J460 Science Writing » Alex Farris http://journalism.indiana.edu/classwork/j460_science_writing_fall2008 Students in a new undergraduate course in science writing report here on the 2008 meeting of the National Association of Science Writers, on new discoveries in science, on the scientists who make the discoveries, and on the science writers who translate these discoveries for the general public. They also review a recent book on science written by New York Times science writer Natalie Angier. Wed, 14 Jan 2009 16:50:24 +0000 http://wordpress.org/?v=2.8.4 en hourly 1 Angier’s Canon Sparkles (Sometimes Excessively) http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/stories-and-reviews/angiers-canon-sparkes-sometimes-excessively/ http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/stories-and-reviews/angiers-canon-sparkes-sometimes-excessively/#comments Thu, 18 Dec 2008 18:31:41 +0000 Alex Farris http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/?p=133 The Canon offers, in the words of the subtitle, a “whirligig tour of the beautiful basics of science.”

She covers all of the beautiful basics in this book, from the atomic reasons why solids have so little give to the unexpected dynamism of our planet to why creationism and intelligent design are pretty much bunk.

But for the most part, she speaks to the choir, which may not win her any new fans, especially those who previously looked askance at science. Then again, we college students, the biology minors and geology majors and PhD candidates, do form part of that choir, and at least for me, it puts to rest any questions about science’s ability to keep learning about our natural world.

The title is a bit misleading. Angier christens the book The Canon, even though she states multiple times that we don’t yet know everything. Historically, a “canon” has been a set of guidelines and beliefs, mostly of a religious nature, that are unchanging, set in stone, or otherwise quite certain. Many of these concepts, though, are incomplete; for example, we do not completely understand how a chain of amino acids bends and folds into an enzyme and how exactly that enzyme changes its substrate. Angier, however, wishes to deal only in the fundamentals of science, and this she does with fascinating skill.

She uses so much skill, in fact, that if one outside of the “choir” were to read this book with an open mind, that reader might join the just sign up to sing. The book bursts forth with metaphors, wordplay, and (a delight to anyone who has trouble grasping science) understandable explanations. It’s just enough to get the reader to see the world from a completely different point of view, like that of an atom.

Of course, being a science writer, she sometimes comes off as too much of a nerd, which may put off some of science’s n00bs. (Okay, I’m a nerd, too, so I liked her quirkiness.) At times, she goes really, REALLY far into the details, and to make those details more appetizing, she showcases a lot of annoying “do you see what I did there?” moments. She deals in excessive alliteration, such as this passage in the molecular biology chapter: “Enamel has enabled many a tooth to last posthumously into posterity.” She does this all the time, and often I did a ::facepalm:: in reaction to its lameness. Regrettably, I have to say that I would rather see those examples of wordplay than not,  because for most readers (including myself) they provide mental candy to convince people to keep reading through the details to get to the really awesome parts.

The most awesome part for me was the chapter on evolutionary biology. This is where the book truly separates the science minds from the non-science minds. She has some harsh words for believers of creationism and intelligent design, quoting a scientist as saying, “You have to be diabolically blinded not to see evolution in everything that we do.” Once the reader (a sufficiently open-minded one, of course, and not a diabolically blinded one!) finishes the chapter, those words are most definitely called for. Through the evolutionary story of life in general, of horses, and of humans, Angier is able to convince anyone that evolution is no crackpot theory or “a fairy tale for grownups,” as a bumper sticker says; it is very scientific, it’s backed up by evidence, and it forms the basis for everything in biology.

Everything Natalie Angier provides in The Canon is a foundation for some scientific field, which makes it such an invaluable read. If you, n00b college student, want to learn more about science, please read this. It’ll do you good.]]> http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/stories-and-reviews/angiers-canon-sparkes-sometimes-excessively/feed/ 0 Alex Farris http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/the-writers/alex-farris/ http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/the-writers/alex-farris/#comments Fri, 12 Dec 2008 05:28:16 +0000 Alex Farris http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/?p=81
Alex Farris is a sophomore at the Indiana University School of Journalism, majoring in journalism and Spanish with a minor in biology. Alex works as a photographer with the Indiana Daily Student, and he also takes senior pictures and other photos just for fun. He is the editor of The Undergraduate Scholar, a magazine that publishes IU students’ theses, lab reports, and long essays. Before attending IU, Alex worked as a research assistant at the Center for Hip and Knee Surgery in Mooresville, IN, where he co-wrote a paper on hybrid total knee replacement for the journal Clinical Orthopaedics and Related Research. He continues to work at the center today and is co-authoring three more papers that cover subjects like the posterior cruciate ligament (PCL) and obesity’s role in prosthesis failure. Alex hopes to mix his interests in the future, combining the emotional allure of photojournalism with the intellectual appeal of science writing, ideally in photo essays and reports for National Geographic or Discover magazines.

Links to Alex’s articles

]]> http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/the-writers/alex-farris/feed/ 0 In “Social” Settings, Avatars Behave Like Real People http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/stories-and-reviews/avatars-behave-like-real-people/ http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/stories-and-reviews/avatars-behave-like-real-people/#comments Fri, 12 Dec 2008 04:58:38 +0000 Alex Farris http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/?p=80 When gamers become characters in online games like Second Life and There.com, they appear to be influenced by the same social cues found in their “first” life, researchers have found.

In a recent study that used a massive multiplayer online game (MMOG), gamers’ avatars responded to requests similarly to how their owners would in real life, whether the request was welcoming or off-putting.  They also responded to racial cues in a way parallel to real experience, although the evidence here was less clear.  The study was published in the March issue of the journal Social Influence.

The researchers from Northwestern University, funded by a grant from the National Science Foundation, used a “virtual field study” model of investigation that could open the field of social psychology to different kinds of people and create another avenue for testing hypotheses.

In the study, 416 random users from the MMOG site There.com were asked a series of requests.  A research assistant posing as a normal “avatar” asked one group of 218 users to teleport to a far-away place and to take a screenshot of the researcher and the surrounding scenery.  The users were told this favor would take approximately two minutes.

The other two groups were subjected to one of two “compliance techniques” that progressed from either a small or a large request to the two-minute screenshot.  In one, called the foot in the door (FITD) technique, the assistant asked if the user could take a quick screenshot of where they were currently standing, followed by the two-minute request.  In the other, called door in the face (DITF), the assistant asked the user to take a two-hour teleporting tour; upon being rejected, the assistant would then make the two-minute request.

The two techniques have been shown to work in real life in studies dating from the 1960s.  The researchers, however, thought the virtual surroundings would affect how the techniques would play out.
The virtual world did not seem to affect rates of compliance.  Mirroring reality, more users agreed to the two-minute request after exposed to a smaller (FITD) or larger (DITF) request than after no previous request.

Paul Eastwick, lead author of the study, said this finding hints at a preservation of self in a virtual world free of most societal restraints.  This conception of self lies at the heart of the two compliance techniques.  FITD, for example, relies on the way the person being asked views himself.

“You see yourself as helpful,” he said, which propels you to fulfill the second request.  “It’s not strictly a game because [how you respond] is linked to self-perception.”

Racial bias was also tested in the study.  Roughly half of each series of requests was performed while the assistant inhabited a “white” avatar, while the other half was performed using a “black” avatar.

Compliance without using either of the two techniques was not affected, nor was compliance while using FITD.  When the user was subjected to DITF, however, compliance dropped when the avatar was black.

Eastwick attributed this finding to the nature of DITF.  Because compliance in DITF is based on how the person being asked perceives the requester, he said, conclusions drawn from the requester’s appearance affects how the other person will respond.  He cautioned, however, that the study could not conclude that skin tone directly affected compliance.

“We can’t say it’s an automatic reaction” to skin tone, he said.  The person being asked may have thought, “‘Why would this person choose to have this skin tone? He must be weird.’
“It’s still bias,” he added, whether or not skin tone directly affected compliance.

Besides There.com, other MMOGs include Second Life and World of Warcraft.  While the latter is based more on completing missions than on the free-form exploration of Second Life and There.com, World of Warcraft features many parallels to reality.  Former World of Warcraft player Pavan Rao found numerous examples of the foot in the door technique during gameplay.

“You can ask random people” for help, he said, “and that’s when you do [FITD]. You can be like, ‘I need help with this mission’ . . . and you just build it up, and eventually it’d be like, ‘Let’s run through every single dungeon in this entire area.’”

Victoria Groom, a student of social psychologist Dr. Jeremy Bailenson, said the study nails down the power of the FITD and DITF techniques in a virtual world.  She took issue, though, with the racial-bias finding.  She said this part of the study was not a pure experiment because it did not control for other reasons why a user would be less likely to comply, and because there was no pre-test that determined the peculiarity of the given race.

Both Eastwick and Groom said that using MMOG sites as “virtual field studies” for social psychologists has yet to gain universal approval.  While this method is not yet considered the “gold standard” for testing social-psychology theories, they said, this study and others like it widen the test pool and include more subjects in tests.
–Alex Farris
]]> http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/stories-and-reviews/avatars-behave-like-real-people/feed/ 0 Among Plants, Fungi, and People: Four days with the Bever/Schultz lab http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/field-notes/among-plants-fungi-and-peoplefour-days-with-the-beverschultz-lab/ http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/field-notes/among-plants-fungi-and-peoplefour-days-with-the-beverschultz-lab/#comments Fri, 12 Dec 2008 00:39:02 +0000 Alex Farris http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/?p=75 2008.11.17

4:00 p.m.

I had been looking for Dr. James Bever’s lab for a full five minutes, frantically wondering where room 149D was in the labyrinth of the biology building. When I finally knocked on the door, a man in an orange T-shirt welcomed me in. Dr. Bever couldn’t see me yet, though, because he was busy. Now that I had found his lab, I was willing to wait a little while and catch my breath.

When he finished, he called me in. My mind still in a rush, I forgot my manners and asked if I could sit in the open chair. “Sure,” he said, and I sat down. Immediately a burst of air rushed out from under me. The chair was amply cushioned, and air escaped through the holes made for the stitches. “That wasn’t me,” I said sheepishly.

Fully aware that things were going OH-SO-SMOOTHLY already, I explained why I had come to his lab: I wanted to follow him and his lab assistants and observe everything they would do over the next ten hours. I wanted to “show what’s behind the public face of science,” I told him. Dr. Bever immediately joked that he wanted to hide behind that public face, which is why his window was covered on the inside from top to bottom with vines.

Fortunately, he was joking (the vines were there, but not for that purpose), and he allowed me to, using his word “spy” on his lab. He introduced me to the lab workers who were there, explained that his wife, Peggy Schultz, also led this lab, and allowed me to sit at a lab table to observe. Now I can really sit down!, I thought…

before another burst of air rushed out from under me. ::facepalm:: More of these chairs? Really? I’ll have to watch myself, too.

4:15

I had not been in the lab for more than five minutes before I found someone to talk to: Benji. …Actually, he found me. With my personality, I was content with simply sitting at one of the black-topped lab tables and observing the people’s work. Benji had other plans, though, and he (gratefully) pulled me into the dynamics of the Bever/Schultz lab and made me an integral part of it for the next ten hours.

 Benji, unlike the other people in the lab, is an undergraduate working on his senior thesis. He’s a shorter guy (just shorter than I), with the most interesting pair of glasses I’d ever seen. The frames were black with an intricate design, but wrapped around that design was what looked like a copper wire, which added a touch of controlled eccentricity to my perception of him. If I had completely forgotten my manners, and if I had not been taking notes, I would have focused completely on his glasses and even asked if I could try them on. They were that interesting.

 The glasses didn’t even compare to his own interesting character, though. He came to IU, and the Bever/Schultz lab, through the Individualized Major Program. His major is Environmental Sustainability, which admittedly is a little redundant, because sustainability is tied intimately into any environment. He could have gone into much more detail with his major, like Fungi and Urban Ecosystems, but he figured such detail was better suited for graduate school. “With an undergraduate degree,” he said, “you want some sort of ambiguity, like biology.”

 I talked to him for almost an hour and a half about the most varied topics. He began with an explanation of his project, which was brought up after another lab worker asked him, “Are your plants still alive, Benji?” (“Yes, they are!” was his answer.) He then looked at me and said, “Now I can use you as an excuse.” I was a little surprised, so he went on.

Benji’s Work

 His project, along with many others in the Bever/Schultz lab, is examining the effect of a certain type of fungus on plant growth. It’s called arbuscular mycorrhizal fungus (AMF), and it plays a major role in some ecosystems. “The prairie system that we see today,” he said, “would not exist without AMF. The way prairies are accustomed to living would be irrevocably changed if AMF were absent.” Why it is important, though, is not completely understood, and this lack of understanding fuels most of the work in the lab.

 Benji’s project looks at certain prairie plants’ interaction with AMF. This interaction is a symbiotic relationship, meaning that each one benefits the other. The plants produce sugars that AMF needs, he said (which makes it an obligate), and while plants do not need AMF, they certainly do better with it.

 Unfortunately, due to the timing of the school year, Benji was unable to plant his study subjects until late into their season, so he’s trying to stretch out their life before the winter knocks them out. He’s done well with his goal, allowing the rain to work its magic and using a tarp to keep the plants under control and under some shelter. (He was using me as his excuse because, until late last week, he was “waiting” for me to go out to his plot on campus with him and help take care of the plants.) Because of this, he will have to adjust his final paper. “With the added stress of late planting,” he said, “I’m going to examine the tough conditions that green plants have to overcome in order to do anything meaningful,” in addition to looking at the relationship between plants and AMF.

The Metaphor

 Now, I’ll admit that some of what he said about the relationship between plants and AMF went over my head. I got a 5 on the AP biology test in junior year of high school, but I’ve never worked extensively with fungi, so I asked Benji to give an example, or even a metaphor, of how AMF and plants interact. In the process, he single-handedly gave me a framework for the remainder of my ten hours.

 In Benji’s metaphor, Dr. Bever (who he called Jim) is the plant, and his lab assistants are the AMF. Jim provides the “sugar” of guidance and encouragement, and the lab assistants help him in his research goals. Jim doesn’t need the assistants, but he is able to do much more work because of them, just as plants don’t need AMF but work much better when AMF is present. Benji cautioned me against using such a metaphor, though, and asked me to check with the other people in the lab to see if it works. “It’s a cool metaphor,” he said, “but it might be a bit too simplified.”

More Conversation

 Before he went back to work at 5:20 (mind you, we started talking at 4:05), we went into topics I wouldn’t have expected in a lab, but that upon closer inspection were bound to come up. Benji mentioned his interest in urban ecosystems, saying that most people agree that cities work better when they have such an environment within their city limits. “New York City would suck that much more,” he said, “without Central Park. But if you don’t have 200 acres in the middle of your city, where are you going to put your urban ecosystems?” He enthusiastically suggested rooftops, which he plans to use in the future.

 We closed with a discussion of the role of science in society, and how the media and politics are integral to that role. “I feel that it’s important to talk to you,” he said, because scientists have an ethical responsibility to talk to the public about their fields. “There are so many avenues for science to affect politics or economics,” he continued. Unfortunately, though, the people whose job it is to travel these avenues do not always understand the details, or even the basics, of science, which can result in a scientist being turned off to talking with journalists like myself. “The scientist can talk to a reporter for an hour,” he said, “think that they got their point across… and the article got everything wrong.”

 Despite this potential for error, according to Benji, scientists must be willing to voice their findings and reasoned opinions if they wish to have a broad positive effect on society. Because they are not legislators, the best way for them to affect policy is to change the voters’ minds, which means going to the mass media. “If they want to affect policy,” he said, “scientists need to go to these reporters and risk the possibility that they could be misinterpreted.” To guard against misinterpretation, he added, two questions must always be asked:

Reporter: “Can you explain that in a different way?”
Scientist: “Do you understand what I just said?”

 After all of this fascinating discussion, Benji went back to work, but not before telling me that he was happy that I understood science. He referenced my minor in biology as reason to believe that if I were to become a science journalist, I would get it right. …I felt pretty good about myself after that.

5:52

 Liz, a graduate technician at the Bever/Schultz lab, prepared to leave at this time. (It was almost below freezing outside, so she needed the extra preparation.) She invited me to follow her tomorrow as she showed some people how to clean and measure plant roots. She said, “It will be dirty.” I was in.

6:00

 This blew my mind, so I think I need to share it.

 Benji was talking to another guy in the lab about the two sources of calculus. Newton developed it for one reason, which Liebniz made his own version independently of Newton to solve an entirely different problem. The two decided to meet for lunch one day and talk about calculus, monads, and multiple universes.

 I was astounded. When I meet someone for lunch, we talk about our days, our families, the stresses of school, and how good and nutritious the food court’s pizza is(n’t). We don’t talk about multiple universes! These guys are definitely science people. They live, breathe, and even eat science.

6:34

 At about 5:15, I had noticed that Jim’s door was closed. As part of my assignment was to observe how the principal investigator interacts with his lab assistants, and as he had his office door closed when it was open previously, I asked Benji, Why the closed door? He said that either the people working in the lab were too loud and distracting, or he was taking a call.

 It was then that I realized something. Wait a minute, I told myself. The people working in the lab might have been too loud? That means they were talking to each other, which means they (gasp!) like more than just the science in this lab.

 Why did I gasp when I thought of that? Did I expect the lab assistants to be bookworms who developed nearsightedness because they looked into the microscope for too long? …Okay, maybe not that extreme, but I know I went into this assignment thinking that they would only be working. But that’s not the case. They actually like each other.

 I don’t know why that was so surprising to me. Science is, at its heart, a human and social enterprise. It is not simply a search for how the world works; it’s also a huge forum for discussing peoples’ observations on how the world works. It’s a way to verify if peoples’ observations are correct, and it requires talking to other scientists. I knew scientists had to talk to each other professionally; why didn’t I think they could talk to each other casually? In Homer’s eternal phrasing, “D’oh!”

6:40

 Jim, Benji, and I were the last one left in the lab. We left at 6:40, with Jim talking to Benji about his future science plans and how science is a never-ending process. As he talked, Jim seemed genuinely interested in Benji’s work and aspirations. Jim really knows and cares about his lab assistants, I thought.

 At this moment, I realized that I had called him “Jim,” not Dr. Bever. I looked back over my notes and saw that I had first called him Jim at 4:25, not even half an hour after my arrival. So, not only were his lab assistants on a first-name basis with him, but I was, too. I was really becoming a part of this lab, and it was thrilling.

 I also realized how much of an even footing Benji was with the rest of the lab. Even though he was a senior amongst graduate students, and even though he wasn’t exactly a biology person, all the people in the lab, and especially Jim, treated him like an equal. I had expected a hierarchy among the lab assistants, but from what I’d observed, this was completely not so.


2008.11.18

12:50 p.m.

 I walked into the lab as they were having lunch. Gretchen, the head of the biology department graduate program, was there, along with Jim, Liz the graduate technician, the guy who set up the lunch meeting with Benji, and other lab workers. As he ate the acorn squash soup that his wife had made for him, Jim introduced me to Gretchen and told me, “You can spy on her, too!”

 I became further convinced that Jim cares about his lab assistants. Contrary to my preliminary fear that the principal investigator would be an aloof character who worried more about getting published than getting to know his students and workers, Jim was very relational. He talked with his assistants about the upcoming Obama inauguration, he reviewed a graduate student’s doctoral proposal, and he just plain cared. I don’t know why that was a shock, but it was a pleasant shock.

 Jim explained to me a little bit of the grad student’s proposal. The student, named Keenan, was examining the evolution of AMF’s benefit to plants. His main focus was the potential for the relationship to get out of balance. Specifically, he asked if it were possible for the balance of beneficence to not be so balanced, because it would be advantageous for AMF to give less help to its host plant. Why would AMF continue to benefit the plant, he asked, if AMF could simply use resources for its own survival and not help its host so much?

 At that point, Keenan walked in. Jim asked him if he could show me a simulation he was working on that modeled the process he was investigating. Keenan said, “Sure,” and he offered to show me at 4 o’clock that day. During this visit to the lab, though, I was going to follow Liz as she showed some people how to clean & measure plant roots…

1:16

 …but before I did that, she allowed me to follow her up to the greenhouses on the roof of Jordan Hall (technically the fifth floor). She was conducting her own experiment, which involved growing different varieties of sunflowers. Her goal was to determine how weedy plants differed from native plants in their gene expression. She hypothesized that weedy plants would use more energy to activate parts of their genome that stimulate fast plant growth and flower production, and that they would use less energy than native plants would for things like stress tolerance.

 We walked in, and I was immediately met with something I hadn’t experienced for a while during November in Indiana: warmth. It was 86 degrees Fahrenheit in the greenhouse, much higher than the near-freezing temperatures outside. I said it was kinda toasty in here, and Liz agreed. “I bring shorts to work,” she said. “It’s great.

Liz’s plants before… and after flowering.
 

She watered her plants, checked on their growth, and we made our way back to the lab, where we met the students she was slated to help. Jim was in the lab. “Did you see real plants?” he asked. “Yes,” I answered, “real sunflowers.” “Did you have to wash pots?” “No.” “Ooo, count your blessings.” …They were going to put me to work! Well, I guess I’m a full member of the lab now.

1:37

The students arrived, and we took the service elevator to the sixth floor this time (the roof has different levels). We walked into a small room (inside, so we were still warm!), and in the room there was a long sink, a compost can, a regular trashcan, and a floor drain. Liz took the plant she had taken from the lab and showed the students how to clean it so that not a speck of dirt was left on the roots. We returned down the service elevator, and she showed the students a scanner that took a picture of a cut root that she had cleaned. She explained that a program called WinRhizo would analyze the root picture and, based on its structure, predict its future growth.

Liz cleans the root… snips off two threads… and places one thread in the scanner.
 
2:10

 Alas, I could not stay for any longer than an hour and 20 minutes, because I had class to attend. As I was leaving, though, I ran into Sarah, the associate instructor from my biology lab last semester. Turns out, she works in the Reynolds lab, right next to the Bever/Schultz lab, so she is in contact with a lot of people within the two labs. I asked if there was a difference between the lab assistants in each lab, and she said, “The Bever lab has a different kind of weirdo than the Reynolds lab. They’re two subspecies.”

 I could not help chuckling to myself. Not only are lab people personable, but they’re also humorously self-deprecating. Given my own frequent self-deprecation, I could fit in well in such an environment.

4:10

 After I returned from class at 4 o’clock, Keenan showed me his simulation.

 Recap: Keenan is examining the evolution of AMF’s benefit to plants. His main focus is the potential for the relationship to get out of balance. Specifically, he is asking if it were possible for the balance of beneficence to not be so balanced. Why would AMF continue to benefit the plant, he wants to know, if AMF could simply use resources for its own survival and not help its host so much? Why would it not just use what the plant gives it and gives no help in return?

 The beginning of his simulation, which was a computer program that performed what he thought fungi did in response to other fungi, seemed to me like a game of Risk. There were two types of fungi: fungi that benefitted the host plant, and fungi that only benefitted itself through the plant and didn’t give anything in return. The fungi were arranged in a lattice, and in each generation, they would create new offspring in adjacent squares. The amount of offspring they created was based on the index of dispersal (d) that Keenan inputted into the system. What made me think of Risk was when the two types of fungi tried to occupy the same space. In this situation, chance, and the number of offspring that each fungi sent into the square, determined which fungus would “own” the square.

 Keenan’s simulation uses two lattices, one on top of the other, and the interaction between each square in the two lattices determines which fungus showed up in the simulation. What results is a picture similar to the one in the figure below, with blue representing a fungus that both gives to and receives from a plant, and red representing a fungus that only receives from a plant. The blue fungus has a higher d-value and is able to create more offspring in each generation, but the red fungus is able to commit all of its resources to its own benefit without giving some for the benefit of the host plant. Thus, it is better individually for a fungus to be “red,” but in order for the system to be full and have at least some healthy variety, much of the fungus must be “blue.” This results in a prisoner’s dilemma: Does a fungus think of its own benefit and be “red,” or does it think collectively and go “blue?” (“Think” is not supposed to be literal, of course, but you know what I mean.)

 Now, my mind works in metaphors, as one could see by my thought of Risk. This part of the simulation, though, got me thinking about metaphysical conceits, comparisons that are a bit broader or on a higher plane. When I saw this part, my mind went to selfishness in society. Is it possible, I thought, that this is a model of what selfishness can do? Since it is better individually to be “red,” would a world where selfishness spreads like this create an environment that does not use its resources right? Must some people remain “blue” so that the world benefits from its contributions to variety and the health of the system?

 Of course, this was high-minded and metaphorical. Science deals in what can be observed, and this simulation does not demonstrate that universal selfishness is bad for society. It is simply a model for how beneficence develops in a fungal population. Still, one’s mind can wander…

^ A picture of Keenan’s simulation. Blue squares represent fungi that help their host plant, while red squares represent fungi that do not help their host. (They’re pretty much free-loaders.) “Red” fungi have a smaller propensity for reproduction, so there are more empty spaces within the swathes of red than there are within the swaths of blue.
 
5:35

 (written in lab)

 Things are much quieter here now than they were yesterday or at lunch today. I don’t know if that’s just because it’s the end of the day, or because there are fewer people, or because it’s Tuesday. Looking at Wittaya [a graduate student looking at previously undescribed species of AMF] work, though, makes me think of another reason.

 Right now, he’s busy at the microscope. He puts one dish under the lens, looks at it, writes down his observations, removes the dish, and puts another dish under the lens. The whole time, he has earbuds in, listening to music. It brings me back to my biology lab last year, when we were counting yeast colonies on Petri dishes. My AI (the one who works in the Reynolds lab next door) allowed us to bring an mp3 player one time, knowing that we would get bored counting the number of yeast colonies on a plate. While I was counting, I made sure that I counted the same way throughout. I was grouping the colonies (I was too lazy to count each one individually!), and I wanted to make sure I grouped them the same way every time, so I could be sure that I counted them right, or at least that I could reproduce my result or realize my mistake after I was done.

 That desire for constancy and universality is an underpinning of the scientific method. In order for others to verify the results of an experiment that someone performs, the methods must be carried out exactly as they were the first time. When a researcher collects data across samples or time periods, he must collect them the same way each time so that he doesn’t introduce a bias to the results. Everything must be done the same way every time, so that only the results, not any outside influence, come through.

 This is the part of science that’s most tedious. Once the results are in, neurons spark, ideas fly, and scientists talk excitedly about what they mean. As the results are gathered, though, everything must stay the same, with little change and little excitement. Scientists fall into a pattern, and a boring one at that. (At least in my little experience.) Always, though, they must keep their eyes on the prize, because if they gather good data, the results will shine for them like diamonds, and all that tedious work at the microscope and data gathering will be worth it.

 Me, though? I have no lofty scientific goal to achieve by patiently watching Wittaya work. I simply have the goal of showing you, Gentle Reader, how science works, and I’m doing my own data gathering through my observation of Wittaya. I’ll continue to do so as long as I need to. So, let’s return to Wittaya. Let’s watch him write down the characteristics of those fungal colonies, knowing that some discovery lies at the end of this long road of tedium.

Was I cheesy? Yes.
Was I excited about science? YES.
 

I left at 6:30. Wittaya was still there, but he had moved to an office computer, so I couldn’t see him work anymore. Besides, the waiting had become too tedious for even my scientific taste. Part of the problem lay with me, though, because I could have made myself more active in the lab. There wasn’t much to do, though, because it was 6:30.


2008.11.20

1:00 p.m.

I missed lunch hour and all its associated banter, so everyone was busy working. Then Jim and his wife, Peggy, walked into the lab, followed by a student who didn’t work in the lab. She was in Jim’s conservation biology class, and she was asking for help with the questions on an exam study guide. I may have been too fanciful, but this brought home even more the point that Jim cares, and even allows students not in his lab group to walk into the lab and ask questions. His lab seemed like an open atmosphere already, but it seemed even more so with this student.

Jim helps a student study for her exam.
 
1:37

 The lab got into a scientific routine again. The science that was going on around me was palpable, yet below the surface, and I didn’t want to interrupt anyone. Jim was in his office, fulfilling his advisor role by discussing a project with a lab assistant, so I didn’t want to talk to him, either. I looked for an opening…

1:42

 …and I found one. The guy who had opened the door for me on my first day stood up to stretch, and after he sat down, I approached him and asked him about his work.

 His name is Doug, and he is researching a specific species fungus, Trichoderma harzianum. This species of Trichoderma has developed a biocontrol agent that knocks out plant pathogens and bacteria. The fungus secretes the agent when it senses competition in its environment. The agent makes Trichoderma a dominant fungus in most environments it grows in. “It plants itself in the soil,” Doug said, “and says, ‘This is now my kingdom.’”

 It is also used in conjunction with AMF to guard a host plant from harmful bacteria, and it is here that Doug is focusing his research. His question is whether the agent that Trichoderma secretes affects the workings of AMF. If the biocontrol agent, which is potently anti-fungal, affects normal strands of AMF, then it may be more effective for planters to use a less helpful strand of AMF that can survive in the presence of Trichoderma. The less helpful strand of AMF may not help the plant as much as the normal strand, but at least it doesn’t die when exposed to the agent that Trichoderma secretes.

 Nobody is sure exactly how Trichoderma affects AMF, but as I’ve discovered through my time at the lab, most scientists don’t know a lot about fungi in general. For instance, Doug pointed out that fungi do weird things with their DNA. Whereas humans, most plants, and almost every other multicellular organism on earth has the same DNA in every cell, one species of fungus often has more than one strain of DNA. Rather, each fungus has multiple DNA strains spread across its network of tubes, called hyphae.

 Doug also pointed out that fungi do not reproduce in the same cycle as either plants or animals. Most multicellular organisms have parts devoted specifically to reproduction, with those cells differing from other cells in the body by having only one, not two, sets of chromosomes. With fungi, however, there is no such division. Sometimes, the whole fungus seems to switch between cells with one set of chromosomes (haploidy) and cells with two sets (diploidy); in others, the switch between haploidy and diploidy is on a cell-by-cell basis with no overall organization. Sometimes, the same fungus will have different methods of switching between haploidy and diploidy.

 Because of the different DNA strands in a single fungus, and because of the different modes of switching between haploidy and diploidy, it’s always difficult to classify fungi. This brought the discussion to the concept of the verb “to seem.” What is certain in science will more than likely turn into uncertainty, because there is always the chance of finding a counterexample. “You can only spout what you’ve observed,” Doug said. “You can’t state anything as fact.

 Unfortunately, we couldn’t follow this tangent as far as possible, because I had a class to go to.

4:40

Liz was back in the lab when I returned. She was cutting the ends off of sunflower seeds from Kansas so that once they burst open after being exposed to water, she could examine the seed and fungal contaminants within the seed and take pictures of their roots using WinRhizo.

 The conversation turned to things outside of the lab. Liz started working in the Bever/Schultz lab in June, but for three years she has held a night job at Options for Better Living, an organization working with the mentally handicapped. She came to the lab after learning about it from a past associate instructor. “I figured I should do something besides social services,” she said, “if I have a degree in biology.”

 I came to another realization that shouldn’t have been shocking: Lab people are very active in their communities. D’oh!

5:07

 Liz was working on another experiment, and she wanted to make sure the pH levels of her soil matched a previous successful experiment. “Do you want to go on a journey to measure pH levels?” she asked me.

 “You had me at ‘journey,’” I responded, stealing a popular line from Jerry Maguire.

5:15

 My mind returned to Benji’s metaphor from the first day. I asked Liz if she agreed that Jim was the plant and the lab assistants were the AMF. She thought it was interesting, so I asked Wittaya, as well.

 He chuckled a bit, which made me think it actually could fit. Wittaya saw Jim’s role as approximating that of the host plant. “He’s providing essential carbon” in the form of grant money and advising, he said. “He’s benefitting us, and we’re benefitting him.”

 “Can AMF live without a plant host?” I asked. He answered with something really interesting: AMF cannot complete its life cycle without the plant. It can stay in its smaller, energy-efficient state for months or a few years, but because it’s an obligate and needs a host, it cannot fully develop. My mind, metaphor-maker that it is, went wild. Maybe, I thought, the lab assistants need someone like Jim to fully actualize them. Without an advisor and principal investigator, they could not advance along their scientific careers, they could not get published, and they could not contribute to the ongoing scientific dialogue. It’s just like AMF not being able to be its full self without the plant, I thought.

 My brainstorming and my excitement were obvious. As Liz was getting ready to leave, I told her that the life-cycle thing was fascinating. She said to me, “I heard you light up when he said that.”


2008.11.21

2:15 p.m.

 I entered on my last day of observation just as Liz was leaving. We said goodbye, and I sat down at my usual spot, which (fittingly enough) had a copy of The New York Times opened to a story on resurrecting wooly mammoths from their preserved DNA. I immediately thought of the journalistic discussion I had with Benji on the first day, and I thought, Beautiful ending. It’s as if the lab had provided me with a wrap-up for these field notes.

3:05

 (written in lab)

 Only now do I feel like I’m an Animal Planet reporter documenting animals in the wild. (The lab people aren’t animals in the same sense, of course, but I’m going more for the reporter-watching-from-the-sidelines link.) That must mean that I was not observing the lab remotely, or from afar, but rather as an active participant in its activities. The surprising thing (although it probably shouldn’t have been surprising) is that the people in the lab were so welcoming and allowed me to watch them work, to participate, to talk, and to listen. I wish I had gotten to know everyone here [at this point, someone walked in whom I had never seen before], but I’m glad for the opportunity that they all gave me to be among them.

 …Now that I’m done waxing romantic, it’s time to go.

–Alex Farris
]]> http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/field-notes/among-plants-fungi-and-peoplefour-days-with-the-beverschultz-lab/feed/ 0 Conversation with Earle Holland, Ohio State PIO http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/nasw-2008/dealing-with-success-and-controversy-a-qa-with-ohio-states-earle-holland/ http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/nasw-2008/dealing-with-success-and-controversy-a-qa-with-ohio-states-earle-holland/#comments Tue, 11 Nov 2008 02:08:14 +0000 Alex Farris http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/?p=48 As director of research communications at Ohio State University, Earle Holland is the public face of Ohio State’s research programs. Since he took the position in 1990, he has explained the scientific process and publicized the findings of Ohio State’s researchers. He has also done damage control, responding to ethical concerns and explaining why the university has acted the way it has in contentious situations. He has managed the fallout from an animal-rights campaign against a veterinary researcher; a dispute over where to return Native American skeletal remains; and most publicly, a controversy in 2005 involving a doctoral student’s thesis.

The thesis, written by high school science teacher Bryan Leonard, sought to examine high school students’ reactions to being taught “the scientific data both supporting and challenging macroevolution.” The student’s dissertation was postponed because of its research methods and difficulties in forming a committee to review his thesis. The Discovery Institute and other proponents of creationism and intelligent design regarded the delay as infringing on the student’s academic freedom, and major news organizations began to cover the university’s handling of the case.


What went wrong with the university’s handling of the situation?

I think fundamentally, any time you have a situation where a student’s path to a degree becomes controversial or questionable, that’s a negative situation. We’re in the business of helping people earn degrees, be they undergraduate or graduate, so in the first place, the fact that his progress toward a degree was ultimately postponed or halted or did not continue is unfortunate, first and foremost from that standpoint.

The second bit of concern is the fact that this was, if you will, a situation “inside baseball.” In other words, it had to do with university administrative procedure that a student agrees to follow when they are invited or accepted into a graduate program. The process is one that is laid down and agreed to beforehand, and in this case, as the process moved along, there were complications with it in that the student and his advisors decided to postpone that process, and that’s where it stayed, in limbo, for a while.

In your opinion, why did this story get so much publicity compared to other situations that you’ve faced?

As you can figure out, we’re talking about news, and news is not only affected by what it entails, but also the environment in which it appears. In this case, this was right after the Kansas hearings that were deliberating whether or not to incorporate intelligent design teaching into the science curriculum for public schools, and it preceded the Dover test case in Pennsylvania, which was looking at the same general issue. The fact that this dissertation could be linked in some way, or at least it was perceived that it could be linked in some way, to intelligent design raises visibility in that regard.


In hindsight, would you have done anything differently to handle the situation better? Could you have done anything differently?

No, I think we handled this as well as could be expected. We looked after and preserved the student’s rights to privacy relative to this; we tried to convey as much information as we could about the process itself without violating federal law or university regulations; we responded to any and all questions or inquiries related to it, to the extent that we could and to the extent that we were allowed by federal law; and the university procedures that involve all facets of this case came into play and ran their course as they were supposed to.


Have there been any other situations, maybe not as public as this one, but maybe in the same degree of difficulty, that you wish you had handled differently?

In the past year, I can’t think of one. A couple of years back, we had a case where there was a massive national campaign by animal rights activists against a researcher at our vet school who was doing work looking into a certain class of retroviruses, and he was pretty much targeted by all the major national animal rights groups and ultimately decided that the harassment was not worth tolerating, and he left the university, and he left research in general. That lasted about three years, that whole process. We were very active in that. My only regret relative to that was the larger issue of how institutions support their faculty in these types of situations where the faculty finds itself targeted and in the spotlight. I don’t think that was our finest hour. Leadership [in] the institution did not necessarily support that researcher to the level that he probably deserved.


What is a normal day for you?

In truth, a normal day is going to have me dealing with something along these lines, maybe a slightly lesser challenge. I’m dealing with eight of these things right now, and probably half a dozen is more of a normal situation on any given day. At the same time, these are ongoing situations that have to run their course.

The majority of my day is built around being the senior editor for the distribution of stories that report on research findings and advances out of the institution. 95% of the reporting we do is based on peer-review publications, journals, or presentations at national meetings where our researchers are reporting on findings or discoveries or advances. We function the same way as a science journalist would inside the boundaries of the institution and report on those the same way that external journalists would, and then feed those out to journalists, both nationally and internationally.

Part of that process is that simply there’s a lot of discussion with my writing staff as to what they’re going to cover, approval of the research that they’re reporting on, line editing, in the sense of initial drafts of stories, a lot that goes on after stories are approved and source-checked by the investigators. There’s also the mechanical transformation of that copy into Web pages and into other distribution points. There’s a whole lot of the machinery of reporting that fills most of the day.

And then there are days when I will spend a considerable amount of time providing advice and counsel to faculty researchers who either have to explain their work or are dealing with a potential problem, or I will spend time trying to persuade them or explain to them the value of their communicating about their work. A typical day normally falls into each of those categories. I gave three presentations the week before last on science communications, I’m advising a graduate student now on science communications, so it’s pretty much wrapped around the whole bushel basket, but they all were translating science research.


What important skills have you honed in your years in science communications?

Well, certainly the standard editorial skills that one has. Being able to be a very good writer is essential, because you can’t advise other writers, you can’t edit other writers unless you are proficient in doing that. Develop a strong ability as a storyteller, to be able to really distinguish what kind of information [is] the best to share with a listening, reading, [or] viewing audience.

Clearly, you develop a sense of a certain level of deduction that allows you to look at this massive scientific material and the necessary way that scientific papers or presentations are given, and be able to pull from that the elements that are necessary to make it useful for journalists. I’ve certainly been able to do that. And I think, to a certain extent, having done this now for more than 35 years, you learn how to be a good mentor and teach and help younger science writers develop in their own ability.


You started out as a police reporter at The Birmingham News. Why did you switch to science communications?

I grew up in a newspaper family. My father was the editorial page editor of The Birmingham News for 25 years, including the civil rights era. We lived in Alabama, in Birmingham, the seat of conflict in that portion of the nation’s history. I had no interest in journalism whatsoever at that point in time and wanted to be a chemical engineer, went to college for that. I had a 35 [on the] ACT in natural sciences and a 17 in math, so my aspirations for being an organic chemist were pretty much dashed after several quarters in college.

Ultimately, I switched majors from chemistry over to journalism. I connected with a number of people who served a strong mentor role for me and opened a couple of doors. This was after my father had long since died, so it was not a case of a father letting his son into the newspaper business; on the contrary, he was gone by the time I had even switched majors.

That was a time in newspaper journalism where you started as a beginning reporter and would work through the beats. It was pretty standard for young reporters to be drawn onto the police beat because there was there was a lot of activity, there was a lot of excitement, and it was a very, very rapid way to learn newspaper journalism. So I did that for a number of years, and I was a general assignment reporter, as well, and then left the newspaper and went back to finish up my degree in journalism.

From that point on, after I graduated from college, I stayed at Auburn University working in a public information role in the College of Engineering. That exposure to engineering over five years whetted my appetite for talking about technology, talking about science and the like. I learned pretty much on the job the difference between standard beat reporting, like police reporting and general assignment reporting, and the specificity of science writing. I transitioned into that, stayed with that university for five years, and then moved up here to Ohio State, and that’s where I’ve been ever since.


What are some “best practices” that one should develop before entering the field of science communications?

I think, fundamentally, that young writers, and especially those who are in college, I think that one of the best things I advise people to do is take as many introduction-to-science courses as you can get. The intro courses to geology, intro to chemistry—well, chemistry and physics are usually required—but to broaden that as much as possible, take as many introductory courses into the sciences, so at least people have a passing knowledge of what that academic discipline is about, so when they come back later on to try to report on it they understand. Science writers have to report on research in botany and biology and chemistry, physics, astronomy, cosmology, geology, and all sorts of –ologies, and if you don’t know anything about them on a general basis, then it’s going to be very hard to report on the research that’s coming out.

So, first and foremost, I think potential writers need to spend as much time with those introductory courses as they can to acclimatize. The parallel I draw is, if you were going to be a foreign correspondent for a major national news outlet, you certainly would have spent the time to learn the language and learn something about the culture if you’re going to function in that vein. The same applies with science writing.
–Alex Farris

OSU Research Web site: http://researchnews.osu.edu/
Earle Holland’s Resume: http://www.nasw.org/users/emhollan/cv.htm
For more information regarding Bryan Leonard’s thesis process, visit http://www.insidehighered.com/news/2005/06/10/osu

]]> http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/nasw-2008/dealing-with-success-and-controversy-a-qa-with-ohio-states-earle-holland/feed/ 0 Session 3D: Why Good Reporters and Institutions Get It Wrong http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/nasw-2008/session-3d-why-good-reporters-and-institutions-get-it-wrong/ http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/nasw-2008/session-3d-why-good-reporters-and-institutions-get-it-wrong/#comments Sat, 25 Oct 2008 19:15:06 +0000 Alex Farris http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/?p=31
But when I walked into the third session, “Why Good Reporters and Institutions Get It Wrong,” I saw only one panelist and one moderator up front. This is not going to be the same, I thought, They’re going to talk, and I’m going to be put to sleep. How many different opinions can come from two public information officers? It turns out that I was thinking one-dimensionally. I neglected to realize that the audience might have something to say.  And boy, did they!

Alex Farris
Ohio State’s Earle Holland
The public information officers (PIOs) did a good job of presenting specific “crisis situations” that they had dealt with at their respective universities, but members of the audience were incisive — and relentless — in their questions. Most significantly, there was a long back-and-forth between Ohio State University’s Earle Holland and the audience over his institution’s handling of a recent doctoral defense dispute involving intelligent design.


The Intelligent Design Incident

A doctoral student (who doubled as a high school teacher) was preparing a defense of his thesis regarding changes in student attitudes as they “are taught the scientific data both supporting and challenging macro-evolution.” One member of the committee for the doctoral defense removed herself after seeing the thesis question and noticing an underlying bias toward intelligent design.  The three other members took issue with the candidate’s use of his own high school students as subjects and asserted that there was no scientific data “challenging macro-evolution.” The defense was postponed due to the first issue, and an inquiry was initiated to examine the second.

The combination brought about condemnation from the Discovery Institute and other proponents of intelligent design, who claimed that the university was, in Holland’s words, “standing in the way of this student’s academic freedom and freedom of expression.” The university couldn’t defend itself as much as it wanted to, Holland said, because of government regulations that prevented it from disclosing much of their students’ records.

Was It Really About Intelligent Design?

What the university could talk about, however, was the doctoral process, which Holland wanted reporters covering the issue to see. If they had dug deeper than the press releases from the Discovery Institute, he said, they would have seen that there were multiple problems with the doctoral committee. For example, two of the set of three members were supposed to come from the department of science education; however, none of the three came from that department, and any challenges to the thesis coming from such a panel would be less substantial than if two science educators had sat on the committee. Also, the committee chair had been sanctioned twice and banned from work with human subjects. According to Holland, no journalists asked to see the faculty members’ records when they were unable to examine the student’s records.

Alex Farris
An audience member asks Holland a question.
The journalists in attendance, while not livid, were certainly animated about what they perceived as Holland’s poor handling of the situation, especially regarding the faculty members’ records. They contended that Holland should have led the journalists to those records directly so that he could help them know what they needed to know.

Holland responded with a point I had not thought of but which was really quite logical: “If you’re not a good enough reporter to understand that you better damn well know what the beat is that you’re covering and the system, then I feel no obligation to tell you which questions there are to ask.” He was willing to answer any question that came up, but he didn’t feel that he should do the reporters’ jobs and provide them with good questions.

My Reaction

To me, this showed the constant and near-universal tension between journalists and PR representatives. On the one hand, public information officers must provide the public with full information regarding any critical situation; on the other hand, journalists must push to find that information and not rely on people who don’t have that investigative call in their job description.
–Alex Farris


For more information about the doctoral dispute, please read Inside HigherEd’s analysis.

Question: Whose side (PR or journalism) do you identify with more? In general?  In this particular case? 

***
Extra!
As I’ve learned through attending this meeting, scientists are people. They do not just do far-off research removed from any social contact. They have human passions, they make human mistakes, and they develop human loyalties.

The last one showed itself most explicitly in this session.

Earle Holland works at Ohio State University; A’ndrea Elyse Messer works at Penn State. That wouldn’t normally be a problem, except that this day, Ohio State was playing Penn State in football. Holland began the discussion with a tongue-in-cheek declaration that there will be no talk of football; A’ndrea playfully objected.

Quick question: Whom do you like better, Ohio State or Penn State? Try to focus on their academics and research, but if you absolutely can’t, go ahead — talk football.

–Alex Farris
]]> http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/nasw-2008/session-3d-why-good-reporters-and-institutions-get-it-wrong/feed/ 0 Friday, 6:42 am: City lights on black http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/nasw-2008/city-on-black/ http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/nasw-2008/city-on-black/#comments Fri, 24 Oct 2008 10:42:50 +0000 Alex Farris http://journalism.indiana.edu/classwork/j460_science_writing_fall2008/?p=49
So imagine my surprise when I, a guy who has never flown in the dark and never out west, wake up at 6:42 Mountain Time and see in my window a sea of darkness, bordered on top by an incomplete rainbow of orange, yellow, and blue. In that sea of darkness, I see the most dots of light arranged in a grid I have ever seen. As of right now, I can’t be sure what city we flew over, but the sight was so spectacular as to have belonged at the end of Field of Dreams. Alas, my camera was in the overhead compartment, so unless I wanted to be really rude and wake up the two people next to me (the perils of the window seat…), I had to be content with capturing the awe-inspiring scene on my cell phone.

Unfortunately, Gentle Reader, you will have to content yourself with pixilated dots on a sea of darkness. Despite its obvious deficiencies, I think the photo conveys enough of the splendor.
–Alex Farris
Alex Farris
I don’t know what city this is, but it’s beautiful.
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