Walkabout Wednesday: doublethink, and starving cancer cells.

My Health

Dr. Malcolm McKendrick always writes great posts, and this one is no exception. He uses some great Orwell quotes to highlight some shenanigans about public data from the European Heart Study. Between 2008 and 2012 they dropped a table showing the relationship between saturated fat intake and per capita deaths due to coronary heart disease. Guess what? The data don't support the orthodoxy.

Understanding the deep evolutionary origins of cancer might help us treat it. The idea is that prior to being multi-cellular, immortality and vigorous cell proliferation were survival traits. Environmental stresses then put cells back into "survival mode", forgetting their evolved functions.

So the team predicts that treating patients with high levels of oxygen and reducing sugar in their diet, to lower acidity, will strain the cancer and cause tumors to shrink.

The fact that they implicate sugar there is interesting, as I also came across another study that found starving breast cancer cells of sugar reverses the phenotype of cancerous cells back to non-cancerous cells. And remember that all carbohydrates in your diet ultimately end up as sugar in your bloodstream.

And as long as I'm thinking about cancer cells, soy protein changes gene expression in breast cells in vivo, and those changes relate to cancer growth rates. This study isn't completely conclusive though, because they did the experiment 7 - 30 days before removing the tumors surgically. As a result we don't know if gene expression changes would in fact have changed tumor growth.

And more on cancer! A large, randomized diet intervention in post-menopausal women found no effect of a low fat diet (< 20% kcal from fat) on risk of breast or colon cancer. 

I'm a fan of breastfeeding babies, and if you need more evidence it is a good thing, here you go. Breastfed babies have lower levels of chronic inflammation as adults.

Your Education

Over the last 2 years or so enrollments in the Fisheries and Wildlife major at UNL have fallen after more than a decade of strong growth. Turns out that reflects a broader trend, and it's at least a symptom of a good thing. For someone. Not us. (ht: Dynamic Ecology)

It's pretty common for professors to share course content around with colleagues. I benefited from course notes and lectures from Helen Regan when I started at UNL. But this article raises a different spectre; taking someone else's hard work on course development and using it without asking them. Made even easier by the widespread use of online course management software. (ht: John Janovy)

A long time ago, in a country far, far away, a University President wrote an op-ed piece bemoaning the surfeit of post-graduate students his faculty were writing into grant proposals. My response, which was actually published, was that it's obvious dude, they are cheap (below the poverty line), highly motivated (willing to work 60 hours a week motivated) and well trained workers. In an environment where funding for public  R&D gets tight, permanent research tech jobs get replaced with postgraduate stipends. Never mind that there's no work for them once they get their shiny PhDs. Now it appears the same perverse incentives are starting to bite here in the USA, with this piece in the Boston Globe highlighting a "glut of postdoc researchers". This quote says it all:

The problem is that any researcher running a lab today is training far more people than there will ever be labs to run. Often these supremely well-educated trainees are simply cheap laborers, not learning skills for the careers where they are more likely to find jobs — teaching, industry, government or nonprofit jobs, or consulting.

Yup. Unfortunately throwing money at this isn't the solution either; a fundamental rethink of how we train researchers and finance public R & D is needed. I guess they could always work as adjuncts, 'cuz that's such a satisfying career. (ht: Natalie West)

Our Environment

Emily Nicholson and Ben Collen have a piece in Science on measuring progress on Biodiversity conservation. I like their point that metrics need to be projected forwards under different policies if they are going to be useful. They also use the excellent approach of virtual ecology (see excellent introduction here) to test how well a biodiversity metric can track reality.

Regular visitors might have noticed that I don't believe improved knowledge leads to changes in behavior. This is a nice little piece summarizing some social science that demonstrates just how bad it really is. One of my FB colleagues wondered what it would mean if applied to scientists. Hint: see the link at the top of this post on disappearing data tables. Scientists are human, unfortunately for science, and the incentives to parrot the paradigm are rampant. (ht: Tala Awada)

Not really about environment, but MotherJones is running a series of charts on income inequality. This one caught my eye because of the increasing variance over time in the income of the top 1%. Rising variance is a signal of an impending tipping point between dynamic regimes in complex systems, as Trevor Hefley's paper in theoretical ecology demonstrates for simple population growth models (which is about our environment!). 

The whole soy?

I've just finished reading "The Whole Soy Story" by Kaayla Daniel. It is a pretty typical offering of the "somethings wrong with our food" genre. In Daniel's case, the something wrong is soy. This book has tons of references to follow up on, but does precious little synthesizing or summarizing. There are plenty of anecdotes from people with horrible soy experiences too, if you're looking for company.

I found the history of soy section pretty fascinating. The takeaway message is that soy based foods are a relatively recent innovation in Asia. Soy was used as a cover crop and fertilizer for millenia, but only in the last few centuries did it start to play a significant role in the food supply. Fermented soy products, like miso and tempeh, have a longer history. Soy oil was a lamp fuel in China! Even now unfermented soy foods like tofu are a small component of the diet, used in conjuction with eggs, fish, poultry and meat. As a population biologist I find it pretty interesting that soy foods increased in importance with increased population size. 

Daniel is pretty clear throughout the book: traditional soy foods are not the target. The fermentation processes used to make miso, tempeh and many others greatly reduce or eliminate "antinutrients" in raw soybeans. Tofu is borderline because the relatively mild processing it receives does not reduce antinutrients to the same extent as fermentation. 

The vitriol is focused primarily on industrial uses of soy in processed foods. If you want to get completely turned off of a product, just read her chapter on first generation soy products. There's clearly a profit motive to using soy everywhere possible, and you won't find me promoting processed foods as healthy. I confess, if you look in our refrigerator you'll find soy dogs with an ingredient list that goes: "Water, Soy based protein Isolate, Soybean Oil, Evaporated cane syrup ..." ugh. Non GMO soybeans though! Nowadays I buy them because they are easy for a teenager to heat and eat, and boy, do teenagers eat. 

The steady introgression of soy products into nearly everything processed is problematic because of the many anti-nutrients associated with soy, and Daniel devotes a substantial amount of the book to detailing these. The trouble with these industrial processes is that they do not reduce antinutrients like phytates and trypsin inhibitors. What about these things in real food, like tofu*? This turns out to be a really good example of how risk tolerance influences the interpretation of data. According to the research Daniel cites, tofu retains 2.5 to 7.9% of the Trypsin inhibitors in the raw soybean. Compare that to 0.3 % retention in Miso and you can see why fermentation is a good thing. Reductions of this magnitude eliminate growth deficits in rats caused by trypsin inhibition. And most of the trypsin in our guts exists in cationic form which is resistant to these inhibitors. So I look at that and say, "well, seems like there's nothing to worry about from tofu." Daniel on the other hand says (I'm paraphrasing) "but it's not ALL gone, and there's SOME effect, and we don't know EVERYTHING." 

But, but, I hear you sputtering, soy is GOOD for us! It's true that these same trypsin inhibitors are being investigated as treatments for cancer. However, the devil is in the details. If you chemically isolate Bowman-Birk inhibitors from soy, treat them to change the relative rates of inhibition of chymotrypsin to trypsin, then feed that chemical product to rats predisposed to get cancer, the rats get less cancer. But that's a long ways from what you're getting in soy food, real or processed. Daniel comes back to the claims that soy protein or isoflavones reduce cancer risk in a later chapter, and similarly, the evidence is equivocal at best, and absolutely in the opposite direction at worst. 

The section that got my attention was the one on phytoestrogens. Soy has a lot, and if you eat a lot of tofu like I do you're getting a pretty hefty dose. The primary negative effect here seems to be on the thyroid gland. Well that's OK, because I had mine removed in 2000 because of Hashimoto's Thyroiditis. What's that? Oh, Hashimoto's has the highest incidence in Japan (hence the name ...), which also has the highest consumption of soy products. Hmmm. Well, correlation doesn't equal causation.

Overall, I call this one a draw. Processed food is bad, yep. I'm with you on that. Infant formula bad, yep, soy infant formula really bad, got it. Breastfeed as long as you can stand it, and then keep going for a few more months please! Easy for me to say, I'm not the one producing the milk. Hey, I tried to do my part by getting up and carting the little devils around after feeding in the middle of the night. 

Am I going to stop eating tofu? Not yet. 

*Yes, I know, tofu is actually processed. However, if I could make it on my kitchen counter then I'm going to call it real food. Like Beer and Wine. :) 

Throwback Thursday: AM and the National Parks system

Way, way back I wrote a paragraph on Tony Prato's research paper on how AM could be used by the National Park System. That post is my all-time-highest visited post! AND, someone provided an intelligent comment on it. So what's Tony up to now?

Walkabout Wednesday: replication, wolves and student evaluations.

Replicating scientific research is important. The ability to replicate a study's results is what sets science apart from other ways of knowing. And sometimes, failure to replicate can overturn an entire paradigm. It turns out that Angus Bateman's classic study on fruit fly sex had a fatal flaw, exposed when Patricia Gowaty* and colleagues attempted to replicate the work after 64 years. And so goes the notion that women are passive objects of male-male competition. Finally. Probably not. Overturning paradigms is hard. 

And here's another example of replication leading to self-correction from physics.

It's been a banner week for replication! Here's a nice article on how Bayesian statistics is helping many disciplines, arguing that Bayesian methods allow checking conventional Frequentist conclusions and therefore improving replicability. Most interesting to me are the references to Andrew Gelman's work on detecting spurious results. However, he takes issue with way those ideas were presented in the article. While I agree there's a "crisis of replication" in science, I'm not sure Bayesian methods are the cure-all the article makes out.  (ht: Jeff Thompson)

I love wolves, and they've provided plenty of fodder for people interested in the intersection of science and policy (see here and here, for example). Now a federal judge has put management of Wyoming's wolves back on the USFWS, calling the handover to Wyoming's state agency "arbitrary and capricious". I gave Wyoming a D- on their AM strategy, so maybe that played a role?

The public regards Scientists as competent but not warm. And they can tell when we're playing "stealth issue advocate" so we should always seek to be "honest brokers". I think stealth issue advocacy is responsible for much of the crisis of replication mentioned above. 

The federal government is preparing to rate colleges and universities to improve students and families ability to make good decisions, and ultimately reduce costs. Here's one op-ed that suggests it won't work, at least at public institutions like mine. "At public colleges, then, the explanation for rising tuition prices isn’t spiraling costs. The costs are the same, but the burden of paying those costs has shifted from state taxpayers to students." (HT: Jeremy Fox @ Dynamic Ecology)

Pre and post testing of physics students at MIT indicates that students taking a MOOC do better than a traditional format.  But: "Although approximately 17,000 people signed-up for 8.MReV, most dropped out with no sign of commitment to the course; only 1500 students were “passing” or on-track to earn a certificate after the second assignment." That's the problem with MOOCs, if it is a problem. The paper is open-access, and uses alot of interesting ideas about how to measure student performance. (HT: Jeremy Fox @ Dynamic  Ecology)

And student evaluations suck. 

This is quite a good talk about Gluten; I hadn't heard of Rodney Ford before but he's a pretty good speaker. I eliminated gluten from my diet completely in early 2014. I will write a post about how I've been feeling since then soon. But here's a teaser: better.

*I was lucky to meet Patty when I was an MSc student at Simon Fraser University in the early 1990's. Really cool work then and now! 

My low fat experience

From 1995 until around 2000 I followed a very low fat vegan diet. The target was to achieve < 10% calories from fat. Kris Gunnar over at Authority Nutrition has a typically well researched blog post summarizing the known effects of a low fat diet.

Water, water everywhere

and all of it regulated. The dustup over a proposed rule by the EPA and USACE to define the scope of water regulated by the Clean Water Act has attracted my interest for some time. Congress has now weighed in.

Remembering Scott Field

Last week I heard the tragic news that a dear friend, Scott Field, had died in a hiking accident in Italy. Since then the tributes to Scott have been pouring across the interwebs, especially on Facebook. I wanted to take a bit of time to look through what images and memories I had of this great guy.

I have none. Really. I guess I don't really take pictures of people. I did come across this picture which comes from circa 2004? 2005? I was on the back side of an extended visit to Oz and spent a few days hanging out with Scott at Waterfall Gully in Adelaide. I believe Brendan Wintle stopped by, and some science happened. Beer was involved, and lots of walks in the Adelaide Hills. I think the intent was to combine our 2004 paper on minimizing cost of managing a declining species with our 2005 paper on detectability issues in monitoring. It never happened; I was getting wrapped up in teaching etc. in Nebraska, and Scott was, as ever, moving onwards towards the bright horizons. Our collaboration was awesome for me. He will be missed.