Sunday, September 28, 2008

A gene to save us from HIV?

Sandra Porter, over at Discovering Biology in a Digital World has a very interesting post up reviewing recent research on a gene that might protect us from HIV and other retroviruses. Well worth reading, given our recent classroom discussions of HIV, and the upcoming lectures where we will address resistance genes, fairly soon! Besides this post is also an excellent model for you to shoot for when writing your own critique/commentary/synthesis for this class!



How would you like to knit Darwin's Tree?

Into your shorts? Like so:


Read More...

Friday, September 19, 2008

Learning from the vapidity of creationists and Conservapedia

Here is an excellent example of how a creationist argument can still help us understand the scientific method! And it starts on a topic we've been discussing in class this week: Homology! Larry Hufford of Washington State University was preparing a lecture on homology, went googling for any new supporting material, stumbled upon the Conservapedia entry on homology, and ended up discussing their creationist claim in the classroom! And the result is something that should make creationists think twice about continuing to demand that biologists (real scientists) give equal time to creationism in the classroom. Its a risky proposition (for creationists) if a competent biologist takes creationism on in such a thoughtful discussion because it is so easy to show why creationism is not a science! Do you want us to keep doing that over and over again? I suppose there is some educational benefit to that - but I'd rather use our class time to explore the real wealth of insights from evolutionary biology, than keep flogging the intellectually dead horse of creationism (or Conservapedia). It is nice therefore to have Hufford's article which lays out the argument with regards to one creationist "claim" about the invalidity of homology. It is worth your while to read the whole story, which starts by outlining what the homology argument is and how a scientific explanation of it can be constructed:




Read More...

Wednesday, September 17, 2008

Darwin gets a belated apology from one church?

That would be the Church of England, which yesterday posted this apology to Charles Darwin on the new Darwin 2009 section of their website:



Charles Darwin: 200 years from your birth, the Church of England owes you an apology for misunderstanding you and, by getting our first reaction wrong, encouraging others to misunderstand you still. We try to practice the old virtues of 'faith seeking understanding' and hope that makes some amends. But the struggle for your reputation is not over yet, and the problem is not just your religious opponents but those who falsely claim you in support of their own interests. Good religion needs to work constructively with good science – and I dare to suggest that the opposite may be true as well.



Maybe you're wondering: who cares what the stuffy old Church of England says? Or, what's the point of apologizing to a man dead for over a century and a quarter? Does the Archbishop of Canterbury even have much resonance with the religious public in the US, which is the real battleground in the anti-Darwin wars these days? Whatever you think of this apology - at least good old Charlie got off lightly compared to some earlier men of science caught in other church crosshairs - like, say, Galileo (who suffered during the latter parts of his life, and got his apology only recently). I guess if you believe in eternal life, you might think it is never too late to atone, so there is perhaps some logical consistency.


But wait, the essay containing the above statement, by Revd. Dr. Malcolm Brown, is not actually an official apology from the CofE, according to a spokesman, but just his personal view! So much for that, then...


Nevertheless, its worth noting that the CofE Darwin 2009 website is apparently sincere in trying to set the record straight, as seen especially in the Darwin and faith section, which uses Darwin's own words to show how he gradually lost faith despite his earlier religious training. I especially like this quote:



“Formerly I was led by feelings such as those just referred to (although I do not think that the religious sentiment was ever strongly developed in me) to the firm conviction of the existence of God, and of the immortality of the soul. In my Journal I wrote that whilst standing in the midst of the grandeur of a Brazilian forest: ‘It is not possible to give an adequate idea of the higher feelings of wonder, admiration, and devotion, which fill and elevate the mind.’ I well remember my conviction that there is more in man than the mere breath of his body. But now the grandest scenes would not cause any such convictions and feelings to rise in my mind.”



The man sure knew how to turn a phrase, didn't he?


And its good to see the church avoid sugar-coating, or quote mining to suppress that last sentence, let alone claiming some ridiculous death-bed conversion! That's something, I'd say; and its nice to have a website from such a major church to point to the next time some devout christian comes around in distress over Darwin or some religion-vs.-science conflict!



E.O. Wilson & James Watson on Charles Darwin

Now here's a conversation worth listening to!
















[Hat-tip: Pharyngula]






Monday, September 15, 2008

The Eye!

Tina Sakha (from Biol 105) shares this video about the evolution of the eye. Here's her summary: The Eye is designed to create images by focusing light into the retina, and sending the signal to the brain. 540 million years ago, the eye had nothing more than photoreceptive patches. It becomes concave but there is very little directionality. In the beginning the eye wasn't concave enough, though it evolved into more concave shape as time passed. Pinhole camera eyes allow for greater directionality. The cornea develops over the eye, as well as a fluid called humour to protect the eye from damage. A lens develops to focus the light, and providing even greater directionality.

If you are in the habit of watching the History Channel (and who isn't?) you might have caught their recent hour-long treatment of the evolution of the eye, which opened their ongoing series "Evolve". Recent episodes of the series are available for viewing online on their website, and you can find older ones, including the one on the eye on iTunes.

Friday, September 12, 2008

Of unlikely black holes and the excitement of particle physics

I'm sure you've seen all the media hype lately over the switching on of the Large Hadron Collider in Geneva earlier this week. And you might also be tired of all the "end of the world" jokes over the teeny-tiny possibility that the particle physicists having all that fun with their $8-billion sub-atomic racetrack might accidently create a black hole that would swallow the earth. Well, the machine is on, no black holes yet, and the media will likely move on, shrugging its shoulders that the world is still here, almost as if they might have preferred reporting from the event horizon of a black hole; what a scoop that would be! But let's not let this teaching moment go to waste, shall we? Let's all learn some more actual physics while the topic is still hot. So, if you are still curious about the true significance of the collider and why all these physics nerds are so excited about it, you should read Brian Greene's op-ed piece in today's NYT: The Origins of the Universe - A Crash Course. And if that crash course whet's your appetite, read Sean Carroll's answer to "What will the LHC find?" where he even gives us the likelihoods of various outcomes, including the detection of the Higgs Boson (95%), Dark Matter (15%), Warped Extra Dimensions (10%), Black Holes - tiny, unstable, transient ones (1%), stable Black Holes that could swallow the earth, along with its worried crackpots (10-25%; yes, that means 0.0000000000000000000000001%), God (10-20%; indeed, more likely than the stable black hole, but not likely enough to make me go to the temple to place Pascal's wager), and a whole list of other possible known and unknown additions to the sub-atomic menagerie. Sean was also live-blogging the momentous switching on of the LHC, and you might want to bookmark Cosmic Variance if you want to keep up once the physicists actually start hurling those protons at each other in a few days (so far they've only been racing the protons all together in one direction, making sure everything is working!). If all that is a bit too much, the visual stylings of PHD comics ought to give you some relief.


Now, that should put you in the mood for the joint Biology-Physics Colloquium this afternoon at 3:00 where Fred Ringwald will talk about "Life Beyond Earth"! So if you are in Fresno, come on by, and maybe we can talk some more about all this afterwards... perhaps even over a drink!



Thursday, September 11, 2008

Time for a pilgrimage, I think...

When's the next bus to Dayton, TN? I could use an image that fills me with an overwhelming sense of logic...




DAYTON, TN—A steady stream of devoted evolutionists continued to gather in this small Tennessee town today to witness what many believe is an image of Charles Darwin—author of The Origin Of Species and founder of the modern evolutionary movement—made manifest on a concrete wall in downtown Dayton.



"I brought my baby to touch the wall, so that the power of Darwin can purify her genetic makeup of undesirable inherited traits," said Darlene Freiberg, one among a growing crowd assembled here to see the mysterious stain, which appeared last Monday on one side of the Rhea County Courthouse. The building was also the location of the famed "Scopes Monkey Trial" and is widely considered one of Darwinism's holiest sites. "Forgive me, O Charles, for ever doubting your Divine Evolution. After seeing this miracle of limestone pigmentation with my own eyes, my faith in empirical reasoning will never again be tested."



Added Freiberg, "Behold the power and glory of the scientific method!"



Read the rest of this amazing story!



Monday, September 8, 2008

Evolutionary ecology of city life at the Central Valley Café Scientifique tonight

Tonight, the Central Valley Café Scientifique presents a talk by yours truly! Here's the announcement:




Of junk food, city jive, & homelessness: the evolutionary ecology of city life



Dr. Madhusudan Katti, Dept. of Biology, California State University, Fresno


Monday, Sep 8, 2008, 6:30-8:30 PM


North India Grill


80 W Shaw Ave.,Clovis, CA 93612 ☎ (559) 325-7788 In the Village Square Shopping Center, S/W of Shaw at Minnewawa.



Go fishing in the bay for dinner, or fish KFC out of the dump - what’s an urban gull to eat? Scarf up the human handouts and you can start breeding early - but can a suburban scrub jay parent raise a family on that kind of food? What’s with the high-pitch songs of the Dutch urban tits? Why are there, often, more birds of fewer kinds in cities than outside them? And why might rich neighborhoods have more bird species than poorer neighborhoods?



As it turns out, recent research on these questions suggests that birds flock to cities (as do monkeys, raccoons and other of our urban commensals) for reasons not all that different from our own. I will draw upon research from my laboratory and elsewhere to explore the evolutionary ecology of how some species may become habitual urban dwellers, and what we might do to allow others to coexist with us amid sprawling cities.



And remember that the Central Valley Café Scientifique meets on the first Monday of every month (except this one because we had labor day last week!).



For more information, visit the website, and/or sign up to the Google Group.





Yet another controversy to teach in our classrooms

And this one is a good analogy to the creationist arguments



The theory of childhood, also known as child origin, is a damnable, loathsome and indefensible lie. How can any thinking person suppose all humans used to be babies once? There is no development path from babies to adults, no transitional forms between these two species. Show me even one baby with the head of a grown man on his body. Can you? No? Not even a bearded toddler? No adults with unfused skullbones, outside unfortunate disorders? Not even a tiny little newborn girl suddenly sprouting a respectable bosom? You can't find them, because they don't exist. There isn't a single transitional form between children and adults, and you will never find one because the theory simply is an unscientific lie.


The development of children has been well-researched in our six-month study following a sample of one thousand children and adults of various ages. We have conclusively proven that while there are minor changes in features like height and body fat, and replacement of deciduous teeth with permanent teeth, incontravertibly still every creature in the study that started out as a child had only slightly more adult features at the end of the observation period than at its beginning. Children and adults are separate kinds and there will never be sufficient changes to change one into the other. We reject any evidence from longer-term studies as we believe the laws of physics have changed within the last year.


To claim people come from children is demeaning and morally degrading. We have observed how children behave. If we acted like small children we'd all be demanding and impatient, and we'd be cheating, lying, and stealing from each other all the time. If the theory of childhood were true there would be no morality, and with no morality to build one on, no society. Childhood is a wicked lie used by charlatans to justify evils such as public schools.


There is no consensus on the theory of childhood in the scientific community. We should teach the controversy. Our children will be served well to learn that the prospect of them becoming adults is merely a theoretical idea. Many children come from families that do not subscribe to the theory of childhood, and they could be disturbed if the theory were taught as fact.


[From metaquotes: ari_rahikkala makes a compelling arguement...]

Sunday, September 7, 2008

Life, The Universe, and Everything Else...

ResearchBlogging.orgJennie Talbot shares her musings following the class discussion last week in Biogeography (Biol 275).

In class we discussed the idea that niches are places that supply a particular organism with all of the resources required for it to thrive. The discussion led to questions regarding how much the niche impacted the species and, in turn, how much the species impacted the niche. For example, a plant species may thrive on the side of a mountain because it is here that the plant can find soil with good nutrients, adequate sun light, and reasonable temperatures. However, as more and more plants colonize the side of the mountain, transpiration will occur at a higher rate, which will produce more moisture in the air and, ultimately cause more rain to fall. The plant’s root system will hold the nutrient-rich soil despite all of the rain. Animals may come and feed on the well-nourished plants and, in turn defecate onto the soil, adding more nutrients for the plants to use. As more and more plants grow in this favorable environment, it is likely that the side of the mountain will get more rain then it did before the plants migrated to this location. Likewise, the side of the mountain may have better soil because of the wildlife that eat the plants. In fact, the wildlife may migrate to this newly colonized region on the mountainside because of the resources available. Therefore, the cycle will continue with more rain, better soil nutrients, healthier plants, and new wildlife. In this way, the side of the mountain, which may at one point have been completely void of life, has become a bustling habitat for multiple species.



Read More...

Thursday, September 4, 2008

Aquatic macroinvertebrate responses to drought

ResearchBlogging.orgA critique submitted by Brett Moore for the Evolution class.


Aquatic macroinvertebrates have received and are continuing to receive considerable amounts of scientific attention. The large amount of diversity within macroinvertebrates allows them to be present in almost all natural freshwater environments (Resh and Rosenberg 1984). The evolutionary adaptations that created the diversity within the group also created the great variety of life histories and physiological requirements, which promote the use of macroinvertebrates in scientific studies and biomonitoring, the use of living organisms and their responses to measure the quality of the environment, (Merritt et al 2008).


Read More...

Post Labor Day Carnivals!

If you are looking for some good evolutionary reading material as you continue readjusting to the start of the new school year, head on over to En Tequila es Verdad for the Labor Day edition of the The Tangled Bank. Some interesting links there, including one to my own post on magnetic cows. And you can find the earlier summer editions of this carnival by clicking on the badge to the right.



Sycamore Canyon has the artsy-fartsy 82nd edtion of I and the Bird, following up on Seabrooke's art gallery approach to showcase the 81st edition.



Let me also, belatedly, note that while I was away on the road trip to Oregon, the 18th edition of Oekologie was hosted by Seeds Aside. Oekologie is yet to find the next ring-master, however, so I'm a bit concerned about its future. If it hadn't been the start of a new semester, I might have hosted it again - but I hope someone else steps up, and soon, for I'm sure you'll find this carnival worthwhile too.



And don't miss the 2nd edition of the Giant's Shoulder, the new monthly event focusing entirely on classic papers in science, hosted by the Lay Scientist.



Now even this little sampling of the many blog carnivals featuring biology should keep you happily occupied and out of trouble for some time! And the next editions of these excellent carnivals will be here pretty soon as well (and I'll try to keep you posted on those intermittently as always), although by that time you might well be distracted by Spore!! If so, happy evolving - and don't forget to let me know how well the game's mechanisms of evolution correspond to what has been documented in the real world.

Wednesday, September 3, 2008

A sample of student writings from past semesters

I already have one submission of a paper critique from the Evolution class (Go Brett!!), but am still waiting for an electronic version of the same (c'mon Brett?!) so I can share it here.



In the meantime, please browse the archives here to see what past students were reading and writing about - it might even inspire you towards your own writing! While this link takes you to the complete subset of student posts, you can also, in the future, pull them all out simply by clicking on the "student post" tag (every post is tagged with some keywords on the bottom, in case you haven't noticed) in the Tag Cloud in the right hand pane here. And the rest of the tags give you some idea of the range of ideas being discussed on this blog.



Have fun!

Blog update in progress

As you may have noticed, I'm changing some things around on this blog, hopefully to make it visually cleaner, and more user-friendly. And that's partly why there hasn't been much new content here for the past week. I will start posting soon - especially if students start submitting their writings! In the meantime, feel free to poke around in this new template, and let me know if something looks strange or broken.

ShareThis

Darwin's tweets

Error loading feed.

Recent ScienceBlogs Posts on Peer-reviewed Papers

Error loading feed.

Current Readers

counter

  © Blogger template Brooklyn by Ourblogtemplates.com 2008

Back to TOP