Showing posts with label evolution. Show all posts
Showing posts with label evolution. Show all posts

Wednesday, June 16, 2010

Evolving Thoughts on Homology



Accompanying the above intriguing illustration, John Wilkins has written a really good essay on the concept of homology, which we are taught (and go on to teach) as a really basic concept in evolution, but has surprising ambiguities and potential circularities (not unlike a few other evolutionary terms I can think of). John very helpfully traces some of the history of the term, and how its application has evolved as we've become better at building and testing phylogenies as hypotheses of evolutionary relationships. I have to agree with him when he says:
The notion of homology is complex, and as we recently saw when I asked about the use in mathematics, it has a slew of other meanings, but the one that seems to me to be consistent across all uses is this: a homology is a mapping or “agreement” of parts of organisms with other parts of organisms. A mapping relation is not a similarity, and it is not the explanation of the relation (such as evolutionary common ancestors, which are proposed to explain the homology). It is an identity relation: this is the same as that. The identity may be an identity of place, of sequence, of developmental process, or just of a shared name, but what it is not is similarity or common ancestry. Similarity may be how we identify homology (and what kinds of similarity depends on what we use), and common ancestry may be how we explain homology, but in both cases homology is the relation itself.
You know you'll be reading the rest of that essay for sure if you are in my class the next time I teach Evolution!

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Wednesday, June 2, 2010

Repeat after me: Evolution is NOT A LADDER and does not lead to any pinnacles!!!!

ResearchBlogging.orgI am more than a little irritated.

This is not how I normally feel after listening to one of my favorite podcastlets "Our Ocean World" broadcast on the local public radio station most mornings.

As a landlubber biologist, I love learning about the fascinating and often bizarre creatures in the ocean, and therefore really enjoy this brief dose of news from the biggest biome on earth. Especially because it typically comes on when I'm dropping my daughter off at school in the mornings, giving us something wonderful to share.

But today's segment (which came on just after I dropped the kiddo off - sorry I was unusually early!) on Tuna, titled Big Fish, Big Sea, really pushed some sensitive buttons. It could be that I had just finished grading finals for my Evolution class, and was particularly touchy about evolutionary misinterpretations. But no, this particular gaffe came from a Stanford Professor of Marine Sciences, no less, and is therefore even less acceptable for being broadcast on the radio!! 

Professor Barbara Block, the tuna expert featured in today's podcast, described these no doubt remarkable fish as being at the top of a bleeping "evolutionary ladder"!! She also said Tuna were "more evolved" than other fish! And that they were on a "pinnacle of evolution"!!!#$*!!!  

More than once! (I checked. I hadn't misheard).

And here I thought we had buried that damned metaphor of evolution being a ladder for good! Heck, I try to bury it ritually for my students every semester in all of my classes, starting with Intro Bio. Yet it keeps rising, like a zombie, even from the mouths of accomplished biologists!! What's it going to take to purge this metaphor entirely from our vocabulary, folks?!

And while on the subject, let's also be clear that no species is "more evolved" than any other. How could they be? If you accept the evidence that we all come from one common ancestor, that the tree of life has one common origin, then every living species has been subjected to the vicissitudes of life on this planet for the same overall length of time, no?! We may have taken different, often surprising and bizarre, twisting branching paths on this journey, but we've all (except those branches that went extinct along the way) traveled the same length of time, have we not? How can any one of us, bacterium to tuna, virus to human to dolphins who say thanks for all the fish, then claim to be "more evolved" than any other species?

Granted there are local peaks and valleys in the fitness landscape for any species, and natural selection may be constantly trying to push us onto the nearest one - but there are no lofty "pinnacles" that we can be proud of conquering! If anything, given the dynamic nature of our world and the new curveballs nature keeps throwing at us, being stuck on any tall pinnacle could lead to the worst sort of evolutionary dead-end. We're probably far better off wandering around local peaks and remaining capable of even drifting across the fitness landscape. Definitely don't want to be stuck on any too tall peak, thank you very much! In fact, as my friend Andrew Jones just reminded meall species evolve to extinction!

Although, now that I think about it, perhaps most other species on this planet, our fellow travelers in the evolutionary journey, are hoping that we humans have reached exactly such a pinnacle, and are, even more hopefully, about to fall off our lofty perch for good. Perhaps from these new ecofriendly smokes.

Meanwhile, repeat after me (especially if you are a biologist):

Evolution, in fact, is best described as a TREE:



And remember, the only thing we are all definitely evolving towards is EXTINCTION!


Thank you!!

Reference:
Andrew R. Jones (2009). The next mass extinction: Human evolution or human eradication? Journal of Cosmology, 2, 316-333

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Sunday, May 30, 2010

Baba Brinkman raps up Geek Week on the Rachel Maddow show!

Visit msnbc.com for breaking news, world news, and news about the economy

It is so cool to see Baba Brinkman hit the mainstream media now, after wowing so many of us in smaller shows around the world. We were lucky to get him on our campus early in the Darwin Bicentennial year, when he was performing at the Fresno Rogue Festival. Great to see Rachel Maddow putting him on to rap up her first Geek Week!

What next? The Colbert Report, dare one hope? I'd love to see that rap duel, wouldn't you?

Posted via web from a leaf warbler's gleanings

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Monday, March 22, 2010

Why are there so many bird species in the Himalayas?

This week, the CSU-Fresno Consortium for Evolutionary Studies brings you another public lecture in our Evolutionary Biology Lecture Series. On the evening of Thursday, March 25, 2010, join us at the Satellite Student Union on campus to hear Prof. Trevor Price of the University of Chicago tell us about his work on the origin, distribution, and maintenance of high bird species diversity in the Himalaya. The public talk starts at 7:30 PM, and you can download the flyer for the talk below. On the following afternoon, Dr. Price will give us another talk in the Biology department colloquium series.

I will try to share podcasts of both the talks - probably over spring break which starts next week. I still have the last few talks recorded that I mean to podcast as well. In my vast spare time...

Posted via email from a leaf warbler's gleanings

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Thursday, March 18, 2010

David Gallo on life in the deep oceans - a TED talk

A lecture accompanied by some astonishing deep sea videos that I showed in intro bio class this week when we were discussing the potential origins of life at hydrothermal vents on the ocean bottom.

Posted via web from a leaf warbler's gleanings

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Wednesday, March 10, 2010

The Jellyfish are coming! En Masse! To... Fresno? Come check it out this friday!

Why yes, we have a Jellyfish mass occurrence... well... occurring on the campus of Fresno State this friday afternoon! Well, ok - I'm not talking about some biblical flood in the valley (its been a wet winter, sure, but not that wet!) or that long anticipated Big One, the earthquake that cleaves coastal California off and converts all our homes here in the valley into beachfront property! No not that - that's not happening this friday (as far as I know). But the jellies will be here in spirit and data form rather than physically present, as we get a seminar from Dr. Michael Dawson of UC Merced just up the road from us. Should be a fun, fascinating talk - here's the relevant info, and you can click on the title below to read the abstract and get further details:

Phylogeny and Ecology of Jellyfish (Scyphozoa) Mass Occurrences
Friday, March 12, 2010
3:00-4:00 PM
Science II, Room 109
CSU-Fresno

And afterwards, you might ask Dr. Dawson what a marine biologist like him is doing in the Central Valley of California... do they know something we don't?

Posted via web from a leaf warbler's gleanings

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Saturday, March 6, 2010

Ooze like an amoeba, float like a bird - wish we could still do that when stressed!

Here's another fun weird science story from NPR, about a creature that might be in the dirt in your own backyard:
20100305 Me 03 by Npr
Download now or listen on posterous
Naegleria-NPR.mp3 (1426 KB)
Naegleria gruberi
Courtesy of Lillian Fritz-Laylan
Naegleria gruberi grows a pair of flagella when under stress. But unlike a sperm tail, it puts these appendages out front, and swims by breast stroke. The organism is stained to emphasize its anatomy.
If you prefer to read the story rather than listen to it aloud, here's the transcript via npr.org.

ResearchBlogging.org
While that behavioral and morphological flexibility is remarkable enough in something we might, from our lofty hominid perch, consider rather "primitive" and "simple", what graduate student Lillian Fritz-Laylan and colleagues found in its genome is perhaps even more surprising. Whle the NPR story focuses on the physical transformation of the organism, cool as that is, the full story is much richer and has far more significance for our own origins from a common eukaryotic ancestor. As they describe in their paper in the current issue of Cell, Naegleria gruberi turns out to have almost 16000 protein-coding genes, which is over two-thirds of what you and I have! A single celled organism with that many genes - no wonder it can transform itself so radically.

Here's an image from the paper illustrating that transformation, which takes a mere 90 minutes or so (far cooler special effects at half the duration of Avatar, if you ask me!):



Figure 1: Schematic of Naegleria Amoeba and Flagellate Forms. Naegleria amoebae move along a surface with a large blunt pseudopod. Changing direction (arrows) follows the eruption of a new, usually anterior, pseudopod. Naegleria maintains fluid balance using a contractile vacuole. The nucleus contains a large nucleolus. The cytoplasm has many mitochondria and food vacuoles that are excluded from pseudopods. Flagellates also contain canonical basal bodies and flagella (insets). Basal bodies are connected to the nuclear envelope via a single striated rootlet. 

Is it just me, or does that upper image, of the amoeboid form, remind you of someone? And... I just realized... that someone also has two apparent flagellae at the top of his head, which unfurl during times of stress!! What better proof do you want of our shared ancestry with Naegleria, eh? No? Oh, what - you mean citing widely published and viewed cartoons is not good enough evidence for you (even though that is a standard of evidence good enough for a third of the good people of Texas)? You want all the boring science-y stuff instead? Well, go read the paper then, which the journal Cell has graciously made freely available!

The paper (luckily for you) turns out to be far from boring. It is indeed quite fascinating because, apart from presenting the complete genome sequence of this remarkable free-living protist, Fritz-Laylan et al also describe several genetic modules for aerobic and anaerobic metabolism (for these guys can do both), amoeboid motility, and a number of other structural and functional necessities of the ecologically diverse lifestyles common to their clade. Further, comparisons with genomes of other protists allow them to predict which genes might have been present in the genome of the common ancestor to all eukaryotes. As the first representative of a fifth (out of 6) major clade of eukaryotes whose genomes have been sequenced thus far, Naegleria holds great promise of generating fresh insights into the early evolution and diversificatiion of eukaryotes. While their lineage diverged from the one we hail from about, oh, a billion or so years ago, understanding their genome brings us closer to understanding and reconstructing the genome of our shared ancestors, those early free-living eukaryotes that gave rise to us both. For it turns out that they contain over 4000 protein families that are similar to ones we have, and therefore were likely found in that common ancestor! That ancestor was presumably also quite versatile and equipped with a set of flexible modules to deal with the diverse environments of that time. And that remarkable flexibility probably underlies the extraordinary diversity of organisms that subsequently evolved from that ancestor. How fascinating and wonderful is that! (Even if some of us later lost the ability to transform ourselves and float away when under stress!)

Let me end with a video where the lead authors talk about what Nargleria's genome can tell us about our own ancestry:



Reference:
Fritz-Laylin, L., Prochnik, S., Ginger, M., Dacks, J., Carpenter, M., Field, M., Kuo, A., Paredez, A., Chapman, J., & Pham, J. (2010). The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility Cell, 140 (5), 631-642 DOI: 10.1016/j.cell.2010.01.032

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Sunday, February 21, 2010

Yet another reason for Israel to become the 51st of the United States of America

For they too have, among the top echelons of their government, "scientists" in charge of public education who do not accept the evidence for evolution or global warming! Wow:
The Education Ministry's chief scientist sparked a furor among environmental activists and scholars Saturday with remarks questioning the reliability of evolution and global warming theory. The comments from Dr. Gavriel Avital, the latest in a series of written and oral statements casting doubts on the fundamental tenets of modern science, led several environmentalists to call for his dismissal.

"If textbooks state explicitly that human beings' origins are to be found with monkeys, I would want students to pursue and grapple with other opinions. There are many people who don't believe the evolutionary account is correct," Avital said yesterday.

"There are those for whom evolution is a religion and are unwilling to hear about anything else. Part of my responsibility, in light of my position with the Education Ministry, is to examine textbooks and curricula," he said. "If they keep writing in textbooks that the Earth is growing warmer because of carbon dioxide emissions, I'll insist that isn't the case."
Now isn't that further evidence of the strong cultural ties between the US and Israel? Doesn't it lend support to the long-argued case for making Israel the 51st state of the US? Further evidence of a shared anathema to science comes courtesy of the NCSE, suggesting that this anti-scientific rot is not limited to the political upper echelons of Israeli government, but may be rather widespread among the general populace as well:
Unfortunately, Avital's views on evolution may be shared by a sizable segment of the Israeli public. A 2006 survey of public opinion in Israel by the Samuel Neaman Institute found that "a minority of only 28% accepts the scientific theory of the evolution [sic], while the majority (59%) believes that man was created by god," while according to the 2000 International Social Survey Programme, a total of 54% of Israeli respondents described "Human beings developed from earlier species of animals" as definitely or probably true, placing Israel ahead of the United States (46%, in last place) for its public acceptance of evolution, but behind twenty-three of the twenty-seven countries included in the report.
And I'm (sadly) gratified to find a shared brotherhood with my biologist colleagues in Israel who find themselves rather unexpectedly having to bat down this kind of inanity.

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Teach the Controversy - sure... but which one?!

Keep pushing teachers to "teach the controversy" - but you may not like what you get when they do! And this teacher didn't even hit upon my ancestral religion!!

Posted via web from a leaf warbler's gleanings

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What rhymes with Galapagos?

Fun to see Baba Brinkman freestyling for Darwin down under... and a pretty good response to the tough question too, although he didn't really come up with a proper rhyming companion word for Galapagos. So what does rhyme with Galapagos?

Posted via web from a leaf warbler's gleanings

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Thursday, February 11, 2010

My blog's strange phylogenetic origin in the Carnival of Evolution #20!

Skeptic Wonder has one of the more creative analytical takes on hosting a blog carnival I've ever seen - an actually phylogeny of the blog posts included in the carnival, based on sequence alignment of each blog post's URL! I'm not sure about some of the results, however... check out where my post on the challenges of teaching evolution ended up in the above tree! How on earth did I end up paraphylizing (if that's a word) Bjørn Østman's blog?!

But, never mind that, this 20th edition of the Carnival of Evolution has plenty of good stuff to read, so head on over there in your spare moments. And pardon my tardiness in bringing this to your attention.

Posted via web from a leaf warbler's gleanings

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Monday, February 8, 2010

Biography of Charles Darwin | Janet Browne's Stanford Lecture

LECTURE DESCRIPTION
Dr. Janet Browne presents a biography on Charles Darwin and explores Darwin's Origin of Species. The lecture is concluded with a panel discussion with Craig Heller and Robert Proctor.

This is the third lecture in the Stanford course on Darwin's Legacy I've been sharing here recently (see parts 1 and 2), and is a good one to start off this week with, as we prepare to celebrate Darwin's 201st birthday next Friday. Janet Browne, of course, is the author of what may be the definitive biography of Darwin, published in two volumes: Voyaging and The Power of Place. Click on those links to pick up your copy if you haven't read them yet - this wonderful biography of a truly remarkable scientist belongs in every respectable library! And I particulary urge those of you who are troubled by evolution and may be suspicious of the old man to set aside your prejudices and read these books to appreciate the fullness of his life and work even if its implications trouble you!

Posted via web from a leaf warbler's gleanings

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Sunday, January 31, 2010

Performance Feedback Revision - a peer-reviewed hip-hop definition of Evolution!

Last year, we enjoyed Baba Brinkman's performance of The Rap Guide to Evolution on our campus when he was in Fresno for the Rogue Festival. His show has gone on to a larger world stage since, as you can see in the above video, from the Hammersmith Apollo in the UK. He was there as a part of Nerdstock: Nine Lessons and Carols for Godless People, which was recently broadcast on television by the BBC! You can watch the whole show on YouTube (if you're outside the UK and therefore not able to use BBC's iPlayer). I thought I should share Performance, Feedback, Revision here for my students since I am going over the basic conceptual framework of evolution in several classes these days - and Brinkman provides a fun restatement of some of the concepts, in rap (and peer-reviewd rap, no less!)! If you haven't done so yet, you really ought to go listen to the whole rap album, available via his website.

Posted via web from a leaf warbler's gleanings

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Friday, January 29, 2010

Seminar today: Step-by-step evolution of the vertebrate blood coagulation system

Friday, January 29, 2010

3:00-4:00 PM in Science II, Room 109


Professor,

Dept. of Chemistry & Biochemistry and Molecular Biology

University of California, San Diego

La Jolla, CA

The availability of whole genome sequences for a variety of vertebrates is making it possible to reconstruct the step-by-step evolution of complex phenomena like blood coagulation, an event that in mammals involves the interplay of more than two dozen genetically encoded factors. Gene inventories for different organisms are revealing when during vertebrate evolution certain factors first made their appearance or, on occasion, disappeared from some lineages. The whole genome sequence databases of two protochordates and seven non-mammalian vertebrates were examined in search of some 20 genes known to be associated with blood clotting in mammals. No genuine orthologs were found in the protochordate genomes (sea squirt and amphioxus). As for vertebrates, although the jawless fish have genes for generating the thrombin-catalyzed conversion of fibrinogen to fibrin, they lack several clotting factors, including two thought to be essential for the activation of thrombin in mammals. Fish in general lack genes for the “contact factor” proteases, the predecessor forms of which make their first appearance in tetrapods. The full complement of factors known to be operating in humans doesn’t occur until pouched marsupials (opossum), at least one key factor still being absent in egg-laying mammals like the platypus.

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Wednesday, January 27, 2010

Genie Scott on Evolution Versus Creationism

This is the second lecture of the course on Darwin's Legacy offered at Stanford in 2008. I posted the first lecture earlier today.

Posted via web from a leaf warbler's gleanings

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Darwin's Legacy: introduction to a course from Stanford University

On NCSE's Facebook page this morning I discovered a link to this wonderful series of lectures on Darwin's Legacy put together as a continuing education course by Stanford University in fall 2008. I will post the whole series here, since it has recently become available online. Or you can get a jump start and go to the source: watch the whole thing in YouTube videos like the one above on Academic Earth or download it to your favorite portable device by downloading it from iTunes U.

While we don't have Stanford's resources or reach, as you may know, we are nevertheless also hosting our own modest Evolutionary Biology Lecture Series under the umbrella of the Consortium for Evolutionary Studies at California State University, Fresno this year. And as some of you may remember, we had NCSE's Dr. Eugenie Scott speaking on campus last month; she's also featured as the second talk in the Stanford course. This friday we'll learn about the evolution of the vertebrate blood coagulation system from Dr. Russell Doolittle of UC San Diego. Join us if you can, or come back here for videos/podcasts - I will try to record and post as many as I can.

Posted via web from a leaf warbler's gleanings

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NOVA | Darwin's Darkest Hour

While the big cinema treatment of Darwin's great pause in publishing "On the Origin of Species" may never make it down to theatres in our neck of the woods, out here in California's Central Valley (not a big market for stories about Darwin, it seems!), the above version on PBS' Nova was actually quite compelling. Having read some mixed reviews of Creation (although most reviews have been positive), I wonder if this televisual treatment may actually be superior in capturing the remarkable intellectual ferment behind Darwin's work. Rather than the movie's dramatic emphasis (from what I've read) on the emotional drama of Darwin's life after the death of little Annie, this Nova biopic choses to focus more on the intellectual turmoil (without downplaying the emotional turmoil at all), and even has Charles and Emma going back and forth in a very compelling way as he develops his arguments. If you're fortunate to be living in a place where Creation was released in theatres (or have managed to score a copy to view somehow), I'd love to know what you think: how does this compare?

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Friday, January 22, 2010

Brain Matters | The Human Spark | PBS Video

The final, and perhaps the most fascinating, part of the series anchored by Alan Alda. Go to the show's website for a lot more information and supporting material.

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Thursday, January 14, 2010

Got a creationist in your face about evolution? There's an app for that!

If you ever argue with creationists, you know that the Index to Creationist Claims is an incredibly useful site, as is the book version, The Counter Creationism Handbook. Life just got a little sweeter: it is now available as a smartphone app for the blackberry and iPhone (just get into the App Store and search for 'creationist'). Well, sweeter for us; creationists will find themselves a little more readily refuted now.

Here's an iTunes link to the Creationist Claims Index app, which at 99 cents might just be the thing I should recommend to my students as I begin teaching Intro Bio (Bio 1B) next week. I just hope I don't have to keep turning to it myself too often. I also wonder if this might have helped last year when I had a creationist grad student in my very lab?! I do have and recommend the paperback version, but having it handy one a phone might have helped others in the lab who got into head-scratchingly odd conversations with that student.

Thanks PZ, and the creators of this app!

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So Human, So Chimp | The Human Spark | PBS Video

This is what had our girls riveted to the television last night - something about all the young 'uns (of various primate species) featured in this episode. What is it about young primates (human and non-human) that fascinates us so much?

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