Wednesday, August 27, 2014

Let’s Chew The Fat

Biology concepts – lipid, saturation, fruit, vegetable, drupe, berry, mesocarp, cotyledon, tuber, fatty acid, triglyceride

To try and get blood from a stone dates back to the 1600’s,
meaning to try and do the impossible. It was first used in a
book by Giovanni Toriano called The Second Alphabet. As far
as the turnip goes, it may relate to a story in the Bible of Cain
and Abel making sacrifices – one a vegetable and one an animal.
The vegetable sacrifice was not as appropriate since it could
not drip blood. Now we often use the phrase for the inability of
getting someone to pay money.
Did you ever hear or use the phrase, “You can’t get blood from a stone?” Sometimes the phrase goes, “You can’t squeeze blood from a turnip.” Item one - gross. Item two, where did the phrases come from? (see picture caption) Basically, they both mean the same thing. You can’t harvest something that wasn’t there to begin with. I use it with creditors – they can’t get money from me if I don’t have any.

You can’t harvest what isn’t there, so that leads to today’s question. If plants are low fat sources of nutrition, how can we use them for cooking oils? There’s corn oil, sunflower oil, cottonseed oil, canola oil, rapeseed oil, olive oil, even coconut oil. How can such low fat organisms provide us with so much fat?

Of course every cell has fats – there are the phospholipids in the cell membrane, and phytophormones made from lipids help the cells communicate and the plant respond to stimuli. Thylakoid membranes for photosynthesis have a lipid (MGDG) that normally doesn’t form a bilayer, but does in the thylakoid. Please refer to this post to show that lipids have a role in almost every cellular activity.

Unfortunately, we don’t get oil from the whole plant, just a little part of it. And even more amazing, the part we get oil from only exists for a short time in the plant’s yearly cycle. When we say vegetable oil, we really mean fruit oil.

The fruit is the part of the plant that grows from the flower after fertilization, including the seed(s). The vegetable is all the other parts of the plant, including the flower bud before it is fertilized. Now you know the true difference between fruits and vegetables.

The fat in plants is almost always associated with its attempt to reproduce itself. Part of the fruit may be fatty, the seed of the fruit may be fatty, or even the germinating plant inside the fruit could be the source of the fat.

The upper image shows the different parts of the berry fruit
avocado. The mesocarp is the part we eat and contains the
fats. The same is true for the olives below. These have had
their seeds removed and replaced with a piece of pimento.
Maybe they thought we wouldn’t notice. No, they can’t grow
them with the pimento there already, but it might be
something Bill Blazejowski could work on, like his idea to
feed mayonnaise to the tuna in the 1982 movie, Nightshift.
Let’s start with the easiest – fruits that are high fat. The oldest is the most famous – olives. The fleshy part of the fruit, the part we eat, is called the mesocarp. In olives, up to 85% of the weight of the mesocarp is fat in the form of triglycerides. Olives have been grown for eating and pressing oil since about 6000 BCE. Olive cultivation predates written language and even teenage vampire movies.

Avocados are also pressed for oil. In locales where olives are harvested part of the year, avocados can be harvested year round, so many olive oil producer make avocado oil when the olives aren’t in season. Even though we use the mesocarp of each fruit for oil, the olive is a type of fruit called a drupe, while the avocado is actually a single-seeded berry. The avocado is just about the only berry from which we harvest edible oil.

In people with metabolic and liver function changes due to diabetes or other parts of a metabolic syndrome, it is known that the monounsaturated fatty acids in olive oil help to normalize many biochemical markers of liver function in people with metabolic syndrome. A 2014 study now expands that to avocado oil. It contains many monosaturated fatty acids, and the researchers found that it has similar positive effects on biochemical metabolic markers as compared to olive oil.

Oil palm (Elaeis guineensis or E. oleifera) fruit are also high in fat. The mesocarp is pressed to make palm oil that is used for eating and cooking, especially in Africa. The seed (kernel) can also be harvested for oil, and this is called palm kernel oil. The differences between the oil from the mesocarp and from the kernel lie in their color (the fruit oil is reddish while the kernel oil is colorless) and the percentage of saturated fats. The kernel oil is higher in saturated (no double bonds) fat.

These differences have an good side for us. Palm kernel oil esters have been shown to pass the blood brain barrier (BBB, see this post) better than other oil esters. So in a 2013 study, the palm kernel esters were combined with the antibiotic chloramphenicol. The resulting emulsion showed properties that could make it useful for treating bacterial meningitis, because more of the antibiotic could be carried across the BBB.

The mesocarp of the coconut is not edible. See the fibrous
stuff being cut away from the coconut? That’s the mesocarp,
or coir. It does have other uses though. You can make good
rope from it, or perhaps you would be more interested in some
biodegradable flower pots – all made with coir.
Another type of palm oil is also used in cooking. Coconut palm oil is pressed from the flaky coconut meat that makes german chocolate cake so irresistible. But the meat isn’t the mesocarp of the coconut fruit. You wouldn’t want to eat the mesocarp of a coconut; it’s the fibrous brown covering that has to be peeled away to get to the nut.
The coconut meat is the endosperm of the seed – the more it grows, the more of the liquid endosperm (coconut milk) turns solid. It turns solid because it is more saturated fat, and like most saturated fats it is more likely to be solid at room temperature. Coconut oil is sometimes used in place of butter.
Other “vegetable” oils come from different parts of the fruit. Sunflower oil uses the entire seed, including the embryonic plant, the endosperm and skin layers – outer (exocarp) and inner (endocarp).
Canola oil is pressed from the seeds of the canola plant. Canola is a plant bred from a type of rape plant, a member of the mustard family. Therefore, there's a really no difference between rapeseed oil and canola oil. The name "canola" was thought up in the 1970’s, using “Can” from Canada, because that is where it was developed, and “ola” as a term for oil. The word “rape” didn’t seem to help sales.

The top cartoon shows how the cotyledons can have different
fates. The brown oval cotyledons can become the first leaves in
epigeal growth, or can stay below ground in hypogeal growth.
Either way, they help the germinating plant get a good start. The
peanuts below show the cotyledons, the big parts we eat, as well
as the germinating plant. The red arrows point to the peanut
nibs; they’re actually the plumule and radicle (stems and root) of
the embryonic plant.
Drupe fruits like olives seem to make good oil. Drupes also include plants like peanuts and soybeans. However, these are different than olives. The fat from most drupes and whole seeds are found in the embryonic leaves, called cotyledons. They often serve as the first leaves of the baby plant, but they also store fat and carbohydrates for the germinating plant.
It occurs to me that the examples above are equal and opposite. On one hand, the fat of peanuts, soybeans, sunflowers, rapeseeds, and coconut serve to nourish the embryonic plant. Fat is a great idea for this function because it stores a large amount of energy in a small volume. Carbohydrates require water for storage, so they take up more room.
On the other hand, the fat of avocados, palm oil fruits and olives are enticements to other animals to eat the fruit. Why do the fruits “want” to be eaten, anthropomorphism aside? The answer - to disperse the seeds held within or on the fruits.
New plants do better when they are far enough away from the parent plant that they will not have to compete with them for resources and sunlight, especially since they will be smaller and in the shade. This is why seeds need to be dispersed. Nourishment for itself or nourishment for a predatory animal, these are two completely different functions for the fat, but both are held in the fruit.

The corn kernel is the fruit of the maize plant. There is starch
(glucose chains), gluten (protein) and the germ, which is the
germinating plant with a single cotyledon. The bottom drawing
shows the difference in constituents of different varieties of corn.
Sweet corn has more sugar, while dent corn has a higher germ to
endosperm ratio.
Given the high enough fat contents of the plant components described above, it makes sense that we could use them for oils. But what’s one of the most common “vegetable” oils used for both cooking and biodiesel? I’ll give you a hint – you probably enjoy some of this fat at the movies.

Yes, corn it is, both as your popcorn and the margarine you slather all over it. We already know that corn is amazing (see this post), but only 10% of corn is fat (dry it and 20% is fat). The sweet corn you eat is a special hybrid that contains more endosperm and less fat, but dent corn is the one used for making oil and feeding livestock. The corn kernel is mostly starch and glucose, but the embryonic plant has the fat. This is called the corn germ and is the only part used to make oil. The germ contains the cotyledon (called a scuttelum for corn) that stores fat for the germinating plant (get it? Germ = germinating plant)

Look at the bottom picture to see how small the germ of the corn kernel is. Because of this, it takes 40 bushels of dried dent corn kernels (at 56 pounds/bushel) to make 500 ml (0.85 lb) of corn oil! It must be cheap to grow corn because that isn’t a very good ratio, yet corn oil isn’t that expensive.

Tiger nut sedge looks a lot like a grass and is considered a weed
in many places. It was cultivated as far backs as 3000 years ago
in Egypt and has been used in cooking for just as long. The tubers
on top left can be eaten as a root vegetable, and are high in
monounsaturated fats. The dried tubers (bottom) can be ground
into flour or used as a spice. However, we might just start to grow
them for biodiesel. I’d line up to buy a tiger nut fueled car – that’s
really putting a tiger in your tank! (a 1960’s Esso gasoline slogan)
Even though this is a summer post, there’s no reason we can’t talk about an exception. Today, it’s sedge oil. The tiger nut sedge (Cyperus esculentus) is being considered as a viable source for biodiesel, but it's used in African cooking as well. Sedge plants reproduce in several ways. They have fruits, but they aren’t significantly high in fat. They have rhizomes and well, but we’re interested in their tubers (serves the same function as a potato).

The tubers are fairly high fat, and they’re a heck of a lot larger than corn germ. On a per plant basis, sedge produce much more oil, which will make C. esculentus a cheaper source of fuel if farmed on a global scale. In truth, since sedge oil comes from a part of the plant other than the fruit, it’s the only true “vegetable” oil we talked about today. I wonder - could we get oil from a turnip? Maybe that’s the blood we should be looking for.

Next week, we'll start a series of posts on just how bacteria get around using flagella. Can flagella be used to prove the existence of a universal designer?

Carvajal-Zarrabal O, Nolasco-Hipolito C, Aguilar-Uscanga MG, Melo Santiesteban G, Hayward-Jones PM, & Barradas-Dermitz DM (2014). Effect of dietary intake of avocado oil and olive oil on biochemical markers of liver function in sucrose-fed rats. BioMed research international, 2014 PMID: 24860825
Musa SH, Basri M, Masoumi HR, Karjiban RA, Malek EA, Basri H, & Shamsuddin AF (2013). Formulation optimization of palm kernel oil esters nanoemulsion-loaded with chloramphenicol suitable for meningitis treatment. Colloids and surfaces. B, Biointerfaces, 112, 113-9 PMID: 23974000

Wednesday, August 20, 2014

Because He Is The One

Biology Concepts – ommatidia, reflex, fly, arthropod, sensory receptors, sensilla, metabolic rate, life span

Neo (Keanu Reeves) learned that he could dodge bullets
at one point in The Matrix. This was before he learned he
didn’t have to. Was he speeding himself up so the bullets
looked to be going slower, or was he actually slowing
down time?
Neo from the Matrix films had the ability, once he learned to accept it, to react so fast that everything around him seemed to be moving slowly. It made for cool cinema, but could it be real? It can seem so, athletes in “the zone” describe their situation as if everything else is moving slower and their task becomes much easier.

Let’s look at a case of this in nature. Today’s question – Why is it so hard to catch or swat a fly? The answer involves fighter jets, optical illusions, and yes, time manipulation.

Ever try to catch a fly? It ain’t easy. Swatting them can be frustrating even though most fly swatters have an area that is more than 350x bigger than the fly itself. It’s even harder to catch or hit them with your hand, and it’s as big or bigger than a fly swatter. We aren’t all as skilled as Pat Morita and his chopsticks in The Karate Kid.

One big reason that it’s hard to catch or swat a fly is because they know you’re coming. It’s not mental telepathy or a glimpse into the Matrix; it’s just that house flies (Musca domestica) and fruit flies (Drosophila melanogaster) as well as many other types of flies have sensory apparatus to let them know something big and powerful is coming at them.

First of all, look at their heads. They are almost all eyes. Each eye is not a single sensory organ, but is made up of 4000 individual ommatidia (omma = eye and tidium = small). Each ommatidium faces a slightly different direction, so all together, they give the fly a 360˚ field of vision. You can’t sneak up on them unless they’re asleep or dead.

The fly eye is a wonder to behold. Technology is using their
design (stealing really) to make smaller, cheaper magnifying
camera lens, to make better robotic eyes, solar panels, and to
reduce glass fogging on windows. The ommatidium on the
right is the basic unit. Fruit flies have about 800 in each eye,
house flies have about 4000.
Each ommatidium senses light changes or objects, so a large moving object (like a fly swatter) will be picked up by several thousand eyes and will alert the fly. The ommatidia aren’t particularly good at resolving objects, but the fact that there are so many of them makes the fly very good at detecting movement. So the fly flies away and you curse under your breath.

Even if you do swing at a distracted, contemplative, or sleeping fly with your rolled up newspaper, book, or hand – you’re still most likely to miss. Flies have sensilla (see this post) on their bodies that contain sensitive mechanoreceptors. The object moving toward them creates an air pressure wave that distorts the receptors. This sends a neural impulse through the giant fibers that make up much of the fly’s reflex arcs, and they immediately fly away.

This is why fly swatters are usually made of plastic or metal mesh. The little holes reduce the amount of air that the swatter pushes toward the fly, so that he's less likely to sense his coming doom. This is also one of the reasons it’s harder to hit them with your hand. Your hand is solid, so it pushes more air toward the fly. But also, the lever arm of the fly swatter (the long handle) creates a greater angular velocity, so it's traveling faster toward the fly than you could move your hand alone.

This is a weird illustration, but work with me. When a
band marches around a corner, they guys on the outside
part of the turn have to march much faster to stay in line.
Now, when swatting a fly, your hand is the guy on the
inside of the turn, and the tuba on the outside, running to
keep up, is the flyswatter. See why it’s easier to hit a
fly with a swatter – more speed.
The quick reaction due to visual or mechanical stimuli is even more amazing when you consider the tarsal reflex. Wing movements are inhibited when the fly is resting on your egg salad. It can't flap when its legs a resting on a surface. A startled fly has to overcome the tarsal reflex inhibition before it can fly away.

Interestingly, the reflex problem for the fly turns into a problem for you. To overcome the tarsal reflex, the mesothoracic (middle) legs push off and the fly jumps. Now it isn’t in contact with a surface and can therefore flap its wings. But the jump is always away from your impinging deathblow. Take a look at this video to see the jump. A 2008 paper showed that the fly plans the jump up to 200 milliseconds (0.002 sec) before its flight, so that it will jump directly away from the approaching object. He’s evading you even before he really starts trying.

Fruit flies and house flies can avoid most attempts at assassination just through these actions, but they have other tools at their disposal as well. For one thing, they can turn away from an approaching object and head off in another direction in only 0.03 seconds. The same group that conducted the 2008 study also showed in 2014 paper how a flying fly avoids visually perceived objects.

Count how few wing beats it takes for these flies to turn
almost 180 degrees –it’s about one and a half. In the top
right turn, you can see how they almost do a loop de
loop, and they all show the subtle changes in wing and
body position need to pull off the turn.
They saw that the fly can bank and turn all the way over or pull up and fly back over its own head in a flipping motion in order to change direction. They move their body, and they counter with subtle wing movements to reorient themselves within just 1.5 wing beats - and they beat their wings over 200 times a second. (see video)

And now we get to the relationship between flies and Neo (other than the observation that Mr. Anderson can fly). To a fly, we mere mortals seem to be moving in slow motion. This phenomenon has to do with their metabolic rate.

It was observed long ago that bigger animals tend to live longer than smaller animals. It was also known that smaller animals had faster heart rates and faster metabolic rates (they make and used energy faster) than larger animals. This led to the rate of living (ROL) hypothesis of life span. The faster your metabolism, the shorter your lifespan. This hypothesis fell out of vogue as oversimplified, but has made a remarkable comeback in the last decade.

In fact, a 2011 study showed that people with slower heart rates and lower resting metabolic rates tend to live longer than people with faster resting metabolic rates. It seems that, “Live fast and die young,” is more than just a macho platitude.

Knock On Any Door was the book and movie that
introduced the phrase, “Live fast, die young, and leave a
good-looking corpse.” Bogart didn’t say the line; he was
the attorney for the kid who did. But “live fast, die young”
has been the title for two movies, three pop songs, and
biography of James Dean.
A 2013 study has taken this observation even further. Small animals with higher metabolic rates tend to process stimuli faster as well. They can sense, process, interpret, and react to a stimulus in the same amount of time a human needs to recognize the snowball that's coming at his head.

It’s as if (not really) time moves slower for the smallest animals as compared to us. This is yet another reason that the fly is likely to avoid reading your People magazine from very close up. Like Neo seeing the bullets in flight or the coming head butt from Agent Smith, flies sense and react on a completely different time scale.

This makes me feel better. Some mayflies live only 5 minutes as a flying adult (see this post), and house flies have a life span of about three weeks regardless of whether you hunt them or not, but this doesn’t have to be so sad. If time passes slower for flies, then maybe their life is long enough to fulfill all their dreams and learn about love, loss, and which wine goes with which meat. What’s important is not the minutes in their life, but the life in their minutes.

Muijres FT, Elzinga MJ, Melis JM, & Dickinson MH (2014). Flies evade looming targets by executing rapid visually directed banked turns. Science (New York, N.Y.), 344 (6180), 172-7 PMID: 24723606

Healy K, McNally L, Ruxton GD, Cooper N, & Jackson AL (2013). Metabolic rate and body size are linked with perception of temporal information. Animal behaviour, 86 (4), 685-696 PMID: 24109147

Jumpertz R, Hanson RL, Sievers ML, Bennett PH, Nelson RG, & Krakoff J (2011). Higher energy expenditure in humans predicts natural mortality. The Journal of clinical endocrinology and metabolism, 96 (6) PMID: 21450984

Wednesday, August 13, 2014

Getting High On Life

Biology concepts – bacteria, climate, respiratory, birds, arthropods, astrobiology, clouds

Carl Sagan wasn’t just the host of the original Cosmos on TV.
He solved the riddles of Venus’ high temperature, the seasons
on Mars, and the color of Titan. He also wrote one of my
favorite speculative fiction novels, Contact. The movie is
good; the book is better.
The astrophysicist Carl Sagan said, “There are naive questions, tedious questions, ill-phrased questions, questions put after inadequate self-criticism. But every question is a cry to understand the world. There is no such thing as a dumb question.” A cry to understand the world – so keep asking the questions, even if they seem silly.

Today’s question might seem a little naive – Is there any life that could escape Earth? But I assure you, there’s more to it than you might think – and no, the answer isn’t an astronaut. Let’s put it another way - is there any living organism that could get high enough on its own to leave our atmosphere?

Well, I guess the first prerequisite for escaping our atmosphere would be an organism that could get really, really high. Some birds can fly at absurd altitudes.

The Ruppell’s Griffon Vulture (Gyps rueppellii) has the highest recorded flight. On November 29, 1975, a Ruppell’s vulture was sucked into the jet engine of a plane flying at 39,700 ft (12.1 km, Mt. Everest is 9.0 km) over the Ivory Coast in Africa. A unfortunate flight plan for the bird, but amazingly the plane landed safely after ingesting a bird with a 10-foot wingspan.

These two pictures are not at the same scale. The Ruppell’s
vulture on the left has a wing span of about 10 ft (3 m),
while the bar headed goose on the right (see the bars?) has
a span of about half that. They should not box one another,
it’s be a slaughter. But still, these are both much bigger than
most birds. Is their longer wing span part of their success at
high altitudes? Songbirds rarely fly above 2000 feet.
We don’t know how often the vultures venture that high, but the bar headed goose (Anser indicus) makes a habit of flying over Mt. Everest. This is a migratory bird that flies over the Himalayas twice a year, sustaining 8-hr flights at more than 28,000-29,000+ feet (8.8 km).

The real question is why birds would fly so high. As you ascend, the air becomes thinner; fewer molecules make the atmosphere less dense. Since bird flight is basically supported by the air, thinner air makes flying much more difficult.

Difficult flying means that more energy is required. Birds live right on the edge of oxygen debt all the time; flying is tough at any altitude. But high in the air, it becomes even harder and requires more energy. And what’s needed to make energy in the form of ATP – oxygen (see this post) – the very thing there is less of at high altitude.

The bar headed goose and his compatriot avians breaks some rules in order to become a high flier. Birds in general are better at oxygenating their muscles, because they can exchange oxygen for carbon dioxide on both their inhalation and their exhalation (this will be the focus of s series soon). But that isn’t all.

Birds can also pant better than mammals. Panting is way to get more oxygen to the muscles, but it comes at a cost - it brings blood vessel constriction in the brain (an attempt to prevent oxidative damage). This makes for poor control, focus and decision making. But birds can pant much longer and harder without constricting brain vessels, so they don’t make stupid decisions - birds aren't bird brained.

Bar headed geese go even further (a 2013 study). The blood vessels in their muscles penetrate deeper and are more extensive. This can supercharge their muscles with oxygen so they can make more ATP and flap more energetically. Finally, the hemoglobin (oxygen-carrying molecule) of bar headed goose red blood cells is slightly different than that of other birds. It grabs onto oxygen molecules easier and quicker, so it does a better job of transporting the maximum amount of oxygen to the muscles.

We humans may not want to flap at high altitudes, but we could learn a lot from the bar headed goose about maximizing oxygen utilization. That’s where we get most of our best ideas – we steal them from nature’s rule breakers.

Many species of spiders, mites, and small caterpillars use
kiting as a means of dispersal. Remember that these are
newborns, and are usually of the smaller species, so these
fellows are awfully small. That makes it possible for a breeze
to catch the silk they spin straight up into the air and carry
them off to new neighborhoods. This is thought to be one of
the primary ways arthropods colonize newly formed islands.
But we shouldn’t restrict our discussion to birds, there may be other things that get high (pun intended). The winds can help out. Some small arthropods disperse themselves as youngsters by ballooning with silk. Spiderlings (newly hatched spiders) risk being eaten by siblings if they hang around after hatching, and too many spiders in one area makes it hard to find food, so they get as high as they can and then shoot out a strand of silk.

The wind picks up the youngsters and deposits them somewhere else. However, the wind sometimes doesn’t want to let them go. They've been know to travel into the jet stream, and have been noted living in weather balloons at more than 16,000 ft (4.9 km).

Bees too have been found on the slopes of Mt. Everest (5.6 km). A 2014 study says bees could theoretically fly at almost 30,000 ft.; they could look down at Mt. Everest if they chose to. The researchers reduced the density of air and the oxygen concentration to match what would be found on top of the world and the bees flew just fine. They compensated not by beating their wings faster, but by widening and lengthening their stroke. Pretty good for an organism that many mistakenly believe shouldn’t be able to fly at all. But just because they could fly at that altitude, doesn’t mean that they do.

For one thing, bees and other arthropods go dormant when temperatures dip into the 40’s ˚F (7-10˚C) they become immobile and if they stay that way, they die. Not a good candidate for escaping Earth, where the temperature approaches -40˚C as you travel through the clouds.

These are the major types of clouds and their average altitudes.
They carry dust, water, chemicals, and apparently a whole lot of
bacteria and fungi. The 2013 paper says the bacteria act as seeds
for cloud formation and can therefore affect the weather.
Powerful beings.
The clouds are up there, could they harbor life? They contain water; life needs water. There are several types of clouds and they sit at various altitudes based on type, topping out at about 13 km (8 mi). The highest clouds are at about the same altitude that the griffon vulture has been known to fly (see picture).

Do all clouds have a living lining? You betcha. A 2013 study has shown that the clouds are actually their own biological environment. Bacteria, some from the ground, some from the ocean, and perhaps some from the air, are living and dividing up in the clouds. The study sampled air at 10,000 feet and found that air over water, had more marine organisms, while air over land had more soil organisms. They also found that hurricane air had many more organisms, so they hypothesize that strong winds pull up more organisms into the upper atmosphere.

But wait you say, the vulture was at 39,000 feet, and these bacteria were only at 10,000 ft. Well, let’s go higher. A 2009 study from India showed that microbes were living as high as 25 miles (41 km) in the stratosphere. This shames the vulture and he makes him feel inadequate. What’s more, the 2009 study found three strains of bacteria in the clouds that are not found on the surface of the Earth!

Meteorites are one way that life might travel from planet to
planet. The organisms would have to survive the jolt that
speeds them to escape speed (bacteria can), and they have to
survive the temperatures of reentry. Interestingly, studies
show that even though the surface of a meteor entering the
atmosphere is several thousand degrees, it feels like a warm
summer day just a few centimeters deeper.
Bacteria are particularly well suited for life in the atmosphere. There are bacteria that can withstand intense radiation, can live in extreme cold temperatures, and can live nearly without water. These sound like good candidates for something that could escape Earth altogether.

A 2012 draft genome of one of these bacteria, Janibacter hoylei, confirms that it is different from any organism found previously on Earth. These bugs might be living their entire existences in the upper reaches of the atmosphere.

But we could look at this from the other direction as well. Could J. hoylei have come from space and is just living in the clouds because it liked the first place it saw when it got here? Astrobiologists are excited to study these high altitude bacteria in terms of whether they could seed other planets or whether life could come here from other places.

The hiccup in all our hypothetical space entering organisms is something called escape speed. In order to leave Earth’s gravitational pull, an object on the ground must travel at 11.2 km/sec. The escape speed decreases as you travel away from the center of mass, but even at 9000 km, an object must travel at 7.1 km/sec. A bullet fired from a rifle travels at about 1.7 km/sec, so you get the idea. It ain’t easy to leave Earth behind, even if you happen to be rugged enough to survive space (as some bacteria and lichens can, see this post and this post).

The Earth’s magnetic field protects life on the planet from many
types of deadly radiation. Near the poles, the earth’s magnetic field
lines bend to pass through the center of the planet. It is here at the
poles that the radiation can interact with the field lines in a position
for us to see. These are the Northern and Southern Lights.
One theory holds that bacteria living in the high atmosphere could be affected by the magnetic field lines of the Earth and sort of ride along a magnetic railway. Tom Dehel, an electrical engineer for the FAA, proposed in 2006 that electromagnetic fluxes, like the solar flares and fields that produce the auroras in the northern and southern hemispheres, could provide charged bacteria with enough energy that they could escape Earth’s gravitational pull. Not one scientist I could find has signed on to this idea. But still, there are no silly hypotheses, they’re all just a cry for the truth.

Next week, another question with a more fascinating answer than you would expect - why is it so hard to catch or swat a fly?

Pawar SP, Dhotre DP, Shetty SA, Chowdhury SP, Chaudhari BL, & Shouche YS (2012). Genome sequence of Janibacter hoylei MTCC8307, isolated from the stratospheric air. Journal of bacteriology, 194 (23), 6629-30 PMID: 23144385
Dillon ME, & Dudley R (2014). Surpassing Mt. Everest: extreme flight performance of alpine bumble-bees. Biology letters, 10 (2) PMID: 24501268

Hawkes LA, Balachandran S, Batbayar N, Butler PJ, Chua B, Douglas DC, Frappell PB, Hou Y, Milsom WK, Newman SH, Prosser DJ, Sathiyaselvam P, Scott GR, Takekawa JY, Natsagdorj T, Wikelski M, Witt MJ, Yan B, & Bishop CM (2013). The paradox of extreme high-altitude migration in bar-headed geese Anser indicus. Proceedings. Biological sciences / The Royal Society, 280 (1750) PMID: 23118436

Friday, August 8, 2014

Biology Position available

I was asked by the Adella Ramirez, the chairperson fo the science department at Waller High School to post the following:

Waller High School in Waller ISD, Waller Texas is in need of an AP and duel credit Biology teacher due to a late resignation (our teacher left to go to a private school). The schedule is quite favorable.

Contact info:
Brian Merrell (Principal)
Waller High School 
20950 Field Store Road
Waller, TX 77484
ph 936-372-3654

Wednesday, August 6, 2014

Fall Leaves And Orange Flamingos

Biology concepts – pigment, carotenoids, flamingos, cyanobacteria, bacteriophage, trophic cascade effect, spirulina, alga

These are the two species of Old World flamingos, the greater
(upper left) and the lesser (bottom right). Their ranges are
included, pointed out by the convenient arrows. Even though
the pictures don’t show it because I couldn’t get them to stand
next to one another, the greater is twice the height of the lesser,
hence the names. Notice the color variation as well. However,
color isn’t based on species.
There are two species of flamingos in Asia and Africa, the greater and lesser flamingos. There are also four New World flamingo species, but let’s focus on the two Old World species for today – the answer to our question holds for the New Worlders as well. Why are flamingos pink? Well, they aren’t always pink. And the reason they can be pink isn’t simple, but it’s something to which we can all relate.

The greater flamingo (Phoenicopterus roseus) is much larger than the lesser flamingo (Phoenicopterus minor) –- that makes sense. Greater flamingos average about 140 cm (55 in) tall, but they only weigh about 3 kg (6.6 lb). They're mostly legs, and there isn’t a lot of meat on those legs. If given a choice at the next flamingo fry, choose a breast over a drumstick.

The lesser flamingo weighs in at only 2 kg (4.4 lb) on average and are half as tall as the greater flamingo. But they make up for this in numbers. There are over 1.5-2.5 million lesser flamingos in East Africa, maybe twice as many as the greater flamingos, even though the larger species has a much broader range.

Flamingos are freaky birds. Their knees seem to bend backwards, but it's just an illusion since those backward bending joints are really their ankles. They tend to stand on one leg, and the reasons for this are not completely known. Some birds do it for camouflage, since on one leg they look more like branches. This probably doesn’t work for flamingos – since they’re pink!

A 2010 study showed that flamingos stand on one leg much more often when they are in water, so they hypothesized that they do it to reduce the amount of body heat that is lost to the water. Also, the scientists saw that the flamingos stood on one leg in the water for less total time as the temperature increased. This was definitive proof for leg position as a method of thermoregulation.

Other theories state that flamingos might stand on one leg because it takes a lot of energy to pump blood down and then back up those long legs Birds live on the edge of starvation everyday; by pulling up one leg at a time, they can reduce the distance and therefore the energy needed for moving blood. Or, they may do it to reduce the fungal and parasite loads on each leg – that last explanation is weak, I think.

All species of flamingos feed by turning their heads upside down.
In this way, they can scoop in some water and filter out their
food. Evolution is funny, they could have just evolved scooping
lower jaws, but for some reason they have scooping upper jaws
and therefore turn their heads over. Remember that evolution is
a point to point exercise in mutation and possible benefit; it
doesn’t move toward simple or toward logical.

Flamingos also have those funky looking beaks, but they’re functional because they eat with their heads turned upside down. As a result, it’s their lower jaw that is fixed and their upper jaw swings free. They don’t use their jaw to chew their food; they don’t really have teeth.

Instead, flamingos are filter feeders. This isn’t unheard of, there are other birds that filter their food to keep only things within a certain size range and then swallow them whole, but they are the biggest of the filter feeding birds. When their two jaws come together, they form a sort of comb assembly on the sides, the wider the distance between the comb’s “teeth,” the bigger the objects that can fit through.

Old studies shows that they use the “teeth” (actually called lamellae) to exclude things that are too big, and then to filter out things that are too small, like excess water. The tongue sits in a deep groove and pulls in and pushes out water and those things it doesn’t eat. This pumping occurs up to 20 times per second in lesser flamingos and 6-8 times/second in greater flamingos (see this video and watch for water squirting out). Different bill shapes and different spaces and lamellae sizes are specific to each species, and each eats according to its filter.

The popular answer for why flamingos are pink is because of their diet. All that stuff we talked about above is related to that answer, but you can now sense that it’s a little more complicated. The greater and lesser flamingos have different filters because they eat different things. Yet they both end up pink.

Here are the major source of nutrition for the Old World flamingos.
On the top left are the brine shrimp that make up the majority of
the diet of greater flamingos. On the bottom is A. fusiformis, the
major calorie provider for the lesser species. On the top right are
spirulina tablets from a health food market, made from dried
Arthospira organisms. Notice that none are pink, yet the flamingos
are pink. Just how do they pick up color from their food?
In the picture to the left you see the foods of the greater and lesser flamingos. Greater flamingos have a tongue/jaw filter that excludes all but the tiny brine shrimp and those things smaller (larvae of aquatic beetles and flies), so this is what they eat. The filter assembly of the lesser flamingo is much narrower, it only lets tiny cyanobacteria (lower image) into their gullet.

Cyanobacteria are sometimes called, perhaps incorrectly, blue-green or red algae. Alga has no clear-cut definition; some consider anything with chlorophyll and no protective cells over their gametes to be an alga, but others exclude all prokaryotes from the classification. I think the term cyanobacteria (Cyanophyta) is much more accurate.

The cyanobacteria that lesser flamingos eat used to be called Spirulina, but are now classified as species of Arthospira. A. fusiformis is the main dietary source of nutrition for lesser flamingos (of course greater flamingos eat them too; their filters let them in and keep them in), but there is also A. maximus. Together, they make up the spirulina that is popular in health food markets today.

We said above that the answer to today’s questions was that flamingos are pink or orangish based on the food they eat. But their food isn’t pink or orangish!! Look at the picture, spirulina is green. The explanation is related to something you see every year, and is something we have talked about before. It’s just like how the leaves turn colors in Autumn.

The green leaves in summer have red and other pigments, but they’re masked by so much chlorophyll (see this post). In fall, the leaves stop making chlorophyll, so the other colors shine through. The spirulina and brine shrimp have red and yellow pigments, but again there is so much green that the other colors are masked.

Here are two lobsters. Actually, it’s one lobster and one dinner.
The only difference is boiling water. The carotenoids in the shell
of the live version are bound to proteins and this changes their
light absorbing and reflecting properties (color). The hot water
denatures the proteins and frees up the carotenoids to be the
color they always dreamed of being.
When digested, the chlorophyll breaks down or is eliminated. But some other pigments, especially the carotenoids, stick around and get deposited in the tissues and feathers, now you can see them because the chlorophyll isn’t there to mask them. Why do the brine shrimp that the greater flamingos eat turn them pink? Because they feed on cyanobacteria that contain carotenoids. Their carotenoids are released when the flamingos digest the shrimp.

There's another reason for the different colors of food and flamingo. The pigments are sometimes complexed to proteins, and this can make them look brownish, bluish, gray, or green – like the many species of brine shrimp, aquatic beetles, and larval flies. This is very similar to lobsters and shrimp. They're bluish or grey when scooting around in the water, but turn red/pink when they are cooked.

Carotenoids come in many varieties; their chemistries run the gamut from alcohols to esters to plain hydrocarbons. We see them in carrots (alpha and beta carotenes - orange) and tomatoes (lycopene - red) for example. Spirulina has many carotenoids, but the one there in highest concentration is called astaxanthin (pink, as in salmon meat). The percentage of different carotenoids and the total amount of them in the diet  determines the color of the feathers and skin. This is why some flamingos can be bright orange, while others are very light pink.

These are just a few of the dozens of carotenoids found in nature.
The longer the carbon chain, the lighter the color, from red to
yellow. This is just a basic generality, different side chains and
rings can alter the color well. And just to let you know, carotene
was named for carrots, not the other way around.
On the other hand, if there is little carotenoid in their diet, the feathers will be white. The pigment is lost over time, so the pigment trapped there when they were produced will fade. But flamingos molt, so that new, pink feathers replace old whitening ones. That is, if they eat their carotenoids. In zoos, their diet is often supplemented with canthaxanthin that keeps them a presentable pink. The exception – babies always start out grey.

For lesser flamingos, their food is sometimes their doom. A 2006 study found that blooms of toxic cyanobacteria produce two different toxins (microcystin and anatoxin) and have been responsible for several die offs in lesser flamingo population over the last 20 years. They have also found that in some instances, the spirulina they eat will also produce toxin, but they don’t know if it is enough to kill them. Microcystin from an algae bloom is the same toxin that shut down the Toledo water system earlier this week.

What may be worse, a bacteriophage (a virus that infects bacteria, see this post) has been increasing in the alkaline lakes where the spirulina grows according to a 2014 study. It infects and kills the A. fusiformis. The kill off of the cyanobacteria leads to a trophic cascade effect; the average adult needs 70 grams of A. fusiformis a day to survive, and that is dry weight, not saturated with water. Lose the base of the food chain and everything else loses too.

Lake Natron is VERY salty, and it contains lots of other minerals.
Natron is a combination of salt and minerals that the Egyptians
used to mummify the bodies of those who could afford it. Not
everyone got to be mummified; if that were the case, we would
have many undead walking around, placing curses on
successful tomb hunters. The minerals are so concentrated that
dead animals that fall in end up mummified and calcified. They
look like gargoyles on a French cathedral.
One last interesting point. While the lesser flamingos can live and eat in several alkaline lakes of eastern Africa, they all fly to one particular lake when it’s time to mate – like a Club Med for pink birds. Lake Natron in Tanzania is their destination. This lake is highly alkaline, hot (nearly 130 ˚F), and just chock full of minerals. The flamingos handle it just fine, but many other birds die from crashing into the highly reflective waters. The carcasses then calcify (basically, turn to stone), and wash up as little gargoyles. Even with all this deadly water, there are two species of fish that live in those waters – I wonder if the stonefish is one of them.

Next week, another question to investigate - can living anything short of an astronaut make it to space?

Anderson MJ, & Williams SA (2010). Why do flamingos stand on one leg? Zoo biology, 29 (3), 365-74 PMID: 19637281

Peduzzi P, Gruber M, Gruber M, Schagerl M. (2014). The virus's tooth: cyanophages affect an African flamingo population in a bottom-up cascade. ISME J. , 8 (6), 1346-1351

Kotut K, Ballot A, & Krienitz L (2006). Toxic cyanobacteria and their toxins in standing waters of Kenya: implications for water resource use. Journal of water and health, 4 (2), 233-45 PMID: 16813016