7.23.2007

Quote of the Week: July 22

A lot has been said about Andrew Keen's new book, The Cult of the Amateur, in which he argues that the products of user-driven content communities (e.g., Wikipedia) often compare poorly to those produced by more traditional institutions.

Over at the Wikipedia Signpost, Wikipedia user Thespian opens his review of Andrew Keen's new book with this quip:
One of the hardest parts of reading The Cult of the Amateur is the temptation to agree with the author, Andrew Keen. It's tempting, when involved in an edit war, to pick up the book, read it, and say, "My god, he's right! People who don't have a clue are RUINING the Internet!", before stepping back and realizing, he's also talking about you.
For some reason, this reminds me of David Gerard's amusing (and doubtlessly true) note that
[M]assive collaboration is hard. The main problem is how to work with idiots you can’t get rid of, who consider you an idiot they can’t get rid of.

Women and Citizendium

Leslie Brooks has a short piece up asking “where the hell are the women in the Citizendium project?” I’m not impressed by the tone of the piece itself, but I think it is a good question (we do have more male than female contributors). Really, I think the question should be expanded to women and wikis in general– I would imagine that Wikipedia may be equally or moreso biased toward male contributors, but it’s just easier to tally up contributions by gender when people are editing under their real names. Regardless, engaging both male and female contributors is something we really need to think about.

I’m writing this as a personal response to Leslie’s blog post, not an official rejoinder.

Dear Leslie,

You can criticize with the intent to help, you can criticize with the intent to explore greater philosophical issues, or you can criticize to produce a neat little snarky blog post. I feel your post straddles the second and third.

Honestly, I think you cover some interesting philosophical ground– maybe wikis can be (tend to be?) biased against women (why is that?). It could be that, by bringing in many academic experts, Citizendium brings some of the biases you mention. I don’t know– but I find these issues interesting and I’d like to hear more.

But you don’t do real dialog about these issues any favors by only linking to criticisms of us (most of which I consider long-since rebutted) and ignoring all the other interesting things and quality dialog going on at Citizendium, nor by ignoring the most valid point of comparison (Wikipedia), nor by not offering any suggestions on what to do.

So I ask you, Leslie– please show your colors. Either make some suggestions on what we can do to help attract female contributors (keeping in mind there are many constraints involved with building an encyclopedia), or don’t. With respect, I submit that- particularly when dealing with volunteers- it takes more to make a positive difference in the world than a snarky blog post.

In the end, I think we’re on the same side. We all want Citizendium to be a welcoming place for female contributors (for philosophical, practical, and moral reasons), and we at Citizendium have thought about the issue and take it very seriously. We’re a group of volunteers that are juggling a lot of initiatives, and sometimes worthy causes don’t get the attention we would like to give them. If you give us a good, easy-to-implement idea, we very well may divert some of our precious, finite resources into it. We would love to have more women editing at Citizendium and are committed to it! And so if you have suggestions on what we can do to bring this about, we’d love to hear them.

But if you do want to suggest changes to Citizendium (and this goes for anyone), please:
1. don’t try to hijack our deliberation process with name-calling like Kali Tal did– she did her cause (a good cause) no favors by her actions– and
2. keep in mind that the vast majority of us are volunteers, that we’re operating under many (and sometimes non-obvious, complex) constraints connected to our main goal, that of building an encyclopedia, and that assuming good faith, being respectful of those you’d like to influence, and meeting people halfway aren’t just platitudes– they’re an important part of effectively working with people and bringing about the change you want.

So, thank you for raising the philosophical issue, Leslie– and I mean that sincerely– but I wish you had put more meat and more respect into your article.


Update, 7-24-07: Interested readers, please see the discussion attached to my crosspost on the Citizendium blog.

Scientific Research (3/5: Dark Energy)

What I'd do with a research lab, part 3:
Test a pet theory regarding Dark Energy

Working hypothesis: There is a fairly elegant modification to gravity that may explain Dark Energy, and that current MOND theories do not touch upon.

We've known since 1929 that our universe is expanding, but in 1998 we discovered that our universe is actually accelerating in its expansion. This flies in the face of accepted understandings of gravity and the Standard Model of quantum mechanics, neither of which allow for any reason that the universe should be expanding. We've come to call this force "Dark Energy" because it pushes the universe apart, just as the presence of energy does, yet we're unable to observe it.

I've been kicking around an idea of how Dark Energy might arise. It is, of course, a low-probability hypothesis, but there aren't really any front-runner theories on Dark Energy[1], the magnitudes involved in my hypothesis make sense, it's unique (to my knowledge), it'd be an elegant way to solve the problems of Dark Energy and inflation if it worked, and I think diversity of effort is very valuable in science. So I'd indulge myself. It's sort of a waiting game at this point since there isn't that much data on the historical expansion rate of the universe, which is really necessary to test these sorts of theories (elegant doesn't mean correct), but I do believe gathering such data is one of the highest priorities in cosmology.

I can hear a physicist in the background snort at my presumption. Quiet, you- get your own blog. :)

[1] Some theories which attempt to explain Dark Energy are listed at the Wikipedia page; physicists are also exploring a promising new option tying Dark Energy, Dark Matter, and inflation to supersymmetrical particles. A reasonably good overview of the new option may be found at Ars. If you're wondering what all this Dark Energy stuff is about, Wikipedia and NASA are good places to start.

Edit 11-7-07: It occurs to me I should put forward something falsifiable in this post.

My theory suggests that a universe with homogeneously distributed mass, in entropic equilibrium, and with no expansion momentum would (setting aside quantum fluxuations that would immediately bring it out of such equilibrum, and
contrary to all gravitational theories I'm familiar with) not collapse due to gravity. Rather, a "dark energy" term would arise which would precisely balance gravity. As the distribution of mass becomes less homogeneous, the dark energy term would naturally increase relative to gravity's effect on the universe's topology.

7.16.2007

Quote of the Week: July 15

From the New York Times article Make Money, Save the World, on efforts to decompartmentalize modern philanthropy by encouraging 'for-benefit corporations' or 'for-profit charities':

“There’s a big movement out there that is not yet recognized as a movement,” said R. Todd Johnson, a lawyer in San Francisco who is working to create an online wiki to engage in the give and take of information for what he calls “for-benefit corporations,” another name for fourth-sector activities. [...] Still, whatever participants call it, the fourth sector faces challenges. Current legal and tax structures draw strict lines between for-profits and nonprofits, and fiduciary obligations prevent asset managers from making investments with any aim other than maximizing profit.

[...] “What we are constantly coming up against is our tax laws and our culture,” Ms. Berry said. “The whole fabric of society wants us to make money on one side and do good with it on the other. What we’re saying is: What if we did both things at once?”

She and others argue that current laws, tax structures and definitions of fiduciary responsibility encourage companies to shift costs onto society.

7.13.2007

Scientific Research (2/5: Anthropic Principle)

What I'd do with a research lab, part 2:
Attempt to generalize the Anthropic Principle to include Dimensionality

Working hypothesis: There are substantial arguments from Physics, Physical Chemistry, Biochemistry, Biology, and Entropy that intelligent life could only arise in a universe with exactly three macroscopic spacial dimensions.

If that seems overly technical, I'm taking a stab at the question, "What's so special about three dimensions? Why don't we live in four dimensions, or two?"

The Anthropic Principle is an argument about why we seem to live in a universe which seems fine-tuned for living creatures. There are 20-plus 'universal constants' (for instance, the speed of light or the strength of the electromagnetic force) which contribute to how matter, energy, and space behave, and it's been observed that if any of them were much different, life couldn't exist--nuclei couldn't form, planets couldn't form, the universe would expand too quickly and fly apart, and so forth. The Anthropic Principle[1] argues that it's not such a big surprise that everything appears fine-tuned for life: if it were any different, we wouldn't be alive to talk about it.

It's a bit of a strange argument, and it's sometimes tough to pin down exactly what the Anthropic Principle is arguing for, especially since there are so many variants. It certainly shouldn't be taken as an excuse to throw up our hands and say, so that's why things are the way they are: the Anthropic Principle is no substitute for hard scientific knowledge about why these constants have the values they do. Used carefully, though, it's a good intuition pump for exploring the intersection between cosmology and biology.

I've sketched out an attempt to generalize the Anthropic Principle to include dimensionality: essentially, I argue that our dimensionality is very fine-tuned, and that any alternate macroscopic dimensional configuration (e.g., any configuration other than our 3 spacial dimensions + 1 time dimension) would likely not give rise to life[2]. It's clear that we don't know all the factors and implications involved in switching our dimensionality for another, but I believe we do have enough knowledge to make certain limited but probable predictions[3]. With these predictions in mind, I've outlined nine arguments to support my hypothesis: five are from the realm of Physics and Physical Chemistry, three from the realm of Biochemistry and Biology, and one dealing with entropy. A major goal of the project, which I have yet to attempt, is to use these arguments to try to generalize the Drake Equation across dimensionalities.

It's a little on the abstract side. And terribly difficult (some would say impossible). But I think the process of working toward this goal could highlight a lot of interesting things about life, intelligence, biology, biochemistry, physics, and cosmology.

[1] My frame of reference is what people call the "weak" Anthropic Principle. I disagree with the "strong" Anthropic Principle, which argues that the universe must at some point generate intelligent life such that the universe will be observed, since it gives an almost mystical, non-naturalistic primacy to observation acts by intelligent beings. Instead of tying physical laws to observation, I would rather see them tied to cosmological natural selection.

[2] The National Academy of Science has recently issued an analysis of (and call for further research on) the prerequisite chemical conditions for life. Ars Technica's coverage of this report is an excellent place to start for anyone who wants to get up to speed on what scientists have identified as enabling conditions for life to arise (though extending some of these chemical principles/prerequisites to other dimensionalities will not be straightforward).

[3] I haven't been able to find much published literature explicitly on this topic of physical and biochemical implications of alternate dimensionalities and I'm grateful to those people with whom I've discussed this.

7.12.2007

Mahalo, Part III

Mahalo, as I noted in my launch coverage back in May, is "a search engine where users get hand-crafted portal-like results for common search queries." Mahalo's founder Jason Calacanis and I are both connected to Larry Sanger, so between that and being fairly intrigued by the idea I've kept my eye on the project.

I like Mahalo. It gives me good content for certain searches, and gosh darnit, it's friendly. But my major philosophical problem with Mahalo, which I laid out here, is that it's not really on the correct side of the technology curve. Having humans make portals for common search terms may work well compared to other options today, but algorithm-based search (e.g., Google) will keep getting better and better in almost every metric whereas human-based search can't*. Google is pretty much guaranteed to improve over time, because it can benefit from iterative algorithm tweaks, large and small, but Mahalo is based on non-iterative human labor and so has to work for every inch of improvement on every page (and simultaneously spend many man-hours battling page rot). I'm not going doom-and-gloom on Mahalo, because I think they've got some really good stuff going on, but let's be honest-- it's a tough spot to be in.

*Granted, I expect Mahalo to do cool things with crowdsourcing additional links on topics and getting editors to filter and sort the best submissions. This sort of strategy has worked for Slashdot-- but it's an unproven technology in search. In some fashion I think Mahalo will be able to crowdsource freshness, but it may not be enough to keep every page as fresh as one would like.

Essentially, I believe Mahalo needs something up its sleeve to stay competitive in the future, something that can connect it to the world of the algorithm. History seems to bear this out: Yahoo's human-crafted web directory looked as good on paper then as Mahalo's human-crafted search portal strategy does now-- but Google's algorithms ate Yahoo's lunch. Similarly, the human-powered DMOZ just couldn't compete against Google. Google's algorithmic approach allows it to have a "special sauce" of algorithms, if/then context switches, and exceptions that it can apply to almost every page on the internet, tweak at will, and combine with sophisticated intent predictors drawn from users' searches to get pretty great search results. This is a very powerful, iterative strategy, and it allows Google to keep its results fresh without any human overhead. I would generalize this as 'Technological progress in search is relentless and algorithms are impressively tweakable, scalable, and improvable compared to human evaluation, and Google is very good at using these these facts to eat peoples' lunches.'

Obviously I don't have The Solution for how Mahalo should try to answer Google. I do think Mahalo is right to try something new, since nobody's had any luck trying to out-Google Google, and I also think Mahalo's on to something with its "search portal" idea. But I can't get away from the feeling that turning one's back on algorithms is trying to swim against the current.

So here's my two-part idea: (1) build a back-end to allow Mahalo to automatically import tagged content into its search portals and (2). use algorithms to figure out what tagged content is worth bringing in.

(1) The tagged-content import system: this setup would draw in relevant, tagged content from elsewhere (like Flickr and Youtube, but blogs, too-- the sky's the limit) to automatically populate e.g., a "content grab-bag" section of Mahalo portals, perhaps heavily weighted toward images, with thumbnails. If someone's at the Mahalo portal for Fugu, most content tagged Fugu will be quite relevant, and there are often powerful indications of how good tagged content is (community ratings, views, links, etc) which could give sorting methods plenty of fodder to work with. Basically, there's lots of great tagged content of all stripes out there, tags enable more streamlined and fresher aggregation, and content aggregation is what Mahalo is all about. It seems like a pretty natural fit.

(2) Using algorithms (not editors) to power the system: by using algorithms, adding this sort of content doesn't add extra effort per page and it also automatically stays fresh. I think it's the perfect complement to the human-crafted search results and would help Mahalo portals stay dynamic. Basically, it's the perfect toehold for introducing and benefiting from algorithms in Mahalo. That said, you could certainly use the tagged content import system with editors making the calls instead of algorithms... it'd just be a lot more man-hours and it wouldn't stay as fresh. And there might not be as much of a point, since the editor could go out, find, and add such content independently. What might be the most attractive option is a hybrid algorithm-editor solution, where algorithms automatically populate sections of Mahalo with tagged content once per day, but editors go through and veto anything that doesn't fit. Algorithms could be tweaked to try to give more 'relevant/informative' content or more 'fun' content, depending on the topic (this might not be in the first system revision!).

Eventually, Mahalo could branch out to become a hub which aggregates all sorts of tagged content on a given topic and displays them based on algorithm, user, and/or editor input... or people could submit various types of content and each Mahalo page could be somewhere between a Digg/Slashdot hybrid for almost any type of content on that specific topic (wouldn't that be cool?). But that's getting a little far afield. In the short-term, I think the combination of human-crafted results and being able to dynamically populate search portals with fun & relevant content would serve Mahalo well. It's a combination that Google can't have, and it'd also give Mahalo a leg up on Wikipedia as a portal to the freshest and most diverse content on a topic.

A tagging back-end would also help integrate some local search capabilities into Mahalo: Mahalo could determine a user's location through various means (whether their search phrase included a location, by tracing their IP, by user preferences, or with a "where are you?" input box), and then return relevant content that was also tagged with their location (and synonyms).

Lest I get ahead of myself, this idea isn't an automatic homerun. It's new and untested- I don't know of anybody who's done this sort of content aggregation based on tags. Largely, this idea would depend on figuring out clever ways to source and sort through tagged content (hey, if you didn't want to roll your own algorithms right away maybe you could somehow use a Google appliance to help sort tagged content!), and the proof would be in the relevance of results. It might be a homerun and it might be a dud. But given the potential benefits (especially in freshness) and near-effortless scalability to all Mahalo pages, it sure seems worth testing.

Bottom line: Mahalo's pretty darn cool as-is (as a Minnesotan, I like how friendly it seems), and I don't doubt that Jason has some further ideas up his sleeve. But using tags and algorithms to aggregate content, though no magic bullet, seems like a promising direction which would allow Mahalo to effortlessly go local, keep pages fresh, and start to take advantage of algorithms while still keeping true to its core vision of being "human-powered search".

Edit, 7-13-07: It seems to me that a good strategy for Mahalo is fostering communities around its portal pages. Communities like dynamic content, thus my suggestion of dynamically bringing in tagged content (it's an inexpensive way to keep things fresh). Per a previous email, I'd also suggest setting up some sort of 'alert' system, where Mahalo sets up automatic Google searches for all the terms they've done, and if any sites that weren't originally in (for instance) the Google top 10 break into the Google top 5, that entry gets flagged as "there's something happening on this search term that might make our portal stale -- have a guide check it out".

Mahalo, Part II

A few months ago I covered the launch of Mahalo, a new "people-powered" search engine which aims to make human-crafted, intelligent portals for the most common search terms (example). I explained the search engine as "based on the theory that many people are searching for the same things, that search engine spam is making Google less useful for common queries, and that humans are still wiser than algorithms at sifting through results and finding the really good stuff." I also noted that I found the real strength of Mahalo to be that the people crafting these portal pages could not only find the best links, but also give really great, human-crafted link context and tell the story about "what you'll find there and why you should take the page seriously" much better than Google can.

I still stand behind all of that. And I still think Mahalo is a very cool project.

However, I also believe Mahalo is staring down the barrel of two pressing questions:

1. How can Mahalo, a human-powered search engine, get on the correct side of AI/algorithm progress? While Google's algorithms are only going to become better, Mahalo's portal system is fairly 'fixed' in its structure and doesn't appear to have that same sort of potential to benefit from progressive tweaks in the code. Aggregated over 10,000+ results and several years, this promises to become very significant.

2. How can Mahalo break into the local search scene? Google's doing cool things with local search, but Mahalo's search results are not local, and are currently not structured such that local results can easily sneak their way in (as with Google).

In what I'd deem a blogsperiment, I'm going to offer possible answers to these two questions *if* somebody puts some money in my tip jar and earmarks it 'Mahalo' (Calacanis, I'm looking at you, though this isn't a shakedown- just a value trade. I figure you of all people will appreciate the incentive structure). Your choice of whether I blog it or email it.

7.11.2007

Quote of the Week: July 8

I wasn't sure about whether to keep up my weekly quotes during this month of science, but since I found one that connects rather ironically with my next science topic, I took it as a sign. This quote is from Jack Cohen in "Is Biology Science?"
In summer 2002, I was at the Cheltenham Festival of Science. Lots of biologists presenting, for sure. But… one very popular event was a presentation by three famous astronomers: ‘Is There Life Out There?’ I prefaced my first question to them by a little imaginative scenario: three biologists discussing the properties of the black hole in the middle of our galaxy. It was very clear that the astronomers really believed that they could discuss ‘life’ professionally, whereas everyone saw biologists talking about black holes as absurd.
Physicists sometimes seem to think they're the superstars of the academy (especially, say, compared to sociologists). Does doing all that rigorous math and modeling give one a special license on truth or just go to one's head? As the son of a physicist, I have no comment. :)

7.07.2007

Scientific Research (1/5: Gut Flora)

I have somewhat of a love/hate relationship with science: on one hand, it provides a uniquely privileged (and fascinating) look into the mechanisms of reality. On the other, the practice of science is often distorted by institutional and financial factors, which can warp what gets studied and who gets to study it away from the ideal and make life pretty miserable for would-be scientists.

Still, I'm drawn to science like a fish to water, and as a hobby I sometimes plan out lines of scientific inquiry I would pursue if I were a scientist and/or rich, particularly on issues which might not come up in normal science funding cycles. Every week in July I'll be posting about one such idea. It'll be a grab bag. Sit back and enjoy it.
----------------------------------------------------------
What I'd do with a research lab, part 1:
Study the effects of diet on gut flora, and the effects of gut flora on physiology and psychology

Working hypothesis: Diet significantly and predictably influences gut flora, and gut flora has a significant influence on physiology, psychology, and in aggregate, perhaps even national character.

Gut flora, as anyone who's read any yogurt labels nowadays knows, refers to the bacteria in our guts which help us digest food and absorb nutrients. The way this is commonly put is that, just as cows have cellulose-eating bacteria in their guts which help them digest grass, we have our own bacteria, or gut flora, which help break down hard-to-digest foods like Twinkies and Big Macs. This sounds simple enough-- but what common wisdom misses about these bacteria in our guts is just how widely important and frighteningly under-studied they are. We know these bacteria not only play a key role in health[1][2]- they may be the primary external factor in immune system function- but can actually influence perception[3]. We also know literally almost nothing[4] about what lives in our guts. So, while the rest of the body is fairly well mapped-out, we have this huge question mark on gut flora, with a scribbled-in note that

1. Whatever does live in our guts outnumbers the 'human' cells in our body about 10-to-1,
2. gut flora is terribly important to body function (perhaps on the scale of a major bodily organ),
3. gut flora likely has some influence on nearly every part of our physiology, and
4. lots of things can go wrong. But we have few reliable metrics to figure out if someone's gut flora has gone wrong, let alone how.

A big frontier in health science is figuring out what sorts of things influence this gut flora we carry around. Scientific wisdom has us getting much of our initial flora as a baby from our mothers, largely from breast milk and the birthing process, and these initial gut ecosystems are thought to be at least minimally stable. We also get bacteria from the food we eat, both from obvious sources such as yogurt but also from bacteria that naturally grow on foods such as grains and produce. Gut flora and mouth flora are linked, as are one's genes and gut flora (e.g., genes influence gut flora, but gut flora also influences gene expression[5]). Taking a cycle of antibiotics is thought to sort of "reroll the dice" on gut flora: most bacteria die off and the survivors must scramble to repopulate the gut before their competitors do. There is, of course, a lot of randomness in all of this.

The nuances and relative contributions of these factors are several frontiers in themselves. Scientists are also starting to explore the indirect contributions of food to our gut flora, or whether different diets stochastically give rise to different biosystems by virtue of changing the competitive landscape for bacteria in our guts. One issue that I think is on the edge of researchers' minds is whether a significant part of America's systemic health problems is not just that we as a nation tend to eat food that's bad for us, but we're eating food (e.g., high-fructose corn syrup, food additives, preservatives (particularly sulfates), low-level food-borne antibiotics and pesticides) that makes the wrong bacteria thrive in our guts.

I think that's probably the case and, getting further afield, what I'd like to do is attempt to look into whether the changes in gut ecosystems caused by changes in eating habits and food manufacturing trends- aggregated over the 300 million people who live in America- could contribute to a stochastic change in national character. Perhaps a significant contributing factor to some of our institutional ills is the food we eat, the corresponding imbalance in gut flora which arises from eating such food, and the subtle yet powerful-in-aggregate dysfunctional personality changes that e.g., biologically-active metabolites of such non-symbiotic gut flora might cause.

I sense some reader eyebrows being raised at this point-- that bacteria could influence, let alone commonly influence, personality may seem quite a stretch. But consider the case of toxoplasma gondii (among other examples): it's a protozoan parasite that spends part of its lifecycle in cats and part in other mammals, and shows clear signs of manipulating host behavior for its own ends. Infected rats, for instance, actually seek out the scent of cat urine, since when the rat gets eaten the toxoplasma can complete its lifecycle in the cat. What's mind-boggling, though, is that humans who show tell-tale immunological signs of a past toxoplasma infection score statistically different on personality tests than do those who have not been infected (infected men tend to score higher in paranoia, whereas for women toxoplasmosis seems to lead to higher levels of social trust and sexual promiscuity). It's unknown how or why toxoplasma causes such subtle personality changes in humans-- though likely it's a result of many generations of toxoplasma getting progressive fitness benefits from honing its initially accidental effects on rat fear/motivation, and since rats and humans are both mammals, some of those same psychological buttons toxoplasma has evolved to exploit in rats are hooked up to things in our brains, too. The fundamental point I would take from this is that there's ample evidence that pathological microorganisms can and do subtly affect personality[6]. Personally? I believe these external pathogenic influences on personality - real as they are - will pale in comparison to that mediated by our gut floras.

Let me be perfectly clear: whether diet-gut flora interaction could be a commonly significant or significant-in-aggregate factor in personality is mostly just an intuition, built on the connections between gut flora and health, and health and personality, how tightly coupled bacteria and their metabolites are to our bodies and the scope of functional possibilities where such metabolites might- intentionally or unintentionally- act as e.g., hormone mimics, how many nerves (100 million+) are in our guts and how connected they are to our brain, the many possible feedback mechanisms between bacteria and neurotransmitters[7], how 'clever' and environmentally manipulative bacteria can be[8], and how connected I think physiology and personality are. A sore tooth can influence personality; surely something that can not only affect our nerves, but many aspects of our biochemistry and nutrition as well, may do the same. I think it's premature to really push any specific hypothesis about this gut flora-personality connection, since a lot of the basic science isn't there to build on. But it's a hypothesis we should be open to, and if I were in charge of the NIH or a well-endowed charitable foundation, I'd heavily prioritize flora research in general, particularly in the context of twin studies: we know so very little about gut flora (other than that it's important) that the expected return is extremely high[9].

Update 10/13/07:

Since posting, there have been at least two major developments on this topic:
1. A theory that the appendix functions as a "safehouse" for good bacteria, especially with respect to repopulating the body's GI tract after diarrhea, has been gaining traction. See

Bollinger RR, Barbas AS, Bush EL, Lin SS, Parker W. 2007. Biofilms in the large bowel suggest an apparent function of the human vermiform appendix. J Theor Biol (in press) doi:10.1016/j.jtbi.2007.08.032

2. A study has linked preference for chocolate with gut flora metabolism. Specifically, people who identified themselves as "chocolate desiring" had significantly different metabolic profiles and significantly different gut flora activity profiles than those who self-identified as "chocolate indifferent". It's both clear that this is an important result, and extremely hard to tease apart the causality involved at this point.


Results to be published in the Nov. 2 issue of American Chemical Society’s Journal of Proteome Research (via PhysOrg).

Update 8/1/10:

A new frontier in gut flora research is exploring the viral symbionts of peoples' gut flora. Recent research points to a viral counterpart to our gut flora which
1. We know very little about (a recent study matched only 20% of the viral biome to existing databases);
2. Varies significantly between individuals (with identical twins having no more similarity with each other vs unrelated people, contra gut flora);
3. Is surprisingly stable (5% change over the course of a year, 1% for the most common viromes-- indicating a benign, possibly functional symbiosis rather than an arms race).

The functional significance of the viral counterpart to our gut flora remains unknown. Presumably, though, it's important.

Footnotes:


[1] http://www.wired.com/medtech/health/news/2007/04/bacteriahacking
"Probiotics (pills containing bacteria) have resulted in complete elimination of eczema in 80 percent of the people we've treated," says Dr. Joseph E. Pizzorno Jr., a practicing physician and former member of the White House Commission on Complementary and Alternative Medicine Policy. Pizzorno says he's used probiotics to treat irritable bowel disease, acne and even premenstrual syndrome. "It's unusual for me to see a patient with a chronic disease that doesn't respond to probiotics."

[2] One of my reasons for being so interested in this topic is that I suffer from celiac disease, or at least have some probably-autoimmune-mediated reactions to gluten and casein, and some think celiac disease may be initially, and perhaps chronically, caused by the presence of 'bad' bacteria in the gut.

[3] http://www.nature.com/nm/journal/v13/n1/abs/nm1521.html
"We found that oral administration of specific Lactobacillus strains induced the expression of mu-opioid and cannabinoid receptors in intestinal epithelial cells, and mediated analgesic functions in the gut--similar to the effects of morphine. These results suggest that the microbiology of the intestinal tract influences our visceral perception."

[4] http://www.sciencemag.org/cgi/content/abstract/312/5778/1355 - with interesting commentary by John Hawks:
"This is really important stuff -- our nutrition is very dependent on these microbes, and there is every reason to think that their ecology affects our overall health status as well. And we know very little about them -- heck, these guys are using the same metagenomic techniques to fine organisms in our bodies that are used to find new unidentified ocean life!" e.g., we're forced to use metabolism and byproduct analysis because most of what lives in our guts can't be cultured in vitro. Edit, 7/13/07: A recent paper came out in PNAS outlining a technique that may at least partially solve this problem.

[5] Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, Gordon JI. Molecular analysis of commensal host-microbial relationships in the intestine. Science 2001 Feb 2;291(5505):881-4.


[6]
Gregory Cochran has argued from an angle of evolutionary fitness load and allele frequency that many things we think of as being caused by genes or behavior (e.g., rheumatoid arthritis) are probably primarily mediated by pathogens.

[7] See
http://findarticles.com/p/articles/mi_m0FDN/is_2_9/ai_n6112781/pg_6 - it's also a good survey of some other complexities in this topic.

[8] This just scratches the surface of the manipulative potential of bacteria, but one such subtle strategy used by bacteria is (briefly) explained here:
http://www.physorg.com/news99220113.html
"The genes responsible for toxin production only seem to be expressed during periods of nutrient deprivation. This is consistent with the view that most disease-causing bacteria express their pathogenicity when they are hungry," says Abraham Sonenshein, professor at the Sackler School of Graduate Biomedical Sciences at Tufts University and at Tufts University School of Medicine, at the 107th General Meeting of the American Society for Microbiology (ASM) on May 24, 2007.

[9] Another related high-return research area which I think is a little better represented in science (but should also get more funding) is examining potential pathogenic influences on personality, e.g., along the aforementioned lines of toxoplasma gondii and
this previous post.


Notes:
- I got to thinking about this when musing about America's social/political/institutional ills. Perhaps this is a longshot for trying to help explain our various institutional dysfunctions. But who knows? It could be a contributing factor. Just because the effects of gut flora are incredibly complex doesn't mean they're neutral when aggregated into larger contexts.
- At this point I don't have solid predictions on what sorts of diets tend to strengthen/weaken what sorts of personalities. Perhaps the safest thing to say is that the significant variation in human personality may have gut flora as a significant contributing factor, and also that the physiological stress of coping with a non-symbiotic flora may e.g. lead to personalities more prone to addiction.
- Though there is plenty of literature documenting correlations between gut flora and various diseases, and specific diseases and personality changes, I haven't found any literature that covers what I would like to study, which is modeling gut flora's influence on personality without the mediating frame of a specific disease.

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7.02.2007

Quote of the Week: July 1

From a column entitled "How To Keep Hostile Jerks From Taking Over Your Online Community":
Teresa invented a technique called disemvowelling -- removing the vowels from some or all of a fiery message-board post. The advantage of this is that it leaves the words intact, but requires that you read them very slowly -- so slowly that it takes the sting out of them. And, as Teresa recently explained to me, disemvowelling part of a post lets the rest of the community know what kind of sentiment is and is not socially acceptable.
Clever.

Now, the astute reader may object that this is more of an anecdote than a quote-- so here's your official quote of the week, from famed neuroscientist György Buzsáki when asked what coursework he might do differently in hindsight: I've often wondered about going into neuroscience so I found this particularly poignant.
We do not quite understand where our curiosity and motivation come from. Occasionally, we dream up an ideal life with constant happiness and success but attempts to define universal happiness and success always fail. Even if I confine your question to the "most effective road to systems neuroscience", it is hard to make up an ideal curriculum. Perhaps, I wish I had learned more math and engineering, and got exposed to a world-class laboratory environment from the beginning. But whereas possession of tools is useful in answering questions, the critical factors in science seem to relate to asking an important question and building up a sufficiently intense motivation to solve it. Living in a suppressive regime at the time when my interest in the brain emerged made me focus on inhibition. This may not have happened under other conditions. Hardship and failure can be as formative of character and creativity as a barrage of positive feedback and supportive advisors. (emphasis added).