Thursday, June 29, 2006

Pedigree collapse

'Everybody has two parents, four grandparents, eight great grandparents, and so on back through time, with the number of ancestors doubling in each generation. Go back 30 generations and the number of ancestors tops one billion. Eventually we arrive at a time when we have more ancestors than there could have been people in the world. How can this be?'

Fortunately we can trust Cecil Adams to give us the Straight Dope on this subject. Now that you appreciate the issue you can appreciate this table which shows some stunning amounts of perdigree collapse in European Royal families. At some level of course we are ALL inbred - geneticists estimate that everyone on earth is at least a 50th cousin to everyone else.

There's another interesting article on the subject here.

"In a population of between three and five hundred people, after six generations or so there are only third cousins or closer to marry. During most of human history, people have lived in small, isolated communities of about that size, and have in fact probably been closer to the genetic equivalent of first cousins, because of their multiple consanguinity. In nineteenth-century rural England, for instance, the radius of the average isolate, or pool of potential spouses, was about five miles, which was the distance a man could comfortably walk twice on his day off, when he went courting- his roaming area by daylight. Parish registers bear this out. Then the bicycle extended the radius to twentyfive miles. This was a big shakeup."

I never really thought of the bicycle as a major advancement in dating technology before.


Wednesday, June 28, 2006

The Y chromosome - more than a wasteland

Here is a link to the Nature website I briefly mentioned today when talking about the Y chromosome. Nature have a series called 'Web Focus' where they provide numerous links to research articles and reviews on a particular topic. This particular one focuses entirely on the Y chromosome although there are others that may be of interest to you.

'The Y chromosome — with the genes to make a man — has been sequenced. Often regarded as a genetic wasteland, the sequence reveals that we may have underestimated its powers.'


It's either a 13 or a 45 or maybe a fish....

Another post of relevance to all the premeds out there.

Color blindness is one of the most common sex linked genetic disorders. It is estimated that around 1 in 12 men suffer from one form or another.

Unfortunately the quick test I put up in lecture today suffered from being scanned, then rendered by my computer then projected by a different device. I would not worry unduly if you couldn't see that image!

This isn't just a problem for projected images, a great many monitors are calibrated incorrectly (ie the displayed color may differ significantly from the intended color). This may render color blindness tests useless so if you suspect you may be color blind you should get yourself tested on printed material where the colors are reproduced accurately.

Having said that, there are plenty of color blindness tests on the web, for example here or here if you prefer the more standard PseudoIsochromatic Plate Ishihara Compatible Color Vision Test

If you work in a clinic or doctor's office, or know someone who does, here is a cool color blindness testing poster for children - diagnosing problems early is important to prevent learning problems. (The answers are here.)

Whilst doing some reading on this issue I came across a couple of interesting programs to help people deal with, understand, and accomodate color blindness. Vischeck simulates colorblind vision so that you can check how pictures and documents on your webpage will appear to color blind people.

Daltonize helps you correct images for colorblind viewers. In many cases the 'true' color of something may be irrelevant but the fact that it is different from its surroundings is very important. This program will alter the contrast and other characteristics of an image to make it more useable for color-blind people.


Thirteen-year old girls storming the Bastille.

I wanted this blog to function as a place I could put links to items I barely had time to mention in lecture. Here is a great example, a fascinating article from the New Yorker on changes in human height, subtitled 'Why Europeans are getting taller and taller—and Americans aren’t.' There is some great writing here and some wonderful images:

"Charlemagne was well over six feet; the soldiers who stormed the Bastille a millennium later averaged five feet and weighed a hundred pounds. “They didn’t look like Errol Flynn and Alan Hale,” the economist Robert Fogel told me. “They looked like thirteen-year-old girls.”


Adding Comments - Please Read

You do NOT have to have an account with Google Blogger to add comments to any post.

When you hit the 'Comment' link at the end of any post a pop-up window should appear. After the space for you to enter your comment is a set of three buttons. You can pick any one of these three (Blogger, Other, or Anonymous). Because the first one seems to be the default it has spaces for your username and password. But if you pick either of the others these disappear. Choosing 'Other' allows you to enter your name, or alias, and choosing 'Anonymous' requires neither.

There is word verification (confirms you are not a robot) and I'm currently moderating posts (only to prevent spam and abuse!) but your post can be anonymous if you wish and you certainly don't need to be a member.

Tuesday, June 27, 2006

Summer reading

Since it is summer I like to suggest a little light summer reading. In class today I mentioned two books that are relevant to the evolution section.

The first was Bill Bryson's Short History of Nearly Everything. This is also on the Berkeley Summer Reading List - Books for Future Presidents. This book covers a suprising amount of the material we cover in the evolution section and a little of the material in the ecology section. Being a mass market book it is a tremendous deal at only a little over $10 for the paperback version.

The second book is a little more obscure and is recommended for fans of the graphic novel. Jay Hosler is both a biologist and a talented cartoonist. The Sandwalk Adventures is the story of a conversation about evolution between Charles Darwin and a follicle mite named Mara living in his left eyebrow. If that sounds a bit wacky, it is, but the book is very clear and you'll learn a lot about both Darwin and evolution. You can read about his books and order them, if you are so inspired, at his website. If anyone asks me really nicely and promises to give it back I'll lend you my copy.


The 'theory' of 'evolution'.

Problems always arise when scientists use a term in a specific way that differs from how the term is used by the general public. Unfortunately both 'evolution' and 'theory' fall into this category (and so the phrase 'the theory of evolution' is just trouble waiting to happen). As we will see in a future lecture, scientists use the word theory to describe a hypothesis that has held up to extensive testing. In general speech, theory tends to mean something much more speculative. ('I don't know why the mail is late today but I have a theory').

Things are perhaps worse when we come to the word evolution itself. Evolution, for scientists, is a measurable change in the heritable traits of a population over successive generations. That's it. And it isn't a theory, it's a fact, because we can measure it. In general speech however evolution is often confused with Darwin's theory of evolution by natural selection. On top of this there is an additional misconception that evolution must involve improvement or progress.

I always thought Pearl Jam and Todd McFarlane had this latter issue in mind when they did the 'Do the Evolution' Video. Comments at the Sony Music site suggest otherwise.


Evolution in ten words

The original question was 'If you had 10 words or less, what would you have the public master about evolutionary theory?' although most people interpreted this as defining evolution in 10 words.

Either way it is entertaining and educational.

I like the answer here that makes a good point about evolution by explaining what would happen in its absence.

I'm curious whether anyone is reading this and whether the comments are working. So do me a favor and post a comment if you find a particularly amusing or educational 10 words or have come up with one of your own.


Monday, June 26, 2006

A wizard did it.

One thing that fascinates me as I learn more about the history of science is what people believed things were before they knew what they really were – or, in a similar vein, what people believed caused certain phenomena before they knew the real cause.

Some of these beliefs were wonderfully inventive and enrich our culture to this day. For example in Monday’s lecture I mentioned the suggestion that pygmy elephant skulls, with no eye sockets and a single, large, and centrally placed socket for the trunk, could have been the basis for the Cyclops myth. There is a nice write-up of this work on the National Geographic website which is based upon the work of Adrienne Mayor. In her book The First Fossil Hunters: Paleontology in Greek and Roman Times, Adrienne Mayor argues that the Greeks and Romans used fossil evidence both to support existing myths and to create new ones: Griffins, Centaurs, Cyclops, Giants etc.

Other explanations were much less inventive and ascribed a wide variety of phenomena (mysterious plagues, poor crops, bad weather etc) to entities such as witches and wizards (or their equivalent in the local culture). In modern popular culture such appeals to generic, and all powerful, entities is considered poor writing. The Simpsons have popularized the phrase ‘A wizard did it’ as an example of an evasive answer to an inquiry, usually with the implication the question is being purposely avoided. The phrase originated when Lucy Lawless responded to Professor Frink's question regarding a continuity error in Xena: Warrior Princess.

Frink: In episode BF12, you were battling barbarians while riding a winged appaloosa yet in the very next scene my dear, you're clearly atop a winged Arabian! Please do explain it!

Lucy Lawless: Uh, yeah, well whenever you notice something like that … a wizard did it.

Frink: Yes, alright, yes, in episode AG04 …

Lucy Lawless: Wizard!

Frink: Oh for glaven out loud.

Due to the wonders of alphabetical order “A wizard did it’ is first in the list of Simpsons neologisms on Wikipedia.

I mention it here because this raises some interesting questions about what makes a good hypothesis. Why do I criticize the 'wizard hypothesis'? I am, deliberately, going to put off detailed discussion of the scientific method until the second part of the class so we won't cover this in lecture for another couple of weeks.

Undoubtedly there are still phenomena around that science does not have a good explanation for. I can think of several but UFO’s would be a good example, especially the alien abduction phenomenon. It is interesting to speculate on how the future will rate our attempts at explanation – as a good attempt given the facts, as part of our cultural mythology, or as just laughable….


Wednesday, June 14, 2006

The politics of Mastodon

Welcome to the Bio1blog.

All the material provided here will be supplemental to that provided in class. I will use this venue to provide some more in depth information, to provide links to research papers and other items of interest. Important notices about the class will always be posted on the main Bio1B website.

If you read any foreign press it is easy to find out what the rest of the world thinks of America. Whether people love America or, let's just say, 'less-than-love' America, I think the one thing they would all agree on is that America, as a nation, has no small amount of self esteem.

So it is perhaps surpising to look back a couple of hundred years, to the period shortly after the American Revolution, when the world had a very different opinion of America.

From the Wikipedia entry on the French naturalist Comte de Buffon:
'Besides his many brilliant insights he is also known for expounding the theory that nature in the New World was inferior to that of Eurasia. He argued that the Americas were lacking in large and powerful creatures, and that even the people were far less virile than their European counter parts. He ascribed this to the marsh odours and dense forests of the continent.'

In this context the discovery of a Mastodon near Newburgh, N.Y. in 1801 had both scientific and political implications. Although this was not the first Mastodon to be discovered in America this one was excavated by Charles Willson Peale and his son Rembrandt (who did the drawing above) who were friends with Thomas Jefferson.

From the Treasures of the American Philosophical Society entry on Peale's Mastodon.
'The mastodon was proof that America could and would sustain large and vigorous life forms, perhaps even larger and more vigorous than Europe. Best of all, it was clear that the mastodon was unique to North America, a symbol of the antiquity of our continent and exemplar of the new nation. Jefferson may well have had the Peales' mastodon in mind when he enjoined Lewis and Clark to scour the western landscape for mastodons, living or dead.'