Recently in Evolution Category
David MacMillan, who wrote an 8-part series on creationism for us, sent us these 4 photographs, along with the following request:
“I recently moved back to central Kentucky. One of the things I came across while visiting my family was this fossilized object I discovered near my home here when I was about 9 or 10 years old.
“Back in the late 90s, we were living in a new development and there was a lot of excavation going on near our house. I believe I found this half-buried in the bottom of a rain-fed creek just after a particularly heavy period of excavation followed by some heavy rainstorms.
“It appears to be a vertebra, due to the shape and orientation of the various spurs, and what seems to be a very large nerve opening going in the side. The exterior is dotted with what appear to be marine fossil concretions, including scallops and similar creatures.
“This region of Kentucky comprises primarily Ordovician limestone and shales, which is puzzling because this would have to be a pretty large marine vertebrate, and there were virtually no large bony vertebrates in the Ordovician. Perhaps this is actually not a vertebra at all and is rather some sort of oddly-shaped shell?
“The largest human lumbar vertebrae are around 13 mm thick, while this measures over 5 cm thick. If it is a vertebra, it would have to come from an animal with a spinal column at least five times the length of a human spine.
“Basically, I’m stumped. Any idea whether any of the readers of Panda’s Thumb might be able to identify it?”
Polish your lenses, oil your tripods, search your archives – the seventh Panda’s Thumb photography contest, begins – now!
We will accept entries from 12:00 CST, June 8, through 12:00 CST, June 22. We encourage pictures of just about anything of scientific interest. If we get enough entries, consistently with Rules 11 and 12, we may assign entries to different categories and award additional prizes, presuming, of course, that we can find more prizes.
The first-place winner will receive a signed copy of Why Evolution Works (and Creationism Fails), which has been donated by one of the authors. The second-place winner will receive a copy of The Devil in Dover, which has been generously donated by the National Center for Science Education.
… June 8. That is, we will accept entries from noon, June 8, to noon, June 22, where noon is defined by the Panda’s Thumb server, which thinks it is still in Central Standard Time, or UTC(GMT) – 5 h. The rules will be essentially the same as previous years’. We have not chosen categories yet, but please be assured that they (or it) will be all-inclusive. So wipe your lenses, grease your shutters, and be ready!
The majority of U.S. medical schools do not require evolutionary biology as a prerequisite for acceptance and do not offer courses dedicated to the subject. But as we talked about last time, adopting an evolutionary perspective on medical issues can potentially give new insights into disease treatment, prevention, and diagnosis. Where do we and should we begin to teach this kind of thinking? What resources are available to teachers and students to learn about evolution and its application to modern day problems?
Evolutionary training can help doctors look at diseases in a different light (Nesse et al, 2006). Take, for instance, sickle cell anemia: carriers of the sickle cell trait, a disease which is highly prevalent in tropical regions, are resistant to malaria, likely as a result of natural selection. This knowledge is helpful in developing ways to prevent malaria and perhaps similar evolutionary links between other diseases or infections and protective traits exist, but examining this hypothesis requires a thorough understanding of evolution and population genetics. Based on examples like this proponents of evolutionary medicine believe evolutionary biology should be considered a core subject for medical students, side by side with anatomy, physiology, biochemistry, and embryology, and that medical license exams should include questions about evolutionary biology.
People with sickle-cell anemia, whose bodies produce abnormal, crescent-shaped red blood cells, also carry genes that protect against malaria. This is most likely the reason sickle cell anemia is so common in areas where malaria is highly prevalent.
Image source: National Health Service
But while most medical schools do not offer much in the way of evolutionary education, there are some resources available for K-12 students and teachers as well as college undergraduates and graduates. One example is the BEACON Center for the Study of Evolution in Action at Michigan State, an interdisciplinary research team working on applying evolutionary principles to a wide range of problems in fields such as medicine, computer science, ecology, and engineering. Along with research, BEACON is focused on evolution outreach and education: researchers are conducting studies to see if integrating undergraduate cellular and molecular biology courses with evolution improves evolutionary understanding. The center also organizes K-12 summer programs, activities for K-12 teachers, and undergraduate and graduate-level courses.
While BEACON is enjoying great success, the NESCent (National Evolutionary Synthesis) Center, a center in North Carolina promoting multidisciplinary evolutionary research, will be closing this year after a decade of operation. Like BEACON, NEScent was also active in public outreach and education, organizing events like Darwin Day for K-12 students and training workshops for graduate students and teachers. But a new center is opening in the wake of NESCent: the Triangle Center for Evolutionary Medicine (TriCEM), which will focus on the partnership of evolutionary biology with human and veterinary medicine.
We’ve made the case for why an evolutionary understanding can improve research in medicine. But if we want to shift the paradigm of medical thought to one that emphasizes evolutionary biology, we need to reevaluate how we teach evolution from the earliest levels of education through medical school.
This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.
Eudyptula Minor – little penguin, Kangaroo Island, Australia. These penguins are nocturnal, but are apparently blind to the red light. Unfortunately, according to Kangaroo Island Penguin Center, “Our nocturnal Penguin Tours ceased in November 2013 due to the very low numbers of Penguins in the Kingscote colony. Predation by the increasing numbers of New Zealand Fur Seals from 2010 onwards has decimated the Penguin Colony, because the seals kill the adult penguins as they swim ashore at night to feed their chicks and therefore the chicks also die. We apologise for this, but the situation has been beyond our control.”
This post is by Joe Felsenstein and Tom English
Back in October, one of us (JF) commented at Panda’s Thumb on William Dembski’s seminar presentation at the University of Chicago, Conservation of Information in Evolutionary Search. In his reply at the Discovery Institute’s Evolution News and Views blog, Dembski pointed out that he had referred to three of his own papers, and that Joe had mentioned only two. He generously characterized Joe’s post as an “argument by misdirection”, the sort of thing magicians do when they are deliberately trying to fool you. (Thanks, how kind).
Dembski is right that Joe did not cite his most recent paper, and that he should have. The paper, “A General Theory of Information Cost Incurred by Successful Search”, by Dembski, Winston Ewert, and Robert J. Marks II (henceforth DEM), defines search differently than do the other papers. However, it does not jibe with the “Seven Components of Search” slide of the presentation (details here). One of us (TE) asked Dembski for technical clarification. He responded only that he simplified for the talk, and stands by the approach of DEM.
Whatever our skills at prestidigitation, we will not try to untangle the differences between the talk and the DEM paper. Rather than guess how Dembski simplified, we will regard the DEM paper as his authoritative source. Studying that paper, we found that:
They address “search” in a space of points. To make this less abstract, and to have an example for discussing evolution, we assume a space of possible genotypes. For example, we may have a stretch of 1000 bases of DNA in a haploid organism, so that the points in the space are all 41000 possible sequences.
A “search” generates a sequence of genotypes, and then chooses one of them as the final result. The process is random to some degree, so each genotype has a probability of being the outcome. DEM ultimately describe the search in terms of its results, as a probability distribution on the space of genotypes.
A set of genotypes is designated the “target”. A “search” is said to succeed when its outcome is in the target. Because the outcome is random, the search has some probability of success.
DEM assume that there is a baseline “search” that does not favor any particular “target”. For our space of genotypes, the baseline search generates all outcomes with equal probability. DEM in fact note that on average over all possible searches, the probability of success is the same as if we simply drew randomly (uniformly) from the space of genotypes.
They calculate the “active information” of a “search” by taking the ratio of its probability of success to that of the baseline search, and then taking the logarithm of the ratio. The logarithm is not essential to their argument.
Contrary to what Joe said in his previous post, DEM do not explicitly consider all possible fitness surfaces. He was certainly wrong about that. But as we will show, the situation is even worse than he thought. There are “searches” that go downhill on the fitness surface, ones that go sideways, and ones that pay no attention at all to fitnesses.
If we make a simplified model of a “greedy” uphill-climbing algorithm that looks at the neighboring genotypes in the space, and which prefers to move to a nearby genotype if that genotype has higher fitness than the current one, its search will do a lot better than the baseline search, and thus a lot better than the average over all possible searches. Such processes will be in an extremely small fraction of all of DEM’s possible searches, the small fraction that does a lot better than picking a genotype at random.
So just by having genotypes that have different fitnesses, evolutionary processes will do considerably better than random choice, and will be considered by DEM to use substantial values of Active Information. That is simply a result of having fitnesses, and does not require that a Designer choose the fitness surface. This shows that even a search which is evolution on a white-noise fitness surface is very special by DEM’s standards.
Searches that are like real evolutionary processes do have fitness surfaces. Furthermore, these fitness surfaces are smoother than white-noise surfaces “because physics”. That too increases the probability of success, and by a large amount.
Arguing whether a Designer has acted by setting up the laws of physics themselves is an argument one should have with cosmologists, not with biologists. Evolutionary biologists are concerned with how an evolving system will behave in our present universe, with the laws of physics that we have now. These predispose to fitness surfaces substantially smoother than white-noise surfaces.
Although moving uphill on a fitness surface is helpful to the organism, evolution is not actually a search for a particular small set of target genotypes; it is not only successful when it finds the absolutely most-fit genotypes in the space. We almost certainly do not reach optimal genotypes or phenotypes, and that’s OK. Evolution may not have made us optimal, but it has at least made us fit enough to survive and flourish, and smart enough to be capable of evaluating DEM’s arguments, and seeing that they do not make a case that evolution is a search actively chosen by a Designer.
This is the essence of our argument. It is a lot to consider, so let’s explain this in more detail below:
As usual I will pa-troll the comments, and send off-topic stuff by our usual trolls and replies to their off-topic stuff to the Bathroom Wall
A pair of recent articles on the Science website seems to think so. Staff writer Robert Service says Researchers may have solved origin-of-life conundrum and writes,
Chemists report today that a pair of simple compounds [HCN and H2S], which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start. Although the new work does not prove that this is how life started, it may eventually help explain one of the deepest mysteries in modern science.
The title is certainly misleading, since the origin of life puzzle is still very far from “cracked.” Showing that biomolecules, even complex biomolecules, can be synthesized under plausible primordial conditions is very different from showing how those molecules could have assembled to produce the first cell. Only then can one claim to have cracked the puzzle.
That seems to me to be essentially correct, but then the author, Walter Steiner, adds, somewhat mysteriously, “Solving that puzzle will require the discovery of some currently unknown natural phenomenon.” Another commenter suggests some kind of broken symmetry.
The creationists, intelligent-design and otherwise, have moved in on the “conundrum” article, which is now about 1 week old and boasts almost 1000 comments, some of which actually make sense.
That is one of the disquieting results of a new survey, Enablers of doubt, by Michael Berkman and Eric Plutzer. The two Penn State professors interviewed a total of 35 students on 4 Pennsylvania campuses in 2013. All the students were training to be biology teachers; many were not comfortable with the theory of evolution, and many were “concerned about their ability to navigate controversy initiated by a student, parent, administrator, or other members of the community.” Indeed, instead of relying on their knowledge of biology, they intended to fall back on classroom-management techniques to deal with creationist students. Notably, these were not education students, but rather biology students who “take a set of required courses in educational psychology, classroom management, and methods of instruction.” Their lack of expertise in science seems not to concern them; to the contrary, they thought they would use their skills at avoiding controversy to avoid any controversies.
PT readers may remember Professors Berkman and Plutzer for their book, Evolution, Creationism, and the Battle to Control America’s Classrooms, which we reviewed here a few years ago. The disquieting conclusion of that book was that only about 28 % of biology teachers actually teach evolution according to recognized standards. The present study may help explain why.
The students, who attended a large research university, an institution that granted degrees at the master’s level, a Catholic college, or a historically Black university (all unnamed), were interviewed in focus groups. The interviews lasted 50-65 min and were conducted by the authors. The focus groups do not provide a statistical sample, but the authors attempted to include several different kinds of educational institution, and they consider the findings “suggestive.” Below the fold, some representative comments.
Or, perhaps more precisely, Did dark matter kill the dinosaurs?, which is the way that an article in ScienceNOW put it.
Readers of PT doubtless know that there have been a half-dozen or so mass extinctions in the history of the earth, and they appear with a periodicity on the order of 30 million years. You can see an early graph here. The vertical arrows are separated by approximately 30 million years. Not every vertical arrow points to a mass extinction, so it might be better to say that the first harmonic of the data set is 30 million years; that is, if the periodicity is real, it sometimes skips a beat.
What is interesting is that some of the extinctions appear to have been caused by collisions with an asteroid, whereas others may be the result of long periods of extreme volcanism – yet all the extinctions occur with the same period of 30 million years.
Imagine that you want to analyze the 3.2 billion bases of the human genome. If you recruited every undergraduate student at ASU, all 70,000 of us, to type those data into a spreadsheet, it would still take about 13 hours. So you develop a computer program that analyzes the data for you. But then you find out that your huge data set amplified small errors in your algorithm and gave you the wrong answer. This is the issue facing evolutionary biologists using genomic data, a practice that is becoming standard to construct reliable phylogenies (see our previous posts about the new bird and insect phylogenies). Our lab, working under Dr. Reed Cartwright, has developed a novel method to quickly analyze genomic data and produce an accurate phylogeny that improves upon previous techniques.
The giant panda genome was assembled using de novo techniques in 2010, but better methods of phylogeny construction are in development. Image: Wikipedia
Historically, scientists have compensated for potential inaccuracies in genomic-size data in two ways: by using better statistical tools to analyze the data after they have been acquired or by acquiring fewer, more informative data.
In the first method, you start with sequenced genomes in the form of short fragments (about 100 base pairs) and develop computational algorithms to compare those sequences to a reference genome for reassembly, like Liu et al. did in their 2003 analysis of primate genomes. The reference genome is one that we know with a high level of confidence; for example, the human genome is reliably known and often used as a reference. If, however, a reference is unavailable or unreliable, you could use a computer program to assemble the sequences with a process known as de novo assembly, which Li et al. used to construct the giant panda genome in 2010. These programs, called assemblers, use graphical techniques (for example, De Brujin graphs) to remove errors in phylogenetic trees and resolve repeated data that are harder to determine in short sequences than longer ones. Algorithms like this can greatly improve the accuracy of conclusions made from genomic data, but de novo assembly without a reference genome requires high quality annotation of the sequences and, once the genome is reconstructed, time-consuming alignments of similar sequences to produce a phylogenetic tree.
Alternatively, you could acquire fewer data in the first place. You would need to determine which markers in a genome are informative and necessary to draw certain conclusions and then only obtain those data. By reducing the size of the data set and eliminating unnecessary information, we improve the accuracy without having to implement sophisticated analytical techniques. McCormack et al. used this principle in 2012 to determine the tree of placental mammals from certain markers. However, the major drawback of this method is that markers appropriate for a particular project or species most likely cannot be reused for other projects. The ability to recycle genomic data reduces the cost and time of phylogenomic studies.
Our lab is working on a program that constructs phylogenetic trees more quickly and easily than either of these methods. The program, called SISRS, combines genome assembly with identification of homologous genes to rapidly reconstruct phylogenies without the need of a reference genome or annotation. In the next post, we’ll go into detail about how SISRS works and what makes it a better way to analyze genomic data.
This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.
Photograph by Jim Foley.
Chelepteryx collesi – white-stemmed gum moth, Canberra, Australia. Mr. Foley writes, “The caterpillar is about 12 cm long! Yet another member of the Australian fauna you don’t want to mess with. … We seem to have more venomous stuff than most places: lots of snakes, stonefish, spiders, jellyfish, blue-ringed octopus, etc., not to mention the crocodiles and sharks.”