Sunday, April 29, 2007
The trip was led by Julie Retrum, geology graduate student and Jonathan Hendricks, a post doctoral researcher from Cornell. The trip's goal was to visit a couple of important sites to collect material for the paleontology collections. We began our trip at 7:15 am in the parking lot behind Lindley Hall at the University of Kansas with Julie and Jonathan providing a briefing about where we were going, and the ground rules for collecting specimens.
We then headed north on 75, not stopping at the world's largest cinnamon roll in Holton and seeing none of the world famous black squirrels in Marysville KS, but going on into Nebraska to our first stop, an old cropping of sandstone-no fossils but as one hunter remarked it was like walking on a beach. There were also interesting nodules littering the site along with crystals of gypsum, but alas no fossils.
The 'beach at the first site(above)
Our next stop was quarry full of tropical soils. Finding tropical soils in Nebraska may seem odd but this spot during the Cretaceous was a tropical rain forest and we stopped specifically to see these weathered soils. Today these soils are quarried for clay used to make bricks. This didn't seem too exciting until we began to notice what looked like pieces of charcoal in the clay.
In a sense that is what they were-the carbonized remains of trees from almost 100 million years ago and yet so fresh the grain of the wood was still visible. Some of the pieces had pyrite (fool's gold) in association with them and were quite large and we joked about use them as Yule logs. The quarry manager said the clay is nice and fires very nicely, except that the pyrite explodes taking little chips of the brick with it and then forming little rust spots on exposure to air.
A piece of carbonized 'Yule log' (above)
Remains of a swamp(below) with some of our
crew digging for plant fossils (below)
From there we went to another site, quite famous for its fossils of early flowering plants and the pictures we saw were quite recognizable to my eye as being related to magnolias. This area during the Cretaceous was apparently a brackish swamp. Along with flower parts the leaf fossils from this site are very complete showing the leaf veins and in some cases the cells through which plants take in carbon dioxide for photosynthesis.
Alas, we mainly found small bits of plant material, no flowers. Also the clay containing the plant material was very damp and fragile, often disintegrating when handled. Let the clay dry and the plant material would blow away in the wind unless sprayed right away with a fixative. Quite a dilemma! Several people did find some nice pieces of fossilized wood in a dry creek bed at the bottom of the site.
Bits of compressed plant material from the brackish swamp site(above)
Wood from this site(below)
In addition to the KU contingent, two local volunteers Lois (Bottom right in the green hat) and John directed us to our last 'dig' , a road cut back in Kansas about 9 miles west of Washington Kansas-that during the Cretaceous was open ocean- guaranteed to have fossil clams.
They were right and we didn't even have to dig. The clams turned out to be all one species of a group of clams called Inoceramids, which are extinct today and we all collected our fill. Some Inoceramids got to be 8 foot long and sometimes fossil fish are found inside the clam, apparently having used the clam for a refuge.
A beach, a jungle, a swamp and a clam bed all within an hour's drive and almost 100 million years away-what a treat-and I found myself imaging Leonardo da Vinci shaking his head at the people driving by these sites daily and yet snug in their view that Genesis explains geology and ignorant of the science he helped found.
The History of the Earth and the History of Life.
Charles Sternberg: fossil hunter.
Friday, April 27, 2007
Sunday, April 22, 2007
"We know you despise all religion.Catholics, Jews, whatever.Its what atheists do. But pretending that you are just promoting science when you are using science as a front to promote your own anti religious agenda is a huge deception.
Mr. Goldstein is associated with a wonderfully imaginative Creationist site at http://www.thebrites.org/ which features the "The Biological Research Institute for Theoretical Evolution Studies"; "The Paley Watch Company "which claims to use natural selection to assemble watches; and my favorite-"Mutation Paste" which accelerates evolution. There is also Darwin Camp where today's Darwin Youth can "live and learn natural selection. "
Great fun and a great teaching moment about the misunderstandings many people have about evolution. Even the name, by the way, is a clever take on an organisation called "The Brights" which is indeed Atheistic in slant. Visit them at http://www.the-brights.net/.
Saturday, April 21, 2007
According to the article, evolution skeptics, such as Father Joseph Fessio, in the Catholic Church argue that there are 3 ways to learn about reality-empirical science, direct revelation from God and natural philosophy which attempts to use reason to discern the hand of God in the universe. I was particularly interested in the split between Roman Catholic thinkers and Orthodox Christian thinkers on natural philosophy, the Orthodox insisting that mystical communion with God is not comparable to the results of reason.
Here I find myself much more attuned to the Orthodox position. For me natural philosophy leads to the temptation to reduce God to a scientific formula which seems to me the very antithesis of what faith is ultimately supposed to be about. That sort of reduction also leads to the temptation to try to let theology do the job of science(i.e. turning the Bible into a science book) and we historically know the outcome of that tact-religion only looses credibility.
By the way there is an interesting defense of the compatibility between Orthodox Christianity and evolution by Fr. Andrey Kuraev. The article defends his belief in the consistency of evolution with Orthodox Christianity. He argues for instance:
"The very essence of the process of the unfolding of Creation remains the same regardless of the speed with which it happens. The view of some, that if we extend the process of Creation in time, "God will become unnecessary" is as naive as that of others who think that creation in anything more than six regular days diminishes the glory of the Creator. We must only remember that nothing stood in the way or limited the creative action, and everything happened according to the will of the Creator. We do not know whether this will consisted in creating the world in one moment, or in six days, or six thousand years, or billions. For "who can number . . . the days of eternity?" (Sirach 1:2)."
Friday, April 20, 2007
MacCallum CJ (2007) Does Medicine without Evolution Make Sense? PLoS Biol 5(4): e112 doi:10.1371/journal.pbio.0050112
If the answer is no, then why is evolution not typically part of the medical school curriculum? MacCallum argues that this is because evolution is often seen as not essential from the point of view of a practicing physician because at the patient level medicine is about problem solving. But MacCallum then makes a case, just as I might do that evolution is important in medicine, noting that:
"As the oft-quoted Theodosius Dobzhansky wrote in 1973, “Nothing in biology makes sense except in the light of evolution” . The time has clearly come for medicine to explicitly integrate evolutionary biology into its theoretical and practical underpinnings The medical students of Charles Darwin's day did not have the advantage of such a powerful framework to inform their thinking; we shouldn't deprive today's budding medical talent of the potential insights to be gained at the intersection of these two great disciplines."
The accompanying cartoon by Nick D. Kim is from the article with permission.
By the way the Howard Hughs Medical Institute does a great job promoting science including evolution and I highly recommend their DVD, Evolution: constant change and common threads, part of the 2005 Holiday lecture series. The DVD is well produced and has a series of highly accessible lectures suitable for high school or college. Order yours through http://www.hhmi.org/biointeractive/. The 2006 series on stem cell research looks equally juicy. The DVD's are free to educators and cover a wide range of topics. Right now I have one each on Genomics, RNA and Ethics in Biomedical Research, waiting for my review.
Tuesday, April 17, 2007
If there is anyone who doubts the evolutionary relationship between humans and the great apes (chimps and gorillas), you might check out these banding pattern comparisons between human and chimpanzee chromosomes originally from:
Yunis, J.J. and Dunham, K. 1980. "The Striking Resemblance of High-Resolution G-Banded Chromosomes of Man and Chimpanzee". Science, 208, 1145-1148.
The Imprimat site has chromosome changes for primates inferred by FISH chromosome painting. In this technique, fluorescent DNA probes from different regions of human chromosomes are applied to chromosomes of other species. The probe will bind to regions of the other species chromosomes that have the same or very similar nucleotide sequences. See http://www.mun.ca/biology/scarr/FISH_chromosome_painting.htm for more information about this technique. Regions of different chromosomes that have the same basic nucleotide sequence and along with that corresponding genes are inferred to be homologous or what cytogeneticists call synteny. Synteny is a kind of homology referring to chromosome regions that have two or more corresponding loci. If you don't get the idea visit this interactive chromosome comparison between human chromosome 22 and the synteny with different mouse chromosomes.
The Imprimat site has this diagram showing the presumed syntenies between the great Apes (Chimps and gorillas) and human chromosomes; the numbering is for human chromosomes. Note for instance that human chromosome 2 is derived from the fusion of two chromosomes present in the great apes (Center box at bottom of figure).
Note that the primitive chromosome number is believed to be 48. Also note that chromosome 14 and 15 are believed to have been originally one chromosome that broke apart. Also in gorillas (GGO) a translocation or exchange of regions between chromosome 5 and 17 appears to have happened.
Another interesting diagram on this site is a cladogram showing inferred evolutionary relationships between the major groups of primates. Notice again the big difference between chimps and humans is the fusion event between what were two separate chromosomes to yield human chromosome 2.
Rhesus monkeys are in the family Cercopthidae on a separate branch from the human like primates which include the great apes, humans and gibbons (Hylobatidae). What's interesting is the great amount of chromosome rearrangement that apparently happened in the evolution of gibbons compared to Rhesus Monkeys.
A closer look at the chromosomes of a gibbon from Koehler et al (1995) is to the left. In their abstract, Koehler et al note that here is a primate that is closely related to humans with a "highly disturbed" pattern of chromosome rearrangements.
Primate Info Net: Primate Evolution.
History of Primates.
A smooth fossil transition in a primate. (Just in case you don't think that transitional fossils exist)
Special online article on the Rhesus Monkey Genome.
Comparison of Human and Great Ape Chromosome 2. The molecular data is exactly what is predicted if human chromosome 2 really is the product of two fused chromosomes!
Lesson plans related to human/chimp chromosome comparisons.
Sunday, April 15, 2007
The big news was that Mr. Stanton is not planning on suing Largo Fla, something he equated with suing his Mom. Also he plans on living as "Susan" at the end of May. The sad thing about all this is that he apparently was taking the sort of steps recommended for transitioning on the job. He was not going to spring this on an unsuspecting city. Unfortunately the area paper got a hold of this and forced his hand. Since transsexualism and gender identity disorder are considered medical conditions, I hope the paper's editors carefully considered the ethics of disclosing this issue.
A good summary of the interview is here. It will be interesting to see how well Mr. Stanton's transition to Susan goes. I know a number of people that have transitioned, and under the best of conditions it can be stressful given the average person's fears and misunderstandings. I hope the press gives him some space. The one thing he has in his favor, if local polls are accurate, is lots of local support.
"Through photosynthesis, green plants and cyanobacteria are able to transfer sunlight energy to molecular reaction centers for conversion into chemical energy with nearly 100-percent efficiency. Speed is the key - the transfer of the solar energy takes place almost instantaneously so little energy is wasted as heat. How photosynthesis achieves this near instantaneous energy transfer is a long-standing mystery that may have finally been solved.
Image from http://www.vdacs.virginia.gov
Note the emphasis on near 100% efficiency. Presumably they are referring to efficiency of conversion of light actually absorbed by the photosystems to chemical energy in the form of ATP and NADPH, not the conversions that take place in the Calvin cycle. According to the news reports, this efficiency results from the ability of individual photons to travel along different paths simultaneously effectively selecting the most efficient path.
**Note: the "pit bull effect" stems from my observation that reports of pit bull bites seem to come in clusters-perhaps because media attention gets focused on the breed because of one spectacular incident such as happened in Lawrence in the 1980's. Suddenly even a pit bull sneezing becomes big news for a time.
Friday, April 13, 2007
"This person is going to die - why not harvest his organs?" he asked. The answer is that "it violates his human dignity," said Brownback, a presidential candidate. "We've got a fundamental debate in this country today, and that's when does human life begin," he said. "They are treating the youngest of human lives as a property and not a person."
So the embryo is the moral equivalent of an adult human? Sorry this sort of anthropomorphism is silly. Were a human embryo really the moral equivalent of a human adult, then we would be spending billions for research to prevent miscarriages. I was going to say, "and in vitro fertilization would be illegal", but I suspect that would be fine in Brownback's mind. I have to ask what about the dignity of a person with Parkinson's? Is the Senator going to deny them a cure simply because he chooses to think that a ball of cells is the moral equivalent of an adult human? Should voters in Kansas continue to support this sort of moral posturing and affront to common sense?
Thursday, April 12, 2007
That said, the Pope seems to have bought into a common misunderstanding about evolution. He is reported to have said:
"Though he did not reject evolution, he noted in the remarks quoted from the book that science could not completely prove evolution because it could not be duplicated in the laboratory."
Granted every instance of evolution cannot be duplicated in the laboratory, but the basic mechanisms of how evolution operates are routinely investigated in laboratory or other controlled situations including field experiments.
Benedict is also quoted in an article in The Catholic News:
"The process itself is rational despite the mistakes and confusion as it goes through a narrow corridor choosing a few positive mutations and using low probability,"
"This ... inevitably leads to a question that goes beyond science ... where did this rationality come from?"
Here again the Pope is buying into some of the probability arguments made about the implausibility of evolution, arguments not supported by science. As noted by many scientists such as Richard Dawkins, Ken Miller, and most recently by Sean Carroll, the probabilities involved only are daunting if you think all the parts, say in an adaptation such as the eye, or all the amino acids in a complex protein, have to come together randomly all at once.
The Pope's thinking here is getting at teleological questions and causality and he clearly understands that these are outside the domain of science, something the intelligent design advocates with their scary sounding references to materialism fail to grasp.
Wednesday, April 11, 2007
The usual response is that maybe plants can't do any better. The problem is plants that have other pigments, such as carotenes and xanthophylls that absorb light in the middle of the visible spectrum at those wave lengths that chlorophyll cannot. Another hypothesis my students often raise is that if plants absorb all the light available to them, they might overheat, much like wearing a black shirt on a hot day. Seems reasonable until you consider that plants in the shade where they ought not overheat are still typically green.
Getting to the news items, the first one from Live Science suggests that photosynthesis arose in a group of bacteria that used a simpler pigment called retinal found today in a group of bacteria (Actually Archeans) called Halobacteria . Shil DasSarma, from the University of Maryland notes that retinal absorbs best in the middle of the spectrum where chlorophyll cannot. Indeed the absorption spectra of the two pigments are eerily complementary as the accompanying figure from American Scientist shows.
DasSarma hypothesizes that retinal was used by the first photosynthetic organisms and that chlorophyll based photosynthetic organisms were able to survive because they could use wavelengths that retinal based photosynthetic organisms cannot. Since chlorophyll is more efficient than retinal, bacteria that used chlorophyll eventually out competed the earlier reddish purple hued retinal using bacteria. If so the early Earth may have been the Purple Planet and looked more like the Halobacteria rich landscape in the image to the left from NASA.
The second article from Scientific American looks at the sorts of colors photosynthetic organisms might be on other planets. Nancy Kiang from the Goddard Space Center analysed the spectra from other stars to attempt to predict what color photosynthetic organisms might be. This seems like an elaboration of a question I ask my students where I present them with a hypothetical planet Munimula (for those who remember Ruff and Ready Cartoons) orbiting a sun that produces light of the wavelengths we perceive as green. I ask the student to predict the color of plants that might evolve on such a planet. They are supposed to get the idea that the plants must be able to absorb the available light so were you to view plants from Munimula under white light, they would definitely not be green because they must have evolved to absorb the wave lengths we perceive as green.
So why are plants green? Maybe the good enough hypothesis combined with DasSarma's hypothesis is on the right track. But plants are still able to fine tune pigments. Indeed algae and other photosynthetic organisms in the ocean where short wavelengths of light penetrate further than long wavelengths, perceived as red, absorb short wavelengths and appear black or red under white light. So it seems terrestrial photosynthetic organisms ought to better fine tune their pigment systems.
I leave you with another idea that I have been thinking about. Maybe for all intents and purposes plants ARE black in the sense of absorbing as much light as possible and that it is our visual systems that have been fine tuned by evolution to be sensitive to what little light that is reflected from the leaves. What ever idea or combination of ideas is involved, sometimes the best and most interesting questions in science are what at first glance are the simplest to state.
One more little tidbit. Retinal is found not just in the Halobacteria, but is found as part of the light detection systems of the eye. So is this convergence in the use of retinal independently hit upon by the early photosynthetic organisms and animals or do we see in the visual pigments of the eye the remnants of the first invention of photosynthesis by early cells maintained in the context of light detection and image formation rather than photosynthesis.
Tuesday, April 10, 2007
I kid you not, OK maybe a little. Check out the Sheep Albedo Feedback hypothesis over at Real Climate. I'm going to throw away my compact fluorescent light bulbs right way. No wait can't do that! What about the the Mercury? The proof is in the accompanying graph! Makes about as much sense as blaming evolution for Columbine and no one would do that? Right?
Actually albedo or light reflected away from the Earth is an important factor in global heat budgets and one of the concerns about the melting of the arctic ice pack is the potential decrease in albedo. Light energy being absorbed by the Earth's surface can indeed increase temperatures. Bad news potentially for those folks who think planting trees is the solution to global warming. See this link from Scientific American for more details.
So sorry you SUV owners can't offset your carbon footprint by planting trees. Besides I suspect lots of these tree planting schemes may merely be about planting quick growing trees that may simply spread impoverished managed tree farms, useless for preserving biodiversity. A related article in Green Business News notes that corporate tree planting schemes have come under increasing attack and don't deliver on their promises as a way to offset our carbon footprint.
How Coldplay's green hopes died in the arid soil of India
Monday, April 09, 2007
Easter is over and it's time for another edition of the Kansas Guild of Bloggers.
Give EMAWKC a hug. He's upset about Bob Huggins, K State's basketball coach, leaving to go to a job at West Virginia. I don't follow sports a whole lot (Baskeball season ended for me when KU lost), but I think emawkc is right to be upset so allow him what he calls his self indulgent crap.
See Joel Mathis' take on Huggins departure at:
I notice that Lady Gunn, my favorite Republican blogger, has been reading Robert Jordon's Wheel of Times series and she is so preoccupied with it that she apparently failed to notice a problem with a painting in her masthead, the sort of thing that gets the FCC to fine networks big bucks. Tisk Tisk! Not familiar with the series she's reading but will look it up-as if I need any distractions as the semester comes to its climax.
Gwynne over at The Shallow End had a veterinary emergency with her dog Smokey and I am glad it turned out better than my dog emergency last fall.
Late April Fool's Joke? Pat Hayes over at Red State Rabble has a somewhat odd report about a special topics class being offered at McCook Community College in Southwest Nebraska on "Creation Science".
Speaking of colleges and learning, Josh at Thoughts from Kansas, co host of KGB. tells us why he blogs and I think he has captured an important part of why we more academic types blog in his article My invisible college.
Which brings us to a bit of analysis by John over at Blog Meridian who examines why he is not fan of Thomas Kincaid.
Continuing the academic thread, I leave the carnival with a brief post highlighting a new discovery about the genetics behind size differences among different breeds of dogs.
Next week the KGB travels over to Blog Meridian...so either contact John with your posts or submit your Kansas related blogging via the KGB submission page.
Friday, April 06, 2007
Now researchers have identified a gene responsible for the great variation in dog height; see here and here. The researchers led by Elaine Ostrander (link to her lab home page)first studied the DNA of Portuguese water dogs. They chose this breed because the breed standard allows for greater ranges of heights than do the standards of other breeds. The small Portuguese water dogs had one variant of a gene called IGF1 related to the production of a protein called insulin like growth factor while larger Portuguese water dogs had other variants of this gene.
What was really interesting is that when they examined other breeds, small breeds apparently have the same variant of this gene while larger dogs have other variants. Also wolves, the ancestor of the domestic dog do not have much size variation and do not have the small dog variant of this gene.
You must be thinking so what? First of all it illustrates again how even single gene changes can lead to big changes in phenotype, so this research is important in understanding evolution. Next, humans also have the IGF1 gene and protein and it crops up in some interesting places. For instance variants of this gene are associated with prostate cancer and related to glucose metabolism in the developing brain.
Fact sheet on insulin like growth factor in medicine
Dog Genome home page
Portuguese Water Dog Club of America
New York Times Article about IGF1 and Dogs
NPR story link(includes Audio report)
Article on the role of IGF1 in growth
Article on the link between IGF1 and Prostate cancer
An article about population genetics of dogs.
Tuesday, April 03, 2007
Is such a bill really necessary? Probably not. After all, Emily Brooker did obtain an out of court settlement from the University, that is valued at $27,000 without this bill. Public universities and colleges already have protections for students who disagree with a professor.
The reporting requirements of the bill has some very interesting language. For instance colleges would be required to:
Encourage a balanced variety of campus-wide panels and speakers and annually publish the names of panelists and speakers;
Sounds good on the surface, but I suppose a university could get into trouble for bringing a pro-evolution speaker to campus without balancing that out with an intelligent design speaker.
Develop hiring, tenure, and promotion policies that protect individuals against viewpoint discrimination and track any reported grievances in that regard;
Are we talking intellectual quotas here? So every time my department hires a biologist we need to hire a creationist to represent diversity of viewpoints on evolution?
Develop methods for disseminating best practices to ensure that conflicts between personal beliefs and classroom assignments that may contradict such beliefs can be resolved in a manner that achieves educational objectives without requiring a student to act against his or her conscience;
Sounds good, but I suppose one of my students should be allowed to opt out of the evolution sections of my biology course because he or she doesn't believe in evolution. Or maybe I need to give equal time to non scientific ideas just because a significant proportion of the population in this country believes them...I don't think so.
Missouri isn't alone here. Similar bills have been proposed in other states including Kansas. These bills are inspired by David Horowitz, a well known conservative activist who has proposed an Academic Bill of Rights. The Students for Academic Freedom site which advocates this bill says in its masthead that "You can't get a good education if you are only told half the story." Now this sounds nice but what is the other half of the story? This sounds suspiciously like saying that all viewpoints are equal in academic discourse. They are not, as undemocratic as that might sound. For instance, many viewpoints and trains of thought, including some that are popular such as Young Earth Creationism just are not supported by critical analysis.
Yes, it is a good thing for students to question and develop their own view points-we cannot compel belief last time I checked, and any professor that would discriminate against students for their view points is not acting in an ethical manner, but a professor has a duty to present his or her honest understanding of a particular issue and expect students to understand the important theories and viewpoints taken in a particular discipline.
Colleges do have an ethical obligation to present diverse viewpoints and foster an atmosphere that encourages intelligent discourse and tolerance for diversity. But these sorts of bills seem to be micromanagement in the interest of "fair and balanced presentation." Horowitz claims his motivation for pushing the Academic Bill of Rights has nothing to do with being a conservative, but the whole thing reeks of the teach the controversy mantra being pushed by advocates of intelligent design.
"As the Academic Bill of Rights states, "Academic disciplines should welcome a diversity of approaches to unsettled questions." That is common sense. Why not make it university policy?"
What is an unsettled question and in whose mind? Is the existence of evolution unsettled? Is the global warming unsettled? Whose job is it to determine this? The result of these bills may not be an increase of academic diversity, but a chilling of academic discourse because professors will be vulnerable to outside political pressure to teach or not teach a certain way or about a certain viewpoint, just as public school biology teachers often are afraid to teach evolution because of pressures from parents.
Sunday, April 01, 2007
Electron micrographs are not yet available but the creature appears to be a single cell with brown cytoplasm (cell goo) and have a nucleus filled with a mixture of DNA and proteins, somewhat resembling marshmallow in texture and taste. The cells' surface is covered with hairs composed of many fused bacterial type flagella and here, run by a sort of egg beater like structure at the base. Most interesting to Dr. Demsy is that the DNA maybe the sort of Z DNA studied by Dr. Beakly at Whynot University.
One feature of the DNAappears to be highly repetitious "satellite" DNA with the sequence 3' TAACUAACT 5' repeating over and over again. Dr. Beakly thinks this is some sort of message but he is not sure what it means except that it may be related to various Bible prophesies obtained by running the King James Version of the Bible through Yahoo's English to Hebrew translator and back again and looking at the reflection of the resulting text in a mirror.
Dr. Demsy has graciously sent me (Why me as opposed to PZ Myers isn't at all clear; does he really think I am not biased?) a specimen to write a formal description which will appear in some sort of peer reviewed journal. Since the organism is entirely new to science I will probably name it Nivosapila kittae in honor of my wife who has an inordinate fondness for a certain confection found at our local Quick Trip.
This is an important discovery lending credence to the notion of panspermia and intelligent design by space aliens. Dr. Demsy notes that the lack of pasta eliminates the Flying Spaghetti Monster (FSM) as being the designer. Neither the monster or it's agent would return my e-mails, but a local Pastafarian said that he thinks the whole thing is a hoax contrived by atheists to discredit Pastafarianism.