Check out this article from MSNBC about the origin of blue eyes.
Thursday, January 31, 2008
I unfortunately started a false rumor about Nicholas Cage being a cycad collector. This, of course, is a preposterous idea. Brad Pitt and David Bowie however are well-known cycad collectors (according to the first article linked to above).
Wednesday, January 30, 2008
Take the chameleon. It's pretty obvious that nifty color changing ability helps camouflage them allowing them to be both protected from predators and to catch more prey. Right? Well, no according to research published this week. Evidence suggests that the color change is for communication not camouflage.
'No one has ever shown that the chameleon's special ability provides camouflage, says Hanlon, who reviewed 100 years of scientific literature on the subject.'
Tuesday, January 29, 2008
The cost is $999, which is far from cheap, but is in the range of pretty standard consumer products such as tv's etc rather than say the cost of a car. Like many products the cost is likely to drop.
Once the cost falls how long before insurance companies offer discounts for customers with the 'good genes'? Which is just a different way of discriminating against people with the bad genes...
Welcome to the future.
If you haven't seen the movie Gattaca, well, you should.
Monday, January 28, 2008
In a bid to demystify the somewhat arcane style of scientific writing, the journal Science has selected a number of scientific articles from that journal and annotated them, illustrating how different parts of each article embody the scientific method. This is part of the 'Keystones of Science project'. The paper also has a nice pop-up glossary if you hold your mouse over any of the green terms.
Sunday, January 27, 2008
If the direct link doesn't work then after you are logged in go to Electronic Journals, search for New Scientist and use the e-links to find the August 11, 2007 issue. The article is on page36.
Oh, and External Testicles are number 10 on the list.
In the interest of academic debate and in the spirit of fair use, I copy an extract below.
A particularly interesting topic for this class, after our lecture on the origin of the eukaryotes, is the discussion of mitochondrial DNA. Bottom line: If you wanted to build humans to last, mitochondria are the last place you'd put DNA.
'Inside every one of our cells are dozens of little sacs called mitochondria, in which sugars are "burned" to produce the energy that powers the cells. The process also produces highly damaging molecules called free radicals, so the interior of a mitochondrion is hardly the safest place for vital DNA - and yet it is home to the genes for 13 crucial mitochondrial proteins.
It's a crazy design: like keeping the repair manual for a steam engine by the furnace, where it inevitably becomes charred and unreadable. The slow loss of function as mutations accumulate in mitochondrial DNA may be the main cause of ageing and, some believe, of many age-related diseases, from diabetes to Alzheimer's.
The DNA is there because of our evolutionary history. Mitochondria are the remnants of a once independent bacterium that formed a symbiotic alliance with our cells around 2 billion years ago. Over time, many of the bacterium's original genes have been lost or jumped to the cell nucleus, but human mitochondria still retain 13 genes.
Anti-ageing research is already exploring ways of moving the remaining genes to the safety of the nucleus. It will not be easy. The 13 genes cannot simply be moved to the nuclear genome, because then the 13 proteins will be made outside the mitochondria where they are needed. A solution might be to get the mRNA recipes for proteins delivered to the mitochondria, so the genes reside in the nucleus but the proteins are still made inside the mitochondria.'
Friday, January 25, 2008
There's a nice essay by Matt Ridley on the PBS Evolution website that discusses the issues. The website has some nice resources apart from this.
Here's a BBC report from a paper in 2004 which takes the issue further and asks whether the Red Queen hypothesis can really explain why we have so much sex...
And to bring us up to date here's a link to a report on a paper from 2006 that argues that the Red Queen hypothesis does just fine if we take into account the maternal transmission of parasites.
Thursday, January 24, 2008
'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 pedigree 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. (Although we are all much more closely related to Kevin Bacon....)
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, January 23, 2008
Tuesday, January 22, 2008
ScienceDaily (Jan. 22, 2008)
To get a good grip on eukarotic diversity try to work out how this arrangement differs from the one I presented in class and the one in your text. It actually looks like the 5 groups in Purves 8th were closer to this new study than some other texts. As I mentioned today Purves already has the Alveolates (apicomplexans, Dinoflagellates and cilliates) and the Stramenopiles (brown algae, diatoms and oomcycetes) grouped into the Chromalveolates. This latest study suggests that the Rhizaria (forameniferans and radiolarians) should also join that group. (If the group called Unikonts doesn't sound familiar it is because we ran out of time to discuss this group - but that's fine because we'll be returning to this group several times since it contains both the fungi and the animals.)
I'd dispute whether the tree of life has 'lost a branch' though or whether one branch joins the tree higher up than we previously thought.
Sunday, January 20, 2008
Jumping into the stillness
Of an ancient pond!
Matsuo Basho 1686
I already hyped National Geographic once so this time I'll just promote their website. Apart from the always excellent photographs their news section contains a lot of items of relevance to this class. Currently, for example, they have Parasite Makes Ants Look Like Berries, Starfish Taking Over Waters in Indonesia and, best of all, One-Ton Rodent Discovered in Uruguay.
The photograph and haiku above is from the magazine article on Japan's haiku master Matsuo Basho, also available on the website.
Saturday, January 19, 2008
Sat 1/19 1:58pm -1.2 (this means 1.2 ft below mean lower low tide)
Sun 1/20 2:42pm -1.5
Mon 1/21 3:23pm -1.6
Tues 1/22 4:01pm -1.4
Wed 1/23 4:37pm -1.1
See the following website for interesting info on tides, etc: http://tidesandcurrents.noaa.gov
Thursday, January 17, 2008
Links to read more on topics from todays lecture.
The appropriately named 'Snowball Earth' website is the go-to place for all your snowball earth information needs. But you should be aware that it is the work of a 'pro-snowball' scientist. The wikipedia article on snowball earth has a good discussion of both the evidence for and against the theory. Here's the news report from, earlier last year that I was thinking of when I said there was some recent evidence against this theory. There are a bunch more links to related stories, half way down on the right. As you can see this is quite a hot topic (no pun intended).
There's a nice article on the purple earth hypothesis here, also from 2007. Here's a similar article that focuses more on the implications for finding life on other planets.
"When we look at these faraway planets, we're not going to be able to spatially resolve them. We won't be able to see continents and oceans. Everything we must learn about that planet will be in a single dot of light."
Finally, the giant sulphur bacteria I briefly mentioned was only discovered in 1999! Here's the original research report from Science and a nice editorial news summary.
Wednesday, January 16, 2008
"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.”
You will be relieved to hear that news, just last week, suggests the Dutch have stopped growing.
Paleontology hit the headlines a couple of years ago when paleontologists discovered a fossil fish, Tiktaalik roseae, that showed the beginnings of digits, wrists, elbows and shoulders, as well as a skull, neck and ribs that resemble those of tetrapods like today's familiar four-legged land animals. Paleontologists suggest that it was an intermediate form between fish which lived about 385 million years ago, and early tetrapods which lived about 365 million years ago. Its mixture of fish and tetrapod characteristics led one of its discoverers, Neil Shubin, to characterize Tiktaalik as a "fishapod". Like any self-respecting fossil Tiktaalik has its own homepage.
The story raised some interesting debate about what is meant by the term 'missing link' - a term that sees more use in the mainstream media than the scientific literature. A better term would be 'transitional form'. The Wikipedia article on Transitional Forms has a nice set of figures showing the number of Hominin species known to science in 1850, 1900, 1950 and 2002 - illustrating how our knowledge has steadily increased and although there are still 'gaps' in the record these gaps become smaller and smaller through time.
A popular term to designate transitional forms with is 'the missing link'. The term is especially used in the regular media, but is inaccurate and confusing. This is partly because it implies that there was a single link missing to complete the picture, which now has been discovered. In reality, the continuing discovery of more and more transitional fossils is further adding to our knowledge of evolutionary transitions.
Tuesday, January 15, 2008
Figured it had to do with a lot of the stuff we've been talking about, or at least stuff we will talk about. Even if I'm wrong its a good read (and you can download the full pdf, its easier than reading from the jstor website).
The fact that the story appears on both the Straight Dope website and Snopes (here and here) suggests that despite dubious scientific evidence it is being passed around more in the form of an urban myth. You might like to think of experiments you could do to work out exactly what mechanisms are at play here (observer bias, 'trails' left in the equipment, worms on 'smart drugs' etc.)
Here are links to the Temple of Nature, and Zoonomia. Select the format you want to download from the panel on the left.
You can also find Erasmus at Project Gutenberg, the first producer of free electronic books. They have Zoonomia and the Botanic Garden. They also have most of Charles Darwin's books, including the more obscure ones.
Whilst I'm pointing out resources I should also mention Librivox, which provides free audiobooks of books that are in the public domain. This includes a nice reading of Darwin's Origin of Species. (Full title: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.)
A short report in Science in 2006 described an 'Early Cretaceous Spider Web with Its Prey'. This was the worlds oldest preserved spider web. Preserved in a large blob of amber the web and the insects caught in it have now been dated to the early Cretaceous - about 110 million years ago.
Although the web is not complete enough for scientists to reconstruct it, enough remains to suggest this was not just a collection of strands and was probably in one plane like an orb web.
As you can imagine finding fossilized spider webs is unusual. We do know that fossilized spiders have had spinnerets for producing silk for closer to 400 million years.
Monday, January 14, 2008
PZ Meyers Pharyngula blog - self-described as 'Evolution, development and random biological ejaculations from a godless liberal'. That seems to describe it fairly well. PZ Myers is a biologist and associate professor at the University of Minnesota (and the pharyngula period is a stage in the embryonic development of vertebrates).
Speaking of the godless, and I mean that quite genuinely, Richard Dawkins has two websites/blogs that are well worth checking out. The official Richard Dawkins website self-described as 'A Clear-Thinking Oasis' and the Richard Dawkins Foundation for Reason and Science (another Clear-Thinking Oasis'). Richard Dawkins holds the Charles Simonyi Chair for the Public Understanding of Science at Oxford University. He came to prominence through his 'Selfish Gene' book in 1976, a book that all Biology undergraduates at my University were recommended to read a decade after its publication - a recommendation I am happy to pass on thirty years after its publication (that makes me 43 if you are curious, I know I look much younger....). Lately Richard Dawkins has been rather prominently involved in the debate between creationism and evolution and is often described, usually by others, as an 'outspoken atheist'. His latest book, 'The God Delusion', combines his work on evolutionary biology and his passionate atheism to ask why, if there is no god, a belief in one so widespread and prominent as to be almost universal? In the hands of an evolutionary biologist this turns out to be quite an interesting question.
Here's a brief news report from last year that ties in to the first two classes.
Gut parasites came from the deep: A genetic comparison finds links between bacteria from deep-sea vents and those from the human body. 7 July 2007.
Saturday, January 12, 2008
"Oh God, no. Oh, Jesus. We thought we had made a big advance with the Scopes monkey trial....My God, evolution is a fact, and if these people are disturbed by being the descendants of monkeys and fishes, they've got a mental problem. We can't afford the psychiatric bill for them. That ends the story as far as I'm concerned."
Apparently not being a front runner gives you more freedom to say what you really think!
Friday, January 11, 2008
Thursday, January 10, 2008
There is a great article about the phylocode proposal and controversy in Discover magazine. I recommend you all read it. It would be interesting to read your thoughts so add a comment to this post if you are so inspired. The actual Phylocode website has both their principles and rules.
Wednesday, January 9, 2008
Here is a link to a really nice website at Cornell for an Introductory Biology class. On the linked page there is a nice description of protobionts and coacervates, and, on the left, some useful links to further origin of life information. Coacervates are one type of protobiont.
Tuesday, January 8, 2008
I mentioned today one of the problems with discussing evolution is that although scientists tend to use evolution in a very specific sense (a change in gene frequencies from generation to generation as we'll see shortly) the public and press tend to wrap three concepts together:
- Evolution as change, in the true biological sense.
- Darwin's theory of evolution by natural selection as a mechanism explaining how and why that change occurs.
- Abiogenesis, the theory explaining the first appearance of life on earth
Evolution may lead to absolute improvement - cheetah probably run faster than their ancestors - without leading to any relative improvement - cheetah don't catch any extra food because their prey is running faster too. Hey, there's the red queen again. Evolution has very little to say about human society and its improvement, or otherwise, despite the fact that at various times people have proposed a 'science' called social darwinism. You should probably be aware of some of the history in this field and the social philosophy of eugenics that it led to. If you haven't thought about this much then the Wikipedia articles I have linked to are a great starting place and are impressively neutral for such an emotional subject. I won't be talking about this in class but as a biologist it is likely that one day you will meet someone who thinks that because you believe in evolution you believe in some form of eugenics (or maybe I just meet all the crazy people).
Okay, I finally get around to eating my lunch so I open this week's edition of 93106 - the weekly faculty and staff newspaper for UCSB - and what is right there on the front page?
'Mica Layers may have hosted life's first cells says new theory'
Research on the origin of life going on right here on campus.
Thanks to the wonderful folks at BoingBoing (a directory of wonderful things) for directing my attention to this fabulous cultural artifact: a Red Queen Barbie doll! Part of a new line of Alice in Wonderland Barbie toys. Buy this one and all your other Barbie dolls will have to run twice as fast just to keep up.
The only disappointment is how, well, static, the Red Queen looks. Perhaps she should come with a catapult launcher.....
Although Barbie is well known for her difficulty with math she has already revealed a fondness for evolution: witness the Paleontologist Barbie. There is a 'Dinosaur Quiz' on the back of the box- 'if you get five or more right you should consider a career in paleontology too!'