Category: Science

App ideas

Micro movement sensing

Use the orientation sensor in a cell phone to monitor small regular movements. For example, the movement due to the heart beat. It might be possible to measure breathing movement. It may also be possible to measure anomalous movements–tremors, the sway due to microadjustments involved in standing.

Also, if the heartbeat moves a phone to a noticeable degree, does this make cell phone photos blurrier? If so, add heartbeat detection to the camera app–have pictures be snapped between heartbeats.

Basically, orientation data would be collected, and a frequency analysis done to detect the freq and amplitude of the movements. I don’t know how fast the orientation can be polled. If it is too slow, it may be possible to use intermittent polling at precise times to identify the frequency of movements.

Shadow boxing

A related use would be as a shadow boxing app. This would clearly be better as a wrist strap standalone device, but might work as an app. Hold the phone in a hand (or strap it firmly to the wrist), and follow the movements of the hand/arm, recording punches and the speed of them. The user would indicate the hand being scored in setup, and then as hands are switched, the punching of the two could be compared. Groups of friends could play together to see who can punch the fastest or do the most punches in 30s.


This app would run simultaneously on two phones. One phone would display bands of pure red, blue, and green. A sample would be placed across one half of the bands. The second phone would take a picture of the first phone. Image analysis would compare the brightness of the control and sample covered regions and calculate absorbance in the three channels. Cell phone displays are either OLED or IMOD. There are a range of displays used in phones, so this would never be super accurate without calibration. The OLED displays seem to have fairly narrow spectrum pure colors while the iphones have broader colors.

This could be used either as an exploration tool–test substances and record spectra, or reference data could be used to make guesses at substances.

Or you could use a diffraction gratings and make a real spec.

Titan landing

At Windycon, I went to a talk by Christian Ready from the Space Telescope Science Institute on the solar system and saw pictures of the surface of Titan. Wow, I didn’t realize that a probe had made a landing!

Surface of Titan

The surface of Titan as seen by Huygens after its landing on January 14, 2005. (credit: ESA/NASA/JPL/University of Arizona)

Book review: Parasite Rex

Parasite Rex: Inside the Bizarre World of Nature’s Most Dangerous Creatures by Carl Zimmer.

Great book. About parasites. What they are, the recent discovery of how big a role they have in ecosystems, how they live, how they have jumped from animal to animal, and of course, which ones afflict people.

Several chapters describe a range of human parasites in amazing and often frightening detail. From botfly larvae to liver flukes, malaria’s Plasmodium to the nematodes that parasitize humans. There is some discussion of microbial parasites, but most of the book covers metazoan parasites. Zimmer tells the stories of some of these parasites–how they find their way to people, what they do once they arrive in a new host, how they escape detection, and the course of the disease. The story of how several parasites were discovered, how they were identified and followed through their changes of form and host are told. And there are pictures!

Word cloud of Parasite Rex by Carl_Zimmer


Notes on water fluoridation and the Fluoride Deception video

I’d heard of the great water fluoridation fight but never looked into it. In the 60’s the John Birchers were saying it was a Commie plot to weaken America’s vital fluids or something of the sort. And it was parodied in the movie Dr. Strangelove…

Let’s start by bracketing things. Fluoride in water can’t be highly dangerous or people would have noticed. Not putting fluoride in water is not a risk-free choice–it prevents cavities. Cavities don’t just make your teeth fall out, they also increase risks of bacteria related heart disease, and the occasional person dies of a tooth abscess. So the question is, is there disease caused by fluoridation, and is it worse than the diseases caused by no fluoridation?

OK, let’s look at the video.
5:42 Suggests that the idea of adding fluoride to water supplies was to hide the dangers of for fluoride pollution or avoid responsibility for damage due to fluoride pollution. Doesn’t really make sense so far. Ah, reading in the history, when government regs made industry stop dumping fluoride in air and water, one thing they did with it was process out fluoride for water fluoridation. Doesn’t sound that damning, after all it would have been cheaper to dump it in a landfill.

~7:00-20:00 Fluoride air pollution can be bad. Some of the early fluoride researchers also worked on and perhaps had a part in the worst cover ups regarding industrial pollutants. What I’ve read of the tetraethyl lead story is appalling. The connection with the lead story is tenuous. Fluoridating water wasn’t a gold mine, I don’t see there being much pressure to push fluoridation back when it started.

21:30 The NRC report (below) discusses Waldbott’s results, concludes that some people are sensitive to typical water concentrations of fluoride and that it appears to be fairly rare.

From the NRC report, it doesn’t appear that the safety of water fluoridation was well-established, certainly nowhere near today’s standards, back when it began. It was safe by 1940’s standards, and had a clear benefit. I’ve probably got an extra tooth in my mouth due to it.

25:00 The NRC report discusses the Mullenix study. Calls it inconclusive, calls for more studies.

The video didn’t have much info. Here are the establishment reference sources:

CDC recommendations

Fluoride reduces cavities by 15-40%, depending on the study. The low figure is an estimate of the benefit of water fluoridation in a population that already uses fluoride toothpaste.

2006 National Academy report (the greybeards)

Here’s the meat! Water fluoridation is 1 mg / L, when the level hits 4 mg / L studies start seeing negative health effects. That’s a pretty narrow window between benefit and danger level, the smallest one for an environmental exposure I’ve run into. YMMV, I’m not an environmental toxicologist.

What hasn’t really been studied are neurotoxic effects of low level exposure. A few studies have turned up disturbing results. Check out the summary on page 205.

Interesting take on differences between Europe and US fluoridation, Pizzo et al. 2008

The bit about Europe in the video is misleading. Europe hasn’t avoided fluoride, it’s just mostly not in water, it’s in salt or toothpaste.

Internet rumors that aspartame is deadly

Many internet sources claim aspartame is dangerous to human health. This is an example:

Aspartame has been renamed and is now being marketed as a natural sweetener

Friday, February 12, 2010 by: Ethan Huff, citizen journalist

(NaturalNews) In response to growing awareness about the dangers of artificial sweeteners, what does the manufacturer of one of the world’s most notable artificial sweeteners do? Why, rename it and begin marketing it as natural, of course. This is precisely the strategy of Ajinomoto, maker of aspartame, which hopes to pull the wool over the eyes of the public with its rebranded version of aspartame, called “AminoSweet”.

Yeah, tell it to the slimehead (aka, orange roughy) or to rapeseed (aka, canola).

Over 25 years ago, aspartame was first introduced into the European food supply. Today, it is an everyday component of most diet beverages, sugar-free desserts, and chewing gums in countries worldwide. But the tides have been turning as the general public is waking up to the truth about artificial sweeteners like aspartame and the harm they cause to health. The latest aspartame marketing scheme is a desperate effort to indoctrinate the public into accepting the chemical sweetener as natural and safe, despite evidence to the contrary.

Aspartame was an accidental discovery by James Schlatter, a chemist who had been trying to produce an anti-ulcer pharmaceutical drug for G.D. Searle & Company back in 1965. Upon mixing aspartic acid and phenylalanine, two naturally-occurring amino acids, he discovered that the new compound had a sweet taste. The company merely changed its FDA approval application from drug to food additive and, voila, aspartame was born.

G.D. Searle & Company first patented aspartame in 1970. An internal memo released in the same year urged company executives to work on getting the FDA into the “habit of saying yes” and of encouraging a “subconscious spirit of participation” in getting the chemical approved.

Of course they wanted their new product approved. Pet peeve of mine: Unsourced quotes of a fraction of a sentence. Often misleading, or copied from somewhere else, and so on leading back to who knows where.

In 1976, then FDA Commissioner Alexander Schmidt wrote a letter to Sen. Ted Kennedy expressing concern over the “questionable integrity of the basic safety data submitted for aspartame safety”. FDA Chief Counsel Richard Merrill believed that a grand jury should investigate G.D. Searle & Company for lying about the safety of aspartame in its reports and for concealing evidence proving the chemical is unsafe for consumption.

A claim! Let’s google around. Here’s some info:

The History of Aspartame by Ashley Nill

This law article has more details of the aspartame approval process. This section is relevant:

The first obstacle that Searle met came from Dr. John W. Olney, M.D., psychiatrist and Professor of Psychiatry at Washington University of St. Louis, and James S. Turner, author of The Chemical Feast, and co-founder of the Center for Study of Responsive Law.[30] Olney and Turner formally objected to the regulation that authorized the marketing of aspartame as a sweetener in foods.[31] Dr. Olney had performed research in animals regarding the toxic effects on the brain of certain Amino acids, including asparatic acid. Both parties objected to the use of aspartame in foods, especially those consumed by children. They asserted that aspartame might cause brain damage resulting in mental retardation, endocrine dysfunction, or both. Turner and Olney also argued that aspartame could be dangerous to persons with the genetic disorder phenylketonuria (PKU), a disorder that prevents the metabolism of phenylalanine, one of the amino acids in aspartame.[32]

These along with other concerns and allegations necessitated a FDA hearing provided for by 21 U. S. C. 348.[33] Instead of having a full evidentiary hearing, which was customary at the time, the parties waived their right and accepted a hearing before a public board of inquiry instead.[34] This was the first time that the FDA had ever used this type of hearing in place of a full evidentiary hearing. Searle agreed to delay marketing of aspartame temporarily, pending resolution of the safety questions.[35]

Before the board could hold a hearing regarding the safety of aspartame as a food additive in response to Olney and Turner’s allegations, however, Searle’s quest for aspartame approval hit another snag. Preliminary results from an audit of the records of certain animal studies conducted by or for Searle, including studies on aspartame, indicated a need for a comprehensive review of the authenticity of the aspartame research data. Apparently, the audit of Searle’s clinical methods revealed “sloppy” research, including some research that was being done on aspartame.[38] The negative publicity that surrounded Searle’s clinical methods bolstered consumer criticism of aspartame, and further clouded the safety issues that had not yet been addressed. Alexander Schmidt, then FDA commissioner, noted that the FDA audit revealed “different discrepancies of different kinds.”[39] Pursuant to 21 U. S. C. 348(e), FDA formally stayed the regulation authorizing the marketing of aspartame.[40]

G.D. Searle & Company submitted its first petition to the FDA in 1973 and fought for years to gain FDA approval, submitting its own safety studies that many believed were inadequate and deceptive. Despite numerous objections, including one from its own scientists, the company was able to convince the FDA to approve aspartame for commercial use in a few products in 1974, igniting a blaze of controversy.

So, the FDA was cautious. Good to hear they don’t let companies put untested new chemicals in the human food supply. G.D. Searle & Company’s safety studies were sloppy, and this delayed the approval of aspartame until 1981, a delay probably costing the company at least tens of millions in lost profits.

It looks like G.D. Searle & Company did what it could to push and influence the approval process through means fair and foul. The worst case interpretation of the company’s actions is put forward here. It’s initial approval application in 1973 was crap but by the time 1981 rolled around enough other studies had been done for aspartame to squeak by to approval.

Wikipedia usually is a poor source for controversies and alt-med claims but its aspartame controversy article at least shows the shape of the debate.

Despite the myriad of evidence gained over the years showing that aspartame is a dangerous toxin, it has remained on the global market with the exception of a few countries that have banned it. In fact, it continued to gain approval for use in new types of food despite evidence showing that it causes neurological brain damage, cancerous tumors, and endocrine disruption, among other things.

OK, let’s look at evidence of:
“cancerous tumors”: As I wrote before 10:1 no cancer:cancer so far. Either not a carcinogen or a very weak one.

“endocrine disruption”: No evidence. The claim traces back to a hypothesis made by Olney in 1975. Basically large doses of MSG can cause stunting and he suggested the aspartic acid in aspartame would have the same effect. There was never much evidence for this idea, and by the time of this 1988 review article it was known to be false. While MSG can make a person head buzz a bit (it has this effect on me), aspartame doesn’t–so it must have a much weaker effect than MSG.

“neurological brain damage”: No evidence I can find.

This claim was rejected during the FDA approval process. Again from the History of Aspartame article:

The board had its first meetings on January 30, 31 and February 1, 1980.[65] On the first question, whether the ingestion of aspartame poses a risk of contributing to mental retardation, brain damage, or undesirable effects on the neuroendocrine regulatory system, the board found that aspartame did not pose an increased risk of brain or endocrine dysfunction.[66]

The Humphries et al., 2008 article I mentioned in the previous post is the recent source for most of these claims on the internet. But the claims in the review article are all hypotheses and maybes and don’t have any evidence behind them. In fact, aspartame’s neurological effects have been studied extensively since the controversy over its approval thirty years ago and there’s still no evidence it causes any damage to the brain.

What countries have banned aspartame? As far as Wikipedia knows, no countries have banned aspartame, certainly not US/Canada/Europe.

The details of aspartame’s history are lengthy, but the point remains that the carcinogen was illegitimately approved as a food additive through heavy-handed prodding by a powerful corporation with its own interests in mind. Practically all drugs and food additives are approved by the FDA not because science shows they are safe but because companies essentially lobby the FDA with monetary payoffs and complete the agency’s multi-million dollar approval process.

From the Wikipedia article: “In 1987, the U.S. Government Accountability Office concluded that the food additive approval process had been followed properly for aspartame.” As the discussion above notes, it was a bumpy approval, but the FDA did scrutinize it.

FDA review and approval is a barrier, the main barrier, to companies selling dangerous or ineffective products. It was designed to work in the face of corporate opposition and evasion. And it works OK–there are only a few cases where the FDA has approved something later shown to be dangerous, and while it is expensive to do the studies to prove a product safe, the FDA makes approval decisions pretty quickly.

That the FDA is a barrier to selling crap is apparent in how happy the alt-med product companies were to get Congress to exclude them from FDA oversight and how hard they lobby to keep their special status (Dietary Supplement Health and Education Act (DSHEA) of 1994).


The artificial sweetener aspartame is about 200 times sweeter than sugar. It is widely consumed in large quantities–diet sodas contain 140-185mg per 12 oz., so a person drinking a lot of diet soda may consume a gram a day. The FDA recommends 40mg per kg body weight as a safe daily dose–about 2 grams per day for a average sized person.

In the human gut aspartame breaks down into three components: two amino acids, phenylalanine and aspartic acid, and methanol. Phenylalanine and aspartic acid, being amino acids, are a normal part of the human diet. Methanol is absorbed from the gut and converted by the liver to into formaldehyde and formic acid, both nasty but non-specific poisons. In the small amounts formed from aspartame they are thought to not be dangerous. Some foods, some normal body processes, and alcohol consumption produce methanol, though I don’t have figures as to how much.

There has been some controversy over whether aspartame is safe. There have been a few studies showing some cancer risk in animals, three recent mouse studies from Soffritti et. al. being the most convincing. Any cancer risk is thought to come from the methanol. Recent studies in animals seem to running about 10:1 no cancer:cancer. As aspartame has been in food for thirty years, there have been some large human studies, and none of them show increased cancer due to eating aspartame.

Here are American Cancer Society and National Cancer Institute pages assessing aspartame.

The other concern brought up is whether the phenylalanine and aspartic acid that aspartame breaks down into have an effect on the nervous system. In addition to being used for making protein, these amino acids are also feedstock for making catecholamine neurotransmitters. There is some evidence that a large ingestion of these two amino acids alone might throw off normal neurotransmitter levels. It’s not clear what, if any, effect this has on human brains–it clearly has no striking consequence. Any effect is of course relative–aspartame is often consumed with caffeine, a substance that clearly effects brain function. :)

This 2008 review article makes a number of alarmist suggestions but has almost no actual evidence. It’s a very odd article. A large human dose of aspartame is about 1 gram a day. The RDA for protein consumption is 0.8 g / kg day, which contains about 2 grams of phenylalanine and aspartic acid. Not all foods have an even balance of amino acids, so animals must have fair ability to buffer a diet rich in one or another.

Aspartame has been well-studied and is safe. It is still being studied–it may turn out to be a very weak carcinogen, too weak to show up clearly in the studies so far. Or have a subtle effect that screws up the rare person’s brain. Risks are relative–aspartame is certainly much better for a person’s health than the sugar it replaces. On the other hand, you can’t go wrong drinking water.

Aging research news

Articel on yeast article
A yeast cells will only divide a certain number of times before it stops–it senesces. When yeast cells divide, the mother and daughter are asymmetric, and the daughter cell has it’s division clock reset. At least part of this is due to extrachromosomal rRNA circles (ERCs) being retained by the mother cell.

New research finds that the septin ring between mother and daughter cells is a selective barrier for membrane proteins. The ERCs can’t pass the septin ring, and are likely linked to a membrane protein.

Z. Shcheprova et al., “A mechanism for asymmetric segregation of age during yeast budding,” Nature, 454:728–34, 2008

A drug that activates telomerase

A team of biotech and academic researchers has found a natural product compound, TA-65, that activates telomerase. Activating telomerase for short period is a way to renew cell populations that stop dividing. This diminishment of renewing cell populations causes some of the human aging phenotypes. If telomerase was turned on all the time, it would lead to cancer. The idea is that short term telomerase activation may have the benefits of renewal without increasing cancer incidence. TA-65 has only had one pilot human pharmacokinetic study where it seemed to have an effect on T-cells.

A Natural Product Telomerase Activator As Part of a Health Maintenance Program. Harley et al. Rejuvenation Research. doi:10.1089/rej.2010.1085. Online Ahead of Print: September 7, 2010

Notes on crystal binding proteins

I’ve had trouble finding info. A google search on “crystal binding proteins” sorta worked.

IgA binds to cholesterol crystals:
Cholesterol crystal binding of biliary immunoglobulin A: visualization by fluorescence light microscopy. Lammert et al. World J Gastroenterol. 2001 Apr;7(2):198-202.

There no doubt are proteins that bind to calcium carbonate shells material, but I couldn’t find info on them. I think shell is formed like bone, by cells increasing the local concentration of Ca++ so it crystallizes out of solution rather than by direct enzymatic action.

DNA sequencing by synthesis

Collected references on DNA sequencing by synthesis and related next-gen sequencing technologies:

SBS history page at Harvard