Introduction to Biology

Molecules and Cells

Chapter 3 - Classification 

Taxonomy is a Side-Effect of Human Nature

Understanding relationships is a critical part of being a human being, and it has been throughout our history.  Who are your close relatives, that you can depend upon for support but probably not for spouses?  Is it safe to eat this plant if it closely resembles one you know is safe?  Animals with high-contrast markings are probably good to avoid.  Also, having language, we love to label things, give them names.  Label and categorize, the science of biological taxonomy, a way of understanding relationships among living things, was inevitable for humans to produce.

Taxonomy as the U.S. government defines it.

When humans first began categorizing Nature and writing down the groups, they often based their groupings on analogies, resemblances in abilities or simple external form.  In such a system, a snake, an eel, an earthworm, and a roundworm would all be included in a "serpent" category, or anything with wings, or fins, would be assumed to be related.  This also led to the first definition of Kingdoms:  one large group for plants, one for animals, one for rocks.  Analogy can sometimes be helpful in establishing relationships, but it is very limited.  Evolution often produces structures that look the same during the adaptation-to-similar-environments process.  This production of superficial resemblance is called convergence or convergent evolution.

The Genesis story in the Bible shows this old way of categorizing - read days 5 and 6.

A bit more on convergence.

Looking closely at animals, especially at their inner structure, suggests that analogy can be misleading.  A bird and a bat support their wings with front arms and bones, but the bones at the tip are very different;  insect wings have no bones at all, and in fact an insect's skeletal structure is outside rather than inside.  The bones of a bat's wings show closer resemblance to our own arms and hands than they do to a bird's wings;  this, and other similarities in basic architecture, places the bats in a group with humans, cows, and dogs (the mammals) rather than the birds.  Similar comparisons make it obvious that whales are not fish, pterosaurs were not dinosaurs, and birds probably are close relatives of dinosaurs.  This architectural similarity is called homology.  It is much more useful than analogy in linking biological relatives together.  Evolution that drives similar architecture to do different tasks - legs to flippers in whale evolution, for instance - is called divergence or divergent evolution.  Divergence to one extent or another is how different types of organisms evolve.

Some homologies in forelimbs (you need much more to truly categorize the groups).

Image of vertebrate embryos at comparable stages.

Homologies, as mentioned above, are not confined to just bones or other obvious adult structures.  Structures that exist early in life, in the first stages of embryos, can hold on to resemblances that have long disappeared in the adults.  There are two probable reasons for this.  First, the earlier a major change happens, the more dramatically changed the eventual outcome is likely to be, and dramatic changes are even more rarely useful than subtle ones.  Second, embryos often have much more similar environments, encased in eggs or seeds, and have needs that haven't changed in eons (flies and humans, for instance, use very homologous genes to determine where their eyes will grow).

Comparisons of embryos was the basis for one of the great cautionary tales of biology history.   In the late 1800s, Ernst Haeckel decided that as a mammal embryo developed, it actually replayed its evolutionary history:  it was a fish for a while, then a reptile, then a primitive mammal, and so on.  This was known as "ontogeny recapitulates phylogeny," and Haeckel stared for hours through a microscope at embryos, making many drawings that were labeled to show off his rule.  But it turns out that he was seeing what worked and ignoring what didn't (a natural human trait that scientists have trouble avoiding);  embryos do show their relatedness to fish and reptiles, but don't actually become them.  Other scientists quickly discovered that Haeckel's ideas were not supported by the evidence, and he is now known for a famous mistake.

Stages in a human's development.

Embryonic resemblances in research. 

More on Haeckel's embryos. 

Some of Haeckel's drawings.

More on HOX genes.

Hox genes in a linear sequence.

Since many molecules have complex structures, including long sequences of components, comparison of molecules is often used in modern biology to detect relationships.  Differences in sequence especially are useful, especially in DNA, which has long bits that can apparently change components with no effects - these point mutations happen, get passed on, and persist down a family line.  How often such changes happen is related to chance, and can be estimated over a timeline - as a family tree separates into different branches, each branch over time will accumulate its own unique point mutations.  The more different mutations, the longer it has been since the tree branched.  These comparisons are called molecular clocks, and are commonly used in evolutionary biology.  They are not perfect;  no one can say for certain that mutation chances stay the same over long periods, or whether different parts of DNA have different mutation rates.  However, they can be useful in establishing how closely related different groups are.  Such a comparison can support the idea that fungi are actually more closely related to animals than plants.
 

More on molecular clocks. 

Some history. 

A critique of believing too much in the regularity of molecular clocks.

A molecular clock leads to an estimate of when humans began to wear clothes.

A System That Everyone Can Use

As the study of Nature became more and more common, with many people speaking many languages adding to the knowledge, it became obvious that some agreed-upon approach to classifying living things was needed.  The one that was eventually worked out, which we still use today, was partly worked out by Carl von Linne (known in publication, since most was in Latin, as Carolus Linnaeus).  He developed the binomial nomenclature method of naming species, using an approach similar to how people get their names.

Here are the rules for species names:

• Species names are always two words.

• The first word is always capitalized, the second one never is.

• The first word is the genus (group the species belongs to), and the second word means nothing by itself.

• The name in English is treated as a foreign phrase - italicized or underlined.

• Species names are commonly abbreviated with the genus' initial and the second word (E. coli is an abbreviated species name).

So what is a species, anyway?  It's a particular type of organism, but what makes it different from closely-related species?  It once was based purely on description.  Later, it was based on reproductive compatibility - different species couldn't make offspring together.  But sometimes they can, but the offspring are often sterile, so the definition expanded to include that.  But...biology is a science of exceptions, which makes rules tough to make.  The latest definition (probably soon to be replaced with one based on genetics) uses behavior:  a group that keeps to itself reproductively under natural conditions.  Basically, we let the species define themselves.

And all of this really only applies to sexual species with a more-than-one-parent system.  The others are much trickier.

Linnaeus brief biography.

Lists of odd species names. 

It's the internet:  Carl's letters. 

The Linnaeus legacy. 

A discussion of defining species. 

With species collected into a genus, what larger group would a genus fit into?  As more and more relationships were determined, a bigger all-encompassing system of groups-within-groups was needed.  Here's how it works:

• Species are collected into a Genus.

• Genera (plural of genus) are collected into a Family.

• Families are in an Order.

• Orders are in a Class.

• Classes are in a Phylum.

• Phyla are in a Kingdom.

To give the system some flexibility, groups can be additionally linked and split through the use of Supergroups (a Superfamily contains Families and would be inside an Order or Suborder) or Subgroups (a Subclass would be contained inside a Class).  This means that if new information is discovered, connections can be added without shifting the entire "ladder" up or down.

The position and relationships of living things is often the subject of debate:  someone thinks that a group belongs somewhere, but others don't.  People have disagreed as to whether giant pandas (Ailuropoda melanoleuca) belonged to the bear family (Ursidae) or the family containing raccoons (Procyonidae).  There are rules here, too:  you can easily propose that a group be moved, or be classified as a smaller or larger type of group, but you can't change the group's name without a long and particular process.  That way, folks may not recognize a group's level, but they will still recognize the name and know what sort or organism is being discussed.

A class getting the group organization down, with rhythm. 

A whole bunch of ways to remember the order of groups.   

Some taxonomic lists showing sub- and supergroups. 

The Six-Kingdom System

In the earliest attempt to categorize Nature, there was the Plant Kingdom, the Animal Kingdom, and the Mineral Kingdom.  It didn't take long to realize that only the first two included living things (although with spontaneous generation, folks thought that members of one kingdom could be generated by members of another, like snails from stones).  It was eventually realized that fungi, which had been included in with the plants, were so different that they deserved their own kingdom.

Then along came the microscope and the discovery that tiny single-celled living things existed.  These often showed combinations of animal, plant, and fungus features and were very difficult to place in the existing kingdoms.  They were eventually split off in their own kingdom, and as more was discovered about them, those kingdoms split into two, then three, kingdoms of single-celled organisms.  Today, basic biology courses generally teach the six-kingdom system, although many people recognize even more, as well as a bigger category, Divisions.

Go On to Next Chapter - Basics of Chemistry

Introduction to Biology - Molecules & Cells.
For SC-135.

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