Edit Sciwrite Demo 7.5

In this next module, I'm going to edit a student's essay from this class. Thanks to everyone who volunteered on the pre-course survey to allow their work to be used for this kind of demonstration. this person responded to the prompt on essay assignment 1 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 the 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, 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 the 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's told very early on what this paper's going to be about. The essay's 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, 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 a 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 speacies, ROS, are highly reactive chemicals often associated with escalating warfare between pathogens and their hosts. 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 with the warfare 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. It's just kind of, that's just kind of hanging there. It's just a, a little bit awkward. It's a, 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 of microbial infection. 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 infection 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, this was, the author uses the term, recently. It's not exactly a recent study. If you look at the reference, it's a 2006 study, not totally recent. So I'm going to say any landmark 2006 study, let's just specify the date rather than saying, recently. Moving on 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, ie, inside the grass. Let's just say that the grass 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. So let's say and this sentence, 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 it's plant host. So I'm actually going to rearrange the sentence just slightly. By moving up that last thought to the beginning of the sentence. The fungus rose 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, the idea of this symbiosis, that grows in perfect synchrony with the plant. And then we can go right in to this idea of colonizing, colonizing, all its leaves. We can say its rather than repeating of the plant, 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 it's cell walls or membranes. And we can end the sentence there. So its 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, branes. And the next two sentences, the author uses the term harmonization. that's a nice word. But I'm, I don't think we need it twice. So I'm going to delete one of those instances of harmonization. And in this next sentence, I think we can just say directly that 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, a couple of nouns that could be verbs here. So we get, the, the, the plant grow 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. We could just say toxins. Which produces toxins that protect the symbiosis from urban wars. The symbiosis, a lot of people may not have heard of symbiosis as a noun like that. I think it may be a little more clear to say, that protect, the toxins that protect both species from herbivores. I also added in a sentence. we were kind of 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 an 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. So I'm going to say 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 here. 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 that appreciation that the author has for this symbiosis, so I'm going to put it in there. the mechanisms underlining 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 get, we're presented with a question. What are the mechanisms? And then the next paragraph starts to address this question. So the reader, write, knows really right away, where, where we're going. So to address this question, Tanaka and coworkers. now we get a whole bunch of details about random, 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 co-workers, how 'bout, randomly, [SOUND] inserted pieces of DNA into the fungal genome. And then we can put in paranthesis 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, in hopes of just of, disrupting genes. Probably more than one gene might be involved. Genes involved, or genes critical to, 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. 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 can say, with a highly, 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 can, I think we can just go into right away, what, 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 pro, proliferation. So this is one of those entran, instances where we've got a noun that can be a verb. So, showed proliferation. We could just say proliferate. And even simpler than the word proli, proliferate, how 'bout if we just say grew. So rather than show pro, proliferation how bout 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 to say, grew profusely throughout the grass. And then I am going to wrap this last sentence in to the previous sentence. So, they grew profusely throughout the grass, whereas. And now let's say what happened to the plants. Whereas, the plants, or the infe, we can say, whereas infected plants. Whereas, infected plants, and 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 a, another instance of a noun being turned, a verb being turned into noun. So, let's turn it back to the verb. So, rather than showed poor growth, how about grew poorly, and often died? Alright, so we've trimmed that a little bit. go on to the next paragraph. Now, what's interesting is this author does a great job with the 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 had caused these aberrations. I'm 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 handholding. 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, we don't always need to hand hold them. Sometimes explicit transtions like that are unnecessary if you've got good logic. So we're going to get rid of that. We're going to g right into using genetic tools. The researchers honed in on the gene the DNA insertion had disrupted surprisingly only a single in, integration event had occurred. notice the use of insertion and integration. probably that's a little repetitive. I think we can just combine this all into one, using molecular tools. The researchers found that [SOUND] and I'm going to say an insertional event, and stick with insertion. And inser, an insertional event in a single gene. I think that's the idea here. An insertional event in a single gene [SOUND], had caused the aberrant growth, or the abnormal growth. And since I deleted aberrant a, a, above, bef, in the one of the sentences above, I'm going to say had caused the, I like that word, aberrant growth. And then we can just end that there. So, they found an insertional event in a single gene that caused the aberrant growth. And now I'm going to make a really small sentence here, a really short sentence, sentence. The researchers named the gene NoxA. Sometimes it's nice to just throw in a short sentence it kind of adds to the sentence variety, the sentence structure 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 genetics tools the researchers found that an insertional event in a single gene had caused the abberant growth, researchers named the gene NoxA. And now I get this again the author wants to kind of tell the reader exactly what's happening next, to get an idea of what that protein does. That the protein made by the gene does, the, 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 alrea, al, just recently talked about the researchers, so we, the, they is assumed to be the researchers, when they compared. its sequence, we've just said the gene, so it's okay to say its 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, what did, what did they find? They noticed that NoxA was very similar to NADPH oxidases, enzymes that are often involved in generating 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 there, that generate ROS. And then, I'm actually going to end this new paragraph right there. Start off another paragraph. And the reason I'm ending there is to kind of punctuate this finding. This is where the researchers realized the link to ROS. So this is wrapping us around to the beginning of the, the essay, to the main point of the essay. So I'm going to punctuate that by ending the paragraph right there. And the next paragraph now starts with indeed, the, the author here likes this transition word indeed. We've already used it once, so I think we'll get rid of that. and actually we can probably, it's saying well, when they next did this, they observed this. We can probably just go right in to 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. I think that would be sufficient there, NoxA mutants. this confirmed, now I'm actually going to change the confirmed that, to the researches concluded that, or the scientists, just for variety, the scientists concluded that. The reason I'm not going to leave 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, I'd rather say that they concluded that, it's a new, 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 the symbiosis. That's the key finding. [SOUND] And we can end it there. Finally in this last paragraph we again kind of get a transition sentence. Well this raises tantilizing questions. Instead of doing that, let's just go into right away what is the open question. So, how ROS enables symbiosis, remains an open question? And notice I've put that in the present tense. I'm assuming that even today, seven years after Tanaka's study, that this is still an open question. We haven't solved it yet. And then we can talk about I might repeat Tanaka's team. I deleted here the, the reference to Tanaka again, so maybe I'll say Tanaka's team. suggest and now this is a, 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, 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 name play role. I want those verbs to be parallel, so may be involved in establishing physical connections between the cell walls of the plankton fungus. Alternatively, ROS might play a role in symbiotic signaling. I'm going to change this colon to a semicolon. It's just, I think, slightly better to have a semicolon here, because the second half of the sentence doesn't amplify the first half. It really is just a kind of, another idea. I could go either way on that, either a colon or semi colon is probably fine. I just slightly prefer a semicolon there, it's 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. So their short life. But maybe we could say it a little shorter. how about their short life, their short half life makes them perfect candidates, for an interspecies Morse code. And then we don't need that helps maintain symbiosis. We don't 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 signaling pathways, how about 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 symbiants and can distinguish them. Notice the lack of parallelism there. Recognize, interact, and distinguish. It would, if we put can distinguish, its 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 aren't always bad players. So I feel like we need a little wrap up here. So I was going to suggest to the, to the author something like, Tanaka's paper fundamentally Changed scientists' view scientists' views or view of ROS. Major shift here. these chemicals are not only weapons of biological warfare. I'm wrapping now. Wrapping back now to the 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. This vivid idea to wrap back to that at the end of the piece. and then I'm 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. If there're any wider implications for biology, even beyond symbiosis. It might be nice if there are, to add that there.