The one about CERN

About a month ago I visited CERN, arguably the most famous research organization in Europe. It is the place where the World Wide Web has been invented, and the home of the Large Hadron Collider. I was very excited about the trip, much like Sheldon Cooper. Here are some facts which were new to me:

... about CERN:

• CERN was founded after the WWII by a bunch of European countries. They were exhausted by the war, and the only way to catch up with the USA and USSR in fundamental science was to join forces.
• The original name was Conseil Européen pour la Recherche Nucléaire (European Council for Nuclear Research), which abbreviated to CERN. Later the name has been officially changed to European laboratory for particle physics, which is both more relevant and less fearful for the locals, however the brand CERN is used now even in official documents.
• There are almost 3,000 full-time employees, but most of them are engineers and not scientists. There are a lot of visiting researchers though.
• There are 20 member states now (primarily EU states), and 6 observer states (such as Russia and the USA).
• CERN's annual budget is about € 1 billion, it is funded by the member states in proportion to their economical power, e.g. Germany gives 20% of the money.
• The budget money are spent to infrastructure and support, all the individual experiments are funded by research groups and their universities.
• In spite of the USA is not a member state, it leads on the number of researchers who work on CERN projects (more than thousand), second is Germany, third is Russia (yes, we still have a good shape in particle physics). It turned out that everybody at CERN spoke Russian, even the janitor. :)

... about the LHC:

• It is in fact a circular tunnel of 27 km in circumference lying 175 m beneath the ground.
• The tunnel was used before the LHC, it was build in 1983 for the Large Electron-Positron Collider. In 2008 it was upgraded to be able to accelerate heavy particles like protons to become the Large Hadron Collider (remind that proton and neutron are thousand times heavier than electron).
• The tunnel is about 4 meters in diameter, one can walk there or ride a bike.
• The tunnel encapsulates two small pipes for the particles that intersect at four points (to make the tracks' lengths equal, like in speed scating arenas). There are more then a thousand of electric magnet dipoles along the pipe. They are not that big as I imagined before.
• It is nearly vacuum and zero temperature inside the tubes.
• Proton beams are not generated inside the LHC. First, they are accelerated in the linear accelerator and almost reach the speed of light c. While the speed is rising, it becomes harder and harder to increase it since it cannot overcome the speed of light. Then they are accelerated in the small circular accelerator, and only after that they are injected into the LHC where during 40 minutes the beams are accelerated to speed as much close to c as possible.
• When accelerated, the beams are being observed during 10 hours. They suffer about 10,000 collisions per second, about 20 pairs of protons collide each time. Since the speed is large, the energy of that collisions is enormous.
• The collisions take place within special locations called detectors. We visited a control centre of one of them, ATLAS. A detector has multiple layers, each able to register certain kind of particles, like photons.
• Ten thousand collision per second would yield really big amount of data, so only few of them are selected to be logged. I don't know how they select those collisions, machine learning might be used. :)
• All the collected data are spread into servers all over the world. An authorized researcher may log in to the grid network and execute her script to analyse the data.

... about Higgs boson:

• Higgs boson is a hypothetical particle, existence of which would prove the standard model of particle physics.
• Higgs boson appears as a result of collision of two protons and large amount of energy. The protons in the LHC are accelerated enough to produce theoretically sufficient energy.
• Higgs boson is very heavy and thus unstable. In theory, it decays into either four muons or two photons. So, if there will be two counter-directed light beams registered by the detector, this will be an evidence of the boson. See the picture below for example of likely detector output in case of the boson shows up.
• Scientist say that if Higgs boson would not be detected, all the modern knowledge on particle physics will crush. They will be obliged to develop a new theory from scratch.
• There are no published results that report on Higgs boson detection so far...

Don't you want to be a theoretical physicist now? =)

Oh noes, it's women CEOs!

Today at Scientopia I discuss the latest debate raging across the pond - hiring quotas to ensure there are more women CEOs of companies.

How NOT to train for the 2011 Soiled Sport Trail Series

Should the snow ever stops falling and temperatures decide to ever rise above freezing, the start of the Soiled Sport 2011 Trail Running Series will start on April 2nd at Meadowlilly Trail.

Our 2010 Trail Series winner, Chuck Edwards, will cut the ribbon at the trail head to start our 31 weeks of trail running bliss.

As always, you will be awarded points for each Saturday trail you attend and complete along with any Ontario Ultra Series race. Bonus points are also awarded when you run or volunteer for London Pacer sponsored events when identified on this blog.

New this year will be aditional bonus points for wearing our series sponsors gear. More details to follow.

So put down the chip dip and start training.

happy weekend.

i feel like this is a good thought to send us off into the weekend....it's easy to get caught up in wanting all the "stuff" and living "the life"...
i need to remind myself that i am ultimately a mom so wiping my children's nose for 100th time is my duty, as well as cleaning spit up off the new rug, hanging out in the doctor's office sick room for 2 hrs, and wearing mix match pj's is just a fact of my life.  even if, in my head, i have a totally different picture!  maybe that is why this blog is such a good outlet :)
*on a side note: since i have been housebound for the last week w/ sick kiddos, i thought i would do something for myself...i got out the real simple i received in the mail yesterday and tried these faces while applying my makeup.  it is suppose to make your makeup look better.  for me, it provided a much needed laugh!  happy weekend.

Polyphenols, Hormesis and Disease: Part II

In the last post, I explained that the body treats polyphenols as potentially harmful foreign chemicals, or "xenobiotics". How can we reconcile this with the growing evidence that at least a subset of polyphenols have health benefits?

Clues from Ionizing Radiation

One of the more curious things that has been reported in the scientific literature is that although high-dose ionizing radiation (such as X-rays) is clearly harmful, leading to cancer, premature aging and other problems, under some conditions low-dose ionizing radiation can actually decrease cancer risk and increase resistance to other stressors (1, 2, 3, 4, 5). It does so by triggering a protective cellular response, increasing cellular defenses out of proportion to the minor threat posed by the radiation itself. The ability of mild stressors to increase stress resistance is called "hormesis." Exercise is a common example. I've written about this phenomenon in the past (6).

The Case of Resveratrol

Resveratrol is perhaps the most widely known polyphenol, available in supplement stores nationwide. It's seen a lot of hype, being hailed as a "calorie restriction mimetic" and the reason for the "French paradox."* But there is quite a large body of evidence suggesting that resveratrol functions in the same manner as low-dose ionizing radiation and other bioactive polyphenols: by acting as a mild toxin that triggers a hormetic response (7). Just as in the case of radiation, high doses of resveratrol are harmful rather than helpful. This has obvious implications for the supplementation of resveratrol and other polyphenols. A recent review article on polyphenols stated that while dietary polyphenols may be protective, "high-dose fortified foods or dietary supplements are of unproven efficacy and possibly harmful" (8).

The Cellular Response to Oxidants

Although it may not be obvious, radiation and polyphenols activate a cellular response that is similar in many ways. Both activate the transcription factor Nrf2, which activates genes that are involved in detoxification of chemicals and antioxidant defense**(9, 10, 11, 12). This is thought to be due to the fact that polyphenols, just like radiation, may temporarily increase the level of oxidative stress inside cells. Here's a quote from the polyphenol review article quoted above (13):

We have found that [polyphenols] are potentially far more than 'just antioxidants', but that they are probably insignificant players as 'conventional' antioxidants. They appear, under most circumstances, to be just the opposite, i.e. prooxidants, that nevertheless appear to contribute strongly to protection from oxidative stress by inducing cellular endogenous enzymic protective mechanisms. They appear to be able to regulate not only antioxidant gene transcription but also numerous aspects of intracellular signaling cascades involved in the regulation of cell growth, inflammation and many other processes.

It's worth noting that this is essentially the opposite of what you'll hear on the evening news, that polyphenols are direct antioxidants. The scientific cutting edge has largely discarded that hypothesis, but the mainstream has not yet caught on.

Nrf2 is one of the main pathways by which polyphenols increase stress resistance and antioxidant defenses, including the key cellular antioxidant glutathione (14). Nrf2 activity is correlated with longevity across species (15). Inducing Nrf2 activity via polyphenols or by other means substantially reduces the risk of common lifestyle disorders in animal models, including cardiovascular disease, diabetes and cancer (16, 17, 18), although Nrf2 isn't necessarily the only mechanism. The human evidence is broadly consistent with the studies in animals, although not as well developed.

One of the most interesting effects of hormesis is that exposure to one stressor can increase resistance to other stressors. For example, long-term consumption of high-polyphenol chocolate increases sunburn resistance in humans, implying that it induces a hormetic response in skin (19). Polyphenol-rich foods such as green tea reduce sunburn and skin cancer development in animals (20, 21).

Chris Masterjohn first introduced me to Nrf2 and the idea that polyphenols act through hormesis. Chris studies the effects of green tea on health, which seem to be mediated by polyphenols.

A Second Mechanism

There is a place in the body where polyphenols are concentrated enough to be direct antioxidants: in the digestive tract after consuming polyphenol-rich foods. Digestion is a chemically harsh process that readily oxidizes ingested substances such as polyunsaturated fats (22). Oxidized fat is neither healthy when it's formed in the deep fryer, nor when it's formed in the digestive tract (23, 24). Eating polyphenol-rich foods effectively prevents these fats from being oxidized during digestion (25). One consequence of this appears to be better absorption and assimilation of the exceptionally fragile omega-3 polyunsaturated fatty acids (26).

What does it all Mean?

I think that overall, the evidence suggests that polyphenol-rich foods are healthy in moderation, and eating them on a regular basis is generally a good idea. Certain other plant chemicals, such as suforaphane found in cruciferous vegetables, and allicin found in garlic, exhibit similar effects and may also act by hormesis (27). Some of the best-studied polyphenol-rich foods are tea (particularly green tea), blueberries, extra-virgin olive oil, red wine, citrus fruits, hibiscus tea, soy, dark chocolate, coffee, turmeric and other herbs and spices, and a number of traditional medicinal herbs. A good rule of thumb is to "eat the rainbow", choosing foods with a variety of colors.

Supplementing with polyphenols and other plant chemicals in amounts that would not be achievable by eating food is probably not a good idea.


* The "paradox" whereby the French eat a diet rich in saturated fat, yet have a low heart attack risk compared to other affluent Western nations.

** Genes containing an antioxidant response element (ARE) in the promoter region. ARE is also sometimes called the electrophile response element (EpRE).

frozen pizza...

since moving a little over a month ago, our family's nutrition hasn't been the best.  when you are surrounded by boxes and you can't find your silverware, you tend to eat not so good for you things.  i think one of our major food groups was frozen pizza.  i'm over convenient food and craving getting back into the kitchen and cooking.  not necessarily fancy meals, but good for you meals.  i think that is why last night, i was practically drooling on my computer when i randomly found the blog- with style and grace.  it has the best looking pictures of food and healthy ways to eat.  i LOVE it and am dying to try some of the recipes out!!  and to make a vow not to eat anymore frozen pizza!!

*images courtesy of pinecone camp and with style and grace

Rabu, 23/02/2011 08:29 WIB

Bawang Putih Mampu Membersihkan Plak di Pembuluh Darah
Vera Farah Bararah - detikHealth


Jakarta, Bawang putih lebih dikenal untuk mengatasi tekanan darah tinggi. Peneliti menemukan mengonsumsi bawang putih bisa berfungsi membersihkan arteri atau pembuluh darah.

Bawang putih bisa memperlambat perkembangan aterosklerosis, yaitu suatu kondisi yang bisa menyebabkan plak dan berbahaya bagi pembuluh darah.

National Center for Complementary and Alternative Medicine (NCCAM) menuturkan sejak ribuan tahun lalu masyarakat sudah memiliki kebiasaan mengonsumsi bawang putih karena dipercaya bisa menjadi obat.

Berdasarkan laporan dari University of Maryland Medical Center diketahui bahwa bawang putih memiliki kemampuan untuk menghancurkan plak yang terdapat di dalam dinding pembuluh darah, seperti dikutip dari Livestrong, Rabu (23/2/2011).

Beberapa studi yang dilakukan terhadap pasien aterosklerosis menunjukkan jumlah plak yang menurun ketika pasien diminta untuk mengonsumsi bawang putih dalam bentuk suplemen. Meski demikian diperlukan penelitian lebih lanjut untuk mengetahui dengan pasti bagaimana cara bawang putih menghancurkan plak.

Studi lain juga menemukan konsumsi bawang putih bisa membantu menurunkan kadar kolesterol darah total dan juga kadar kolesterol jahat (LDL), sekaligus meningkatkan kadar kolesterol baik (HDL) sehingga mengurangi risiko plak menumpuk di arteri.

Selain itu, hasil penelitian yang dilakukan oleh Linus Pauling Institute menuturkan bahwa bawang putih juga memiliki kemampuan untuk mencegah pembekuan darah di arteri serta mengurangi jumlah trombosit dalam darah yang bergumpal.

Sedangkan bawang putih yang dikonsumsi dalam bentuk bubuk atau minyak tampaknya juga efektif untuk mencegah penggumpalan darah di arteri yang bisa menyebabkan serangan jantung atau stroke.

Bila seseorang ingin mengonsumsi bawang putih untuk membersihkan arteri, UMMC menyarankan untuk konsumsi 2-4 siung bawang putih segar setiap harinya, atau bisa juga bawang putih tersebut dicampurkan dalam makanan.

ver/ir)

NB: SehatHerbal menyediakan kapsul bawang putih (GARLIC). harga 50rb/45 kpsul, sdh BPOM, halal. Pemesanan : budiprakoso98@gmail.com / 081310343598

NCCDC is coming - My favorite time of year

Once a year the fine folks at the National Collegiate Cyber Defense Competition invite a team of people to participate in their event as red or white team members. I'm happy to announce that I've been asked to return as captain of the red team this year again on April 8-10 in San Antonio, Texas. I got my start as a professional in network security and though I speak about computer forensics publicly we at G-C still do network security for select clients.

For those not familiar with CCDC it is a national competition that pits teams of college contestants who have to defend their network while continuing to deploy new business services against a team of people who are looking to ruin their day.While there is always a team who wins the national title I've always felt that it's the red team who always wins since we have the most fun.

Getting involved with CCDC is something I've always enjoyed doing and would recommend others do as well, if you are looking to volunteer as either a good guy or a bad guy you should go here http://www.nationalccdc.org/index.php?option=com_content&view=article&id=58&Itemid=70 to get involved at either the national or local levels.


If you are company looking to recruit the best talent emerging out of today's universities you could also benefit by sponsoring, as we have, the event and get access to these students before they can write their own ticket. To sponsor go here:  http://www.nationalccdc.org/index.php?option=com_content&view=article&id=59&Itemid=37

dream home

today i am over at la dolce vita sharing my idea of a "dream house"....hope to see you over there! thanks so much paloma for letting me dream...it's kind of nice considering currently i am surrounded by runny noses, laundry, and dirty dishes :)

Sorry, but don't apologize

One of the bits of advice floating around for scientists is, "Don't apologize for your work". Usually this advice is dispensed within the context of giving a presentation - don't start a presentation with, "Sorry", don't apologize for unreadable graphs, etc.

But I think this advice should be extended to all professional scientific communication. If you hurt someone's feelings or spill their coffee, absolutely you should apologize. Of course you should speak considerately and professionally to all people. But when it comes to communicating science don't apologize for yourself. Don't degrade your expertise, don't qualify your statements.¹

You can qualify presentations of information, for example, "This work is preliminary" or "This was just a first step to exploring this problem area." But that is very different from saying, "I realize I am only a masters student" or "Sorry, I am a n00b here" or "I know my undergraduate degree is in French literature, but..."

Be bold! Yes, you will probably need to wave the white flag sometimes. But don't start out with your flag waving. Start out strong.

---

¹ Unless you work in a country where apologizing is the norm for professional communication, in which case, I'm sorry for this post. ;-)

Youth Training Announced for Green Code Meetings

The next round of Green Code meetings has been announced! The meetings will take place between Monday, February 28th and Saturday, March 5th. Check out the map to find the meeting closest to you!

HKHC Buffalo has been working closely with its partners to determine the best ways to get Buffalo youth out to the meetings. We have met with many community groups and youth leadership groups - including the Buffalo Public Schools Inter-High Council - to talk about the importance of the youth voice at the Green Code meetings.

Our youth representatives, Adriana and Robert, told us that students will need some help finding their voice around issues of land use and zoning. When we asked how, they responded that a youth-led training could help students find buddies to attend the meeting with, learn about land use and create talking points so they could convey a clear message. We listened.

A free training for Buffalo youth interested in participating in the Green Code meetings will take place this Thursday, February 24th from 5:00 - 8:00 pm. Dinner will be provided to all attendees, and the training is open to middle- and high-school students. The meeting will take place at the Innovation Center at 640 Ellicott Street.

We know school is out this week - and that students are excited for time off and families are relaxing together. We have worked with the youth leaders to make this training fun - and students can count the meeting attendance toward their community service requirement! Plus, participating in the Green Code process is too important to pass up. We need to hear from youth and their families about what they want most out of their city.

RSVP for the training to Erin at 882-5327 or sharkey@mass-ave.org. You can download the flyer here. See you there!

my new "grab bag"

i have something new going on at the Designer's Attic on Fridays now....it's my version of an instant room!  i had a lot of fun making the first one...i hope y'all will enjoy it too!  thanks jenny for the twitter shout out, i'm honored you like it ;)

New year, New book!

Hello Readers,
                       I thought I'd take this weeks post to announce that I just signed the contract with McGraw Hill to write a new book. It will be called 'Computer Forensics, A Beginner's Guide'. It's meant for those of you already in the IT field who are looking for a jump start into your first computer forensics investigations. I'll post more details as I finish the manuscript but we are currently set to have in stores in early November.

Prescient spam

I work in area X. I recently wrote a paper on area X_1, and submitted it to a conference. It was rejected. So I revised it and resubmitted it to a more topic-relevant conference, and it is currently under review. There is absolutely nothing in the public sphere indicating that I have done work in field X_1 that I am aware of.

Today I got a spammy email from one of those shady journals that spams anyone who ever published something in IEEE Xplore or the ACM Digital Library, saying:

Dear Dr. FCS,      // Not a bad start, calling me "Dr." instead of "Ms." (or "Mr.")

Our Journal of X has a special issue coming up on X_1. Given your expertise in this area we would like to invite you to submit something. 

Sincerely,

Editor in Chief of Shady Journal

Mostly I am fascinated that they somehow know I am working in area X_1. Looking at the editorial board of the shady journal and the PC of the two conferences this paper has been seen by, I see no obvious overlap.

The funny thing is, this journal never spams me on areas of X_2, X_3, or X_4 (none of which I work in, but they publish in), so this is fairly deliberate spam.

So how did they know about my new professional foray? Clearly this is evidence that they are psychic. Or one of my reviewers blabbed. I'd say it's a 50/50 probability of either.

Those who trade security for coffee deserve neither

A recent article reports results from a survey which shows, among other things, that companies are spending more money on coffee for their employees than securing their "web applications", whatever that means. (In this day and age, is there any application that doesn't have at least some network-facing capability?)

In any case, being an advocate of both strong coffee and strong encryption, I can understand the dilemma. You need to caffeinate your sysadmins so they can keep up their daily grind of writing Javascript, while still allowing them to esperesso themselves that, actually, not beaning standards compliant is going to cause a latte problems.

(Coffee pun hat tip)

these past couple of sunny days can do wonders for a girl.  grey days totally mess with my mood!!  i am longing for spring...i hope these pretty days are here to stay...

*images courtesy of suzie beezie, emily henderson, design darling, my home ideas, emily henderson

Gallaudet University plans to cut Computer Science

Read this, and tell me if anything looks unusual to you:

Be it resolved that the Board of Trustees, recognizing the need to strategically reallocate resources, approves the recommendation of the university administration to close the following major degree programs:

• Ed.S. Change Leadership in Education
• M.S. Administration
• Ph.D. Special Education Administration
• M.A. Deaf Studies: Deaf History
• M.S. Leisure Services Administration
• B.S. Computer Information Systems
• B.A. Chemistry: Chemical Technology
• B.A./B.S. Computer Science
• B.A. French
• B.A. International Government
• B.A. Theatre Arts: Educational Drama

Two of these things are not like the others. I've made them red. (Not because I'm angry, I just like the color.)

I can understanding cutting French and Leisure Services Administration - I doubt there are a lot of jobs in these fields.  Same also for International Government and Theater Arts, though I suspect both of those fields could stand to have a higher representation of people who are deaf and hard-of-hearing. I don't know anything about the fields of Education, Administration, or Deaf Studies so I can't comment on those. As for the Chemical Technology major, given its stated purpose is to prepare students to be laboratory technicians and given the rumors of large numbers of people with Chemistry PhDs scrambling to get lab tech jobs, I'm not entirely surprised to see the major cut.

But CS and CIS? Why?

Why on earth would a university cut CS programs in this economy? If anything, those are the majors most likely to yield jobs for undergraduates. An undergraduate degree in Computer Science is a golden ticket for a job from now until 2018. Here's what the Computing Community Consortium has to say about this (boldface and italics are theirs):

Looking at all science and engineering occupations — “Computer and mathematical,” “Architecture and engineering,” and “Life, physical, and social science” — computer science occupations are projected to be responsible for nearly 60% of all job growth between now and 2018. The next largest contributor — all fields of Engineering combined — is projected to contribute 13.4% of total growth. All of the life sciences combined: 5.6%. All of the physical sciences combined: 3.1%. In other words, among all occupations in all fields of science and engineering, computer science occupations are projected to account for nearly 60% of all job growth between now and 2018.

So, I am puzzled by Gallaudet's decision. And troubled.

Check yo self

FSP's post today on getting blogged about reminded me of something I meant to write about awhile ago. And that is - ways to actively monitor how others talk about you publicly.

I highly suggest setting up several Google Alerts. This is a great service that emails you whenever someone mentions your name on a site Google indexes*. You can set this up for general search results, as well as for blogs, twitter, and news articles.

You also can set up citation alerts in Google scholar, which will tell you if someone has cited you generally, or you can set one up for individual papers if you're so inclined.

For these alerts, I have quite a few variations of my name, for example:
(Ada A. Lovelace) OR (A. Lovelace) OR (Lovelace, A.) OR (Lovelace AND Analytic Engines) 
etc.

I've found these alerts invaluable, because over the years I have given several talks where my privacy requests were violated. This happened along the lines of:
"Can we have a copy of your slides?"
"No."
"Pretty Please? It's for those poor undergraduate students who couldn't attend your talk today."
"No."
"Pleeeeease? We promise not to put it on the internet."

Because I'm a pushover when it comes to pleas about wee undergraduate students, I acquiesced, and sure enough two weeks later, surprise! There are my slides.

But these alerts have also relayed good news, for example, I've learned of news articles about my research I didn't know existed, learned of entirely unexpected paper citations, and, I also discovered a really juicy paper basically trashing one of the subfields I work in. (Not trashing me specifically, just saying something factual about my publication frequency).

So, these alerts are worth setting up. Unless you're the academic equivalent of Lindsay Lohan, in which case I do not recommend this service.

(*) If you're a Bing person, sorry - there are no Bing alerts at present. Their academic.research.microsoft.com site offers RSS subscriptions, though I imagine there is a fair bit of overlap with Google scholar. 

questions answered...

i had several questions and emails about painting my kitchen so i thought i would do one last post and then you don't have to hear about it anymore :)

painting: while i would love to say that i was cool enough to tackle this project myself, i'm not.  i left it to the professionals but i did buy all of the supplies so i can guide you a little on what they used.  our cabinets were a light stained wood so to get the paint to adhere they first started w/ sanding all of them.  next, they used zinsser cover stain.  this stuff is heavy duty and so we moved out of our house for 4 days while they painted.  it's an oil based primer that covers really well over wood, knots, etc. here is a pic of the can if you need a visual:

my paint colors were Benjamin Moore from the Classic Color collection.  the cabinets were oil base, which is not my favorite thing to use but the durability is a lot better.

cabinets: Vapor Trails 1556 (this is actually one shade lighter then Sally Wheat's kitchen)

and the walls: Northern Cliffs 1536

a lot of people also asked about my chair fabric....its one of my spare DR chairs and the stripe is lulu dk's catwalk light blue w/ brown.  

thanks a million for all of your sweet comments!  it was fun sharing the process and even more fun to get the "after" product!  

and i can't end w/out saying happy valentine's day!!  seriously, can this cake make its way into my kitchen so i can eat it?!! xoxox

Top Secret Rosies

A special "rose" for you for Valentine's Day - I've just posted at Scientopia about the incredible new documentary "Top Secret Rosies: The Female Computers of WWII."

Polyphenols, Hormesis and Disease: Part I

What are Polyphenols?
Polyphenols are a diverse class of molecules containing multiple phenol rings. They are synthesized in large amounts by plants, certain fungi and a few animals, and serve many purposes, including defense against predators/infections, defense against sunlight damage and chemical oxidation, and coloration. The color of many fruits and vegetables, such as blueberries, eggplants, red potatoes and apples comes from polyphenols. Some familiar classes of polyphenols in the diet-health literature are flavonoids, isoflavonoids, anthocyanidins, and lignins.

The Case Against Polyphenols

Many diet-health authorities seem pretty well convinced that dietary polyphenols are an important part of good health, due to their supposed antioxidant properties. In the past, I've been critical of the hypothesis. There are several reasons for it:

1. Polyphenols are often, but not always, defensive compounds that interfere with digestive processes, which is why they often taste bitter and/or astringent. Plant-eating animals including humans have evolved defensive strategies against polyphenol-rich foods, such as polyphenol-binding proteins in saliva (1).
2. Ingested polyphenols are poorly absorbed (2). The concentration in blood is low, and the concentration inside cells is probably considerably lower*. In contrast, essential antioxidant nutrients such as vitamins E and C are efficiently absorbed and retained rather than excluded from the circulation.
3. Polyphenols that manage to cross the gut barrier are rapidly degraded by the liver, just like a variety of other foreign molecules, again suggesting that the body doesn't want them hanging around (2).
4. The most visible hypothesis of how polyphenols influence health is the idea that they are antioxidants, protecting against the ravages of reactive oxygen species. While many polyphenols are effective antioxidants at high concentrations in a test tube, I don't find it very plausible that the low and transient blood concentration of polyphenols achieved by eating polyphenol-rich foods makes a meaningful contribution to that person's overall antioxidant status, when compared to the relatively high concentrations of other antioxidants in blood* (uric acid; vitamins C, E; ubiquinone) and particularly inside cells (SOD1/2, catalase, glutathione reductase, thioredoxin reductase, paraoxonase 1, etc.).
5. There are a number of studies showing that the antioxidant capacity of the blood increases after eating polyphenol-rich foods. These are often confounded by the fact that fructose (in fruit and some vegetables) and caffeine (in tea and coffee) can increase the blood level of uric acid, the blood's main water-soluble antioxidant. Drinking sugar water has the same effect (2).
6. Rodent studies showing that polyphenols improve health typically use massive doses that exceed what a person could consume eating food, and do not account for the possibility that the rodents may have been calorie restricted because their food tastes awful.

The main point is that the body does not seem to "want" polyphenols in the circulation at any appreciable level, and therefore it gets rid of them pronto. Why? I think it's because the diversity and chemical structure of polyphenols makes them potentially bioactive-- they have a high probability of altering signaling pathways and enzyme activity, in the same manner as pharmaceutical drugs. It would not be a very smart evolutionary strategy to let plants (that often don't want you eating them) take the reins on your biochemistry. Also, at high enough concentrations polyphenols can be pro-oxidants, promoting excess production of free radicals, although the biological relevance of that may be questionable due to the concentrations required.

A Reappraisal

After reading more about polyphenols, and coming to understand that the prevailing hypothesis of why they work makes no sense, I decided that the whole thing is probably bunk: at best, specific polyphenols are protective in rodents at unnaturally high doses due to some drug-like effect. But-- I kept my finger on the pulse of the field just in case, and I began to notice that more sophisticated studies were emerging almost weekly that seemed to confirm that realistic amounts of certain polyphenol-rich foods (not just massive quantities of polyphenol extract) have protective effects against a variety of health problems. There are many such studies, and I won't attempt to review them comprehensively, but here are a few I've come across:

• Dr. David Grassi and colleagues showed that polyphenol-rich chocolate lowers blood pressure, improves insulin sensitivity and lowers LDL cholesterol in hypertensive and insulin resistant volunteers when compared with white chocolate (3). Although dark chocolate is also probably richer in magnesium, copper and other nutrients than white chocolate, the study is still intriguing.
• Dr. Christine Morand and colleagues showed that drinking orange juice every day lowers blood pressure and increases vascular reactivity in overweight volunteers, an effect that they were able to specifically attribute to the polyphenol hesperidin (4).
• Dr. F. Natella and colleagues showed that red wine prevents the increase in oxidized blood lipids (fats) that occurs after consuming a meal high in oxidized and potentially oxidizable fats (5).
• Several studies have shown that hibiscus tea lowers blood pressure in people with hypertension when consumed regularly (6, 7, 8). It also happens to be delicious.
• Dr. Arpita Basu and colleagues showed that blueberries lower blood pressure and oxidized LDL in men and women with metabolic syndrome (9).
• Animal studies have generally shown similar results. Dr. Xianli Wu and colleagues showed that whole blueberries potently inhibit atherosclerosis (hardening and thickening of the arteries that can lead to a heart attack) in a susceptible strain of mice (10). This effect was associated with a higher expression level of antioxidant enzymes in the vessel walls and other tissues.

Wait a minute... let's rewind. Eating blueberries causes mice to increase the expression level of their own antioxidant enzymes?? Why would that happen if blueberry polyphenols were protecting against oxidative stress? One would expect the opposite reaction if they were. What's going on here?

In the face of this accumulating evidence, I've had to reconsider my position on polyphenols. In the process, and through conversations with knowledgeable researchers in the polyphenol field, I encountered a different hypothesis that puts the puzzle pieces together nicely.  I'll discuss that in the next post.


* Serum levels of polyphenols briefly enter the mid nM to low uM range, depending on the food (2). Compare that with the main serum antioxidants: ~200 uM for uric acid, ~100 uM for vitamin C, ~30 uM for vitamin E.

Sejarah Linux/unix

Nama Linux merupakan kombinasi unik antara nama penciptanya dan nama
sistem operasi yang menjadi targetnya (UNIX). Semuanya
berawal dari sebuah
sistem operasi bernama Minix. Minix dibuat oleh Profesor Andrew Tanenbaum.
Minix adalah sistem operasi mirip UNIX yang bekerja pada PC.
Torvald adalah salah seorang mahasiswa di Universitas Helsinki yang
menggunakan Minix. Walaupun cukup bagus, ia belum menganggap Minix memadai.
Kemudian pada tahun 1991 ia membuat sistem operasi yang merupakan clone UNIX,
yang diberi nama Linux.
Seperti halnya Minix, Linux tidak menggunakan kode apa pun dari vendor
UNIX komersial, sehingga Torvalds mendistribusikan linux di internet secara bebas
dan gratis.
Pada Oktober 5 1991, Torvalds mengeposkan sistem operasinya di newsgroup
comp.os.minix. Ia mengumumkan bahwa source code Linux tersedia dan meminta
bantuan programmer-programmer lain untuk ikut mengembangkannya. Ketika itu
Linux masih setengah matang, sistem operasi ini hanya bisa menjalankan sedikit
perintah UNIX, seperti bash, gcc dan gnu-make. Saat Linux 1.0 diluncurkan pada
1994, sistem operasi ini telah cukup stabil dan memiliki banyak feature, seperti
preemptive multitasking (kemampuan untuk membagi sumber daya CPU untuk
banyak aplikasi) dan symmetric multiprocessing (kemampuan untuk membagi tugas
di antara banyak CPU). Linux bahkan memiliki maskotnya sendiri yang oleh torvalds
Dijelaskan sebagai "seekor penguin yang menggemaskan dan ramah, yang kekenyangan setelah
banyak makan ikan hering".

Pada 1996, tim pengembangan Linux yang ada diseluruh dunia mulai
memberikan hasilnya. Tahun itu mereka telah membuat versi Linux untuk sejumlah
versi hardware, dari Atari ST sampai Macintosh.
Linux terus berkembang pesat, utamanya karena ada sejumlah distributor
(seperti RedHat, Caldera, dsb) yang berkompetisi untuk berebut pangsa pasar. Oleh
karena itu dibentuk kelompok bernama Linux Standard Base. Kelompok ini bekerja
untuk memastikan bahwa beragam distribusi Linux yang ada tetap bisa menjalankan


aplikasi yang sama dan saling berinteroperasi. Saat ini ada tujuh distribusi Linux
paling terkenal, yaitu :
1. RedHat Linux, distributor paling populer di AS dan salah satu yang paling
mudah digunakan.
2. Mandrake Linux, distributor yang menambahkan update dan patch untuk
RedHat Linux.
3. Caldera Open Linux, distibrusi Linux dengan instalasi dan lingkungan
pengguna berbasis grafis yang bagus.
4. Suse Linux, distribusi Linux paling populer di Eropa yang juga
menyediakan perangkat instalasi dan panduan berbahasa Indonesia.
5. Slackware Linux.
6. Debian GNU/Linux.
7. TurboLinux, distribusi Linux paling populer di Asia yang menyediakan
dukungan untuk set karakter khusus Asia.

Oh no, it's GroupWise!

Hi there Reader,

For many years when I talked to a client about their network environment, these would be my words 'Oh no, it's GroupWise!' but not anymore!

Read more »

Dear Randall

You are, truly, the reason why Computer Scientists* make fantastic comic writers. Thanks for making me laugh today.

♥,
FCS

(*) I guess technically you're a physicist, but really, what's a few bits and atoms between friends?

http://xkcd.com/859/

My Gluten-Free January

I've been avoiding most gluten, particularly wheat, for over a year now. I never had obvious symptoms that I could clearly link to eating wheat, although I had my suspicions. I've made many changes to my diet over the last decade, and I feel much better than I did ten years ago, but it's hard to disentangle all the factors. I don't think I ever went an entire month without eating any gluten at all before this January. After posting Matt Lentzner's challenge to go gluten-free this January, I felt obligated to do it myself, so I signed up!

I succeeded in avoiding all gluten for the month of January, even though it was a pain at times. I felt good before January, and didn't start with any health or body weight problems, so there wasn't much to improve. I also felt good while strictly avoiding gluten this January, perhaps a little better than usual but it's hard to say.

At the end of the month, I did a blinded wheat challenge using the method I described in a previous post, which uses gluten-free bread as the placebo (1). I recorded my blood sugar at 30 minute intervals after eating the bread, and recorded how I felt physically and emotionally for three days after each challenge.

The result? I think the bread gave me gas, but that's about it. I'm not even positive that was due to the wheat. My energy level was good, and I didn't experience any digestive pain or changes in transit time. There was no significant difference in my blood glucose response between the bread and the gluten-free bread.

I decided that I didn't have any symptoms, so I celebrated by having a porter (1) with friends a few nights later. I slept poorly and woke up with mild digestive discomfort and gas. Then I ate wheat later in the week and slept poorly and got gas again. Hmmm...

Some people might say that the body adapts to any food, and wheat is no different. Go without it for a while, and the body has a tough time digesting it. But I can go for weeks without eating a potato, a chicken thigh or broccoli, and all will digest just fine when I eat them again.

I'm pretty sure I don't have a severe reaction to gluten. I think I'm going to stick with my mostly gluten-free habits, and eat it occasionally when I'm offered food in social situations.

Did anyone else do a blinded wheat challenge? Describe it in the comments!

The Role of CS Postdocs

The Computing Research Association (CRA), the major professional organization for Computer Science in the US, has a new white paper on the role of postdocs in CS Research. It's excellent, very thorough, and has several interesting graphs. (Including who's hired in what areas over the past few years.) The white paper is up for people to leave comments if they are so inclined, until March 15th.

I haven't had time to read the report in depth, but a few things jumped out at me as interesting:

• 42% of all CS PhD graduates are hired into industry immediately after completing their PhDs. (I affectionately refer to this as the Google Slurp). However, there is a large category of "other", which sadly includes the unemployed. So maybe that old statistic that less than 1% of PhDs in Computer Science are unemployed is no longer true, eh? 

• Here's the graph of who got hired in what. Everybody is going downhill, but it looks like Architecture and Theory people are hurting the most in hiring. Which correlates with my anecdotal information. 

(Why aren't Security, CS Education, or Ubicomp listed as fields? I would not consider any of them to be subfields of any of these really. They are their own fields).

• This table is really interesting. Compared to other fields those of us in CS/Math hardly postdoc at all:

Anyway, interesting stuff - check it out and leave comments if you have them. CRA is a well-run organization, if you comment I strongly suspect your opinions will be taken into account - not just for future white paper drafts, but also for recommendations they make to Congress and various funding agencies. (I know CRA and NSF in particular are usually fairly kissy kissy. CI Fellows anyone?)

Phew!!

it's taken me long enough but i think my kitchen is finally okay to show y'all. when we moved in the previous owners had a lot of green accents throughout the house so the kitchen color made sense with their design scheme (real estate listing pic).

when our stuff moved in, the color stuck out a little (and a bomb went off obviously)...

i debated and debated on what direction I wanted to go with the paint colors. i posted lots of pictures.  ultimately, i decided to go w/ my gut, even though it scared me, and go greige on the cabinets and a darker greige on the walls.  here is the picture that inspired my kitchen:

and now, here is my kitchen....and i can officially say i love her!

thanks so much for all of your help- for convincing me to take a leap and not stick w/ white.  i am one happy camper.  next on my list is to find a good, faded oushak rug to plop in front of the sink :)

Gluten-Free January Raffle!

Hi, Gluten-Free January participants. Matt, Janine and I have collected about 200 survey responses at this point. So far, the results are very interesting! But we want to get as many responses as possible, because the more responses we get, the more informative the data will be for all of us. So please fill out the survey Matt sent you by e-mail, no matter what your results were, and no matter whether you stuck with the diet or not! The survey is strictly about your GFJ experience, not investment opportunities, timeshares, ShamWows or anything else. It will take you less than 5 minutes, and it's totally anonymous. The deadline is Feb 15th. Big thanks to everyone who has taken it so far.

To encourage participants to complete the survey, we're organizing a raffle. Matt and I have five Gluten-Free January T-shirts we're ready to give out for free. These shirts were designed by Matt and they're really cool. I have one myself, and the print and fabric quality are top notch. Here's what the logo looks like:
If you've completed the survey and want to be included in the raffle, please e-mail Matt to let him know you've completed it. Anyone who has already e-mailed Matt to let him know they completed the survey will automatically be entered, so no need for a second e-mail. So far, very few people have written Matt, so your probability of winning a shirt is high!

Punch Beating

Recently, two different people have told me they were all excited about a revolutionary new idea, went to the literature to read about it, and found someone had already invented it.

I said: "Great!"

They said: "Great?"

I say "great!" for several reasons:

1) You clearly had a great idea if somebody else already came up with it.
2) You are capable of lots and lots of great ideas and will have more
2.1) People who only have one great idea usually have very dull careers following their accolade.
3) At least you didn't spend five years building something you were hoping to patent only to find out it exists and is currently being sold in three countries.

In my area of research, I am always delighted to learn somebody has studied one of my ideas, particularly if they've done a satisfactory job of exploring it, because it means I can spend time more working on other ideas.

Anyway, I'm sure there is some good research-zen koan for this one. Maybe... hold each idea in your hand like a grain of sand, cling too tightly and someone else will patent it.

i can see the light at the end of the tunnel and it makes me truly happy...
my kitchen is 99% done...i need to clean it up, hang some pictures, and squirt some mrs. meyers and it will be ready to go.  can't thank my dad and hubby enough for doing the backsplash and lighting this weekend!  hope y'all are having a wonderful monday...i can finally say i am :)

Scientopia

The folks over at Scientopia have kindly invited me to join their blogging community. I have accepted, and created a new blog called The Difference Engine.

I've decided to keep this blog going, because as much as the Blogger UI drives me nuts I actually kind of like it. And I like that I can metaphorically and literally paint the walls purple here without troubling anyone.

So over there I will post occasionally (weekly I hope), probably more about Computer Science than I do here, but perhaps about other things as well. We'll see how it goes.

As for how this affects you? Not in the slightest. When I post over there I'll post a pointer here, so if you don't want to add another RSS subscription you don't have to. (But if you do want to, here is a link).

Assorted Thoughts About the 2010 Dietary Guidelines

In the past week, I've been rooting through the USDA's 2010 Dietary Guidelines (1). Here are a few of my thoughts.

Positive

One of the things I've been enjoying recently is watching health authorities shift away from a nutrient-oriented philosophy in favor of a more food-oriented philosophy. For example, I recently read a nice editorial by Drs. Dariush Mozaffarian and David S. Ludwig (not associated with the USDA) that encapsulates this (2). Here's a quote:

Nutritional science has advanced rapidly, and the evidence now demonstrates the major limitations of nutrient-based metrics for prevention of chronic disease. The proportion of total energy from fat appears largely unrelated to risk of cardiovascular disease, cancer, diabetes, or obesity. Saturated fat—targeted by nearly all nutrition-related professional organizations and governmental agencies—has little relation to heart disease within most prevailing dietary patterns. Typical recommendations to consume at least half of total energy as carbohydrate, a nutrient for which humans have no absolute requirement, conflate foods with widely divergent physiologic effects (eg, brown rice, white bread, apples). Foods are grouped based on protein content (chicken, fish, beans, nuts) despite demonstrably different health effects. With few exceptions (eg, omega-3 fats, trans fat, salt), individual compounds in isolation have small effects on chronic diseases. Thus, little of the information found on food labels’ “nutrition facts” panels provides useful guidance for selecting healthier foods to prevent chronic disease.

In contrast with discrete nutrients, specific foods and dietary patterns substantially affect chronic disease risk, as shown by controlled trials of risk factors and prospective cohorts of disease end points

Although this approach may seem radical, it actually represents a return to more traditional, time-tested ways of eating. Healthier food-based dietary patterns have existed for generations among some populations.

Tell it! Although he doesn't use the word nutritionism, that's basically what he's arguing against. Dr. Mozaffarian seems to represent the less reductionist school of nutrition, which is a more informed version of what nutrition pioneers such as Sir Edward Mellanby, Dr. May Mellanby, Dr. Weston Price and Sir Robert McCarrison advocated.

Although the 2010 guidelines are too focused on nutrients for my taste, they do spend some time talking about food groups and eating patterns, for example, recommending an increase in the consumption of vegetables, fruit, whole grains and seafood. They also recommend Mediterranean and plant-focused eating patterns. Although I don't think their recommendations quite hit the mark, they do reflect a shift in thinking.

Another thing I enjoyed about the Guidelines is the table on page 12 of chapter 2, which shows just how messed up the average American diet is. The number one source of calories in all age groups is "grain-based desserts". The next five in adults are yeast breads, chicken dishes, soda/sports drinks, alcohol and pizza. To see typical American food habits presented like this just blows me away. They call this the "obesogenic environment"; the idea that we're surrounded by tasty but unhealthy food and situations that favor the consumption of it. I agree.

The Guidelines also contain a surprisingly accurate one-sentence review of the glycemic index literature:

Strong evidence shows that glycemic index and/or glycemic load are not associated with body weight; thus, it is not necessary to consider these measures when selecting carbohydrate foods and beverages for weight management.

Negative

The first problem is the creation of the category "solid fats and added sugars", abbreviated SoFAS. With the creation of this term, they lump pastured butter together with Crisco and Red Hots. If they've been hiding the evidence that pastured butter, virgin coconut oil or red palm oil contribute to heart disease, I'd like to see it so I can stop eating them!

Another problem is their list of recommendations to curb the obesity epidemic. They say:

The current high rates of overweight and obesity among virtually all subgroups of the population in the United States demonstrate that many Americans are in calorie imbalance—that is, they consume more calories than they expend. To curb the obesity epidemic and improve their health, Americans need to make significant efforts to decrease the total number of calories they consume from foods and beverages and increase calorie expenditure through physical activity.

Looks like we have Sherlock Holmes on the case. Now that we have this information, all we have to do is tell overweight people to eat less and they'll be lean again! What's that, they already know and it's not working?? Someone should tell the USDA.

Jokes aside, I do think energy balance is a huge issue, perhaps even the central issue in chronic disease risk in affluent nations. The basic problem is that Americans are eating more calories than is optimal, and they have a very hard time stopping. It's not because they have less willpower than their stoic ancestors, it's because their bodies have decided that overweight/obesity is the new lean, and they defend that higher level of fat mass against changes. Simply telling an overweight person to eat fewer calories, without changing the dietary context, is not very effective in the long term, due to compensatory mechanisms including hunger and increased metabolic efficiency (fewer calories burned for the same muscular exertion).

What does the USDA recommend to lose fat or maintain leanness?

• Count calories. Doesn't work for most people, although I acknowledge that it is physically possible to lose fat (and lean mass) by restricting calories.
• Reduce sweetened beverages. Thumbs up.
• Serve smaller portions. As far as I know, this rests exclusively on very short-term studies that showed that food consumed at a single meal or three is reduced if portion size is smaller. I guess it can't hurt to try it, but I'm not convinced it will have any effect on long-term body fatness. I think restaurant portion sizes have probably increased because people eat more, rather than the other way around, although both could be true.
  
• Eat foods that are less calorie dense. I think vegetables are healthy, but is it because they're less calorie-dense? Why is dietary fat intake generally not associated with obesity if it's the most calorie-dense substance? Why do many people lose body fat eating energy-dense low-carbohydrate diets? Not convinced, but I'm feeling open minded about this one.
• Exercise more and watch less TV. Exercise is good. But don't let it make you hungry, because then you'll eat more!

Overall, I think their recommendations for fat loss are not very satisfying because they don't address the core reasons Americans aren't in energy balance. Eliminating sweetened beverages and exercising are the most solid advice they offered in my opinion. The rest strikes me as wishy-washy advice that's offered because they have to say something.

At one point, they talk about changes in the US diet that have corresponded with the obesity epidemic:

Average daily calories available per person in the marketplace increased approximately 600 calories, with the greatest increases in the availability of added fats and oils, grains, milk and milk products, and caloric sweeteners.

Let me edit that so it's more complete:

Average daily calories available per person in the marketplace increased approximately 600 calories per day, 250 calories of which were actually consumed (USDA and NHANES). Added fats increased, due to a large increase in seed oil intake, but total fat intake remained approximately the same because of a roughly equal decrease in fatty meat and whole milk consumption (USDA and NHANES). Grain intake, predominantly wheat, increased, as did the consumption of refined sweeteners, predominantly high-fructose corn syrup (USDA).

It reads a bit differently once you have a little more information, doesn't it? Animal fat intake declined considerably, and was replaced by seed oils, in parallel with the obesity and diabetes epidemics. Maybe it contributed, maybe it didn't, but why not just be forthright about it? People appreciate honesty.

Conclusion

Although the 2010 USDA Dietary Guidelines show some promising trends, and contain some good information, I hope you can find a better source than the USDA for your nutrition advice.

Cryptocontributions

John Regehr of Embedded in Academia has a great post about Cryptocontributions in writing:

Even when interesting and unexpected results make it into a paper (as opposed to being dismissed outright either by the PI or by a student doing the work) the discussion of them is often buried deep in some subsection of the the paper. When this happens — and the interesting development is not even mentioned in the abstract or conclusion — I call it a “cryptocontribution.” Sometimes these hidden gems are the most interesting parts of what are otherwise pretty predictable pieces of work. When authors are too focused on getting the thing submitted, it’s really easy to shove interesting findings under the rug. Certainly I’ve done it, though I try hard not to.

I like that in his post, there is a little bit of a cryptocontribution, and that is - by being so conference deadline-driven, Computer Science is, as a Science, still a bit immature. If I have time I'll write more about this topic next week, because it's an idea I've been pondering for awhile.

---

PS - A note to John and other bloggers who run WordPress type-things - I seem to be unable to leave IP-anonymous comments on your blogs via Tor. I try, and try, and try, and am thwarted. So I've given up! But do know I'd love to comment if I could. Maybe this summer if I have some free time I'll write a Tor browser plugin that works with WordPress.