Saturday, May 19, 2012

N-3, Fructose And Rat Cognition

The LA Times headlines this rather interesting study with typical j-school "science" journalism idiocy.

Fructose makes rats dumber. What sugars should we avoid?

The problem with the LA Times article is that the study doesn't actually compare sugars, it compares combinations of fructose and n-3. It's too bad, actually, that they didn't add in glucose also, I'm genuinely curious what the effects on cognition would be vs fructose. Nevertheless it is an interesting study.

I would love to give this study the Petro Dobromylskyj  treatment, but since I lack the knowledge and motivation I will just give it the brand X treatment.

Okay, so here's the abstract:
We pursued studies to determine the effects of the metabolic syndrome (MetS) on brain, and the possibility of modulating these effects by dietary interventions. In addition, we have assessed potential mechanisms by which brain metabolic disorders can impact synaptic plasticity and cognition. We report that high-dietary fructose consumption leads to an increase in insulin resistance index, and insulin and triglyceride levels, which characterizeMetS. Rats fed on an n-3 deficient diet showed memory deficits in a Barnes maze, which were further exacerbated by fructose intake. In turn, an n-3 deficient diet and fructose interventions disrupted insulin receptor signalling in hippocampus as evidenced by a decrease in phosphorylation of the insulin receptor and its downstream effector Akt.We found that high fructose consumption with an n-3 deficient diet disrupts membrane homeostasis as evidenced by an increase in the ratio of n-6/n-3 fatty acids and levels of 4-hydroxynonenal, a marker of lipid peroxidation. Disturbances in brain energy metabolism due to n-3 deficiency and fructose treatments were evidenced by a significant decrease in AMPK phosphorylation and its upstream modulator LKB1 as well as a decrease in Sir2 levels. The decrease in phosphorylation of CREB, synapsin I and synaptophysin levels by n-3 deficiency and fructose shows the impact of metabolic dysfunction on synaptic plasticity. All parameters of metabolic dysfunction related to the fructose treatment were ameliorated by the presence of dietary n-3 fatty acid. Results showed that dietary n-3 fatty acid deficiency elevates the vulnerability to metabolic dysfunction and impaired cognitive functions by modulating insulin receptor signalling and synaptic plasticity.
tl;dr: n-3 no fructose did the best, n-3 deficient diet with fructose did the worst.

See this? This is my shocked face. Still, it's easy to have one's preconceptions confirmed, and it's easy to be less than skeptical of studies that confirm them.

Exhibit A:

Interesting that the n-3/fructose rats were the fattest with the highest caloric intake.

Table 2:

Interesting the triglyceride level differences between the n-3 and n-3 deficient diets.

And now we get to the meat of things:

According to graph A, there was a wide divergence on days one and two, with everyone pretty much converging on latency times after 5 days. The n-3 group seems to have the highest latency times on average so I'm not sure how they ended up so kick-ass in graph B.


The interesting thing for me is how the n-3/fructose diet represented by the x's have so much larger of a scatter than the other diets. The more unhealthy the diet the wider the range of responses, it seems.

Tuesday, May 15, 2012

Interview With Ana Navarrete

A while back I wrote about a recent paper in Nature challenging the expensive tissue hypothesis. The lead author of the paper, Ana Navarrete, contacted me, sending me supplemental data, since I didn't have full access to the Nature paywall, and she agreed to do an interview about her paper.

Ana Navarrete got her PhD at the Anthropological Institute and Museum of the University of Zurich. She is currently a research assistant at the University of St Andrews.

Your recent paper in Nature apparently demolishes ETH as proposed by Aiello and Wheeler. Could you give us a lay summary of the paper and it's conclusions?

You say that our study “demolishes” the ETH, but that sound really harsh. Although our results show that there is no evidence for the ETH in mammals and primates, but that does not mean that the significance of the ETH should be minimalized. Its presentation in 1995 fuelled the field of the study of the costs of encephalization, which is actually growing and focusing lots of interest. We were therefore very happy when Leslie Aeillo turned out to be one of our reviewers and provided us with very interesting feedback. We coincided that the results show that mammals do not show energetic trade-offs between tissues, but that the ETH could still highlight aspects of human evolution, although this will need at some point further demonstration.

To summarize our study, we used data obtained from the dissections of a sample of 100 mammal species, which included 23 primate species, to test possible correlations between brain size and the size of other expensive organs. We found no evidence for a correlation between brain size and digestive tract size in these groups. Moreover, we found no correlation between brain size and the size of heart, kidneys and liver, which are traditionally considered expensive organs. In this aspect, we rejected the Expensive Tissue Hypothesis. However, when analyzing correlation between brain size and other less expensive, but more abundant tissues, which also could consume high quantities of energy, we found a negative correlation between brain size and the accumulations of adipose tissues. We interpret here that having big brains and large adipose depots are strategies which can be beneficial for survival, but most animals either take one or the other because both options are costly. Big brains are associated with higher cognitive abilities, but need lots of energy. Large adipose depots can help to buffer periods of unavoidable starvation, but in great quantities they can be very costly in terms of locomotion. Therefore, most mammal species either increase their brains or accumulate more fat. However, species with types of locomotion which allow them to transport more fat with less costs should be able to combine both strategies. It would be the case of aquatic or bipedal animals, like humans. We humans have large brains and large accumulations of adipose tissue. 

You write: "However, species with types of locomotion [bipedal and aquatic] which allow them to transport more fat with less costs should be able to combine both strategies." I realize birds aren't mammals, but I thought of the ostrich as a bipedal animal that might be able to employ this strategy also, yet is not famous for its brain size. Any thoughts on this?

First of all, our results refer to mammals specifically. We suppose that brain evolution is constrained energetically in birds, as well, but these energetic constrains must be different. In birds, we do not observe the correlation between brain and metabolism that we observe in mammals. Additionally, the correlation between brain and adipose tissue is unlikely to be present in birds because the size of adipose accumulations is restrained so that it does not hinder locomotion efficiency. Previous work of Karin Isler and Carel van Schaik, however, shows that there is a negative correlation between the brain size and the size of the pectoral muscle, the most important muscle involved in flight. In birds, locomotion efficiency also constrains brain size, but not in the same way as in mammals.

Now, ostriches don't fly. They are bipedal like humans. They have small brains. My guess here is that, although these animals lost the capacity to fly, which allowed them to accumulate more fat, their ancestors lived under conditions where enhanced cognitive abilities were not a requisite for survival. Both encephalization and fat storage are strategies to avoid periods of unavoidable starvation. This means that, if a species is relying on ephemeral food, it has either to get smarter o get fatter to survive. But species that rely on low-quality food that is always available (grass, leaves, etc) or species that live in habitats where seasonality is low, may be able to survive without using either of these strategies. As a matter of fact, in our sample of mammals, be found that there was no correlation between brain mass and fat storage mass in tropical species. We concluded that this was caused by the fact that habitats in the tropics are less seasonal.

Could you talk a little bit about the special case you saw for primates and the data from wild vs captive species?

We expected to find the same negative correlation between brain mass and adipose tissue in primates as we found in mammals, but, as you saw in our publication, we were not able to provide this correlation. This has awakened criticisms about the credibility of our results. However, we are convinced that the negative correlation must be there, but that we were not able to find it because our specimens were animals whose total adipose tissue accumulations I wasn’t able to measure directly, so we had to set a proxy based on abdominal fat. We suspect that our approximation underestimated the amount of fat of these animals, which would not be strange considering that they were captive individuals. Future study either using carcasses of wild primates or using complete measurements of captive primates will be needed to test the correlation anew.

Captivity is known to influence body composition. Captive animals do not perceive environmental fluctuation, such as food scarcity or changes in temperature. They also tend to be less active as wild specimens because lack of space. Moreover, diet composition in captivity tends to differ significantly from diet composition in the wild. A combination of these factors (different diet, reduced mobility and immunity to environmental fluctuations) is often called to explain either overweight or underweight in captive individuals or differences in internal morphology between wild and captive individuals of the same species. We therefore controlled for captivity effects. Our results showed captivity weakens the correlation between brain mass and adipose tissue, because the correlation between these two variables turned stronger when only wild specimens were included in the analyses, and it disappears when only captive specimens are analyzed.

ETH has been used by the paleo/ancestral diet community as a justification for a diet high in animal products. Likewise, your paper was recently argued by vegans (such as PaleoVegan) as proof that animal products weren't responsible for encephalization, hence unnecessary for a modern diet even from an evolutionary standpoint. Would you care to speculate on what you see as the larger dietary implications of your paper?

I always found interesting that people would use the ETH for this paleodiet debate, because the hypothesis only refers indirectly on diet. And I also find interesting that people are arguing about what our results mean for the debate. Additionally, there is the fact that the whole debate is mainly used to discuss how the diet of actual humans should be. And here we incur into the risk of forgetting that our ancestors lived in very different circunstances, under very different pressures, exploited different resources and lacked of other resources available to modern man.

Just to make clear our impact in this debate: our results on the ETH just disprove the expected morphological trade-off between brain mass and digestive tract mass. Our study does not make any verdict on the diet of our ancestors. In our framework, we still consider that diet quality played an important role in human brain evolution, and a higher quality in diet would have been achieved through meat consumption, but with the introduction of cooking, which would have reduced overall costs of digestion and granted access to other high quality items of non-animal origin, such as tubers, which are hardly edible when raw. I would say that the addition of high quality resources of animal AND vegetal origin allowed us to increase our brains.

Dr Navarrete noted separately, "Also, I really had problems answering your [last] question. Although I am familiar with the paleodiet debate, I am really uncomfortable when the ETH (or our study) is cited in it because I consider that its reference is misplaced (it just discuss morphological trade-offs, but does not discuss diet but as a possible factor triggering gut reduction). This is also the reason why we did not concerned ourselves to speculate about it." 

Saturday, May 12, 2012

Guest Post At Free The Animal

I have a guest post up over over at Richard Nikoley's blog about being a long-time expat.

Thursday, May 10, 2012

Free Speech, Twitter, And Obnoxious Neurosurgeons

Emily Deans just wrote about the recent Kruse kerfuffle, which prompted me to write a somewhat lengthy comment there on free speech that I'd like to expand upon. I won't go into the Kruse details, Emily mentions them and David Csonka wrote them up here.

Now, I'm no Constitutional scholar. Then again, Obama is, yet he signed NDAA into law (among other egregious assaults upon civil liberties), albeit with 'reservations' (how nice that he at least had reservations).

I don't know if the FBI or DHS or whatever considers the person who ran this parody Twitter account (@shitkrusesays) to be culpable of anything. Given the ever-increasing police state climate in the US this past decade it's easy to jump to the conclusion that they would, but hopefully this is all Kruse trying to avenge himself or stir up more publicity for himself.

What's clear to me is that whoever was running that Twitter account most definitely is not culpable of any violation of the law, ie, they are, or ought to be protected under the First Amendment. And I don't believe that the account ought to have been shut down under any sort of pressure from the government (perhaps the person running it shut it down themselves), although that seems somewhat unlikely as Twitter is being defended by the ACLU for refusing to hand over the details of one of its users.

I know it's really quaint these days to actually quote from the Bill of Rights, but I'm going to do it anyway:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
Is all speech in reality protected, or ought to be protected? No. There's a gray area there, of course, which is summed up pretty well here:
[O]ver the past century the courts have carved out or tolerated dozens of “exceptions” to free speech. These exceptions include: speech used to form a criminal conspiracy or an ordinary contract; speech that disseminates an official secret; speech that defames or libels someone; speech that is obscene; speech that creates a hostile workplace; speech that violates a trademark or plagiarizes another’s words; speech that creates an immediately harmful impact or is tantamount to shouting fire in a crowded theatre; “patently offensive” speech directed at captive audiences or broadcast on the airwaves; speech that constitutes “fighting words”; speech that disrespects a judge, teacher, military officer, or other authority figure; speech used to defraud a consumer; words used to fix prices; words (“stick ’em up — hand over the money”) used to communicate a criminal threat; and untruthful or irrelevant speech given under oath or during a trial.--Richard Delgado, Campus Antiracism Rules: Constitutional Narratives in Collision, 85 Nw. U. L. Rev. 343, 377 (1991).  Quoted from Volokh.

Now I don't agree with a lot of those exceptions, for example regulating speech on the airwaves, but that's a pretty fair summary of the legal state of free speech in the US (and a pretty good baseline for many Western European countries as well).

One certainly can't consider a Twitter follower a member of a 'captive audience'. The Twitter feed was obvious parody to anyone in the paleosphere who's been following this even remotely (like me), hundreds of thousands of people at least. Was that clear to DHS or whoever was apparently grilling Kruse for hours. No, but about five minutes of research ought to have made it clear.

Next we have the person who contacted Carnival security tarring Kruse as a terrorist threat. I think that person is maybe culpable for something. Perhaps they ought to be charged the price of a plane ticket to fly Kruse back to rejoin the ship. They most definitely ought not to be face extended prison time. If Kruse suffered anything more than a mild inconvenience for all of this, then the only party to blame, the party that is really culpable for that are the authorities.

For example, if I report, out of spite, that my neighbor is beating his wife or doing illegal drugs, and the police break down his door and end up shooting the guy should I be held culpable for murder? No. This kind of stuff actually happens. But the culpable party here is the police, not the person who made the call. They are the ones who pull down a nice salary with full benefits and an early retirement. They are the ones who are supposed to be trained to deal with this sort of stuff.

These distinctions are what really matter, as far as I'm concerned, not whether or not Kruse is a blowhard or a quack.


More on free speech by Eugene Volokh from the same post quoted above:
But as the exceptions become more plentiful, they may begin to seem like they swallow the rule. As Justice Scalia noted in the Fourth Amendment context, once a rule (there, the warrant requirement) “become[s] so riddled with exceptions that it [is] basically unrecognizable,” it is easy to see new exceptions not “as some momentous departure, but rather as merely the continuation of an inconsistent jurisprudence that has been with us for years,” and to conclude that the rule needs to be jettisoned altogether. California v. Acevedo, 500 U.S. 565, 582-83 (1991) (Scalia, J., concurring in the judgment). We recognize that there is disagreement about whether indeed the warrant requirement should be retained, despite its exceptions; our point is simply that the multiplication of exceptions (from “only * * * a few specifically established and well-delineated exceptions,” Katz v. United States, 389 U.S. 347, 357 (1967), to a vast array of such exceptions) undermines the normative force of the rule.

For this reason, the creation of a large array of free speech exceptions ought to be avoided. Having a dozen exceptions for subcategories of knowingly false statements may seem more speech-protective than having a general exception for all knowingly false statements. But such a proliferation of exceptions may ultimately prove to be less speech-protective, because it may open the door to more exceptions that will not be limited to knowing falsehoods.
 Has free speech been jettisoned altogether? Not yet, but that's the endgame.

Wednesday, May 09, 2012

A Brief Jack Kruse Rant

I don't use Twitter so I'm not usually hip to things like the latest Kruse kerfuffle, but I did see Richard talking about it, so I reluctantly went to the circle jerk known as PaleoHacks to see how much stupid was happening (I don't watch reality television so this is my guilty pleasure).

Plenty of it all around, as it turns out.

For those not in the know, someone made a parody Twitter account of Kruse apparently, and someone else (or perhaps the same someone) apparently reported Kruse to the fascist ever-vigilant and hard-working authorities. Blah blah blah, he was arrested, blah blah, then let go, blah.

Are you still awake? Because I'm not sure I am.

Anyway, I got to this comment on PaleoHacks by someone calling themselves PaleoVenus and I got annoyed enough to wake up and write this rant.
I can't believe someone made a twitter account dedicated to making fun of this guy. He's already an outcast here. I don't put faith in what he says, mostly because I can't understand it, but whoever is behind this twitter account has crossed a line by tweeting about a bomb/bio threat. What a thoughtless thing to do. It's totally foreseeable that it would end with an investigation. As for JK himself and his behavior, what did you expect? He is who he is.
I could give a flying fuck about Kruse or his haters but this comment really encapsulates more sheep-like idiocy than I care to digest in one sitting.

Someone crossed the line by making a fake twitter account? Or by making a joke on that fake Twitter account that was construed by the fucking idiots at Homeland Security as a terrorist threat?

You know what? Fuck Homeland Security. I'm embarrassed to even have been born in a country that has a government organization with the word homeland in it. If I hadn't already left the country a long time ago, I'd leave it again. Why don't they just call it Fatherland Security? Seriously, go fuck yourselves.

Guess what fuckers? I want to bomb the US by smuggling dynamite up my ass and kill the President. Am I a terrorist threat? Am I joking? Better to be safe and 'request' that Google delete my fucking blog you fascist cunts. I live in Prague 6, Czech Republic, I'm sure you can figure out the details, why not send a drone over to wipe out me and any non-combatants in my vicinity just to be safe.

Collateral damage, it's what's for breakfast.

Tuesday, May 08, 2012

Day of Liberation

Today is a national holiday here in the Czech Republic, Den osvobození or Day of Liberation, otherwise known as VE day. For the Russians, tomorrow is the official end of the war in Europe and it is a big celebration there from what I've heard.

Both my grandfathers suffered bodily harm in world wars. My father's father was gassed in WWI (he died from emphysema before I was born, but to be fair he smoked like a chimney), he was actually taken for dead and woke up among a bunch of corpses, but managed to throw up some fuss and get recognized as still amongst the living. My mother's father was sent home from the Western theater of WWII after contracting some strange disease or parasite.

Here's a picture of my mother's father holding my mother right before he left after he came back from fighting in the Pacific Theater. 

Man, look at that chiseled face. I totally got screwed in that department.

I don't consider myself to be special because my grandfathers both fought in these wars, I've certainly never experienced anything like what they must've gone through, but I would like to acknowledge, on this national holiday, that they both suffered considerable hardship serving their country.

Allergies and Growing Up On A Farm

When my wife was pregnant, her sister, who is a doctor, told her that we should get rid of three of our four cats, cause it wasn't healthy for babies to be exposed to too much cat, apparently. A little Google research later I found out that kids who grow up with pets are less likely to have allergies and asthma.

Color me surprised.

We kept the cats and my son has yet to have any problems (my wife had life-threatening asthma as a child that mostly disappeared with puberty).

Now there is this recent study showing that Amish farm kids have a much lower incidence of allergies than city kids.  To quote from this writeup:
They studied 157 Amish families, 3,000 Swiss farming families and another 11,000 Swiss who did not live on farms. All had children aged 6 to 12.

Only about 10 percent of all Amish children show sensitization for allergies – mostly dust mites and grass; about 25 percent of all Swiss farm children tested positive to allergies — mostly cats.

Overall, the Swiss have the same allergy sensitization rates as Americans – about 44 to 50 percent. Only about 20 percent of those who show sensitization develop allergy symptoms.

Researchers also found that only 5 percent of Amish kids had been diagnosed with asthma, compared with 6.8 percent of Swiss farm kids and 11.2 percent of the other Swiss children.
They go on to talk about the possible positive correlation of the Amish kids drinking raw milk. Now I don't have a problem with the idea that raw milk is healthier than the pasteurized stuff---but, I think the difference between Swiss and Amish farm kids is to cats could have a lot to do with diagnosis and the relative reclusiveness of their cultures. I think it is telling that the asthma rates are much more similar.

The biggest news here, hormetic stress to the immune system seems to lower incidence of autoimmune disease. It wasn't that long ago that our peasant ancestors* were sleeping with their animals and while that probably is not optimal for human health, neither is living in a sterile environment and obsessing over anti-microbial soap.

*Actually, your peasant ancestors, not mine. I'm descended from royalty according to my long departed peasant Irish grandmother.

Sunday, May 06, 2012

Start With The Tycho Brahes

I was reading an interesting editorial in the May issue of Analog magazine (unfortunately not online) about the scientific method, by editor Stanley Schmidt.

Schmidt, who holds a PhD in physics, pointed out that there are a lot of scientific fields where the classic experimental method is untenable, for example astronomy.
But what about astronomy, which practically everybody considers clearly one of the most basic and important of sciences? Who has ever set up an experimental pregalactic gas cloud to watch how stars and planets form? Or even a protostar in a laboratory to test a theory of stellar evolution?

So astronomers and astrophysicists, in general, can't do controlled experiments. the have to make do with observing what nature provides--and they can't even get close to that. As astronomer and SF writer Michael Brotherton succinctly put it at Launchpad[...], "Everything we know about stars we know by analyzing light [in the broad sense of 'electromagnetic radiation,' of any wavelength] from very far away."
And this is what struck me the most:
But if the earliest students of what we now call physics and chemistry had disdained to study them because they weren't understood with twenty-first-century rigor, they would never have gotten off the ground. No science starts off at that level; somebody has to do the groundwork before rigorous theories can be formulated, tested, and refined. As my brother Dennis (a computer professional with a strong interest in psychology) once said, "I used to think psychology needed a Newton. Now I realize it isn't ready for a Newton. First it needs a Tycho Brahe"

By the way, Tycho Brahe is said to have died from from drinking too much wine and not being able to relieve himself due to court etiquette (although recent evidence suggests it might have been simple mercury poisoning), Brahe certainly wasn't the last person to drink too much in Prague. I think the Tycho Brahe analogy is especially apt when it comes to nutrition research. Brahe wasn't a theorist but a collector of data, greatly ahead of his time in astronomical accuracy. Brahe was the equivalent of a modern experimental astrophysicist with Kepler being the theoretician. 

When I see nutritional studies quoted that use self-reported data, or don't control for people who dropped out of the study or other idiotic things that are supposed to pass for science I have to shake my head in wonder. What's so annoying is to see the language of science used in these papers, statistical regressions, big words, blah blah blah, when the raw data is nonsense.

What many of the 'soft' sciences need more than anything else is good data. Maybe a better way to put it, what many of the complicated sciences need is better data, better controlling for variables. 200 similar studies with 60 participants are not nearly as effective as one study with 1200 participants. Let's say you divide the participants into three groups, intervention A (say low-carb), intervention B (low-fat) and a control group (no intervention). All these small similar studies with 20 people per group are going to vary somewhat in implementation so they will be less effective than a single large study. Rigorously measuring 1200 people in a dietary study is, of course, very expensive. But no more expensive than all the small studies that are now done that are essentially statistical noise.

Instead we are left with meta-studies, AKA the cherry-pickers utopia. Okay, not all meta-studies suck, but even the most conscientious meta-study is simply not going to be able to control for all the study variances and hence is going to skew the data.

The real problem is that accurate data is extremely difficult to collect in complicated fields like nutritional or health studies (or economics or psychology). Just as there's no crying in baseball, there's no placebo effect in physics. Or maybe there is? Perhaps that's the secret of the Theory of Everything! I'm off to write a grant proposal.

This reminds me of a recent criticism I made of archaeology. I wrote:
So a problem I see with the paper from Miki Ben-Dor who has a blog entitled Paleo Style, or with archeology in general it is pretty easy to cherry-pick or insert one's biases, because it's all in retrospect and the data is so scant.
What I was really thinking is that archaeology is observational hence not as rigorous as experimental science. But the reality is that archaeology is much like astrophysics. It is about uncovering data and analyzing that data based on increasingly rigorous methods and frameworks (such as genetic analysis, population modeling, etc). So, my bad.

No one has ever seen a black hole, but we have plenty of indirect evidence they exist just from observing photons that reach us from distant parts of the universe. Likewise, these same observations have led astrophysicists to postulate dark matter and dark energy, opening up some of the most interesting new topics in the world of physics today.