Spoiler Alert – It Wasn’t Aliens

I really like fiction. Fiction is fun in part because it doesn’t have to stick to the facts.  However fiction is also compelling because it reflects who we are.  I heard someone say that all fiction is a lie but good fiction reveals the truth about who we are.  In addition in order for fiction to be believable it cannot stray too far from reality including the realities of the physical world. 

A few years back there was a lot of controversy over The da Vinci Code by Dan Brown.  A lot of people argued about the content of the book and a lot of people read the book too, including me. Boy was that a fun time. One of the best outcomes of reading The da Vinci Code was that I sought out more page turners by Dan Brown and others.

One of Browns earlier titles was Deception Point. The premise of the book is that scientists in the arctic found a meteorite buried below layers and layers of ice and that there were alien fossils imbedded in the meteorite.  As it turns out the meteorite wasn’t genuine and science was used as a weapon of deception but ultimately revealed the truth. 

So what’s the point? I’m not sure.  Maybe it’s that science is everywhere. Maybe it’s that science and fiction are cool. I’m really not sure.  I’ll sleep on it and have to come back to it.

When 9-13 < 1

The astute mathematicians in the readership might be wondering, “When doesn’t it?” but rest assured it does.  For example:

9-13<1 when T≥0

But

9-13>1 when T≤ 0

Huh?

It all depends on the frame of reference you read from.  First, read the statement again. Did you read nine minus 13 is less than 1 when T is greater or equal to zero? If so you may have read correctly but again maybe not. The statement could also be read nine to thirteen is less than one when T is greater or equal to zero.  If you know T is temperature in degrees Celsius and 9-13 is inches of snow predicted, a new picture starts to take shape. In other words if a bunch of snow is predicted but then the temperature stays above the freezing point there will be very little snow (<1 inch for example).

Looking at the scenario laid out in a table can make the example even clearer. 

Predicted Snowfall	Actual Snowfall	Temperature
9-13 inches	<1 inch	>0⁰ Celsius
9-13 inches	>1 inch	<0⁰ Celsius

I recently read an article by Isaac Asimov titled The Relativity of Wrong.  Through the essay Asimov describes how our frame of reference including the data and tools we have available impact how right we can be at a particular time in history.  In The Evolution of Adam Peter Enns describes a similar scenario in terms of the frame of reference, and ability to be right scientifically, of the ancient Hebrew culture that produced the book of Genesis. 

When asked, “Is the world flat?” Asimov reminds us, yes it is (practically) and if we don’t have a frame of reference or tools to tell us otherwise are we really that wrong?

When asked, “Was there a global flood?” Enns reminds us, yes there was when the boundaries of the known world were covered and the limits of the flood were beyond perception.

It might seem like our understanding and ability for understanding is as clear as it has been throughout history.  However each passing day, each passing year, each passing generation brings us farther away from the past we have emerged from.  Because of this there are some things we have to work at understanding. We have to be intentional about not thinking from our frame of reference. We have to see through the eyes of the past to understand what is not always clear in the present.

The Essentials: Of Mice and (Wo)men

In 2004 researcher Jonathon Tilly presented evidence that indicated an ability in mice to regenerate egg cells.  This finding flew in the face of the century old thought that mammalian females are born with a certain number of eggs and that no new eggs are produced.  In next month’s edition of the journal Nature Medicine Tilly will report experiments that show he and his team have found the same ability in human women.

That this similarity between mice and humans was found is not really that surprising.  Mice have similar genes and gene sequences as humans. The evolutionary explanation for this commonality is that humans and mice genes come from the same source DNA.  It would be expected then that similarities would be found both in sequence and function and that any differences that do exist between humans and mice are due to accumulated mutations.  This type of commonality can be seen to varying degrees in all organisms. The fewer the differences in sequences the closer organisms are related.

MPR had a story about the Tilly research this morning that you can read or listen to here. http://minnesota.publicradio.org/features/npr.php?id=147344258

The Essentials: Disambiguation with an Unfortunate Loss of Meaning, or Not

Are these two sequences the same?

⁞A⁞B⁞C⁞D⁞E⁞F⁞G⁞H⁞I⁞J⁞K⁞L⁞M⁞N⁞O⁞P⁞Q⁞R⁞S⁞T⁞U⁞V⁞W⁞X⁞Y⁞Z⁞

⁞A⁞B⁞C⁞D⁞E⁞F⁞G⁞H⁞I⁞J⁞K⁞L⁞W⁞N⁞O⁞P⁞Q⁞R⁞S⁞T⁞U⁞V⁞W⁞X⁞Y⁞Z⁞

According to the X-MenWikipedia page, “Creator Stan Lee devised the series title after Marvel publisher Martin Goodman turned down the initial name, "The Mutants", stating that readers would not know what a "mutant" was.”

I have to agree with Martin but at the same time X doesn’t explain much either.  There are two schools of thought on the etymology of the X.  Some say X is an homage to the founder of the troupe, professor Xavier, while others believe X is for extra abilities (and that Xavier would never have been so conceded to name his team after himself).  As I scoured the fandom for more answers I came across a message board response to a different ambiguity that covers my question as well. It reads as follows.

“It's made up, it's ALL MADE UP."

Thank you cripticgeek you couldn’t have cleared it up any better. That’s the beauty of fiction and science fiction. It’s not real and it doesn’t have to be. 

Science on the other hand by definition must stay in the realm of the real and therefore it seeks a clear understanding of terms and conditions.  Mutation is a term and a concept that is explained by science and also helps us answer the question at the outset of this post.

Are these two sequences the same?

⁞A⁞B⁞C⁞D⁞E⁞F⁞G⁞H⁞I⁞J⁞K⁞L⁞M⁞N⁞O⁞P⁞Q⁞R⁞S⁞T⁞U⁞V⁞W⁞X⁞Y⁞Z⁞

⁞A⁞B⁞C⁞D⁞E⁞F⁞G⁞H⁞I⁞J⁞K⁞L⁞W⁞N⁞O⁞P⁞Q⁞R⁞S⁞T⁞U⁞V⁞W⁞X⁞Y⁞Z⁞

A legitimate scientific answer to this question is, “Yes – but it has a mutation.”

Mutation is in fact a primary factor in creating the variety in populations that I’ve been describing throughout The Essentials series. The mutation in the alphabetical sequence above would be classified as a mutation within a gene, or, a point mutation.  As described earlier in ATCG: The ABC’s of DNA, the alphabet that composes the genetic code isn’t made up of 26 characters but of 4 nucleotide bases.  Still it is mutations of these sequences that creates genetic diversity and makes evolution possible.

The Essentials: The X-Flies

A friend of mine told me that he was comped two drinks a while back.  The first was because there were fruit flies in the glass and the second for the same reason.  He speculated that the establishment neglected to cover their bottles over night and the flies enjoyed their own free drinks.  The story immediately reminded me of a study that showed how an attraction to alcohol was advantageous to the flies.

Fruit flies could have just as easily been named bar flies because their habits lead them to imbibe in alcohol on a regular basis.  Fruit flies dine on over ripe, and therefore fermenting, fruit.  The fermentation process converts the fruit sugars into alcohol and in that way alcohol becomes part of the fly’s daily diet.  The study showed that alcohol consumption increased the flies fitness because it helped them ward off attacks from a would be predator.

The foiled predator is of the most insidious and sneaky kind.  This predator attacks undetected (possibly) and from within. This predator is a parasite: specifically a parasitic wasp. The strategy of the wasp is to get its eggs into the fly, then once the eggs hatch, the newborns feast on the fly from the inside out.  As a result the wasp has a buffet of fresh fly guts to feast on and the fly dies from the inside out.

The fly has no real defense against the parasitic attack.  There are no fly surgeons to extract the unwanted wasps and left untreated the prognosis that accompanies diagnosis for an infected fly is certain death.  That is unless the condition is caught early enough and the correct preventative measures are taken.  In this case the best medicine is one of the oldest remedies around, booze.

The increased alcohol in the fly’s system creates an environment inhospitable for the development of the wasps and the fly lives to eat another banana. This conclusion isn’t a simple conjecture made by the authors of the paper but is actually backed up by experimental evidence.  You can read more about the study in the New York Times article that presented it to the general public.

(I experienced some inconsistencies with the first link so if that doesn't work try this one from the Huffington Post.)

What is amazing to me is that the defenseless flies found a solution to their parasitic problem.  Of course flies don’t create committees around public health or engage in research to find cures to diseases. Flies main concern (concern is probably to anthropomorphic – instinct is probably better) is the same as all other organisms - live and reproduce.  Just like every other organism the solution comes from the variability that is already present in the.  Variety results in some individuals being more fit to survive and ultimately those fit individuals pass on their genes to their offspring. 

If you are reading this and are suddenly experiencing déjà vu it is probably because I keep coming back to this point.  Populations are made up of individuals and those individuals are all different.  It is the presence of these differences, and the realities of limited resources, that drives species to evolve. But where does this variability come from?

The answer is that, just like the flies, we are all mutants. We are all X-Men, mutated at random and against our will or control. We are mutated without our knowledge and without knowledge of the consequences.  Though we can’t shoot laser beams out of our eyes or move metallic objects with our minds, the collective mutations of ours, and every species, have shaped us into who we are today and have given us the super power of survival.

The Essentials: Skin, Kidneys and the Rest of the Inconsequential Organs

If you’ve ever received an email from me composed on my iPod you may have seen one of my favorite quotes.  The excerpt is from a The Lives of a Cell by Lewis Thomas and the extended passage reads as follows.

“Nothing would save me and my liver if I were in charge, for I am, to face the facts squarely, considerably less intelligent than my liver. I am, moreover, constitutionally unable to make hepatic decisions and I prefer not to be obliged to, ever. I would not be able to think of the first thing to do."

I like the respect and admiration for the complexity and internally programmed aptitude of the human body Lewis expresses, but I’m most impressed with the humility that comes from an appropriate view of science.  In light of the quote, and the light it sheds, why create a post title that depicts the body with such contempt? My text book told me so.

When reading in Essential Cell Biology about how genes and genomes evolve, the first point the authors make is that in terms of evolution our body doesn’t matter, only our germs. Again a clarification is needed. 

There are two basic types of cells in humans (and mammals and other organisms): somatic cells and germ cells.  Somatic cells make up the bulk of the body including skin, kidney, liver, heart, brain and bone. Basically everything except sperm and eggs are somatic cells. So that just leaves sperm and eggs in the category of germ cells.  Germ cells are the reproductive agents of the body and therefore the only cells of any consequence when passing on genetic information.  As my textbook puts it, “In this sense, the somatic cells can be considered to exist only to help cells of the germ line survive and propagate.”

Of course germ cells have all of the information that lead to somatic cells, but anything that happens after the line blossoms into a body will not have an impact on the next generation of reproductive cells that follow. The only events that can impact the germ line are sex and mutation.

Science Fiction, Social Justice, Science

If one good thing came out of the cable snapping on the Martin Olaf Sabo pedestrian bridge it’s that it added about an hour to a public transportation commute that is typically just under two.  That may not sound like a great thing but it opened up a great opportunity to catch up on some podcasts. I finished a few Stuff You Should Know Episodes but the best podcast was from my guy Neil deGrasse Tyson’s StarTalk.

The episode, A Conversation with Nichelle Nichols, was as enlightening as it was entertaining.  Typically Star Talk takes on a more jovial mood but this particular episode broke that form to deliver a full interview with Nichelle Nichols, the actress who played Chief Communications Officer Lt. Uhura on the original Star Trek.  I grew up, not so much a Trekkie but certainly enjoying the occasional rerun and well aware of the impact of Star Trek on geek culture. What I never appreciated was the positive results the show had on the greater culture of its day.

In the interview Nichols recounted a sequence of events following the first season of the show.  With her eye on Broadway, Nichols went to Gene Roddenberry (the creator of the epic space serial) with a letter of resignation and news of an opportunity to be featured in a Broadway show.  Roddenberry was not pleased and asked Nichols to think about her decision over the weekend.  That weekend Nichols attended an event and was asked if she would be willing to meet with someone claiming to be her number one fan.  

To her surprise the next thing she knew Dr. Martin Luther King Jr. approached her with a rare smile. He announced himself as her number one fan and went on to tell her how meaningful her character was to him, his family and the cause of civil rights.  What I never picked up on, but what Dr. King was acutely aware of, was that Lt. Uhura’s character didn’t have to be black, a woman or even a human. But she was. The vision of the civil rights movement was reflected in Rodenberry’s vision as it played out in Star Trek.

There is no substitute for hearing the story for yourself so if you have 45 minutes or so, maybe in the car or on an extended bus ride, I highly recommend listening to the full episode.  If you do, you may be drawn into the next episode in which the interview continues and turns to the impact Nichols had on NASA.

The Essentials: Same or Different?

Are these two sequences the same?

⁞A⁞B⁞C⁞D⁞E⁞F⁞G⁞H⁞I⁞J⁞K⁞L⁞M⁞N⁞O⁞P⁞Q⁞R⁞S⁞T⁞U⁞V⁞W⁞X⁞Y⁞Z⁞

⁞A⁞B⁞C⁞D⁞E⁞F⁞G⁞H⁞I⁞J⁞K⁞L⁞W⁞N⁞O⁞P⁞Q⁞R⁞S⁞T⁞U⁞V⁞W⁞X⁞Y⁞Z⁞

There is more than one possible answer. I’ll give just two for now.

Possible Answer 1: No. The letter in the 13^th position is different so the sequences are not the same.

Possible Answer 2: Yes.  The sequences are practically identical; the 13^th letter is just flipped upside down.

How do you answer the question?

The Essentials: Homology (Not Techmology – That’s a Different Subject)

An analogy explains one thing by showing how it is like another.  For example DNA is like an instruction book for building living things. DNA isn’t really a book, it is a molecule, but equating it with an instruction book makes it easier to understand the concept.  Learning and communicating science is full of analogies because comparing complex concepts to every day experiences makes them more accessible. Analogies don’t necessarily show a real connection between the things in comparison but they show how they are similar.  

There is another type of comparison in biology called homology. Homology doesn’t illustrate similarities in functionality by comparing the unfamiliar to the familiar it actually shows how things are the same when their function is different. Where analogies are illustrative of function homologies demonstrate actual similarities between organisms that appear diffierent.

Analogy shows how different things are similar.

Homology shows how things that appear completely different are actually the same. 

The Essentials: ATCG – The ABC’s of DNA

From courtroom dramas to disturbing episodes of Dateline NBC, DNA has entered into the public vernacular. There has been a huge popularization of the genetic molecule in the last 20 years or so but I’m not sure how much the general public really knows about DNA.  I really don’t know. 

In my mind when I hear terms like base pair, nucleotide, nitrogenous bases, codon, intron, exon, DNA, RNA, mRNA, tRNA, rRNA, central dogma, transcription, translation, polymerase, peptide bonds, ribosome, etc. (as in etcetera) I am transported to the early days of my biology education when I first fell hard for science.  I realize that for many people these words might insight a different response, something a little closer to, “Nucleowho? Ribowhat?”  

Advancements in our understanding of DNA have impacted many areas of our lives including our understanding of evolution. While DNA can bolster the evidence for evolution in many ways it can’t make a case if it is incomprehensible.  

One of the big challenges with science is that the technical language can be a big barrier.  In my Essential Cell Biology textbook the authors disambiguate any confusion about ribosomes with the helpful section heading “The Ribosome is a Ribozyme”. Thanks authors, that clears everything up. Before I describe how DNA supports the case for evolution I’ll explain a few key ideas that will help later on.

DNA – DNA is the molecule that stores all of the information for making and running living things.  Like all molecules DNA is made up of smaller parts.  The main structure of DNA is like a ladder.  The rail of the ladder is made up of alternating phosphate and sugar molecules.  The rungs of the ladder are made up of nucleotides which extend out from each rail and meet in the middle.  The ladder is twisted which gives DNA its famous “double helix” shape.

Nucleotides – Nucleotides are the functional part of DNA and are the “coding” elements of the molecule. There are only four different nucleotides in DNA. This might not seem like enough to create all of the instructions for making and controlling a life but the possibilities for complexity are astounding. If you think of binary code, the basic computer language which uses combinations of 1 and 0 to code for everything ever done on the internet or a computer, you can see how four “digits” could create an incredibly complex message.  The nucleotides that create the DNA code are indicated by the letters ATCG (Adenine, Thymine, Guanine and Cytosine).  A,T,C and G are refered to as bases.

To see an example of the two digit binary code in action copy the sequence below and paste it into the converter at this link.  There may be a bonus in it for you as well.

010000100110100101101110011000010111001001111001001000000110001101101111011001000110010100100000011101010111001101100101011100110010000001110100011101110110111100100000011001000110100101100111011010010111010001110011001011100010000001000100010011100100000100100000011101010111001101100101011100110010000000110100001000000110010001101001011001110110100101110100011100110010111000100000010000110111001001100001011110100111100100100000011100100110100101100111011010000111010000111111001000000100010101110110011001010111001001111001011101000110100001101001011011100110011100100000011011110110111000100000011000110110111101101101011100000111010101110100011001010111001001110011001000000110111101110010001000000111010001101000011001010010000001110111011001010110001000100000011000110110000101101110001000000110001001100101001000000110001001101111011010010110110001100101011001000010000001100100011011110111011101101110001000000111010001101111001000000011000110010010011100110010000001100001011011100110010000100000001100001001001001110011001011100010000001001001011011100110001101101100011101010110010001101001011011100110011100100000011101000110100001101001011100110010000001011001011011110111010101010100011101010110001001100101001000000111011001101001011001000110010101101111001011100010000000100000011010000111010001110100011100000011101000101111001011110111011101110111011101110010111001111001011011110111010101110100011101010110001001100101001011100110001101101111011011010010111101110111011000010111010001100011011010000011111101110110001111010101001001101010001011010110111101101011011101100100110001001101001100110110011101010101

The Essentials: Evolving Under Our Nose

While Crichton’s bacterial population boom is an unsettling thought the idea of limits to the populations growth is even more problematic.  As discussed previously the population of bacteria will inevitably face limits and with these limits will come competition.  The individuals most fit to survive will pass on their genes to the next generation and the next generation of bacteria will consequently be more like the survivors.  The selection pressures will effectively shape the appearance of the population over time. In other words the population will change, or evolve. 

Antibiotics are a strong selective pressure on populations of bacteria. These powerful drugs target bacteria for destruction in order to get us healthy when we are sick. However the populations of bacteria that make us sick have variety in their individuals and some of these individuals are more resistant to the effects of the antibiotics. These antibiotic resistant bacteria are the survivors in the population and over time the population will be comprised of all resistant individuals.  In just a few days the population can have a very different composition.

This is evolution and it happens all of the time.  In a few days bacteria can show us how the mechanism of natural selection works and gives us a glimpse of how it has been playing out for the last several million years.

The Essentials - Pop Science

"The mathematics of uncontrolled growth are frightening. A single cell of the bacterium E. coli would, under ideal circumstances, divide every twenty minutes. That is not particularly disturbing until you think about it, but the fact is that bacteria multiply geometrically: one becomes two, two become four, four become eight, and so on. In this way it can be shown that in a single day, one cell of E. coli could produce a super-colony equal in size and weight to the entire planet Earth."

Michael Crichton (1969) The Andromeda Strain, Dell, N.Y. p247

I knew this postulation existed, just not exactly where, so a quick Google search provided an example.  This surely isn’t the only example but the website that provided the quote also does a nice job of laying out the mathematical reasons for why the claims are valid. The site also points out some of the critical questions beyond the validity of the mathematics especially the possibility of ideal circumstances.

In the late 1700s Thomas Malthus famously wrote, “That the increase of population is necessarily limited by the means of subsistence,” and in expounding on this notion influenced Charles Darwin and others as the theory of evolution by natural selection was being formulated.  Malthus counters the idea of ideal circumstances with the realities of the economies of life and ecosystems.  If Malthus would have read Crichton I suspect he might have written a polite yet firm letter, sent by post, informing him that, while mathematically sound his example was all but impossible. 

This isn’t to take anything away from the awesome growth potential of populations (and I should say that  Crichton’s point was really about the risks of rapidly spreading disease and I suspect he is well aware of Malthus) but it is to say that populations have natural limits. This realization is one of the bits of inspiration that drew Darwin closer to his evolution conclusions.  His thinking was that if populations are limited then there will be competition for those limited resources and in competition the strongest survive. 

Remember that being strong, or fit, for survival doesn’t necessarily have anything to do with big muscles or being the best fighter. Evolutionary fitness simply refers to the ability to pass on genes by having offspring.  This could mean that as a population approaches its limits the most fit individuals will be those that go dormant for a period while others in the population die of starvation.  Or perhaps the most fit individuals will exhibit a behavior that opens up another food source to them. (I wrote previously about the skittish vs. trusting wolves as an example of a new food source opening with a change in behavior.)

There are a few things that I like about this whole population business.  To begin with I like how math can be used to describe the natural world very accurately.  I also like how three academic areas come together to create a better understanding of the world around us.  Math shows us how it could play out, demography describes how it really happens then science comes in to tie the two together with an explanation that is descriptive, predictive and can even be tested.  

As an additional like I’ll add that in this example we see a science fiction author in Crichton, an Anglican clergyman in Malthus and a naturalist in Darwin all engaged in a conversation that has spanned the centuries.  Science and society share an unbreakable bond and our degree of investment in science literacy, both personally and as a society, determines if that bond is restrictive or empowering.

Observations from the First 23% of The Evolution of Adam

One of the great things about science and technology is the elegance of the solutions that emerge out of innovation.   I’m reading The Evolution of Adam by Peter Enns on a Kindle. Like other e-readers the Kindle allows for font and text size changes which makes page numbering problematic. As the texture of the text changes so does the number of pages in the book. Yet the total length of the book never changes, just the number of swipes required to read to full resolution.  So what magical methods do the makers of tech texts devise? Fractions! Well specifically percentages.  

Maybe I’m goofy for liking stuff like this but I do.  I’m also enjoying The Evolution of Adam and today I’ll share a few observations from the first 23%.

I was fortunate to participate in a call with Peter Enns last month in which he discussed some of the central issues in his latest book. In a previous post I shared some notes from that call.  My notes covered two main areas; the purpose and place of the Genesis text and Paul’s treatment of and relationship with Adam. The first 23% of The Evolution of Adam deals with the perceived conflict between Genesis and the science of Evolution and also begins to shed light on Genesis in terms of authorship, genre and its role in defining Israel’s national identity.

The first thing I was impressed by, at the time of the original phone conversation and in the introduction of the book, is Dr. Enns’ respect for Christian tradition and especially opposing points of view.  He makes it clear that the Bible is the inspired Word of God but also that as long as it has been read it has been discussed and has incited questions and disagreement.  I’m grateful for the example provided for confidently expressing convictions while still respecting opposing points of view.

It is made clear within the first 5% however that not all Biblical interpretation is equal. The limitations of these views are described in the following quote.

These other views, rooted in a precommitment to read the Bible literally at virtually every point despite evidence to the contrary, avoid engaging science by reinterpreting it to conform to that conviction. To the contrary, it is clear that, from a scientific point of view, the Bible does not always describe physical reality accurately; it simply speaks in an ancient idiom, as one might expect ancient people to do. It is God’s Word, but it has an ancient view of the natural world, not a modern one.

Much of the first 23% describes Genesis and the rest of the Pentateuch as a declaration by ancient Israel of their National Identity and their role in the world as God’s chosen people.  In this description the authorship of the Pentateuch is fleshed out as a compilation of several authors over centuries of time. As Enns points out, this is not a new conclusion but is as old as the Old Testament itself.

The discussion around the Bible’s beginnings is described as self generating as there are internal conflicts within the text itself.  When I read this section the questions and conflicts resonated so deeply with my own experience with the Scriptures that I’m confident I would have audibly expressed my agreement if not for being on the train and surrounded by strangers. 

Enns remarks that questions and discussions around Genesis should be expected because Genesis generates its own questions. Why are there two completely different creation accounts? Where did Adam’s offspring’s wives come from? Why does God need to ask where Adam and Eve are in the Garden? Why is Genesis so repetitive?  The presence of these conflicts, repetitions, parallelisms and stylistic deviations are evidence that Enns and centuries of Biblical scholarship point to when claiming multiple authors and the nationalistic purpose of the texts.

This is an important point because it takes Genesis and the Pentateuch out of the realm of pure historical account (and therefore out of conflict with modern science) and into a complex assemblage for the shaping of Israel’s relationship with God and the world.  

The book returns often to the impact of reading Genesis well on our view of science and as I move toward the 24^th% and beyond a discussion of genre and calibration with similar ancient texts is taking shape.  I’ll continue to process the book and report more as the fraction of the total book read approaches 1/1.

Pop(ulation) Quiz

What is the total human population?

How many bacteria populate your gut?

How long would it take to cover the world in elephants if their population was allowed to grow unrestricted?

Write your answers on a lined piece of paper and turn it into my desk by the end of the period.  If you are into the whole paperless thing you can turn in your answers to the comment section.

The Essentials – A Survival Story

Last April I walked across the parking lot into work after a long spring nights soaking and was greeted by thousands and thousands of worms.  I couldn’t help but walk in a little slower that morning as I pondered the worms paristalticly parading across the pavement.  

This is what I remember observing and thinking that day.

As I walked from my car to the front door at work one rainy April morning I noticed 100s if not thousands of worms sprawled across the expanse of the parking lot.  There were small worms and big worms, and all were completely stretched out, presumably in an attempt to not drown in the supersaturated earth.  My first thought was that if a guy wanted to collect worms this would be a great time to do it.  This in fact is a favorite childhood past time for many people. I remember a lot of good times collecting worms on a rainy day or soaking an area of the lawn to collect worms before going fishing. As useful as this phenomenon is for would be fisher kids, to a worm this is a survival mechanism.

 I don’t know enough about the biology of worms at this moment to comment very specifically but I am aware that worms have a nervous system and a capacity for some sensory responses but they are not on level with mammals or fish or other higher organisms in terms of intelligence, decision making or anything like that.  What worms do have is a survival instinct.  They have an instinct that triggers a response if they are in danger of suffocating because the ground is filling with water just as people have a survival instinct of getting out of water if we are being held under water and couldn’t breathe. Our instinct, like the worm’s, is to get out.  Worms don’t have the capacity to want. Worms have an instinct (or nature or biochemistry or whatever you want to call it) to get out in order to survive.

As a result of this instinct, as I was walking into work that rainy April morning, there were thousands of worms within 100 feet of me that were surviving the rain. They were surviving this horrible situation, making an attempt to avoid drowning in the murky soil below. Their home had become inhospitable and as a result they fled.

Fast Forward through 8 ½ hours of work,  five delicious cups of coffee, three pieces of peanut butter toast, a bowl of delicious lasagna supplemented with hard boiled eggs and tobacco sauce, I emerged from work having survived it (having satiated my instincts for survival by eating all of that food of course).  I emerged to find, not all of the worms, but many of the worms, as worm carcasses, splayed out across the blacktop. Dead.  These worms were not survivors. They followed an instinct to get out of a situation that would have surely caused their death but their response also caused their death.

Not all fleeing worms however, remained to die on the blacktop. Some of the worms went back to the soil, some of the worms found higher ground or found a moist place that would not consume them and fill their little membranes with the aqueous poison that would subsequently claim their fallen comrades. In short, they survived. This is the battle worms fight every time there is a rain, every time their home becomes inhospitable to life. They have to survive it.

Those worms that return and continue burrowing through the ground once it dries out a bit and especially those worms that procreate (that is go have little worm babies) with other worms, those worms survived.  Not just as individuals and not just in terms of their family name or to live another day.  Their specific genetic makeup survived the flood and those genes became more likely to be passed on to the next generation of worms.

 Perhaps if there is something about the survivors genetic make up that caused them to have an affinity for higher ground or sensed a finer range of moisture levels that would be hospitable or if they just got lucky, their genes will go on and the genes of their mates on the blacktop will not.  

So some of the worms survived, some of them did not, some of the gene variations will be passed on, some will not. In this story, and in an evolutionary sense, genes are the ultimate survivors.

While this is quite a harrowing tale it is certainly not the picture of survival of the fittest that is painted by some authors regarding cruelty or violence between organisms.  There is certainly no direct conflict or fight between two individuals.  This is not the story of the lion tracking and stalking a gazelle to catch it and rip open its throat to subdue and eat it (though that is certainly also an example of something surviving and something not surviving and ultimately linked to the survival of genetic material).

The worms give us a survival story with evolutionary consequences but not the type of survival we always think of. This is characteristic of evolution in a lot of ways. To understand and accept evolution we have shift our paradigms toward those of greater and more minute scales than we often have the mental capacity to comprehend (I know it’s the case for me). 

How long is a billion years?  What is a gene? How is a gene expressed and what impact does that have on me? These are mind bending questions and questions that we ultimately have little to no frame of reference to answer unless we examine them intentionally and with tools that are useful for exploring them.

The Essentials - What is Survival and who are the Fittest?

I can't believe that Survivor has lasted 24 seasons.  But then again I can't believe Ben gave Courtney a rose last night. I mean how could he be so blind? Wait... strike the last two sentences from the record. In the show Survivor, contestants have to be strong or smart or sneaky or some combination of those traits. But that's just a dumb TV show.  What does it mean to be a survivor from an evolutionary perspective? What is a survivor and who are the fittest?

These terms have created some backlash, especially for Christians, as they stir up images of ravenous lions tearing the flesh off of an innocent, majestic, bounding antelope. I've heard several people say that they couldn't believe in evolution because God wouldn't work through such a violent and senseless mechanism. While I won't speak to the theological implications of the conclusion this unfortunate image produces, in the next few posts I will try to shed some light on the two evolutionary concepts of survival and fitness.

The Essentials - Where Does He Get Those Wonderful Toys?

The Joker was impressed by the cool grappling guns, smoke bombs and armored PJs Batman wielded but those were not the reason the Caped Crusader was a great crime fighter. Batman was good at his job because he was motivated and he was a detective.  While Joker saw Batman as a flawed fighter (because he knew that Bruce Wayne, like any (hu)man is capable of good and evil) what the clown overlooked was the cunning and diligent detective work that unraveled the mysteries of the joker’s schemes and ultimately brought the truth to light and the criminal to justice.

Scientists are a lot like Batman.  Sure they have cool tools.  Who wouldn't want to go to work every day to a lab filled with lasers and liquid nitrogen or at the heart of a rainforest or the bottom of the ocean? But it is not just the tools that scientists have, but how they use the tools to unravel mysteries, that give them super powers.

For much of history a rational understanding of the world has largely been a mystery scientists have diligently worked to unravel.  Like Batman’s detective work, the work of science often reveals new areas to investigate.  As these new areas are investigated new techniques develop and understanding grows. 

How do scientists learn about the age of the Earth? It’s elementary my dear Watson, specifically isotopic elements.  How do you observe a time that has faded into the past? See the forest for the trees, while making careful comparisons of the rings they have accumulated.

Radiometric dating and dendrochronology are examples of detective tools that scientists have used to reach into the past.  However simply counting rings or measuring and comparing ratios of isotopes doesn’t do anything.  These tools have helped us understand events and scales of time that were unobservable.  Natural history is a mystery and scientists are the sleuths that can solve it.

The Essentials - The Original Dating Game

Radiometric dating is relatively new to other methods for determining the age of old things.  There are two others that are far more low tech but yield reliable results and also insight into the question of Earth's age.  These two methods are based on the regular accumulation of strata, or layers in the earth and in a group of living organisms- trees.

Dendrochronology is the science of aging (that is, determining the age of)trees.  In its simplest form this discipline counts the rings revealed in the cross section of a tree.  One ring is formed per year of the trees life so then the total number of rings equals the total number of years the tree has been around.  If you have ever counted the rings of a tree I recommend you take a moment right now to say, "Hey, I'm an amateur dendrochronologist." If you'd like, and you're feeling crafty, you can make yourself a badge to wear the next time you go tree ring counting.  

There is a bit more to the science of tree ring counting but at its heart it really is as simple as
1 ring = 1 year of growth so the total number of rings = the age of the tree. 

Dendrochronologists can use this simple relationship to gain insights beyond the life span of a tree.  The size of the rings reveals information about the climate of the year that it was formed. If there was plenty of water and suitable temperatures the tree will grow rapidly and a wide ring will result.  Similarly a narrow ring reveals more harsh growing conditions such as drought or perhaps colder than normal temperatures. 

This discipline can also reach back beyond the life of a tree.  By comparing tree rings of overlapping age, chronologies have been created that stretch back tens of thousands of years.  The usefulness of this is best understood in an example. 

Say a wood tool is found in an archeological dig site.  The archeologists want to know when the people who used that tool populated the site.  By comparing the ring structure revealed on the wood tool to the known tree ring record the tool, and the people who used it, can be placed in their proper historical time.


The smaller samples have common sections that are alligned to assemble a lengthy chronology. The dig sample is compared to the known chronology to determine its position in history.

Tree ring chronologies can also be used to validate radio carbon dating by comparing the estimated age, based on the ratio of C14 to N14, to the known age based on the tree ring chronology.
Geological strata (layers in the Earth) can be used like tree rings for but can go much farther back than tree chronologies.   

The Essentials - Old Man River’s Got Nothin’ on You Earth (Part 2.2)

Clocks in the rocks

Carbon 14 (C14) predictably decays to Nitrogen 14 (N14) at a rate of half of the total sample every 5,000 years (OK fact checkers not exactly 5,000 but it will make the math easier in a few sentences. You should also brace yourself because I’ll use some even more ridiculously simplistic numbers in the next paragraph). This decay rate is called the half life. As you savvy readers may have realized the half life can be used to estimate the time since the rock was formed.  If you’re not so savvy, (Don’t worry if you’re not. I’m still trying to wrap my mind around the math of it) When I’m feeling underwhelmed by my understanding I find it helpful to work through a scenario. So let’s do this thing.

1) Let’s say a rock has 512 C14 and 512 N14.  From this ratio, and the known 5,000 year half life of C14, we can deduce that the rock started with 1024 (512 +512) C14 and is 5,000 years old.  In other words half of the C14 is gone so we know one half life has passed.

2) Now let’s say the rock has 256 C14 and 768 N14. From this ratio, and the known half life of C14, we can deduce that the rock started with 1024 C14 and is 10,000 years old. In the first 5,000 years the original 1024 C14 were halved to 512 leaving 512 N14.  In the second 5000 years the remaining 512 C14 was cut in half to 256 C14 and the 256 newly created N14 were added to the original 512 from the first 5,000 years for a total of 768 N14.

3) 5,000 years later (15,000 years in total) there will be 128 C14 and 896 N14. This C14 halving and N14 accumulating will continue until all of the C14 is gone (or there is not enough to discernibly measure).  The chart below carries this logic through to the end of its usefulness. After 50,000 years there isn’t enough C14 to measure, or be halved, so at this point we can only say that the rock is older than 50,000 years.

Total Age	Total Remaining C14	Accumulated N14
>50000	<1	>1023
50000	1	1023
45000	2	1022
40000	4	1020
35000	8	1016
30000	16	1008
25000	32	992
20000	64	960
15000	128	896
10000	256	768
5000	512	512
0 (The rock is formed)	1024	0

While this was a simplistic example, and the C14 numbers should be a lot bigger, it does show how the half life of an isotope like C14 can be used to estimate the age of a rock. In fact the usefulness of C14 for dating does have an upper limit of around 50,000 years.  If C14 was the only available isotope, the upper reliable limit of our Earth age estimation would be 50,000 years.  This wouldn’t mean that the Earth could only be 50,000 but rather we could only reliably say the Earth is older than 50,000 years old. THere may be a term for the case when the effectiveness for dating sails over and beyond the horizon of physical observability but I don't know it.  I think I'll call it "The at least hypothesis."

Fortunately there are many types of isotopes with a wide range of half lives, some very short and some very long. By using a range of isotopes with half lives of millions and billions of years scientists have estimated the age of the Earth at about 4.5 billion years.