Tuesday, February 5, 2013

Biology Rewriting History

The mitochondria; primary function being producing ATP energy for the cell.  The mitochondria contains circular DNA which is only passed down from the mother.
In the news this past week I have come across two instances where biology has recently rewrote history.  The first and most publicized story has to do with the discovery of Great Britian's King Richard III  (Click for news story here).  Scientists, through the use of forensic skeletal evidence were able to show the skeleton in question had similar features to what history tells us about the king.  The final and most absolute evidence came in the form of mitochondrial DNA.  The mitochondria is an organelle within cells that produces ATP energy for running the cell.  The mitochondria contains a relatively small amount of DNA that is circular in shape.  This DNA is unique in that it is independent from DNA contained within the nucleus of the cell and that it is only passed down from the mother and not the father.  DNA in the nucleus is a combination of half coming from the father and half from the mother, so the offspring is a unique combination of DNA from both parents.  With DNA of the nucleus, every individual person has a unique combination of DNA, except in the case of identical twins which have identical DNA.  In mitochondrial DNA, all offspring have identical DNA to their mother, even if they have different fathers.  In the case of King Richard III, a direct match of mitochondrial DNA was found between the skeleton in question and a present day descendant of King Richard III's sister.  So to break this down, King Richard and his sister would have had identical mitochondrial DNA because they had the same mother.  Identical DNA would have then been passed down through the maternal side of all of King Richard's sisters descendants.  To find a direct match in mitochondrial DNA is undeniable evidence that two people are directly related to each other and that the skeleton must be King Richard III.

The second and far less publicized story has to do the Mary Ingalls, the sister of Laura Ingalls Wilder wrote the "Little House on the Prairie" books.  The question being asked about Mary Ingalls in this investigation was why really did Mary go blind (Click for news story here) .  In the books, Laura claims that Mary went blind as a result of scarlet fever.  With modern medicine we know that scarlet fever rarely causes blindness and if it does the blindness is only temporary.  So the idea that scarlet fever cause blindness is only a myth from the past.  A medical doctor examining this went through the many letters and writings of Laura Ingalls-Wilder in order to find what illness may have actually caused Mary's blindness.  In the letters, the doctor came across what appears to be Mary having spinal meningitis, which causes swelling of the central nervous system.  This swelling could have easily caused damage to the optic nerves and therefore causing blindness. 

Friday, February 1, 2013

Legumes: Self Fertilizing Plants

The green stem of the legume palo verde tree in the Sonoran Desert.
Determining how to fertilize a plant can be quite the difficulty.  You may have heard that most people over water their plants, but it is also true that most people over fertilize their plants.  Certain plants however never need to be fertilized simply because they have "figured" out a way to fertilize themselves.  Bean plants, also called legumes, form a symbiotic relationship with a bacterium known as rhizobium.  The air we breath is about 70 percent nitrogen, an essential nutrient for plant fertilization.  Atmospheric nitrogen however cannot be used by plants, it must be converted into a different form called ammonium.  Rhizobium bacteria has the ability to take nitrogen gas and convert it into ammonium.  This changing of nitrogen gas into ammonium is known as nitrogen fixation. 

Using legumes in the garden can be quite a useful way to fertilize your plants naturally.  Farmers in the Midwest will often alternate between corn and soybeans, taking advantage of the fact that soybeans naturally replenish the soil with nitrogen fertilizer that the corn can use.  In deserts, which have soils that are naturally deficient in nitrogen, plants must either be adapted to living in soils with low nutrients or have the ability to fix their own nitrogen.  For this reason, legumes are extremely common in desert ecosystems.  Legumes are not just your typical bean plant, they also grow into bushes and trees.  In the Sonoran Desert palo verdes, mesquites, ironwoods, and acacias are all small legume trees that form bean-like pods.  Typically, these legume trees will form islands of soil under their canopy that are rich in nutrients compared to soils beyond the canopy.  Because of the slightly richer soil many smaller plants will often be growing in this micro-environment. 
The darker growths on these plant roots are tumors infected with rhizobium bacteria.
Legumes and Rhizobium bacteria form their association with each other in the soil-root environment.  Rhizobium are naturally occurring soil bacteria but don't really do much if they haven't infected a legume.  When bean seeds germinate and begin to grow, rhizobium already present in the soil infects the new plants roots.  Points of rhizobium infection in the roots form into tumorous-like growths which are like little nitrogen fixing factories.  Typically we think of tumors as unhealthy but be assured, this type of plant tumor is very healthy and beneficial to not only the infected plant but also to the entire environment.  Legume plants that for some reason are not infected become extremely anemic with stunted growth and yellow coloration. 

Monday, January 28, 2013

Tuzigoot National Monument

Desert grassland surrounding the Tuzigoot ruins.  National Parks website photo.
When it comes to living off the land as the ancient Sinagua Native Americans did, Tuzigoot National Monument near Cottonwood, Arizona has it all.  Landscape diversity is essential when it comes to finding the products essential for life and Tuzigoot is especially rich when it comes to the landscape.  Think about it.  If you were to live off the land and not be required to wonder around searching for things constantly you would need a variety of different types of habitats that support a variety of different types of plants and materials necessary for life.  You would need food, building products for shelter, material for clothing, and water at least.  At Tuzigoot, all of these things are highly concentrated in a relatively small area. 

If you visit Tuzigoot National Monument you can see four major habitats that would have provided nearly everything the ancient Sinagua's would have needed within about 50 acres, which is about the size of a very small farm.  Tuzigoot is located in the desert grasslands of the Upper Sonoran Desert.  The desert grasslands surrounding these ruins would have provided yucca plants which provided some fiber and some food for the Native Americans.  Food would have been in the form of plants such as cacti fruits that could have been gathered or animals for hunting.  The desert grasslands are the least productive habitats though of this area.  Even more productive would have been the mesquite and acacia bosque downslope and closer to the river and wetland.  This thick brushy habitat grows where soil moisture is higher than in the grasslands and where the river has deposited deep soils.  The mesquite trees provide huge amounts of food in the form of mesquite beans every summer.  These bean pods were ground-up and made into cakes.  Mesquite wood also provided materials for building and tools.  The deep soils of the mesquite bosque are also likely where farming took place.  Of course, farming in these areas provided food mostly in the form of corn, beans and squash, but it also provided cotton to make clothing.  The mesquite bosque was also a great place for animals to hide and was therefore very good for hunting. 
Tavasci Marsh. Photo from National Parks website.
Slightly down slope from the bosque two extremely important habitats can be found.  The first is the large marsh.  The marsh is today known as the Tavasci Marsh and is dense with grassy wetland plants.  The marsh would have provided essential habitat for all kinds of animals that came to it for both water and food, both of which were scarce in the surrounding desert grasslands.  The Native Americans would have used the marsh as a hunting area as well as an area to gather food from plants.  For example, the cattails in the marsh provide huge amounts of potato-like food in their root systems.  Lastly, the perennial flowing Verde River would have provided trees for building materials, water to drink and for watering plants, and wildlife for eating.  Across all of these habitats there of course can be found an abundance of rocks that the Sinagua used for building. 

Friday, January 25, 2013

Organ Pipe Cactus National Monument

View from the visitors center trail at Organ Pipe Cactus National Monument.  In this photo jumping cholla, saguaro, and organ pipe cacti can all be seen with the Ajo mountains in the background.
Organ Pipe Cactus National Monument is located right on the boarder of Mexico as far south as you can go in Arizona. The monument is quite a ways off the beaten path and probably the most dangerous monument in the national park system. There are multiple boarder patrol checkpoints that are actually in or near the park and boarder patrols can be found all over the park. Tragically, a few years back a park ranger was killed in a boarder incident and things were quite dangerous within the park. Today however, a barrier fence has been put into place along the monuments boarder and dangerous sections of the park have been closed to visitors. The park is significantly safer today than it was several years ago. Unfortunately, Senita Basin, the only population of the columnar senita cactus is currently closed due to these issues. Fortunately, other sections of the park such as the Ajo Mountain Drive are open and offer spectacular views of the Sonoran Desert. For a desert, the monument is quite green and hope to a decent amount of vegetation. This unusually green desert is a result of this particular desert being one of the wettest deserts in the world. Organ Pipe receives about 10 inches of rain annually with significantly more falling at higher elevations. Both winter and summer rainfall seasons also contribute to the amount and diversity of vegetation here.
View along the Ajo drive in Organ Pipe Cactus National Monument
A total of 28 species of cacti can be found within the park. Several of these are at their northern most limits, and are prevented from migrating further north due increased number of days with freezing temperatures to the north. Organ pipe cacti are one of these species and can be found in abundance within the park. The amazing diversity of cacti can be found on the Ajo Mountain Drive, and it is spectacular for organ pipe viewing. Most commonly, the organ pipe is found on upper slopes facing south. The sun warms southern slopes just enough to prevent colder freezing temperatures that prevents the cacti from growing on colder northern slopes. Upper slopes also are slightly warmer due to warm air rising up these slopes. If the growing tissue of an organ pipe freezes for too long of a period of time or too many times in the winter it will kill the plant. So these slightly warmer areas give the cacti an added edge so they can become established. I also have a strong suspicion that organ pipes prefer soil types typically found on upper bajada slopes. Even with this added warmth however, conditions are not absolutely perfect. The organ pipe sill needs some help from what is called a nurse plant. Small shrubs, mesquites, ironwoods, and palo verdes all help protect young organ pipes from the intense summer heat and sun. The cooler temperatures and shady conditions also help hold the water in the soil for longer. On occasion, large rocks can even provide these added benefits of shadier, cooler, and slightly wetter conditions. Nurse plant associations can be found for several different species. The saguaro cactus has very similar nurse plant requirements. A different type of nurse plant association that can be found within the park is that of the jumping cholla and pincushion cactus. The jumping cholla is a rather large shrubby-tree like cactus that looses an abundance of spine dense joints. These joints naturally fall from the cholla and often will form a mat around the mother plant. Nothing really wants to go close to these piles of spiny cactus joints making it a perfect place for the small pincushion cactus to live.
Organ pipe cactus

Monday, January 21, 2013

Tassel Ear Corn

Tassel-ear that another garden produced.
Back in July we planted several blocks of corn in our college garden.  July is the normal time to plant corn in the Arizona Sonoran Desert.  The corn we planted was a normal desert adapted variety that was supposed to mature in about 70 days and grow to about five feet.  This would mean we would harvest our corn about the first of October.  Some of the corn grew exactly as we expected.  Most of it however just kept growing and growing and growing until December (150 days) and never reached maturity.  The corn grew to over 10 feet tall and produced weird tassel-ears at about five feet.  Oddly, this extremely tall tassel-ear corn was the exact same variety as the corn that grew to only five feet and reached maturity in 70 days. 

Why the extreme difference?  We wondered if we had messed-up by planting some other seeds instead.  But we could find no evidence of that.  We also wondered if we had some mutant corn.  Again, no evidence.  We also wondered if we had planted to late in the season.  Probably not since the varieties of corn we planted normally are planted that time of year.  So what was mutating this corn into a gigantic tassel-ear plant?

With a little more investigation we found that the soil where our gigantic mutant corn grew had extremely high clay content and was very commonly saturated with water.  Water was often found pooling in this area.  Areas where the corn grew as would normally be expected also had slightly lower clay content but were not saturated with water and did not have pooling issues.  But we had no good explanation for why poorly aerated, high clay content, water saturated soils would produce gigantic mutant tassel-ear corn.  So we took to the internet, where answers to all good gardening questions are found of course...

What we found was the condition of tassel-ear corn.  This is where corn cobs also form tassels, just as our corn did.  Our corn appears to be an extreme example of this condition though with the corn cob actually becoming very elongated and forming mostly tassel.  Apparently this condition is common where corn plants are growing under poor soil conditions, just like ours.  No one knows what triggers tassel-ears but from what I read, all corn cobs start off as both male and female, or both tassel and corn cob.  Hormonal changes in the cob during development normally cause the cob to become fully female and produce seed and not a tassel.  For some reason, tassel-ear corn does not have a hormonal change and the result is a corn cob that is both male and female.  This condition does not however explain why our corn grew twice as tall and for twice as long as it should have.  I could find no explanation for these weird problems though.  For now, I'm simply blaming poor soil conditions on everything.

Friday, January 18, 2013

The Truth About Genetically Modified Corn

There is an increasing amount of hype about genetically modified organisms. And for good reason, without us really knowing it, genetically altered foods have invaded the grocery store. For example, 90 percent of corn grown in the United States is genetically altered. This necessarily means that a huge proportion of corn products within the grocery store are also genetically modified.  Considering corn or corn products are found in seemingly everything, that's a lot of grocery store products that have genetic modification as part of them.  The question is, is genetic modification really a problem I should be concerned about?  To be sure, there really isn't a perfectly straight forward answer.  Mostly, the answer is we simply don't know.  Corn amazingly has 32,000 genes, nearly 12,000 more genes than humans.  That means there are 32,000 genes that could be modified, or added to or subtracted from.  In reality there are potentially millions of ways to genetically modify corn or any other organism.  There is no way we could say that all of these tens of thousands of potential gene modifications are harmful, and there is no way we could say all of them could be helpful.  Its sort of complex.

For example, Bt corn has a gene added to it that produces a pesticide.  This gene was taken from a naturally occurring bacteria that infects insect larva.  Bt corn therefore produces this pesticide and kills potential insects that might eat the crop and therefore decreasing the harvest.  So Bt corn becomes extremely beneficial to corn production but has negative impacts on insect populations.  You may initially think that this is a good thing, who really cares about those annoying insects anyway?  Well, some of those insects are bugs that people love and are very important to the environment such as monarchs and other butterflys.  Bt corn can and is having very negative results on the environments we live in.  Beyond that and into our homes, there is evidence that Bt corn is causing elevated immune responses which means increases in auto immune disorders and allergies.  A number of studies though suggest there is no negative health consequence to Bt corn.

Another common corn genetic modification is round-up ready corn.  This is corn that can resist being killed by the herbicide round-up, so farmers can spray there fields of corn killing only the weeds and not the corn.  Again, corn production is greatly increased but the environmental and health consequences are negative.  It not clear though if the actual genetic modification is actually causing the health problems however.  Residue round-up herbicide is however causing at least some of the health problems though.  These health problems are very serious in lab rats and include kidney and liver damage, and cancer.  It is very likely humans have very similar health problems with round-up ready corn.

Other genetic modifications are likely less harmful to the environment or health and may even be extremely beneficial.  For example, modification of a heat shock protein in corn could allow it to tolerate drought better.  The heat shock protein would likely have no consequence on human health.  Corn could also be modified to have higher levels of vitamins.  Whether these so called 'good' modifications are actually 'good' would be very difficult to actually determine, and may only be in the eye of the beholder.

Currently in the stores, nearly all corn products are genetically modified.  Only corn that is labeled as non-GMO or organic can normally be assumed as being GMO free. 

Friday, January 11, 2013

Science Style

OK, its official, everyone is doing some version of Gangnam Style.  When lab geeks such as those in the above video take the time to do a parody of a popular song, you know something is wrong.  Not to criticize lab geeks, I suppose I am one also, but as I said, lab geeks are kind of geeky.   What I love about this video is not that it is a Gangnam Style parody done in a genetics lab, but that the word of this parody share about how science really takes place.  The part of real science that is shared in this video can be summed up in one word: frustration!  While it is not commonly know, science is completely frustrating.  Take Thomas Edison for instance, he made over one thousand attempts to make the light bulb before he succeeded.  The same type of failure is true for other areas of science also.  In genetics it can take years of trying to design a good experiment before it actually works right.  Then, once it is working it might stop working for no known reason.  In science it is very common for things to work once than never work again or for things that worked for years to stop working. 

Tuesday, January 8, 2013

White Tank Mountains Goat Camp Trail

Desert grassland with mainly tobosa grass located at the top of the White Tank Mountains west of Phoenix, Arizona.
Goat Camp Trail in the White Tank Mountains west of Phoenix is the longest trail in the park.  It can be done as a 13 mile loop along with the Mesquite Canyon and Bajada trails or a 12 mile hike from trail head to end and back.  The trail head is just past the park entrance on Black Canyon Road.  The first mile and a half of this trail is pretty easy starting at 1600 feet in elevation and hiking up a bajada.  This bajada is fairly interesting.  It has been highly disturbed by some major flood events along the dry washes that come out of the mountain canyons.  This disturbance is evident increasingly as you hike towards the mountains by the presence of large boulders laying on the surface.  Normally, these boulders would be sitting lower in the sediments of the bajada being at least partially buried in the dirt.  Large floods however coming from the canyons washed away a lot of these sediments but were not strong enough to wash away the larger and heavier rocks.  So the rocks remained in place while the finer textured sediments washed downslope.  These unburied boulders become increasingly common upslope where the flood, or floods, were more powerful.  These floods resulted in increasingly variable disturbed soil conditions higher up on the bajada and closer to the mountain.  As a result of the more variable soil conditions plant diversity also increases up slope.  Sections of undisturbed soils typically have triangle leaf bursage while the disturbed sections brittle brush.  Other species such as palo verde and jojoba also seem to like the flood disturbed soils.

After a mile and a half or so, the trail begins to head up the mountain.  This trail has an elevation gain of about 1700 feet, topping out around 3300 feet.  With the elevational gain, average annual temperature decreases several degrees and rainfall increases several inches.  At the mountain base, rainfall averages about 8 inches annually.  At the higher elevations rainfall probably averages around 14 inches annually.  There is a rain gage at the top of the White Tanks but apparently gusty winds around the peak prevent it from collecting rain properly, so it is difficult to get an exact measurement of rainfall at the peak.  Regardless, the vegetation tells us that rainfall is significantly higher and temperatures slightly lower.  In the past decade or so I have seen snowfall above 3000 feet in the White Tanks only one time and never below that level.  The lower temperatures, specifically lower freezing temperatures in winter, make conditions less ideal for cacti such as the saguaro.  Saguaros are not able to survive freezing tempertures for longer than 24 hours.  While the saguaro does grow near the peak it is quite rare in comparison to lower elevations.  This is at least partially due to the increase in the amount of time freezing temperatures occur at the higher elevations.

I think there may be another, possibly better, explanation for the decrease in cacti towards the top of the White Tanks though.  Around 3000 feet the vegetation strongly shifts towards a desert grassland dense with tobosa grass.  Tobosa increases because of the increased rainfall and because it can survive the freezing temperatures quite easily.  Dense tobosa grass is possible out competing the cacti at these higher elevations.  Another indicator of a problem for cacti at these higher elevations is the presence of charcoal.  Obviously charcoal indicates fire has been present in the area at sometime in the past and cacti in general do not survive fire very well.  Grass, such as tobosa, however, are very flammable and actually encourage fire to some extent.  Grass, unlike cacti, are very adapted to fire through.  While I have never seen or heard of a grass fire at the top of the White Tanks, the charcoal is evidence that it has happened at some time in the past.  Even if fire happens only once every few decades, that is enough to severely limit the population of cacti in the area.

A few other plants that are relatively common at the higher elevations include desert agave and crucifixion thorn.  Most of the desert agaves are pretty small and almost all appear to be clones that have grown from root sprouts of older plants.
Crucifixion thorn.

Desert Agave