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Jeffrey Martz
Poncha Springs CO USA

This is a blog about paleontology (the study of the history of life on Earth through the fossil record) with an emphasis on vertebrate paleontology, the study of extinct vertebrates (animals with backbones). The methodology and findings of paleontology will be discussed, as well as related issues such as evolutionary theory. The blogger is a vertebrate paleontologist specializing in the Triassic Period, the Beginning of the Age of Dinosaurs.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Saturday, March 26, 2011

Sorry about the delay.  The last couple months have involved some major changes and frenetic activity, and this post also expanded considerably in scope from what I originally had in mind, evolving (if you will) from a straightforward explanation of Linnaean taxonomy to an extremely detailed answer to the question "how do we know that we are descended from apes?" Since the post was so gigantic, I've split it in half.  Here is part one.  Read it, get some sleep, the next will be up in a couple days.  I have one or two posts on taxonomy I want to do after this one, and then we should move right into evolutionary theory.


The first scientist to call human beings animals and primates was a Christian creationist.

Carl Linnaeus (1707-1778) was a Swedish biologist, and like most Western natural scientists of his time, he was a Christian who believed all life was divinely created by God, more or less in its present form (he suggested that there might be little changes due to hybridization). He was also the inventor of what is usually called "Linnaean taxonomy" (remember that "taxonomy" is just the practice of giving names to organisms).  This basic system of naming and classifying living things would persist for two centuries after Linnaeus' death, although many modifications have been made to it in that time.  Today, most biologists and paleontologists prefer to use what is called "phylogenetic taxonomy," which I will discuss in the next post.

There are two parts to Linnaean taxonomy:

1. Binomial ("two name") alpha taxonomy, which I have been talking about in the last couple posts.  Linnaeus popularized this system, in which the species is the basic unit of classification, and species are contained within genera.  Linnaeus used both genus and species names together when naming a plant or animal (e.g. Homo sapiens), and this is still the practice today.

2. A hierchical, ranked, or "nested" classification system.  Creationist or not, Linnaeus recognized that there were patterns to life on Earth which were impossible for him to ignore, and these patterns formed the basis for his classification system.  As discussed in the last blog, multiple species may be similar enough to each other (and different enough from all other species) to group into genus.  However, particular genera may also share enough similarities that they can be grouped into a bigger category, called a family.  Under Linnaean taxonomy, Tyrannosauridae (the suffix -idae is used for families) is a family, and its members are all tyrannosaurids: Tyrannosaurus, Tarbosaurus, Gorgosaurus, etc... The ability to unite groups based on anatomical similarities does not end there.  Families can be grouped into orders, which are grouped into classes, which are grouped into phyla (plural, the singular is phylum), which can be grouped into kingdoms, which are grouped into domains. Moreover, there are all kinds of intermediate ranks (e.g. suborders, infraorders, subfamilies, etc...) which can be introduced as needed.  For example, if you group a bunch of genera inside a family, and then realize that some of the genera have more similarities to each other than to others, you can stick a couple subfamilies inside the family and separate the genera into those. Here is a diagram giving an outline of the basic system.


Linnaean taxonomyOne reason why most modern biologists and paleontologists don't use Linnaean taxonomy anymore is because the exact ranking is a little arbitrary, just as it is with genera (discussed in the last blog).  For example, there is no question that the genera Tyrannosaurus and Gorgosaurus should be grouped together within a bigger group (family Tyrannosauridae) and that this group lies within a group containing all carnivorous dinosaurs (suborder Theropoda).  However, why are Tyrannosauridae and Theropoda a family and suborder?  Why isn't Tyrannosauridae a suborder and Theropoda an order?  Just as with saying a bunch of similar species are in the same genus (instead of just being really closely related genera), it is an arbitrary exercise.  When I discuss different animal groups below, I'll use rank names to start with, but as I go from bigger groups to smaller and smaller subgroups, there is more and more disagreement as to which rank names should be used.  Eventually, I'll stop using them altogether.

Now, here are a couple of interesting questions: Do humans fall somewhere in this hierarchy, or are we so unique that we stand apart from all other living things?  And why is it even possible to group organisms in such a tidy manner?  I'll answer the first question here, and the second down the road.

Let’s start with domains and kingdoms.  The most common system in use after the 1960s (in the waning days of Linnaean taxonomy) recognized five or six: Animalia (the animals), Plantae (the plants), Fungi, Protista (single-celled or very simply multicellular organisms sharing certain characteristics with animals, plants, and fungi; more on that in a second), Bacteria, and Archea (the latter two containing all other single-celled organisms, which were once collectively all just called "bacteria" or "monerans").  Animals, plants, fungi, and protists all have cells with a bunch of little complex structures enclosed by membrane, which are called organelles, and which perform various jobs to keep the cell running. This type of cell is called a eukaryotic cell.  The nucleus, which is sometimes described as the defining feature of eukaryotes, is an organelle which encloses the DNA.  Complex organelles (including the nucleus) are absent in other single-celled organisms (bacteria and archeans).  So, because if these similarities at the cellular level, another rank (Domain) was invented to enclose the kingdoms with eukaryotic cells.  Animalia, Plantae, Fungi, and Protista were put in within Domain Eukarya. Humans don't have cells like eukaryotes, bacteria, OR archeans.  We have a special and totally unique kind of cell called the SuperAwesome Cell, which has a little nuclear reactor and gears and- Ha ha, just kidding.  We have a typical eukaryotic cell.  Here is a drawing of one; most of the labelled features are organelles.Eukaryotic cell

Now, animals, plants, and fungi are all multicellular (which is to say, they are a mass of several different kinds of cells which work together to keep the organism alive).  Plants are autotrophs, meaning they get energy and raw materials from non-living sources, specifically sunlight, and (like protists) some have cells which usually have two or more flagella (a flagellum is sort of like a little tail that some cells have that can be used to either propel the cell through fluid, or to generate a current).  Animals and fungi are both heterotrophs, meaning they get energy (and raw materials for building and repairing themselves) by consuming the cells of other organisms.  Animals and fungi also possess flagellate cells, but these only have a single flagellum; on the basis of these similarities, animals and fungi are grouped together in a group called Opisthokonta.  However, animals differ from fungi in mostly being mobile at least some stage of their life, and differ from nearly all other types of eukaryotes (protists, plants, and fungi) in lacking a rigid wall around their cells. Human beings don't require food OR sunlight, because we run on magic, and are just made of one big magic cell with hard walls of pure titanium.  Ha ha, just kidding.  We are mobile, multicellular, heterotrophic eukaryotes without cell walls, and produce a type of flagellate cell with a single flagellum (I'll give you a hint: only males produce them).  The eukaryote below is NOT photosynthesizing, and you can see that the cells in the picture on the right only have a single flagellum.

AnimaliaAmong animals, sponges have the simplest organization, are are placed into a subkingdom called Porifera.  They have a few different types of cells, but the cells do not have any special organization within the sponge.  All other animals have many different types of cells which are organized into groups of the same kind of cell, called tissues (e.g. Muscle and skin are tissues, aggregations of muscle cells and skin cells respectively). Animals with organized tissues are grouped into subkingdom Eumetazoa.

Among Eumetozoans, some animals have radial symmetry, meaning you can cut them half in many different directions in which both halves are mirror images; these are placed in a group called Radiata.  This group includes jellyfish; picture a jellyfish from the top, and you can see that you could cut it into several different directions which are (almost) mirror images, like a pizza.  Most other animals can only be cut in half in one direction in which both halves are (almost) mirror images; these are placed in a group called Bilateria.  Bilaterians also have more types of tissues than radiatans, which only have a couple.

Human beings, being specially created, have one type of cell (remember, the SuperAwesome Cell), and can be cut in half in exactly 12 different directions in which both halves would be mirror images. Ha ha, just kidding.  We have organized tissues (skin, muscles, nerves, etc.) and are bilaterally symmetrical (if we are cut in half in any direction except right down the middle, the two halves will not be mirror images).  No more joking around.

Eumetazoans and bilateransBilaterians (like all animals) start off at fertilization as a single cell (the zygote), formed by the fusion of a sperm and egg.  This single cell then begins to divide, forming a hollow ball of multiple cells called a blastula, which has an opening at one end, called the blastopore, which later forms one end of the digestive tract.  In some bilaterians, the blastopore forms the mouth, and the anal opening forms later, and these are placed in a superphylum called Protostomia.  In other bilaterians, the blastopore forms the anus, and the opening for the mouth forms later, and these are placed in a superphylum called Deuterostomia.  There are other consistent developmental differences between the two groups that we won't get into. Human embryos follow typical deuterostome development in which the blastore forms the anus first.

Protostomes and DeuterostomesThere are several groups of deuterostomes, but I'll just mention a couple.  One group, phylum Chordata, differs from other deuterostomes in several ways.  Chordates have a hollow nerve chord (the spinal chord) and a stiff rod of cartilage (the same stiff but flexible tissue in your ears and nose) called a notochord.  Both extend through the back of the animal, with the nerve chord being more dorsal (closer to the back) than the notochord.  Chordates also have pouches behind the mouth called pharyngeal pouches which develop into gills in some forms, and a tail behind the anus, as well as segmented muscles running down the length of the body (think about a fish filet) .  Another group of deuterstomes, phylum Enchinodermata, have hard plates of a mineral called calcium carbonate protecting the outside of the body, and (although the larvae have bilateral symmetry like other bilaterans) develop pentameral symmetry later in life; this means that you can cut them in half exactly in FIVE directions in which the two halves are mirror images.   Enchinoderms include starfish, sea urchins, and sand dollars.  Human beings have a hollow spinal chord, and early in our development as embryos we also have a notochord, pharyngeal pouches, and a tail, which disappear in embryos later in development.  That's right, you used to have "gill slits" (though not actual gills) and a tail. This is getting weird, huh?  You also have segmented muscles running down your body (think about the six pack on a bodybuilder; that is a series of abdominal muscles).  You don't have pentameral symmetry or hard plates of calcium carbonate on the outside of your body, so at least you aren't a starfish.

Chordate embryosMost chordates have a hard case of cartilage protecting a mass at one end of the nerve chord (the brain); we refer to this protective case as a "cranium" or "skull."  Most of these also have a cranium also protect the nerve chord itself with a series of segments made of cartilage as well, called "vertebrae", with the whole series of vertebrae being called a "spine" or "backbone."  It is also notable that these hard parts are all inside the body, surrounded by soft tissue, instead of the hard parts being entirely on the outside of the body like a clam, crab, or sea urchin.  We put chordates with an internal skeleton with a skull and vertebrae in subphylum Vertebrata.  I don't think I need to tell you that you have a skull and backbone, or that your bones are inside your body.

In the picture below, the human vertebra is upside down compared to the sauropod vertebrae; the spinous process of the sauropod verts is pointing up, which is how it would be in life.  Since we stand upright, ours normally point back.

VertebraeOK, so we are eukaryotic, multicellular, bilaterally symmetrical heterotrophs with organized tissues, which develop from a blastula in which the blastopore forms the anus, and which later develops pharyngeal pouches, a notochord, and a postanal tail, and protect their central nervous system with a hard skull and backbone.  So, this would make us animals, and more specifically, vertebrates.

We aren't just descended from animals.  We are animals RIGHT NOW.  But that doesn't necessarily mean that we are descended from apes, right?

Let's keep moving....

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Blog Comments
Mike Taylor

Guest Comment

Great work, Jeff, this is a sensational series of posts.

Is it wrong that on seeing the final picture, I instantly recognised (from left to right) a posterior dorsal vertebra of the diplodocid Supersaurus, previously thought to have been an anterior dorsal from a brachiosaurid named Ultrasaurus and subsequently renamed Ultrasauros due to preoccupation, a dorsal vertebra of Argentinosaurus with controversial hypantra, and a mid-to-anterior dorsal vertebra of Supersaurus initially considered the holotype of its own genus Dystylosaurus?  They are just SUCH distinctive shapes.


Guest Comment

Hahaha, love the sarcastic "humans run on magic" bit.

Jeffrey Martz
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It's not wrong at all considering that I got the photo off SV-POW, so the least I can do is post a link:

Mike and his partners in crime Darren Naish and Matt Wedel maintain the "Sauropod Vertebra Picture of the Week" site, which discusses thier own investigations into sauropod dinosaurs and various related topics.  Darren also maintains "Tetrapod Zoology", which I have linked from time to time, which is probably my favorite site for learning new things about different vertebrate groups that I didn't know before:


Guest Comment

Great (first) article, a lot to soak in but still understandable for the layman just interested in learning more. Didn't catch me with the "cutting humans in 12 directions" either since I initially thought you were talking about the human cell, ha!


Guest Comment

Well, thats just sad.

First of all taxonomy is not limited to living organisms or even to biology. Try soils. bed rock, meteorology, just to name a few. I was truly amazed at how fast you blew by complex cell structures PERFORMING VARIOUS TASKS to KEEP A CELL RUNNING, not to mention DNA. Just how does a complex group of molecules (organelles) perform these tasks? Such as constructing other molecules guided by information obtained from DNA, (which can only be described as intelligent acts). Perhaps it is a tiny little magical brain inside each cell that as you put it "keeps it running". Maybe you should just face the fact that where there is an intelligent design there must be an intelligent designer! Would you believe that a tornado could blow through a boeing plant and drop a fully functional 747 on the runway? Anyway keep searching. eventually even you will find something so extraordinary that you won't be able to dismiss it.

Good Luck,



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