You Must First Invent the Universe…

By Rich Feldenberg

This year Carl Sagan Day is being celebrated Saturday, November 14th. Sagan, who was born on November 9th, 1934 has been an inspiration to generations of scientists and science enthusiasts. Unfortunately, he passed away on December 20th, 1996 at the age of 62. Way too young, and certainly way too soon for a world that desperately needed his carefully measured dose of rationality, skepticism, and his poetic style of revealing the awe of the cosmos we inhabit together.

There are many great and inspiring Sagan quotes, or Saganisms as they’ve come to be known, but one of my favorites is, “If you want to make and apple pie from scratch, you must first invent the universe”. The meaning, of course, gets one to think deeper about where the origin for all the things we take for granted actually came from. The ingredients for an apple pie may include things like apples, flour, sugar, eggs, salt, etc. But where to these ingredients come from? To get these ingredients you must first invent a universe with laws like our own, that can lead to the formation of galaxies full of stars, which can fuse hydrogen atoms into heavier elements, which can then form planets. Some of these planets must have conditions that allow life to arise, which can evolve into things like apple trees and chickens (for the apples and eggs respectively) and for the evolution of intelligent beings that can put them together to make an apple pie. Some of the ingredients, like the salt (NaCl) and water (H2O), are relatively easy to produce, and just require the hundreds of millions of years necessary for stars to produce the heavy elements oxygen, sodium, and chloride (the hydrogen for the water was produced in the Big Bang itself). The other ingredients require billions of years in the making, for life forms and their evolution to take place. How brilliant and wonderful and simple a statement to make. Many people around the globe, that continue to honor and remember Carl make it a tradition to eat a slice of apple pie on Carl Sagan day. I know I plan to have a piece this year!

Sagan was an Astronomer, and one of the first astrobiologists. He was involved in important scientific research on the atmospheric composition of Venus and Mars. He played a major role in the Viking mission to Mars and the Voyager probes to the outer solar system. And, of course, he made communicating scientific findings to the public, and demonstrating the importance of the scientific process, a priority.

When I was growing up, the book Cosmos and the mini-series, by the same name, came out. Both were inspiring, thought provoking, and in some ways life altering, and Sagan tackled everything from Astronomy, evolution, the brain, and the importance of being skeptical of pseudoscientific claims. He had a mesmerizing way of delivering his message with intelligence and passion. The TV series was recently redone by Astrophysicist and science communicator, Neil Degrasse Tyson, who didn’t attempt to remake the original episodes, but who did an excellent job of continuing on where Sagan left off.

Sagan also wrote quite a few other excellent books. These included, “The Dragons of Eden”, “Broca’s Brain”, “The Demon Haunted World”, and “Billions and Billions”. These books really fueled my scientific curiosity growing up, as I’m sure they have done for many others who grew up to love science. After all these years, his books are still worth reading, if you haven’t done so already. He also wrote the science fiction novel, “Contact” that was made into a motion picture in 1997 with actress Jodie Foster. In the novel he attempted to show what first contact with an advanced alien species might be like.

I did have the opportunity to see Carl Sagan in person on one occasion. At the time I was a chemistry major in the mid-1980s at The University of Missouri – St. Louis. Sagan came to deliver a lecture to our university on the dangers of nuclear war and the importance of nuclear disarmament. He was a great dynamic speaker and the lecture hall was completely full. I think, at the time I was hoping he was going to talk about astronomy, but in retrospect I now understand the importance of his social concerns for our future and continued existence.

Sagan also introduced me to the concept of scientific skepticism, at a relatively early age. He was critical of how to tell the difference between science and pseudoscience (something now called the demarcation problem). He showed us that there are no beliefs that should be immune to skeptical inquiry, including religious belief. He came up with the “Baloney Detection Kit” that everyone should have in their skeptical toolbox.

Carl passed away right when the first exoplanets were just being discovered. Now we know of more than 1000 planets that circle other stars. We have made a much more thorough exploration of Mars and the moons of the outer solar system. We have strong evidence for liquid water deep under the crust of the moons Europa, Enceladus, and Ganymede. There is liquid methane on Saturn’s moon Titan. These discoveries make the possibility for life in our outer solar system a little more likely, and for life outside of our solar system very likely, by the sheer number of planets in our galaxy alone. At the same time the skeptical movement has gained momentum and is going strong. We have learned more about cognitive psychology and our innate biases and predisposition towards distortions of memory and perception. Flaws we must recognize in ourselves if we are to take the first steps to learn to become a more rational species and rise out of our superstitious past. I believe Carl would find all this fascinating and exciting. We could really use Carl’s wisdom now, but at the very least we still have him with us in the form of his writing and video.     

Happy Carl Sagan Day. Have some Apple Pie and be sure to learn something new today!
References and other items of interest:
1. Carl Sagan Wikipedia article: https://en.wikipedia.org/wiki/Carl_Sagan
2. Article detailing the “Baloney Detection Kit”: https://www.brainpickings.org/2014/01/03/baloney-detection-kit-carl-sagan/
3. Trailer for the movie “Contact” based on the book by Carl Sagan: https://www.youtube.com/watch?v=jl7Xe80_0MY
4. The Demarkation Problem on the Rationally Speaking Blog.
http://rationallyspeaking.blogspot.com/2013/08/philosophy-of-pseudoscience.html
Also check out the excellent “Rationally Speaking” podcast. The current host is Julie Galef, and excellent skeptic and teacher of all things rational! The previous host was Massimo Piglucci and scientist and philosopher and all around brilliant guy. Well worth checking out!
5. The Rationally Speaking Podcast with Julia Galef: http://rationallyspeakingpodcast.org
6. Some great Julia Galef youtube videos on rationality: https://www.youtube.com/user/measureofdoubt
7. Massimo Piglucci’s homepage: https://platofootnote.wordpress.com/massimo-central/
8. My contemplations on the possibility of what it would take for life to evolve on Titan:
http://darwinskidneys-science.com/2015/08/05/musings-on-the-biochemistry-on-saturns-moon-titan-part-i/

Mutation Monday: Lactase Persistence

Welcome back to your Mutation Station.
by Rich Feldenberg

Today we will examine the importance of the LP-mutation (Lactase Persistence-mutation), and its impact on human survival and global colonization.  Creationist like to ask the tiresome question, “name a mutation that increases the information content of a gene”.  I don’t think they really understand the question that they are asking, but today we will give one example of a simple mutation in human DNA that offered an advantage through natural selection to our species.  There are other examples, and we’ll address some of them in later blog entries.

Lactose is a carbohydrate found in mammalian milk.  It is composed of two simple sugars bonded together.  Humans and other mammals evolved to be dependent on mother’s milk during infancy, but then to be weaned off milk once the animal was mature enough to begin finding food on its own.  In order to digest lactose the enzyme lactase is required.  Lactase is produced in the digestive tracts of the infants and young mammals, but after weaning is generally no longer produced.  This is to conserve resources in the sense that it makes no sense to keep making an enzyme or other protein that is not being used.

This was true of early humans, as well, but a mutation occurred about 7500 years ago that allowed the lactase enzyme to remain expressed much longer throughout human life.  This mutation would then make drinking milk possible by adult humans, whereas prior to this, adult humans would not have tolerated drinking milk.  It is probably no coincidence that this mutation took place around the same time as the domestication of cattle and goats – sources of milk.

The mutation, itself is due to a simple switch of one DNA base in the gene coding for lactase, for another base – a single nucleotide polymorphism (SNP).   This lead to a change in the regulation of expression of the gene so that it wasn’t shut off when it normally would have been.  To our stone age ancestors, this would have been a wasteful and useless mutation, but with the development of an agricultural society it became indispensable as a way to increase ever rare nutritional sources.  It may have been responsible for allowing humans to migrate into and successfully inhabit Europe.

References:

1. “The Milk Revolution”, Andrew Curry; Scientific American special collector’s edition.  July 2015.

Mutation Monday (Your Mutation Station): Thymine dimers

by Rich Feldenberg

Welcome back to your mutation station.  Today we’ll look at a harmful effect on your DNA due to ultraviolet light, which leads to dimerization of the nucleotide bases thymine (T).  If there are two T bases next to each other in the DNA strand and they absorb UV light they can undergo a photochemical reaction that causes them to link-up.   The double bonds in the base break and then form single bonds to their neighbor.

This blocks normal base pairing on to the other DNA strand of the double helix, and results in a mutation.  Fortunately there are cellular repair mechanisms that can find and fix these errors, but some errors escape detection and cause major harm.  Some melanomas are thought to be due to thyimine dimers caused by the effect of UV sunlight.

Thymine dimers are actually a more specific form of what is called pyrimidine dimers.  The bases thymine and cytosine (T and C) are pyrimidines.  Two pyrimidines can dimerize under the same conditions leading to the same sort of DNA mutations.  You could have T-T dimers (thymine dimers), but also T-C, and C-C leading to the same problems.   So, remember to use sunblock and be careful about exposure to the sun!!

Fossil Friday: Dickinsonia

by Rich Feldenberg

Welcome to the long forgotten Ediacaran Period (635-542 Million years ago) in the Precambrian.  An assortment of unusual and fascinating fossils have been found dating to this time period, when multicellular life was just getting large enough to make good fossil imprints.  It is sometimes known as “The Garden of Ediacaran” because it is thought that at this early stage of animal evolution most creatures were basically filter feeders, and no major predation had yet developed (including the tools used by predators such as teeth, eyes, or sophisticated brains).  In that sense it may have been a very peaceful and “innocent” chapter in the history of life, before an evolutionary arms race between predator and prey began in the Cambrian and continues on to this day.

One common fossil found in rocks of this age is that of Dickinsonia.  This little guy was round shaped with a bilateral symmetry – something that shows some level of sophistication from the even earlier radially symmetric ancestors.  It seems to have had a head-end and a tail-end and was divided into segments.  It is not clear what kind of animal Dickinsonia really was, and there is a great bit of controversy in the scientific community in regards to its proper placement on the tree of life.  It seems to have been capable of movement over the ocean floor, as there have been fossilized tracts found that are thought due to its movements.   It may have belonged to a phyla that went extinct by the end of the Ediacaran period, or alternatively it may be related to modern day creatures.  Some experts have speculated that it is related to modern day jellyfish and some even think it may be related to animals that eventually became vertebrates.  Others have even gone so far as to say that it was not an animal at all, but part of a short lived, and ultimately unsuccessful evolutionary experiment in some type of multicellular life form that went extinct half a billion years ago.  What ever Dickinsonia was it made beautiful fossils!

Why Brontosaurus being back challenges my ability to change my mind

Why Brontosaurus being back challenges my ability to change my mind.

by Rich Feldenberg

 

 

Ok, here’s the thing.  I grew up dino-crazy.  From the time I was in 3^rd grade onward, I had a love for the prehistoric beasts we know as dinosaurs.  I’m not saying that a lot of kids don’t come down with dino-fever when they’re little (it is a common childhood illness after all), but it seems that for the vast majority of people it is a mild self-limiting disorder that is really nothing to worry about.  I didn’t fall into the category with the majority of inflicted, I was in the small percentage of patients where the condition became chronic.  There is an even smaller percentage of chronic dino-fever sufferers that go on to become paleontologists (so yes, there are some out there that have it worse than me).  I didn’t grow up to become a paleontologist, like I thought I would in 3^rd grade, but I continue to have an interest in learning more about my extinct darlings (all extinct that is except for the avian variety – birds!).  Of all the dinosaurs I knew about in 3^rd grade – and there are a lot more known today than there were then – brontosaurus was definitely one of my favorites.  It would certainly be amazing to be able to see what a living animal would have looked like.  Here’s hoping for Jurassic Park or Jurassic World technology one day – minus the rampaging raptors and out of control T. rex, of course!

Brontosaurus was one of the long-necked dinosaurs or sauropods.  They were a varied group and some, like brontosaurus, grew gigantic.  The sauropods were the biggest land animals to ever walk the earth.  Only blue whales are larger, and those whales are cheaters (literally, the “biggest” cheaters) because they use the buoyancy of the salty ocean water to prevent their tremendous weight from crushing the life out of them.  Not good old brontosaurus, they were built to take it.  In case you haven’t noticed, whales don’t last too long on dry land.  Back in my day (you know 3^rd grade) we thought that brontosaurus probably had to live in lakes and other bodies of water to support their mass, but over the last few decades it has become clear that isn’t so.  They roamed the dry land in herds.  Their legs and backs had to hold up under the unrelenting gravity of planet earth.  Their lungs had to expand to fill with air and their hearts had to pump blood through a super long neck leading to a brain (alright, so it was a tiny brain) with the weight of their own tissues constantly trying to flatten them.  A pretty impressive physiology had to be set in place by the wonder of evolution, and it is amazing to speculate on what environmental pressures lead to such crazy gigantism through natural selection.

So what does all this have to do with brontosaurus being back, or me having a tough time changing my mind?  Well, back during my paleontological training in 3^rd grade, brontosaurus was the most famous of the sauropod dinosaurs.  We did know about sauropods like diplodocus and brachiosaurus, but brontosaurus was the one most often portrayed in drawings and paintings.  Little did our young minds realize at the time, but there was a scientific controversy on the nomenclature of brontosaurus.  It seems that brontosaurus was named by the famous paleontologist Charles Marsh in 1879, but Marsh had already named a different skeleton of sauropod Apatosaurus in 1877.  Marsh, of course, thought that these two animals were different kinds, but in 1903 another scientist, named Elmer Riggs, studying the fossils, concluded that the two specimens were, in fact, one and the same species.  Even though Marsh was the discoverer of both specimens, the rules of dinosaur nomenclature state that the first named is the true name.  In other words, there was no brontosaurus, just apatosaurus.

Scientists had known, and basically accepted this since 1903, but it didn’t seem to trickle down to the general public until a long time later.  I’m not really sure when it became generally well known that brontosaurus was out and apatosaurus was in.  It may have been the 90s or early 2000s.  All I remember was being devastated that brontosaurus was no longer a thing!  The name was already well engrained in my mind, and it seemed annoying to have to now call brontosaurus, apatosaurus, but I was already scientifically trained by that time and was willing to do the right thing.  I began using the name apatosaurus when talking or thinking about the great beast.

Now new research has revealed that the bones of brontosaurus and apatosaurus really are two different kinds of animals.  So, just this year, brontosaurus is back after 112 years of mistaken identity.  When I saw the reports of the research teams conclusions I was overjoyed.  Yay, brontosaurus is back!  I love you brontosaurus!  Then the joy I felt at going back to a well engrained fact made me think about the difficulty humans have changing their minds.  The cognitive strain caused by having to accept new facts as true, and our emotional need for a stable, unchanging view of the world.  Darn, there are no free lunches after all!

Changing gears just a bit from the bones of the Thunder lizard to the frontal cortex of the “wise man” (Homo sapiens), research in cognitive psychology by nobel laureate Daniel Kahneman reveals that we rely on two systems to construct our view of reality, and to update that view as new information is processed.  These systems are called system 1 and system 2.  So much for creative naming.  System 1 is our quick thinking system.  It is similar to intuition or a gut feeling.  You don’t really have to think about the situation, the answer just comes to you.  Some of it is just evolutionary programming that is triggered by certain stimuli, like face recognition for example.  It allows us to rely on certain heuristics that may be right a lot of the time, so we can make snap decisions.

System 2 on the other hand is our slow thinking system.  It is dependent on more careful thinking and consideration to detail.  Applying statistical analysis or the scientific method to a problem would draw on system 2.  Unfortunately, system 2 is slow, expends a lot of mental energy, and is therefor expensive from a survival point of view.  In reality we use both systems everyday.

I think that since I learned about brontosaurus from such an early age, I formed a sort of heuristic of recognition when I saw or read something about apatosaurus.  There was a cognitive strain associated with placing apatosaurus in the memory location where brontosaurus was supposed to live.  The article that validated the uniqueness of brontosaurus as it’s own species gave me a sort of permission to use my old tried and true heuristic for recognizing the creature – much like recognizing a familiar face of a friend or celebrity.  A relief of the cognitive strain meant that I didn’t have to rely on system 2 each time to draw upon the fact that there is no brontosaurus, only apatosaurus.

This seemed a bit disappointing to me, since I consider myself someone who values system 2 type thinking a lot.  And this was only about the name of the brontosaurus.  Think of all the many beliefs deeply embedded in our minds due to having been placed there from an early age.  It makes it difficult, though fortunately not impossible, for us to self-examine facts that we take for granted.  But science teaches us that individual facts are updated, revised, and sometimes even completely changed as new evidence accumulates.  This is not how our system 1 evolved to interpret the world our distant ancestors woke up in.  The things our intuitions inform us of, that seem like common sense, are not always a good model of truth.  Getting my brontosaurus back told me that it is really hard to change your mind and update your model of the world.  Being open to change means feeling comfortable with some degree of uncertainty.  Not an easy thing, but something we can train ourselves to get better at accepting.  I was lucky this time, but the next beloved fact that is overturned will probably not be set back to zero again.  Oh well, I’m a scientist and I will continue to try my best to embrace the changes that are coming as science sheds new light on our world.    In the meantime, welcome back brontosaurus, I missed you!

Why the Horta would not have looked like a rock monster

Why the Horta would not have looked like a rock monster.

By Rich Feldenberg

 

 

In the original Star Trek series the U.S.S. Enterprise, on its heroic five year mission to explore strange new worlds, to seek out new life and new civilizations…, comes across many fascinating and unusual alien species.    In one episode in particular, “The Devil in the Dark”, they make contact with a creature with an entirely different kind of biochemistry from the typical carbon based biochemistry seen elsewhere on earth and throughout the galaxy.  Captain Kirk and the crew of the StarShip Enterprise first encounter the alien after they respond to a distress call sent from a mining colony on the planet Janis VI.  When the Enterprise arrives, Kirk learns that routine mining operations have been disrupted by a strange life form native to the planet.  The creature doesn’t register as a life form on the tricorder, lives deep in the darkness of the mines, and can eat through solid rock due to it’s highly corrosive nature.  Once Spock learns that the mines contain a multitude of spherical shaped silicon nuggets, he has a hunch.  As usual, Spock’s hunch turns out to be correct.  The round silicon nuggets are the eggs of a silicon based life form.  Spock is able to use his mind melding abilities to communicate briefly with the creature, and learns that it is called a Horta, and that the miners have been destroying its eggs, causing it to face total extinction.

While I applaud the episode for thinking outside the box when it comes to attempting to imagine “life as we don’t know it”, I suggest that making the silicon based Horta, essentially a living rock, showed a poor understanding of both organic and inorganic chemistry.  So first let me say what was outstanding about the idea before I lay into it with my chemistry degree equivalent of a phaser set on kill.  

Ok, it was great that there was any attempt at all to speculate on the astrobiology of an organism that was not carbon based back in a 1960s TV show.  By non-carbon based I’m not talking about energy beings here, but legitimate speculation about an alternative chemical system, as we’ll discuss below.  This certainly went well above the usual laziness and poverty of imagination of portraying an alien as a human with pointy ears, or a green girl, or, as in the case of the klingons, with angry eyebrows (they hadn’t evolved there forehead ridges yet!).  Now don’t get me wrong, I don’t have anything against a green blooded pointy eared Vulcan.  In fact, Mr. Spock may be my all time favorite fictional character, but it really isn’t terribly creative when you consider how life forms on different worlds would likely have evolved down completely different pathways leading to completely unique body plans.  In other words, even if most life in the universe is carbon based, like us (probably still a good guess), intelligent aliens wouldn’t necessarily appear anything like humans.  Ok, I get it, there were budget issues!

Now, all life on earth is carbon based.  Carbon chains form the backbone of all the major classes of biomolecules, such as DNA, protein, carbohydrate, and lipids.  Because carbon can form so many complex molecules, it has it’s own special branch of chemistry devoted to it – organic chemistry.  The chemistry of every other element falls under the heading of inorganic chemistry.   That seems really unfair, right?  I mean one element out of the 92 naturally occurring elements, and it gets it’s own branch of science!  Well it actually is fair when you consider that the number of possible organic molecules far exceeded the number of inorganic molecules combined by orders of magnitude.  There are an estimated 10 million carbon compounds in existence.  There are a lot of ways that carbon can react depending on what other atoms are near it on a molecule.  Carbon is element number 6.  It has 6 electrons in orbitals around a nucleus containing 6 protons and 6 neutrons (at least for carbon12, the most common isotope).  Because carbon is in group 14 of the periodic table, its electron configuration is 1S², 2S², 2P².  Each S orbital can only hold two electrons but the P orbital can hold up to 6 electrons so there are 4 vacant spots in carbon’s P orbital.  There is a tendency for an element to move towards a noble gas configuration, meaning that for reasons related to finding the lowest energy state, and hence the greatest stability, the element will either shed electrons or gain them to mimic the electron configuration of the closest noble gas atom.  This is known as the Octet Rule.  

Metals typically lose an electron to this end, and non-metals typically gain them.  In the case of the non-metal carbon, if it fills its four vacant orbitals with electrons it will have the electronic configuration of the noble gas neon (Ne) with 10 electrons, and, ah that feels so good!   Well, how is poor carbon to get four more electrons?  That’s where covalent bonding comes in.  It shares electrons with other atoms, so carbon will try to form 4 bonds with up to four other atoms.  These could be 4 single bonds, in which case carbon is attached to 4 different atoms, or it can also form a combination of single, double, or triple bonds.  Both single and double bonds are very common in organic chemistry.  The reactive double bonds in carbon based molecules account for a lot of the action in organic chemistry.  The really special thing about carbon compounds are that carbon can bond to another carbon, which can bond to another carbon, and so on.  In fact, it is very common to see very long chains of carbon bound together making something like a huge protein or DNA molecule, for instance.  This would seem to make carbon the best suited element in the periodic kingdom for producing life forms.  I’m surprised nature never thought of that, oh wait it did!!

So what about the poor Horta?  The Horta is silicon based.  Silicon (Si) is in group 14 of the periodic table.  Hold on, thats the same column as Carbon (C)!  It also means that like carbon, silicon will also want to gain 4 electrons to fill it’s orbitals.  By the way, this is why the periodic table is so useful.  You can tell a lot about an atom by where it sits on the periodic table.  The reason you can go around the table to the next row down and find another element like the one in the row above it is why it is periodic!  There are repeating patterns.  Anyway, silicon is element number 14, and its electron configuration is 1S², 2S², 2P⁶, 3S², 3P².  If it can just gain four more electrons it will have the stable electron configuration of the noble gas Argon (Ar).  It is for this reason that people have speculated that if there is any other element in the periodic table that could cast a little carbon-like magic, it would have to be silicon.  The other great thing about silicon is that it is common, really common.  It is the 8^th most common element in the universe (carbon is the 4^th most common element in the universe), and is second only to oxygen, as the most common in the earth’s crust.  It is found in rock and sand all over the earth.  You certainly wouldn’t want to have a life form based on a very rare element like Lanthanum (element 57), for instance, where there isn’t enough of it around to make anything  useful.  You want your building materials to be lying around everywhere.

                                                                                           

Unfortunately, the problems faced by silicon based life forms would be many.  First of all, while silicon is capable of forming a variety of silicon compounds, and even forming chains of silicon (silanes) that resemble the long chain alkanes of carbon, the number of actual silicon compounds is far lower than for that of carbon.  The Si-Si single bond is weaker than a C-C single bond due to the silicon atom being larger, and thus the silicon atoms are further apart.  This makes silicon bonds unstable, and you don’t see very long chains of Si show much permanence.  They break apart quickly, and in fact, are so reactive that they will spontaneously combust in an oxygen atmosphere.  Really very bad for any oxygen breathing lifeforms.  Also, whereas, carbon readily forms double bonds, silicon is less likely to form many double bonds, which again limits the kind of chemistry it can undergo.  Double bonds expose electrons to “attack” by other molecules – this is the beauty of organic chemistry – so fewer double bonds in Si lead to fewer potential chemical reactions.  Again, boring chemistry equals inert substances, not vibrant living materials.

Carbon also loves to form carbon rings, even rings that include double bonds that provide a special stability due to a property called resonance associated with the electrons in the ring system.  This is a bit like a little electric circuit in the molecule where the electron can have room to move around and make the bonds between atoms even stronger.  These kind of compounds are called aromatic compounds and are extremely common in living things on earth.  Si doesn’t form rings very readily so the equivalent sorts of aromatic Si compounds would be unlikely to exist.    

Remember, life is all about lots of interesting chemistry.  Interesting chemistry may not explain the purpose of life, but it’s one way to sum up what life is.  It seems most likely that life would only thrive and evolve if it’s chemistry allowed a lot of diversity and potential to form many varieties of stable compounds.  Limitation in the number and stability of compounds and number of reactions is like a death blow to the odds of life.  But what about the Jurassic Park law of biology that says, “life finds a way”?  Yeah, that may be so, but it found carbon chemistry out of all the other useless junk on the periodic table.   

In addition to these problems, there is the problem of how silicon would be recycled throughout it’s biosphere.  Carbon is well suited for recycling due to it’s ability to form the simple gas CO2 (carbon dioxide).  As we all know, CO2 is taken up by plants, and using the energy of the sun, uses the carbon to make glucose (a carbon compound in a ring shape) and releases the waste product molecular oxygen (O2).  Animals eat the plants, thereby gaining the glucose for energy and delivery of a carbon source to make more kinds of carbon compounds.  For both animals and plants the glucose can be oxidized – burned in the presence of oxygen in the tiny midi-chlorians in the cell (sorry, I meant mitochondria)- to release the energy stored in the carbon bonds.  This is the process of chemical respiration.  Once the animal dies, its body decomposes (oxidizes!), and CO2 is released back into the atmosphere where plants can take it in again.  This is the carbon cycle, and it makes life on earth sustainable for billions of years.

For silicon life forms there would need to be some sort of silicon cycle.  This is problematic since SiO₂, while common, is solid and not a gas.  It is also not soluble in water, so how it would circulate through the biosphere to become accessible to the silicon life forms that need it may create an insurmountable dilemma.  With no silicon cycle, even if silicon based life could somehow get a foothold with it’s weak and limited bonding capabilities, it would quickly shut down once the available silicon became trapped in all the dead silicon organisms.  

Ok, so I’ve tried to illustrate why silicon based life forms probably won’t exist to begin with, but let’s say, for the sake of argument, the Horta really was based on Si chemistry.  Why wouldn’t look like a big rock?  This is the thing that really irks me!!  The whole point of invoking the possibility of Si life is because silicon has some chemical similarity to carbon due to its similar electron configuration.  So our imagining a Si based creature to be essentially a living rock is analogous to an intelligent silicon based species speculating that carbon based life forms would be like living lumps of coal or dangerous diamond creatures that can scratch glass.  It might make for a good episode of space Sci-Fi for our silicon based friends to watch on TV, but you can see that this is obviously an incorrect interpretation.  There is a huge diversity of life on earth but we don’t have living coal or diamond creatures.  The reason, of course is that carbon forms very complex compounds with itself and with lots of other kinds of atoms.  Coal and diamond are basically crystallized forms of carbon.  Crystals are not suitable for the basis of life because they don’t allow a lot of rapidly changing chemistry to happen within them.  

If the Horta was silicon based, the whole point would be that Si would be mimicking the complexity and diversity of carbon, and its tissues should be no more rock-like than earth creatures are diamond-like, but instead have soft squishy muscles, nerves, intestines, kidneys, blood, and so on.  It could be conceivable that the Horta could have a hard outer shell made of silicon dioxide (SiO₂) but it’s whole body would not be silicon based rock.  This misinterpretation was brought home when Dr. McCoy was asked to treat the phaser wounded Horta and replied, “I’m a doctor, not a bricklayer”.  Captain Kirk appropriately reprimands McCoy telling him, “Your a healer, there’s a patient, that’s an order”.  

At the end of the Star Trek episode, Kirk realizes that the Horta was only a protective mother and didn’t wish to harm the miners or their equipment.  The crew of the Enterprise is able to make the miners understand that the Horta means them no harm if they leave her eggs alone.  In fact, the natural mining abilities of the Horta could make a collaboration between the miners and the Horta very profitable.  As the Enterprise leaves orbit, the many Horta eggs are getting ready to hatch.  Too bad that due to their silicon chemistry they are likely to spontaneously combust when they are exposed to the oxygen rich atmosphere that the humans are breathing!    

References:

1. Wikipedia entry on silicon:  http://en.wikipedia.org/wiki/Silicon

2. General Chemistry, Principles and Modern Applications, third edition

By Ralph H. Petucci.

3. Inorganic Chemistry; third edition,  by James E. Huheey.