Archive for the ‘Science’ Category

Nature Futures

Wednesday, April 2nd, 2014

Earlier this year, the journal Nature created a writing competition asking for short science fiction stories of only 200 characters. Today Nature announced the winners and I am one of the five runners up.

It’s an honor to be published in one of the most prominent scientific journals. I can only hope that in the future I will be published not only for my writing, but also for my research. Nature also publishes Scientific American magazine. Here is my winning entry:

Cynthia was learning faster than anyone had predicted. The apparently totipotent cells continued to proliferate at an exponential rate. Today would be the last time they would refer to her as a mouse.

Congratulations to the other winning entrants. Keep writing!

23 and Me

Tuesday, February 12th, 2013

One of my Christmas gifts was a DNA profile from 23 and Me, a service that genotypes your DNA and evaluates, among other things, your traits, risks for certain diseases, and ancestry. It takes some time to process (you mail them a saliva sample), so my results just came in today. There weren’t many surprises and my ancestry information is still processing, though it shows a completely European background. I found the disease information to be most informative and potentially useful.

My highest risk for disease is Alzheimer’s. I have genetic markers indicating a doubled risk compared to the general population. There is long list of diseases for which there are markers, though this was the highest risk disease for me. In contrast, my lowest risk for disease was melanoma (skin cancer) and pulmonary embolisms, which has to do with blood clots.

My DNA profile accurately predicted that I have straight blond hair and blue eyes. It also accurately predicted my blood type and that I have fast-twitch muscles (I was a sprinter in high school). I have genetic markers indicating a higher likelihood of living to 100 and having a lower body mass index and low tendency to overeat. I currently weigh 132 pounds with a goal weight of 125, the lowest weight someone of my height can have without being underweight based on body mass index (BMI). I have a lower than average likelihood of developing male pattern baldness and I am likely to consume more caffeine than the average person. I have a higher than average tendency to develop addictions to alcohol and nicotine, though I neither drink nor smoke so that has never been an issue for me. I have markers indicating that I have an increased sensitivity to pain.

Other information includes my likely response to certain drugs and medications (nothing real significant) as well whether I carry any disease risks (I’m not a carrier for any diseases). Much of the information was very accurate, like my physical traits, while other information is more probabilistic, such as my likelihood of developing Alzheimer’s. My grandmother is currently in a nursing home with full stage Alzheimer’s, yet otherwise she’s extremely healthy and is 85 years old. My great-grandfather lived to 94 and my great-grandmother lived to 89, so I do have longevity in my family.

The information has to be taken with a grain of salt – genetics is just one facet of health. The other major elements are behavior and environment, the latter of which is very complicated and filled with confounding factors. For example, Maine has the highest rate of cancer of any state in the US. Is that because we have the second highest per capita geriatric population in the US? Is it because of radon leaking out of Maine granite? I’m a strong believer in personal choices, individualism, and self-determination, so I lean toward behavior being the most important factor. I exercise, stay active (rollerblading, archery, tennis, etc.), and hold to a fairly strict diet. I don’t drink, smoke, or use illicit drugs. I do what I can to have fun, reduce stress, and maintain a positive outlook on life. Mentally I challenge myself all the time with computer programming and science projects, lots and lots of reading (especially scientific journals), and creative projects. I also take several health supplements. I recently read a book called The Longevity Project, by Howard S. Friedman, PhD, and Leslie R. Martin, PhD. It was based on an 80-year study of behavioral patterns associated with life span. They found that the number one predictor of long life was conscientiousness. I consider myself to be extremely conscientious and I have been told that I am often conscientious or principled to a fault, so I was happy to read their findings.

I’m still waiting on the ancestry results, which will give me a profile of my racial and ethnic background. I suspect that I have significant Native American ancestry on my father’s side, though we’re not sure. I’m also waiting on the “relative finder” to process, though I assume that for that to work, my relatives must have also had their DNA profiled through this service. I think it applies to very distant relatives, too, so that significantly expands the possible matches. There is still a LOT more information for me to explore and they are adding more stuff all the time. There are well over 100 different traits with in-depth explanations, so I’ve got a lot of information to explore!

New Year

Saturday, December 29th, 2012

Well the world did not end and it seems there wasn’t anyone crazy enough to make it a self-fulfilling prophecy. I’m just old enough to vaguely remember Y2K and the Hale-Bopp comet and I’m grateful December 21st shared little in common with those events. The date seemed to have passed by without much notice at all and ensured that Christmas was safe, even if the American economy isn’t 😀

I had a nice Christmas with my family. I got an iPhone, a FitBit, a whole bunch of lab supplies / lab books, and some clothes. It will be good having an iPhone because right now I really need 24/7 internet access and I’m still developing an iPhone game. I’ve been very busy with other things so I haven’t had a lot of time to program and create graphics, but the game is coming along well. It’s more work and more fun than I ever expected it to be! I also got a DNA kit to have my genes sequenced – technically it will look for genetic markers that correlate to specific disease risks and may give me some insight into my ancestry. I had to fill a vial with spit and then mail it in, and it will take a month or so to process, so I’ve got some waiting to do.

In the meantime I successfully hand-pollinated two of the three blue orchid blooms, which are already beginning to swell (and the flowers of which almost immediately died). Plant science is probably boring to most of you, but I’ve always loved plants and my new lab supplies will help me emulate much of the work I did at the University of Maine working with transgenic rice and Arabidopsis. Unfortunately I lack a laminar flow and a thermal cycler (for PCR). As a result, contamination is a significant problem when I’m plating media at home, and whatever results I obtain won’t be especially scientific since I can’t actually do any genotypic analysis. Still, there is a lot I can do with what I have, including my two microscopes, plant hormones, agrobacterium cultures, and some colchicine. NOTE: Colchicine is a chemical that can halt cellular mitosis by interfering with spindle / microtubule elongation. It is very useful for essentially “freezing” phases of mitosis and also inducing mutation in plants. Even though colchicine used to be derived from plants, it is extremely toxic and I don’t recommend using it without experience with toxic chemicals. Always read the MSDS if you’re going to work with an unfamiliar chemical.

I will publish some of what I’m doing on my Plants and Labwork page in the future. Most of my work will probably consist of plant tissue culture / cloning, which is fairly accessible even to people like me who don’t have multimillion dollar laboratories. One of the most common examples is African Violet, which readily develops new whole plants from partial tissues taken from a donor plant. This species and several others require little to no hormonal treatment to induce such growth. I’m also going to attempt growing orchids from seed on plated media. The vast majority of commercial orchids are clones (“mericlones”) originating from tissue cultures. Human comprehension of orchid seed germination, which is the result of a symbiotic relationship with a fungi, is relatively recent. In the early days of orchid collecting, nobody understood how to germinate orchid seeds. Orchid seeds lack endosperm, which can be thought of as “food” for the seed during germination. As such, they rely on various fungi species for germination and these fungal species are very specific to the orchid species itself, no pun intended. The prevalence of mericlones has more to do with cost-effectiveness, product consistency, and logistics, however; most orchids require at least 7 years from seed to flowering. Between plant genomics and paleogenetics, I can’t think of anything else I’d rather devote my life to.


Monday, August 6th, 2012

As of my writing this, Curiosity just landed on Mars and made contact with Earth! The complex sky crane touchdown worked out well and it seems the Mars Science Laboratory maneuvers were a success. The first images were just sent to Earth moments ago…

This is a video from NASA that discusses the difficulties involved in this mission…


Monday, June 11th, 2012

Summer’s here and we’re finally getting through the rainy season that hit us and threatened to wreck my garden. My family and I got to Monhegan Island over the weekend, which is just as beautiful as ever. I highly recommend it. I got some awesome photos that I posted in a Google Plus album: Monhegan Island 2012 As I said I probably would, I also posted the album that played at my grandfather’s funeral. Here is the link for the online album Memorial Album of Harland Nickerson

My hair’s longer than it’s ever been. I tried putting it down the other day and everyone says they like it better longer, though it’s a real pain to deal with. I posted pics in my Google Plus profile and Flickr. I might cut it, IDK. I love how my highlights came out and I don’t want to lose those.

June 5th was the once-in-a-lifetime Venus transit across the Sun. Despite the overcast sky here in Maine, there were several breaks that allowed me to get a clear shot of the Sun. I put the telephoto lens on my Canon EOS, added an IR filter, and set the shutter speed to 1/4000 of a second. I got some beautiful photos of Venus silhouetted against the Sun and one of the best ones is right here:

I’m really excited, too, because my garden, greenhouse, and indoor plants are coming along really well. My Tricyrtis (toad lily, which looks a lot like an orchid), which I grew from seed, just bloomed. I’ve got some red bell peppers growing inside – I never knew that green, red, and yellow peppers are all the same plant, just different maturation times. Tons of stuff in my garden coming up. And perhaps most exciting is that I succeeded in pollinating my Encyclia orchid from Florida – it’s now developing seed pods!


Friday, January 27th, 2012

The puppies opened their eyes recently. They don’t look like puppies, in my opinion; more like smug little bears. The brown and white one yawns a lot. They are of course still suckling, though Bebe is much less protective of them and checks in on them only occasionally. That said, if she spots any of the other poms going into the bedroom, there’s always pomeranian drama, lol. Puppy pictures are below ^-^

My plants are doing well. I finally decided to cut back the belladonna, which almost immediately grew new leaves from the 1/2″ stems I left. I’ve been wanting to start some Black Pearl Peppers (the leaves are black instead of green) and Easter Egg Radishes, the latter of which may help me with one of my graduate projects. I transplanted the belladonna outside when it was relatively warm the other day. I’m hoping the roots may survive the rest of the Maine winter, especially since the species is native to Europe. I also have some blue water lilies growing and although their stems are about a foot long now, their growth, much like that of the Colchicaceae plants, has virtually halted, though they remain healthy. I have them under a grow light, but I’m not sure it’s helping.

Two of my three orchids are shooting, an odd time considering the light is at a minimum right now. One of them, an Encyclia orchid I got from R.F. Orchids in Florida nearly two years ago, will bloom for the first time in its life. The flowers supposedly smell of chocolate, so I’m excited! I will post pictures when they bloom.

Among my Christmas presents were two microscopes – a dissecting scope and an objective microscope with 2,000X power. It’s my fourth objective microscope, but this one includes an attachment for dark-field microscopy, which is great for certain microorganisms with transparent bodies. I had to cut some infected leaf tissue from one of my Phalaenopsis orchids the other day and I was able to view the stomata, chloroplasts, nucleus, and nucleolus very clearly even though I don’t have any stains yet. Just by adjusting the diaphragm, I was able to observe changes in the cytoplasmic streaming of the chloroplasts.

Unfortunately UMaine doesn’t offer any courses in plant histology, so I’m on my own when it comes to using my microtome and figuring out what stains I need to order. There are a lot of good resources online, though. I’ll post pictures when I get some good ones. I also ordered a camera mount while I was in California, so now I can take time-lapse videos. I’m hoping to (very carefully) slice open a dicot plant seed in order to photograph the embryonic developmental stages (embryogenesis), which are very distinctive. This Summer I’ll likely take some time to document the cleavage stages of amphibian eggs and their embryonic development as well. In the meantime there’s limitless things to look at for fun, like my red and white blood cells, cheek cells, hair, and microorganisms, many species of which I can find in the standing water around my orchids. Sometimes I’m lucky enough to come across Daphnia, my favorite. I bet they will show up well under the dark field.