monday's should always start off with something pretty....these pretty much fit the bill.

*images courtesy of zinke design, la dolce vita

Saturated Fat, Glycemic Index and Insulin Sensitivity: More Evidence

Insulin is a hormone that drives glucose and other nutrients from the bloodstream into cells, among other things. A loss of sensitivity to the insulin signal, called insulin resistance, is a core feature of modern metabolic dysfunction and can lead to type II diabetes and other health problems. Insulin resistance affects a large percentage of people in affluent nations, in fact the majority of people in some places. What causes insulin resistance? Researchers have been trying to figure this out for decades.*

Since saturated fat is blamed for everything from cardiovascular disease to diabetes, it's no surprise that a number of controlled trials have asked if saturated fat feeding causes insulin resistance when compared to other fats. From the way the evidence is sometimes portrayed, you might think it does. However, a careful review of the literature reveals that this position is exaggerated, to put it mildly (1).

The glycemic index, a measure of how much a specific carbohydrate food raises blood sugar, is another common concept in the diet-health literature. On the surface, it makes sense: if excess blood sugar is harmful, then foods that increase blood sugar should be harmful. Despite evidence from observational studies, controlled trials as long as 1.5 years have shown that the glycemic index does not influence insulin sensitivity or body fatness (2, 3, 4). The observational studies may be confounded by the fact that white flour and sugar are the two main high-glycemic foods in most Western diets. Most industrially processed carbohydrate foods also have a high glycemic index, but that doesn't imply that their high glycemic index is the reason they're harmful.

All of this is easy for me to accept, because I'm familiar with examples of traditional cultures eating absurd amounts of saturated fat and/or high-glycemic carbohydrate, and not developing metabolic disease (5, 6, 7). I believe the key is that their food is not industrially processed (along with exercise, sunlight exposure, and probably other factors).

A large new study just published in the American Journal of Clinical nutrition has taken the evidence to a new level (8). At 6 months and 720 participants, it was both the largest and one of the longest studies to address the question. Participants were assigned to one of the following diets:

1. High saturated fat, high glycemic index
2. High monounsaturated fat, high glycemic index
3. High monounsaturated fat, low glycemic index
4. Low fat, high glycemic index
5. Low fat, low glycemic index

Compliance to the diets was pretty good. From the nature of the study design, I suspect the authors were expecting participants on diet #1 to fare the worst. They were eating a deadly combination of saturated fat and high glycemic carbohydrate! Well to their dismay, there were no differences in insulin sensitivity between groups at 6 months. Blood pressure also didn't differ between groups, although the low-fat groups lost more weight than the monounsaturated fat groups. The investigators didn't attempt to determine whether the weight loss was fat, lean mass or both. The low-fat groups also saw an increase in the microalbumin:creatinine ratio compared to other groups, indicating a possible deterioration of kidney function.

In my opinion, the literature as a whole consistently shows that if saturated fat or high glycemic carbohydrate influence insulin sensitivity, they do so on a very long timescale, as no effect is detectable in controlled trails of fairly long duration. While it is possible that the controlled trials just didn't last long enough to detect an effect, I think it's more likely that both factors are irrelevant.

Fats were provided by the industrial manufacturer Unilever, and were incorporated into margarines, which I'm sure were just lovely to eat. Carbohydrate was also provided, including "bread, pasta, rice, and cereals." In other words, all participants were eating industrial food. I think these types of investigations may be limited by reductionist thinking. I prefer studies like Dr. Staffan Lindeberg's paleolithic diet trials (9, 10, 11). The key difference? They focus mostly on diet quality, not calories or specific nutrients. And they have shown that quality is king!


* Excess body fat is almost certainly a major cause. When fat mass increases beyond a certain point, particularly abdominal fat, the fat tissue typically becomes inflamed. Inflamed fat tissue secretes factors which reduce whole-body insulin sensitivity (12, 13). The big question is: what caused the fat gain?

Comic strip: 10%

Last summer, during my internship at CMP in Prague I drew some xkcd-style comic strips, and I want to share some of them here. I considered starting a different blog for that, but there are too few of them, and they do suck (at least in comparison to Randall's work). However, most of them are programming/research related, so they are appropriate here.

I planned to use them when I would have nothing to post about. This is not the case now (I am planning a couple more posts in a week or so), but this one is topical. It was originally drawn in September 1, 2009 when GMail was not operating for a few hours. From the recent news: Google shuts Google Wave down, admitting their failure predicted by some sceptics (see the image title text).

Happy Friday.

*images courtesy of happnstance, fiddlesticks and funny girls

2nd visioning session a success!

The second visioning session was a great success. 20 community members turned out to revise the draft statement created by the individual adult and youth visions from the August 3rd event.

Community members worked in small groups to ensure that the shared vision incorporated everyone's ideas and priorities - while remaining true to the HKHC goals.

As we move forward, we will begin planning for the third and final session in our visioning series. We will display the art created by our youth attendees, both craft pictures and photographs, as well as launch our newly crafted vision. We hope the final session will be a celebration for all of Buffalo - and the launch of the HKHC initiative in the city.

my daughter's favorite song isn't old mcdonald had a farm or twinkle twinkle little star...it's not hot dog, hot dog, hot diggity dog from the mickey mouse clubhouse or ring around the rosie. nope, not my 3 yr old. when we get into the car, she strictly wants me to play eminem (or rather M&M) and rihanna love the way you lie.....i am sure her teachers will really appreciate that when she sings it at school.

First HKHC Report - Check it out!

As a part of the HKHC program, we are conducting an ongoing assessment of the healthy eating and active living environment in Buffalo. As a part of this assessment, Kailee Neuner - the research coordinator from the University at Buffalo for HKHC - produced a policy brief that outlines the current conditions. Please take a few minutes to read this very important document - and get involved. You can always contact me with any questions at jhersher[at]bnmc.org.

Download the document here.

Why men still get more promotions than women

Very interesting article in The Harvard Business Review on male vs. female mentoring, and the difference it can make in business contexts.

All mentoring is not created equal, we discovered. There is a special kind of relationship—called sponsorship—in which the mentor goes beyond giving feedback and advice and uses his or her influence with senior executives to advocate for the mentee. Our interviews and surveys alike suggest that high-potential women are overmentored and undersponsored relative to their male peers—and that they are not advancing in their organizations. Furthermore, without sponsorship, women not only are less likely than men to be appointed to top roles but may also be more reluctant to go for them.

The article is a bit anecdotal in parts, but has some underlying interesting ideas in it that are grounded in research. I'm not sure how applicable it is to academic careers, but having a mentor who in addition to giving you advice can help sell you and your ideas to others (institutional peers, editors, etc) is almost always, in my experience, a helpful thing.

2nd Visioning Session Tonight!

After a very successful first session, the HKHC community will meet again tonight to work on the draft community vision for a healthy Buffalo. Adults and youth came together on August 3rd to provide their personal visions for a healthy Buffalo, and these prioritized themes and ideas have been compiled into a draft vision.

Please come out tonight and help us finalize our vision! Everyone is welcome - health is important for all of us! See you tonight.

Check out some photos from the first session - some of our representatives are presenting their ideas...

coming soon...

these pics serve as a reminder that fall is right around the corner.....

on another note, jazzercise was a success. i actually really enjoyed it. i think it would do the company some good to "reinvent" themselves/aka change the name from jazzercise. it's just a dance workout class that last an hour and it works your butt off! and for the record, there were no sweatbands or leg warmers in the room (i was kind of disappointed)! we did however, do an occasional jazz walk but no jazz hands ;)

*images courtesy of lonny, la masion boheme, cottage living, everything leb

If horses were wishes

Photo by Stuck in Customs

Sometimes I wish I had a cadre of graduate students to help me out with my research. The irony is that in order to prove to future employers that I am able to supervise graduate students, I need to prove that I am capable of "independent research". But the grim reality of independent research in my subfield means sitting in the lab all day and all night alone, toiling away. I do get help along the way, I do "outsource" when I can, but in the end it's up to me to wrap together the whole kit n' caboodle and make the magic happen.

I guess it's different in the biosciences or physics where a whole team of people are working late in the lab on an experiment. But in my field you pretty much fly solo. Even when I collaborate with other researchers, somehow it's still just me writing the bulk of the software, collecting the data, analyzing the results, and writing the paper. (And, apparently, complaining on my blog :))

How collaborative is your work?

i'm wishing....

for a happy monday.....and that i don't fall on my face tonight at jazzercise b/c my neighbor is making me go (yep, i said it- jazzercise...i bet you thought it ended in the 80's...i'm practicing my jazz hands as we speak).

*images courtesy of unknown, suzie beezie, amelia handegan

Tropical Plant Fats: Coconut Oil, Part II

Heart Disease: Animal Studies

Although humans aren't rats, animal studies are useful because they can be tightly controlled and experiments can last for a significant portion of an animal's lifespan. It's essentially impossible to do a tightly controlled 20-year feeding study in humans.

The first paper I'd like to discuss come from the lab of Dr. Thankappan Rajamohan at the university of Kerala (1). Investigators fed three groups of rats different diets:

1. Sunflower oil plus added cholesterol
2. Copra oil, a coconut oil pressed from dried coconuts, plus added cholesterol
3. Freshly pressed virgin coconut oil, plus added cholesterol

Diets 1 and 2 resulted in similar lipids, while diet 3 resulted in lower LDL and higher HDL. A second study also showed that diet 3 resulted in lower oxidized LDL, a dominant heart disease risk factor (2). Overall, these papers showed that freshly pressed virgin coconut oil, with its full complement of "minor constituents"*, partially protects rats against the harmful effects of cholesterol overfeeding. These are the only papers I could find on the cardiovascular effects of unrefined coconut oil in animals!

Although unrefined coconut oil appears to be superior, even refined coconut oil isn't as bad as it's made out to be. For example, compared to refined olive oil, refined coconut oil protects against atherosclerosis (hardening and thickening of the arteries) in a mouse model of coronary heart disease (LDL receptor knockout). In the same paper, coconut oil caused more atherosclerosis in a different mouse model (ApoE knockout) (3). So the vascular effects of coconut oil depend in part on the animals' genetic background.

In general, I've found that the data are extremely variable from one study to the next, with no consistent trend showing refined coconut oil to be protective or harmful relative to refined monounsaturated fats (like olive oil) (4). In some cases, polyunsaturated oils cause less atherosclerosis than coconut oil in the context of an extreme high-cholesterol diet because they sometimes lead to blood lipid levels that are up to 50% lower. However, even this isn't consistent across experiments. Keep in mind that atherosclerosis is only one factor in heart attack risk.

What happens if you feed coconut oil to animals without adding cholesterol, and without giving them genetic mutations that promote atherosclerosis? Again, the data are contradictory. In rabbits, one investigator showed that serum cholesterol increases transiently, returning to baseline after about 6 months, and atherosclerosis does not ensue (5). A different investigator showed that coconut oil feeding results in lower blood lipid oxidation than sunflower oil (6). Yet a study from the 1980s showed that in the context of a terrible diet composition (40% sugar, isolated casein, fat, vitamins and minerals), refined coconut oil causes elevated blood lipids and atherosclerosis (7). This is almost certainly because overall diet quality influences the response to dietary fats in rabbits, as it does in other mammals.

Heart Disease: Human Studies

It's one of the great tragedies of modern biomedical research that most studies focus on nutrients rather than foods. This phenomenon is called "nutritionism". Consequently, most of the studies on coconut oil used a refined version, because the investigators were most interested in the effect of specific fatty acids. The vitamins, polyphenols and other minor constituents of unrefined oils are eliminated because they are known to alter the biological effects of the fats themselves. Unfortunately, any findings that result from these experiments apply only to refined fats. This is the fallacy of the "X fatty acid does this and that" type statements-- they ignore the biological complexity of whole foods. They would probably be correct if you were drinking purified fatty acids from a beaker.

Generally, the short-term feeding studies using refined coconut oil show that it increases both LDL ("bad cholesterol") and HDL ("good cholesterol"), although there is so much variability between studies that it makes firm conclusions difficult to draw (8, 9). As I've written in the past, the ability of saturated fats to elevate LDL appears to be temporary; both human and certain animal studies show that it disappears on timescales of one year or longer (10, 11). That hasn't been shown specifically for coconut oil that I'm aware of, but it could be one of the reasons why traditional cultures eating high-coconut diets don't have elevated serum cholesterol.

Another marker of cardiovascular disease risk is lipoprotein (a), abbreviated Lp(a). This lipoprotein is a carrier for oxidized lipids in the blood, and it correlates with a higher risk of heart attack. Refined coconut oil appears to lower Lp(a), while refined sunflower oil increases it (12).

Unfortunately, I haven't been able to find any particularly informative studies on unrefined coconut oil in humans. The closest I found was a study from Brazil showing that coconut oil reduced abdominal obesity better than soybean oil in conjunction with a low-calorie diet, without increasing LDL (13). It would be nice to have more evidence in humans confirming what has been shown in rats that there's a big difference between unrefined and refined coconut oil.

Coconut Oil and Body Fat

In addition to the study mentioned above, a number of experiments in animals have shown that "medium-chain triglycerides", the predominant type of fat in coconut oil, lead to a lower body fat percentage than most other fats (14). These findings have been replicated numerous times in humans, although the results have not always been consistent (15). It's interesting to me that these very same medium-chain saturated fats that are being researched as a fat loss tool are also considered by mainstream diet-heart researchers to be among the most deadly fatty acids.

Coconut Oil and Cancer

Refined coconut oil produces less cancer than seed oils in experimental animals, probably because it's much lower in omega-6 polyunsaturated fat (16, 17). I haven't seen any data in humans.

The Bottom Line

There's very little known about the effect of unrefined coconut oil on animal and human health, however what is published appears to be positive, and is broadly consistent with the health of traditional cultures eating unrefined coconut foods. The data on refined coconut oil are conflicting and frustrating to sort through. The effects of refined coconut oil seem to depend highly on dietary context and genetic background. In my opinion, virgin coconut oil can be part of a healthy diet, and may even have health benefits in some contexts.


* Substances other than the fat itself, e.g. vitamin E and polyphenols. These are removed during oil refining.

cooking part II

or rather take two!! good thing i have another year to perfect my skills....see i'm all smiles in the pic b/c i think i have mastered the empanada (which is seriously a fancy word for hot pocket)...until my husband reads the recipe and says we're suppose to have 12 and we only have 6. whoops! reading the instructions correctly is always a plus when cooking. they had twice as much dough as they were suppose to but it didn't ruin dinner. i am not giving up on my quest. i want to try them again and this time, i should lay off the wine until dinner :)

ps. seleta, thanks for my bracelet...i love her ;)

cooking...

i'm 31 and i want to cook. i mean, i can cook; warren and i enjoy doing it but i want to learn to really cook. according to julia, i have one year left before i really have to get down to business. i'm making homemade empanadas (thanks sis-in-law) for supper tonight....i figure i need the practice :)

*images courtesy of high street market, the city sage, apartment #34, urban electric, southern living

Tropical Plant Fats: Coconut Oil, Part I

Traditional Uses for Coconut

Coconut palms are used for a variety of purposes throughout the tropics. Here are a few quotes from the book Polynesia in Early Historic Times:

Most palms begin to produce nuts about five years after germination and continue to yield them for forty to sixty years at a continuous (i.e., nonseasonal) rate, producing about fifty nuts a year. The immature nut contains a tangy liquid that in time transforms into a layer of hard, white flesh on the inner surface of the shell and, somewhat later, a spongy mass of embryo in the nut's cavity. The liquid of the immature nut was often drunk, and the spongy embryo of the mature nut often eaten, raw or cooked, but most nuts used for food were harvested after the meat had been deposited and before the embryo had begun to form...

After the nut had been split, the most common method of extracting its hardened flesh was by scraping it out of the shell with a saw-toothed tool of wood, shell, or stone, usually lashed to a three-footed stand. The shredded meat was then eaten either raw or mixed with some starchy food and then cooked, or had its oily cream extracted, by some form of squeezing, for cooking with other foods or for cosmetic or medical uses...

Those Polynesians fortunate enough to have coconut palms utilized their components not only for drink and food-- in some places the most important, indeed life-supporting food-- but also for building-frames, thatch, screens, caulking material, containers, matting, cordage, weapons, armor, cosmetics, medicine, etc.

Mainstream Ire

Coconut fat is roughly 90 percent saturated, making it one of the most highly saturated fats on the planet. For this reason, it has been the subject of grave pronouncements by health authorities over the course of the last half century, resulting in its near elimination from the industrial food system. If the hypothesis that saturated fat causes heart disease and other health problems is correct, eating coconut oil regularly should tuck us in for a very long nap.

Coconut Eaters

As the Polynesians spread throughout the Eastern Pacific islands, they encountered shallow coral atolls that were not able to sustain their traditional starchy staples, taro, yams and breadfruit. Due to its extreme tolerance for poor, salty soils, the coconut palm was nearly the only food crop that would grow on these islands*. Therefore, their inhabitants lived almost exclusively on coconut and seafood for hundreds of years.

One group of islands that falls into this category is Tokelau, which fortunately for us was the subject of a major epidemiological study that spanned the years 1968 to 1982: the Tokelau Island Migrant Study (1). By this time, Tokelauans had managed to grow some starchy foods such as taro and breadfruit (introduced in the 20th century by Europeans), as well as obtaining some white flour and sugar, but their calories still came predominantly from coconut.

Over the time period in question, Tokelauans obtained roughly half their calories from coconut, placing them among the most extreme consumers of saturated fat in the world. Not only was their blood cholesterol lower than the average Westerner, but their hypertension rate was low, and physicians found no trace of previous heart attacks by ECG (age-adjusted rates: 0.0% in Tokelau vs 3.5% in Tecumseh USA). Migrating to New Zealand and cutting saturated fat intake in half was associated with a rise in ECG signs of heart attack (1.0% age-adjusted) (2, 3).

Diabetes was low in men and average in women by modern Western standards, but increased significantly upon migration to New Zealand and reduction of coconut intake (4). Non-migrant Tokelauans gained body fat at a slower rate than migrants, despite higher physical activity in the latter (5). Together, this evidence seriously challenges the idea that coconut is unhealthy.

The Kitavans also eat an amount of coconut fat that would make Dr. Ancel Keys blush. Dr. Staffan Lindeberg found that they got 21% of their 2,200 calories per day from fat, nearly all of which came from coconut. They were getting 17% of their calories from saturated fat; 55% more than the average American. Dr. Lindeberg's detailed series of studies found no trace of coronary heart disease or stroke, nor any obesity, diabetes or senile dementia even in the very old (6, 7).

Of course, the Tokelauans, Kitavans and other traditional cultures were not eating coconut in the form of refined, hydrogenated coconut oil cake icing. That distinction will be important when I discuss what the biomedical literature has to say in the next post.


* Most also had pandanus palms, which are also tolerant of poor soils and whose fruit provided a small amount of starch and sugar.

Theorem 8.10. P ≠ NP.

Nearly two weeks ago Indian-American mathematician Vinay Deolalikar, the employee of HP Labs, sent a letter to a group of mathematicians asking them to proof-read his attempt to prove P ≠ NP. The pre-print was eventually distributed over the Internet, so a lot of people became aware. Later two major flaws were found in the proof, so it is now considered wrong. Nevertheless, Vinay has removed the paper from his page and commented that he fixed all the issues and is going to submit a paper to the journal review. You can download the original paper from my web-site [Deolalikar, 2010].

We'll see if he is bluffing or not. In any case, it is very pleasant to me that the main role in the proof is played by... the graphical probabilistic model framework. Yeah, those graphical models we use in computer vision! It was surprising indeed, since the problems in computational complexity are usually discrete and well-posed. So, this post is devoted to understanding why a graphical model emerges in the proof.

First, I am going to review some key points of the proof. It is far from being exhaustive, just some rough sketches that are critical for understanding. Then I report on the flaws found in the proof, and then I end up with a methodological note on the whole P vs. NP problem.

k-SAT and d1RSB Phase

In order to prove P ≠ NP, it is enough to show the absence of a polynomial algorithm for some problem from the class NP, e.g. for some NP-complete problem (which are the "hardest" problems in NP). The boolean satisfiability problem (SAT) addresses the issue of checking if there is at least one assignment of the boolean variables in the formula, represented in conjunctive normal form (CNF), which makes it TRUE. The k-satisfiability problem (k-SAT) is a particular case of SAT, where all the clauses in the CNF have order k. For example, (x˅y)&(¬x˅y)&(x˅¬y)&(¬x˅¬y) is an instance of 2-SAT which has the answer 'NO', since any boolean values of (x, y) makes the formula false. (x˅y˅z)&(¬x˅u˅v)&(¬x˅u˅¬z) is a 3-SAT over 5 variables (x, y, z, u, v), which is satisfiable, e.g. on the input (1,0,0,1,0). 2-SAT is in P, but k-SAT is NP-complete whenever k > 2. The Deolalikar's idea is to show that k-SAT (with k > 8) is outside of P, which (if true) proves that there is a separation between P and NP.

The space of possible k-SAT solutions is analysed. Let m be the number of clauses in the CNF, n be the number of variables. Consider the ratio α = m/n. In the border case m = 1 (α is small), k-SAT is always true, there are usually a lot of inputs that satisfy the CNF. Consider an ensemble of random k-SATs (the following is statistical reasoning). With the growth of α, the probability of the CNF to be satisfiable decreases. When a certain threshold α_d is reached, the "true" solutions set breaks into clusters. This stage is known in statistical mechanics as dynamical one step replica symmetry breaking (d1RSB) phase. Moving further, we make the problem completely unsatisfiable. It turns out that d1RSB stage subproblems are the most challenging of the all k-SAT problems. The effect could be observed only if k > 8, that's why such problems are used in the proof. [Deolalikar, 2010, Chapter 6]

FO(PFP) and FO(LFP)

In the finite model theory there are recurrent extensions of the first-order logic. The predicate P_i(x) is evaluated as some second-order function φ(P_i-1, x), where x is a k-element vector, P₀(x) ≡ false. In the general case, either there is a fixed point, or is P_i looping. For example, if φ(P, x) ≡ ¬P(x), then P₀(x) ≡ false, P₁(x) ≡ true, P₂(x) ≡ false, etc. Here x is meaningless, but it is not always the case. Consider the following definition: φ(P, x) ≡ max(x) ˅ P(x) // recall x is a vector, in the boolean case 'max' is the same as 'or'. If x contains at least one non-zero element, P₀(x) = false, P₁(x) = true, P₂(x) = true, etc. Otherwise, P_i(0) = false for all i. In the case of looping, let's redefine the fixed point to be constantly false. FO(PFP) is a class of problems of checking if there will be a loop for some x, or a fixed point. They are actually very difficult problems. FO(PFP) is equal to the whole PSPACE. Suppose now that φ is monotonic on P. It means that P(x) only appears in the formula with even number of negations before it (or zero, as in the second example). This means that once P_i(x) is true, P_j(x) will be true for any j > i. This reduces the class to FO(LFP), which is proven to be equal to the class P. So, the global problem now is to show that k-SAT is outside of the class FO(LFP).

ENSP: the graphical model for proving P ≠ NP

So how a graphical model emerges here? Graphical model is a way to describe a multivariate probability distribution, i.e. dependencies of covariates in the distribution. Recall now the definition of NP. If we somehow guess the certificate, we are done (i.e. have a polynomial algorithm). If the space of certificates (possible solutions, in terms of Deolalikar) is simple, we can probably get a polynomial algorithm. What is simple? This means that the distribution is parametrizable with a small amount of parameters (c.f. intrinsic dimensionality), which allows us to traverse the solution space efficiently. This is twofold. First, the distribution is simple if it has a limited support, i.e. all the probability measure is distributed among a limited number of points of the probabilistic space. Second, it is simple if the covariates are as much conditionally independent as possible. In the ideal case, if all the groups of covariates are independent (recall that pairwise and mutual independence do not subsume each other!), we need only n parameters to describe the distribution (n is the number of covariates), while in general case this number is exponential. See [Deolalikar, 2010, p. 6] for examples.

How to measure the degree of conditional independence? Yes, to build a graphical model. It is factorized to cliques according to Hammersley-Clifford theorem. Larger cliques you get, stronger dependency is. When the largest cliques are k-interactions, the distribution can be parametrized with n2^k independent parameters. Finally, Vinay shows that FO(LFP) can deal only with the distributions parametrizable with 2^{poly(log n)} parameters, which is not the case for d1RSB k-SAT (its solution space is too complicated).

In order to show it strictly, Deolalikar introduces a tailored graphical model describing LO(LPF) iterative process, the Element-Neighborhood-Stage Product model (ENSP):

There are two types of sites: corresponding to the variables on the stages of LFP (small circles) and corresponding to the elements of witty neighbourhood system (some closure over Gaifman graph; big blue circles). When a variable is assigned 0 or 1, it is painted with red or green respectively. The last column corresponds to the fixed point, all the variables are assigned. Thus, this model is easily factorizable to the small cliques, and it cannot describe the imaginable LFP process for some k-SAT. See [Deolalikar, 2010, Chapter 8] for the details.

So what's the problem?

Neil Immerman, an expert in the finite model theory, noticed two major flaws. The first one is that Vinay actually model only monadic LFP, which is not equal to P, as assumed. He thus proved that there is a gap between NP and some subclass of P, which is not obligatory equals P. The second major flow deals with modelling k-SAT as a logical structure. I do not fully understand this step, but some order-invariance assumptions are wrong. Here is a discussion in Lipton's blog. According to it, the flaws are really fatal.

The third way

It seems that it is really difficult to prove P ≠ NP. The most of scientists think that P = NP is improbable, and that's why the hypothesis P ≠ NP is generally adopted now. But there is one more option: neither P = NP nor P ≠ NP is provable. As every mathematical theory, computational complexity is a set of axioms and statements, which are usually could be proved to be correct or not. But there are sometimes some statements formulated in terms of the theory, which could not. Moreover, according to the first Gödel's incompleteness theorem, in any mathematical theory based on our natural understanding of natural numbers, there is either a statement that could be proved both true or false, or an unprovable one. I know no actual reasons why this could not be the case for P ≠ NP (although I have feelings there are some since it is not usually taken into account).

Suppose it is really so. This would mean that the whole theory should be reconsidered. Some axioms or definitions will change to make this fact provable. But may be anything else will become unprovable. Who knows...

Regarding Quotas

In my post on nurture vs. nature, thehackerfairy asked about my thoughts on some comments left after a recent Guardian article on this topic. The article helps support my claim that really it's a social problem we're facing in CS, not some difference due to biology. And the article cites my favorite developmental neuroscientist, Lise Eliot, as support.

I couldn't find the particular comment HF was alluding to, but I think the basic idea was, "Well, if men and women are biologically equal, let's get rid of quotas / affirmative action / encouragement initiatives / etc." I've seen this argument pop up in other communities of underrepresented people as well.

Here's my opinion: I am more than happy to see all of these inclusion initiatives be eliminated... once the groups of people they're targeting stop being systematically discriminated against. And for anyone who doesn't think women, people of color, people with disabilities, and LGBT people are being systematically discriminated against in STEM, I say: please come out from under that rock.

Khasiat Pegagan untuk Tumpas TBC (Tuberkulosis)

Testimoni Pegagan
Seorang teman bercerita, betapa frustrasinya ia menumpas tuberkulosis (TB) paru-paru. Digempur pakai obat-obatan medis, si penyakit tetap saja eksis. Ia juga panik, karena katanya, bakteri TB bisa kebal terhadap gempuran obat yang diracik apotik. Untunglah, saat nyaris frustrasi, ia “menemukan” pegagan.

Menjalani “takdir” sebagai penderita TB paru-paru memang tak gampang. Jika tidak ulet, alih-alih sembuh, pasien bisa mati bosan. Maklum, proses penyembuhan TB, selain cukup sulit, juga makan waktu lama, berkisar 3 – 6 bulan. Itu pun dengan catatan, pasien berdisiplin minum obat dan rajin memeriksakan diri ke dokter.

Lamanya pengobatan itulah – apalagi jika disertai kendala biaya – yang kerap menyebabkan pasien frustrasi. Ya frustrasi minum obat, ya bosan menanggung derita. Padahal, disiplin minum obat menjadi faktor penentu dalam proses penyembuhan. Pengobatan yang tidak tuntas dapat menyebabkan bakteri TB resisten terhadap beragam obat konvensional, termasuk obat kombinasi.

Dengan kata lain, pasien TB sebenarnya dilarang keras menoleransi kata bosan, apalagi sampai putus asa. Itu sebabnya, buat teman tadi, perjumpaan dengan pegagan dan kawan sejawatnya menjadi sangat berarti. Paling tidak, ia merasa tak “sendiri” lagi menghadapi tuberkulosis. Ketika banyak sanak saudara dan handai taulan menjauh lantaran takut tertular, pegagan dan kawan-kawan menjadi teman paling setia.

Yang paling penting, harga mereka murah dan tak membuat kantung cekak jika dikonsumsi dalam kurun waktu lama.

Pegagan Menghambat & menghancurkan

Pegagan atau nama kerennya Centella asiatica itu tumbuhan liar yang ada di dataran rendah, sampai sekitar 2.500 m di atas permukaan air laut.

Secara empiris, biasa digunakan sebagai tonik, antiinfeksi, antirematik, penenang, mempercepat penyembuhan luka, dan diuretik. Berbagai penelitian telah dilakukan guna mendukung manfaat empirisnya.

Misalnya, penelitian yang merujuk pegagan sebagai antiinflamasi, antioksidan, antitumor, atau untuk meningkatkan daya ingat (susunan saraf pusat), eksem (luka terbuka), dan hepatitis. Hal itu berkaitan dengan kandungan senyawa yang dimiliki pegagan, yaitu asiaticiside, thankuniside, medecassoside, brahmoside, brahminoside, madastic acid, vitamin B1, B2, dan B6.

Dari berbagai penelitian in vitro terhadap pegagan menemukan kemampuannya menghancurkan berbagai bakteri penyebab infeksi, seperti Staphylococcus aureus, Escherechia coli, Pseudomonas aeruginosa, Salmonella typhi, dan sejenisnya. Sementara dalam bentuk infus atau ekstrak etanol, tumbuhan ini dipercaya dapat menghambat pertumbuhan bakteri.

Laorpuksa A. dan kawan-kawan dalam penelitian pada 1988 membuktikan, estrak air pegagan dapat melawan bakteri yang menyebabkan infeksi pada saluran napas. Sementara Herbert D. dan kawan-kawan dari Tuberculosis Research Center di India mencoba efek pegagan pada bakteri tuberkulosis H37Rv secara in vitro. Hasilnya, pegagan tidak langsung berefek pada bakteri tuberkulosis. Namun, Herbert menyarankan penelitian lebih lanjut terhadap senyawa aktif asiaticoside.

Feeling Herbert terbukti benar. Berdasarkan penelitian lanjutan, senyawa aktif pegagan itu ternyata dapat melawan Mycobakterium tuberculosis dan Bacillus leprae (Oliver-Bever, 1986). Penelitian berikutnya yang dilakukan Walter H. Lewis juga menyatakan, pegagan termasuk kelompok tanaman yang menghasilkan zat seperti antibiotika dan asiaticoside.

Uji Keampuhan Pegagan
Keampuhan pegagan juga telah diuji coba oleh Boeteau P. dan kawan-kawan, yang menginokulasi binatang percobaan marmut dengan bakteri basilus tuberkulosis selama 15 hari. Injeksi 0,5 ml 4% asiaticoside yang diberikan pada marmut, terbukti dapat mengurangi jumlah lesi tuberkular di paru-paru, hati, dan limpa. Senyawa asiaticoside membuat pegagan tak hanya dapat menghambat pertumbuhan bakteri tuberkulosis, tapi juga berpotensi sebagai imunomodulator – peningkat daya tahan tubuh.

Secara empiris, pemanfaatan pegagan untuk membasmi tuberkulosis paru-paru dapat dilakukan dengan berpedoman pada resep berikut. Cuci 30 – 60 g pegagan segar, lalu rebus dalam 3 gelas air sampai tersisa 1 gelas, dan diminum 3 kali sehari. Untuk TB kulit, lumatkan pegagan, kemudian tempelkan pada bagian yang sakit.

NB:
Utk atasi TBC herbal yang direkomendasikan terdiri dari :
1. Cakar ayam
2. Sambiloto
3. Pegagan
MInum 3x1 selama 1 bulan kemudian jeda 1 minggu dan lanjutkan lagi.
Info lebih lanjut bs contact : 081310343598 , budiprakoso98@gmail.com atau YM : budi_prakoso98

Sumber:
http://cintaherbal.wordpress.com (dikutip dari Khasiat Pegagan, dari penumpas TBC sampai peningkat daya ingat, www.depkes.go.id)

white wash....

loving these white wash spaces.....they feel so clean and crisp. if only i didn't have sippy cups, crayons, and grape jelly to deal with :)

*images courtesy of donna griffith, unknown, the city sage, unknown

hello everyone!! i have lots of stuff to do today since i have been away for a week but i love this quote and thought it would be a great way to start off monday!! and i couldn't help throwing in a pic of walker on vacay!! his dad, uncle, and grandfather caught some crab and so he thought he would show them off :)

*images courtesy of forever love stoned, me

Image Parsing: Unifying Segmentation, Detection, and Recognition

Recently I have posted about the connection between object category detection and semantic image segmentation. While delving into this problem more deeply, I have found the paper denoted in the title of this post.

The ICCV 2003 paper by Tu et al. was among the three Marr prize winners. And it is really a prominent piece of work! In the introduction to the special Marr prize IJCV issue, Bill Triggs featured the paper as one that "would have been particularly pleasing to David Marr", because of "its bold attack on the central problem of perceptual organization and whole scene understanding". Here is the journal version of the paper.

The authors combined discriminative and generative models, which resulted to the unified framework for image parsing. For each image the corresponding parsing tree could be found. The root of the tree represents the whole scene. On the next level, nodes represent semantic fragments, such as human faces, text, or textured regions. The leaves of the tree correspond to the pixels of the image.

The approach differs drastically from the vanilla CRF framework in the way that the structure of the parsing tree is dynamic while the CRF structure remains constant and just interaction models between the pairs of sites may change. The goal is to obtain the tree that maximizes the posterior probability given the image. The directed search in the space of valid trees is performed by means of Markov chain Monte-Carlo (MCMC). The possible tree changes like split and merge of regions, varying the border between regions, are defined. Such changes are described in terms of learnable Markov chain transition kernels.

What they actually did is they effectively combined top-down and bottom-up approaches. In a nutshell, the bottom-up (discriminative) method generates the hypotheses of pixel labels and object positions using the local neighbourhood, and the top-down generative model is then built making use of those hypotheses. The latest guarantees the consistency of the output and the optimum of its posterior probability.

Okay, what does it mean for the issue of detection and segmentation convergence? Because the shapes of objects are determined implicitly during the recognition, and stuff regions are detected by their colour and texture, the problem of semantic image segmentation is actually solved. Moreover, multi-scale semantic segmentation is performed during the parsing. Therefore, image parsing seems to be the most general formulation of image recognition problem.

The nodes of a parsing tree, which belong to the same depth level, are not connected (right, because it is a tree). This means that spatial interactions could not be modelled directly. A totally different approach was introduced in another Marr prize winning paper by Desai et al [2009]. They also use bottom-up tests to generate hypotheses on the object locations and then use CRF over those location to take spatial context into account. They model different kinds of inter-class and intra-class interactions. Thus, they ensure that the objects in the image (described by their bounding boxes) are arranged correctly, e.g. a cup is likely to be on a table (spatial arrangement), while a train could not be close to a ship (mutual exclusion).

It seems that the two papers exploit the two different forms of information (aggregation vs. spatial interactions), which are mutually redundant to a certain extent, but do not completely exhaust each other. It seems that the group of researchers who will successfully combine those approaches will receive some 201x Marr prize.

Can a Statin Neutralize the Cardiovascular Risk of Unhealthy Dietary Choices?

The title of this post is the exact title of a recent editorial in the American Journal of Cardiology (1). Investigators calculated the "risk for cardiovascular disease associated with the total fat and trans fat content of fast foods", and compared it to the "risk decrease provided by daily statin consumption". Here's what they found:

The risk reduction associated with the daily consumption of most statins, with the exception of pravastatin, is more powerful than the risk increase caused by the daily extra fat intake associated with a 7-oz hamburger (Quarter Pounder®) with cheese and a small milkshake. In conclusion, statin therapy can neutralize the cardiovascular risk caused by harmful diet choices.

Routine accessibility of statins in establishments providing unhealthy food might be a rational modern means to offset the cardiovascular risk. Fast food outlets already offer free condiments to supplement meals. A free statin-containing accompaniment would offer cardiovascular benefits, opposite to the effects of equally available salt, sugar, and high-fat condiments. Although no substitute for systematic lifestyle improvements, including healthy diet, regular exercise, weight loss, and smoking cessation, complimentary statin packets would add, at little cost, 1 positive choice to a panoply of negative ones.

Wow. Later in the editorial, they recommend "a new and protective packet, “MacStatin,” which could be sprinkled onto a Quarter Pounder or into a milkshake." I'm not making this up!

I can't be sure, but I think there's a pretty good chance the authors were being facetious in this editorial, in which case I think a) it's hilarious, b) most people aren't going to get the joke. If they are joking, the editorial is designed to shine a light on the sad state of mainstream preventive healthcare. Rather than trying to educate people and change the deadly industrial food system, which is at the root of a constellation of health problems, many people think it's acceptable to partially correct one health risk by tinkering with the human metabolism using drugs. To be fair, most people aren't willing to change their diet and lifestyle habits (and perhaps for some it's even too late), so frustrated physicians prescribe drugs to mitigate the risk. I accept that. But if our society is really committed to its own health and well-being, we'll remove the artificial incentives that favor industrial food, and educate children from a young age on how to eat well.

I think one of the main challenges we face is that our current system is immensely lucrative for powerful financial interests. Industrial agriculture lines the pockets of a few large farmers and executives (while smaller farmers go broke and get bought out), industrial food processing concentrates profit among a handful of mega-manufacturers, and then people who are made ill by the resulting food spend an exorbitant amount of money on increasingly sophisticated (and expensive) healthcare. It's a system that effectively milks US citizens for a huge amount of money, and keeps the economy rolling at the expense of the average person's well-being. All of these groups have powerful lobbies that ensure the continuity of the current system. Litigation isn't the main reason our healthcare is so expensive in the US; high levels of chronic disease, expensive new technology, a "kitchen sink" treatment approach, and inefficient private companies are the real reasons.

If the editorial is serious, there are so many things wrong with it I don't even know where to begin. Here are a few problems:

1. They assume the risk of heart attack conveyed by eating fast food is due to its total and trans fat content, which is simplistic. To support that supposition, they cite one study: the Health Professionals Follow-up Study (2). This is one of the best diet-health observational studies conducted to date. The authors of the editorial appear not to have read the study carefully, because it found no association between total or saturated fat intake and heart attack risk, when adjusted for confounding variables. The number they quoted (relative risk = 1.23) was before adjustment for fiber intake (relative risk = 1.02 after adjustment), and in any case, it was not statistically significant even before adjustment. How did that get past peer review? Answer: reviewers aren't critical of hypotheses they like.
   
2. Statins mostly work in middle-aged men, and reduce the risk of heart attack by about one quarter. The authors excluded several recent unsupportive trials from their analysis. Dr. Michel de Lorgeril reviewed these trials recently (3). For these reasons, adding a statin to fast food would probably have a negligible effect on the heart attack risk of the general population.
   
3. "Statins rarely cause negative side effects." BS. Of the half dozen people I know who have gone on statins, all of them have had some kind of negative side effect, two of them unpleasant enough that they discontinued treatment against their doctor's wishes. Several of them who remained on statins are unlikely to benefit because of their demographic, yet they remain on statins on their doctors' advice.
   
4. Industrial food is probably the main contributor to heart attack risk. Cultures that don't eat industrial food are almost totally free of heart attacks, as demonstrated by a variety of high-quality studies (4, 5, 6, 7, 8, 9). No drug can replicate that, not even close.
   

I have an alternative proposal. Rather than giving people statins along with their Big Mac, why don't we change the incentive structure that artificially favors the Big Mac, french fries and soft drink? If it weren't for corn, soybean and wheat subsidies, fast food wouldn't be so cheap. Neither would any other processed food. Fresh, whole food would be price competitive with industrial food, particularly if we applied the grain subsidies to more wholesome foods. Grass-fed beef and dairy would cost the same as grain-fed. I'm no economist, so I don't know how realistic this really is. However, my central point still stands: we can change the incentive structure so that it no longer artificially favors industrial food. That will require that the American public get fed up and finally butt heads with special interest groups.

Open peer review done right

There's been a lot of talk recently on the idea of open peer review, open source science, and so on. arXiv was sort of intended to serve this role, but at least in my subfield it's uncommon to put papers on there before they've been accepted by a "proper" conference/journal. In general we use it for open archival purposes, but not for initial peer review.

Image by Network Osaka

However, I recently saw a really nice use of open peer review. Vinay Deolalikar of HP Labs sent a manuscript to a few of his colleagues which was a proof of P ≠ NP. This is one of the most fundamental unsolved problems in CS, in fact it's such an important problem that The Clay Mathematics Institute offers a $1 million prize to anyone who can solve it. I won't burden you with the details of the problem or proof because that's not what this post is about, and will instead refer you to this excellent summary in New Scientist if you are interested.

So Deolalikar sent this proof to his colleagues, and Greg Baker (with permission) posted the manuscript on his blog. Somehow the blog post got Slashdotted and next thing you know everyone was talking about it. What I find really remarkable was how in many places there was a nice, civil discussion among the theory types about the strengths and weaknesses of the proof. (You can read about this in Richard Lipton's blog starting here).

What I especially loved was the peanut gallery. People were just thrilled to be watching the action. Even people with no background on the topic were offering support and encouragement. Here are some comments from Lipton's blog:

 Go Vinay!

I agree with the spirit of this posting. I am not an expert in complexity theory so I am unable to provide any feedback (not even elementary). However, I like it that there are researchers like Vinay who are not afraid of tackling the hardest problems. I am anxious to know what are the consequences of Vinay’s work.

-Anon@ 11:23pm

And these two really made me say, "awwww" (boldface is mine):

Professor Lipton,

Your accessible and well-written writings motivate me to continue studying mathematics. I develop software for a living; to stay sharp, I try to study ‘real’ proofs in my spare time. Complexity is an amazing field… I cannot wait to see what we’ll learn about computation (and its relation to physics, and to everything else).

Thanks for the inspiration!

-Robert W 

“P.S. I hope these discussions are helpful to the community at large.”

This member of the community at large can’t understand a word you say, but is nevertheless fascinated by every new post and comment. Seeing the review process unfold in public has rekindled my long-dormant interest in mathematics. I intend to register for a class this fall and (who knows?) perhaps pursue that Ph.D. after all these years.

Don’t infer from the paucity of experts who can contribute to the public conversation that you might as well confer entirely in private; on the contrary, public discussion is an immense service to the community. Thank you.

-Fritz Juhnke

I applaud Lipton for cultivating a positive exchange of ideas and place for civil discussion and making the review public for all to watch. Even though things got heated at times, in general the discourse was constructive and positive. Top complexity theoreticians came together to help Deolalikar out, for no reason other than they think it's a cool problem and they're nice people, and I think that's just fantastic.

ALTERNATIF HERBAL UNTUK ATASI LIMFOMA....

Limfoma atau kelenjar getah bening dicirikan adanya benjolan yg biasa terdapat di bagian leher atau bagian-bagian tubuh lainnya terutama di bagian lipatan seperti ketiak, kaki dll. Penyakit ini biasanya pada tahap awal berupa tumor dan bila tidak cepat diatasi akan berkembang ke stadium lanjut berupa kanker.. dan kanker juga berkembang cepat ke stadium yang makin lama makin tinggi.

Limfoma ini sebenarnya bisa segera diatasi, terutama bila masih dalam stadium awal. Pemicu utama dari Limfoma ini banyak faktor mulai dari makanan dan lingkungan. Makanan yang mengandung pemanis-pewarna-pengawet buatan, vetsin, softdrink,makanan yang dibakar, ikan asin, daging dll. sedangkan lingkungan bisa menjadi pemicu kalau lingkungan tersebut terkontaminasi oleh logam berat.

Limfoma tidak saja diidap oleh orang dewasa tetapi juga bisa diidap oleh anak-anak, hal ini karena dipengaruhi oleh jenis makanan yang dimakan mengandung zat-zat yang menjadi pemicu terjadinya limfoma.

Pengobatn secara medis biasanya dengan melakuan penyinaran atau paling akhir dengan kemoterapi. bagi masyarakat yang biasa ke-2 pengobatan ini akan sangat membebani karena biaya yang sangat besar dan hasilnya kadang belum pasti.

Berdasarkan pengalaman saya selama ini, saya sering membantu masyarakat yang mencari alternatif herbal untuk menyembuhkan atau meringankan sakit akibat limfoma tersebut. Herbal yang saya rekomendasikan sudah standar yaitu :
1. Lhiforcan (keladi tikus, temu putih dan sambiloto)
2. Tapak dara
3. Rumput mutiara
Semua sdh bentuk kapsul sehingga memudahkan untuk dikonsumsi.Semua herbal tsb diminum selama 1 bulan penuh dgn dosis 3x1-2 (tergantung dari kondisi sakitnya), kemudian jeda 1 minggu dan lanjutkan lagi.

Dari beberapa informasi orang yang konsumsi herbal tersebut, ternyata hasilnya sangat memuaskan dan alhamdulillah sudah banyak yang teratasi. Berikut informasi yang disampaikan via tlp k saya sbb :
Pagi ini, jam 10.00 WIB tgl 21 Juli 2010 sy ditelepon Bp. Wasidi- Sragen,Jawa Tengah (085711284440) salah seorang pemesan herbal utk LIMFOMA, beliau ingin pesan lagi herbal utk limfoma. setelah sy tanyakan kondisi terakhirnya, beliau menyatakan banyak kemajuan setelah minum herbal tsb


Wass
Prakoso,budi
081310343598
YM : budi_prakoso98