Evolutionary Thinking

Final Marks Final Update

2011-04-27T09:38:00.001-04:00

I submitted the final marks to the registrar for BIOL-433 yesterday, but still have not been able to post them to Moodle nor have I posted the comments there yet either. I will do my best to post everything to Moodle before the end of the month. Watch this space for further information.

FINAL UPDATE
Your marks and my comments for the Annotated Darwins and the Philosophy Essays are now available on Moodle. I can't see what you can see so please let me know if something is not visible.

The comments for each of these are the notes I made as I was reading your work, and are just in the order I wrote as I read. If you want me to return your paper with detailed comments, please send me an email after 1 May and I will return your paper within about a month f receiving your request.

Many of the Annotated Darwins and some of the essays were amazingly good—thoughtful, well written, interesting. I hope you enjoyed doing those two exercises and learned something in the process.

Have a great summer and a fulfilling life, filled with wise, exciting, and interesting (if not entirely free ;) ) choices.

Marking progess

2011-04-17T20:56:00.000-04:00

I have finished marking your philosophy essays and, on the whole, they were pretty good. I am awaiting a couple of late submissions from students who were/are incapacitated so won't be posting the final marks for a week or so, as I leave for France on Tuesday, and want all the marks completed before I post them.

When I do post the marks, I will also post a brief summary in Moodle of comments that I made while marking your essay. I just realized that I can do that and will add my comments on your Annotated Darwins later today. Please understand that these comments are in no particular order but are just things that struck me while I was reading your work. If you want detailed feedback your Annotated Darwin and/or your philosophy essay, please send me an email after 25 April requesting that feedback and I will send your paper back to you with further comments on the pdf before 3 May 2011.

The marks for this course look pretty good, with the class average hovering around 80%, and a reasonable correlation between Roz's marks for the tutorials and mine for the lecture half of the course. You would not really expect a high correlation because they were based on very different skills and requirements, but the fact they are correlated at all is encouraging, I think. will post some more details about the marks when I post the marks for the philosophy essays on Moodle next week.

Who to vote for?

2011-04-14T11:26:00.002-04:00

Far be it from me to tell you who to vote for in the upcoming election but I thought the following quotes might interest (amuse?) you, from the Green Party's, just-released, VISION GREEN statement. They promise to:

Provide funds to expand provincial health insurance to cover proven alternative therapies that are less expensive and invasive such as chiropractic, massage, acupuncture.
Expand healthcare coverage to include qualified complementary/alternative health professionals such as naturopaths, acupuncturists, homeopaths, licensed massage therapists, chiropractors, and dietitians.
promote complementary health care – through support of chiropractic, naturopathic, homeopathic, and other non-western practices.

Needless to say, the bolding is mine. I think Tim Minchin (see previous post) said everything that needs to be said about homeopathy and alternative medicine.

Stormy Weather

2011-04-14T11:04:00.001-04:00

This animated beat poem by Tim Minchin just about covers everything we talked about in the last half of BIOL-433.

Marks-a-lot

2011-04-14T09:41:00.002-04:00

Marks for Annotated Darwins are now posted on Moodle. Apologies for the delay but I was awaiting a late submission, and then had trouble with Moodle. Your Annotated Darwins were generally excellent and I gave a few people bonus marks that will not appear on Moodle as there is a ceiling on the marks I can enter there.

Marking is an inexact, somewhat subjective process but I am confident that the rank order of marks in this course is highly repeatable and fair. Because you are marked on so many things, any small inconsistencies on our part are almost always cancelled out. Some of you have complained about participation marks but I can assure you that these were assigned fairly and in rank order. The problem (for you, I suppose) is that even though you may have thought you participated well, others in the class participated more and better so your mark might not reflect your impression of your own contributions. I am happy to discuss this with any of you.

I marked about half of the Philosophy essays so far and they too are very good, on the whole. I will try to post those marks in the next week or so.

Conscious yet?

2011-04-12T11:21:00.003-04:00

In case you would like to explore the ideas about consciousness and free will further, here are some of the references I mentioned in class:

Dennett D 1991 Consciousness Explained. Little, Brown & Company, Boston
Edelman G 1992 Bright Air, Brilliant Fire. Penguin
Kringelbach ML, Berridge KC 2009 Towards a functional neuroanatomy of pleasure and happiness. Trends in Cognitive Sciences 13: 479-487
Cashmore AR 2010 The Lucretian swerve: The biological basis of human behavior and the criminal justice system. Proc Natl Acad Sci USA 107:4499–4504.
Brembs B 2011 Towards a scientific concept of free will as a biological trait: spontaneous actions and decision-making in invertebrates. Proc. R. Soc. B published online 15 December 2010 doi: 10.1098/rspb.2010.2325
Nichols S 2011 Experimental Philosophy and the Problem of Free Will. Science 331, 1401 DOI: 10.1126/science.1192931
Tenenbaum JB et al. 2011 How to Grow a Mind: Statistics, Structure, and Abstraction. Science 331, 1279; DOI: 10.1126/science.1192788

I hope you find this stuff interesting, not that you have any choice, really ;}

Fledging

2011-04-05T11:53:00.000-04:00

It's 11:30 on Tuesday, immediately after class, and it looks like the baby hummingbirds are still there but about to fledge: http://phoebeallens.com/nochat.html

Thanks for making the course so interesting and rewarding for me. I assume you will all have lots to think about in the coming months and years. To those of you actually fledging at the end of this term, I hope your next step is exciting and fulfilling. For those of you still here for another year, don't hesitate to drop in to see me any time.

I will be making a few more posts on this blog in the next week or two, and will leave it up as long as possible, just adding to it next time I teach this course.

Books on Scientific Misconduct

2011-03-28T18:03:00.002-04:00

Last week I mentioned a few books about scientific misconduct. Here they are:

Garfield B 2007 The Meinertzhagen Mystery—The life and legend of a colossal fraud. Potomac Books. [a great read and a really scholarly assessment of one of the great frauds of the 20th century]
Koestler A 1971 The Case of the Midwife Toad. Hutchinson [about Arthur Kammerer and his attempt to support Lamarck's ideas]
Reich ES 2009 Plastic Fantastic: : How the Biggest Fraud in Physics Shook the Scientific World. MacMillan [an interesting and surprisingly sympathetic look at Jan Hendrick Schön]
Judson H 2004 The Great Betrayal: Fraud in Science. Harcourt [an overview of scientific fraud and what it does to science, by Olivia Judson's dad—Olivia is Dr Tatiana of sex secrets fame]

Also Tim Birkhead and I wrote an article about fraud in science that you can download here. We will do the survey in Tuesday's class.

This week—21 March

2011-03-20T11:02:00.002-04:00

Spring equinox at 19:20 EDT on 20 March 2011. Supermoon last night rose at 1940 last night (19 March).

Earthquakes, tsunamis, heavy snowfalls. Coincidence? Astrologers don't think so.

This week we'll be talking about scientific misconduct. Who, when, where and how. This is a big topic that's been in the news almost every month for the past decade. Lots to think about and talk about.

Philosophy Essay

2011-03-19T13:09:00.003-04:00

Now that you are in the final stages of ~~thinking about~~ writing your philosophy essay, here are some details to guide you. I have talked about most of these things in class, and will be happy to clarify anything here on Tuesday next:

STYLE

maximum 5000 words, minimum probably about 2000 words; I doubt that you can say everything that needs to be said in less than 2000 words; there will be rewards for clarity and conciseness, there will be penalties for unnecessary rambling and repetitiveness
single-spaced, serif font, saved as pdf
you are welcome to use pictures, graphs etc., but please provide captions and integrate them into the text near where you first refer to them
provide references and source material at the end of the essay (these are not included in the word count
make sure the organization of both your essay, and your paragraphs is clear; at least a few of you appear not to have fully grasped the concept of a topic sentence, or of having logical links between sentences in a paragraph. It would be no exaggeration to say that some of you write like this: "I am taking 4 courses this year. American robins lay blue eggs...."
subheadings are welcome but not necessary
see Moodle for more formatting details, under 'Philosophy Essay' and 'Style Guide for Essays'

CONTENT

biology: your essay must include a heavy dose of biology, in the form of biological facts, ideas, concepts. I will take marks off if you get the biology wrong.
history: not necessary but most of you will benefit from having some historical treatment of the subject. In some cases most of what you write will be in a historical context
philosophy: ideas, the more the merrier. And controversies. I am particularly looking for some evidence that you have given your subject lots of thought and that your own ideas come through loud and clear
conclusion: this is or at least may be the hardest part, so pay particular attention to ending your essay in a logical and thoughtful manner. An abrupt ending that comes to no logical resolution, or ideas for the future, etc, is not good.
uniqueness: I particularly do not want to see an essay that I think you could (or could have, or actually have) submitted to another course in biology. In other words, I don't want an essay about a subject that does not include a philosophical component. A mere recitation of facts about climate change, or animal welfare, or stem cells, is not good enough and will result in a failing grade. I want you to take a critical view of the material rather than just reporting facts at face value

DEADLINE

pdf uploaded to Moodle by 5 pm Kingston time on 8 April 2011

MARKING

I leave on 7 April for a conference in NY city, then to the Pyrenees for a few months to work on rock ptarmigan, writing, and wine-tasting
I will upload your mark to Moodle so you can see your own marks for the course by the end of April and will submit them to the registrar before the deadline in early May
I will provide you with some brief comments about your essay by email when I post the marks
I will not return your marked essay unless you specifically ask me to by email after I have posted the marks and before 15 May 2011
I will be marking your essay out of 25 with about 15 marks for content (as outlined above) and 10 for style, again as outlined above. This may seem like a lot of marks for style but, honestly, the most brilliant ideas will be lost if you do not express them in an organized and clear fashion. I will also take off a mark or two for basic spelling, grammar and layout details, including typos

News of the Week

2011-03-19T10:23:00.003-04:00

In Thursday's lecture I mentioned several recents science news items that are relevant to things we've talked about in class. They are listed below with links to the originals but note that some of these links will not work unless you are on campus or linked to the Queen's library through the Queen's proxy link:

the discovery of 13,000 year old artifacts on Santa Rosa Island off the coast of California, suggests that some early migration of humans after ~~they~~ we crossed the Bering Strait may have been by sea [the podcast is freely accessible]
the faking of fossils in China has caused a stir; the link is to a recent letter so check out the articles that this letter refers to
a new study on tooth wear in fossil horses shows that we can actually learn something about behaviour from the fossil record
a molecular phylogeny of annelids finally provides a consistent view of annelid evolution and helps explain some apparently enigmatic aspects of the evolution of their morphology, solving a problem originally identified by Ernst Haeckel
lamp shell embryos react to light, demonstrating that even simple organisms composed of a few cells can have primitive 'eyes' [that link is to a blog post describing the study; the reference to the study itself is at the bottom of that post]; the picture below shows the embryos and the location of the light sensitive 'eyespots'

This Week—14 March

2011-03-12T20:45:00.005-05:00

This week we are going to talk about alternative medicine, which seems like a nice segué from talking about religion. Last Thursday the Doc Zone on CBC was called Magical Mystery Cures and focussed on various ways to reduce the effects of aging. It's an excellent introduction to this week's topic and you can watch it at http://www.cbc.ca/video/#/Shows/1221254309/ID=1836464814

I plan to discuss homeopathy, vitamin therapies, vaccination, naturopathy, chiropractic, acupuncture, and faith healing. I would appreciate it if you would think about and read up on those topics in advance so that you can contribute to the discussion.

You might also want to check out one or more of the following blogs and blog posts: Science Based Medicine, Trust the Evidence, KevinMD, PLoS, and Evidence Based Nursing and Midwifery.

What is science?

2011-03-11T09:12:00.001-05:00

That might be the most important philosophical question we deal with in this course. That, and what is religion?

To try to make sense of that question, I will post below a series of quotes that I think are relevant to answering the question "What is science?". I will add to this list as I find relevant material.

Scientists are responsible for truth, knowledge, wisdom, and understanding. Truth is what is—it is the underlying reality of all existence. Knowledge is what we think we know about truth. Knowledge, however, is always an imperfect assessment, and is always subject to revision and improvement. The realization that there are discrepancies and weaknesses in knowledge is wisdom. Wisdom leads to a process, called the philosophy of science, through which knowledge is modified to better fit the truth. Philosophy means the love of wisdom, and doctors of philosophy are supposed, before all else, to be experts in wisdom. Understanding, as defined in Job (28:28), is the effort to avoid evil. We may think of understanding as what we use in order to adequately apply our wisdom and our knowledge in guiding our actions. While applied scientists seek understanding, basic scientists seek knowledge.

from Fretwell SD 1975 The impact of Robert MacArthur on ecology. Annual Review of Ecology and Systematics 6:1-13

Ontological Argument

2011-03-10T21:17:00.000-05:00

Over at the blog Cosmic variance, Sean Carroll (a different Sean Carroll from the one who wrote "Remarkable Creatures") has an excellent discussion about the ontological argument for he existence of deities. Have a look.

No Thursday Lecture

2011-03-07T19:54:00.000-05:00

In case you missed it in the last post, there will be no lecture this Thursday, as I am off to Toronto for a few days.

Take this opportunity to ~~sleep in~~ work on your philosophy essay.

This week—7 March

2011-03-06T21:38:00.000-05:00

This week we will be talking about religion and writing on Tuesday. I ran out of time last week to get into the relationship between biology and religion, and I think that will make for lively discussion. I also want to spend some time telling you a bit about your essays and writing style.

There will not be a lecture on Thursday as I have to go to Toronto for a couple of days and will not be back in time. Use the time to work on your seminars!

Monophyly revisited

2011-03-02T10:49:00.001-05:00

Darwin, Annotated

2011-02-26T11:52:00.001-05:00

As you are all undoubtedly in the final throes of your Annotated Darwin project, I thought it might be useful to pass on some answers to questions that people have been asking me over the past week or so:

your submission is due, in pdf format, at 5 pm Monday (28 Feb) via Moodle
there's no upper limit to the number of annotations you can do, but the lower limit is 50 unless you can provide me with a convincing reason as to why you couldn't reach that goal
my preference is that you have all your annotations as endnotes, following the whole chapter, but there are no marks off for not doing exactly that (some people will have already done them following each page etc, and I don't want you to waste time changing that, if that's what you've done)
your name and student no. in the page header, not mine
provide clear details on where the chapter is from
there's no limit to how long each annotation should be
refer to pictures, graphs, books, websites, etc at the end of the annotation in which you refer to them. You can just write "SOURCES:" and list them in a standard format
do not copy and paste off the web, or anywhere else for that matter as that is plagiarism and will not be tolerated. Put everything you write in your own words

I will start marking them right away at the rate of about 2 per day and thus should be finished by 15 March. I will provide you with a mark and a brief assessment in writing about your annotated chapter but will not provide detailed feedback unless you specifically request it. Your mark (out of 15) will be based upon:

meeting the minimum requirements
the appropriateness of what you decide to annotate, concepts are better than people and places, but people and places are better than simple facts that most people should know. A few annotations that provide the sorts of details that are not easy to come by should be highly valued
the quality of your annotations, especially with respect to the thoughtfulness of your material (the less you simply paraphrase what you could get from a single website, like wikipedia, the better)
your wise use of illustrations to enhance your annotations (in other words, there's nothing to be gained by using gratuitous illustrations that do not really add anything useful)
the clarity of your writing; your annotations should be clear, concise, and informative, not confusing, awkwardly written, or wordy
creativity; it's not easy to be creative in this sort of exercise but if you do something creative you will be rewarded

There are no marks off for formatting details per se, but anything you can do to make things easier for the reader will undoubtedly be rewarded indirectly.

Gould Lewontin Redux

2011-02-25T14:53:00.000-05:00

Over at Sandwalk, Larry Moran (Biochem, UofT) has a nice discussion going on the Gould and Lewontin paper you read for the tutorial this term. Makes for interesting reading and Richard Dawkins ways in with his pithy 2 cents worth. Moran is about as anti-adaptationist as it gets for an evolutionary biologist but I like to read his stuff mbecause he makes me think, especially about how wrong he is.

I mentioned this to Richard Dawkins—that I like to read Moran's blog because he annoys me—in Brasil in the summer of 2009 (we were both there for a conference). Richard said 'oh piffle' or something like that, and claimed he wouldn't waste his time. But I guess he now has time to waste, or sees the wisdom of assessing arguments you don't agree with.

The picture shows my postdoc Troy Murphy discussing something—no doubt pithy—with Dawkins in Brasil.

Books

2011-02-20T14:56:00.000-05:00

Over the past 6 weeks I have mentioned these books in class:

The Tiger: A True Story of Vengeance and Survival by John Vaillant: about the Amur (Siberian) Tiger and conservation in far eastern Russia, by a Canadian writer

Darwin's Dangerous Idea by Daniel Dennett: all about Darwin's ideas by one the the leading philosophers of our time

The Species Seekers by Richard Conniff: great stories about naturalists who searched the world for new species. Conniff has had weekly columns in the New York Times, drawn from this book, for the past couple of months

The Inner Bird by Gary Kaiser: a detailed exploration of bird anatomy, especially with respect to dinosaurs, written by a biologist with Environment Canada and the Nature Conservancy

Charles Darwin: vol. 1 Voyaging, vol 2 The Power of Place by Janet Browne: the definitive biography of Charles Darwin, in two volumes.

Egg and Sperm Race by Matthew Cobb: about the discovery of eggs and sperm in the 17th century

The Oxford Handbook of Philosophy of Biology edited by Michael Ruse: essays by different experts on philosophy in different areas of biology

Style, 10th ed by Joseph Williams and Gregory Colomb: some lessons on how to write (very) well

The Growth of Biological Thought by Ernst Mayr: a wide ranging treatise on the history and philosophy of biology by one of the 20th century's outstanding evolutionary biologists

Abstract Marks

2011-02-19T09:13:00.000-05:00

The marks I provided for your philosophy essay abstracts may seem, well, abstract. They are marked out of 5 with 1 mark for writing and 1 mark for ideas and 3 marks for doing the work, handing it in on time and having a consistent theme. Everybody got those 3 marks. If you got 5/5 then I think you are on the right track and if you hand in an essay written just as well, and using the abstract as a guide you will probably get an A.

If I gave you 0.5 for writing I think your writing needs some work—in most cases this means that you need a more logical sentence ad paragraph structure. If I gave you 0 for writing, you need a lot of work. It probably means that your writing is intelligible but not up to the standards I would expect for a senior undergrad student. Unfortunately, there's not too much I can do to help you with your writing style at this stage. I am happy to give you some detailed feedback (make an appointment) in person, if you want it, but my experience has been that these sorts of writing issues cannot be fixed overnight.

If I gave you 0.5 for ideas, it means that you had some semblance of ideas, concepts, and opinions in your abstract but too little for the purpose of this essay and course. If I gave you 0, I could not detect any focus on ideas. In general I am looking for a paper that you could not submit to another course. Thus a paper on global warming that just laid out the facts would not be good enough. I am looking for different ideas and where they came from, and best of all why. One way to do this is to focus on the development of ideas, or controversies, and try to figure out why there is a conflict of ideas.

I also want you to focus as much as you can on biology. Thus a paper on global warming that talks only about sea level changes, and glacial reduction is not good enough. I want to know the biological aspects of the issues and, if possible, how a better knowledge of biology can help to resolve them.

Do not hesitate to come and see me about your paper. I am available virtually every afternoon from now until the end of term, including Reading Week, and I can give you much better feedback in person. Also, if I gave you less than 1 for either writing or ideas, feel free to rewrite your abstract and send it to me, as I am happy to provide you with additional feedback.

Reading Week reading

2011-02-17T19:49:00.000-05:00

When you get tired of working on your Annotated Darwin during Reading Week, you can read section 3 in Remarkable Creatures because it is sort of relevant to what we are going to talk about in the second half of the course. Also I would suggest spending some time reading about atheism and creationism as there's a tom of discussion about these issues on the blogosphere and we'll be discussing those topics the first week back.

I would also suggest watching the remaining 3 parts of Darwin: The Voyage That Shook The World at http://www.trinity.edu/tmurphy/trinity/darwinfilm.html

During Reading Week I will be posting further thoughts on the philosophy essays and a few book reviews so check back here from time to time.

Enjoy your break!

Annotating Darwin on his Birthday

2011-02-12T09:32:00.000-05:00

I have posted on Moodle both instructions for preparing your Annotated Darwin paper, and a short example to show you what to do.

The example is a pdf document that I prepared using Word by copying the first page or so of a chapter from his Different Forms of Flowers book. My annotations are mostly copied and pasted from things I found on the web, but I want you to actually write things in your own words as copying and pasting is plagiarism, as you are not doubt aware. I estimate that you might want to spend about 10-15 min per annotation on average, so make sure you leave yourself enough time to do this project well. Some will take much less time, but a few will take much more, especially if you take care to avoid plagiarizing.

Here are a few things that will help to make the process go smoothly:

Do all the formatting first; don't start annotating until you have the original all set up in final form, with Darwin's annotations in italics, pictures sized properly, header and tile done, etc
I would strongly recommend marking all the text for annotation before you start and keeping track of the number of words/phrases you have marked for annotation. That way when you get that done you will know whether you have too many or too few things to annotate. I would then go through and either add or delete markings (bold or underline) on text so you get more or less the required number (50). Note that you are quite welcome to do >50 annotations if you have the time and inclination.
set up the endnote numbering style when you do the first annotation (choose the number format you want to use, etc). If you don't know how to do this the Help function in your word processor will show you.
In Word and Open/Neo Office, you can split your document on the screen so that you can view the text on the upper half and the endnotes on the lower half of the screen. I found that this really makes it easy to read and annotate at the same time. If your screen is too small to make this feasible, print out your marked text before you begin annotating so you can see the place where your annotation belongs while you are typing the annotation itself.

Today is Charles Darwin's birthday.

No readings this week

2011-02-07T21:36:00.001-05:00

This week I need to catch up, lay some foundations for next week and beyond, tell you a bit about systematics, and give you time to get your essay abstract done by Valentine's day so there is nothing for you to read.

For next week, though, I would like you to read the chapters in Remarkable Creatures that tell stories about paleontology and paleontologists (Roy Chapman Andrews, dinosaurs, bird fossils, etc). That is, you need to read all of Section 2 "The Loveliest Bones" before Tues 15 Feb. Note that chapter 10 "It's a Fishapod" is about the Canadian Arctic!

Due Dates

2011-02-03T19:45:00.001-05:00

As Andrew pointed out to me after class today, the due dates for assignments was muddled on Moodle. I think I have fixed them. The correct due dates are:

Philosophy Essay Abstract due 14 Feb at 5 pm

Annotated Darwin due 28 Feb at 5 pm

Philosophy Essay due 8 April at 5 pm

Don't hesitate to let me know if something online does not jibe with what I say in class.

Eagle Sex

2011-01-31T13:21:00.002-05:00

Like most birds, eagles copulate for such a brief period, and without intromission, that copulation is called a 'cloacal kiss'. Most birds don't have a penis and this makes them unique among animals that fertilize internally. Obviously a peis is not needed for sexual reproduction, so what's it for, you might well ask.

If you are lucky you can see eagles mating, live, on the Eagle Cam at http://www.wvec.com/marketplace/microsite-content/eagle-cam.html

Even if they don't mate, they are fun to watch as they get their nest ready for eggs.

Sex Week

2011-01-31T08:21:00.001-05:00

Well, Reproduction Week, at least. There are no readings for you to do this week as I will spend the entire week on the history of human knowledge about reproduction. This topic is not covered in Remarkable Creatures but some of the amazing discoveries from the 1600s are detailed in Matthew Cobb's Egg and Sperm Race, if you are interested in reading in depth on this topic.

We will also talk a bit more about your Philosophy essays and seminars. Remember that the working abstract for your essay is due on Valentine's Day, before 5 pm.

Plagiarism 101

2011-01-22T10:54:00.001-05:00

I discovered today a pretty good webinar from Queen's on PLAGIARISM at http://library.queensu.ca/qlc/video/Avoiding_Plagiarism/Avoiding_Plagiarism.htm

Plagiarism is a problem that I want you all to be aware of (and to avoid) so I would strongly recommend you watch that short presentation, and be prepared to discuss this and ask questions when we do our session on scientific misconduct after Reading week. There's even a nice little quiz at the end of this presentation.

To read

2011-01-21T10:05:00.001-05:00

I forgot to mention (remind you) in class yesterday that you should read PART ONE in REMARKABLE CREATURES before next week's lectures. I will assume you have read this as background for what I am going to talk about.

I hope (trust) you will all take it upon yourselves to read The Origin this term. There are 14 chapters so just about exactly one a week will get you through it, and the Costa annotated volume makes it more interesting I think, than the raw text. Reading it will also give you good ideas for your own annotations.

A (The?) Scientific Method

2011-01-20T18:44:00.002-05:00

In the December 2010 issue of THE SCIENTIST magazine Kevin Kelly (cofounder of WIRED magazine) had an interesting little article <http://www.the-scientist.com/article/display/57831/> on the present scientific method and how it has accumulated historically to what we do today. This method, shown below is what scientist use to gather knowledge that other can verify and to use that knowledge to understand the physical and natural universe by testing hypotheses and developing theories. As he nicely points out there really is not a single 'scientific method' but rather a toolbox that has accumulated about how to learn about things using a variety of tools.

I showed this timeline in class today but it was too small and I was running out of time to discuss it fully. You can click on the picture below to see a bigger version in a new window.

Topics for assignments

2011-01-18T20:58:00.000-05:00

When you decide on a topic for your philosophy essay, your annotated Darwin chapter, and your history of biology seminar, send your suggestion to Roz Dakin or Bob Montgomerie by email. We will decide if it is appropriate and if so we will enter your choice(s) on the topic list which we have made in Google Docs, which you can access via Moodle.

This list is just for your information; you cannot edit this list.

We will assign topics on a first come, first served basis. We would prefer that you each choose a different chapter to annotate but will allow up to 2 people per chapter if necessary. History of biology topics must be unique. We will allow up to 3 people on each of the broad philosophy topics but each one must be focussed on a different narrower subject.

This week—17 Jan

2011-01-17T12:35:00.000-05:00

I will try to post a notice like this every Sunday night to let you know what's happening in the coming week, so you might want to check here first thing Monday morning.

This week in lectures we will be discussing Charles Darwin and his life and contributions both to biology and science in general. We'll talk about his contributions to human affairs after Reading Week. On Tuesday I will spend some time showing what you need to do and how to do it for the Annotated Darwin assignment. You should probably bring your copy of the Origin (Costa annotated version if you have it) to class.

On Thursday, we will talk about some of Darwin's books other than The Origin of Species, and I will spend some time outlining what is required for your Philosophy of Biology essay, as you will need to start thinking about that soon.

Tutorials this week focus on three papers on the evolution of colour patterns in the pepper moth. Remember that you need to submit your critiques via Moodle by 5 pm Monday. If for some reason Moodle does not work properly, send your critique to Roz as an email attachement and explain exactly why the Moodle process did not work, so we can fix it. This is our first experience with Moodle and we are still working out some of the bugs.

Moodling

2011-01-13T11:22:00.000-05:00

I have made the course available to students on Moodle but have no way to ensure that you can actually log on. Please contact me immediately if you have any problems with Moodle.

We will use Moodle to provide information about assignments and other aspects of the course. You will also submit assignments on Moodle, and all of your marks will be posted there.

This is our first experience using Moodle so there will be some growing pains but we hope to give birth (if that's not mixing too many metaphors) to a full-fledged Moodle experience by the end of next week.

First week

2011-01-12T21:39:00.000-05:00

We are gradually putting together all of the resources and calendar for this course on Moodle. There you will find a brief outline of the course (Syllabus), the lecture and tutorial schedule, assignments and readings. So far we have only the times of lectures and tutOrials but we will add some details for each one once we figure out how to do that.

As mentioned in the first class, this blog/noticeboard is the place to look for ongoing notices and information about the course, as well as the occasional article on subjects relevant to the course material.

The Thursday lecture will begin promptly at 08:30

WINTER TERM 2011

2011-01-01T10:58:00.000-05:00

The first class will be held at 10:00 on Tuesday 11 Jan 2011. Pleaser check this blog on the morning before each class for reminders about topics, readings, and other news about the day's class.

Final set of readings

2009-03-28T14:57:00.000-04:00

For this, the last week of classes, the readings are:

Tues 31 March

Ghiselin: chapt 9 Sexual Selection

Darwin: excerpt from The Descent of Man and Selection in Relation to Sex, chapt 6 [this is the longest excerpt I have given you to read, at 12 pages, but it's well worth reading the whole thing]

Fri 3 April

Ghiselin: chapt 10 Conclusions

Darwin: excerpt from The Descent of Man and Selection in Relation to Sex, chapt 8

The excerpts from Darwin's books are posted on the course schedule webpage.

Readings for 24 and 27 March

2009-03-20T19:45:00.000-04:00

Please read the following for class:

24 March

Ghiselin: chapter 7 Variation

Darwin: excerpt from Variation of Animals and plants under Domestication

27 March

Ghiselin: chapter 8 An evolutionary psychology

Darwin: excerpt from Expression of Emotions in Man and Animals

The excerpts from Darwin's books will be posted on the course schedule webpage.

Readings March 17th and 20th

2009-03-15T09:49:00.000-04:00

This week's readings are:

17 Mar: chapters 4 and 5 in Ghiselin. In class we will read a page or two from Darwin's Barnacles

20 March: chapter 6 in Ghiselin, and a short piece from Darwin's Different Forms of Flowers on Plants of the Same Species (now available on the course schedule page)

I am going to get Drs Lougheed and Eckert to come and discuss these chapters with us on Tues and Fri, respectively. I would prefer that you focus on the Ghiselin readings in advance of those lectures.

Marking scheme

2009-03-07T10:49:00.000-05:00

As I mentioned a couple of times in class, I have modified the marking scheme to better reflect the amount of effort (both time and intellect) that I expect you to put into each assignment. To be entirely fair, since it is rather late in the course to be changing the marking scheme, I will calculate your final mark both ways and give you the higher of the two

Annotated Darwin

2009-03-07T10:06:00.000-05:00

I have now posted an example for the Annotated Darwin project here and some more detailed instructions here. Don't forget that this is due on 15 March, to be sent to me as a pdf attached to an email.

As I mentioned in class, I am really looking for some variety in the annotations and figures, and for annotations that have some depth (not just definitions, although a couple of these would be OK, especially if they are interesting). I would also prefer that you don't rely on wikipedia for all of your info and pictures.

Finally, please be careful that you do not plagiarize stuff from the web. That means you are not allowed to lift sentences from websites, and simply change a couple of words. Everything must be written in your own words. I apologize to those of you who are tired of hearing about plagiarism but, for reasons I do not completely understand, a few students just do not seem to get the point. On the example I posted, I deliberately used only wikipedia but I made sure that everything I took from that source was reworded well enough that there would be no hint of plagiarism, so that you could see an example of what is acceptable.

Attendance

2009-03-06T19:10:00.000-05:00

I am sorry to see that attendance has fallen off to about 2/3 since Reading Week. Don't forget that participation is an important part of this course, and you will miss what I think is the most useful, and painless, as pet of this course if you miss class.

Readings: Mar 10th and 13th

2009-03-06T19:04:00.001-05:00

This week we are focusing on arguments about natural selection in the Origin. That means we will be reading only chapt 3 in Ghiselin, plus two different readings from Darwin:

10 Mar: the first part of chapter 4 (Natural Selection) in the Origin

13 Mar: an excerpt from the middle of chapt 7 in the 6th edition of the Origin, where he deals with various objections to his theory that were raised by a prominent zoologist of the day, St. George Jackson Mivart (see picture to the right)

The first Darwin reading is rather short so I would suggest reading all of the Ghiselin chapter before the tuesday class

As always, pdfs for the Darwin readings are posted on the course schedule

Readings: first week of March

2009-03-01T10:35:00.001-05:00

The readings for this week are:

For Tues 3 Mar

Ghiselin: Chapt 1 Geology

Darwin: Coral Reefs, last part of Chapt 6

For Fri 6 Mar

Ghiselin: Chapt 2 Biogeography and Evolution

Darwin: Origin, Chapt 12 [note that the pdf for this is largish because it is a copy of the actual book, first edition; if you want a smaller text only version there are several places where you can get this on the web]

As always, pdfs for the Darwin readings will be posted on the course schedule as soon as I can get them ready

Readings for FRIDAY 27 Feb

2009-02-25T09:38:00.000-05:00

For Friday's class please read:

Ghiselin: everything up to the beginning of Chapt 1.

Darwin: Chapter 17 in Voyage of the Beagle (available here as a pdf)

I suggest you print out the Darwin reading and bring both it and your copy of Ghiselin (Triumph of the Darwinian Method) to class.

As usual, you can read for the first 20 min of the lecture, but you will probably have to do some reading in advance to get both of these read by the end of that 20 min period.

All of the readings will be available on the course schedule.

Happy Birthday CHARLES DARWIN

2009-02-12T16:49:00.000-05:00

Today is the 200th anniversary of Charles Darwin's birth, and we are celebrating it with a symposium in Grant Hall at 7:30 pm. Everyone is Welcome.

Come and hear some interesting short talks about evolution by Drs Eckert, Friesen, Martin and Chippindale.

Delinquents

2009-02-08T19:30:00.000-05:00

I am surprised to see that many of you have not yet chosen a book to review or a chapter in one of Darwin's works to annotate. Please try to get those to me this week, and decide on your second biography to post as well. I would like to get those lists completed before Reading Week.

Readings Week of Feb 2nd

2009-01-31T08:47:00.001-05:00

For your tutorial this week we will be reading Chapter 5 in The Egg and Sperm Race called "The Rules and Theorems of Generation". In many ways this is the central chapter in this book.

In lectures we will be reading Chapter 5 ("Where the Dragon Laid her Eggs") on Tues, and Chapter 6 ("The Day the Mesozoic Died") on Friday. These two chapters are both about dinosaurs and fossils

Videos, Websites, Books

2009-01-31T08:30:00.000-05:00

Here are the links to the various videos and websites, and a list of books, that I have either shown or referred to in classes during the past couple of weeks:

VIDEO 1: Dan Janzen talking about how he became a naturalist

VIDEO 2: Dan Janzen and Paul Hebert talking about the Barcode of Life project

Site 1: Dan Janzen's page on caterpillars in the tropical forest

Site 2: Consortium for the Barcode of Life

Site 3: Piltdown man

Books

Koestler A. 1971. The Case of the Midwife Toad, ISBN 0-394-71823-2. [An account of Paul Kammerer's research on Lamarckian evolution and what he called "serial coincidences".]

Bates H.W. 1863. The naturalist on the river Amazons. 2 vols, Murray, London.

FRIDAY Jan 30th

2009-01-28T15:27:00.001-05:00

I forgot to mention in Tuesday's class that we will be reading and discussing Chapt 4 JAVA MAN in Carroll's INTO THE JUNGLE book this Friday. As usual we will start off the class with a 20-minute reading period so you should try to ensure that you have completley read this chapter by the end of that reading period.

Week of Jan 19th

2009-01-16T23:14:00.000-05:00

As I mentioned in class today we will be focussing on Chapter 3 in Cobb in the tutorials. The tutorials will begin with 30 min in which you can read but if you don't think you can read the entire chapter in 30 min then please do as much reading in advance as you will need to get through the whole chapter by the end of that 30 minute reading period.

In lectures we are going to begin discussing the chapters in Carroll's INTO THE JUNGLE. Please read CH 1 on Darwin before the Tues lecture and CH 2 on Wallace before the Friday lecture.

Student Blog Problems

2009-01-14T19:13:00.001-05:00

The student blog (Giants of Evolution) has been having problems this week as have all of the blogs at edublogs. They have been having a serious slowdown due to some server malfunction and have promised to get it fixed asap. Be patient, if you find it slow to upload your biography, or to even get on the blog.

If you find that there is an uploading problem close to the midnight Sunday deadline, simply email your bio to Dr Montgomerie or one of the TAs before the deadline.

Tutorials Week of 12 Jan

2009-01-10T12:38:00.001-05:00

This week please go to your assigned tutorial session at all possible. If you need to siwtch tutorial sessions please consult with your TA.

For this week's tutorial, please read Chapt 1 of Cobb's Egg and Sperm Race in advance, and BRING your copy of this book with you to the tutorial session.

The TAs offices are both in Room 4325 in BioSciences

* MON - Philina English: email paenglis@lakeheadu.ca
* TUES - Lori Parker: email 6LDP@queensu.ca

When sending emails to your TA or to Dr Montgomerie, please put 433 somewhere in the subject.

Pictures for Biographies

2009-01-10T12:07:00.000-05:00

I would like everyone to include at least two pictures in their blog biographies. Unfortunately you cannot upload images to the blog post yourself, so you have two options:

link to the image you want to use from another website—you will need to copy and paste the URL of that image (note that this is the image URL and not the web page URL. Remember to adjust the image size so that it fits well on the page
send the image to your TA and they can put it into your bio for you. Just send it as an email attachment, preferably already adjusted to the size you want, and they will put it into your bio as soon as they are able.

I will make the bios public (i.e. visible on the blog, as soon as I can after you post them but they may lack pictures for a few days until the TAs can get to them. Both the bios posting and the pictures are due by midnight on the day of the deadline.

Ads by Google

2009-01-06T21:37:00.001-05:00

You will notice that our Giants of Evolution blog often has Ads by Google. These are inserted by Eublogs onto our blog and this is the price we pay for getting this blog for free from Edublogs.

Course update

2009-01-06T20:03:00.001-05:00

If you have already looked at the Syllabus etc I showed you in class today, please look again as I have just updated all those pages to include a little more info as we discussed in class today, and to include info on how to do the Annotated Darwin project.

There's nothing to read for Friday's class.

Prof's blog

2008-12-31T08:05:00.000-05:00

This is a blog that I use as a noticeboard for BIOL-433. Unlike other blogs that you will read, there are no comments on this one so this is really just a place for me to put up notes about the course. I strongly suggest that you bookmark this blog, visit it daily, and use it as your window onto the course material. The latest post is always at the top of the blog.

Links to all other course material are listed in the right-hand sidebar. You might even want to get an RSS feed to your favourite newsreader (huh? If you don't know what I'm talking about I'll explain this in class).

I will post to this blog at least once a week and more often if time permits. My intention is to post here:

info about course scheduling—if I have to cancel a class (snow, emergencies, unavoidable duties) it will be posted here at least a half hour before class begins
cool things that I have read on-line or in books and papers that are relevant to the course material
instructions about projects, tutorials and readings that were mentioned in class (or not)
feedback on emails or comments you make about the course, if I think that everyone would be interested
links to videos, pictures, papers, websites, etc, that refer to things we talk about in class

There will be no tutorials the first week but there will, of course, be lectures. See you at 08:00 Tuesday mornings.