A Poorly Illustrated Guide to Genetically Modified Organisms

Anybody in the mood for a tasty meal? I’ve been slaving over a hot stove all morning working on the main course: a heaping casserole of haute SCIENCE! On the side, I’ll be serving up a generous spread of odiferous fruits, sinfully steamed vegetables, and decadent meats… but there’s a catch! All of my splendid victuals hold a dark secret: someone has been tampering with their very DNA. That’s right, I’m inviting you over for a dinner of Genetically Modified Organisms. I hope you’re hungry.

These chimeras of the kitchen, these degenerates of digestion, are showing up in produce departments worldwide. But what exactly are they? GMOs are creatures whose genetic makeup has been altered in order to confer a useful change in anatomy and physiology. These organisms are created by taking existing genes from one critter and inserting them into the genome of another, usually by means of a viral vector. Examples include corn that produces its own pesticide, cows with increased milk production, glow-in-the-dark kittens, soybeans immune to certain herbicides, and bacteria that synthesize pharmaceuticals.

Did you say glow-in-the-dark kittOHDEARGOD.

Genetic engineering isn’t all recombinant kittens and spliced rainbows; there is a vocal group of concerned individuals ardently opposed to the proliferation of GMOs. These organisms are despised by many, especially within the organic and natural foods movement. Yet there are many that hail GMOs as nearly miraculous boons to society. What are you to make of this discord, Dear Reader? Are GMOs a blessing, a curse, or more complex? I’ll do my best to stir this pot of biological soup and explore the many flavors of this very issue over the course of my next 3 articles, hopefully adding a subtle note of Skepticism to the bouquet. In this series, I’ll be looking at the potential impacts of GM technology. Specifically, I will be addressing the many criticisms leveled against GMOs. These arguments fall into 3 broad categories, and I’ll be dealing with each in separate articles. The categories are:

1. Hazards to human health

2. Effects on the environment

3. Offenses against Nature and Decency

Won’t you join me, Dear Readers? I’ll even let you take home the leftovers.

Part 1: GMOs and human health

A Poorly Illustrated Guide to the Tree of Life: Part 3

Hello again. My name is James, and I like science. It’s been a while, but I’m back with some more words and drawings to tickle your every fancy. Our gradual climb up the Tree of Life continues. Where it will lead, none can be certain. What we can be certain of, however, is this: you’re about to become uncomfortably familiar with one of the Animal Kingdom’s most wondrous creatures: the Ctenophore. These mysterious undersea jellies may not be as cuddly as a kitten or a bunch of dudes with beards, but don’t fret, Dear Reader. By the time you finish this article, I promise you’ll discover that you’ve been in love with Comb Jellies all along.

(And if you haven’t yet, be sure to check out Part 1 and Part 2)

Part 3.1: The Ctenophore

 

Comb jellies are ocean-dwelling invertebrates belonging to the phylum Ctenophora (it’s roughly pronounced “ten-o-four;” the ‘C’ is silent for some reason I can’t even begin to understand), which is Greek for comb-bearer. They come in a variety of shapes and sizes: some are inconspicuous specks of plankton, while others are brightly colored, downright gaudy little deep-sea vixens. The average Ctenophore is a transparent aquatic oblong with several rows of hair and a pair of long tentacles. If you’re unfortunate enough to have never seen one of these majestic beasts before (or you’re too lazy to look on Wikipedia), kindly observe this image painstakingly constructed with the latest rendering technology (i.e. Mac Paintbrush).

Behold!

Although Ctenophores are a strictly marine taxon, with no known freshwater species, they’re an extremely adaptable bunch. Comb jellies can be found near the coasts, in the middle of the open ocean, inside shallow inland seas, and in the crushing abyssal depths. Their versatility is a result of their simple but elegant design. The following section contains a brief account of the basic anatomy and physiology for an idealized Ctenophore, but be warned, Dear Reader; there are many variations and exceptions to these descriptions, some of which I’ll address in later on.

Anatomy of a Deep Sea Degenerate

Comb jelly. Get it? He's got a greaser hairstyle, because the ocean is just like the 1950s.

Ctenophores have partial bilateral symmetry, with a distinct top and bottom but no front or back. The top bears the entrance to the creature’s gastrovascular system (i.e. the mouth) and is designated as the oral surface. The bottom, known as the aboral surface, houses a set of anal pores and a sensory structure called the statocyst. Each jelly is equipped with 8 rows of cilia combs, or ctenes, that extend along the length of their bodies from near the mouth into the statocyst. These cilia move in a rhythmic motion that propels the jelly anywhere it fancies while simultaneously producing dandy little moving rainbows across their surface.

Side view of a single ctene. It's also probably the worst drawing I've ever made ever, and that's counting stuff like this: http://musasha.files.wordpress.com/2011/11/awfulspongefig.png.

The statocyst, which is itself comprised mainly of 4 stiff tufts of cilia, provides the jelly with information about its position relative to the pull of gravity. Each of the tufts is physically contiguous with 2 neighboring ctenes and supports a small grain of calcium carbonate, the statolith, in the center of the statocyst. The whole structure works sort of like a simplified human inner ear: when the comb jelly is perfectly vertical with respect to gravity (looking up or down for you non-sciency types), the statolith exerts equal pressure on all 4 tufts; whenever the jelly is tilted horizontally (like your mom after a night of appletinis and cooking wine), the pressure in increased on the lower tufts and decreased on the upper tufts. The variations in pressure are translated into electrical signals which pass into the Ctenophore’s nerve net and are interpreted by what can only be described as magic. Neurobiology isn’t my forte.

A very realistic close-up of a statocyst.

Just like sponges, the bulk of a Ctenophore’s volume is composed of water suspended in a gel-like matrix of proteins, the mesoglea, sandwiched between sheets of epithelium. Unlike sponges, comb jellies have fewer cells embedded in their middle layer and possess unambiguous and persistently interconnected tissue layers, although there is some disagreement in the scientific literature as to whether there are 2 or 3 layers (some authors have squared this circle by positing that comb jellies have 2.5 epithelial layers. Good job, Science).

Comb jelly anatomy: they're a series of tubes. 1. Statocyst; 2. One of many anuses; 3. Tentacle; 4. Transverse canal (i.e. some kind of tube); 5. Tentacular canal (also a tube); 6. Tentacle sheath (rather tube-like if you ask me); 7. Pharyngeal canal (i.e. another random tube); 8. Mouth (i.e. eating hole); 9. Pharynx (tube city); 10. Meridional canal (so many tubes); 11. Digestive tract (yep); 12. Mesoglea

Additionally, Ctenophores have fibrous myoepithelial (i.e. muscle) cells, a feature that may shed light on the evolution of the middle tissue layer which gives rise to muscle tissue in triploblastic animals like me and you, Dear Reader. Cells composing the outer surface of the jelly form the epidermis, which functions to protect and provide support to the animal’s interior bits. The epidermis also houses a network of neurons that act as the Ctenophore’s nervous system.

A Neapolitan ice cream representation of Ctenophore tissues. Strawberry indicates the outer ectoderm layer, with the yellow squiggles (butterscotch, perhaps?) representing the nerve net and purple (a drizzle of red wine reduction?) standing in for muscle. Vanilla represents the mesoglea, a mostly cell-free aqueous gel that gives the beast some structure. The final chocolaty layer is the endoderm, which lines the jelly’s various internal cavities, including the pharynx. Please note that I don't actually know what any of these structures look like, so don't go eat a comb jelly and expect it to be a creamy, non-traumatic experience.

Ctenophores, despite being totally bereft of a brain, are actually pretty good at moving around in and reacting to their environment; gently cruising the ocean and snatching up unfortunate sea-critters with their inscrutable tentacles. They accomplish this feat by using their nerve net to both process signals from their sensory organs and coordinate the actions of their comb rows and muscle tissue.

"Baby, your aboral surface sure does make my cilia beat rhythmically... and by cilia, I mean my penis."

Although this biological circuitry is about as powerful as a digital watch (and not the kind with a built-in calculator), it nonetheless makes comb jellies far more intelligent that the most scholarly and erudite sponge. Most species possess a single pair of feeding tentacles, which protrude laterally from the body and can be retracted into protective sheaths. The tentacles are covered colloblasts, a specialized type of cell that releases a gooey adhesive to adhere to prey items upon contact.

A cross-section of a single colloblast embedded in a Ctenophore's ectoderm. The reddish spheres at the top contain an adhesive that is released on contact. The coiled gray structure probably acts like a cellular shock absorber to protect the jelly’s tentacle as the prey helplessly thrashes and convulses in anguish. Ctenophores simply love killing.

Captured food is reeled in and licked off the tentacles by the jelly’s endoderm-lined mouth, where it passes into the muscular pharynx to be crushed and digested into a nutritive slurry which then flows into the beast’s stomachy canal system to be absorbed. These cilia-lined canals branch and radiate throughout the Ctenophore’s body (especially under the ctenes; see unwieldy cross-section above), allowing the rich broth to fuel its various tissues and functions, or be stored in elongated vacuole cells. Despite possessing several perfectly good anuses (=D), the jelly expels most of its metabolic waste by regurgitating it through the mouth (D=).

Sorry folks, I just couldn't bring myself to draw a detailed Ctenophore anus. Maybe next time.

While we’re on the subject of anuses, it’s worth mentioning that the sex lives of Ctenophores are rather tame; nearly all are hermaphroditic (and most of these are believed to be self fertile) and simply expel reproductive cells haphazardly into the surrounding water column in hopes of making more tiny jellies. A few species retain the developing Ctenophore larva in their endoderm, releasing them after a short gestation period. The juvenile jellies, called cydippids, are usually just miniature versions of the adults that gradually grow in size until they reach sexy-time maturity.

A larval Ctenophore, or cydippid. I usually just call them jelly kittens.

So, are you tired of comb jellies yet? No?

Good, me neither! In the next installment of APIGttTOL, we’ll explore Ctenophore diversity and evolution. Until then, Dear Reader, stay curious and rather gooey.

"Come on, Doll-face; these hermaphroditic manparts ain’t gonna fertilize themselves unless I decide to ingest my own sperm.”

James is a graduate of the University of Missouri, Columbia. He is a research biologist specializing in the molecular evolution of invertebrates. Feel free to visit his subpar research blog.

A Poorly Illustrated Christmas Card

Merry Shrimpmas to All!…

...And to Arthropod, a Good Night!

James is a graduate of the University of Missouri, Columbia. He is a research biologist specializing in the molecular evolution of invertebrates. Feel free to visit his subpar research blog.

A Poorly Illustrated Guide to the Tree of Life: Part 2

Hello again, Dear Reader. I hope you enjoyed reading Part 1 as much as I enjoyed pretending I didn’t write it; if not, please go back and read it again and again until my words become like a fine spiced beverage soaking through your brain. Also, reading Part 2 without the benefit of context will probably render my already muddled narrative wholly incomprehensible. You’ve been warned.

Part 2: Animals are Confusing: Sponges and Choanoflagellates

Now that we know what an animal isn’t, how do we move forward? As promised in Part 1, there are actually traits joining all animals in a nice clean monophyletic taxon, and they shall be presented herein.

This flow chart made more sense right after I drank all that absinthe.

Well, the taxon isn’t actually so nice. Or clean. In fact, the line between true animals and not-quite-animals gets quite murky, as we shall soon see. However, fear not, Dear Reader: Although things may get rather messy, the rain-scented, foaming-action of phylogenetics and molecular biology will probably save the day.

But first, let’s talk about our good friend, the Sponge!

This is a sponge.

This photo-realistic image depicts one of the sea’s most familiar denizens. Proud, noble, and perhaps mildly arousing, the sponge has quite an impressive history of scrubbing grimy Ancient Greeks, absorbing many an unsightly puddle, and inspiring today’s youth. Yes, I hardly need shower accolades upon the sponge, so great has been its contribution to humanity. So why have I decided to digress and take up valuable your-mother joke space discussing their merits? Sponges straddle the line between different types of organism; they are asymmetric, largely amorphous, and altogether alien to land-dwellers like us. There’s nothing quite like them, and a brief look at sponge biology will inform our understanding of what makes an animal.

Kitchen sponges don't contain any actual sponge; not since the Great Sponge Aggression of the '78.

Their habitat spans all the world’s oceans wherever sediment-free water is found; from pole to pole, along the coasts, down continental shelves, and across the ocean floor to the abyssal depths. A few species can even be found in freshwater environments, including everybody’s favorite continental rift lake: Lake Baikal.

The slightest pretext to draw Eurasian bodies of water is all I need.

The sponge body plan is quite variable, ranging from inconspicuous crusts to gigantic barrel-shaped cylinders. Internally, sponges are, for lack of a better word, untidy. Most of the sponge’s body is composed of a non-cellular gel, called the mesohyl, and some kind of scaffolding material.  The exact composition of this scaffolding is variable (including silica spikes called spicules, protein fibers, and several forms of calcium carbonate) and is important in the classification of the major types of sponges. These two substances are collectively known as the extracellular matrix, or ECM.

A sampler of some example sponge body plans: potbellied (left), sad cactus (center), and bluish amalgam (right).

Sponges lack anything readily identifiable as proper organs or organ systems, although a cross-section reveals an extensive network of hollow spaces that I’m willing to call organs if you’re willing to call the blackened space within my chest a heart. In the typical sponge, these channels begin as small tube-shaped cells (porocytes) along the external surface of the sponge and gradually expand into a series of increasingly spacious chambers until reaching a large central cavity, which ends in a terminal vent, called the osculum. This system serves three important functions: feeding, material exchange, and reproduction.

I couldn't agree more, Mr. Fish. 1. Water and food particles enter through a pinacocyte (not shown); 2. Water then enters the central chamber and is filtered by choanocytes; 3. The water finally exits through osculum; 4. All the while, nutrients are dispersed into the mesohyl.

Understanding how the sponge works its magic requires a close look at the cellular level. There are two very broad types of cell in sponges; external and internal. External cells line the parts of the sponge in direct contact with the surrounding water, including the previously mentioned hollow channels. Internal cells are embedded within the jelly and fibers that make up the actual sponge body.

A very rough map of sponge cell types in relation to the environment. A very, very rough map.

External cells can be further divided (Yay, isn’t biology fun?) into protective skin-like epithelial cells called pinacocytes and fancy flagellated cells, known as choanocytes, that line the channels. Like all true gentlemen cells, choanocytes wear a ruffled Victorian collar of cilia around their stately flagella visages. The choanocytes spin and flex their flagella to generate tiny water currents inside the sponge interior, pulling in fresh water, food particles (mainly bacteria, algae, and plankton), and, somewhat disturbingly, sperm; all the while expelling dissolved waste products out of through the osculum.

A single choanocyte embedded inside mesohyl (yellow). The flagellum (light blue) wiggles like an excited kitten tail, pushing water and food particles through the collar of cilia whiskers (dark blue). Food is captured by the cilia, carried down to the cell body, absorbed as a vacuole (i.e. phagocytosis), and digested in the cytoplasm.

There are several types of internal cells with subtly different functions, including cells that secrete materials (such as collagens, polysaccharides, and silica), facilitate changes in shape (sponges can actually contract and shift position, albeit slowly), produce gametes (them’s sexy-time cells), and act as a primitive immune system that attacks and engulfs foreign particles. Internal cells are generally amoeboid in shape, and their functions can sometimes overlap. The sponge equivalent of a stem cell is the totipotent archaeocyte, which can mature into any cell type.

A close up view of a slice of delicious sponge cake: 1. Pinacocyte; 2. Porocyte; 3. Secondary Chamber; 4. Mesohyl with Spicules; 5. Archeocyte; 6. Choanocyte; 7. Inner Chamber.

True tissues, defined as ‘a part of an organism consisting of an aggregate of cells having a similar structure and function’ and derived from a common cell lineage are generally believed to be absent from sponges; an understandable yet misinformed belief resulting from the erroneous notion that sponges are simply a chaotic heap of primitive organic material. Although certainly lacking the localization of vital functions found in most ‘higher’ forms of life (breaking a sponge in half effectively creates two perfectly happy new sponges), the various layers of cells are structurally and developmentally similar, well organized, and only function by virtue of their spacial arrangement. If that doesn’t qualify as a tissue, I’d venture to say that there exist no true tissues in biology. Different individual cells, especially the external type, appear physically joined to one another in a variety of configurations similar to those of higher multicellular organisms. Indeed, sponges resemble us sophisticated animals in more ways than that.

A Venus' Flower Basket sponge, Euplectella aspergillum, here looking like some kind of poorly rendered black tornado. These are almost cool enough to warrant looking at an actual picture... almost.

Sponge reproduction is a sordid and lusty business, and can take place either sexually or asexually. Each individual sponge is hermaphroditic, producing both sperm and egg cells. Sperm are ‘broadcasted’ (a subtle euphemism for penis-less ejaculation) out of the osculum of one sponge and absorbed by the inner cells of a different individual, where they are transported to an egg. Kinky, right? The fertilized zygote develops into a sphere of undifferentiated cells, a blastula, which in turn develops into a ciliated embryo that may be retained within the sponge or released into the water. Asexual reproduction involves the production of a detachable structure, called a gemmule, made of a mass of archeocytes surrounded by a protective envelope. The gemmule floats away, settles on a substrate, and the archeocytes multiply and diversify into the various cell types, producing a miniature adult. This development is accomplished thanks to the sponge’s complement of regulatory genes, called homeobox genes. These act like genetic switches, turning other genes on and off in different part of the sponge and at different times.

Sponge sex is hotter than one might expect.

I know what you’re thinking, “Wow, thanks for teaching me about sponges. I always wanted to know about porocytes and oscula and sperm or whatever. But tell me: What does this have to do with animals?” Your concerns are duly noted, but before I get to that, please take a look at another critter for seemingly no reason:

A single choanoflagellate in all its glory.

This little darling is a single-celled aquatic organism known as a choanoflagellate. These fellows spend their days flapping their long central flagella round and round, generating tiny water currents that pull food particles into a ring of basal cilia and circulate gasses while expelling waste.

A collared, uniflagellated cell that captures edible material from the surrounding water? Now why does that sound familiar?

Remember me?

Oh yeah!

The structural and functional similarities between choanocytes and choanoflagellates are more than just an artifact of my poor illustrating abilities: Microbiologists have noticed the uncanny resemblance between these two organisms for well over a decade, and only the most experienced are able to tell the two apart in vitro. Perhaps the most intriguing aspect of this relationship is the existence of a number of colonial choanoflagellates. These colonies can consist of a simple string of neighboring individuals attached at the midsection to spherical structures possessing multiple cell types suspended in a sponge-like gel matrix.

A few different colonial forms of choanoflagellate. The most recent common ancestor of all animals may have been similar to a creature similar to one of these.

Finally, we return to our discussion of animals. What are the shared characteristics that unite all animals into the Kingdom Animalia and distinguish them from all other living organisms? If you’ve read the entire article up to this point, then you may be surprised to learn that you already know what those features are. That’s right; and you thought I was just wasting your time with sponge-related nonsense. Sponges are animals; in fact, they make up the oldest linage of extant animals (actually lineages, but I’ll get to that). Choanoflagellates are not animals, but are closely related to sponges. Presumably, the differences between the two groups should illuminate what qualifies as a uniquely animal trait.

Being an animal depends on possessing 4 shared characteristics that were present in and derived from the most recent common ancestor that all animals share; features meeting this definition are known as synapomorphies. Precursors to these 4 traits have been located in other organisms, consistent with the gradual process of evolution, but their particular metazoan functions evidently evolved only once and are represented to some degree in modern sponges. Keeping with conditions (1) and (2) as laid out in Part 1, these 4 characteristics (1) describe all animals, and (2) describe only animals.

1. Blastular development:

At some point during the embryonic development of all animals, there is a stage where the cells form a hollow sphere, the blastula. This structure plays an important role in the formation and growth of animal germ layers. In sponges, the blastula generally drifts in the water column, directed in some limited capacity by its ciliated surface.

2. Metazoan multicellularity:

There are several groups of multicellular organisms; true plants, fungi, some bacteria, and a variety of protists (i.e. slime molds, seaweeds and other algae); however, the particular way animals achieve multicellularity is unique and readily identifiable. Metazoans possess a number of cellular junctions and attachment structures not found in other groups, facilitating everything from selective permeability of organs and body cavities to cell-cell communication.

There are three broad classes of animal cell junction: occluding, adherens, and communicating. Occluding junctions allow sheets of cell to form impermeable or semipermeable membranes. Adherens junction are the cellular equivalent of bolts, fastening cells to one another using proteinous bits of the cytoskeletion. Desmosomes and hemidesmosomes are chief among these, binding cells to other cells and the ECM, respectively. Communicating junctions, as you might expect, facilitate cell-to-cell communication (think neurons and the like). Plants and fungi have similar structures (the plasmodesmum in plants and septate junctions in fungi) that allows two cells to trade cytoplasms and other substances, but they are evolutionarily unrelated to those of animals.

Sponges don’t rely heavily on junctions to achieve their multicellularity. Although rudimentary, some sponge cells are connected in the distinctive metazoan configuration (including some desmosome-ish structures in pinacocytes). Choanoflagellates possess many of the same genes used by animals to attain multicellularity, but they don’t provide the same function; indicating an important evolutionary change in the shared common ancestor of all animals. Communicating attachments (gap junctions and synapses) aren’t known in sponges.

3. Extracellular matrix:

Lacking the ridged cell walls found in other creatures, animals rely heavily on secreted, non-cellular materials for structure and cohesion. The most ubiquitous of these materials is collagen, a protein found in great abundance in both sponges and most other animals. These fibers link together and into a lattice, serving as an anchor for surrounding cells and other neighboring extracellular matrix. Like those involved in multicellularity, sponges and choanoflagellates share many of the genes, but their specific functions differ significantly (although the colonial forms of the latter may represent a significant exception).

4. Structural regulatory genes:

Animals, being relatively complicated things, require some special instructions for building their bodies. These instructions are encoded in special genes called homeobox genes. These genes are translated into a specific kind of protein, regulatory factors, that bind to other genes in the genome and regulate whole groups of other genes responsible for growth and development. Metazoan homeobox genes come in a few different flavors, the most well studied being Hox genes (homeobox genes are found throughout eukaryotes and aren’t unique to animals, but Hox genes are). Hox genes are responsible for the segmentation observed in many animals, and even have a tendency to be spatially arranged in the proper order on the chromosome. Sponges appear to lack true Hox genes (unsurprising considering their lack of segmentation), but possess a related class of regulatory genes known as NK genes. NK genes are not exclusive to metazoa, but there is compelling evidence that they are the progenitors of true Hox genes. All of these observations make structural genes a somewhat tenuous and arbitrary synapomorphy; I present it here because it works with a little bit of imagination.

————————————————————————————-

These 4 traits are present, in some form, in all animals; including our spongy friends. Although sponges and choanoflagellates are very similar, sponges are more closely related to all other animals than they are to choanoflagellates, which are not animals but are just outside the Animalia clade (also referred to as the clade Metazoa). In fact, choanoflagellates are the most closely related group of non-animals to the metazoans (the two groups actually form their own clade, Filozoa), and the hypothetical proto-animal ancestor of all animals was probably similar to modern choanoflagellates. If you take a few evolutionary steps backwards, it turns out animals and their other Filozoan brethren share a common ancestor with the fungi. This group, collectively called Opisthokonta, is defined by the synapomorphy of a single posterior flagellum (in case you’re wondering where your posterior flagellum is, you lost it once your paternal half stopped being a sperm cell and became a zygote). This nested hierarchy of taxa and traits has some very significant evolutionary implications (and makes a mockery of the tired notion of the ‘common design, common designer’ argument creationists are so fond of putting forth to explain the unity of form shared by all earthly organisms), and the recently sequenced genomes of representative sponges and choanoflagellates is shedding light on the evolutionary origins of multicellularity, genetic regulatory mechanisms, connective proteins, immune systems, and embryonic development.

A phylogenetic tree of the Domain Eukaryota made of that scientific gold I was talking about earlier. Emphasis is placed on the Opisthokonts, the large blue taxon. The creatures in the 'etc...' group include fungi, slime mold, and lots of other weird and unspeakable thing: If you exclude this group, you've got the clade Filozoa (light blue). Excluding the choanoflagellates yields the clade Metazoa (slightly lighter blue).

You might remember a third condition from Part 1: All animals must ‘consist of a monophyletic grouping of creatures united by common ancestry.’ Does the Kingdom Metazoa, as described here, actually represent a group fitting condition 3? After all, a collection of very similar organisms can be incredibly similar morphologically, behaviorally, ecologically, and cellularly while still being the result of convergent evolution rather than recent common ancestry.

For example, take these creatures:

Remember us?

That’s right: Sponges! Has your brain liquefied from astonishment? Sponges, the very paradigm of biological integrity, do not qualify as a valid evolutionary clade (these animals were formerly placed in their own phylum, Porifera; a term I’ve avoided using until now on account of its dubious status). The 3 or 4 major assemblages of sponges form genetically distinct taxa whose most recent common ancestors are nearly as old as the Kingdom Animalia itself. One of these groups, Hexactinellida (glass sponges like the Venus’ Flower Basket), is probably the oldest. Another, Homoscleromorpha (the bluish amalgam illustrated above) , may be the sister group to the rest of the Metazoa.

I’ll address this vexing topic, as well as provide evidence that Metazoa meets condition (3), in Part 3. Until then, enjoy this final illustration and these fine references:

A highly simplified phylogeny of the Eukaryotes. Animals and Fungi (as well as choanoflagellates, slime molds, several kinds of amoebae, and a few other protists that don’t quite fit into those two groups) unite to form the monophyletic taxon Opisthokonta. Plants (and their algal friends) represent a sister group.

Carr, M., Leadbeater, B.C.S., Baldauf, S.L. (2010) Conserved Meiotic Genes Point to Sex in the Choanoflagellates. Journal of Eukaryotic Microbiology. 57(1)

Fahey B., Larroux C., Woodcroft B.J., Degnan B.M. Does the high gene density in the sponge NK homeobox gene cluster reflect limited regulatory capacity? (2008) The Biological Bulletin. 214(3)

Gazave, E., Lapébie, P., Renard E., Vacelet, J., Rocher, C., Ereskovsky, A.V., Lavrov, D.V., Borchiellini, C. (2010) Molecular phylogeny restores the supra-generic subdivision of homoscleromorph sponges (porifera, homoscleromorpha). PLoS One. 5(12)

King, N. et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. (2008) Nature. 451

Lang, B.F. et al. (2002) The closest unicellular relatives of animals. Current Biology. 12(20)

Nielsen, Claus. Animal evolution: interrelationships of the living phyla. (2001) Oxford University Press, New York. 2^nd Ed.

Snell, Elizabeth et al. (2001) Hsp70 sequences indicate that choanoflagellates are closely related to animals. Current Biology. 11(12)

Valentine, J.W. On the Origin of Phyla. (2004) University Of Chicago Press. Chicago.

James is a graduate of the University of Missouri, Columbia. He is a research biologist specializing in the molecular evolution of invertebrates. Feel free to visit his subpar research blog.

A Poorly Illustrated Guide to the Tree of Life

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_________________________________________________________________________

Hello everybody. My name is James, and I’ve been working on a little something. I want to explore some fundamental questions about life, and I want you, Dear Reader, to accompany me on this journey. To facilitate this desire, I’ve written some words and drew some pictures, but I didn’t do either particularly well. In fact, my creation has caused me no small quantity of shame. So much shame…

So, without further ado, I present the first part of what I can only hope will be a short series of pieces answering the most important questions ever. Dear Reader, kindly ask yourself:

 

Part 1: What the hell is an animal?

 

I made all of these with a broken laptop touchpad. This snail took me 7 hours.

 

Animals: what are they? This seems like an easy question: After all, we see animals all the time at zoos, in backyards, on the street, in adult movies, and every time we look in the mirror. Animals are all around us; scheming, searching, squirming, and doing things so degenerate I hardly dare speak of them.

Ask a child (or an adult religious fundamentalist) what an animal is, and they’ll probably tell you an animal is a creature that moves, breathes, thinks, eats, reproduces, and reacts to stimuli (or some variation of those traits). This sounds like a pretty good non-technical definition; certainly almost every animal encountered by most people on a regular basis fits these criteria. Indeed, the Latin root of the word animal, animalis, means the quality of having breath (it’s also the root of the words animate and, for you Jungians, anima). From a scientific perspective, however, this definition is totally and unequivocally wrong. We need something a bit more robust before a proper treatment of the animal kingdom can begin. Time to unleash the Semantic Cracken.

 

"No wait, I meant 'Whom!'

 

Much like the words human, fish, bird, plant, and fungus, the word animal is an attempt to define a category. A good definition of a category is precise and inclusive, defining every quality of the category while excluding every quality outside of it. For example, take the following definition of the category people who are your mother: any unattractive person willing to anonymously dispense sexual favors for a reasonable price.

This is a poor definition of the category your mother, as there are many such individuals in the world who fit those criteria, such as your sister and grandmother. And perhaps your mother charges a hefty premium during the holidays to earn a little extra money to buy you Christmas presents. This definition is neither precise nor inclusive. A better definition would be “the female person who gave birth to you.” This too has potential complications, as it clashes with the colloquial definitions of the word when considering adopted children and surrogate mothers, but it gets the job done (much like your aforementioned parent). It is both precise and exclusive: Anybody who did not give birth to you is not your mother, and only your mother gave birth to you.

 

I got a couple of these every month; I made a scrapbook.

 

We can extrapolate these general criteria to any categorical definition, with some special provisions for categories that describe groups of organisms, like the word animal. While we can create an endless number of arbitrary categories for living creatures (e.g. creatures that swim, creatures that are fuzzy, creatures that are delicious), the evolutionary history of all life enables us to group organisms based on shared ancestry. These special groups, known as clades or monophyletic taxa, contain a common ancestor of a group of organisms and all of that ancestor’s descendents (there are several other flavors of evolutionary groupings, such as grades, paraphyletic and polyphyletic taxa, but we’ll ignore those for now). If we want our idea of an animal to have any sort of scientific heft, it should define a monophyletic clade. As it happens, there is good evidence supporting this notion.

 

The tree on the left is monophyletic, while the tree on the right is delinquent on it's student loans.

Our proper definition of an animal must now satisfy three conditions: It must (1) describe all animals, (2) describe only animals, and (3) consist of a monophyletic grouping of creatures united by common ancestry. Condition (3) is its own field of study and a bit beyond the scope of this exercise, but I’ll be addressing it sometime in the future. For now, let’s address (1) and (2): what are the necessary and sufficient conditions for an organism to qualify as an animal? In other words, what defines all animals, and just animals? Let’s return to our erroneous colloquial definition of a creature that moves, breathes, thinks, eats, reproduces, and reacts to stimuli. All 6 of these characteristics fail to adequately satisfy conditions (1) and (2) as they are not precise and/or inclusive. To illustrate, let’s dissect each one.

 

Meh.

1. Movement: At first, this character seems fairly solid: Animals are wily critters with important shit to take care of, and it seems to draw a clear distinction from plants and fungi. Movement, however, is a fairly subjective and vague quality. Does growth count as movement? It entails a change in position, however slight. What about tropism, the direct growth of a plant or fungus towards some kind of stimulus or gradient? Non-animal organisms are capable of orienting themselves in relation to a variety of environmental factors such as light, chemicals, or the pull of gravity. Even if we don’t classify tropism as true movement, there are plenty of animals with mobility comparable to that of a plant. Corals, sponges, brachiopods (lampshells), many mollusks, some echinoderms (the group containing sea-stars and its relatives), a few insects, and a variety of internal parasites simply stand (or encrust) idly as the world passes them by. Motility fails both conditions, as (1) not all animals are capable of movement, and (2) movement is found in many non-animals.

 

They're lungs... or really gross angel wings.

2. Breathing (respiration): Depending on what is meant by breathing, this character is either bad or awful at defining animals. If you mean the process of using lungs to pump air into and out of the body, it’s worth noting that the vast majority of animals (fish, insects, marine mollusks, and practically every other invertebrate) do not have lungs in the proper sense, thus failing condition (1) (gills, swim bladders, and tracheal tubes don’t count). Breathing is, at its most basic level, the act of gas exchange. Specifically, it is the process of utilizing Oxygen to facilitate metabolism while removing Carbon Dioxide from the body. But even this definition sucks and violates condition (2), as all know forms of life on this planet use some form of respiration (some bacteria swap out Oxygen for other electron-accepting atoms, but I digress).

 

This is what thinking looks like, I promise.

3. Thinking: For a quick and entertaining treatment of this idea, simply look at any discussion about the ethics of eating meat to get a taste (wink wink) of the popular sentiment. Although some non-experts may debate where exactly to draw the line between thinking and non-thinking animals (if eating a chicken is unethical, than killing a cuttlefish is tantamount to cold-blooded murder), scientific opinion squarely puts animals like sponges, cnidarians (jellyfish, coral, and sea anemones), and other creatures lacking much of a nervous system in the non-thinking camp, thus violating condition (1).

 

Yes, the bird goes into the cat. It's science.

4. Eating: Surely eating is a worthy qualifier for defining an animal. If watching the world’s fattest married couple devour 2000 kilograms of hotdog on the 4^th of July doesn’t strike you as the most animalistic activity imaginably, what hope do we have of finding a predicate worthy of the kingdom Animalia? Well, I’m not here to pass judgment on how your parents spend their holidays, but I will tell you that eating is about as good a character as thinking or breathing (i.e. bad). Again, depending on our choice of definition, eating is either a poor or terrible feature. If you consider a stomach necessary equipment for eating, then we need only look towards the innumerable examples of digestively-impaired animals, including sponges, several kinds of parasitic worm (e.g. tapeworms and flukes), and cnidarians (provided your idea of a stomach isn’t a gastrovascular cavity) to disqualify eating on condition (1). If eating means heterotrophy, deriving substance consumption of other living organisms (as opposed to autotrophy, deriving chemical energy via photo- or chemosynthesis), then it fails on condition (2), as many bacteria, all fungi, and even some plants must obtain organic Carbon from other living creatures.

 

I made 8 different drawings symbolizing reproduction. This was the only one without a penis.

5. Reproduction: I’ll cut your mother some slack and simply say that there is reproduction going on all around us and in every kind of organism, invalidating this feature on the grounds of condition (2)…

 

…

 

Your mom’s a whore.

"Bad Kitty! Ethnic slurs aren't allowed at the dinner table."

6. Reaction to stimuli: See the dissection of Character 1 and replace the words “movement” with “reaction to stimuli”; “plants or fungi” with “mom and dad”; and “towards some kind of stimulus or gradient” with “towards some kind of snack cake or bacon fat.”

 

So, what the hell is an animal? I assure you, there are several traits that do actually meet conditions (1) and (2). What are they? You could look in a zoology textbook, which is boring and difficult and risk revealing your crippling illiteracy, or you can just wait and I’ll tell you; not with stupid words, but with a series of bitchin’ pictures. Huzzah!

Ultra-Bitchin'

James is a graduate of the University of Missouri, Columbia. He is a research biologist specializing in the molecular evolution of invertebrates. Feel free to visit his subpar research blog.

Jesus for a Day

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I have joined the small but ever-growing list of people who know what it is like to be a Messiah. For a short time, I had become Christ in the flesh. And I must tell you, dear reader, it felt good. Really good.

Before the Holy Spirit wholly abandons me and I return to a mere mortal, I’ve taken the time to write down a few of my Holy revelations and experiences.

I entered the Sacred Circle of Speaking to the sound of trumpets and angel’s tears, the scent of feathers and heavenly spices thick on the breeze. My children were all there with eager faces and open hearts. I could feel their love filling my mind, body, and soul in ways you could not imagine and in places so deep and dark I dare not mention them. Yes, those places.

Touchdown Jesus!

But I was not alone. Others were there with me, spreading a false gospel of deceit! They were the Jedites: Brother Jed and friends! And there was much clashing and gnashing of teeth.

It will come as no shock to learn that one of Brother Jed’s ilk, a certain gentleman I’ll refer to only as Mr. BC, was displeased with my presence; however, even I was surprised at how little time passed before he began simultaneously accusing me of being both a demon and a flaming homosexual monster. It was almost instantaneous.

For those of you who are unfamiliar with Mr. BC, he is evidently a world renowned multimillionaire polymath gentleman scholar with a heart of gold who, despite only having formal training in computer science, has mastered the fields of biology, physics, mathematics, logic, geology, anthropology, archeology, and ufology. He is not shy about letting you know the scope of his expertise, as an endless stream of facts and truth can exit his mouth at a continuous rate for hours upon hours. Even when his words render your eardrums into a bloody heap of mismatched tissues and your brain into an unrecognizable hematoma of sorrow, his voice goes on and on.

Additionally, he has a bottomless repertoire of supernatural abilities at his fingertips, including the ability to control the weather and communicate with animals, thanks to his devotion to the Lord. His supercomputer-like brain is so sharp he could literally disembowel you with a mere though. I’m certainly lucky he took pity on me and only resorted to calling me a ‘faggot.’ Such mercy and tact.

Anyway, knowing that I was in the company of a leviathan of human understanding, I kindly and humbly asked him to prove that I was not, in fact, Jesus reborn. His response was that the real Jesus would be able to name all the stars in the sky.

Considering that there are roughly 400 billion stars in the Milky Way (most of which do not have anything resembling a proper name, let alone the rest of the stars in the universe), and that there is no list of stars in the bible or any Christian holy book, I’m not really sure what he had in mind. I suspect his encyclopedic knowledge of both physics and astronomy and unprecedented mental processing power would have enabled him to properly distinguish the true Christian names of stars from the false secular ones. Nevertheless, I created my own alphanumeric and completely arbitrary naming convention for celestial bodies on the spot and began stars in a very authoritative manner. I could tell that, at least for a few fleeting seconds, it seemed like he actually thought I was labeling the heavens, but this quickly gave way to more accusations of Satan being my father.

Ad hominem attacks are the last refuge of those with no case and no class, but the poor guy didn’t even bother letting me eviscerate his feeble little arguments. He is one of the few individuals in the world you can stand next to while you are dressed as Christ Jesus and still not feel like an arrogant bastard.

 

So Many Goddamn Stars!

I received only one condemnation for my actions from somebody without a messianic complex. At the SASHA table, a gentleman expressed his misgivings and commented on his dearth of respect for my performance. I gathered he was a theist; likely a Christian by his later comments on the specific origins of the universe and the veracity of evolution which were, as one might expect, vapid and malformed. To paraphrase:

“I can understand presenting your cause at this ‘Ask an Atheist’ table, but mocking Jesus? I cannot respect that. It’s offensive. Why have you singled out Christianity when other religions are just as absurd in your eyes?”

For anybody not paying attention, I’ll point out that I was actively attempting to offend on some level. I thought that was fairly clear after I had claimed to be an expert at performing fellatio on both the Heavenly Father and the Holy Ghost. However, I find it hard to believe it took me dressing in a white robe and talking about sexual congress with the Holy Spirit for him to become offended. I suspect the combination of my very existence and my position on the existence of his favorite deity are sufficient to cause him offence on some level.

Besides, causing such individuals discomfort and ire is pretty much the only thing that warms my blackened heart. You will soon learn that about me should you ask about my thoughts on, say, the Intelligent Design movement. On request, I will gladly let it be known that I have no more respect for your thuggish fictional god than I do for your childish beliefs in that cretinous bastard.

The Holy Ghost - Artist's Rendition

I had hoped the reasons for singling out Christianity in particular were clear enough, but I will briefly elaborate. First, there were no Buddhist, Jain, Muslim, or Zoroastrian preachers out on that particular day, so my choice in topical messiah guises was quite limited. Second, I have never seen preachers from those particular religions out on any given day in Missouri, so I fail to see much utility in ridiculing them. Besides, why bother offending Zoroastrians when I am surrounded by easily outraged Christians? I’m not one to pass up low hanging fruit, and there are only so many nice days I wish to squander combating the stupidly unleashed by the faithful. Third, I would gladly wear prosthetic Hobbit feet and dance a merry jig if Tolkenism suddenly became the predominant religion* in the United States. No, I know all too well that the most common species of believer in my county are of the Christian genus.

I want to close by thanking all the Apostles and Roman centurions who helped me spread the good word. Although the Jesus you met and loved has departed, he will remember your good works and reward you in the hereafter…

 Because Jesus never forgets.

 

James is a graduate of the University of Missouri, Columbia. He is a research biologist specializing in the molecular evolution of invertebrates. Feel free to visit his subpar research blog.

Helpful resources:

Godisimaginary.com
Iron Chariots Wiki
Skeptics’ Annotated Bible / Skeptics’ Annotated Qur’an
AtheismResource.com
TalkOrigins.org

YouTubers: Evid3nc3, Thunderf00t, TheAmazingAtheist, The Atheist Experience, Edward Current,NonStampCollector, Mr. Deity, Richard Dawkins, QualiaSoup

Blogs: Greta Christina, PZ Myers, The Friendly Atheist, WWJTD?, Debunking Christianity, SkepChick

and don’t forget… other SASHA members! We are here for you, too! 

*Anybody interested in actually making this happen should contact me immediately.

Blind to Detail: How Your Fictitious God Makes You Look Like an Idiot

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In my opinion, the two biggest flaws of the religious person’s thought process are 1) a deficiency of good information (or a complete lack thereof), and 2) the inability or unwillingness to examine details. The causes and impacts of the former are well known and have been thoroughly discussed, by myself and others, elsewhere on this blog and across the furthest reaches of the internet. I believe there are still some interesting and, as of yet, unexplored points to address in regards to the second of these two flaws.

What exactly do I mean when I claim that Christians (and I do mean all Christians) are blind to detail? To illustrate, let’s look at an example scenario combining Christian belief and geology: specifically, the vast layered collection of materials which form the geological column.

*I must first issue a warning: I’m about to engage in a brief thought-experiment where I make some fairly broad generalizations. I’d like to point out that, although it might not pertain to everybody, it most certainly does pertain to you, dear reader.*

If you dig a hole anywhere on planet Earth, it will come as no great shock to find the soil, rock, and other materials form discrete layers. Astounding, right? The earth is made of layers and layers within layers and more damn layers. We live on a layered planet. Moreover, most people are aware of this fact and take it more-or-less for granted.

Layers!

Now, add to this equation an average American Christian advocating for the veracity of the Christian bible. They need not be a strict biblical literalist, but they must be somewhat vocal and hold the general believe (as most American Christians do) that god is the master architect and craftsman of the universe.

If pressed, there is a good chance my hypothetical Christian will state some or all of the following:

1) The layers of the earth do not contradict the truth of the bible or the existence of god.

2) God could have created some of these layers, or they are part of his grand design.

3) The layers of the earth are positive evidence for specific aspects of the bible, such as Noah’s flood.

4) The layers of the earth can only be explained in the context of an all-powerful Christian god.

More damn layers!

I suspect most Christians of the type I’m referring to would not disagree with any of these claims. Indeed, I’ve purposely limited their scope for simplicities’ sake: I’m sure many would take this list to its natural conclusion: god created everything and everyone. Here’s the catch: notice I didn’t specify any sort of formal education or working knowledge of geology for our Christian straw man, and you can assume they have none.  Why? As I stated earlier, we’re assuming an average Christian, with an average level of education. That entails a high school diploma and perhaps some college level or technical education (http://www.census.gov/hhes/socdemo/education/data/cps/2009/tables.html), but most likely no in-depth training in the geological sciences.

As far as the typical Christian living in the United States is concerned, there is no minimum amount of background needed in geology in order to conclude that god is the designer of the Earth and is, therefore, responsible for all observable facts within geology. No mechanisms are needed. Not only is this true in regards to every other scientific disciple, but there appears to be no lower limit to knowledge of the bible and Christianity necessary to come to the same conclusions.

Like some kind of debased logical wizards, Christians are able to conjure certainty and objective facts about the natural world out of thin air. I have personally spoken to individuals who will freely admit they have never read even the introductory paragraph to a geology text book, yet claim privileged divine scientific insight to every facet of the field. They say the signature of god is practically inscribed on every single rock in sight, even if they are unable to tell me whether that rock is igneous or sedimentary. If starting from their preferred deity renders doing any actual work unnecessary, why bother with understanding the details? They simply don’t matter.

A banded iron formation, of BIF. If you can tell me a plausable mechanism for their formation that doesn't totally contradict the biblical flood, I'll give you a cookie and 100 Science Points.

In any other situation, somebody attempting to do this would qualify as “a jackass,” “being full of bullshit,” or “a goddamn idiot.” I am a gentleman and a scientist, so I would never say those sorts of things; but I can assure you that I’m thinking them.

I invited those creationists, and I now invite you, dear reader, to actually look at the ground. Most of us, including myself, are not formally trained geologists, but that doesn’t preclude us from learning about and enjoying geology. Pick up an elementary geology textbook or a rock field guide. Find a cut-away hill along a road and look at the bones of the Earth up close. Look at the layers and think about what they are made of and how they got there. Are they sandy, muddy, smooth, rough, rocky, or full of fossils? What kinds of patterns can you see? If you want to get extra sciency, look at the soil in a floodplain, take notes, and use that information to try and find evidence of a global flood.

If you are so convinced that your god’s handiwork is everywhere, why not actually look for it?

Little known fact: most creatures killed in the flood were snails

James is a graduate of the University of Missouri, Columbia. He is a research biologist specializing in the molecular evolution of invertebrates. If you would like to pay James to do science for you or your laboratory, please post in the comments. Also, feel free to visit his subpar research blog.

Murdered by Jesus (or possibly Dracula)

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Meeting: Tomorrow (Wednesday 8/31/11) at 5:30 PM in the Arts & Science building, room 103

James here.

Some interesting developments regarding my faith of late. Two, in fact. I don’t know how much time is left, so I’ll be blunt: First, I have reluctantly been forced to abandon my atheism. Second, I’m presently trapped under my mattress and boxspring by what I can only assume is an enraged avatar of Jesus Christ.

As you’ve probably already determined, these two events are causally connected. Although I suspect being flayed alive by our Lord and Savior is no worse than I deserve, the reality of it all is only now sinking in. It all started this past Sunday…

Like most good atheists, I was spending my Sabbath day at a butcher’s shop, browsing the selection of goat and lamb innards. The butcher, sensing the vacuous confine of space that once held my mortal soul, was visibly upset and doing his best to hurry me along and out the door. Admittedly, I was holding up the line quite severely, mainly due to the difficulty I was having in calculating the perimeter of a blood pentagram using just a bone-ash pencil and the back cover of a Necronomicon. But I have my rights just like everyone else. I finally left with a plastic bag of hallowed goodies and returned to my shanty alone… so I thought.

I had barely started my ritual sacrifice to Atheismo, the nonexistent three-headed god of atheism, when I heard a loud tapping at my window. Before I could even unzip the eye-holes of my S&M mask to look out, a tremendous gust of wind toppled my homemade alter and blew out my demonic black-flame candles. The alter, which made of transitional fossils and beneficial mutations and was, therefore, incredibly light and fragile, shattered into pieces. Then I saw him. Standing just outside my partially demolished wall was a tall, dark figure suspended in midair. He floated in and immediately demanded I repent, or else face an ‘unholy pistolwhipping from beyond the grave.’

This shall be my immortality.

At first, I was nearly certain it was either Dracula or perhaps an urban bigfoot. Now, the truth couldn’t be more obvious: god is real, and he works in very mysterious ways.

I’ve been stuck for almost a day now. Jesus just keeps staring, taking the tiniest steps towards me every time I close my eyes. Reading Ann Coulter’s book Godless: The Church of Liberalism (available at fine stores everywhere) aloud seems to calm the creature, but I’m down to the last few pages and it isn’t exactly content heavy. I’ve repented in terms agreeable to every Christian denomination I can think of, so I should be on the fast-track to Heaventown. I think the end may be near, but I’ll continue to liveblog from under my bed for as long as I hold out.

In other news, Michele Bachmann is a moron.

Oh god! The beast awakens! See you on the other side, godless scum!

James was a graduate of the University of Missouri, Columbia. He was a research biologist specializing in the molecular evolution of invertebrates. If you would like to pay James to do science for you or your laboratory, please travel back in time and post in the comments. Also, feel free to visit his subpar research blog.

Creationism is Cancer

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Bad ideas are like diseases.

Some ideas are viral; they emerge from dark corners of the world and spread from person to person. They move in chaotic but predictable ways. Certain populations can be more susceptible, and others are wholly immune. Some are benign, some are fatal. Some are static, and some change so quickly they become unrecognizable. There are many examples, religion being the most abundant and variable.

Others are more like parasites, leaching the blood of more useful ideas. The best example of this is the way the ridiculous and bigoted prejudices of the political right have become engorged off the sensible notions of fiscal conservatism.

And some ideas are malignant tumors on society.

Real cancer is caused by a defect in the genetic code of a cell. The mutation results in the unregulated growth and division of the cells, or the failure of the cells to die when their usefulness is exhausted. When these cells divide and propagate, so does the defect. Soon, the cells begin corrupting the body which contains it, eventually supplanting the surrounding tissue, overwhelming the organs, and killing the host.

Creationism is an ideological cancer. It is deeply rooted in our society, and it grows and festers slowly. It fractures and becomes lodged in unexpected places. Many cancers are the result of mutagens in the environment, but some are facilitated by viral infection. The human papillomavirus (HPV) is strongly linked to cervical cancer. Hepatocellular carcinoma, a cancer of the liver, can be caused by the hepatitis virus. Likewise, viral religion weakens the mind of infected individuals, making them more susceptible to the growth of metastatic creationism.

A mind that willfully denies the collective evidence of biology, geology, physics, history, chemistry, and every other legitimate modern field of discourse is suffering from a sickness. If you believe in creationism, your brain is diseased.

But unlike its biological equivalent, this type of cancer can be readily cured by a sufficient force of will. If you are afflicted, I strongly and sincerely hope you seek the proper treatments:

http://www.pbs.org/wgbh/evolution/

http://evolution.berkeley.edu/

http://www.talkorigins.org/faqs/comdesc/

 

Stay healthy friends.

 

James is a graduate of the University of Missouri, Columbia. He is a research biologist specializing in the molecular evolution of invertebrates. If you would like to pay James to do science for you or your laboratory, please post in the comments. Also, feel free to visit his subpar research blog.

DIY Science: Build Your Own Molecular Phylogeny

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Greetings, friends. My name is James. Today, I’m going to turn everybody who reads this blog into an evolutionary biologist in a few easy steps. How will I do that? Simple: I’m going to teach you how to make your very own evolutionary tree using DNA sequences. I’ll start by answering some basic questions.

“What is an evolutionary tree?”

An evolutionary tree, or phylogeny, is a graphical representation of the relatedness of organisms. A phylogeny is made up of bifurcating (spitting into two) branches joined together by nodes. They can be built using physical characteristics (morphology) or molecular sequences (DNA, RNA, or protein). These trees can compare different species, different individuals or populations within a single species, or even different genes within the same organism.