Biology 284a : Patterns in Life's Diversity -

Course Content, Structure & Resources

©Paul Handford 2008

Content:  A description of the Primary Themes of this course.   See also the Course Overview page for a "bird's-eye view".

Structure:  The components of the course:  Lectures, Tutorials and Examinations. 

Resources:  Recommended text and video materials and where to find them.   There are also many useful weblinks here

But before all that, a few words about the overarching principle which informs the whole course:
 

Background to this assertion:

Nature's diversity has impressed humanity from our earliest days, and its exuberant abundance and remarkable fit to conditions of life have always called for explanation.  In a pre-Darwinian world, the explanations offered were imprecise and, as we would now say, unscientific, often involving various aspects of divine providence - "The Almighty made it that way."

But continuing exploration of the world led to the realization that nature is not only astonishingly diverse and seemingly "well-designed," but also shows other strange characteristics, notably a clear and natural "patterned order" in the levels of resemblance among organisms, and a seemingly irregular distribution of their kinds about the globe (no tigers in South America, no kangaroos in North America, and suchlike.)  And there were abundant and diverse fossils - ancient life, now extinct....... The explanation of all life's manifestations through supernatural agency became more and more unsatisfactory as the facts of the earth itself and & biota and its distribution in space and time accumulated, and it also became clear that a rational explanation of it all required us to avoid the employment of unobservable factors, and to reject the miraculous.

That rational explanation is provided by the deployment of the idea that both the earth itself, and all the life that it supports, have changed, sometimes in profound ways, and that life has diversified dramatically since its simple origins.  This process of change & diversification is called EVOLUTION, and one of its primary engines is NATURAL SELECTION, which leads organisms to become progressively adapted to their conditions of life, as they may change through time.

One of the keys to the development of Darwin's explanatory hypothesis of evolutionary change and diversification was the discovery and deployment of the notion of deep time:  The earth and its contents all had a very long history.  The Earth and its contents did not, after all, spring into existence in some short-term spasm of creation;  rather they developed, through a process called evolution, over an immense time.

We now see earth's biotic diversity as having developed, through the evolutionary diversification of uninterrupted ancestor-descendent lineages, across huge expanses of time - much longer than most could imagine only a century or so ago.  This has all taken place against a backdrop of shifting global geography and chemistry.

The physical world's changes, such as continental drift and climate shifts, are to some extent independent of the biota (though far from completely independent, since the biota impacts on climate, as we now know only too well), providing, as it were, a template upon which the biota is lain;  the biota, however, always responds to earth's physical template, through the process of natural selection.  But to some degree, and often in profound ways, the physical earth and the biosphere interact, and affect one other.

This course is intended to permit students to gain a basic awareness and understanding of:

• the diversity of earth's organisms,
• the processes that have produced this diversity,
• the resulting patterns of evolutionary inter-relationship among the organisms,
• the patterns in the organisms' distribution through time and space, 
• the patterns in the organisms' adaptation to the physical factors that they encounter.

Thus, a knowledge of the processes of change & diversification and how they work does not allow us to deduce all of the patterns in which life is deployed about the earth through time & space - much about these patterns is unique and specific to circumstances or, as we say, contingent.

Necessarily, then, much of the content of this course is what you might call "information-intensive":   one can't simply learn about the basic principles and then figure out any particular thing from them, as is possible in much of chemistry and physics.  

This course aims to answer such questions about life as:  what's out there?  what happened?  where are things?  how many are there?  These are EMPIRICAL MATTERS - that is, the answer is just what it happens to be, not what may be deduced from theory.  This means that there is no substitute for simply learning about these things;  once learned, one has a broad base upon which to build a firm understanding of other patterns and processes in the study of life.

Life on Earth is astonishingly diverse, and getting some grasp on that diversity is a formidable task.  To aid us in this struggle, we use frameworks of various sorts, upon which to organise things, and to help us gain some notion of the overall shape of life's manifestations.

Life - earth's organisms - may be displayed along many different axes, or dimensions, all of which provide us with some power in our efforts to see life's big pictures.

The diversity of organisms is generated by the processes of evolution:  Life evolves and diversifies through time and space.  This short sentence suggests the most useful structures upon which to array life's phenomena, the better to comprehend it:

What has evolution produced?  What is the range of form and life-style of earth's organisms?  how many of them are there?    We might call this the organismal dimension of diversity.

How has this diversity come about? how are organisms related in evolutionary lineages, and how should we classify them? We might call this the taxonomic/phylogenetic dimension of diversity.

What happens to life's diversity through time?  What patterns are there in earth's changing biota?  How do extinction and diversification interact?  This is the historical dimension of diversity.

What happens to life's diversity in space?  What geographical patterns are there in life?  This question has two distinct aspects:


First, what are the distributional patterns in evolutionary lineages?  and what causes them?  This is the evolutionary-biogeographic dimension of diversity.

Second, what are the geographic patterns in life's adaptation to conditions?  how do organisms respond to the demands of their physical environment?  how do organisms respond to one another?  what sorts of organisms are typically found in association?  what is the nature of these associations? This is what we might call the ecological dimension of diversity.

Familiarity permits understanding, and with understanding may come humility:  such a progression has led us, by steps, to a better appreciation of our place in the universe.  From the conceit that our earth was the centre of the cosmos, and that we were the pinnacle of creation, we have arrived at the scientific understanding that our planet orbits but a commonplace star, one of 100 billion (10 E+11) in our galaxy alone, and that we, and all the diversity of other life, have evolved by descent from common origins in a far distant past.  Thus, a profound unity underlies this diversity.

Lectures - the sequence of topics

The first lectures consider basic tools for the comprehension of diversity:  recognition of species, the idea of a natural classification, and evolutionary processes & relationships.  The next lectures provide an overview of organismal diversity - the range of form, funtion, and life-style of the organisms themselves.  Next we consider the diverse patterns in which this diversity of organisms is deployed about the planet through time & space, and the factors that generate these patterns.  Finally, we look at the nature and origins of some selected biomes.

LECTURE PRESENTATIONS     

The link above takes you to a restricted area;  you will be required to enter a login name and password to reach the index page. 
When you get there, you'll find:

1. a string of numbered folders each containing html versions of the lectures.  These are quick and easy to load in the browser, so you can see the lecture's content. These versions cover the content well, but they aren't exactly what you'll see in class, since every year I alter things a bit, and these html files are a few years old.
2. at the bottom of that string is a folder called 284.pdfs.  Click on that and you get downloadable pdf versions of each class as it appeared last year, formatted at 6 slides per page.  These are ideal for printing for use in class, but they might take a while to download.  I often edit the slide shows a little just before we get to them in class, so what we work with in class might be a little different from your printed copy.  But that's fine, since the primary reason for my making the slides available in this way has always been to save some of the labour of scribbling, not to make attendance dispensible.

Below is a list of the lecture titles, broken down by major course themes.
 
Associated with some of these titles you'll find links to sites which I either used in setting up the presentation or are of general use in illustration of the material.  I update this periodically:  it's a good idea to check back now and again.

Remember:  these lecture titles just give the topics and their sequence; they do not link to the presentations - you must go via the link above.
 

Introductory classes       

      Introductory - course nuts & bolts  

Patterns in Organismal Form - the biota, its composition, and its relationships

      Taxonomy and Classification - naming and sorting
      Classification & Phylogeny - how should classifications relate to genealogy?
      Deep Time - the scope of evolutionary time and its major landmarks - an introduction.

Discussion of TIME, and a display of the text's TIME CHARTS is to be found here.  

Such time charts often provide a challenge to students, but please remember:  all we are concerned with in this course is achieving a reasonable knowledge of (a) the relative location of major events in the history of earth's biota - what happened before/after what, and (b) a rough notion of how long ago these events occurred.  By "rough" I mean sufficient precision as to avoid confusion with neighbouring time periods.  

The Time Charts used in this course show numerical time scales that pretty much correspond with what the geologists and paleontologists tell us, but they make no great claim to absolute accuracy or precision, since this is not my aim here.  For Bio 2484a purposes, you may treat the following table as an easy-to-remember, sufficiently-close-to-true guide to the dating of the primary component periods of earth's history.  You will see that most of the Periods of the Phanerozoic eon (where we see the clearest signs of complex life) have a duration of roughly 50 million years - a pretty easy number to remember.  To find the duration of any given period, look at the corresponding number and the one in the row above, e.g. the Jurassic runs from ~200,000,000 years ago to the start of the period above it – the Cretaceous – at ~150,000,000 ago, which roughly equals ~50,000,000 years.  Remember:  these numbers are ROUGH, but close enough to stay out of trouble.

Period / ERA / EON	YEARS AGO WHEN the PERIOD BEGINS
The 3 Eras of the Phanerozoic are colour-coded below: Cenozoic (blue), Mesozoic (orange) & Paleozoic (purple).	10x	all the zeros
Quaternary	2x106	2,000,000
Tertiary	6.5x107	65,000,000
Cretaceous	1.5x108	150,000,000
Jurassic	2.0x108	200,000,000
Triassic	2.5x108	250,000,000
Permian	3.0x108	300,000,000
Carboniferous	3.5x108	350,000,000
Devonian	4.0x108	400,000,000
Silurian	4.5x108	450,000,000
Ordovician	5.0x108	500,000,000
Cambrian	5.5x108	550,000,000
PHANEROZOIC eon (all the above)	5.5x108	550,000,000
PROTEROZOIC eon	2.5x109	2,500,000,000
ARCHAEAN eon	3.5x109	3,500,000,000
Beginning of Life	3.8x109	3,800,000,000
HADEAN eon  = Age of the Earth	4.5x109	4,500,000,000
BIG BANG = Age of the Universe	1.5x1010	15,000,000,000

The Biota     http://www.ucmp.berkeley.edu/help/taxaform.html

A great site is to be found at Discover Life.  Among the items on the menu on the left, you can click on All Living Things to go to an index of pages carrying images and basic information about various groups of organisms or on Tree of Life to go to a great modern tree.

A more technical, but terrific, comprehensive site dealing with the entirety of life is found at the Tree of Life (ToLWEB) website. 

      Bacteria - the Prokaryotes
Resources:  http://144.92.49.43/GenInfo.html
               http://www.bact.wisc.edu/Microtextbook/index.php
                  http://lifesci.ucsb.edu/~biolum/organism/photo.html

For an overview of all Eukaryotes see http://www.tolweb.org/Eukaryotes/3

      Protoctists - the basal lineages of eukaryotes
Resources:  http://megasun.bch.umontreal.ca/protists/gallery.html
                  http://www.ucmp.berkeley.edu/help/taxaform.html  

        Fungi
Resources:  http://www.tolweb.org/Fungi
                    http://www.ucmp.berkeley.edu/fungi/fungi.html
                    http://www.mycolog.com/

      Plants

 

A terrific though detailed site on plant phylogeny is to be found at:

http://www.mobot.org/MOBOT/research/APweb/

Other resources:  http://www.science.siu.edu/landplants/
                http://www.dipbot.unict.it/sistematica/xIndex.html
                http://www.botany.hawaii.edu/faculty/carr/phylo_fpfamilies.htm

        Animals
Resources:  http://tolweb.org/Animals/2374
  
              

      Patterns in species numbers - the biota's inventory

Patterns in Time & Space

      Patterns in species richness - how many species are where?
      Patterns in time - extinction & biotic change 

Resources;  http://www.scotese.com/earth.htm
                  http://www.amnh.org/exhibitions/Fossil_Halls/Timelines/

      Patterns in biogeography - different lineages live in different places:  
                                                       much of this explained by continental drift,
                                                       illustrated in these reconstructions:
Resources:  http://www.scotese.com/earth.htm
                 http://jan.ucc.nau.edu/~rcb7/global_history.html
                http://jan.ucc.nau.edu/~rcb7/globaltext2.html
                  http://www.ucmp.berkeley.edu/fosrec/Metzger3.html

Patterns in Adaptation

      Patterns in global climate - the biota's environmental context
Resource (it's all in german, but it's pretty easy to figure it out):  http://www.klimadiagramme.de/
An absolutely brilliant aid to understanding seasons is at this site.

      Patterns in adaptation - how the biota evolves in response to climate
      Patterns in major ecological assemblages - the world's biomes
Resource:  http://www.blueplanetbiomes.org/world_biomes.htm
                    http://www.runet.edu/~swoodwar/CLASSES/GEOG235/biomes/intro.html
This comprehensive site looks at the detail of the relations between world climate and vegetation                    

This great site looks at North American biotic assemblages:  http://www.cas.vanderbilt.edu/bioimages/ecoframe-map.htm

      How North American climate has evolved through time
Resource:  http://www.scotese.com/climate.htm

Biomes

      Tundra and Taiga

      Grasslands and Deserts
     
      Tropical Forests

Tutorials – one every two weeks

There are 5 different 2-hr tutorials, each ocurring every second week:  you attend one, then skip a week. 
Choose a section that suits your timetable;  there is rarely any problem in switching sections - just check with the TA.

There will be some discussion led by the tutorial-leader, sometimes illustrated by slides and/or video materials.

2)  The Biota - the main characteristics of the diverse lineages of organisms.

3)  Evolutionary processes which generate many of the big patterns in diversity:  Adaptive Radiation and Evolutionary Convergence.  The interaction between chance, phyletic descent & selection.

4)  Global patterns in Time:  Extinction, Diversification & Biotic turnover through earth's history.

5)  Global patterns in Space:  Biogeography, Climate, Life forms, Biomes.
 

Course Credit

The lecture sequence pretty much follows that of the Bio 2484a Lecture Notes, which is the only REQUIRED TEXT MATERIAL, but the lectures do not simply reiterate these Notes - lectures often have extra material, and sometimes they look at the material from a  different perspective than do the Lecture Notes.

The suggested supplementary text Cox & Moore - Biogeography  (Call no. - QH84.C65 1993), provides useful further detail for part of this course.

I have also placed course copies of two other useful books on 1 day loan.  One concerns biogeography, and is an alternative to C&M - Patterns of Life - by Mielke;  the other concerns the diversity of organisms - Five Kingdoms by Margulis & Schwartz (there are also copies of this book in the bookstore).  The library has its own copies of both of these texts, and their call nos. are:  Mielke - QH84.M54 1989;  Margulis & Schwartz - QH83.M36 1988

Finally, there are video resources which should be useful:  first, the library has a set of six VHS videos looking at the five kingdoms, filed under QH315.3.VC  1990, tapes 1- 6.  Then the course has copies of two different video sets produced by David Attenborough and the BBC.

The 2 VHS video sets produced by David Attenborough are not in the library, rather, they may be signed-out from me directly in COLLIP Rm. 111.

Life on Earth comprises two 2-hour tapes, which look at organismal diversity, taking an evolutionary history/complexity approach.  They show excellent footage of many organisms which you are unlikely to see easily elsewhere.  Here is an index to the contents of these two tapes;  it is the same index that is shown on the video itself, and the section numbers (further broken down into subsections) are shown in the corner of the screen for easy location of particular segments:

Life on Earth : Tape 1
 1.  Intro.;  Darwin's discovery;  Beginning of life;  First complex cells;  Cell colonies, Jellyfish, Corals. 2.  Flatworms;  Molluscs;  Echinoderms;  Crustacea. 3.  First plants;  Millipedes, arachnids, insects;  Conifers;  Insect flight. 4.  Insects;  First flowers & pollination;  various insects. 5.  Fish origins;  Sharks & rays;  Bony fish. 6.  Origins of tetrapods;  Amphibians.

Life on Earth : Tape 2
 7.   Reptiles 8.   Feathers, birds & flight. 9.   Marsupial and  Placental mammals. 10.  Insectivores to whales. 11.  Ungulates & predators in E. Africa 12.  Primates 13.  Human evolution.

The other set of videos is Attenborough's The Living Planet, and it deals with the major ecological divisions of life on earth - more or less the biomes which we shall be discussing in class.  There are twelve 50-min. tapes in the whole set, though they are not all directly relevant.  Below is a list showing the subject matter of each tape, and an asterisk (*) indicates those tapes of direct importance to this course.

The Living Planet Series.
1. Earth process. 2. *Tundra. 3. *Boreal forests. 4. *Tropical forests. 5 *Grasslands. 6. *Deserts.
7. Air. 8. *Freshwater. 9. *Shores. 10. Islands. 11. *Oceans. 12. Humans.

THERE IS ALSO AN ABUNDANCE OF GREAT RESOURCES ON THE WEB. CLICK HERE TO GO TO A PAGE OF LINKS.