As Many Exceptions As Rules

Wednesday, August 10, 2016

Gimme Some Dihydrogen Monoxide

Birds need water just like the rest of us,

but beaks make it harder. They may suck

it up like a straw or scoop it up like a bucket,

or by leaning back and letting the rain fall in.

At some point or another we've all said, “I’m about to die of thirst.” Of course we can only survive for a few short days without water, but do you know why?

Cells are full of salt water (saline), but are also crowded with proteins, carbohydrates and lipids (saline + organic molecules = cytoplasm). This suggests the importance of H₂O, but it doesn’t say anything about the reasons behind its importance.

Water is the solvent (the liquid part of a solution), while the proteins and carbohydrates are the solutes (the solids dissolved in the solvent). Lipids (a type of fat) are insoluble in water; therefore, they are good for building cell membranes. They help keep what is in in, and what is out out. With a lipid membrane, our cytoplasm doesn't leak out on to the floor.

Cytoplasm isn’t water plus some organelles. As shown in

this electron micrograph, it is more like a gel, packed

with organelles, proteins, minerals, sugars, and nucleic

acids. There is water, but just enough to separate the other

constituents. Photomicrograph credit: Dr. Jeremy Burgess/Science

Photo Library.

The intracellular solutes are surrounded by water. It’s like the green jello with pineapple that your Aunt brought every Christmas, except that it's packed to the gills with pineapple. Cytoplasm is more crowded than the public pool on a 104˚F day when the ice cream vendors have gone on strike. In some cases, there may only be a few molecules of water separating different cellular components, but this water layer is crucial.

Water is the solvent in which most cellular reactions take place. Water is made up of an acid (H⁺) and a base (hydroxyl, OH^-). Together, they are two hydrogen atoms and one oxygen, H₂O! Having the H⁺ around keeps the bases in check, while the OH^- keeps the acids in check. This helps keep the cytoplasmic pH within a small range (buffers it), about 7.35-7.45. Buffering the cytoplasm ensures that that reactions proceed in the proper direction and at the proper rate.

Water transports materials within the cell, from cell to cell, and through the blood and lymph. The partial negative and positive charges, the high surface tension, and the cohesive properties of water make it good at its jobs.

Water being sucked up in a capillary tube

uses cohesion (water sticking to water) and

adhesion (water sticking to the glass tube).

Water likes to bond to itself (cohesion) via hydrogen bonds formed between the positive H⁺’s of one water molecule and the negative OH^-‘s of two others. Cohesion is what makes water form drops as it rains, and what gives water its strong surface tension. Surface tension is why some insects can land on water and take off again. Water striders (family Gerridae), walk on water and you can actually see the depression in the surface, like when you stand on your bed. They are helped out in this endeavor by hydrophobic (water-fearing) tiny hairs on their legs and feet.

Water also likes to hydrogen bond other surfaces; this is called adhesion. If you pour water into a small diameter glass, you can see it cling to the side (meniscus, Greek for crescent), and even seem to rise up the side of the glass (see the image above). If the glass tube is narrow enough, like in a capillary tube, the water will climb up the tube against gravity. The force that drives this is adhesion.

Water striders spread their weight over a large area to

reduce their pressure on the water. They are also helped

by the hydrophobic proteins on their legs. But mostly, the cohesive

force of the water raises the surface tension so the strider

remains on the surface.

The adhesive force is driven by the bipolar (a negative end and a positive end) nature of water, just as with cohesion. The positive H⁺ is attracted to any negative molecules, and the negative OH^- is attracted to anything positive. Together, they are attracted to most everything, not just other water molecules.

Hydrogen bonding and the adhesion and cohesion they produce are important for plants. How does water absorbed by a redwood’s roots get to its leaves way up high? The mechanism has several features, the most important of which is suction. When water in the leaves evaporates, it creates negative pressure that actually pulls the water up from the roots through the plants vessels.

The negative pressure alone isn’t strong enough to keep the water moving against gravity, but when you add in the cohesion of water molecules to one another, and adhesion of the water molecules to the sides of the vessels, it all works out. The sum total of these actions is called transpiration, and is responsible for moving water against gravity in plants.

Water also participates in many cellular reactions, most famously photosynthesis. During the Calvin cycle of photosynthesis (dark reactions) glucose is produced, water is split into hydrogen atoms that are incorporated into the growing carbohydrate and gaseous oxygen (O₂) that is released. It is this transformation of water to gas that drives transpiration. In cellular respiration, when carbohydrates are used to produce chemical energy (ATP), the exact opposite occurs – water is formed from oxygen and hydrogen.

Other cellular reactions, such as the hydrolysis (hydro = water and lyse = split) of fats or proteins are occurring inside cells all the time. In these types of reactions, a water molecule is split into H and OH while the target molecule is also split in two; one part gains a hydrogen and the other gains a hydroxyl group. This is crucial for the normal degradation of cellular proteins by protease enzymes, amongst other things.

If that wasn’t enough, water acts as temperature buffer, helping organisms hold a more constant temperature. Water does not warm up fast and it does not cool down fast; it tends to keep an even temperature. It has a high specific heat (1 calorie/gram C˚), meaning that you must add a lot of energy in order to change its temperature. Water’s high specific heat evens out temperature fluctuations in the body and allows reactions to proceed in a controlled fashion.

Finally, many organisms use water pressure to hold their form, an example of the turgor pressure we learned about several weeks ago (Plants That Don’t Get A Good Night’s Sleep). For instance, you return home from a trip to find your plants have turned brown and are drooping in their pots. Your goldfish are belly up, and the expensive six-pack in your fridge is now a two pack – the neighbor you asked to look after them did a bang up job. If you’re lucky, the plants stand back up a few hours after a good soaking, especially if you fertilize them with your goldfish carcasses. Your plants need the water for everything we have discussed, but also because the water pressure in the cells keeps them the plant stem and leaves standing rigid.

The tube feet of starfish and other eichinoderms have a

suction cup on the end of the podia. The internal portion

is the ampulla, the tube that holds water to regulate the

tube movement.

In a similar fashion, starfish store and move water through a series of hollow tubes to form a hydrostatic skeleton. In the general sense, this type of skeleton is any fluid filled cavity surrounded by muscle, in which the actions of the muscles work against the fluid pressure in the cavity. Worms, and many other invertebrates have this type of support system.

But starfish take the concept a bit further. Not only is water used to maintain the form and structure of the animal; it makes up the water vascular system for locomotion (tube feet), food transport, and respiration. By moving water in and out of specific tubes in the different arms, the muscles contract and extend the tube feet, pushing them against a surface. The movement of water in and out of the tube feet is also the primary way to move oxygen into the tissues of the starfish, and the water pressure can be used to evert their stomach (it will protrude out their mouth and turn inside out) to surround and engulf food. Ugh!

Many types of animals use hydrostatic skeletons, where the pressure of water substitutes for a rigid skeleton. Muscular movements are generated against the in agonist/antagonist form against the pressure of the water, using muscular fibers positioned in several planes. A recent review by William M. Kier demonstrates how the hydrostatic skeletons and muscular arrangements of several different animals work to generate stiffness as well as movement.

For instance, in the tube feet of the starfish, Ludia clathrata, muscular fibers are oriented in longitudinal and circular directions, allowing for extrusion and contraction. But he also discusses the connective tissue fibers that are just as important for the limiting of movement and generation of tension.

We always knew water was crucial for life, and now we know why. Its importance is reinforced when you consider how much water there is in different organisms. Humans are about 60% water by mass, but it varies from person to person. Younger children are normally have a slightly higher percentage of water, maybe 70%, while morbidly obese people have much less water, remember that fat is stored in the absence of water (Is it Hot in Here or is it Just My Philodendron?).

The golden barrel cactus has ribs that can expand and

contract, depending on the hydration state of the plant.

It is also called a mother-in-law’s cushion….that’s just mean.

Plants require even more water. Cactuses can be more than 90% water after a good rainfall. The places where cacti grow have variable water availability, so when water is present, they must take advantage. The endangered golden barrel cactus has ribs that can expand to take in more water. In addition, the golden barrel cactus is round to reduce surface area and has a thick waxy surface, both of which reduce water loss.

Despite these dehydration prevention measures, cacti still lose water over time, and it might not be replaced for a long time. Therefore, cacti have evolved mechanisms to withstand the loss of almost 60% of their water without any negative ramifications. In this area, they are the exception. Typical flowers and trees can only withstand a 20% water loss without damage; however, this is still much better than humans can do.

No matter what your personal water percentage might be, you can only afford to lose about 5% of your water without suffering symptoms. At mild levels of dehydration (5%), you may feel groggy or get a headache. Higher levels of water loss will bring tingling in the muscles, nausea, and confusion. If the loss reaches 10-15%, there can be muscle spasms, delirium, and the kidneys may be permanently damaged (if water loss is held for a sufficient period). Held above 15%, dehydration is usually fatal. However, athletes can lose up to 30% of their body water in the short term, but it must be replenished immediately so that performance or normal function will not be compromised.

When we say normal function, we mean those functions of water we have mentioned, but also several others we haven’t. Water, along with surfactant proteins, works to keep our lungs absorbing oxygen. Water lubricates our joints and tissues to avoid friction damage. People with xerostomia (Greek, xero = dry and stoma = mouth) or xerophthalmia (dry eyes) use artificial saliva or tears to prevent damage to mucous membranes. Finally, water acts as a cushion, absorbing pressure and force to protect our organs from traumatic damage, like a punch to the gut.

Damage can come in many forms when water is low, so all living organisms require water intake to function and remain safe, right?……Or is just most organisms? Next time.

Kier, W. (2012). The diversity of hydrostatic skeletons Journal of Experimental Biology, 215 (8), 1247-1257 DOI: 10.1242/jeb.056549

For more information, classroom activities, or laboratories about water in biology, the properties of water, transpiration, or the Calvin cycle, see:

Water in biology –

http://www.amnh.org/exhibitions/water/?section=lifeinwater&page=lifeinwater_f

http://www.everydayhealth.com/water-health/water-body-health.aspx

www.coastalcoolers.com/body.pdf

http://www.chemcraft.net/wbody.html

http://www.rawfoodexplained.com/water/waters-role-in-the-body.html

http://www.weightlossunit.com/Pages/Healthy_eating_articles/role_of_water_in_human_body.html

properties of water –

http://www.uni.edu/~iowawet/H2OProperties.html

http://faculty.rcoe.appstate.edu/goodmanjm/asuscienceed/background/waterdrops/waterdrops.html

http://hyperphysics.phy-astr.gsu.edu/hbase/surten.html

http://daphne.palomar.edu/jthorngren/water.htm

http://www.youtube.com/watch?v=LrNwcxMWJ68

http://www.physicalgeography.net/fundamentals/8a.html

http://propertiesofwater.org/

http://www.watereducation.utah.gov/WaterScience/Properties/default.asp

http://aquarius.nasa.gov/prop_fresh_sea.html

www.uas.alaska.edu/attac/ampdf/activity3.pd

www.edinformatics.com/math_science/water_ice.htm

transpiration –

http://ga.water.usgs.gov/edu/watercycletranspiration.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transpiration.html

http://www.phschool.com/science/biology_place/labbench/lab9/intro.html

http://www.biologymad.com/resources/transpiration.swf

http://extension.oregonstate.edu/mg/botany/transpir.html

http://www.eoearth.org/article/Transpiration

http://www.youtube.com/watch?v=U4rzLhz4HHk

www.ucar.edu/learn/1_4_2_18t.htm

http://www.sciencebob.com/blog/?p=162

http://beckyboop.wordpress.com/2011/03/22/plant-transpiration-lesson-plan/

http://www.learnnc.org/lp/pages/3600

calvin cycle –

http://www.science.smith.edu/departments/Biology/Bio231/calvin.html

http://www.bio.umass.edu/biology/conn.river/calvin.html

http://highered.mcgraw-hill.com/sites/0070960526/student_view0/chapter5/animation_quiz_1.html

http://www.youtube.com/watch?v=_NIhg1qa_L0

http://www.khanacademy.org/video/photosynthesis---calvin-cycle?playlist=Biology

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CalvinCycle.html

http://sites.bio.indiana.edu/~hangarterlab/courses/b373/lecturenotes/photosyn/carbon/c3.html

http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/dark.htm

http://www.johnkyrk.com/photosynthesisdark.html

http://www.educationalrap.com/song/photosynthesis.html

Wednesday, August 3, 2016

No Introductions Necessary?

Biology concepts – introduced species, invasive species,

The United States is a melting pot, and it is one of our

greatest strengths. The questions is, is it also a good

idea for plants and animals?

The United States is an amazing place to live; nearly everyone’s family is from some place else. But if you ask the people you meet on any given day, they will likely say they are from the USA. Most have had time to assimilate and find their niche in their family’s adopted homeland. Can you name a place on Earth where this situation applies to its animals and plants?

If a place like this existed, it would probably be some place young. It would probably also be someplace isolated, where the exchange of species would not have been easy. Sounds like an island to me; probably a volcanic island(s), something like the big island of Hawaii, in a chain that is only 300,000 years old….. O.K., it is the big island of Hawaii.

Hawaii is the biggest and youngest of the Hawaiian Islands.

Formed from five active volcanoes, it is growing larger

everyday.

Since they are islands, it makes sense that many of Hawaii's species came from somewhere else. A key question is, how did they get there? If seeds were brought by migratory birds or washed up on shore, or if an animal wasn’t quite dead when a predatory bird dropped it on the island, that’s one thing. But if humans brought plants or animals and released them by accident or deliberately, that is something else.

History shows the latter mechanism has been responsible for most of the diversity in Hawaii. Estimates are that the rate of species introduction in Hawaii has outpaced the natural rate of diversification by 2 million times. Over half of the island’s plants species are there because of people, not nature.

Many of the plants and animals that have been brought to Hawaii were introduced deliberately, but that is not the definition of an introduced species. Whether an organism is imported and released to serve some specific purpose, or whether it is a stowaway on a ship or otherwise unknowingly allowed to get loose, it is an introduced species (also called neozoon, alien, exotic, non-indigenous, or non-native species). Introduced species are those plants and animals living outside their native range due to some human intervention, whether intentional or not. For Hawaii, this began in the 19^th century.

The Hawaiian monk seal is known as

Ilio‐holo‐i‐ka‐uaua in Hawaiian,

meaning, “the dog that runs in

rough waters.” They are critically

endangered, with only about 1100

remaining individuals.

Hawaii has only two native mammals, the Hawaiian monk seal (Monachus schauinslandi) and the Hawaiian hoary bat (Lasiurus cinereus semotus), and no native terrestrial (land) mammals. Many other mammals were introduced in the name of making money, like cattle and goats, while others were brought in specifically to make hunting more enjoyable.

In the last few posts, we have been discussing the activity patterns of different organisms, and we suggested that the organisms that interact most likely have the same or overlapping activity patterns. A tragic story illustrating this concept has played itself out in Hawaii since the late 1800’s.

Ladd & Company (from Maine) had established a lucrative sugar industry on the big island by 1834, and this increased the ship traffic in and out of Hawaii. The ships brought rats, an all too common introduced species.

In Jamaica, the problem of rats in the sugar cane fields was an old one. A successful sugar planter, W.B. Espeut, thought that introducing the Indian mongoose to the sugar cane fields could help with their rat problem. Apparently it did, and Espeut told everyone he could find. Subsequently, 72 mongooses were brought to the big island in 1883. There were some objections raised in the local papers, but as with most good ideas, they were roundly dismissed.

It is sad that mongooses

in Hawaii are causing damage, while

at the same time, mongooses are

endangered in their native India

due to habitat loss.

The problems became apparent not too long after mongoose introduction. In Jamaica there is a predator that eats mongooses, the fer-de-lance snake, but no such predator in Hawaii. What is the number one cause of death for mongooses in Hawaii? Old age!

No predator means unfettered reproduction, and female mongooses can have two litters each year. The result has been lots of mongooses, all looking for a meal and a mate.

Did all these Hawaiian mongooses do their job, did they get rid of the rats? Not really, and this is where a biology class could have helped. Mongooses are diurnal, they hunt during the day, but the rats on Hawaii are nocturnal. Oops. You would have thought someone might have noticed that beforehand.

I’m sure the odd mongoose runs into the odd rat as one goes to bed and the other begins its day, but that isn’t enough to force either species to adapt; everyone is happy keeping to his old schedule. Now Hawaii has too many rats and too many mongooses.

Mongooses (mongeese?) will eat almost anything (fruits, snails, mammals, insects, amphibians, lizards, spiders), but they really like bird eggs. Many species of bird in Hawaii, including the Nene (Hawaiian goose, the state bird) are on the brink of extinction because of the mongoose.

The story of the mongoose and the rat illustrates another point. Not only are there few mammals on Hawaii, there are even fewer native predators. As a result, many animals and plants that happen to be from Hawaii originally (or least for a long time) have adapted to this lack of predators by not developing defense mechanisms. This is an advantage, in that energy normally spent on defense can be saved for other metabolic or reproductive activities. Nature always wants to reroute energy if it is being used unnecessarily.

But, if predators are then introduced (and they were by the bucketful after Western Europeans and Americans became involved) the native animals are particularly at risk. The lack of native predators and the introduction of alien predators is illustrated by the case of the western yellow jacket. Though often mistaken for a bee, the yellow jacket is actually a wasp, and a nasty one at that.

Western yellow jackets have a smooth

stinger, so they can sting multiple

times. However, they rarely sting when

away from their nest.

The yellow jacket is an example of an accidentally introduced species, arriving in a shipment of Christmas trees. Law required that a percentage of the trees be shaken to knock off insects before shipment, but the required percentage of shaken trees was apparently too small, or the time shaken was too short, because it didn’t work.

In the continental U.S., the yellow jacket forms an annual nest and starts over building a colony each spring, but in the warmer climate of Hawaii, the species has become perennial, with nests as large as an SUV – more like a Lincoln Navigator, not the small Honda CR-V.

The yellow jacket is a carnivorous wasp only as a larva. The adults eat only nectar, but acquire meat to feed their young. This has decimated native Hawaii insect species, which in turn has reduced the amount of food available to bird species. In addition to insects, the wasps will devour dead birds and other large vertebrates, but will kill lizards and amphibians to feed their young.

In addition to accidentally introduced species, there are many feral (fera in Latin = wild beast) species on the big island. Feral species are animals that were domesticated, but have returned to the wild and propagated there. Their freedom could have come by accident or on purpose, as with cats and dogs in the cities. We call them strays, but they are correctly referred to as feral.

The stories of sewer alligators inspired sculptor

Tom Otterness to create a slightly scary piece in

bronze. It is located in a14^th Street subway station

in NYC.

All those alligators in the sewers of NYC aren’t feral, because they were never domesticated. And yes, alligators have been caught in the sewers of NYC; the latest Time and Post articles I could find were from August of 2010. They don’t live for years, grow to be monsters, or reproduce - but small ones, probably recently released, are found just about every year.

In most cases, feral animals cause problems and don’t offer many advantages. They can act as reservoirs of disease, compete with native species for resources, prey on indigenous species and eat native plants.

If there are benefits to feral animals, they will depend on your view of things. Some ranchers can make money by rounding up feral cattle or horses. Feral canines provide an income for the town dogcatcher. Stray cats can help keep the rodent population down; there seem to be many advocates for feral cats. There is even a website that advertises all the wonderful things about sterilized feral cats. Really? They want to catch them, sterilize them, and then release them again?

Literally, thousands of plants and animals of all kinds have been introduced to the big island, and now we get to the crux of the issue – introduced species that become invasive species, ie. those that do damage to the natural ecosystem by becoming dominant by killing or displacing native species. The question is – which is the exception, introduced species that become invasive and do damage, or introduced species that do little damage or even result in a benefit?

On the negative side, we have talked about the Hawaiian mongooses, rats, and yellow jackets. There are others; feral pigs and cattle graze on native grasses and other plants. The Formosan ground termite causes millions of dollars of damage to trees and structures each year. Alien plants, such as Florida prickly blackberry and molasses grass smother native vegetation and prevent their re-establishment. As a result of these and other invasives, Hawaii has more endangered species per square mile than any other place on earth. This is due, at least in part, to invasive species.

Other introductions have been moot. For instance, over 4,600 species of plants have been introduced into the Hawaiian Islands over the last 200 years. However, only 86, less than 2% of the total, have become serious problems for native ecosystems.

Horses were introduced to the Americas

by the Spanish in the 16^th century, as were sheep and

cattle. De Soto brought 13 pigs to Tampa Bay in

1539; these were the ancestors of the razorbacks

of the Southeast… and the University of Arkansas.

Some introductions have been wildly successful. Indeed, most of the cultivated crops (except for corn, turkeys, tomatoes, potatoes, and peanuts) and livestock animals in the continental U.S. are introduced species. Your pet cat, dog, bird, fish, or snake is probably an introduced species as well.

Of the approximately 5,000 alien animal and plant species in Hawaii, only about 300 to 500 have gone on to wreak significant damage and some have been beneficial. So the question remains, which are the exceptions- the failures and accidents that have resulted in destruction, or the successes and the accidental introductions that have had negligible effects?

Websites are full of lists of invasive species, the species they are displacing and the lost resources due to their introduction. We don’t see lists of introduced species that have worked out just fine. Perhaps this is as it should be; attention should be paid to those problems that need to be resolved. Attention should also be focused on the failures as a learning opportunity when future introductions are contemplated. But don't assume that a species is a problem just because it was introduced.

Lemoine NP, Burkepile DE, & Parker JD (2016). Quantifying Differences Between Native and Introduced Species. Trends in ecology & evolution, 31 (5), 372-81 PMID: 26965001

Nelson FB, Brown GP, Shilton C, & Shine R (2015). Helpful invaders: Can cane toads reduce the parasite burdens of native frogs? International journal for parasitology. Parasites and wildlife, 4 (3), 295-300 PMID: 26236630

For more information, classroom activities and laboratories on introduced and invasive species, see:

Introduced species –

http://www.gcrio.org/CONSEQUENCES/vol2no2/article2.html

http://amphibiaweb.org/declines/IntroSp.html

http://alic.arid.arizona.edu/invasive/sub2/p7.shtml

http://www.flmnh.ufl.edu/fish/southflorida/introducedspecies.html

http://www.saburchill.com/hfns02/chapters/chap022f.html

http://www.physorg.com/news/2011-01-australian.html

http://www.hawaiianencyclopedia.com/polynesian-introduced-plants.asp

http://www.expedition360.com/australia_lessons_esd/2001/09/introduced_species_the_rabbit.html

Invasive species –

http://www.invasivespeciesinfo.gov/

http://www.fs.fed.us/pnw/invasives/index.shtml

http://ei.cornell.edu/ecology/invspec/

http://www.invasivespeciesinfo.gov/resources/educk12.shtml

http://www.oar.noaa.gov/spotlite/archive/spot_illinois.html

http://www.nationalgeographic.com/xpeditions/lessons/14/g68/newsinvasive.html

http://www.fws.gov/invasives/is-activities.html

http://www.nhptv.org/natureworks/nwep15tg.htm

http://www.utoledo.edu/nsm/lec/gk12_grant/Invasive_Species_Game_.html

Saturday, July 30, 2016

What Do You Know, I Wrote A Book!

This post has little to do with biological exceptions, but if you find the writing on this blog at all appealing, then perhaps you will like this topic as well. I have finished a book for Springer Scientific Publishing, and this book is now ready for pre-ordering and e-book sales. The book is entitled, The Realization of Star Trek Technologies: The Science, Not Fiction, Behind Brain Implants, Plasma Shields, Quantum Computing, and More.

A new Star Trek movie was just released, and September marks the 50th anniversary of the airing of the first episodes of the original Star Trek series. To mark the occasion, I have investigated just how close science is to producing all those great technologies introduced in the various Star Trek series and movies.

As I started my research, it soon became apparent that some technological goals presented in the shows have been met and even surpassed (cell phones, tablet computers, talking computers, hand held scanners, etc.). But more surprising was how far science has come in producing working versions of larger technologies.

Would you believe that lasers have been produced that can pull objects toward the source of the light. That's a tractor beam to you people less interested in Sci-Fi. Even more amazing, brain implants are on the market right now that can restore vision to the blind, a la Geordi's VISOR. They even have the ability to see beyond visible light, just like Commander La Forge could.

Perhaps the two most amazing advances are in the areas of cloaking devices and teletransportation. Engineers and physicists can render objects invisible to wavelengths of light, allowing someone to sense what is behind the object as if it weren't there at all. That's a true cloak, not a trick with mirrors or cameras. And finally, transporters may be decades away, but scientists have begun to teletransport energy, atoms and information from one place to another - without ever existing anywhere in between. The distance record is now farther than what would be needed to transport things from space to the Earth's surface.

In all, nine Star Trek technologies are discussed in the book, including how they are used in the franchise, how they are explained to function, and how prophetic the creators were - the ways things really work is so close to how they were predicted.

The hard copy, e-book, and individual chapters can be pre-ordered from Springer Scientific Publishing: http://www.springer.com/us/book/9783319409122

or from Amazon Books: https://www.amazon.com/Realization-Star-Trek-Technologies-Intelligence/dp/3319409123/ref=zg_bs_226507_8

The hard copy of the book should be available for shipping in September.

Here endeth the commercial.

mark

Wednesday, July 27, 2016

The Nature Of Science Of Nature

I have judged many a science fair project in my

day. It is a learning experience, so adherence to

the steps of the scientific method taught in most

classes is O.K. But the students should realize

that there isn’t just one scientific method. This

young lady’s strategy was to take all the available

time and be the only project that got judged;

therefore, she's the winner.

A summary of the usual (but hopefully disappearing) lecture on the scientific method –

1. Define a problem

2. Research what is known

3. Hypothesize a cause

4. Test your hypothesis

5. Analyze your results

6. Support or refute your hypothesis

In the next few class periods, a few examples are identified and the class works through them. And there is always the "design an experiment to prove your hypothesis."

The question of the day:

Is this the only method to conduct science?

I don’t have room to go into all the things that are wrong with the process as it is enumerated above, but let’s hit a couple.

One big problem is the idea of supporting or refuting your hypothesis (hypo = under, and thesis = proposition; a supporting basis for an argument). True, your experiment may do one or the other, but it doesn’t have to. Many experiments end up with ambiguous results, especially if the scientist is doing his or her job.

I am using this picture because I couldn’t find a

way to work the quote into the post. But in truth,

science is like life, better results often come from

many trials. So... science is like life which is like
science.

The design of the experiment should minimize any confounding effects that would render the results less than explicit. But, as the old saying goes, “You don’t know what you don’t know.” The middle of an experiment is often a learning moment. It is when you get into a study that you find the things that are going to make the study useless. Then you go back and design a better experiment.

Let’s say you have designed an experiment that will have a definitive result. What result are you going for? Most will say that you are trying to see if your hypothesis is supported. But anyone can design an experiment to give a desired result. Your hypothesis says “A” should occur if you do “B,” so you design an experiment to make sure “A” occurs. It doesn’t even have to be a conscious effort, your design will just tend toward that result.

A truly scientific experiment is designed to REFUTE your hypothesis. You design an experiment to prove your hypothesis is not true. If, under those, conditions, your hypothesis is still supported, then you really have something. If a scientist tries his/her best to refute their own hypothesis and can’t, the chances that the hypothesis is correct go way up. Then you report your results and let other scientists try to design an experiment to show your hypothesis is wrong. If they can’t do it either, then you are really onto something. Real scientists try to prove themselves wrong, not right. The big idea - you can never PROVE a hypothesis, you just have data to support it. But the next experiment may refute it. You can always design another experiment to test the hypothesis, so no hypothesis is ever proven absolutely. True science proceeds when you refute a hypothesis; only then can you make a concrete change to move closer to the truth.

Negative results and refuted hypotheses are the basis of science;

too bad they get a bad rap. Can you think of another profession

where being wrong is your goal?

This leads to the next problem implied by the process outlined above. It is usually taught that negative data is a bad thing. Even people in the profession often downplay the importance of negative data; ie. data that does not give a result that is publishable.

Editors don't get excited over studies saying we tried this and it didn't work. But, an experiment that doesn’t work isn’t necessarily bad – you can learn a lot from it and so can other scientists. Unfortunately, journals don’t like to publish this data, so those who might learn from it don’t get to hear it.

This is one reason why it is important for scientists to have meetings and talk to one another personally, not to just write journal manuscripts and funding applications. Case in point, it turns out that studies that show new drugs aren't cure-alls, that they don't do what they say or don't do it as well as they say don't published. Ben Goldacre gave a recent TED talk on the subject, and has numbers to back up his assertions that negative data studies on drug efficacies hardly ever see the light of day.

In fact, negative data is the most common data and often the most useful. Refuting your hypothesis is a type of negative data. When faced with this result, you modify or discard your hypothesis and try again. You can design a thousand experiments that support your hypothesis and still not prove that your idea is the true mechanism - you may just not have thought of the experiment to disprove it yet. Like we discussed above, just one experiment that DISPROVES your hypothesis results in a step forward. Like Thomas Edison said, "If I find 1000 ways something won't work, I haven't failed. I am not discouraged, because every wrong attempt discarded is another step forward."

Negative data truly moves us forward, in fact failing is the only way we move forward. But this still leaves a problem with the way science is taught. Is there good data that is neither positive or negative? We tend to think of data only as that information that supports or refutes a hypothesis, but do you have to have a hypothesis?

This is the black walnut tree (Juglans nigrans).

The one in our front yard is about 70 feet tall and

produces over 200-300 kg (500-650 lb) of fruit.
Black walnut dye comes from the husk, not the
nut, and is yellow when immature and black
when mature.

Consider an experiment I have been conducting for the last 13 years. We have a black walnut tree in our front yard, and I have been counting the number of black walnuts it drops every year since we moved in. I had no mechanism I was trying to define, I just wanted to know how many walnuts the tree produced.

Here is my data:

Year # of walnuts

2003 3662

2004 604

2005 3508

2006 368

2007 4917

2008 0

2009 6265

2010 0

2011 6395
2012 6
2013 2140
2014 159
2015 1825

Now, we can ask a question and hypothesize a mechanism? What is responsible for the pattern in nut production, and why do the results keep diverging? Does that mean that my original observations aren’t science? True – you could say that I was answering a question about how many nuts the tree produces, but I did not have a hypothesis that I was trying to dispute. This is true science, but not the kind we teach in school. Is the change in the pattern during the middle years accounted for by weather? Do the fewer nuts later mean that the tree is dying?

Black walnut meats are expensive because
they are hard to get out of the shell. But the

shell is also economically important, used in

paints, oil wells, explosives, cosmetics, cleaning

and polishing agents, and jet blasting of metallic

and plastic surfaces.

Try this experiment at your school. Find a tree and start to count the nuts, or find a sapling and count the leaves each year. You can keep this experiment going over a number of years, with each class adding their data.

But the real learning is in defining the limits and possible confounding effects that could lead to errors. Did the tree lose a limb and therefore produce fewer nuts the next year? Was there an explosion in the squirrel population, and they stole all the nuts before you could count them? What was the weather over the time period you observed, could a change in weather account for a change in number? Is there another walnut tree too close, and the nuts are getting mixed up? Am I just getting better at finding and counting the nuts each year?

Squirrels are kind cute, if you forgive them for

carrying rabies. Here, he represents one source

of possible error in my black walnut counts. Can

you assume that every year they steal about the

same percentage of nuts before I can count them?

I have asked these questions and am observing multiple parameters to see if they account for the pattern in nut production. But there may also be a biologic reason, something to do with energy output versus opportunity to produce offspring. All these items can be investigated and used to better explain the observations.

Each might be considered a hypothesis – the weather affects nut production, so you try to show that different weather years had the same nut production – hypothesis refuted. The squirrel population exploded – talk to the local nature experts, if the number has been fairly constant- hypothesis refuted. There is an almost infinite number of possible confounding effects, and your class can come up and test as many as their brains can think up. Now that is a true scientific method!

Ben Goldacre (2012). What doctors don't know about the drugs they prescribe. TED MED 2012

Wednesday, July 20, 2016

Take Off Your Coat And Stay Awhile

Biology concepts – thermoregulation, ectothermy, endothermy, genetic mutation

Let me introduce you to the most wondrous animal on the surface of the Earth, or under the surface of the Earth – the naked mole rat, Heterocephalus glaber (hetero = different and cephalus = headed, refers to the fact that it lives in a colony where different members have different jobs; glaber = smooth skin).

Why, you ask, is this pruny thumb with two eyes the most incredible animal? Its odd looks and cutsie pink color belie the fact that this rodent is the most heinous rule breaker in all the biological world. It hasn’t meant a convention it wouldn't defy or a norm at which it wouldn’t thumb its nose.

Meet H. glaber, the naked mole rat. He has teeth, pink skin, and a probable

inferiority complex. The right image shows that H. glaber is not much bigger

than the thumb he resembles.

Take for instance, its name – NAKED mole rat. It is a mammal, but it’s naked. Mammals are always covered with hair or fur, but not his guy. Even we humans, the most hairless of all the apes (except for Robin Williams, he looks like he wears a sweater into the pool), look like we’re covered in fur compared to this rodent.

Look at yourself in a mirror. There’s hair on top of your head (well at least most of you). There is fine, unpigmented vellus hair (vellus = fleece in latin) that we know as peach fuzz, on your arms and legs when young and more coarse hair when older. You see eyebrows, and nose hairs as well. There is hardly a spot on us that isn’t hairy, save the palms of our hands to increase friction for gripping, and the soles of our feet, probably to keep it from tickling when we walk.

H. glaber eschews all this hair, but even he isn’t completely naked. From the picture, you can see the several sets of whiskers protruding from the wrinkly pink face that only a very devoted mother could love. The whiskers are crucial to helping the mole rat make its way in its surroundings, and therefore have not been lost, but why on Earth is it nearly naked?

The horn of Africa, a great place not to be noticed, and hot enough

to make underground living a plus.

The reason lies in how and where the naked mole rat lives. Found only in the desert of the horn of Africa (Ethiopia, Kenya, Somalia, Eritrea), this rodent that is neither a mole nor a rat lives underground its entire life. It burrows to find roots to nibble on, and they can be few and far between – it’s a desert for crying out loud!

In its tunnels, body hair imparts no advantage, and can contribute to negative outcomes, such as carriage of parasites (this is why scientists believe humans lost most of their hair), overheating, or getting stuck in narrow spaces. The mole rat’s skin helps with this last problem, although it seems counter-intuitive. Defensive lineman in football like to wear very tight uniforms so that the offense has nothing to grab a hold of, and it would follow that a tight skin on the naked mole rat would also help it slide around and not get caught on anything.

But the advantage to big skin is that the rat can turn around almost completely in its uniform, and dig from any direction to move itself along. Like the owl that can turn its head 270˚, the naked mole rat can rotate its whole body to get out of a jam. That loose skin is also helpful in traffic jams; mole rats can slip past one another in a tunnel without even slowing down.

The whiskers serve to guide the mole rat around in its dark environment. It feels its way, it feels for its food, and it feels other mole rats that it may meet in the tunnels. Therefore, the hairs it has kept serve a definite purpose, and one can see why there are whiskers along its entire body, as opposed to just around its nose (see photograph above).

Other mammals might appear to hairless, some even have it in their name, but they don’t match H. glaber for nakedness on an overall basis. Rhinoceroses, elephants, pigs, they all have coarse hair on many parts of their bodies, so they can’t compete for the world hairlessness title. Even marine mammals like whales and dolphins have some hair (mostly when they are younger) and have nose hairs as well (so I’m told – I never looked up a dolphin’s nose). The Sphynx cat is supposedly hairless, but its entire body is covered in vellus hair.

Dolphins have whisker as infants, and the whisker pits help sense electrical fields. The Sphynx cat was revered by the ancient Egyptians, which was fine, because the Egyptians shaved off most of their own hair. On the right, the Xoloitzcuintli was said by the Aztecs to guard human souls in the underworld. It looks intimidating enough to be good at that.

Finally, there is the Mexican hairless breed of dog, properly called the Xoloitzcuintli or Xoloitzcuintle. While some of these dogs are completely hairless, it is a mutation rather than normally occurring. Hairlessness is the dominant form of the mutation, but even most of these animals have hair on their heads and tails. It is less common that the dog is completely hairless.

Powder was a 1995 movie about a young man with alopecia

universalis amidst other issues, like psychokinesis and a lack

of sun exposure.

Humans can also be hairless, called Alopecia universalis (alopecia is Greek for “fox mange” and universalis means everywhere). The condition is an autoimmune disorder, meaning that our own immune system has decided that our hair follicles are no longer part of us and are attacked as being foreign. Many human diseases can be autoimmune in origin, including diabetes and muscular dystrophy.

But of all the animals mentioned, H. glaber takes the crown as hairlessiest! And it serves a good purpose. Along with living underground, living in a community, having smooth skin, living in a desert, and having a limited food source – these features have contributed to another decision nature has thrust on H. glaber, it is ectothermic! It doesn’t warm itself, rather it assumes the temperature of its surroundings. Is that any way for a self-respecting mammal to behave?

In the cold, hair traps air and keeps it close to the body to act as thermal insulation. However, H. glaber is communal, and they have larger chambers in which they all huddle together during sleep. Over the course of the cold desert night, the mole rats will rotate positions, so no one animal is on the outside for too long, much like penguins do in Antarctica. This keeps them warm and negates the need for hair as an insulator.

The communal sleeping is just one aspect of the social life of H. glaber. There are one of only two eusocial mammals. The have a queen and a caste system, like many bees and ants. A recent study shows that the queen is very important to the building of the tunnels, as well as all aspects of H. glaber life.

The tunnels of each worker may be widened to form sleeping chambers or pup rearing chambers, but which. The 2012 study indicates that the presence of the queen will increase the dirt moving by all castes, while workers will work more than the others if she is not present. What is more, the odor of the queen is enough to increase the dirt moving in a particular area, so her movements do influence the geometry of the nest.

An arrector pili muscle is attached to every hair on your body. You can

see that if it contracts (shortens), the hair will stand up. Thank you,

black cat for the Halloweenish demonstration.

Hair can also act to dissipate heat. In most mammals, each hair is attached to a small muscle (arrector pilori; pili is the plural) that can stand the hair on end and release the trapped warm next to the body, cooler air will then carry the heat away from the skin and the hairs, thereby reducing the temperature of the animal. Interestingly, this same action is seen when we get scared. The fright or flight release of adrenaline causes the arrector pili muscles to contract; think of how a cat’s tail gets bushy and the hair on its back stands up when scared. The arrector pilli muscles will also spasm in an effort to produce added heat when the skin gets cold (goose bumps).

Being underground all the time means that H. glaber is protected from the most intense heat of the desert day and therefore needs fewer thermoregulatory mechanisms. So, the naked mole rat doesn’t need to dissipate heat via the arrector pilli action.

Finally, by practicing ectothermy, the naked mole rats reduce the amount of food they have to consume; they don’t need all that energy to produce heat and maintain a constant temperature. This works out well for them, since they live in the desert where there isn’t a heck of a lot food for them anyway. Could H. glaber have ended up as anything other than ectothermic? Its design just makes too much sense for its environment. We could learn a thing or three from how nature has tweaked its design.

And we have only scratched the surface of the ways that this rodent refuses to conform to established biological norms. Future posts will introduce more aspects of this amazing animal’s physiology, including longevity, pathology (or lack thereof), social structure, senses, immunity, biochemistry, and reproduction.

But you’ll have to wait for those stories. Next time we will turn our attention to a necessity of all life, sleep. But aren’t we learning that no single characteristic applies to ALL life – there’s always an exception.

Kutsukake, N., Inada, M., Sakamoto, S., & Okanoya, K. (2012). A Distinct Role of the Queen in Coordinated Workload and Soil Distribution in Eusocial Naked Mole-Rats PLoS ONE, 7 (9) DOI: 10.1371/journal.pone.0044584

For additional information, classroom activities or laboratories on H. glaber, animal hair, alopecia universalis, arrector pili:

H. glaber –

http://www.digimorph.org/specimens/Heterocephalus_glaber/

http://animals.nationalgeographic.com/animals/mammals/naked-mole-rat/

http://nationalzoo.si.edu/publications/zoogoer/2002/3/nakedmolerats.cfm

http://www.npr.org/2011/10/13/141313080/-re-exposed-naked-mole-rat-genome-sequenced

http://www.bristolzoo.org.uk/naked-mole-rat

http://www.pbs.org/wnet/nature/lessons/ugly-says-who/lesson/422/

www.brookfieldzoo.org/pagegen/inc/whattodo.pdf

http://www.torontozoo.com/ExploretheZoo/AnimalDetails.asp?pg=622

http://www.sciencedaily.com/releases/2009/03/090305171903.htm

http://www.youtube.com/watch?v=AX94UtcRu14

http://www.youtube.com/watch?v=fj48ewrkSFQ