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Andrew Gelman's advice on writing research articles

As they say here in NZ, good as gold.
 

Advice on writing research articles

From a few years ago:

Both the papers sent to me appear to have strong research results. Now that the research has been done, I’d recommend rewriting both articles from scratch, using the following template:

1. Start with the conclusions. Write a couple pages on what you’ve found and what you recommend. In writing these conclusions, you should also be writing some of the introduction, in that you’ll need to give enough background so that general readers can understand what you’re talking about and why they should care. But you want to start with the conclusions, because that will determine what sort of background information you’ll need to give.

2. Now step back. What is the principal evidence for your conclusions? Make some graphs and pull out some key numbers that represent your research findings which back up your claims.

3. Back one more step, now. What are the methods and data you used to obtain your research findings.

4. Now go back and write the literature review and the introduction.

5. Moving forward one last time: go to your results and conclusions and give alternative explanations. Why might you be wrong? What are the limits of applicability of your findings? What future research would be appropriate to follow up on these loose ends?

6. Write the abstract. An easy way to start is to take the first sentence from each of the first five paragraphs of the article. This probably won’t be quite right, but I bet it will be close to what you need.

7. Give the article to a friend, ask him or her to spend 15 minutes looking at it, then ask what they think your message was, and what evidence you have for it. Your friend should read the article as a potential consumer, not as a critic. You can find typos on your own time, but you need somebody else’s eyes to get a sense of the message you’re sending.

Also,
(a) Don’t write something unless you expect people to read it.
(b) This principle holds for tables and figures as well.

More at the above link.


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Here are my thoughts about using Prezi for Teaching a Class

Using Prezi for Classroom Teaching

I usually teach using powerpoint or the whiteboard. Today for a change I started using Prezi an online presentation creation and demonstration tool. I downloaded the presentation after creation to my notebook computer for presentation but this was not necessary. Prezi is a different implementation of a show and tell environment and I will be using this more frequently in my presentations.

In a sense, Prezi is more like a dynamic poster presentation than a presentation software that runs linearly through the slides. It is a flash based and browser dependent application, so that it can be shown nearly everywhere, and no additional hardware needs to be installed. In that sense, a prezi presentation is quite a nice and hassle free application; besides it is possible to embed images, videos, audio clips (I think through the sound bytes), and of course texts and images that then become dynamic entities that gain focus.

It takes a while to get used to create presentations in Prezi. Basically you need to start with an outline, and I found that you cannot think while you work on Prezi. Think about your presentation beforehand, lay it out on a mind map (which is what I usually do for any writing), then either transfer that mind map as it is on a word processor or text document (use textedit/textwrangler on mac or any other word processor/text processor on other platforms) and then work from there, i.e., copy and paste or write on the prezi template.

Basically the way it works is this:

  1. You develop the idea of the presentation first
  2. Populate Prezi using word boxes, add pictures, add voice or other files, video, etc
  3. Link the “units” using a path selector

The combination of your own boxes/text/image/multimedia and paths creates a unique pathway based or learning pathway based implementation of what you want to show and when. On screen the elements will keep on being exhibited according to the magnification you want them (in turn depending on what you want to highlight). You can highlight individual words or phrases, and you can play on them. Or you can dynamically link individual elements within picture units. They are not “slides”, as nothing really slides anywhere but display units glide around and it creates quite a unique effect. I am not sure how learners may interact (coming to it).

The first couple of times I tried to use the Prezi templates that were prebuilt, it did not work. First of all, the templates were somewhat complicated for me to use for a first timer, and second, it was a pain to identify and select the path. Second, understanding this path structure is quite complex. It seems that it is suited to edit and modify paths after creation, but it was quite difficult to do this in the first shot. So I ended up adding to the path component after every two to three element creation. There is a panel that will let you reorder your panels to show.

Did I like it? I think I did. It has almost all the interactivity and elements of powerpoint, but the paradigm is different. It is more of a dynamic story telling. You got to have a story first and then build the elements around the story. Some people may not like the way the screen rotates and refreshes (may make people dizzy). One of my students got confused in setting up the iPad in the middle of the presentation as it asked her to log in. She just downloaded the app on her iPad without registration. These need to be fixed.

Overall, good tool to work with. I quite like it. Need to figure out some more productive ways to use it.

Filed under  //   presentation   teaching  
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Guy Kawasaki writes a great manual on Google Plus titled, "What the Plus!"

Just finished reading +Guy Kawasaki ’s latest book on Google plus, “What the Plus!”

I tend to keep a manual at hand. To that extent, it’s a much needed manual for Google+, and I guess there’s something to learn from this book for everyone. Besides, the book is very readable. Easy, fast, sharp.Some lessons I got out of the book from my first read:

  1. Participate, and take it for a spin (aim for like five posts a day). Get a good profile (he suggests what features to consider for mugshots like forehead and chin)
  2. Write often, write clearly, must embed figures and links in your post.
  3. Comment on other people’s posts and provide helpful advice, and remain positive.
  4. He cites several ways to find meaningful posts and people including using google’s social search (I leave you to read the book to find out what they are, nitfy tricks like “circles shared with me” in the search boxes)
  5. When writing long posts, break up and use bullet points.

I think he could have expanded on the hangout section. Perhaps more will come in the next iterations. There are also other tricks and shortcuts that he could have listed (he has listed several shortcuts). A nifty feature in this book is how he has described features in Google plus that stack up with Twitter and Facebook.

I know google+ keeps on changing all the time. Social web is powerful, and I feel that at least I need a strategy to negotiate with the plethora of information. Lately (and quite significantly), we had quite a few books coming out, one of the best to my mind is +Clay Johnson ’s book “Information Diet” (I think it’s really well written, another must read for anyone interested in information management).

Some people complain about sparseness of Google+ interactions, perhaps it is, but it’s a different ecosystem that needs some handholding (which this book does eminently). But it’s also true that it’s largely built around what we are interested in and how to find and interact with contents, much more than intereacting with people in our immediate social networks.

It’d be good to have some insights in these processes, but I guess this was not the book’s purpose. As Guy writes in this book, that fine grained differentiation between perspective (twitter), people (facebook), and passions (google+) is important. I quite liked this typology. There are overlaps on all three, but this is perhaps as good a way to think about what people do on social media as it gets.

Overall, good job, +Guy Kawasaki .

(This was also posted on my google+ here: https://plus.google.com/117270655453846612117/posts/b5RzAamnKoL)

Filed under  //   book review  
Posted by Arin Basu 

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Watch this moving video on the ethical dilemma of robotics

Quantic dream's KARA is a very moving video on the ethical dilemma of
the robotics. Surreal and but it moves you in the end where they are
going to disassemble the robot because "it/she" wants to "live":

https://plus.google.com/109602109099036550366/posts/ZmTM6FQSPSU

Disturbing.

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Converting a PDF to a readable format on small devices

It's a pain to convert a pdf to an epub for reading and optimizing on
a tablet device, and unfortunately there are no reliable programs that
can get the work done. Note the steps:

1. First of all, the pdf has to be truncated to remove white spaces.
Fortunately, there are programs such as briss that helps to get the
job done. Nothing else quite works.
2. Next, use Calibre to convert the pdf to ePub format
3. Edit the epub in sigil because in 99 out of 100 cases calibre does
a sloppy job in the conversion process.
4. Finally, reconvert it back to mobi fomat
5. Upload to the device for reading decently.

Who cares? Way too much work.

Much better to plug in iPad and use iannotate to read the damn pdf.

I am quite disappointed with amazon kindle touch.

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Why Brainstorming Doesn’t Really Work according to this "New Yorker" article

It's a longish reading, but well worth it. It essentially pulls up examples from other research studies and claims that the two basic tenets of brain storming "freewheeling" and uncritical acceptance of all ideas to solve problems or come up with creative ideas may not be the best after all, and that, solo thinkers produce more ideas which can then be pooled, OR, groups of people who debate and criticize ideas often come up with a range of ideas and diverse creative solutions more often. 

Possible. But ideas and nature of the demand on creative outcrop of ideas change with time. 

http://www.newyorker.com/reporting/2012/01/30/120130fa_fact_lehrer

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Excellent info graphic, I think, on the dangers of Fracking

Posted by Arin Basu 

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NIcholas Carr writes on Facebook and Saint Zuck

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How scheduling a writing time and gathering a group who write together can work wonder for your writing habits

Heather Whitney wrote about her experience in following Silvia's book on productive academic writing and describes what she did on streamlining her time and writing management. I think there are some interesting lessons for many of us who find writing and reading stuff as part of our daily routine. For me, most mornings are spent in reading my blog feeds and planning writing. 

<--- Here's the post in full. There are some lessons here for us to follow ---

ProfHacker 3/02/12 2:00 AM Heather M. Whitney Productivity Profession gtd productivity science

In a previous post, I described how reading How to Write a Lot: A Practical Guide to Productive Academic Writing proved to be beneficial to me, a fairly skeptical scientist, in increasing my writing productivity. (A brief summary of my post: the book recommends scheduling writing time and participating in a writing group. Do it. It works.)

I also alluded to the fact that reading the book has boosted my productivity in other ways, which I’ll now describe in this post. But first, a disclaimer. I’m a science faculty member at a small liberal arts college, and I work solely with undergraduate students. My semesters are primarily focused on teaching (which can include classroom and instructional lab time) and mentoring, with some institutional service thrown in. Research theoretically is partitioned to the summer, but in my world (doing experimental nuclear magnetic resonance research without postdocs or grad students, a fact which makes others in the field blanch upon hearing) I have to fit research in the school year to ensure productive summer work. I mention all this to note that what I’m about to write about may not work for everyone, because the description “professor” can have an amazing number of variations. But it is my hope that the methods that have worked for me, a scientist for whom the typical advice about “getting things done in academia” has always seemed to not relate, might in some way help ProfHacker readers who are in a similar scenario.

Back to the topic of my post: how scheduling writing led me to change up how I schedule my work in its entirety. You see, before I began scheduling writing I filled in my calendar according to other people’s claims on my time: classes, meetings, office hours. That left me with misleadingly wide open “slots” in which I could theoretically get everything else done: prep for each class period, prep for meetings, do the tasks that resulted from meetings, follow up on questions that came up in office hours, read, do the aforementioned writing (which I now realized for me was not just journal article writing but essays, grant proposals, grant activity reports, abstracts, and more), planning the writing, answering email, acquiring data, evaluating the data, etc. You get the picture.

Overall, I had previously felt that I was a fairly productive person. I was getting a lot done, but I had periods, especially on the weekends, in which I felt panicky and could not rest because I sensed that there were work-related items that I should have been doing. After reading How to Write a Lot, I realized that my change in thinking about writing — purposefully scheduling it so that it has a dedicated place in your schedule, and protecting that time — could (and really, should) apply to everything else I need to get done.

So several weeks ago I began sitting down on Friday afternoons and carefully evaluating my schedule for the week to come. At the beginning of the semester, when I put in recurring events for standing class, meeting, and office hour times, I also put in recurring slots for reading, writing, research efforts, and class prep/grading. I review those on Fridays to remind myself that in the coming week, those activities deserve the time allotted. I also review my tasks list, which I maintain in Remember the Milk (RTM), to see what tasks I’ve specifically tagged according to the standing time slots. For example, each week I have to look at the lab we will do with students the following week, make sure we have all the items, make edits to the lab as necessary, and then upload it to Blackboard for students to access; all of these items are recurring tasks in RTM, tagged for the time slot “intro lab administration.” Sometimes I’ll need to enter newly ordered items into our lab database, or fix a piece of equipment. That to-do will be tagged for lab and I’ll know to attend to it in my scheduled intro lab administration slot the next time it comes up. Next, I look at other more general to-do’s that have made their way into RTM and fill in time slots in which I will attend to other miscellaneous responsibilities that don’t happen regularly, such as arranging for clicker use in a faculty inservice day. After this weekly review period, I know I’ve set myself up for spending enough time on all the things I need to do in the coming week, and don’t have to worry that I’m somehow misappropriating my time.

There’s still room for flexibility, an absolute must, with this system. For example, when meetings get scheduled out far in advance they go into the calendar, and then when I do my weekly review I know to work around them as they come up. But the value is that I definitely know I’ve got to work around them and make up for the lost time somewhere. There’s a lot less ambiguity and overestimation of available time in the future. And at the same time, I am less likely to schedule meetings that interfere with my reading, writing, and research time and displace them in the first place.

I’ve been amazed at how this change in thinking has improved my semester thus far. I believe that previously I had a false sense of how much time was available to do everything that is a part of work. I do now have some Friday afternoon moments in which I’m gasping in awe at the sheer volume of things to get done the next week and how little time there is to do them. But now I feel more sure that I’m doing the best that I can with the 24 hours in a day I have. I also feel more motivated to continue to seek out ways to make my work and home life more efficient, to really and truly rest when I am able, to be honest when someone asks me to take on something that is outside of my work and life priorities, and to encourage students to protect their time as well.

Maybe you’re thinking, “she just needlessly reinvented the wheel.” If you already have found a similar process to work for you, then congratulations! But I felt compelled to write about this at ProfHacker because so much of the hacker-type advice seems to be written by those not in the sciences, and I have felt that advice hasn’t related to me. I’ve always thought to myself that those who write about hacking the academy don’t have to set up demos before class and then take them down afterwards, grade quantitative problem sets for both accuracy and appropriateness of solution strategy, make time-sensitive samples that will degrade if you don’t image them soon enough, get a stubborn machine to work, create data before you can even begin to think to write about it, and thus what they’ve suggested (which often is read by me as “just write” or some other oversimplification)  doesn’t translate to my work. The few resources that are available for improving productivity in science are often produced by those with administrative help or course releases that allow them to protect their time, which doesn’t relate to me either. So if you’re in this boat with me, this post is for you. Even though “just schedule writing time” may not be directly applicable, there’s a principle there of protecting your time and giving it the attention it deserves that is helpful. I offer this perspective as a possible way to rethink getting things done in the sciences, especially in the small liberal arts college setting.

...>

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How Can Asians Eat So Much Rice and Not Gain Weight? Because they exercise a lot and rice is not the only thing ...

So writes Mark Sisson in his blog: "daily apple". 
I think Mark got a point here. Where he writes that it's just not rice per se, but a combination of rice, regular aerobic exercise like slow walking at a constant pace for long time, and other adjunct highly nutritious food items consumed as well relates to their rice "binge" but not getting fat. I think though that the food patterns are changing and it's getting closer to the Western dietary patterns, at least that's what I get to see in what flies out of the supermarket shelves off Calcutta (Bengalees are the other group in India who are great rice eaters).

Thoughts?

Here's the full story for you:

Mark's Daily Apple 2/02/12 5:00 AM Mark Sisson Carbs Diet Health Low Level Aerobic Activity Nutrition

How the Primal community loves the concept of a dietary paradox. How we eagerly point to its various manifestations as supportive evidence for our way of eating, living, and moving. You know the French Paradox and how it confounds the experts. To mention all those smug surrender monkeys with their brie and their butter and their duck confit and their Gauloises and their seeming imperviousness to heart attacks is to make Dean Ornish binge on bran and pull out tuft after tuft of frizzy hair. And then there’s the lesser-known Israeli Paradox, which attempts to answer why Israelis have skyrocketing rates of heart disease despite a skyrocketing intake of “healthy” omega-6 fatty acids. In its wake, Walter Willet might be found weeping into a mug of safflower oil. There’s even an American Paradox – those who ate the most saturated fat had the least coronary heart disease – that had the minds of researchers thoroughly boggled.

All those paradoxes work out in “our favor.” Saturated fat gets off pretty much scot-free and omega-6 vegetable oils get raked over the coals (and, presumably, oxidized). And if people were honest about things, they would see these paradoxes not as paradoxes, but as reasons to reevaluate previously-held beliefs about health and diet.

But what about the Asian Paradox? How can Asian countries consume so much white rice and so many noodles and remain so thin? If carbs make you fat, how do they eat so many of them? This is a question I get from Mark’s Daily Apple readers all of the time, so it’s about time I gave a thorough response.

First of all, I want to confirm that Asia eats a lot of rice. It may be a “side dish” or not the main course, but there’s no dancing around the fact that a lot of rice gets eaten – the stats (PDF) are pretty clear on Asian rice consumption. I briefly covered the Asian Paradox in the rice post, but I think the subject deserves more than a brief paragraph. So, today, I’m going to explain why the Asian Paradox (like all “paradoxes,” really) isn’t actually a paradox, and why I consider it to happily coexist with all of the other Primal-friendly paradoxes. I’ll also explain why I think the Asian Paradox offers us Primals a chance to evaluate our own beliefs (because that’s the only honest thing to do).

They Move(d) Frequenty at a Slow Pace

Whenever I’m in a large city with a sizable Asian immigrant population, I notice a different approach to walking. For instance, Carrie and I were recently visiting San Francisco’s Golden Gate Park. We spent the day just walking around and getting sort of lost, and we both noticed the difference. Of all the multitudes of people walking, jogging, and otherwise being active, everyone but the older Asian folks seemed to be actively exercising. Exercising on purpose. Trying to “burn calories” or “improve VO2 max.” We noticed as a young mother with strollered child powerwalked down the path, wearing compression tights, a baseball cap, and the latest running shoes, while the elderly Chinese grandma she passed wore some keds and a knit sweater. Two seemingly identical joggers (one in Vibrams!) with Bluetooth earpieces jabbed at each other with business-speak opposite a pair of old friends strolling along and loudly speaking (in another language) of politics and times long past (again, it was another language) in well-worn suits and loafers. A group of cyclists could have passed for pros with all their gear and advertisements and special cycling shoes, while an older Asian gentleman wearing a collared shirt and slacks cruised by on a simple ten-speed. I got the distinct impression that walking or cycling or just getting around using your own limbs as the vehicles was simply a way to get from here to there for the older Asian folks. It wasn’t a special occasion. It was an everyday occurrence. It was normal. For everyone else, it was exercise. It was a big event that you had to get geared up and spend money for. Exercise is great, and walking with intent of getting healthier is great – I do it all the time. But my observations speak to a huge cultural difference between the way older Asian folks who immigrated over (and, presumably, the cultures back at home) and Americans treat moving frequently at a slow pace.

People living in Asian countries have historically been more active than people living in the States. It’s not that they’re all lifting weights and running sprints and joining gyms; it’s that their average daily activity levels are higher. And as everyone here probably already knows, the simple act of walking on a regular basis does wonders for one’s health. Daily walking is consistently associated with (among other health benefits) improved insulin sensitivity (better tolerance of carbohydrates like white rice), better moodlowered blood pressure and triglycerides, and greater longevity. America is a car country, and has been for about a hundred years. We don’t – and haven’t for over 50 years – have to walk to get around. Heck, oftentimes we can’t walk to get where we want to go even if we wanted to walk, since many of us live in a kind of suburban sprawl that requires the use of cars just to buy groceries or take the kids to school. The result is a country that takes fewer steps per day than the rest of the world. As Asians start buying more cars, relying more on vehicular transportation, and moving further away from labor-intensive work, I suspect you’ll see more carbohydrate intolerance, fat gain, and general ill health begin to emerge. It’s already happening, as you’ll see.

I think daily activity levels are probably the biggest determinant in tolerance to carbs. In American cities where walking is required or more convenient than driving, like New York, people are generally healthier, slimmer, and longer-lived. Things are changing, though. In 1989, 65% of Chinese performed heavy labor on a daily basis. By 2000, that proportion had dropped to 50% – still far more than in Western nations, but the downward trend is clear. You’ll notice on that same page that the proportion of overweight children also increased by the year 2000.

An Otherwise Unprocessed, Nutritious Diet

Traditional Asian food is highly nutritious. Go to a Vietnamese noodle house and the signature dish is pho, a big bowl of homemade beef marrow bone broth, tripe, tendons, brisket, and rice noodles. Go to a real Thai restaurant and get bone broth soup with cubes of pork blood, greens, rice noodles, and a duck egg. Go to a Chinese restaurant and get sauteed (alas, in soybean or corn oil these days) pork kidneys with Chinese broccoli and rice on the side. Go to a Japanese restaurant and get wild caught salmon eggs rolled with seaweed and rice, mackerel sashimi, and some fermented miso soup with kelp strips. Go to Korean barbecue and eat a dozen different kinds of kimchi, grilled short ribs, beef tongue, and liver all wrapped in lettuce, with rice on the side. In all these foods, rice is present, but so are real bone broth, fresh meat, fermented cabbage, offal, and vegetables. The presence of rice does not invalidate or negate the presence of every other nutrient.

Of course, that’s restaurant food. If you want to get an idea of how Asian folks cook at home, go to their supermarkets and note what people are buying. It’s not as fancy or flavorful, but it’s just as nutritious. Stand by the register and you’ll see twenty kinds of whole fish; live oysters, mussels, clams, crabs, snails, and sea urchins; a http://www.marksdailyapple.com/tails-tendons-and-tripe-a-guide-to-discovering...">pig’s entire digestive tract; buckets of chicken feet; bags full of strange leafy green things and exotic vegetables like bitter melon; all sorts of herbs, roots, and teas; fermented, pickled foods; a dozen different kinds of http://www.marksdailyapple.com/difference-yams-sweet-potatoes/#ixzz1l5OaJqzD">root vegetable; and yes, rice. If you want to isolate the rice from that list of nutrient-dense offerings and say “What about that?” be my guest, but not me. I’ll be admiring the handsome beef foot oozing collagen and marrow and imagining all the wonderful dishes it could make (while I mentally compare the contents of shopping carts in Asian markets to the contents of shopping carts in standard American grocery stores… guess who wins).

Before recently, Asians ate less refined sugar and used animal fats for cooking. Sugar intake is rising now, of course, and cooking oils made from corn and soybean have largely replaced lard and tallow, but rice in the context of a low-sugar, no-HFCS (remember, the oft-cited 55/45 fructose/glucose breakdown for HFCS is highly misleading and actually quite often incorrect), low-vegetable oil, nose-to-tail nutrient-dense diet is (or was) acceptable. You can’t reduce a food down to its constituent parts and focus on, say, the bit of fructose in a blueberry and then condemn the entire berry because of it. Similarly, you can’t reduce a diet down to a single constituent food and condemn – or praise – it based on that single food. You have to look at the entire picture, and the Asian diet is largely a nutritious one.

More Rice, Less Wheat

Thanks to regular monsoons, 90% of the world’s rice production is located in Asia. It’s been cultivated in the region for close to 10,000 years, so the region’s occupants tend to eat a fair amount of the stuff.

Luckily for them, rice, especially white rice (the favored type across most of Asia; as a Thai friend of mine who grew up there and came to Hollywood in the 60s told me, “rice bran was for the chickens”), is a mostly non-toxic source of glucose. On the grain spectrum, where wheat and other gluten grains reside at one end, rice relaxes at the opposite end. It’s not “good,” but it’s also not “bad.” It just is. It’s pretty much neutral. Whether you can handle (or need) the glucose load is another thing, but you can rest assured that white rice will be generally free of gut irritants, phytic acid, and deleterious lectins. If you’re eating wheat, on the other hand, you have gluten, wheat germ agglutinin, and a host of other antinutrients with which to contend. And, as Ned Kock’s masterful (and under-appreciated) series of stats posts on the China study data suggests, rice intake is associated with a reduction in cardiovascular disease while wheat flour intake is associated with an increase in cardiovascular disease. The upper level of rice intake did correlate with a slight increase in CHD, however, but not a major one.

All else being equal, people will be healthier on a rice-heavy junk food diet than on a wheat-heavy junk food diet.

Is Asia Even All That Healthier Anymore?

Healthy, long-lived Asia isn’t so healthy and long-lived. Both China and India are facing diabetes epidemics. In Taiwan, KoreaVietnam, and Thailand, diabetes is also increasing. The perfect storm – of sedentary living, processed junk food full of carbs and bad fats, and poor sleep – that has ravaged America and other industrialized nations for almost a century and led to a host of debilitating illnesses is beginning to descend upon Asia. Cooking oils have displaced traditional animal fats and sugar intake is rising. People walk less and eat more wheat.

Even the low BMIs of Asian countries are misleading. At equal BMIs, Asians generally have more body fat than other groups (PDF). So, on average, the American or the Pacific Islander with a BMI of 25 has less body fat than the Chinese guy with a BMI of 25. It’s not clear whether these higher body fat levels (at lower BMIs) correspond to increased risks for certain diseases, but it does suggest that BMI is an unreliable barometer for a country’s leanness on a particular diet. You can be skinny-fat with a low BMI – and it appears that significant numbers of Asians with low BMIs fit that profile.

So, like every other one before it, the Asian Paradox topples: there is actually no paradox. Asian countries remain lean (if they’re actually lean, that is) on a rice-heavy diet by virtue of lots of low-level aerobic activity to promote insulin sensitivity, lots of nutrient-dense food to go with that rice, and because rice is the least offensive grain.

Any questions? Fire away!

Posted by Arin Basu 

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