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!
Sunday, September 28, 2008
Into your shorts? Like so:
And if you know how to make/modify patterns, you might want to make it more authentic: add "I think" at the top of the tree and label some of those branches! Here's a photo I was lucky enough to take of the original several years ago:
[Hat-tip: John Wilkins]
Friday, September 19, 2008
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:
Homology is basically a proposal of equivalence. If we say that the arm of a human, the arm of a chimpanzee, and the wing of a bird are homologous, then we are hypothesizing that these corresponding structures are somehow equivalent. The somehow of that equivalence is what a biologist wants to explore and to explain. In a facile manner, I could say that homology of the arm of a human, the arm of a chimpanzee, and the wing of a bird is explained because they are all modifications of a corresponding structure in their most recent common ancestor, which is to say that we have homology because of evolution.
A less facile explanation would require us to explain how common position within bodies and possible similarities in development, including perhaps similar genes being expressed to control development, of humans, chimpanzees, and birds lead to a hypothesis of homology. We might also be expected to explain how intermediate structures in the lineages ‘between’ humans and chimpanzees as well as between them and birds help to demonstrate the transformations that could have occurred since their divergence from a common ancestor. Formulating this set of explanations to propose an hypothesis of homology is sometimes called a ‘homology argument.’
After laying out that excellent explanation, Hufford went looking for examples:
As I wrote my lecture on Monday, I wanted to look for new examples of homology arguments—so I googled ‘homology argument.’ One of the top links that Google returned in the search was for an entry in the Conservapedia, which subtitles itself as “The Trustworthy Encyclopedia.” The link took me to the Conservapedia entry for homology, which it defined as “. . . the theory that macroevolutionary relationships can be demonstrated by the similarity in the anatomy and physiology of different animals.” While I don’t regard that definition as accurate, it’s neither egregious nor exactly untruthful.
It was the section below the Conservapedia’s definition of homology that caught my attention—it was labelled “Invalidity of the Homology Argument.” How could the homology argument be invalid, I wondered? After all, a homology argument is a method of comparing and reasoning rather than an assertion of truth.
The explanation offered by the Conservapedia for the invalidity of the homology argument is straightforward: “Creation scientists claim that similarity can just as readily be explained by a common Designer as common ancestry, and that homology is therefore not evidence that can be used to support the evolutionary view.”
So a "claim" from creationists is sufficient to dismiss out of hand a logically constructed and repeatedly well tested scientific argument? And they claim that scientists are the ones acting in an authoritarian manner when keeping creationism out of the classroom? Interesting. Anyway, the above "claim" then led to a useful class discussion on what separates scientists and creationists:
We discussed in class a critical difference between a scientist and a creationist. Creationists think they have THE answer from the beginning, whereas a scientist has only a question in the beginning. While a creationist may accept absurd dogma and simplistic dismissals of rational ideas, a scientist looks for a way to test ideas. That willingness to test and to infer from the results of those tests the best explanations distinguishes the scientific method from the creationist method. [A great untruth of the Conservapedia’s entry on homology was its claim that there are creation ‘scientists’—creationists offer religious explanations and dismiss the results of repeatable scientific studies rather than using a scientific method.]
Once this very basic difference between the two approaches is recognized, is there really any reason to keep discussing all the other creationist arguments in the classroom?
Wednesday, September 17, 2008
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!
Now here's a conversation worth listening to!
Monday, September 15, 2008
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.
Friday, September 12, 2008
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
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!"
Monday, September 8, 2008
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!).
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
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.
So then I have to ask the question, “Was earth created for life or did life mold the earth into what it is today?” Of course, people may say, “Yes, the earth was created for life.” Well, Harold C. Urey submits that the earliest atmosphere of earth was composed mostly of hydrogen, methane, and nitrogen with only trace amounts of other elements such as carbon and oxygen. Over time a bunch of chemical reactions occurred (if you want to know all of the reactions, read Urey’s paper) and the earth’s atmosphere changed from being predominantly hydrogen and methane based to being highly oxidized with a lot of free energy created from oxidation reactions. The available free energy made it possible for a few primitive organisms to thrive. From here on out, those small organisms began to colonize earth. Current literature suggests that heterotrophic cells evolved 3.5 billion years ago followed by autotrophic cells (somewhere around 2.7 billion years ago), eukaryotes (2 billion years ago) and then multicellular organisms (Kardong, 2005). Because of the newly formed organisms on the planet, compounds that the earth had not seen yet (like isotopes of sulfur) were made and the compounds that were available already could be molded into something that could be used by another organism (Urey, 1952; Kasting, 1993).
So what does all of that mean? It seems to me that when the earth was created, it was completely uninhabitable. Which may mean the earth was not created for life and it is because of life, that the earth is habitable now. When the earth first came to be, there were atmospheric elements that began to interact with one another. From this energy was released, organic molecules were formed and the genesis of life began. At this point in the story, organisms have done nothing to alter the earth. However, with the birth of the first autotrophic cells (and the use of photosynthesis), living organisms began to transform the earth into something that could sustain life. Since then life has molded the planet into what it is today. Of course, it is likely that life has not molded the entire planet (as in, I am not sure that living organisms have any impact on the core of the planet itself…but this is science, so you never know, something could be discovered ☺) and who knows about our impact on the entire solar system. Nevertheless, in terms of niches within our range of exploration on the surface of the earth, it seems that living organisms can have a drastic, sometimes detrimental, impact on their habitats. Image what the world would look like if there was no deforestation or animal poaching. Imagine if the mosquitoes that bite us incessantly were not provided with stagnant water supplies in the rims of old tires and so could not reproduce in new habitats and spread deadly diseases to the inhabitants of those places. What if plumes of dinoflagellates did not blanket the ocean and poison thousands of fish each year. What if asparagus seeds did not float on water? What if fungus did not decompose leaf litter on the forest floor? What would the world look like without millions of species changing the world into a place called home?
Okay, so the end of that paragraph was a little cheesy. But truly, without life shaping the planet what would the planet look like? From these thoughts, I believe, at least for now, that living organisms have morphed the earth into what we know today. Without life on this planet, the earth would look completely different.
Kardong, Kenneth V. 2007. An Introduction to Biological Evolution. 2nd ed. Boston: McGraw-Hill Companies, Inc., 49-54.
J. Kasting (1993). Earth's early atmosphere Science, 259 (5097), 920-926 DOI: 10.1126/science.11536547
Harold C. Urey (1952). On the Early Chemical History of the Earth and the Origin of Life Proceedings of the National Academy of Sciences, 38 (4), 351-363
Thursday, September 4, 2008
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).
Ecosystem disturbances, whether anthropogenic or natural phenomena such as drought, can create changes in aquatic macroinvertebrate communities by altering habitats and the physiochemical conditions they have adapted to live by. Thus, disturbances can have a large effect on the community structure of aquatic biota. However, many studies have shown that even after a single event disturbance that does not chronically alter habitat, such as a drought and the drying of aquatic habitats, aquatic macroinvertebrate taxa richness can make a rapid recovery (Boulton 2003, Wallace 1990). The fast recovery is most likely the result of the evolutionary history of drought in aquatic environments (Boulton 2003).
Boulton and others have done several studies addressing the effects of drought, drying, and intermittent streams on aquatic macroinvertebrates. In Parallels and contrasts in the effects of drought on stream macroinvertebrate assemblages, Boulton observed the effects of drought as an intermittent stream disturbance and the ecological changes that occurred. As riffle habitat dried and the stream turned into isolated pools, species assemblages changed favoring the species more adapted for lower oxygen levels, higher temperatures, and predation on other invertebrates. When flow commenced recovery of the species assemblages began to take place. Recovery rates were rapid for species that had strategies for surviving drying. Two main strategies were identified: 1. Species were adapted for finding refuge. 2. Species had a life history strategy for dry conditions (Boulton 2003). Strategies for finding refuge include being mobile, or being able to bury into damp substrates, while some life history strategies to survive dry conditions include having a terrestrial winged adult stage of the species existent during dry conditions, having desiccation resistant forms of eggs, or having tendencies for downstream drift once flow commences (Boulton 2003, Wallace 1990). Therefore, immobile invertebrates without life histories to survive drying should be heavily effected and take longer to recover from a stream drying disturbance. Several studies have been able to show this. For example, mollusks, which do not have a winged adult stage and are fairly immoblie compared to other invertebrates, have been shown to be among the last taxa to recover following disturbances (Wallace 1990).
Boulton (2003) acknowledges the linkages between the history of drought and the evolutionary adaptations of aquatic macroinvertebrates. However, there are still information gaps and questions that need to be answered. Boulton states that most of the data that exists about the effects of drought on aquatic biota is short term, and the lack of pre-impact data exists because studies are opportunistic and droughts are phenomenological events. Understanding the life histories, life cycles, behaviors, and the genetic structure of aquatic macroinvertebrates is also extremely important, however much of the information is still poorly known. Also, several questions still need to be clarified or answered such as: Does frequent drying select for life histories and certain community assemblages? Do the same responses occur across most geographical regions (Wallace 1990)? Once more information becomes available about the evolutionary adaptations of aquatic macroinvertebrates science may have a better understanding of evolutionary processes and what may happen to biota in the future if global climate changes occur.
Andrew J. Boulton (2003). Parallels and contrasts in the effects of drought on stream macroinvertebrate assemblages Freshwater Biology, 48 (7), 1173-1185 DOI: 10.1046/j.1365-2427.2003.01084.x
Merritt, R. W., K.W. Cummins, and, M.B. Berg (eds.). 2008. An introduction to the aquatic insects of
North America, 4th ed. Kendall/Hunt, Dubuque, Iowa.
Resh, V.H., and D.M. Rosenberg (eds.). 1984. The ecology of aquatic insects. Praeger
Publishers, New York, NY.
J. Bruce Wallace (1990). Recovery of lotic macroinvertebrate communities from disturbance Environmental Management, 14 (5), 605-620 DOI: 10.1007/BF02394712
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.
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
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.
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.