Episode 5: Elephants, Cats, and Ticking Clocks

Posted in Individual Podcasts and Transcripts with tags , , , , , , , , , , , on October 24, 2011 by Dr. Matt Bonnan

Unlike a lizard where the limbs are sprawled out to the sides, most mammals have drawn their limb bones vertically beneath the body.  What are the functional advantages of such a posture? And what does all this have to do with Dr. Bonnan almost being creamed by an African elephant?

Podcast Teaser: I learned the real meaning of the word “awesome” during a close encounter with an African elephant.  A colleague and I were in an animal park in South Africa, and we had spied a large, lone male elephant walking towards our car.  As I was taking pictures of the elephant, our car was suddenly traveling in reverse with my colleague uttering frantic expletives.  It was at this point I noticed that the elephant was picking up speed and coming right for us.  On attempting to turn the car around, we became stuck, and now our fate was left to a very large mammal.  In my cleverness, I rolled up the car window, as if that would protect me from 6 tons of muscle and bone!

References / Further Information

Advertisements

Episode 4: A Brief History of Meat

Posted in Individual Podcasts and Transcripts with tags , , , , , , , , , on October 14, 2011 by Dr. Matt Bonnan

Many of us enjoy eating meat, but few of us pause to think about how important its pre-meal form, skeletal muscle, is for vertebrate life.  Or why you eat different parts of fish and tetrapods for that matter.

Podcast Teaser: I don’t know about you, but I enjoy a good steak, especially fillet minion.  In fact, many of us enjoy eating meat, but few of us pause to think about how important its pre-meal form, skeletal muscle, is for vertebrate life.  Unless you injure your skeletal muscles, you barely notice them – of course, if you’re a body builder, you probably notice them a lot more.  But the contractions of skeletal muscles across the joints in your skeleton do everything from keeping you upright to preventing nasty falls.  Believe it or not, meat is so universal among vertebrate animals that muscles in one area in a fish do very similar things in the same area in your body.  This is because, long ago and 540 million years away, our common ancestor developed two important traits …

References / Further Information

Transcript Available Upon Request.

Episode 3: How Do You Make a Snake?

Posted in Individual Podcasts and Transcripts with tags , , , , , , , , , , on October 11, 2011 by Dr. Matt Bonnan

It seems only fitting that a podcast series called Along the Backbone should discuss the formation of the backbone in one of lengthiest vertebrates: snakes.

Podcast Teaser: Snakes are lizards.  More specifically, snakes are limbless, eyelidless, earless lizards with megakinetic skulls and well-developed salivary glands that often produce venom.  Among the many standout features of snakes, perhaps the most fascinating is how these vertebrates routinely develop a body that will have 120 or more rib-bearing vertebrae and no limbs.  It turns out that a simple but profound difference in the timing of the expression of developmental genes called HOX genes renders snakes limbless, whereas an increase in the frequency of another set of clock-like genes generates their amazing number of vertebrae.

References / Resources:

Transcript available upon request.

Episode 2: Why Pedigrees Are Not Just For Dog Shows

Posted in Individual Podcasts and Transcripts with tags , , , , , , , , , , , , , , , on October 10, 2011 by Dr. Matt Bonnan

When we talk about reconstructing the vertebrate family tree, we are also trying to develop a pedigree of relationships. This pedigree, in turn, helps us understand how anatomical changes have taken place over time.

Transcript of Episode 2: Why Pedigrees Are Not Just For Dog Shows

Our family has a miniature pinscher named Squirrelbella.  You can ask my six-year old daughter about that name.  Squirrel, for short, is no show dog, and so as much as we love this little tail wagging, occasionally yippy carnivore, we do not have pedigree papers for her.  In the world of dog shows, pedigrees are important to establish the blood line of the dogs which end up being winners.  To make future money, you as a serious breeder would want to have offspring that descended from the winners and not the losers.  In short, you want a reliable pedigree: a family tree.

When we talk about reconstructing the vertebrate family tree, we are also trying to develop a pedigree of relationships.  Formally, such a pedigree of relationships is known as a phylogeny.  A phylogeny is a hypothesis of relationships, based on data, which is open to testing and which predicts the shared common ancestry of various groups.  This means that any phylogeny is not permanent – it will either be supported, modified, or rejected when new data surface.

If our goal is to understand how vertebrate form and function has changed in different groups, or even to define what a vertebrate is, we have to understand the order and appearance of these skeletal features.  For vertebrates, we typically reach an understanding of changing function by comparing the anatomy of several related groups to see what has changed (what traits are special to our group of interest) and what has remained the same (what traits are present in all vertebrates).  This requires an understanding of the relationships of vertebrates.

We establish vertebrate phylogeny on traits, the attributes or features of particular animals.  Simply put, a phylogeny is a hypothesis of relationships established using trait data.  But traits are not self-evident – they are not labeled neatly on fossils or written on the tags of pickled museum specimens.  So, how do we select informative traits?

The simplest approach to reconstructing vertebrate phylogeny would be to survey as many animals as possible and then compare the distribution of similar traits.  We could then tabulate up all the similarities, and group together vertebrates which share more traits in common.  For example, we group all known vertebrates together because they all possess specialized back bones called vertebrae.  We could continue comparing similar traits, divvying up the vertebrates into smaller subgroups possessing more exclusive shared traits.  Fish have gills, amphibians have a moist skin, reptiles are scaly, birds have feathers, and mammals have hair.  By doing this, we would eventually have a phylogeny, a hypothesis of relationships among the living vertebrates.

Yet, not all similar-looking traits are related to common ancestry.  For example, a shark and a dolphin both have a stream-lined body form with fins.  At face value, we might conclude that these traits were evidence that sharks and dolphins shared a recent common ancestor.  However, on closer inspection, we would begin to notice some large discrepancies.  The skeletal structure of the shark is cartilaginous whereas that of the dolphin is bone.  A shark’s skin is rough and covered in tooth-like scales, yet that of a dolphin is smooth and overlies a layer of blubber.  Sharks breathe using gills, but dolphins have lungs and must surface occasionally to take in fresh air.  Dolphins nurse their young on milk from mammary glands while shark pups must fend for themselves.

Eventually, it would occur to us that, more likely, the similar shapes of the shark and dolphin were not due to common ancestry but instead to a common environment: water.  Water is denser than air, and there are only so many “solutions” to swimming fast in it.  The shark and dolphin have converged onto a similar functional solution, the streamlining of their bodies and the possession of fins, to move fast in a dense medium.  So, overall similarity is not good enough: we must be able to distinguish between traits inherited through common descent and those that are due to convergent evolution.

Traits are not static.  Under the theory of biological evolution, traits are inherited and modified during descent from a common ancestor.  Traits, the key features we are establishing vertebrate relationships on, are plastic and malleable – to wit, they change.  Although the plasticity of traits seems at first to be a stumbling block to establishing vertebrate phylogeny, it is in fact a great asset.  This is because traits have states – that is, they have an original form and one or more variant forms inherited and passed down to different descendants.

The original form or state of a trait is referred to as primitive, whereas a trait is considered to be in a derived state if it has changed from this original condition.   It is the change from the primitive to the derived trait state which reveals evolution and pedigree.  For example, one type of trait is that of possessing appendages.  The appendages of the earliest jawed vertebrates were fins.  Therefore, fins are the primitive appendage state, and modern jawed fishes would be said to retain the primitive appendage condition.  In contrast, amphibians, reptiles, birds, and mammals have changed the original condition (a fin) into a new structure (a limb with digits).  So, in this example, fins are the primitive (original) appendage type, and limbs with digits are the derived (changed from the original) appendage type.  All vertebrates possessing the derived appendage state of limbs with digits are grouped together as tetrapods.  We would hypothesize that all tetrapods share a closer common ancestry with each other than any of these animals would with fishes.

The word primitive is often confused with something inferior or less developed.  It is important to note that all living vertebrates today actually possess a complex combination of primitive and derived traits.  To dispel you of equating a primitive trait with inferiority, imagine being thrown into a tank with a hungry shark.  Yes, the shark has primitive appendages (fins), and you have derived appendages (limbs with digits), but which of you will swim well?  Which of you will be the diner, and which the dinner?

But how does one determine whether or not a trait is in its primitive or derived state?  The answer is something called polarity.  Because trait states are changeable, they have polarity, or a direction of change from primitive to derived.  Polarity is an arrow of change pointing in the direction that a particular trait evolved.

Polarity is inferred in a number of ways.  In one approach called outgroup comparison, the trait state of interest is noted over a large number of animals outside the ones being studied.  If one particular state is widely distributed over these so-called outgroups, the researcher may conclude that this is the primitive state.  This reasoning would follow from evolutionary theory: all vertebrates should share certain general trait states, followed by different descendant groups that possess more exclusive trait states.  Therefore, commonality may indicate that a particular trait is in its primitive state.

Another approach to determining trait polarity would be to note when certain anatomical features appeared during embryonic development.  The idea here is that more general, foundational trait states should appear earlier in development, whereas more derived states of various traits should develop at a later time.  For example, all vertebrate embryos develop throat (pharyngeal) slits during development, but these are only retained as spaces for gills in fishes; the slits anneal and contribute to other structures in tetrapods.  Since all vertebrates develop these pharyngeal slits before these features transform into more specialized structures within each group, the retention of these slits in fishes would be considered primitive, and the annealed versions would be called derived.

The modern biologist or paleontologist thus collects trait state data and, using specialized software, analyzes the distribution of primitive and derived trait states.  The relationships of the vertebrates are determined by how many derived trait states they share in common, and this is translated into a branching diagram of relationships: the phylogeny.

The phylogeny is established on trait states that are independent of the chronological order of their appearance in the vertebrate fossil record.  This means that the fossil record can serve as an independent check or test against the phylogeny.  Since the assigned polarities are hypothetical, the chronological sequence of when certain trait states appear in the fossil record can either support or call into question whether something is indeed primitive or derived.  For example, the earliest jawed vertebrates in the fossil record possess fins, whereas it is not until much later that we see the first fossil vertebrates possessing limbs with digits.  This observation independently bolsters the assignment of fins to the primitive appendage state.  Through careful analysis of both traits and the fossil record, a reasonably consistent phylogeny of vertebrate animals has emerged, even if my little min pin doesn’t appreciate it.

Episode 1: Who’s Afraid of Evolution?

Posted in Individual Podcasts and Transcripts with tags , , , , , , , , , on October 8, 2011 by Dr. Matt Bonnan

In the first podcast of this series, we define the theory of biological evolution and discuss effective science communication in the current socio-political climate.

Transcript of Episode 1: Who’s Afraid of Evolution?

As we travel along the backbone of vertebrate anatomy in this podcast series, I thought I should define the theory of biological evolution in this first podcast.  Biological evolution is not simply “change over time” as is often claimed.  Your watch changes over time, but it certainly does not evolve.  The biological theory of evolution can be stated as descent with modification from a single, common ancestor.  In other words, all life on earth is related through a great family tree.  Different branches of the family tree have inherited modified characteristics unique to their portion of the pedigree through a process of natural selection.

Unfortunately, too often various anti-evolution sentiments and activities permeate the media, generating a public perception that evolution is, at its heart, anti-religious.  These sorts of challenges to science and science education are not new, and the reactions to them tend to be the same.  As scientists we say, “why don’t people accept the evidence for evolution?” and in popular media two talking heads will shout at each other over the issue, usually with a title like, “Science Versus Religion!”  Seeing the continuing frustration and hand-wringing of my colleagues and friends over this recurring issue prompted me to make this the first episode in this podcast series.

As scientists, we typically respond to challenges about evolution the way we would respond to a colleague questioning our data or methods: we give lots of information.  Scientists are taught to defend their hypotheses by providing data which can be evaluated by others, and this is one of the great strengths of our discipline.  However, if you assume that those opposed to teaching evolution will be swayed by a lot of scientific data, you will be very disappointed.  Here, I dissect what I have come to learn about the creation-evolution argument in the public sphere, and give some thoughts on how my colleagues and I can be more effective science communicators.

First, clear definitions matter.  What, for example, do you mean when you say, “creationism” or “creationist”?  To a scientist, those terms generally translate into someone with a very narrow, fundamentalist view of the world, including those who may take a holy text literally.  But I guarantee these words translate very differently in the public sphere.  For example, many people feel that if you believe in a creator, then you are a creationist.  This is a very important difference!  To many people the word “creationist” means “people of faith” – so if you believe that a scientist is debunking creationism, they are therefore debunking your faith.  Yet, many people of faith accept evolution as a valid theory.  From this perspective, it is easy to see why many spiritual and religious people are uncomfortable or angry with scientific “debunking” of creationism.  So carefully defining our terms from the beginning is extremely important.

Second, this is not about data: it is about fear.  There are many reasons for why people reject evolutionary theory, but in my experience the primary one seems to be the fear of loss: losing the spirit, losing the soul, and dehumanization.  If you believe that accepting evolutionary theory is tantamount to rejecting your faith, your family, and your humanity, I doubt you will be willing to listen to a scientist give you facts about evolution, let alone be persuaded that the theory has merit.

Third, both the public and the scientific community tend to conflate various things together under the banner of “science” or “evolution” or “religion,” and this leads both to more confusion and anger on both sides.  Here’s where the problem lies.  Let’s say you are an atheist and you conflate science with atheism.  It would then be appropriate to ask, where does the science end and the atheism begin?  But we often don’t make these distinctions, and this leads to the false impression that evolution is a theory whose purpose is to reject religion.

Instead, science is merely a tool for understanding the natural world.  It is certainly a powerful tool, but nonetheless a tool just the same.  Science is not about making God go away.  Science is not an antidote to religion, it cannot replace faith, and one does not live by scientific tenets.  But this cuts both ways, because faith cannot and does not replace science as a tool for understanding the natural world

Given these realities, how can we be more effective science communicators, particularly about evolutionary theory?

First, assuaging fear is critical.  We as scientists will get nowhere in general public discourse if we mock, belittle, or talk condescendingly about faith while proclaiming the value of science.  Having respectful discussions with those willing to engage with us will probably accomplish a lot more.

Second, that said, let’s stop trying to convince the unconvincible, and instead focus on the majority.  For example, there are people who still believe that the earth is flat, despite all evidence to the contrary.  Why on earth (pun intended) would you waste your time as a geographer or cartographer trying to convince that small group of people otherwise?  Wouldn’t your time be better spent arguing for better geography classes and better public awareness on how the use of maps influences our culture, politics, and resource management?  Which of these options is likely to be more fruitful in the long term?  By the same token, there are those who doubt evolution and have gone so far as to claim that plants are not alive for convoluted reasons arising from a literal interpretation of one section of Genesis.  Don’t believe me?  Go to the Institute for Creation Research and search for “are plants alive?”  I ask you, how can you convince someone about the importance of evolution or science if they won’t even acknowledge that plants are living things?  Not believing plants are alive would undermine the very underpinning of our human civilization: agriculture.

Third, I realize that there will always be those in positions of power who will question science, especially evolution, and the necessity of teaching these tools.  In these situations, showing the links in the chain from basic research to practical matters is always more beneficial than talking about how well evolution is supported.  Going back to the flat earth example, let’s get practical here: if you are an airline pilot and you don’t believe the earth is round, you are going to chart a course that will take longer to complete, may not even put you where you want to be, and certainly will gobble up more fuel.  Let’s turn to geology and paleontology and get practical here, too: it is the concept of an old earth and the distribution and sequence of rocks and fossils that oil companies rely on to find their fuel.  If paleontology and geology were equivalent to flat earth concepts, why would companies invest billions of dollars searching for fossil fuels where the sciences of paleontology and geology say that they are?

And what of teaching evolutionary theory?  Let’s get practical again: biological evolution states that all living things are descended with modification from a common ancestor.  In medicine, this means it is practical and desirable to look outside the human body for solutions to anatomical defects, disease, and developmental problems.  You might choose to not accept the genetic and fossil data that support a close relationship between primates like ourselves and rodents.  However, you would then have to consider why pharmaceutical companies and medical researchers would bother studying and testing drugs on rats and mice if there were no relationship between these animals and humans.  Wouldn’t’ it would be a huge waste of money?  And what about disease itself?  Acknowledging evolution means you also acknowledge that diseases are often caused by living things which descend with modification and adapt to their host’s body.  A static view of disease-causing bacteria or viruses would get you nowhere with drug research: if there was nothing to evolution, it would seem awfully foolish and wasteful for pharmaceutical companies to invest millions of dollars into drug research.

Ultimately, the controversy over evolution is not about data but about fear.  In my experience, the biggest barrier for many people to accept evolution is accepting that we are related to other living things, and that we share a close, common ancestor with chimpanzees.  I acknowledge that this can be a deeply disturbing thought for some.  As a scientist, I would say that this is where the data consistently point us.  But as a fellow human being, I would say, even though humans may share a common ancestor with chimpanzees, we still have value, there can still be a God, there can still be morality, and people can still love and be loved.  As scientists, we must become better at conveying our data along with our shared humanity.

Note – this first podcast and its transcript were derived with some revision from an earlier post on my Jurassic Journeys blog.  I felt this was such an important topic that it bore repeating.  Future podcasts and their transcripts will consist of wholly new material not featured elsewhere.

Welcome to Along the Backbone

Posted in Along the Backbone Information with tags , , , , on October 7, 2011 by Dr. Matt Bonnan

This blog is a companion to a podcast series, Along the Backbone, by Dr. Matthew Bonnan, that explores the evolution of vertebrate anatomy, from bones to brains, through deep time.  The text of the audio essays will appear here, there will be links to the podcasts, and this blog will provide a forum for comments and discussion.

Stay tuned … the first essay and audio podcast will be posted soon!