Thursday, May 26, 2011

DCA: A cure for cancer?

The molecular structure of DCA, Dichloroacetic Acid (CHCl2COOH), a potential drug to cure cancer. 
DCA, or Dichloroacetic Acid, has recently been in the news as a potential cancer cure.  The commonly used chemotherapy drugs kill rapidly dividing cancer cells by hindering cell division.  Thus DCA differs completely by targeting cancer cell metabolism.  Most cancer cells are anerobic, meaning they function without oxygen, while normal healthy cells within the body are aerobic, meaning they function with oxygen.  DCA shifts cancer metabolism from anerobic (without oxygen) to aerobic (with oxygen).  This means DCA restores mitochondria function of the cell where aerobic metabolism (respiration) takes place.  The mitochondria, sometimes known as "the powerhouse of the cell", is an organelle that uses oxygen and glucose sugar to produce energy for cellular function.  Once mitochondrial function is restored  the cell can go through apoptosis, or programmed cell death, and the cancer cell kills itself.

Source from Hubpages.  I'm not sure where this image came from originally. 
 Summary of how DCA ideally works:
-Most cancer cells function without oxygen while healthy cells function with oxygen.
-DCA shifts cancer cells away from functioning without oxygen towards using oxygen.
-Once cancer cells start using oxygen again the mitochondria portion of the cell will kill the cancer cell.
-DCA ideally restores normal function of cancer cells so they will kill themselves.  So in effect the body (or the cells) kill cancer, not the drug.

Currently there is a lot of propaganda and hype surrounding DCA as a cure for cancer and conflicts with drug companies.  I am sure this is true at least in part but I don't know enough information to speak on it.  I simply want to present a scientifically based explanation of DCA cancer treatment that the general public can understand without political or corporate stigmas.  To be sure though, DCA is a very promising drug but it is not a cure all drug.  Clinical testing has shown it effective in some situations and not in others.  Based on my experience with science it is extremely unlikely this will end all cancer as some people seem to be spouting on the internet. 

Most of this research is coming from the University of Alberta DCA research.  This is a great website that will give you scientifically based, down to earth, information on DCA cancer treatment.

And Wikipedia has a good review of Dichloroacetic acid (DCA)

Tuesday, May 24, 2011

A few Iowa fungi and mushrooms

On my recent May hiking trips through Iowan woodlands I cam across a few interesting fungi.  Being Iowa has had a very cool and wet spring there is an abundance of certain types of mushrooms and an absence of others. 

An unknown bracket or polypore fungus growing on dead wood.  I believe this is Polyporus squamosus, or Dryads Saddle, but never positively identified it. 

I came across an abundance of a bracket or polypore fungus growing on dead wood throughout the woodlands.  Bracket fungi are shelf shaped and almost always grow on dead wood.  They are also called polypores because of the small holes or pores they contain on their underside.  Most familiar fungi that you might see in the grocery store have gills, or lines of fleshy material on their undersides, instead of the pores found on these mushrooms.  This fungi also had brownish scales on their top side and a very short stem.  I believe (I don't know for sure!) the particular type I found in the greatest abundance is known as Dryads Saddle or Polyporus squamosus.  This particular mushroom is generally not considered edible being it toughens up considerably as it ages.  It is not poisonous and some people do eat before it toughens up.  I didn't positively identify this fungus so I was not about to eat it, and neither should anyone else if they do not positively identify it! 

I also came across a slimy orange/white fungus growing on a dead grape vine.  I have no idea what it was.  Was the orange/white stuff on the surface of the vine mycelium the root like structure of mushrooms?  Or was this the immature fruiting body?  I would have had to come back at a later date to figure it out.  But even so, it was pretty interesting. 

An unknown orange/white fungus growing on a dead vine.

In very short supply were the Morel Mushrooms this spring.  Unusually cool weather apparently has prevented them from popping up in the woodlands this spring.  Hopefully slightly warmer weather will cause some to come up soon.  I however, am not a skilled Morel hunter...  so it may just be me...

Monday, May 23, 2011

Mid-May eastern hardwood forest wildflowers

May in a mature eastern hardwood forest, Indian Creek Nature Center near Cedar Rapids, Iowa.  Most of the trees in the photo are White Oak (Quercus alba) and Bur Oak (Quercus macrocarpa). 
One of the first sure signs of spring in the Midwest is the waking up of the forest floor.  You would expect sunny grassy areas to spring up greenery first but oddly, the cooler shaded forest floors seem to wake up usually late in April.  These plants bloom quickly before the trees leaf out and shade the forest floor.  Then through the end of May or so, depending on how warm it is, the forest is full of a wide variety of wildflowers.  While these flower shows do not dramatically cover forests with brilliant blooms, there are always an abundance of flowers.  Most notable though may be the intense green that blankets the entire landscape.  The best flower shows will always be in mature upland hardwood forests.  These mature forests are often characterized by large inter-spaced oak trees and need to have a forest floor that is not disturbed by grazing, erosion, or flooding.

The Indian Creek Nature Center outside of Cedar Rapids Iowa has many acres of prime mature eastern hardwood forest.  I recently went hiking there a few times on a short trip visiting relatives.  The nature centers land is extremely healthy and well maintained.  There are great examples of upland forest, bottom land forest, and wetlands.  It is also part of Northeastern Iowa's Silos and Smokestacks National Heritage Area

Here are some of the flowers and plants I found on a recent trip. 
Virginia Bluebells



May Apple
Poison Ivy

Prairie Trillium

Wild Geranium

Thursday, May 19, 2011

Mid-May in the Sonoran Desert

The desert is still quite active during the middle of May.  We have had some unseasonably cool weather lately which is extending out some of the blooms over the past few weeks.  We have had several days with highs around 80 degrees so far this month which is weird considering highs are normally in the mid 90's or so.  We even had a little rain last night, which is extremely unusual for the month of May.  The big flower show of Foothills Palo Verde is done for the most part and the desert is moving on to Ironwood and Saguaro.  While both Ironwood and Saguaro are less abundant than Palo Verde they still keep desert bugs and birds quite active during the morning hours.  Here are some pictures from my recent hikes.

Catclaw Acacia (acacia greggii) in flower.  Common lower on north facing slopes and in basin washes around Phoenix.

Catclaw Acacia flowers.

Ironwood (Olneya tesota) flowers.

Ironwood and Saguaro (Carnegiea gigantea) both in flower.

Saguaro cactus flower.
The Ironwood flowers should die off within the next week or so while the Saguaro flowers will last another couple of weeks.  Once Saguaro flowering is done we head into June, the driest month and second hottest month of the year.  When June hits, the desert more or less seems to go dormant during daylight hours until the end of the month.  At the end of June, Saguaro fruit ripens and desert life goes crazy gorging itself on the fruit.

Biomimicry: possibilities only limited by nature itself

Biomimicry is the emulation of natural forms and processes to solve human problems.  The tremendous diversity of the natural world has a seemingly infinite number of forms and processes that naturally and often passively take care of everyday problems we encounter as humans.  Water filtration, pollution control, recycling, antibacterial surfaces, waterproofing, water transportation, and water conservation are only a few of the processes that organisms do everyday seemingly without notice.  These are also processes humans deal with everyday.  Biomimicry is an amazingly diverse field of study incorporating nearly every field of study including biology (of course), math, physics, electronics, art, sociology, business, and the list goes on.  We have barely scratched the surface of this science.  In a sense, biomimicry is as Johann Kepler said "Thinking God's thoughts after him", and then using them for our benefit.  The potential of this scientific field of study is only limited by the tremendous diversity and complexity of the natural world.

A number of organizations and people are beginning to tap the natural world in hopes of finding something to mimic.  The Biomimicry Institute is one of those organizations, with the goal of "inspiring, educating, and connecting biomimics throughout the world."  They have a very good website you can check out here:

Janine Benyus is one of the pioneers of this movement.  She has authored a number of books including one on biomimicry and frequently gives lectures on the subject.  She has given several TED lectures over the past several years.  Here is one of her latest ones, and is both interesting and inspiring.

As I have been thinking about biomimicry I realized it is already in use in many different situations, even when we don't realize it.  I personally am interested in ecomimicry, which I think is much easier for the average person out there.  Permaculture I believe is a form of ecomimicry, mimicking ecosystems and their processes.  Permaculture mimics ecosystem processes through landscaping and gardening in order to create a "permanent culture", or rather a sustainable culture.  By mimicking natures use of water conservation, shade, sunlight, planting, soil processes and structures we can create a better, healthier environment.

Wednesday, May 18, 2011

Sauerkraut disaster

My batch of sauerkraut a month ago with cabbage fresh from the garden.
About a month ago we harvested 16 pounds of cabbage from our garden.  I was quite proud of our cabbage being we started it from seed back in October.  The cabbage tasted excellent and had minimal bug infestations, which as cabbage growers knows is quite an accomplishment.  So it was exciting to preserve the cabbage by fermenting it into sauerkraut.  Everything went as usual and I expected to have fresh kraut in about two weeks.

Normally, sauerkraut fermentation bubbles for a little over a week before finally stopping.  This time however, the kraut continued bubbling for four weeks and would have went longer. 
My bad sauerkraut.  Smelled funny, had a slimy limp texture, and looked off color compared to good sauerkraut.  Needless to say, I threw it out.
After four weeks of bubbling I finally looked at what was happening to the sauerkraut.   In the crock I found unusual smelling, slimy, limp, and off color kraut.  All of these things indicate a kraut gone bad.  I have a feeling it somehow was contaminated with yeast or mold.  And of course, I threw it all out.  Which was quite a disappointment.  I mean, who wouldn't be if their normally tasty sauerkraut went bad?

All this was not a waste though.  This is the only batch of sauerkraut I have ever had go bad on me but I think I learned a few things from it.
1. If bubbling of sauerkraut is extended for any longer then two weeks just throw it out.
2. Off smell, slimy or limp texture, and off color all indicate a bad kraut.
3. Fermenting at higher temperatures (in this case around 75 degrees) can be more difficult and lead to contamination.  I generally like to ferment kraut between 60 and 70 degrees.  This situation confirms my fermentation temperature preference.
4. Be sure to cover the crock well to prevent contamination.
5. Don't get too attached to your experiment.  Projects and experiments fail all the time, learn from it and try again with your new knowledge on how not to do something.

Friday, May 13, 2011

High fructose corn syrup, sugar and your health

A table sugar (technically called sucrose) molecule model.   Sucrose is made of 50% glucose and 50% fructose.
There has been a lot of controversy in recent years centering around high fructose corn syrup (HFCS).  Public opinion appears to be turning against it and current research also does not appear to favor it either. Considering in the 80's HFCS replaced table sugar in many processed foods as a better, healthier option, it is interesting that the public now may want regular table sugar instead of HFCS again.  Recently a coworker informed me of a recent New York Times article published last month.

While the article is long, it is excellent and full of great science based information.  Well worth reading all the way through.  As the title suggests it is not simply about HFCS but sugar in general and its negative health consequences.  The negative consequences of table sugar and HFCS do however center around fructose.  While HFCS is typically 55% fructose and 45% glucose, table sugar (technically known as sucrose) is 50% glucose and 50% fructose.  So there really isn't much difference between table sugar and HFCS.  According to the article the problem with fructose is in how its processed by the body.  Here is a summary of what's in the article:

-The average american eats 90 pounds of refined sugar annually (includes both table sugar and HFCS).
-While glucose is processed by every cell of the body, fructose is primarily processed by the liver.
-When the liver processes fructose much of it is converted into fat which is deposited in and around the liver.  Fat is also deposited around the mid section.
-A fatty liver is connected with heart disease and insulin resistance. 
-Type 2 diabetes is a result of insulin resistance.
-Cancer may also be connected with these negative health consequences.

Other research has also found 1/3 of HFCS products contaminated with mercury (click here).  This contamination is likely due to the processing of corn into HFCS.

I personally have eliminated nearly all sugar and HFCS from my diet for these reasons but I would be interested in what other people think.  How does this information affect you if at all?  

Tuesday, May 10, 2011

Update for April garden

We continued to make a lot of progress in the garden this past April.  We are still hurting some from some poor planting decisions I made last fall but I continue to learn how to productively garden.  Weighing and recording everything that comes out of the garden seems to be the key.  April continued to be a dry month and always marks the beginning of our annual spring/summer drought that ends with July's monsoon season.  We recieved 0.25 inches of rain and had pretty nice weather for most of the month.  The last week of April however we had highs in the mid to upper 90's which required a little extra watering.  

Here are the stats:  All prices are based on local Fry's or Sprouts organic produce.
College garden
Cabbage 16 lbs, $15.87 ($0.99/lbs),
Beets 8lbs 1oz, $24.11 ($2.99/lbs),
Chard  2 lbs, $10.00 ($2.50/8oz bunch)
Cilantro  4oz, $1.38 ($0.69/2oz bunch)
Total hours: 4
Total calories burned: 1224
Calories produced: 3721
Net calories:  2497
$ spent: $0.00
$ produced: $51.36
Net $: $51.36

Home Garden
Green onions  1 lbs 10 oz, $8.97 ($0.69/2oz bunch),
Beets  4lbs, $11.96 ($2.99/lbs),
Chard  2lbs, $10.00 ($2.50/8oz bunch)
Carrots  2lbs 8oz, $2.48 ($0.99/lbs)
Chives 8oz, $6.76 ($1.69/2oz bunch)
Basil 3oz, $2.84 ($1.89/2oz bunch)
Garlic 1lbs 4oz, $6.00 ($0.75/head)
Tomatoes 8oz, $1.50 ($2.99/lbs)

Total hours: 4
Total calories burned: 1224
Calories produced: 2376
Net calories:  1152
$ spent: $2.99 on basil plant
$ produced: $50.51
Net $:  $47.52

Totals since October 2010
College garden: 
$ Totals: $59.72+$51.36=$111.08
Total hours worked: 18.75
Calorie totals:1654+2497=4151

$ Totals: $56.15+$47.52=$103.67
Hours worked: 21.25
Calorie totals:556+1152=1708

So April was a pretty good month for our gardens.  May should produce a lot of tomatoes, zucchini, beans(?), peaches, garlic, chard, and carrots.  May is normally a good month for gardening in Phoenix.  While it is dry and the temperatures are getting pretty hot, the temperatures are not so hot that it harms plant production.  June and July are when we really have to protect plants from extreme heat and sun. 

Friday, May 6, 2011

What's the difference between these Palo Verde trees?

As usual, this spring I have spent quite a bit of time hiking the desert near my home.  For the past week the Foothills Palo Verde trees (Parkinsonia microphylla) have been in bloom, dotting the hill and mountain sides with yellow.  The Palo Verde is typically the most abundant and important upland trees within the Sonoran Desert.  Every spring it is filled with flowers, which attracts swarms of insects (especially bees), and the insects in-turn attract lots of birds.  The blooming Palo Verde literally becomes a buzzing, chirping, swarm of activity each spring.  However, as I was walking I noticed a peculiarity, some of the Palo Verdes were blooming while others were not.  Why was this?  Here is some of what I observed.
Some of the Palo Verdes were blooming like this one.

Others had very few flowers or none at all like the one above.
So why the difference between the above two Palo Verde trees?  The trees both received the same amount of rain and both were in the same type of soil.  The answer to the difference in blooms lays in the pictures above.  So I hypothesized that the Saguaro was out competing the Palo Verde for water, resulting in the Palo Verde not having enough water to produce flowers (second photo).  The Palo Verde in the top photo was not associated with a Saguaro, and according to my hypothesis would have plenty of water.  To test this I decided to survey Palo Verde trees associated with and without saguaro cacti to determine how flowering was affected.  So, spending about a days worth of hiking around a mountain side I recorded the percent flowering of Palo Verde trees associated with Saguaros and not associated with saguaros. 

This is what I found.  Palo Verdes associated with Saguaros (Saguaros had to be at least three meters high) averaged 30% flowering within their canopy.  Palo Verdes not associated with Saguaros averaged 42% of their canopy flowering.  For all us statistical nerds, yes this was statistically significant for one-tailed, two-tailed, and paired t-tests!  So the test does support our hypothesis that Saguaros are our competing Palo Verdes for water.  Thus Palo Verde flowering is reduced.

This is all quite odd considering the Palo Verde is a well know nurse plant for the Saguaro Cacti.  A nurse plant aids the establishment and growth of another plant, "nursing" another plant to life.  The shade, nutrients, reduced temperature, and greater moisture under a Palo Verde are well known to "nurse" the establishment of young Saguaros.  But apparently the Saguaro "bites the had that feeds it" later in life, out competing the Palo Verde for water and eventually killing it (according to other researchers).

Tuesday, May 3, 2011

Accidental aquatic biology in an aquarium

In the biology lab we have had an aquarium for keeping aquatic plants for probably about six years.  All was going well until about two years ago when we purchased some aquatic plants from a new vendor.  These new plants were unfortunately inhabited by a few hidden snails.  Resulting in a snail population explosion in our tank.  The snail population probably peaked somewhere around several hundred snails in our ten gallon tank.  Large bunches of the aquatic plant elodea could be eaten in a matter of days by these snails.  We fought this snail population for about two years by trying to starve them to death, but ultimately it was unsuccessful. 

Snail on the side of our fish tank.

Snail eggs on the side of our fish tank.

 Thinking that maybe snails were coming in on each of our shipments of aquatic plants we tried a new vendor.  Well this third vendor was worse than the previous one.  Snails still proliferated in the tank but apparently mosquito eggs or larva, and some sort of daphnia zooplankton came in with our latest shipment of plants.  This resulted in a rather large swarm of mosquitoes in our tank and huge numbers of daphnia swimming around in the water.  Fortunately, we had a good lid on the tank so the mosquitoes did not escape.

Mosquito larva in our tank.  The tiny dots are either sediment or tiny daphnia swimming around.
As a result of all this we finally had to dump the tank out and start over.  But in the process we got to observe some pretty interesting things: snail and mosquito life cycles, exponential population growth and subsequent crash, control of food on the snail population, and even some microbiology.  A pretty cool accidental aquatic biology experiment if I don't say so myself.  Next time we are going to stick with our first vendor, and if we have the same problem I think we'll introduce a small fish into the tank to see what happens.

Global warming? Climate change? What is going on?

A coworker of mine recently introduced me to a new PBS documentary called "Earth: The Operators' Manual".  This video is full of great science, awesome video footage, answers to our climate change questions, and practical solutions for climate change problems.  The documentary is very logical, straight forward, and easy to understand.  One of the best things this video has to offer are practical solutions and a positive outlook on the future, something that is quite rare in climate change discussions.  The website has some excellent resources on climate change and the documentary for free (at least for now).  Check it out: