plant" and then we can go right into this idea of colonizing. "Colonizing all its leaves". We can say, "its" rather than repeating "of the plants" so "colonizing all its leaves". But, "and then the hyphae sprout only sparsely in tissue". We don't need all of that. I think we could just go right into "but never breaching its cell walls or membranes". So we can end the sentence there. So it's just a little bit streamlined. "The fungus grows in perfect synchrony with the plant, colonizing all its leaves but never breaching its cell walls or membranes." The next two sentences, the author uses the term "harmonization". That's a nice word, but I don't think we need it twice; I'm going to delete one of those instances of "harmonization". And in this next sentence, I think we can just say directly, exactly what happened. So "the grass directs resources to the fungus, the fungus produces a toxin that helps them both". I think we can be a little more direct. So I'm going to delete this "exquisite harmonization of the fungus and the plant" and just say, "the plant", and then we get a couple of nouns, it could be verbs here, so we get "the plant growth directs resources to the production of fungal toxins". Right, "growth" and "production", those could be verbs. So I think we can just say "the plant". We could even just delete "the plant growth". "The plant directs resources to the fungus which produces", we don't need "fungal toxins" actually, we could just say "toxins", "which produces toxins that protect the symbiosis from herbivores". "The symbiosis." A lot of people may not have heard of "symbiosis" as a noun like that. I think it might be a little more clear to say "the toxins that protect both species from herbivores". I also added in the sentence, we were talking about the role of the fungus in the previous sentence. For a little transition here, I added "the plant, in turn, directs resources to the fungus, which produces toxins that protect both species from herbivores." Finally, in this last sentence, I'm just going to read it here. "But how this harmonization is achieved and what its underlying mechanisms are, have remained a mystery. Notice it's a little awkward to say "are" and then "have". Notice also that we get "how the harmonization is achieved" and what its underlying mechanisms are. Those are kind of related concepts. It's a little bit repetitive. So I think we can cut one of those and just talk about the underlying mechanisms. The other thing is, I'm going to add a "but until Tanaka" here because remember this is a 2006 paper. Up until Tanaka, it was a complete mystery. Tanaka actually maybe solved some of that mystery, so I think we have to acknowledge that. So "but until Tanaka, the mechanisms underlying this", how about we say "exquisite harmonization". We don't really need that word "exquisite", but the author had used that term "exquisite harmonization" before. It just kind of shows the appreciation that the author has for this symbiosis, so I'm going to put it in there. "The mechanisms underlying this harmonization just have remained a mystery." And that will end that paragraph. So we get a nice summary of the background. And then we have a lovely transition here. We're presented with a question, "what are the mechanisms", and then the next paragraph starts to address this question, so the reader knows really right away where we're going. So, to address this question, "Tanaka and coworkers," now we get a whole bunch of details about when and how they generated random mutants of the fungus. I think the first sentence and second sentence of this paragraph can actually be combined into one. It's a little repetitive and we probably can put it all into one sentence. So we get that they generated random mutations in the first sentence and then we get how they did it in the second sentence. I think we can combine those by just saying that Tanaka" and coworkers", how about "randomly inserted pieces of DNA into the fungal genome ". And then we can put in parentheses what the name of that method is. It's good to have that in there but it's probably extra information. "They randomly inserted pieces of DNA into the fungal genome" and then, why did they do that? "In the hopes of disrupting," and then we get "a gene resulting in observable growth changes in symbiosis." This is a little wordy. How about if we just say "in hopes of disrupting genes," probably more than one gene might be involved, "genes involved" or "genes critical to the symbiosis." And I think the reader can infer that if you disrupt those genes that are critical to the symbiosis, you would observe changes. So we don't need to spell that out so much for the reader. Then we get "they indeed found a mutant showing a highly unusual growth pattern." Nice use of the colon here to say exactly what that growth pattern is. I'm going to just make one tiny change. I just prefer "indeed they found" rather than "they indeed found" that personal preference. Both are fine. "Indeed they found a mutant", and I think I'm going to say "a mutant strain". "A mutant strain showing", I think we could say "with a highly", I slightly prefer "with a highly unusual growth pattern" here. And then we get this colon. Now, we get this. "Unlike the synchronous growth of the wild type fungus." Well we've already talked about the synchronous growth of the wild type fungus in the previous paragraph. I actually don't think we need to repeat that. I think we can just go into right away what's different about the mutant. So we can just start with what's different about the mutant. We don't necessarily need that hyphae again, the technical term for the fungal cells. I think we can just say "mutant fungal cells". It's not important to get the technical term, again in this context, since the essay is mostly about reactive oxygen species, so just "mutant fungal cells". And then we get a "showed profuse and abundant proliferation". So this is one of those instances where we've got a noun that could be a verb. So "showed proliferation", we could just say "proliferate" and even simpler than the word "proliferate", how about if we just say "grew". So rather than "showed proliferation", how about "proliferated" or "grew" and then we can say they "grew profusely and abundantly", but actually "profusely" and "abundantly" are kind of the same thing, so I'm just going to say "grew profusely throughout the grass". And then I am going to wrap this last sentence into the previous sentence, "so they grew profusely throughout the grass, whereas", and now let's say what happened to the plants. "Whereas the plants", we could say "whereas infected plants". "Whereas infected plants" we don't have to say that they were infected by the mutant, that's implied. "Whereas infected plants" and now we get another "showed growth", which could be just "grew", right, it's another instance of a verb being turned into a noun. So let's turn it back to the verb. So rather than "showed poor growth", how about "grew poorly and often died". All right, so we've trimmed that a little bit. Going to the next paragraph. What's interesting is, this author does a great job with the logic and the flow again. They actually almost give too many transitions that aren't really necessary. So notice in this next paragraph it starts, "this set the stage for the next step. Finding the genetic changes that cause these aberrations", actually going to delete that entire sentence. The author here has a tendency to want to start every paragraph with a little guidepost, a signpost for the reader to tell the reader exactly what's coming up in the paragraph. That's a good instinct but, in fact, the logical flow is so nice here that the reader doesn't need this kind of hand-holding. You can just go right into how the researchers figured out what the genetic change was. The reader doesn't need that entire sentence. So, trust your reader a little. You don't always need to hand-hold them. Sometimes explicit transitions like that are unnecessary if you've got good logic. So, we're going to get rid of that. We're going to go right into "using genetic tools, the researchers honed in on the gene the DNA insertion had disrupted. Surprisingly only a single innovation event had occurred." Notice the use of "insertion" and "integration". Probably that's a little repetitive. I think we can just combine these all into one. "Using molecular tools, the researchers found that", I'm going to say "an insertional event", let's stick with "insertion", "an insertional event in a single gene". I think that's the idea here "the insertional event in a single gene had caused the aberrant growth or "the abnormal growth" since I deleted "aberrant" in one of the sentences above, I'm going to say "had caused the" like that word "aberrant growth" and then we just end up there, "So they found that an original event in a single gene had caused the aberrant growth". And now I'm going to make a really small sentence here, a really short sentence. "The researchers named the gene noxA. Sometimes it's nice to just throw in this short sentence. It kind of adds to the sentence variety this and that structural variety here. It kind of punctuates this finding a little bit. So think about that. Occasionally throwing in a short sentence like that has a nice effect. Now I have a really short paragraph here so I'm going to fold this paragraph here in with the next paragraph. These can be brought together. So, "using molecular genetic tools, the researchers found that an insertional in a single gene had caused the aberrant grown. The researchers to name the gene noxA". Again the author wants to tell the reader exactly what's happening next. To get an idea what that protein does, the protein made by the gene does, the team did X Y and Z. I think we can actually jump right into what the team did and what they found, all in one and get rid of this little signpost here. So I think we can just say "When they compared". We've just recently talked about researchers so the "they" is assumed to be "the researchers" when "they compared its sequence", we just said "the genes", so that it's OK to say "it's sequence", we'll know we're referring to the gene. "When they compared its sequence with those of enzymes with known activities", and then let's just fold that right into the next sentence; let's hear what they did find. "They noticed that noxA was very similar to any NADPH oxidases enzymes that are often involved in generating our ROS in cells". I think we can say just shorter than that, "enzymes that generate ROS" and I don't think we need the "in cells that generate ROS" and then I'm actually going to end this new paragraph right there, set off another paragraph. And the reason I'm ending here is to punctuate this finding. This is where the researchers realize the link to ROS. So this is wrapping us around to the beginning of the essay, to the main play of the essay. So I'm going to punctuation that by ending the paragraph right there. And the next paragraph now starts with "Indeed", the author here likes this transition word. "Indeed," we've already used that one so I think we'll get rid of that. It's saying well when they next did this they observe this. We can probably just go right into what they observed. I'm going to say "further testing revealed that ROS accumulates in plants infected by the wild-type fungus but not those infected by the noxA disrupted mutant". I think we can say this shorter" but not those infected by the noxA mutant". That would be sufficient there, "noxA mutants. This confirm that", I am actually going to change the "confirmed that to "The researchers concluded that" or "the scientists concluded that". The reason I'm not going to leaved confirmed in here is because this is a really novel discovery I think. And so "confirmed" implies like other people had suspected it before but this I think is really novel and so I'd rather say that they concluded that it's a totally new thing as opposed to a confirmation. And then, "that noxA is involved in ROS production required for proper functioning of the symbiosis". I don't think we need all that. I think we can just say that "ROS is a critical player in this symbiosis". That's the key finding, and we can end it there. Finally, in this last paragraph, we again get a transition sentence, "Well, this raises tantalizing questions". Instead of doing that, let's just go into, right away, what the open question is, so: "How ROS enables symbiosis remains an open question." Notice I've put that in the present tense. I'm assuming that even today, seven years after Tanaka said it, this is still an open question we haven't solved it yet. I might repeat "Tanaka's team" I deleted here, that the reference to Tanaka again, so maybe I'll say, "Tanaka's team suggests", they probably suggested or speculated about this in the past when they published their paper, so I think it should be a past tense. They speculated back then, when they published that paper, that "ROS could be involved", I'm going to change this to "may be involved" just because the next sentence has a neat play rule. I want those verbs to be parallel so "may be involved in establishing physical connections between the cell walls of the plant and fungus". "Alternatively, ROS may play a role in symbiotic signaling." I'm going to change this colon to a semi-colon. It's just I think slightly better to have a semicolon here because the second half of this sentence doesn't amplify the first half. It really is just another idea. I could go either way on that, either a colon or something colon and it's probably fine. I slightly prefer a semicolon there. So a new idea, so, "their short half-life predisposes them for cellular communication, perhaps facilitating an interspecies Morse code," that's kind of cool language "is their short life" but maybe we could say it a little shorter. How about "their short half-life makes them perfect candidates for an interspecies Morse code." And then, we don't need "that helps maintain the symbiosis". We don't need to repeat that because we already know that we're in a paragraph about how the symbiosis is maintained, so we can get rid of that extra completely. The reader doesn't need that. "If so, identifying the plant sensor and signalling pathways". What if we just say, "if so, breaking the code", kind of playing on the Morse Code idea from the previous sentence, "If so, breaking the code could provide deeper insights into how plants recognize and interact with beneficial symbionts and can distinguish them". Notice the lack of parallelism there, "recognize, interact, and distinguish", what if we put "can distinguish". It's not parallel, so I'm going to eliminate that "can". And then, finally, I feel like we need to add a little tiny paragraph at the end here, just to provide a nice conclusion to wrap back to the beginning. Remember the focus of this paper is this new discovery that ROS are always bad players. So I feel like we need to wrap-up here. So I was going to suggest to the author something like, Tanaka's paper fundamentally changed scientists' view of ROS. Major shift here. These chemicals are not only mean weapons of biological warfare, I'm rapping now, wrapping back now to that metaphor that was given at the beginning but also "agents of peace and cooperation". Sometimes it's nice to, if you start with kind of a metaphor nice vivid idea to wrap back to that at the end of the piece. And then I am going to ask the author of this piece to maybe think about, are there any wider implications for biology of the fact that ROS are not always bad players? Is there any wider implications for biology even beyond symbiosis? It might be nice if there are to add that there.
