More than meets the eye

What is color?

If you’ve ever wondered if colors were really out there in nature or if they only existed in our minds then listen to last month’s Radiolab episode on Colors, “where Jad and Robert tear the rainbow to pieces.” Given its audio format, one of the standouts in the episode is the sonic interpretation of how a rainbow might appear differently to a dog, a human, and a mantis shrimp.

Comparison of the visible color spectrum of humans vs dogs.

Dogs, like most mammals, are dichromats–their eyes only have 2 types of photoreceptors: blue and yellow. This puts dog color vision on par with humans that are red-green colorblind. Humans, on the other hand, are trichromats, having a third photoreceptor for red in addition to blue and yellow.

Putting all of us to shame, the mantis shrimp has a whopping total of 16 types of photoreceptors (hexadecachromat anyone?), allowing them to see polarized light and into the UV spectrum (and perhaps appreciate each other’s pretty colors!)

Now imagine being a dog and not being able to appreciate this…OR imagine being a mantis shrimp and what a total mindbomb this would be:

The rest of the episode explores genetic engineering experiments that confer trichromacy to monkeys, the hunt for the fabled human “tetrachromat,” the mysteriously violent history of gamboge (a brilliant, yellow dye), and why blue is the last color to be attributed a word in nearly every culture.

Vertical stripes: The new black

Black clothing has a slimming effect due to an optical effect known as the “irradiation illusion, in which a black rectangle surrounded by white looks smaller than the same rectangle in white surrounded by black.”

The central squares are the same size, despite appearances given by the “irradiation illusion”

Another optical illusion suggests that horizontal stripes would also have a slimming effect. But amateur scientist and participant in Radio 4’s “So You Want to Be a Scientist?” Val Waltham disagrees. She put this effect to the test in 3-D by dressing models in outfits consisting of either vertical stripes, horizontal stripes, or plain black. Based on surveys she found that, “vertical stripes make people look taller, while horizontal hoops make them look wide – but plain black was the most slimming of all.”

Mental images

Close your eyes. Now imagine that you’re at the beach. Picture the sun, the sand, and the waves. Ever wonder how your mind creates these mental images? Neuroscientists at UTHealth are studying the neural mechanisms that allow us to form these images with the ultimate goal of designing a visual prosthetic to help the blind “see.”

Your eyes can play tricks on you

Have time to kill? Try this mysterious eye experiment.


Some Post-Father’s Day Reflecting: Old Dads Having Kids.

Recently, my dad has been dropping some not-so subtle hints and our conversations, over lunch or on the phone, have been following a certain formula:

“How’s work going?”

“It’s ok. I’ve been really busy with experiments.”

“I see. Is that why you’re dragging your feet on having kids?”


“Is there a Bruins game tonight”

“Yes, Dad, I’ll pick you up at 8 tonight.”

“Great. Would love to watch hockey with my grandkids someday.”

And even somtimes:

“Have you rescheduled my colonoscopy?”

“Yes. It’s for next Tuesday.”

“See? Who is going to do these things for you when get older, huh?

Despite his insistence, I try to tell him that it’s not that I don’t want children–I’m just not ready for children. For one, I’m not married. Two, I’m still in grad school making a pittance that barely supports myself, nevermind a family. Let’s face it, these figures aren’t exactly making a case for having kids either. And three, quite frankly, I’m just not ready to make that lifestyle adjustment.

My arguments, however, are never good enough for my dad. He often counters with a 1-2 punch consisting of a “who’s going to take care of you when you get older?” jab to throw me off guard and set me up for the ultimate guilt trip uppercut: “All I want is to hold my own grandchild. Then, I can close my eyes and die a happy man.” The first punch is a legitimate point seeing as how I am both his secretary and chaffeur when it comes to doctor’s appointments. And, admittedly, the thought has crossed my mind as to who would be driving me when it came time for my own colonoscopies. His second point, however,  is one-part selfish and one-part low blow.

Then, last week I saw the following fortuitously-timed headlines: “Older Dads Have Healthier Kids?“(h/t @LaurenAMichael) “Older dads may pass along a longer lifespan to their child.And,Kids of Older Fathers and Grandfathers May Inherit Longevity.” Seeing that Sunday would be Father’s day, I was excited to have new biological ammo to use against my dad.

Much to my disappointment, however, I was thwarted on two fronts. First, Father’s Day came and went without so much as a peep from my dad about the lack of grandkids, although, he might have been preoccupied with programming the clock on the microwave I had given him as a present. And second, a closer look at the reported research immediately tempered my excitement. In this study, researchers at Northwestern University found that the average length of telomeres, the tips of chromosomes, were longer in children of older fathers. They also found that this effect was cumulative, in that the telomeres were even longer in children if their fathers were themselves children of older fathers. The researchers point out that the increase in telomere length in children of older fathers is might be due to a known phenomenon where the telomeres in sperm cells increase with age.

With each cell division the ends of chromosomes are progressively shortened due to the peculiar inability of the enzymes responsible for DNA replication to do its job at the very tips of chromosomes. This is known as the End Replication Problem.

In order to protect chromosomes from deteriorating, an enzyme called telomerase “sews” to the end of chromosomes some “slack” DNA, which gets shortened instead, during cell division. Once telomeres reach a certain length it can signal to the cell to self-destruct through a process called apoptosis. For that reason, telomerase tends to be highly active in cells that are rapidly dividing since they are at the most risk for telomere shortening. Consistent with this, telomerase is very active in the testes (the site of sperm division), but how this might contribute to increasing rather than just maintaining telomere length is unknown.

While shortened telomeres have been linked to aging and age-related diseases, like cancer, and longer telomeres have been associated with longevity, this study did not examine any potential health benefits of older fathers bequeathing longer telomeres to their children. It is known, however, that as paternal age increases so does the risk of autism, schizophrenia, and other disorders in their children. Furthermore, the researchers were only able to measure the average length of telomeres. Since we inherit half of our chromosomes from our mothers and half from our fathers, its most likely that only the telomeres on the paternal chromosomes are longer.

After Father’s Day dinner with my dad, I went home and started thinking about how old he was when I was born. My dad was 46, making him one of many who followed an increasing trend (Table 21) of waiting to have kids. When I reflect back on my childhood, absent are those idyllic “father and son scenes” of playing catch with a baseball or tossing around a football. Or shooting hoops on a warm, Sunday afternoon– Ok, so maybe I’m guilty of employing a bit of “American-esque” dramatic license here, since I’m pretty damn sure my father’s never touched a baseball, football or basketball in his life. But my point is that he was sort of too old to do those things with me when I was a kid. That’s not to say he was a deadbeat, either. He was there for the spelling bees, the plays, the musicals (that’s right, I was a drama kid), and all of my hockey practices and games–but in the end, it just would have been nice to have been able to skate and pass the puck around with my Old Man. And when I start thinking about it that light, for a brief moment, it makes me want to have kids sooner rather than later.

Related Reading

Nobel Prize Press Release “How chromosomes are protected by telomeres and the enzyme telomerase

It Seems the Fertility Clock Ticks for Men, Too

Telome Health of Menlo Park tests age of DNA (I think they mean nucleotides and not amino acids.)

On Fatherhood: Proud Primate Papas

Moo Burps vs. ‘Roo Farts


With most of the attention on cutting greenhouse gas emissions from things like cars and power plants, we often overlook an odiferous offender: cow burps. Belching from ruminants, which include cows, sheep, and goats, releases methane, which is a greenhouse gas that can dramatically trap more heat than carbon dioxide (CO2). Over a 100-year period, methane’s heating trapping potential is 25 times greater than CO2’s potential!

According to the EPA, livestock farming of ruminants produces methane to the tune of about 80 million metric tons annually, which is roughly “28% of global methane emissions from human-related activities. An adult cow may be a very small source by itself, emitting only 80-110 kgs of methane, but with about 100 million cattle in the U.S. and 1.2 billion large ruminants in the world, ruminants are one of the largest methane sources.” This is supported by a Food and Agriculture Organization study, which concluded that livestock farming accounts for 18% of global greenhouse gas emissions. In contrast, the same study found that vehicles account for only 13% of global greenhouse gasses, the majority of which is CO2.

Ruminant Digestion

The source of the methane is actually microbes found in the cattle’s rumen, the cow’s “grass fermenting tank.” Cows and other ruminants lack enzymes that break down fiber (cellulose) found in grass and, therefore, depend on microbes to digest it through fermentation. One of the byproducts of this process is methane. While most of the methane is released by burping or rising from manure, some of the gas is also passed when ruminants “break wind.”

These facts have spurred scientists and cattle farmers to try and cut greenhouse gas emissions by adjusting the cows’ diet:

Another way to dramatically reduce methane emissions, as suggested last week in a Freakonomics podcast, is to switch from a cow-centric to a kangaroo-centric diet–an idea that has been bloated around before.

“You could also switch from eating beef to eating kangaroo — because kangaroo farts, as fate would have it, don’t contain methane. But just imagine the marketing campaign that would be needed to get Americans to take up ’roo-burgers. And think how hard the cattle ranchers would lobby Washington to ban kangaroo meat. Fortunately, a team of Australian scientists is attacking this problem from the opposite direction, trying to replicate the digestive bacteria in kangaroos’ stomachs so it can be transplanted to cows.” [links added by me]

Someone should tell the Freakonomics guys that Eight Mile Creek in New York has been serving kangaroo since 2010. Apparently, kangaroo meat is very lean and tastes “just like sweet filet mignon.” [h/t @brainofrich]

‘Roo meat

As it turns out, however, marsupial farts DO contain methane. In a recent study, red-necked (refraining from red neck jokes) wallabies were housed in special respiration chambers that had air constantly pumped in, which allowed the researchers to measure the amount of methane coming out of the chamber. The wallabies produced between 25-33% of the expected amount of methane that would be produced by ruminants fed the same diet. “Based on the uneven release of CH4 with time” the researchers concluded that the gas mainly came from farting rather than breathing, which would have produced a constant stream of methane. The drop in methane production could be due to the presence of certain gut bacteria that can help break down plant matter without making methane.

One friend, however, pointed out that kangaroos are much smaller than cows. Given the size difference, how much feed would be required and, consequently, how much methane would be produced in order to get an equivalent amount of kangaroo meat? Might the methane “savings” be a wash? While another friend suggested, “They’ve got this all wrong, you put a balloon on the cow’s ass, collect methane, and then burn it for energy. Yes this really happens.” Ask and you shall receive:

Related Reading and Videos:

‘Gas-less’ kangaroo secret sniffed out

Dinosaur gases ‘warmed the Earth’ (

China’s emissions estimates don’t add up

Tackling belching cows (Video)

Urging our Senators to Support NIH Funding: Does it Work?

Last night, before leaving lab I received this email:

Urge Your Senators to Support for $32 Billion for NIH in FY 2013

Dear Colleague,
The Senate Appropriations Committees will soon consider the Labor, Health and Human Services (LHHS) bill that will provide fiscal year (FY) 2013 funding for the National Institutes of Health (NIH). FASEB is urging Congress to increase the NIH budget to $32 billion in FY 2013 as the first step of a program of sustained growth that will keep pace with the increasing scientific opportunities, continue our progress in improved heath, and foster economic competitiveness. We need your help to ensure that your Senators hear from the research community about why it is important to provide $32 billion for NIH in 2013!
Please go to to email your Senators today to urge them to support $32 billion for NIH in the FY 2013 LHHS Appropriations bill. Together, we can make a difference for science!
Joseph C. LaManna, PhD
FASEB President

Normally, I fill these out without question, but after clicking the link I wondered whether I was just preaching to the choir. Being from RI, I know that funding the NIH and research in general has the support of my representatives and senators. In a few days I’m sure that I will receive a canned response from Sen. Reed and Sen. Whitehouse pledging their support.

So how effective is it? Has letter writing ever changed the minds of senators who oppose research funding increases? Or do they just picture this when they receive these emails:

Has anyone ever received a reply from a senator expressing why they oppose research funding or why they’ve changed their minds and now support it? If so, I’d love to hear your story. Better yet, if you responses from your senator please share and I’ll attach it to this post.

UPDATE 6.15.12

As anticipated, Senator Reed has responded with a letter expressing his support for NIH Funding: (bold mine)

Dear Mr. Le:
     Thank you for contacting me regarding federal support for medical research.  I appreciate hearing from you.
     To further our understanding of diseases and conditions and improve our nation’s health, I have consistently supported the work of the National Institutes of Health (NIH), which is the leading federal agency for medical research in the United States, as well as public health programs at the Centers for Disease Control and Prevention (CDC).  Scientific research, coupled with greater public education and awareness, has produced significant results with respect to disease rates in this country.
     The Consolidated Appropriations Act for Fiscal Year (FY) 2012, which I supported and was signed into law on December 23, 2011, provides over $30 billion to the NIH and $6 billion to the CDC.  You may be interested to learn that I recently joined a number of my colleagues in sending a letter to the Senate Appropriations Committee in support of biomedical research funding for the NIH in FY13.  For your review, I have enclosed a copy of this letter.
     It is my hope that strong federal support for medical research will continue to advance our knowledge of diseases, genetic disorders, and chronic conditions.  You can be assured that I will keep your thoughts in mind as I continue to support robust federal investment in medical research.
     Again, thank you for contacting me, and please do not hesitate to write, call, or visit my website,, in the future for information regarding this or any other matter.
Jack Reed
United States Senator

Here’s a copy of the letter to the Approriations Committee: FY13 NIH support

I think the statement, “As NIH grants get more competitive, researchers can easily spend half their careers working before receiving a grant, resulting in promising, talented young researchers being discouraged from biomedical research and some young investigators deciding to abandon scientific research altogether or to conduct their research outside the United States,” will resonate with most of my peers.

Histamine, Hygiene Hypothesis, & Hookworms

If you’re like me and millions of other Americans you’ve spent this spring being an itchy, sneezing, mucous-y mess. In this week’s Worldwide Wednesday I’m talking about allergies– the immune system’s reaction to pollen and otherwise harmless substances (dubbed allergens) and the ruiner of my favorite season.

Scanning electron microscope image of pollen grains from a variety of common plants.


We’ve all heard of them before, but what is histamine and what does it do? Histamine is a chemical compound produced by cells of the immune system, such as mast cells, and is the primary culprit that causes the miserable symptoms of allergies. That is because histamines induce capillaries to leak out fluids resulting in sneezing, watery eyes, and a runny nose. Learn how the release of histamines from mast cells is triggered by allergens and how anti-histamine drugs work:

(Note: I liked the videos about allergies and antihistamines on better, but I couldn’t figure out a way to embed them.)

Hygiene Hypothesis Challenged

As I mentioned, allergies are actually an immune response and the main players have other roles in immunity. For instance, the class of antibodies called Immunoglobulin E (IgE), which bind to allergens and triggers the release of histamines, appears to be the main line of defense against parasitic infections. Histamine, on the other hand, is part of the inflammatory response.

So what would cause the immune system to react to otherwise innocuous substances? One widely accepted explanation that takes into account the prevalence of allergies in developed countries is the hygiene hypothesis. Since we have effectively eradicated parasitic infections and live in increasingly cleaner and relatively sterile environments, we have reduced our exposure to infections pathogens and parasites especially during childhood. As a result the body’s immune system, which would normally be pre-occupied dealing with parasitic infections, becomes “bored” and starts mistaking harmless substances for potentially hazardous ones. Recently, however, some scientists have begun to look at allergies not as our immune system going rogue but rather that “runny noses, coughs and itchy rashes keep toxic chemicals out of our bodies, they argue, and persuade us to steer clear of dangerous environments.”


The concept underlying the hygiene hypothesis has inspired some squirmy solutions. Some people, desperate for allergy relief, have turned to infecting themselves with parasites such as the hookwormNecator americanus. The idea behind this treatment, known as helminthic therapy, is to keep the immune system’s hands tied up dealing with the parasitic infection so that it can’t trigger allergies.

N. americanus. “What’s it going to be, me or allergies?”

While there is some evidence that this therapy works, its efficacy is still being studied. But that isn’t stopping this doctor from experimenting on himself. Neither is it stopping Jasper Lawrence, who deliberately infected himself to combat allergies and asthma. You can catch the story of how he took it one step further and started selling hookworms as a business and how shortly after he had an ominous visit from the FDA.

Related Reading:

While most allergy treatments focus on blocking histamines, Finnish scientists are taking a different approach: vaccination.

Scientists at the University of Eastern Finland led by Professor Juhu Rouvinen, in cooperation with Professors Kristiina Takkinen and Hans Söderlun from VTT, a technical research center in Finland, discovered unique IgE‐binding structures in allergens. They say these structures can be genetically modified so they do not bind IgE anymore, but they can still induce the production of the immunoglobulin G (IgG). IgG protects you from allergic symptoms by actually prohibiting the formation of IgE-allergen complexes and could, in theory, prevent the degranulation and histamine release from white blood cells. The modified allergens are produced using modern molecular biology and biotechnology.

It seems a little vague since I can’t find anything published, but it would appear to be a lot of work since I imagine for the vaccine to prevent all allergies it would require modifying ALL allergens.

Meanwhile, a study from the Fred Hutchinson Cancer Center links allergies to higher blood cancer risk. But as the report concedes, “the added risk is so small that no new screening guidelines are currently planned.” Which made me wonder why this was even reported on the first place. As with the vaccination report, I couldn’t find anything published to read and evaluate.