Merry Christmas and Happy New Year

I'm taking a short break from the blog over the holidays but will be back in January!

Mistletoe: The Kissing Parasitic Plant with a Gross Background...

This is a post from two years ago but I thought it worthy of reposting.  Mistletoe has such a fascinating background and considering the time of year...

For many years now, every time I see mistletoe hanging-up around Christmas time I find it sort of humorous.  Most people think of mistletoe as the "kissing" plant.  While I also think of it as the "kissing" plant, I also think of its complex parasitic life-cycle.  Yes, mistletoe is a parasite, and is pretty common in western forests and deserts.

A clump of mistletoe growing in the center of a juniper tree.

However, parasitism is only the beginning of the story.  Even more interesting is how the mistletoe got on the tree in the first place.  Mistletoe produces red or white berries which are possibly toxic to humans but extremely tasty and nutritious to birds of all types.  Many types of birds will gorge themselves on the berries and as a consequence carry the seeds to new locations.  In-fact, a southwestern bird known as the pheinopepla was found to eat around 1100 berries a day when berries were available.   Eating all those berries means a lot of seeds being transporting to new plants that baby mistletoes can parasitize.

Phainopepla, found to eat around 1100 mistletoe berries per day when berries were available.

Seeds are transported in the birds digestive tract but also on their beaks.  Mistletoe berries are covered with a very sticky substance causing seeds to stick to the birds beak, which the birds wipe off onto trees and shrubs where a new plant can grow.  The sticky seeds also pass through the digestive tract of birds and when defecated on a plant can germinate and parasitize the new plant very quickly.

Desert tree severely parasitized by mistletoe.

From all this you may think that mistletoe is a severe problem taking over and destroying our forests, but things to not always as they first appear.  In many cases mistletoe actually benefits the forest.  First of all the berries provide food for bird species that live in the area, increasing the number of birds and number of bird species an area can support.  Secondly, some trees, such as the junipers, when parasitized actually produce more of their own seeds.  This also increases the food available for birds and animals, thus supporting greater numbers of animals and greater diversity as well.  Parastized trees also form deformed 'witches brooms' which many birds and animals prefer for nesting sites. 

So the next time you see mistletoe hanging in the doorway, wow your "kisser" with this knowledge and they may never look at mistletoe in the same way.  They may not want to kiss you after their new found knowledge either though...  But this may be a good thing...

December Ephemeral Drainage Flow

A dry wash the morning after a flash flood came though.

The mid-December rain is the most reliable rainfall we receive here in the Sonoran Desert.  This rainstorm is almost like clockwork.  Every December, usually around the 15th or so, a strong Pacific frontal storm system brings rainfall in from the northwest.  One-half to one inch of rain pretty much falls across the entire desert with higher totals in the mountains.  Of the past ten Decembers, only one failed to produce any rainfall and that was during one of the driest winters on record in Arizona.  This year was picture perfect with one-half to one inch of rain falling in the Sonoran Desert between December 13th and 15th.  With this rain being almost like clockwork, the flow of the normally dry washes also flow during this rain almost like clockwork.  This year was a little odd in that the rain was spread out over a three day period making flows a little weaker than normal.  Typically, dry washes require a significant amount of rain over a short period of time in order to generate enough runoff to supply a flow.  A lot of drainages did flow at least a little though. 

Of course, a lot of rain over a short period of time helps these washes to flow in the desert, but there are other factors involved also.  Geology, or geomorphology, are probably the most important factors in determining flow.  Geomorphology is simply a scientific term that describes how landforms came about and how they function.  One of the functions of geology and geomorphology in the landscape is to determine how and where water flows.  For example, shallow unbroken bedrock is going to prevent water from seeping down into the soil and therefore will result in greater amounts of runoff.  Type of soil also matters in the amount of runoff produced.  Rain seeps very slowly into clay soils so a lot of runoff can be generated.  Sandy soils however can quickly absorb a lot of rain so not much will runoff.  Number of rocks also makes a difference.  Soils with fewer rocks have more runoff than soils with more rocks.  Rocks on a soil surface slow the speed of runoff and with slow speeds of runoff the water has more time to be absorbed into the soil.  Size of the dry wash also makes a difference with smaller washes flowing more frequently than larger washes.  However, larger washes tend to run longer than small washes when they do flow.  Larger washes simply need a lot more water to flow. Depending on the combination of these factors some washes will flow a few times annually while others will only flow a few times a decade.

All of these things factors also determine what lives where along a dry wash.  Flow is normally very short in duration in a wash.  This is simply because flowing water quickly is lost as it is absorbed into the sediments of the stream bed.  Though flowing water is lost, the water is not entirely lost.  Water is stored in these sediments for long periods of time after surface flow ends.  Depending on the depth of this moisture and the depth of the sediments differing plants will occupy the area.  Typically, deep sediments with relatively frequent flows will be occupied by blue palo verde and desert willow.  Areas of fewer or shorter flows typically have yellow palo verde.  Other plants such as acacia's, ironwood, wolfberry, and mesquites can be somewhere in-between. 

Fall Leaves in a Sonoran Desert Riparian Zone

A Sonoran Desert riparian area in fall along Cottonwood Creek.

The desert is most definitely not known for spectacular fall colors.  Fall colors do however, find their place along some of the wetter desert water courses.  If perennial water sources are available, even if it is hidden below ground a short distance, the roots of large deciduous trees will find there way to it.  Sycamores, cottonwoods, and willows are all relatively common along streams and washes with perennial sources of water.  Even Arizona walnut and ash trees can be found in some of the more stable riparian zones.  These trees do not display the brilliant hues of red and orange common to eastern forests but do show off bright yellows that are in stark contrast to the dried out browns and greens of the desert.    Desert fall leaves are quite a rarity and are quite unique.  Typically, perennial water sources are considered perched water tables.  A perched water table simply is water that accumulated above the surrounding water sources, most often a result of bedrock that prevents water from penetrating deeper into the soil and out of reach of plant roots.

A recent hike I took demonstrated this concept extremely well.  The hike was along Cottonwood Creek near Lake Pleasant north west of Phoenix.  The majority of this hike is along Cottonwood Creek, which really isn't much of a creek considering water only flows in this creek a few hours every year.  The rest of the year the wash remains mostly dry, except for a few locations.  Nearly all washes in the desert are called dry washes, and for good reason: they are completely bone dry the majority of the year.  A few washes, such as Cottonwood Creek are fortunate enough to have areas that always remain wet.  Cottonwood Creek owes this moisture to its underlying geology.  First off, the creek bed lays at the base of two small bajadas between two small mountain ranges.  One bajada lays to the north of the creek bed and one to the south.  These bajadas and bedrock of the mountains are relatively steep and provide ample runoff to Cottonwood creek so it will run during periods of heavy rainfall.  Moisture is quickly lost into the deep sediments of the bajada and placed out of reach of deciduous tree roots.  In areas where bedrock are shallow though, moisture cannot penetrate deeply and remains closer to the surface within reach of plant roots.  Bedrock can also push water flowing underground towards the surface.  At these locations large deciduous trees take advantage of the shallow moisture and can in a few places form small but beautiful wooded areas.

Wildlife may not be obvious in these small wooded areas, but if you look at the ground you are sure to see evidence of animals.  Javelina and mule deer heavily utilize these small areas and their hoof prints are normally abundant.  In some area, such as along Cottonwood Creek, wild donkey's are also abundant and heavily utilize these areas.  The abundance of shade, food, water, and cooler conditions during hot dry summers gives great value to these areas for every creature.

Preventing Illness This Winter

Its the season for getting sick... A part from the normal concerns of the holiday season, we have the additional concerns of catching a cold or the flu this time of year.  Apparently, this years strain of flu is especially bad.  Specifically, the flu virus is H3N2 and has increased the number of hospitalizations for the flu compared to normal flu seasons.  The thing I always want to know this time of year is how I can prevent myself from getting sick.  There are a number of things that can be done to help prevent illness.  Of course we always hear to get vaccinated and to wash your hands.  But in addition to that, studies have shown reducing stress, meditation, getting enough sleep, exercising, drinking lots of fluids, maintaining a healthy weight and limiting sugar intake all help strengthen your immunity.  Unfortunately, this may be the worst time of year for getting enough sleep, reducing stress, and limiting sugar intake.  So I guess we'll all have to do our best.  Other interesting things I found were that the ideal house temperature for reducing illness is 68 to 72 degrees with about 50% humidity.  Viruses can survive longer inside with the lower indoor humidity this time of year, so having a humidifier is beneficial to your health.  There is also a lot of various information out there on how much exercise is ideal for boosting immunity.  From what I have read and sort of averaging a bunch of reports and research together, exercising thirty to sixty minutes, three to five times a week boosts the immunity the most. 

The Biology of Bread Making

The process of making bread is an extremely biological process.  Good bread bakers are experts at controlling the biological processes involved in making delicious bread, even if they don't know it.  There are two major biological components to bread, first is the wheat flour and specifically gluten, and secondly the yeast.  A typical bread recipe is very simple and includes water, sugar, salt, wheat flour, and yeast.  All of these ingredients work together to create an environment for the yeast that creates bread.  I will explain each of these components and discuss how they can create the ideal bread making environment.

First we will talk about sugar.  Sugar is very easy for yeast to consume and therefore helps the dry yeast off to a quick start.  This helps the yeast to quickly start growing and reproducing, causing the bread to rise.  Yeast also can consume the carbohydrates in the wheat flour, but these are harder to consume.  Depending on how much sugar is added, the yeast will normally consume all of the sugar in the dough.

Water in the bread making process is not extremely interesting.  It is of course a requirement for all of life and without it the bread would never form.  In bread making tough it is important to balance the amount of water to the amount of flour to get the right consistency in the dough.

While sugar helps speed-up the reproduction and function of yeast, salt slows it down.  By balancing the salt and sugar in the dough recipe we can balance the growth of the yeast, not too fast and not too slow.  Without salt, the dough would rise too quickly and collapse.  With too much salt though the bread would rise extremely slow. 

Wheat flour of course is what actually composes the bread.  I say wheat flour specifically because wheat is the only type of flour that contains the protein gluten.  Without gluten the flour would not rise into a spongy loaf of bread but rather would turn into a dense heavy mass of cooked flour.  Gluten is a long sticky molecule that sticks to other gluten molecules.  This allows the yeast to form air bubbles in the dough, making it rise.   Gluten molecules stick together, making the flour in the dough to stick to itself so it can rise.  Without gluten, bubbles couldn't form and the dough would not stick together and the dough would not rise.  Flour also provides carbohydrates for the yeast to grow and function.

Lastly, yeast produces carbon dioxide that helps form bubbles in the dough, making it rise.  As yeast consumes sugars and carbohydrates it releases carbon dioxide.  Without the carbon dioxide produced by the yeast, the dough would not rise.  Yeast functions best at warmer temperatures so more time is needed for bread to rise when temperatures are lower.  When you finally bake your bread, the high temperatures of the oven actually kill the yeast and solidify the gluten and dough structure.   Baking ends the biological processes of bread making so it is ready to eat.

A lot more can be said about the origin of yeast and gluten as we find them in our breads today.  But the above are the essentials of the biology making bread.  Knowing these things can greatly aid your ability to come up with your own recipes and make the perfect bread.  Using the above, you can also come up with your own scientific process or experimentation in bread making by varying water, sugar, salt, and yeast amounts.

Science Education Crisis

Looking around the world today, its easy to see a significant number of science related problems. Climate change, ocean acidification, resource depletion, overpopulation, invasive species and so on, the list is depressingly long. On the positive side though, there are relatively straight forward solutions to a lot of these problems. Straight forward doesn't mean simple to implement through. For example, renewable energy has potential to easily offset burning of fossil fuels and therefore providing solutions to climate change, ocean acidification and resource depletion. Implementation of renewable energy though very plausible, will take a lot of work and changing of peoples mindsets. Probably the largest hurdle in this is simply education of the general public. I have worked in science education and biological research for about a decade now and have seen huge discrepancies between the two. Researchers with all their vast knowledge of extremely important scientific information that has the potential to help humanity simply don't communicate their concepts well to the masses. Scientists also have isolated themselves from the masses with the general belief that most people just can't understand science. The average high school or even college biology 101 textbook doesn't really paint the big picture for students to learn, but instead focuses on overly compartmentalized concepts. The average high school biology teacher's knowledge of the subject also seems quite limited to these overly compartmentalized concepts. As a result, the masses really don't get what is going on with subjects pertaining to science. I personally am of the belief that even though science is hard to understand, the average person is able to understand at least some of the more complex concepts. Students must be taught by teachers who know the concepts in the first place, and in a way that connects students to the bigger picture. Regardless of what anyone says, science is extremely interesting and people who say science is boring simply have a poor science education. Science is so diverse it can literally engage every field of interest possible, there is absolutely no room for boring with this great diversity. I'm not saying everyone should become scientists, I am simply saying that science should engage everyone in whatever profession they choose. Currently, science is highly compartmentalized in our society with the educationally elite. This should not be so and is highly damaging to our society. The educationally elite scientist is absolutely necessary to science but I would suggest needs to greatly improve communication of their research with the masses. Improving scientific communication and education with the average non-scientist is the goal of the Practical Biology blog. Hopefully I have begun to do this. I feel there is a lot more that can be done and a lot more depth that can be given to non-scientists, or even scientists, through this blog. Knowledge is power and scientific knowledge has potential to greatly benefit individuals as well as society.

Global Climate Change: Thawing of the Arctic Tundra

The above is a great short video about the effects of the warming planet on Arctic tundra.  Tundra by definition is ground that is permanently in a frozen state.  During the short and few summer months, tundra only thaws on the surface.  Deeper down however, the ground remains frozen year round.  This only allows for small shallow rooted plants to grow and prevents larger plants such as trees from ever taking root into the frozen ground.  The constantly frozen ground also does not allow plant materials to decay once they die.  Dead plant materials simply die and other plants grow on top of them.  This causes a thick accumulation of dead, un-decayed plant materials to pile-up, forming peat.  The great expansiveness of peat in Arctic tundra is a gigantic holding place for a huge amount of carbon dioxide.  The carbon dioxide simply remains locked up in the peat because of the cold and frozen conditions.  Recent warming of tundra peat however has caused some thawing and therefore allowing decay to take place in this peat.  As the decay takes place, carbon dioxide that was held in the peat is released into the atmosphere contributing to increased global temperatures.  Anyway, check out the above video for a short look on a scientific experiment and some of the potential effects of a warming climate.

Huricane, Superstorm, Frankenstorm Sandy... What Made This Storm So Bad

Watch Inside the Megastorm on PBS. See more from NOVA.

The science and story behind the development of Superstorm Sandy is fascinating.  The above video does a great job of explaining the development of this storm and how so many different weather elements came together to make this storm so bad.  The combination of a hurricane, absence of the Bermuda High, higher than usual ocean temperatures, a Nor'eastern storm, high pressure of the coast of Greenland, an adjusted jet stream, and the storm making landfall at the full moon high tide all came together to make this frankenstorm.  A hurricane or nor'eastern storm are bad enough, but the combination of these two along with everything else made this storm devastating.  Though Sandy was quite a dramatic weather event, the above video gives a great education on weather in general.  The big question now is, will superstorms like Sandy become more common in the future?  In the next 100 years temperatures are expected to warm by about four degrees which would likely increase the number and intensity of storms throughout the world.  Are storms like these a preview of what is to come in the future?

Thanksgiving and the Food Pyramid (or Choose My Plate)

The average Thanksgiving meal is about 3000 calories, or about one and a half days worth of calories.  The average American eats about 4000 calories or more on Thanksgiving day, about twice as much as what is recommended daily.  Of course, everyone is talking about all the extra calories eaten during Thanksgiving but I want to talk about how the average Thanksgiving meal lines up with the latest food pyramid.  The latest food pyramid is actually a plate called Choose My Plate and can be found here.  To do this we must first identify what actually is found in an average Thanksgiving meal.

An Average Thanksgiving meal
Turkey: 8oz.
Stuffing: 1 cup
Green bean casserole: 1/2 cup
Mashed potatoes and gravy: 1 cup
Cranberry sauce: 1 slice
Sweet potatoes: 1/2 cup
Pumpkin pie: 1 slice
Total calories: about 3000

The above meal contains about 1 and 1/3 times the recommended daily intake of protein, at most 1/5 the daily recommended intake of fruits and veggies, about two times the amount of recommended carbohydrates, and the absence of healthy oils and dairy products.  So pretty much, the typical Thanksgiving meal is extremely carb and protein heavy.  The bad thing about carbs is that they are less filling than protein and oils or fats, which means you can end up eating a lot more of them.  So it is possible that the reason there are so many carbs in a typical Thanksgiving is because they are less filling, so people just end up eating more.

We won't even go into how to calculate how many hours of exercise it would take to burn these extra calories off, which is about 6 hours.  But hey, this is only one meal a year so its not something to really beat yourself up over, especially if you are eating healthy on a regular basis.

Echinocereus sp.: The Hedgehog Cactus

Echinocereus engelmannii

The hedgehog cacti are probably my favorite group within the cactus family.  I find their forms, including shapes and spines very interesting.  Their flowers come in an assortment of beautiful colors ranging from pink to red to white to yellow to purple.  Flowers also survive quite a few more days than other cacti flowers.  The scientific name for hedgehogs is Echinocereus.  Fittingly, echino means "hedgehog", and cereus means candle.  I suppose the individual stems may look somewhat like a hedgehog or candle, but I consider them to look more like a cucumber standing upright.  The stems of hedgehog cacti most often are clumped together but with several species they are individual or forming mounds.  Hedgehog cacti are common throughout SW United States and NW Mexico surviving in the low deserts to the high mountains.  The full extent of hedgehogs ranges from South Dakota to Central Mexico.  Identifying these cacti can be a little tricky at times and knowing flower color as well as spine density, length, and coloration is essential.  Even within species there can be considerable variation of traits.  For this reason, botanists have been confused and arguing over classification of different hedgehog cacti for decades.  As time goes on, these botanists seem to discover more and more species, or identify new species out of already existing groups.  Hedgehog fruits are also typically very tasty and Native Americans would eat the fruit as they came across them.  The cacti do not seem to produce a lot of fruit though, so I suppose they were eaten more like a snack.   

Echinocereus coccineus

Echinocereus engelmannii

Joshua Trees, Ice Age Sloths, Extinction, and Climate Change Today

With the end of the Ice Age, the giant Shasta ground sloth became extinct in our American Southwest deserts. This extinction happened as a result of the warming of the continent and invasion of humans into the land 13,000 years ago.  Today, the sloth is long gone, but the consequences of its extinction are still being seen to this day.  The Shasta ground sloth was intimately intertwined with every organism they ate, use, or associate with.  Of course, all organisms that inhabit this earth are intertwined in the same way with all the organisms they eat, use, and associate with both directly and indirectly.  This can be extended to show that all organisms are in one way or another connected.  If one organism is removed from an ecosystem, such as the ground sloth, every other part is affected and must adjust their life accordingly.

Unfortunately, not every organism is able to adjust to every change in an environment.  Such was the case of the Shasta ground sloth.  As the climate warmed, plants that inhabited the Southwestern deserts changed, changing the sloths food sources.  As food sources changed, the sloth could not adjust and as a result became extinct.  As a result, the plants and animals affected both directly and indirectly by the sloth had to adjust to "life after the sloth".  For example, the Joshua Tree was a major part of the sloths diet.  At first it may seem that extinction of something that is eating you might be a good thing.  At first, I could guess, the Joshua tree might have benefited greatly by the absence of a giant animal consuming it.  Long term however, the Joshua tree suffered greatly and continues to suffer to this day.  As the sloth ate the Joshua tree, of course this injured the plant.  However, as the sloth ate, it also consumed the Joshua tree seed which would pass all the way through the sloths digestive tract without being damaged.  Once passing though the sloths digestive tract the seed would find itself in a moist pile of fertilizer, which is an extremely ideal location to find yourself if you are a desert seed in desperate need of moisture and nutrients.  

With this association of the sloth and Joshua tree, the sloth benefited with food by eating the tree.  The
Joshua tree made a trade-off though, being damaged by the sloth as it was eaten, but benefiting from the sloth into the next generation.  The sloth aided the success of the Joshua Tree by likely aiding germination and by carrying the seeds to new locations up to ten miles away.  After the extinction, and up to the present day, only desert squirrels and packrats move Joshua tree seeds today, and only at a pace of about six feed per year.  As a result, the Joshua tree cannot adjust its range anywhere near as quickly as it could before and its range has been shrinking for over 10,000 years now.  How do we know all this?  Scientists in the Southwest have examined caves where sloth dung which tells us what the sloth ate.  Ancient packrat middens also have been examined which tell us where the Joshua tree was and when over the last 10,000 plus years.

With the ability to only change their range six feet per year, the Joshua trees range will continue to shrink in coming decades.  Currently, the climate is warming far to fast for the Joshua tree to keep pace.  This does not mean however the Joshua tree will go extinct.  It will be able to survive in cooler high elevation locations.  As the range of the Joshua tree is reduced however, organisms dependent on it will have to adjust.  For example, many species of rodents are dependent on moisture from the tree during times of drought.  These organisms access water from the tree simply by chewing through the bark to access water.  With the trees gone however, there will be far less water available to support rodents.  And so we see the continued consequence of the extinction of the sloth.

How to Make Sauerkraut

Every fall I start thinking about making my own sauerkraut.  Making your own sauerkraut is really a very simple process once you are familiarized with the steps required.  The process is very similar to making kimchi but kimchi is much more complicated in regards to spices and different steps, and for that reason I prefer to make sauerkraut.  I have written about the process before on this blog (How to make sauerkraut) and will summarize briefly here:

1. Shred your cabbage.
2.  Thought mix shredded cabbage with sea salt by hand.  The salt will draw the liquid out of the cabbage.  Do this in a crock or straight walled jar.  There is not set ratio of salt to cabbage, this is simply a taste preference.  You do need enough salt though to draw enough water out of the cabbage. 
3. Weigh and press down the cabbage so it is below the liquid mark.
4. Cover the entire container so dust will not contaminate the process.
5. Wait until bubbling stops before removing weight to taste sauerkraut.  Press down on the weight daily to push out gas bubbles given off by fermentation. Bubbles generally stop before two weeks.  
6. Sauerkraut can be stored for weeks at or below room temperature if it is submerged below the water level.

 And that's the basics of making sauerkraut.  The first time is most definitely the scariest time.  But after that it gets pretty easy.  Here are some tricks to making sauerkraut:

• More salt will slow the entire fermentation process significantly but will preserve the sauerkraut for longer periods of time.  It takes very little salt though to make sauerkraut and to preserve kraut with low salt, simply place it in the fridge.  Adding more salt and refrigerating after bubbling has stopped a few days is the safest way of making sauerkraut for the first time.  After doing this you can experiment with adding less salt.
• If temperatures are going to higher, say above 75 degrees add more salt.  This helps control yeast and microbial growth.
• Lower temperatures require less salt because the lower temperatures help control yeast and microbial growth. 
• Different temperatures and amounts of salt will change the flavor of the sauerkraut.  Play around with these in different batches to see what tastes best to you.  I prefer sauerkraut when average daily temperatures are in the 60's and with a low salt content.
• You can add any seasoning or vegetable to your batch as long as it doesn't add to much sugar or starch.  For example, peppers, onions, garlic, radishes, and ginger can all be added.

Some things to watch out for:

• If your batch of kraut goes on bubbling for a long period of time after the initial two weeks, throw it out, it has gone bad.  Do the same if it stops bubbling and then starts again.
• The sauerkraut should be a pale color unless you add veggies that have color in them like purple onions or purple cabbage.  Then the sauerkraut will take on a purple color.  If the sauerkraut takes on an off color or is brownish it has gone bad and you need to get rid of it.
• If the sauerkraut is slimy or smells weird it has gone bad.
• Any sauerkraut exposed to the air and not submerged under the liquid will go bad.  

Easy Enzyme Experiments Anyone Can Do

Three catalase enzyme experiments.  More bubbles demonstrate more catalase enzymes. On the left, catalase extract from beef muscle, middle beef kidney, right beef liver.  Liver has the most catalase, second most is kidney, and muscle has hardly any at all. 

The easy enzyme experiments have been some of the most popular posts on this blog so I'll be posting a summary of them today.  These experiments really are easy enough for nearly anyone to do and to use to demonstrate the amazing work these molecules do.  Unfortunately, most enzyme experimentation is extremely difficult and must be done in a science lab.  I have come across several though that are rather simple and I am always looking for more simple enzyme experiments to post here.  

Enzymes, you can't see them, but you can't live without them.  Some scientists have seen the rough outline of larger enzymes using scanning electron microscopes, but they still haven't actually seen one.  In-fact, no one has ever seen one, they are simply too small.  So how do we know they exist?  Molecular scientists use special complex scientific techniques to determine the shapes and structures of enzymes without actually looking at them directly.  More practically though, we see proof of enzymes every single day, every single second.  The very fact that we, or anything else is alive, is owed to these amazing molecules.  Without these molecules hardly any of the chemical reactions that take place in our body would ever happen.  And without these chemical reactions, life would never happen.  All of the cells in our bodies are loaded with dozens of enzymes of different types, all making life possible.   A few of these enzymes are easy for us to extract and observe the work they do very clearly.  Anyone can do these experiments with some basic equipment, even in a kitchen.  

One of the most common and easiest enzymes to work with is catalase.  This enzyme is found in potatoes, spinach, and liver in high concentrations.  To extract it all you have to do is blend some of these materials up with some water.  Catalase functions to convert hydrogen peroxide into water and oxygen.  This protects the body from the harmful effects of hydrogen peroxide, which is commonly produced as a metabolic by-product. You can conduct your own catalase experiments simply by adding hydrogen peroxide to your extract.

Another great and easy enzyme experiment is that of rennet and cheese making.  Cheese is actually made by the enzyme called rennet.  You can buy rennet off of Amazon, follow the directions that come with the packet, and make cheese in the process.  Without rennet, we would only have a few different types of cheeses.  

A very practical enzyme to our digestion is protease.  Without this enzyme it would be impossible for us to digest protein of any kind.  Protease can be found naturally in fresh pineapple, or in meat tenderizer (which contains protease found in pineapple).  The reason fresh pineapple cannot be used in making gelatin is because the protease in the pineapple digests the gelatin protein, preventing the gelatin from solidifying.  Pineapple or mango protease are also placed in pills that aid digestion.  

Lastly, amylase is another protein that is important to carbohydrate digestion.  By mixing ground-up crackers with spit (where amylase is typically found), you can actually witness how your spit digests carbohydrates.  

If you know of other simple enzyme experiments, please let me know.  

Barrel Cactus Part 2

California barrel cactus, Ferocactus cylindraceus.

Barrel cacti are kind of as their names imply, barrels full of water.  The problem is, the water isn't just hanging out in the cactus like a big glass of water.  The water is stored inside of the cells that fill the interior of the cactus.  The best way to get this water is to eat the tissue, though it won't taste very good and probably will make you sick.  The thick layer of hooked spines will also deter any person or animal from easily accessing this water though.  In drought however, the barrel cacti is one of the best sources of water for desert animals there is, that is, if they can get through the spines.  Small animals like rats, chipmunks, or mice can avoid spines by burrowing underground slightly to where there are no spines and then eating up into the cactus.  I have actually found a few barrel cacti that have been entirely hollowed out by rodents, yet have there skin and spines fully intact.  Larger animals such as deer have no such luck though accessing moisture from a standing barrel cactus though.  The spines become just too big of a deterrent.

Red spines of the barrel cactus show up after being wet by rain.

Fortunately, for larger mammals the barrel cactus has a fatal flaw.  As a barrel cactus grows it generally leans towards the southwest, which is the direction from which the most intense sun comes from.  Nearly all barrels lean to the southwest, just as a compass always points north, thus the common name compass barrel.   It might seem that leaning in the direction of the brightest sunlight might mean the cactus is trying to gather as much sunlight as possible.  This is however the exact opposite of what it is doing.  With the top of the cactus pointing directly at the most intense sun, spines at the top actually shade out much of this light and all sides of the cactus actually avoid this direct sunlight.  The sides however gather the most sunlight from the sides, as the sun comes up or goes down, when the sun rays are less intense and therefore less damaging to the cactus.  Pointing tops towards the most intense sunlight is therefore actually a protection mechanism, rather than a gathering mechanism, against intense sunlight.

A barrel cactus that fell over due to leaning towards the southwest.  Even though this cactus fell over, it continues to grow.

Leaning is an important adaptive strategy of the cactus, but is this strength also lays a huge weakness.  As the barrel cacti grows and leans it becomes very off balance.  Older, large cacti will often simply fall over.  Oddly, even when the cactus falls over it will continue to live and grow as it lives laying on the ground.  Once the barrel cactus falls over, the underside of the cactus is exposed which is unprotected by spines.  Large mammals will often start eating the barrel from this unprotected portion during drought.  

Flower of the California barrel cactus Ferocactus cylindraceus.

Barrel Cactus Part 1

Compass Barrel cactus

The barrel cactus is one of the most common cacti in the Southwest.  There are four different species common to this area of the country, the most common of which are the compass barrel and the California barrel.  It can be extremely difficult to distinguish between these two common species of barrels.  In southern Arizona, such as around Tucson, the compass barrel is the most common of the two cacti.  In central Arizona such as around Phoenix, southern California, and even into the depths of the Grand Canyon the California barrel cactus is the most common.  Their ranges overlap in central Arizona and their similarities are pretty extensive.  Without closer investigation you may not be able to determine what specific species a particular barrel is, there are however a few differences that may help in identification.  First off is shape.  Of course, barrel cacti are all sort of barrel shaped.  The compass barrel is a little more wide and plump than the California barrel.  The California barrel  is a little skinnier.  The second way to distinguish between the two is by looking at the spines.  Both have very interesting spines which are often red colored.  This red coloration gives a sharp contrast to the dark green of the cacti's body, especially after a rare rainfall.  Both cacti also have flattened central spines that have a ribbing pattern on them.  The central spines are also hooked, giving both cacti another common name of fishhook barrels.  Compass barrel cacti spines are however considerably more hooked than California barrels.  Compass barrel central spines are a full "fishhook" shape and were in-fact used as fishhooks by some Native Americans.  California barrel central spines are closer to a 90 degree curve than an actual fishhook.  These are the best ways, though not necessarily foolproof ways of distinguishing the two while out in the desert.

In our next post we will talk about the leaning habit of barrel cacti.

California barrel cactus front left of picture.

How To Identify a Cactus

The columnar saguaro cactus.  Note the huge column like shape and ribs lined with spines traversing from the bottom to top.

Cacti are one of the most diverse and interesting plant families in the plant kingdom.  Cacti are native only to North and South America but are prized worldwide by plant enthusiasts.  I once worked with a PH.D who was from England but came to the United States specifically to work with cacti.  While you can go to just about any botanical garden in the world to observe cacti, the Southwestern United States and Mexico are probably the best places to observe cacti in the wild (in North America at least).  Within the United States, cacti can be found in the wild in just about every state.  Where I grew-up in Iowa, every once in awhile I would come across plains prickly pears growing in a dry prairie.  Now, living in the Southwest I come across cacti every single day.  The Sonoran Desert is loaded with all kinds of different cacti ranging from the 50 foot Saguaro cactus to the six inch tall pincushion.  Cacti are really not that difficult to identify, at least to the genus or "group" level.  Just about anyone can learn the major groups of cacti simply by looking at three major traits; the shape, ribs, and spines.

Barrel cacti in foreground.  Named after their barrel like shape.  Barrel cacti also have ribs lined with spines.

Shape is possibly the easiest and best way to categorize a cactus.  The most common cactus group is the prickly pears.  These cacti have stems that are sectioned into flat, pear or pancake shaped pads.  The overall prickly pear plant is joined together by these pads typically forming a shrub shape.  Cholla cacti are similar in that the plant is made up of sections, but instead of these sections being flat and pear shaped, they are cylindrical, and the overall plant also is shrub shaped.  Barrel cacti are barrel shaped.  Columnar cacti such as saguaros form tall columns. Tiny pincushion cacti are small and often shaped like an actual pincushion.  Hedgehog cacti are sort of like small columnar cacti that only grow a few feet tall at most, with the small stems bunching together.

A cylindrical cholla cactus section.

Ribs are the next important way of identifying a cactus.  Saguaros and other columnar cacti have long ribs or pilleates that stretch from the bottom of the cactus to the top.  Hedgehogs and barrels also have ribs.  Pincushions, prickly pears, and chollas do not have ribs. 

Prickly pear cactus with flat pear shaped sections.

Lastly spines.  Spines don't always help us distinguish between different groups of cacti but are extremely useful in determining the actual species of cacti.  A few spines like the tiny hairlike glochid are only found on prickly pears.  Glochids are the tiny spines that get stuck in your skin and have to be taken out with a tweezers.  Pincushions typically have tons of white spins which helps give them a "pincushion" like appearance.  Spine color, number, and shape are essential in learning to distinguish specific species of cacti.

Hedgehog cactus

Pincushion cactus.

Bringing Back the Dinosaurs... Sort Of...

Picture of a hadrosaur based off of findings from the dinosaur mummy "Leonardo".

In our last post we discussed how it has recently been discovered that some dinosaur fossils contain remnants of soft dinosaur tissue. In this post we will discuss the discovery of a fossilized dinosaur mummy.  Specifically, this dinosaur is a hydrosaur, or a duckbilled dinosaur, that died and was quickly buried in sediments before it could decay.  The burial process mummified the dinosaur, preventing decay and eventually the mummy was fossilized.  This dinosaur mummy is different from say human Egyptian mummies in that the dinosaur is actually fossilized and rock.  Egyptian mummies are simply well preserved tissues of the human that died.  As a result of the dinosaur mummy fossilizing, all of the parts of the dinosaur present in the mummy are still present today in rock form.  The process of fossilization of dinosaur mummies is exceedingly rare and have only been found a handful of times.  The awesome thing about mummies is that they preserve the soft tissues such as internal organs or skin which normally decay away long before any scientist can observe them.  The difficulty with fossilized mummies though is the fact that all of the soft tissues are now actually rock, which obviously is extremely difficult to dissect.  The documentary movie "Secrets of the Dinosaur Mummy" shows how modern day paleontologists "dissected" Leonardo without hacking him up.  The movie is a great demonstration of real scientists doing real science.  As a result of the "dissection", the scientists were able to find out all kinds of interesting biology about the dinosaur.  Huge changes in what we believe about dinosaurs in how they look and how their body functions have come about because of the investigation shown in this movie.  Also interesting, since the movie has been filmed, soft tissues like we talked about in our last post also have been found in Leonardo. 

Secrets of the Dinosaur Mummy
 

Actual fossilized dinosaur mummy "Leonardo".

Is Jurassic Park Possible? Bringing Back the Dinosaurs

Dinosaur soft tissue found in a fossilized T-Rex leg bone.

Is Jurassic Park really possible?  For nearly twenty years scientists have been telling us that the science behind the movie Jurassic Park is possible in theory, but not really possible in practice.  Why?  No one has ever or would ever be able to find intact dinosaur DNA from ancient fossilized bones, or mosquitoes for that matter.  Oddly though, about the time the movie was coming out, a paleontologist discovered the remains of some organic soft dinosaur tissue in a fossilized dinosaur bone.  How in the world would tissue survive such long periods of time and the fossilization process?  The answer to that question is that no one really knows, but several scientists working independently of each other have been able to verify the presence of dinosaur tissues in fossilized bones.  Organic molecules, including blood cells, have been found and confirmed in these specimens.  These samples open up a totally new area of paleontology and biology that has previously never been open for scientific examination before.  For example, through the examination of protein sequences, specifically collagin, scientists have been able to find that dinosaurs were closely related to birds.   Several different proteins have also been found in these fossils.  These proteins may open doors to understanding dinosaur physiology such as if they were warm or cold blooded.  Currently though, the field of studying ancient tissues from fossilized specimens is still highly controversial.  Even though there has been a lot of evidence to support the existence of this tissue and that it is not simply environmental contamination, the fact remains that it is still nearly unbelievable that organic soft tissues would survive decay over such long periods of time.  Though proteins have been found, no intact DNA has been found.  This makes sense considering protein molecules are significantly more stable than DNA.  So unfortunately, the search for dinosaur DNA and for Jurassic Park continues.  But with this discovery, we will get a lot closer to determining what a real dinosaur was like and what a real Jurassic Park would be like.

http://www.smithsonianmag.com/science-nature/dinosaur.html

In my next post I will discuss another, even more recent dinosaur finding which is even more amazing than this discovery.

Time To Plant Gardens In The Sonoran Desert

October in the Sonoran Desert means the start of a very long and productive growing season in the garden.  I have already planted garlic, green onions, carrots, beets, and lettuce.  I am planning on planting peas, tomatoes and potatoes very soon.  Most of these garden plants should grow through May.  Only tomatoes and potatoes will require a little frost protection if it does freeze this winter.  Typically I find at my house it freezes about two out of every three winters, but never for more than a few hours at a time.  I normally do not grow tomatoes during the winter but am giving it a try this year.  If they survive through the winter they should produce heavily March through July.  I am also planning on planting potatoes above ground in straw and compost, I'll post more on this at another time.  The earlier everything is started the more productivity we can get out of the garden.  If we wait a week or two it will be to cool for plants to grow very quickly, greatly reducing productivity.  If we start earlier, the bugs eat everything.  I am still trying to find a good solution to bugs eating all my new sprouts.  

We have had two years of drought which has been rather hard on gardening here.  This summers monsoon season broke that drought at least for the near future.  Fortunately, it is expected that this will be an El Nino winter, which often means more rain for the Southwest.  Even with irrigation it always seems that the garden grows best with rain.  

Bacteria: They're everywhere, and they're not your enemy

Bacteria are absolutely everywhere.  On the floor, on your desk, in the air, on you skin, in your stomach, and on absolutely everything else.  There is basically nothing that doesn't have bacteria in or on it.  Well, that is unless you cook it for long enough at a high enough temperature.  But we're talking about uncooked things here.  Us modern humans often thing bacteria is the enemy.  We like to make sure everything is perfectly cleaned with antibacterial soap so we feel safe.  Unfortunately, this is a big fat lie, antibacterial soap does not make us perfectly safe.  In-fact, it really isn't safe in itself and isn't really that great of a cleaner.  Fortunately, the fact that antibacterial soaps aren't that great and that they probably shouldn't be used is probably a very good thing. 

So first off, why is antibacterial soap so bad?  There has been a lot of research showing negative negative health consequences of antibacterial products.  Negative health consequences include neurotransmitter interference, increased allergen sensitivity, and immune system response.  I am not sure how conclusive a lot of this research is but there is a lot of it out there.  There is also good potential that antibacterial soaps with the antibacterial agent triclosan in them are mutating natural bacteria into bacterial superbugs that are resistant to antibiotics. 

Secondly, bacteria isn't as scary as you might think.  The fact that bacteria cover nearly everything is actually a good thing and only a very small percent of those bacteria are actually scary.  For example, dirt is absolutely loaded with bacteria.  But, if you were to eat dirt you probably would not get sick from all the bacteria.  The reason for this is because the bacteria in dirt is environmental and not necessarily infectious to humans.  Of course, there is some infectious bacteria in soil but it is a rarity relative to all the other bacterias.  Some research even suggests that eating a little dirt will help boost your immune system, but...  I don't suggest you do that.  We probably all tried a little when we were kids.  Bacteria that naturally lives in dirt lives there because it eats the stuff in dirt.  The bacteria in dirt does not normally live in or infect humans because it does not eat the stuff in humans.  The type of bacteria we have to worry about are infectious bacteria.  Infectious bacteria infects humans because they eat the stuff inside of people!  Typically, we come in contact with infectious bacteria through other humans, or infected water or food.  This is why we must wash our hands and not sneeze on everything or stay home when we are sick! 

No matter how hard and how many times you clean yourself with antibacterial soap, you are never going to rid yourself of bacteria, and that's a good thing. Your skin is normally covered with bacteria that helps keep your skin healthy.  Your digestive tract is filled with all kinds of bacteria that also keep you healthy.  Probiotics have in recent years become increasingly popular as people have discovered their positive health benefits.  Things like fresh yogurt and sauerkrout are loaded with the healthy lactobacillus bacteria which are one type of probiotic.  Lactobacillus bacteria are shown to improve the health of both the digestive tract and skin.  Probiotic bacteria can actually prevent us from getting sick.  Removing these probiotics from the body can have negative health consequences.  So, bacteria are friends, not enemies to be feared.

What Makes a Chili Pepper Spicy?

The chili pepper was first cultivated and bred for its spiciness in Central America, hundreds of years before any part of the rest of the world enjoyed it.  During this time, ancient Americans spiced all kinds of food with the chili.  In the southwest United States, Native Americans would gather wild chiltepine chilis and protect the plants for future use.  Aztecs were said to enjoy hot cocoa spiced with chili peppers.  When explores from the Old World began visiting North and South America in the 1500's they brought the chili to the rest of the world.  Now, the spiciness of the chili pepper has captured the taste buds of nearly the entire world.

It is amazing how the spiciness of the chili has been utilized in nearly every cuisine possible.  Even if a recipe is not made with the spice of chilis many people will put some sort of spicy sauce on it.  Think about Tabasco Sauce. people will put it on just about everything.  There is probably someone that puts it on there cold cereal in the morning.  The odd thing is, spicy flavor is painful and for some reason people like the pain (myself included).  Enjoying the spicy pain is a learned taste and some people can build-up quite a tolerance.  At least for decades, if not for centuries and millenniums, people have been trying to breed the next spiciest chili pepper.  It seemed for years the habanero held the record for spiciest chili.  In recent years a number of chili's have claimed to be the spiciest in the world.  Recently, the ghost pepper, also known as the naga bhut jolokia, from India held the title of worlds spiciest chili.  Now the trinidad moruga scorpion pepper holds the official Guinness World Record for spiciest chili. 

The secret to the chili's spiciness is the molecule capsicum.  This molecule is secreted by the white tissues holding the seeds inside the pepper.  Capsicum binds with pain receptors in the mouth responsible for detecting heat, therefore giving the spicy heat chilis are known for.  The body then responds by increasing perspiration, raising heart rate, and releasing endorphins.  Capsicum also has been shown to kill certain types of cancer cells and may indirectly aid weight loss.  In the wild, birds love spicy chili's, and mammals generally hate the spiciness (except for some humans of course).  When birds eat chili's the seeds pass through their digestive tract undamaged and can therefore germinate and grow if deposited in an ideal location.  The chewing and digestive tract of mammals however digests the seeds, preventing them from passing through the digestive tract.  This is exactly why chili peppers were spicy to begin with.  Caspicum deters mammals from eating them and to encourage birds to eat them, thus allowing the perpetuation of chili plants.  Cultivated varieties of chili's however are increasing in spiciness simply because humans are selectively breeding only the spiciest chili's in order to produce an even spicier chili. 

How to Identify a Rock

Gneiss.  A banded foliated metamorphic rock with coarse grain.

As with anything, such as plants, birds, or animals, rocks can be quite difficult to identify.  There are however, far fewer rocks to identify world wide than there are living organisms.  At a local scale there may be only one or two major rocks that need to be identified while there may be several dozen species of plants or birds.  On top of that, there is likely whole lot of rocks of the same type at a particular location which helps aid identification.  Plants of particular species may be few and far between while birds and animals fly or run away before you can ever get a good look.  So rocks may be one of the easiest things to identify in any particular habitat.  That doesn't always mean they are easy to identify though.  It is fairly typical for someone to just flip through page after page of a field guide trying to identify a rock, bird, or plant.  Then, after flipping through the entire guide realizing you couldn't find what you were looking for.  Likely the species is in the guide but you just didn't know what you were looking for.  There are several things you can do to help narrow down your search for a rock, these include color, texture, and structure.

First color.  Is the rock light, medium, or dark colored?  Of course these are generalizations and the rock might be pinkish or tan or brown.  But, even if it is pinkish it is likely a light colored rock such as granite, quartzite, or possibly rhyolite.  The rock may also have both dark and light specks through out it.  If the rocks are sort of an even "salt and pepper", with approximately even amounts of light and dark, it would be considered medium in color, such as diorite.  Even light colored rocks will have some dark specks in them or dark colored rocks some light colored specks.  The key is determining the overall generalized color of the rock. 

Granite.  A coarse, light colored igneous rock.

Secondly consider rock texture.  Is it fine grained where you can hardly see any crystals such as with the dark colored basalt or light colored rhyolite?  Is it coarse grained where you can easily see individual crystals such as with light colored granite or dark colored gabbro?  Other rocks may have lots of holes in them such as scoria or pumice.  These holes are a result of lava quickly cooling and forming air bubbles called vesicles. 

Third, what is the overall structure or pattern of the rock.  Does the rock show irregular banding patterns such as gneiss, or no pattern such as with granite?  Does the rock break into plates like with schist or slate?  Or are there many long parallel bands which are called bedding planes such as with sedimentary rocks like limestone. 

Limestone.  A light colored sedimentary rock that forms bedding planes.  No bedding planes visible in this picture. 

Also, narrowing a rock down to igneous, metamorphic or sedimentary can help a lot.  Igneous rocks are volcanic in origin and have interlocked crystals that range from coarse to fine.  The crystals have flat surfaced and fit together like a puzzle with no air spaces.  Typically there is not overall structure or pattern to igneous rocks.  Metamorphic rocks are formed by heat and pressure.  They also are made of crystals that interlock and have flat surfaces.  They do however form banding patterns of light to dark, or break into plate like pieces.  This banded or plate like structure is called foliation.  Not all metamorphic rocks are foliated such as with marble and quartzite.  Sedimentary rocks do not have interlocking crystals.  They often contain fossils and form bedding planes.  Bedding planes are thin parallel bands.Sedimentary rocks are formed through the accumulation of sediments such as sand or clay that turn into rocks.

Sandstone cliffs.  A coarse textured sedimentary rock made or sand.  Individual sand crystals do not interlock.  Sandstone forms bedding planes that run parallel to each other as seen in this picture.

By narrowing your choices down using color, texture, structure as well as igneous, metamorphic, and sedimentary, finding the right rock will be a lot easier.  Here is another great resource to help identify rocks more specifically than I have done here:

http://geology.about.com/od/rocks/a/Rock-Tables.htm