Science & Nature Archive

Wednesday, November 10, 2010

Celestial Videos

Astroscan TelescopeEvery year, I get an Amazon gift card from my mom for my birthday. This year, I used it (along with some of my own money) to buy the Celestron NexImage Solar System Imager - an attachment for a telescope that lets you digitally capture what you would normally see through the eyepiece. It also comes with software that lets you 'stack' frames from a recorded video, and then the software will clean that up to give you a good still image.

I took it out to play with for the first time last night. I still have a lot of learning left to do, but at least I could see on the monitor something resembling what I saw through the eyepiece. Just for the hell of it, I decided to post two of the videos I captured last night. The cool thing these videos show is just how fast the Earth is moving. I wasn't moving my telescope at all (except for the big jumps and the one change of focus). The motion of the objects across the frame is due solely to the Earth's rotation.

In case you haven't figured it out, what you're seeing in the two videos above is Jupiter and some of its moons. The second video is with the NexImage directly where the eyepiece would normally go. The first is with a 2x barlow lens. For reference, I'm using an Astroscan telescope (which explains the jumpy movement when I have to re-aim).

Like I said, I still have some learning to do. Those videos are definitely overexposed - through the eye piece, I could just make out one of the bands on Jupiter, and I could make out the overall color better. I've found some info on websites with some helpful tips. So, one of these nights, I'll get out there and try them out, and hopefully get some better video. Once I have that, then I'll start playing around with the video processing software to see how good of a still I can get.

Friday, September 10, 2010

Book Review - Archaeopteryx: The Icon of Evolution

On a recent trip to the Houston Museum of Natural Science, I bought a ticket to see the the exhibit, Archaeopteryx: Icon of Evolution (related link). The exhibit was a fascinating collection of fossils from the Solnhofen region of Germany, with an archaeopteryx known as the Thermopolis specimen as the centerpiece. The archaeopteryx fossil was very interesting, but there were two things about it, in particular, that I was struck by. First was the size. For some reason, in my mind's eye, archaeopteryx had always been a big bird, something along the lines of an eagle. The archaeopteryx fossil at the museum was about the size of a crow (more on this below). Second was the level of detail in the feather imprints, which photos just don't do justice to. It's not that the feathers were imprinted perfectly in their entirety, but in the regions where the preservation was best, it was very obvious that you were looking at an actual feather.

Thermopolis Specimen
The Thermopolis Archaeopteryx, With a Hand for Comparison to Show Size

So, after I left the exhibit, I went to the museum gift shop to find a souvenir. About the only thing they had that was appropriate for an adult was the book, Archaeopteryx: The Icon of Evolution, by Peter Wellnhofer*.

Before I get started with my own review, let me note that the publisher has a great section for the book. Perhaps best for someone considering buying the book is the section of sample pages. The pages shown are not anomalous - nearly every page had many illustrations, which was great. Also note the small text size and amount of text per page. Even though the book was only 208 pages, it was an information packed 208 pages.

The book was divided into several sections. The first was a short description of the locale where the fossils were found, the Solnhofen region of Bavaria, in Germany. It was the sort of description you'd expect from a chamber of commerce.

Next came a brief description of the geology of the Solnhofen region, and what this tells us about the ancient environment of the area. All of the archaeopteryx specimens found so far have come from Solnhofen Jurassic limestone deposits. It turns out that these deposits were from lagoons in shallow seas. The water was apparently fairly calm, and formed stratified regions with very low oxygen levels at the sea floor - no multicellular life could survive in those anoxic conditions. The mainland was not very close, but it's possible there were islands nearby. So, the limestone deposits were necessarily not the native habitats of any of the terrestrial animals found there. It's possible that the archaeopteryx were blown out to sea during storms, and didn't have the strength to fly back to land (the fact that all archaeopteryx found thus far are juveniles supports this idea).

Horseshoe Crab Death March
Death March of a Horseshoe Crab, Which Died after Wandering into an Anoxic Lagoon

After that came a discussion of the history of fossil discovery in the Solnhofen. Obviously, being a marine environment, most of the fossils from the region are from sea creatures, with the fossils of terrestrial animals being very rare. Because of the way the fossils were formed, the preservation is excellent, and Solnhofen fossils have been prized for centuries. They were regular inclusions in the curiosity cabinets of medieval Europe, which emerged in the 16th century (some of the best collections served as the start of modern museums).

Next came the heart of the book - 83 pages discussing the known archaeopteryx specimens in detail. If you think 83 pages of discussion sounds like a lot - it was, and it was a bit dry. I think of myself as a fairly knowledgeable layperson when it comes to evolution and biology, but much this section was a bit advanced for me. The fossils were described in technical terms (radius, ulna, meta carpal, flexor tubercle, pneumatic foramina), which would have made a firm grounding in anatomy useful in understanding this chapter.

This section started with a discussion of how the urvogels (a common name for archaeopteryx from German, meaning proto bird) likely became fossils - they floated in the sea for a few days before sinking to the sea floor, where they were covered with a microbial film before being covered by sediment. One fact I found interesting is that the feathers formed an imprint in the sediment before decomposing, and then this imprint was transferred to the adjacent layer of sediment after the feather decomposed. So, when a slab containing an archaeopteryx is split, both new slabs show only one side of the feathers.

After discussing fossilization, this section moved on to the controversy in the nomenclature and taxonomy of archaeopteryx. The rules of taxonomy state if a species is named twice, the first description has precedence, even if it was obscure and few people heard of it, or if the type specimen wasn't as complete as the later one. (This, for example, is why brontosaurus is now referred to as apatosaurus, since apatosaurus was the first name used, even if it wasn't as widely known). An early archaeopteryx specimen, not being recognized as a bird, was named Pterodactylus crassipes, so crassipes should be the species name. But before that specimen was recognized as a bird, a fossil feather was discovered and used as the original type specimen for Archaeopteryx lithographica. Once subsequent archaeopteryx were discovered, they were named after the feather, even though it's not certain if the feather is actually from the same animal. Another ealy genus name was Griphosaurus. In the end, most people referred to the animals as archaeopteryx, so a special petition was made to the International Commission on Zoological Nomenclature in 1977 to make the London specimen the type specimen, and to make Archaeopteryx lithographica the official genus and species names.

There is, however, some controversy as to whether the archaeopteryx specimens found so far are actually all from the same species. Most notable is the size difference between the specimens, but there are also differences among the details of the anatomy. The size and some of these differences could be explained by the urvogels being different ages at their times of death, along with individual variability, or even sex differences. But, it's possible that the fossils represent more than one species.

Comparison of the Size of Various Archaeopteryx Specimens
Size Comparison of Archaeopteryx Specimens

Next came the discussion of each fossil. For each fossil, Wellnhofer gave a brief overview of how the fossil was discovered and brought into public light, followed by a detailed physical description, which as I already mentioned, was rather technical when it came to anatomy. Besides the feather (which may or may not be from an archaeopteryx), there have been 10 archaeopteryx specimens discovered so far, of differing levels of completeness and preservation. Most are now housed in museums, and are known by the city in which they're permanently located. In order of discovery (though not necessarily public knowledge), the specimens are the feather, London, Berlin, Maxberg, Haarlem, Eichstatt, Solnhofen, Munich, Burgermeister-Muller, the 9th, and Thermopolis specimens.

The first, and one of the most complete, was what is now known as the London specimen. It was discovered in 1861, just two years after Darwin published On the Origin of Species, and made quite a stir being such an obvious transitional form. Also notable is the Maxberg Specimen, which has gone missing since its owner's death. Luckily, casts were made of the fossil before it was lost, but casts are not as useful as the real thing.

Once all the fossils had been described, the next section was a sort of synthesis, describing as much as we can know about archaeopteryx from the fossils we've found. Wellnhofer started with the subject with the most certainty, the skeleton, and moved on from there through less certainty and more conjecture - plumage, physiology, then lifestyle.

The remaining four chapters were all related - discussing early bird evolution, and the role of archaeopteryx in understanding that story. Archaeopteryx is, after all, the oldest bird yet known (though not the first bird, as is too often mistakenly said). Wellnhofer discussed some of the leading hypotheses on the ancestor of birds, including the thecodont hypothesis and the crocodile hypothesis, along with a few more 'imaginative' theories. But the leading hypothesis, which is pretty much certain, is that birds are a lineage of dinosaurs, closely related to the maniraptoran theropods. They're so similar, actually, that there's some discussion as to whether some animals traditionally classified as non-avian dinosaurs are in fact birds that have secondarily lost the ability to fly (in the same manner as ostriches, but back when birds still had teeth and clawed hands).

One of the things that struck me is just how much more dinosaur-like than bird-like archaeopteryx was (yeah, yeah, I know - birds are dinosaurs, but I think my meaning is clear enough). In fact, the Solnhofen Specimen was originally mistaken for a Compsognathus theropod by an amateur collector. I've included two pictures from the book below to dramatically illustrate this (I apologize for the quality of the scans, but like I said in another review, I wasn't about to ruin the binding on my book just to make it lay flat in the scanner).

Comparison of Bambiraptor, Archaeopteryx, and a Modern Chicken
Comparison of Bambiraptor, Archaeopteryx, and a Modern Chicken - not to scale

Comparison of Archaeopteryx to a Modern Eagle
Comparison of Archaeopteryx to a Modern Eagle - not to scale

Take a close look at those skeletons. If you had to pick which other animal archaeopteryx was most closely related to, it seems pretty obvious that it would be the bambiraptor. Archaeopteryx still had clawed hands, a hyperextensible 'killer' claw on its foot (though not shown in the above reconstruction), a long bondy tail, gastralia (the bones under the stomach), a more theropod pubis, and teeth in its mouth. Just as important is what archaeopteryx didn't have - a pygostyle, a keratinous beak, a large keeled sternum, fused hand bones, a fused tibiotarsus, or a fused tarsometatarsus. It also seems pretty likely that archaeopteryx lacked a bastard wing. And those are just some of the differences between archaeopteryx and modern birds.

I hadn't realized just how many ancient birds have been discovered that are younger than archaeopteryx. There are quite a few. In fact, the evolutionary story of birds following archaeopteryx is pretty well understood. The family tree below illustrates this. Note that archaeopteryx is most likely not actually the ancestor of today's birds. Like most animals, it was in a lineage that went extinct, which means it had a few traits it had evolved that set it apart from the surviving avian lineage. However, it's still a very valuable specimen for understanding what early birds were like.

Avian Family Tree
Avian Family Tree

This discussion also helped to put into perspective the K-T mass extinction. You often hear that birds were the only lineage of dinosaurs to survive that event, which makes it seem like there must have been something extra special about birds. But look at that phylogenetic tree. Most birds died at the end of the Cretaceous along with their non-flying relatives. There may have been some advantage that the surviving lineage of birds possessed, or they may have just gotten lucky (similarly, most mammals also died out at the end of the Cretaceous).

Despite there not being any known birds older than archaeopteryx, in recent years, paleontologists have discovered quite a few feathered dinosaurs. The book discussed a few of those dinosaurs, and compared the structure of their feathers to those of archaeopteryx and birds. The dinosaur feathers are more primitive. Some are just a downy covering, but some more advanced feathers do resemble the flight feathers of birds, only lacking the asymmetry. While the downy feathers were likely used for insulation, the function of those flight-like feathers is still uncertain.

Wellnhofer also covered the ground up versus trees down debate on the origin of flight. Up until I heard of this debate a few years ago, I'd always assumed that avian flight must have evolved from the trees down. It didn't seem plausible that it would have developed any other way. But many people have made compelling arguments for how it could have evolved from the ground up, where the wings would initially have been used for balance, and then maybe flapped for extra thrust to increase running speed, before fully developing flight. It's interesting that the flapping motion of a bird wing is very similar to the motion possible in a maniraptoran arm (most likely used to capture prey).

Perhaps the best evidence for the ground up hypothesis is that archaeopteryx very strongly appears to be a fully terrestrial animal, with no special adaptations for an arboreal lifestyle. Since archaeopteryx wasn't the first bird, it's possible that archaeopteryx secondarily evolved a terrestrial lifestyle, but given its similarities to the theropods, this seems unlikely. One proposed evolutionary stage in the ground up scenario, wing-assisted incline running, is supported by observation of living birds. The idea has also been proposed that flight may have evolved from jumping and parachuting from cliffs or other elevated points, followed later by gliding, as a sort of reconciliation between the trees down and ground up hypotheses, but eliminating the trees.

The ground up hypothesis certainly seems to be the more likely at this point, but as Wellnhofer pointed out, all ideas on this are speculative for the time being, since we haven't found the fossils of earlier birds.

Archaeopteryx: The Icon of Evolution was a very interesting book. It's very informative and detailed, and I learned quite a bit from it. I wouldn't recommend it for everybody, though. The target audience is quite a bit higher than the general layperson. Although some sections would probably be interesting to many people, if you only have a passing interest in archaeopteryx, maybe Wikipedia is a better choice. But if you happen to have a really strong interest in avian evolution, and don't mind reading technical jargon, then this is the book for you.


Update 2011-08-02 - A new fossil, xiaotingia zhengi, has been found that sheds further light on the evolution of archaeopteryx like animals. A cladistics analysis using this fossil suggests that archaeopteryx might not be quite as closely related to birds as previously thought. You can read more about it in a new entry, Is Archaeopteryx Still a Bird?

Update 2010-09-28 - I reworded several sections to make them more clear, particularly the section on the origin of flight. I also added a bit of information to the section on the origin of feathers.

* Although I commonly buy books as souvenirs from museums, this one was a little more expensive that I was willing to pay, so I walked out of the museum without it. However, my wife and daughter, seeing how interested I was in it, bought it without me noticing, and gave it to me later as a Father's Day present. Actually, it was my daughter's girl scout troop leader who bought the book, who then gave it to my wife when I wasn't looking. The full story is that we were at the museum as part of a girl scout trip. My wife was an official full time chaperon for the trip, and although I helped with chaperoning duties for most of the time, since I wasn't officially one, I was free to go off and do my own thing if I wanted to. Since the tickets to the archaeopteryx exhibit cost extra, it was out of the budget for the girls, so I went through the exhibit by myself. I would have liked to have taken the girls, but to be honest, I think they were all fossiled out after the museum's main exhibits. At the least, they definitely wouldn't have taken as much time as I had.

Friday, August 6, 2010

Genetic Determinism

DNAI got into a discussion with a few co-workers last week on a topic that I'd thought most educated people agreed upon to a large extent - the limits of genetic determinism. In the old argument of nature vs. nurture, I thought most people realized that who we are is a combination of both influences. However, in that conversation, I was the only one who thought environment played a big role, while the other two thought it was mostly down to genetics. Anyway, a few days after our conversation, I sent them an e-mail explaining how environment can contribute to our traits, and decided that it might be worth posting a modified version of it here on the blog. So, to anyone who puts too much stock in genetic determinism, here's some information on how environment also plays a strong role in our development.

First, there's an example that's so obvious that we almost forget about it - muscle size. Genetics gives us a potential muscle size & strength, but our actual muscle size can be greatly affected by diet and lifestyle, particularly by being active or working out. This is a clear example of genetics and environment interacting to produce a trait.

Here's an article on height (since that was one of the traits my coworkers and I discussed specifically). Based on studies between twins and other relatives, it looks like genetics is 60 to 80% responsible for height, and environmental factors, particularly nutrition, are responsible for the remaining 20 to 40%.
http://www.scientificamerican.com/article.cfm?id=how-much-of-human-height

Here are a couple more links on height.
http://en.wikipedia.org/wiki/Human_height
http://www.newton.dep.anl.gov/askasci/mle00/mole00125.htm
http://jn.nutrition.org/cgi/content/full/135/9/2192

One important caveat on twins that doesn't get mentioned in many of these articles - identical twins don't look so similar solely because of their shared genetics (although that is the biggest reason). It is also due to the shared environment in the womb. That's why fraternal twins look more similar that siblings that didn't develop together. So, it's not enough to look at identical twins in these studies - you have to use fraternal twins as a control for early developmental factors.


Here's a really good site on the 'nature vs. nurture' debate that focuses on intelligence. I'm giving the link to the conclusion, but if you follow the links on the site, you can find the evidence they list. To quote part of that site:

Through the research we have done, it seems that heredity, as well as environment plays an important role in humans’ mentality; but these are not exactly equal in influence. A person’s entire environment seems to be more effectual in determining his mental ability than heredity is. The most fundamental way to explain our opinion is quite comprehensible. It is that heredity determines one’s potential, but environment determines how far one will reach that potential during his lifetime. In other words, every individual has a destined mental potential, but how much of that potential the individual will be able to gain solely depends on the environment that the individual grows in.

http://www.macalester.edu/psychology/whathap/ubnrp/intelligence05/Rconclusion.html


Here's another article that touches briefly on genetic determinism, mentioning an experiment where cloned plants (i.e. genetically identical) were grown in different environments, and the plants grew differently depending on the environment they were in.
http://scienceblogs.com/pharyngula/2009/10/richard_lewontingenetic_determ.php


Another point against genetic determinism is the fact that our cells aren't perfect machines, where given inputs give precise outputs. Cells are a cluttered stew of molecules inside a membrane. Depending on how molecules are dispersed throughout the cell, two genetically identical cells may have different reactions to the same conditions. Carl Zimmer's book, Microcosm, has a good explanation of this, if you ever get a chance to read it. A good example, one which made headlines, is the first cloned cat. Although it has identical nuclear DNA to its mother, it has a different color pattern, because the activation and inactivation of the responsible genes is more or less random.
http://www.accessexcellence.org/WN/SU/copycat.php


Here are two more links, dealing with related themes that we discussed. The first link is to an article on the Flynn Effect (the fact that IQ scores have been increasing). We also discussed abstract thinking, and whether or not it's a learned skill. The second link below includes a discussion of a study done in Uzbekistan which seems to confirm that abstract thinking is learned (though the article also mentions potential problems with the study).
http://www.americanscientist.org/bookshelf/pub/the-domestication-of-the-savage-mind
http://www.cscs.umich.edu/~crshalizi/slothblog/484.html


Okay, so what's my point in all this? Genetics plays a significant role in who we are, but so do environmental factors, and even random chance has a part. So, given the long complicated history that has led to the current conditions in the world, unless two people have had very similar upbringings, it would be nearly impossible to tell how much of the difference between them was due to genetics.

Friday, July 9, 2010

New Comments

Well, I don't have anything really substantive for this week. I did leave two decent comments, though, in response to visitors. First is a discussion of why humans should be considered apes. Second is a bit of politics in response to a guy who didn't like my response to Gary Hubbell's anti-liberal article.

Thursday, June 17, 2010

Book Review - The Tangled Bank

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

So ends Darwin's Origin of Species, giving the inspiration for the title of Carl Zimmer's latest book, The Tangled Bank: An Introduction to Evolution. It is described as a textbook on evolution for non-biology majors, and it is very good.

The term, 'evolution', is pretty broad. In general, when people talk of biological evolution, there are two broad categories they're referring to. The first is the concept of common descent with modification - that all life on this planet is related, and that populations of organisms change over time. The second is the theories describing how that works, with natural selection being the most famous. Pretty much every book that covers evolution will cover both areas to some extent, but often times they will focus on one area over the other. The Tangled Bank covers more of the latter subject. Of course, it uses examples, but it is more about how evolution works rather than a fossil by fossil account of the evidence for common descent (for that type of book, read Donald Prothero's Evolution: What the Fossils Say and Why It Matters - also, realize that there's much more evidence for evolution than just fossils).

Let me give an example of one of the concepts I learned about - Hardy-Weinberg Equilibrium. This term is probably familiar to biology majors, but it's not something us non-biologists generally read about in most popular books or magazine articles on evolution. The concept has to do with allele frequency. As a refresher, an allele is a variation of a gene. Think back to your high school biology class, and the genetic experiments of Gregor Mendel. For example, Mendel discovered a certain gene* that controlled pea color - one version would make them green, while the other would make them yellow. Each version is called an allele. Remember further, that us eukaryotes carry two copies of a gene (actualy, at least two - it can get a bit more complicated than this). So, individual plants in a population of all green peas might all carry two copies of the green allele - GG, and individual plants in a population of all yellow peas might all carry two copies of the yellow allele - YY. Now, if you were to bring those two populations together, the alleles woud start mixing, and you'd end up with three different combinations that the plants could have - GG, YY, and GY (GY and YG are the same thing). What Hardy-Weinberg equilibrium tells us, is that according to just random mating and chance distribution, these allele combinations should all be present in certain ratios. In this example, half of the plants would likely be GY, one quarter would be GG, and the remaining quarter would be YY. But what if you checked up on your pea population, and found that it didn't match the Hardy-Weinberg equilibrium? What if less than a quarter of the plants were GG, and more than a quarter were YY? Well, then we could conclude that something about the Y allele was advantageous to the plants, and that natural selection was pushing the population to have more plants with the Y allele.

This concept of Hardy Weingberg equilibrium can be applied to more complicated scenarios. It doesn't have to be just two alleles, and the initial distribution doesn't have to be 50/50. However, for any combination, the Hardy Weinberg equilibrium is the distribution you'd expect if there weren't any natural selection, and measuring how much the actual distribution varies from the Hardy Weingberg equilibrium is a measure of how strong the selection is.

To me, that's a pretty interesting concept, and it wasn't something I'd given much thought to before reading Zimmer's book. However, the book didn't go into much more detail than what I just gave in my summary. If you're not of a technical bent, that may be all you need. I realize that Zimmer's goal was to provide a book for non-biology majors, so maybe that's all the detail he felt was necessary. However, to someone like me, who may not be a biology major but wouldn't mind seeing a little light math, Zimmer's explanation was a little too superficial. I mean, if you follow that Wikipedia link I provided and read the explanation of Hardy Weinberg equilibrium, the math isn't all that hard. It's just a bit of algebra. Maybe as an engineer who works with equations all day long I'm a bit biased, but it's not as if you need to understand any calculus or differential equations to follow the basics of Hardy Weinberg equilibrium.

I can't discuss this book without mentioning the illustrations. Practically every page of the book has a figure or a graph. I'm sure that the printing cost associated with this contributed to the $50 price tag for the book, but it really makes it easy to understand certain concepts that would be difficult to get across with just words.

This book was published right around the same time as Richard Dawkins' The Greatest Show on Earth: The Evidence for Evolution, so there were inevitably comparisons. But the truth is that they're just not the same kinds of books. In my discussion above on the broad meanings of evolution, I said that Zimmer's book covered more the theories of evolution. Dawkins' book was more of a look at the evidence itself. Zimmer's book was a textbook with color illustrations on each page, while Dawkins' book was a popular book with few illustrations. Comparing the two is comparing apples to oranges.

If you'd like to get more of a taste of the book, I've found two excerpts available for download online. Chapter 1, Evolution: An Introduction is availabe from Carl Zimmer's own site. Chapter 10, Radiations and Extinctions is available from the National Center for Science Education. You can also read Zimmer's announcement of the book on his blog, to hear his intentions in his own words.

All in all, The Tangled Bank was very good. It was a nice broad introduction to many of the theories and mechanisms of evolution, but without getting too technical for those of us that don't plan to go into careers in biology. Unfortunately, being a textbook, it's a bit pricey. You may try going to your library to check it out, find it used, or maybe be lucky enough to be able to borrow it from a friend. However you manage to get your hands on a copy, I definitely recommend this book.


*Mendel's insight was that there were units of heredity, now known as genes, as opposed to the prevailing concept at the time of blending inheritance, but he didn't actually know the mechanism responsible. It wasn't until later that other scientists discovered that genes were contained on chromosomes, and later yet that scientists discovered that chromosomes were made of DNA.

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