Mystery Monday
Time for another Mystery Monday. Whenever I look at this fossil, I always think of cheap tenement housing. Can you guess what it is?
What has evolution done for me lately?
“I have a dream…”
Zach Weiner. SMBC.
Almost everyone will have heard this most famous line by Martin Luther King, Jr. in the past few days. In honor of the holiday, rather than introduce another fossil, review a book, or some such thing, I thought I would do something a little different. I have a dream too, one in which teachers are not afraid to talk about evolution within the classroom, one in which people don’t recoil from the word because they think it goes against their religion, a dream in which everyone embraces the concepts, not because some scientist or teacher tells them they have to, not because they think it is part of a body of education they need to sound smart, but because they see the logic of evolutionary theory and the application of it in their everyday lives, because they understand how it affects them every day in ways they normally never even think about. In this essay, I am going to discuss a few of the many ways evolutionary theory helps us in practical applications. Next post I will discuss why I think most people deny evolution (it’s not what most people say, what people say and really think are often entirely different things), and why that denial is something we need to get past.
Cancer is an inescapable fact of life. All of us with either die from it or know someone who will. Cancer is so prevalent because it isn’t a disease in the way a flu or a cold is. No outside force or germ is needed to cause cancer (although it can). It arises from the very way we are put together. Most of the genes that are needed for multicellular life have been found to be associated with cancer. Cancer is a result of our natural genetic machinery that has been built up over billions of years breaking down over time.
Clonal evolution of cancer. Mel Greaves. http://www.science-connections.com/trends/science_content/evolution_6.htm
Cancer is not only a result of evolutionary processes, cancer itself follows evolutionary theory as it grows. The immune system places a selective pressure on cancer cells, keeping it in check until the cancer evolves a way to avoid it and surpass it in a process known as immunoediting. Cancers face selective pressures in the microenvironments in which they grow. Due to the fast growth of cancer cells, they suck up oxygen in the tissues, causing wildly fluctuating oxygen levels as the body tries to get oxygen to the tissues. This sort of situation is bad for normal tissues and so it is for cancer, at least until they evolve and adapt. At some point, some cancer cells will develop the ability to use what is called aerobic glycolysis to make the ATP we use for energy. Ordinarily, our cells only use glycolysis when they run out of oxygen because aerobic respiration (aka oxidative phosphorylation) is far more efficient. Cancer cells, on the other hand, learn to use glycolysis all the time, even in the presence of abundant oxygen. They may not grow as quickly when there is plenty of oxygen, but they are far better than normal cells at hypoxic, or low oxygen, conditions, which they create by virtue of their metabolism. Moreover, they are better at taking up nutrients because many of the metabolic pathways for aerobic respiration also influence nutrient uptake, so shifting those pathways to nutrient uptake rather than metabolism ensures cancer cells get first pick of any nutrients in the area. The Warburg Effect, as this is called, works by selective pressures hindering those cells that can’t do so and favoring those that can. Because cancer cells have loose genetic controls and they are constantly dividing, the cancer population can evolve, whereas the normal cells cannot.
Evolutionary theory can also be used to track cancer as it metastasizes. If a person has several tumors, it is possible to take biopsies of each one and use standard cladistic programs that are normally used to determine evolutionary relationships between organisms to find which tumor is the original tumor. If the original tumor is not one of those biopsied, it will tell you where the cancer originated within the body. You can thus track the progression of cancer throughout a person’s body. Expanding on this, one can even track the effect of cancer through its effects on how organisms interact within ecosystems, creating its own evolutionary stamp on the environment as its effects radiate throughout the ecosystem.
I’ve talked about cancer at decent length (although I could easily go one for many more pages) because it is less well publicly known than some of the other ways that evolutionary theory helps us out in medicine. The increasing resistance of bacteria and viruses to antibiotics is well known. Antibiotic resistance follows standard evolutionary processes, with the result that antibiotic resistant bacteria are expected to kill 10 million people a year by 2050. People have to get a new flu shot every year because the flu viruses are legion and they evolve rapidly to bypass old vaccinations. If we are to accurately predict how the viruses may adapt and properly prepare vaccines for the coming year, evolutionary theory must be taken into account. Without it, the vaccines are much less likely to be effective. Evolutionary studies have pointed out important changes in the Ebola virus and how those changes are affecting its lethality, which will need to be taken into account for effective treatments. Tracking the origins of viruses, like the avian flu or swine flu, gives us information that will be useful in combating them or even stopping them at their source before they become a problem.
Another place that evolutionary theory comes into play is genetically modified organisms. I won’t get into the arguments about whether or not they are safe to eat, other than to say that there is very little evidence to indicate GMO food is any more dangerous than normal food (i.e., yes, there are certain dangers, but nothing that you won’t find in regular, non-GMO food). There are two things about GMOs that I do want to discuss here. First is the belief that GMOs are somehow altogether different from natural organisms. In truth, DNA is swapped between unrelated organisms all the time. Horizontal gene transfer, such as this DNA swapping is known, has been well known in bacteria for over a hundred years. In the past few decades, it has also been found throughout the plant kingdom and even (what people like to call) higher order animals. It has been estimated that as much as 8% of human DNA comes originally from viruses that made their way into our cells, some of which allowed the evolution of the placenta. We even have bacterial DNA in us.
(a) Red aphids get their color from red carotenoid pigment. Genes necessary to make this pigment are present in certain fungi. Scientists speculate that aphids acquired these genes through HGT after consuming fungi for food. If genes for making carotenoids are inactivated by mutation, the aphids revert back to (b) their green color.
http://www.boundless.com/biology/textbooks/boundless-biology-textbook/phylogenies-and-the-history-of-life-20/perspectives-on-the-phylogenetic-tree-135/horizontal-gene-transfer-545-11754/
GMOs also may have an effect on natural ecosystems. They can and do occasionally escape into the wild. Genes from the GMO oilseed rape plant that provide herbicide resistance has spread into wild mustard plants. These plants have spread quite far. Herbicide resistant weeds are springing up all over the world, to the detriment of our farmers and food supply. What was once only a concern for agriculturists is now a concern for anyone concerned about conservation of natural ecosystems. How much of an effect? Unless you understand how evolutionary changes can spread through an ecosystem and what ramifications that may have, you are simply guessing, which is of no use to anyone. People often think of this as a genetics problem or an ecology problem, but this is the effects of evolution at the ecosystem level.
The problems we see in GMOs are not really related to the fact that they are GMO, as evidenced by the natural horizontal gene transfer we see. We see similar problems with no GMOs involved. Pests becoming resistant to pesticides after generations (of the pest) of exposure is a common issue farmers need to address. Weeds will become resistant to herbicides on their own, with no help from GMOs needed. Evolutionary theory will help deal with this problem, guiding us to solutions we may never have reached otherwise.
Another highly controversial topic these days is climate change. Whether we caused it or not is really beside the point and is not a topic we will discuss here. It is undeniable by a quick glance at the evidence that the earth is getting warmer. We will have to deal with it, and so will every other living thing on the planet. Organisms respond to climate change in one of three ways: adapt, move, or die. There are numerous accounts of animals and plants shifting ranges in response to climate change. This is most easily seen in highly mobile organisms. Plants are not generally considered mobile, but pollen and many seeds have huge dispersal potential, so some plants can spread surprisingly quickly. The difference in dispersal ability is a big factor in how the plant communities adapt to climate change. This is not biological evolution in the strict sense of the word. However, over time, these shifts will cause evolutionary change as the population spatial patterns are disrupted.
Unfortunately for many animals and plants, humans have so sliced up the land that mobility is limited (for others, it is greatly expanded, but that is chiefly for things we don’t want to expand, like fire ants or zebra mussels and numerous other invasive species). For these organisms, they have the options of adapt or die. Obviously, this isn’t a conscious choice they make, but conscious or not, these are the options available to them. For these, if we want to know how they will respond to climate change, we need to know their evolutionary potential, what is their ability to adapt and how fast can they adapt. This will depend (assuming similar selective pressures based on climate change) in large part on the genetic variation within the species, their generation rate (the shorter the time between birth and reproduction, the faster evolution can function), and population size. As a result, their conservation depends on our understanding of their evolutionary potential.
Not a good candidate for evolutionary adaptation to climate change. http://inhabitat.com/evolution-cant-keep-pace-with-climate-change/
A critical component here is time. It can be hard to tell whether or not evolution is occurring or more simple phenotypic plasticity (the ability of an organism to respond to changes via changes in gene expression rather than actual genetic change) without substantial genetic study. If an organism has a high phenotypic plasticity, they will be able to adapt quickly. However, if it requires real evolution in the strict sense, that takes time, meaning they will be less likely to adapt in time to prevent extinction. Again, this is a question that can only be answered by proper application of evolutionary principles.
These are just a few examples of how scientists are using evolutionary theory to save lives by improving medical treatments and protect our food supply and environment. I did not provide much in the way of specific examples of these processes, as that would expand this essay far beyond comfortable reading times. However, the links throughout the essay will lead to you several specific examples. Some people may argue that these examples are all microevolution and adaptation, not true macroevolution. In truth, there is no significant difference between the two. Microevolution and adaptation are simply subsets of a larger concept, processes that cause macroevolution over longer time frames.
More importantly, the argument doesn’t matter anyway. It is not important that doctors and farmers know the evolutionary history of earth. The application of evolutionary theory is the same whether one is looking at the present or eons in the past. One can incorporate evolutionary thinking and utilize the theory without ever having to deal with things that are millions of years old, but only if one understands the theory in the first place. Evolutionary theory touches on so many aspects of our lives that if we want to be able to make good decisions on many of the most pressing issues of our time, we need to have some basic understanding of how evolution works. If we do not teach evolutionary theory to our kids, we are crippling our future doctors, farmers, conservationists, fish and game managers, coastal development planners, lawmakers,…
Fossil Friday. Soak up some information
Were you able to guess what the image was? It is a common animal almost everyone has at least a synthetic version of in their home. Yet they make terrible fossils.
Yes, this is a sponge. It is a small one, but typical for a fossil of a sponge. If they preserve well, they look like little balls, or pancakes (the squished ball sponge), or cylinders. All in all, visually very simple.
“Porifera body structures 01” by Philcha – Own work. Licensed under CC BY-SA 3.0 via Wikimedia Commons – http://commons.wikimedia.org/wiki/File:Porifera_body_structures_01.png#mediaviewer/File:Porifera_body_structures_01.png
Sponges belong to the the group called Porifera, so named because they have a lot of pores through which water flows through. Even though they may superficially look like some colonial organisms, they are true multicellular animals. Sponges have no true organs, or even tissues, but they do have specialized cells to handle various functions, such as reproduction, producing the materials needed for growing, and cells that act as a primitive immune system. The body organization is about as simple as you can get. Water flows through the pores into a central chamber, which has an opening at the top for water to flow out. As the water flows through, the sponge cells filter out nutrients, generally consisting of bacteria, plankton, and the occasional small animal, and excrete waste products.
Traditionally, sponges have been considered the most primitive of metozoans, the group comprising multicellular animals. There has been some research indicating that comb jellies are more primitive, but that work has been disputed by new research.
“92 ANM Glass sponge 2” by Randolph Femmer – National Biological Information Infrastructure 6259. Licensed under Public Domain via Wikimedia Commons – http://commons.wikimedia.org/wiki/File:92_ANM_Glass_sponge_2.jpg#mediaviewer/File:92_ANM_Glass_sponge_2.jpg
Sponges are normally divided into three different types. Demospongia is the largest of the three (although this may be because it includes sponges that may not be as closely related as typically thought). They form a “skeleton” out of small, pointed cylinders called spicules, made from either silica or a protein called “spongin”. The glass sponges, or Hexactinellid sponges, also make silica spicules, but these spicules are noticeably different from the demosponges. The third group of sponges make their spicules out of calcium carbonate and so are known as calcareous sponges. For more information on sponges, the wikipedia article is surprisingly good, so I will not belabor the points here.
It is these spicules that make fossils of sponges so problematic. When the sponges die, the soft tissues decay away and the spicules become little more than sand. Finding an intact fossil sponge is relatively rare. Thus, the vast majority of research done on fossil sponges is done through painstaking microscopic work on the spicules.
The fossil record of sponges goes back possibly as far back as 750 million years, although they do not become common until about 540 million years in the Cambrian and have been found all over the world. In Arkansas, the record of sponges is rather poor, mostly because very few people have worked on them and no one is looking for them. There are currently only four named fossil sponges and a few indeterminate sponge spicules.
Boring sponge, Cliona swpp. Photograph Forest Rohwer, San Diego State University. http://www.sms.si.edu/irlspec/Cliona_spp.htm
Demospongia is represented by three species. Haplistion sphaericum and Virgaspongia ichnata are demosponges found in the Bloyd Formation in Washington County. The Bloyd Formation is a Pennsylvanian aged formation found in the Ozark Mountains, a fossiliferous unit consisting of silty shale to massive sandstones, representing a relatively shallow marine environment with fluctuating sediment influx. Cliona, is a Late Cretaceous demosponge found in the Arkadelphia marl Formation in Hempstead County. Cliona is known as a boring sponge, not because it is uninteresting, but because it has a habit of boring holes into shells. This formation is mostly a limey mud best known for its mosasaurs, but also has a diverse assemblage of marine fossils. Stioderma hadra is the long glass sponge known from Arkansas and was also found in the Bloyd Formation.
The First Mystery Monday of 2015
Time for the first mystery fossil for the year. Can you figure out what this humble little sphere is? Specimens of these little fellows have been around for over 500 million years, but I bet you have a reasonable facsimile in your house.
Leave your thoughts in the comments section and come back Friday for the answer.
Dinosaurs by Aliki, Part 2
Last post, I reviewed two books by Aliki Brandenberg, called Fossils Tell of Long Ago and Dinosaur Bones. They mostly got good ratings, despite being 25 or more years old. They are still better than many books that are much more current. This time I will look at two more, Digging Up Dinosaurs and Dinosaurs are Different. These books are even older, but Digging Up Dinosaurs continues to be a favorite book by many, despite its age.
Digging Up Dinosaurs
by Aliki Brandenberg
Publication Date: 1981, 1988
Harper Collins Publishers. ISBN: 0-690-04714-2, 0-06-445078-3 (pbk)
AR Book Level: 3.6
This book covers much the same ground as the first two books, but focuses on the path from living dinosaur to being on display in a museum. Appropriately then, the book starts with her in a museum looking at Apatosaurus, or as she states, once known as Brontosaurus. She also looks at a few other dinosaur skeletons, which are mostly drawn reasonably well, although the Tyrannosaurus rex is in the old and inaccurate Godzilla pose.
Drawn by Darren Naish. Available through him on a T-shirt.
The next page briefly discusses dinosaurs in general. Sadly, this page does not hold up well, despite its generality. The dinosaurs are drawn in old, toy-like fashion that would not have been considered accurate in the 1980s, much less now. This book suffers the most from inaccurate and simplistic drawings. The dinosaurs are drawn with “bunny hands”, in upright poses dragging their tails, and featherless, along with other problems, such as the giant sauropods having their noses on top of their heads. Even during the 1980s, the drawings were somewhat anachronistic. Now, they are woefully out of date. For a good description of the changes that have gone on in dinosaur art based on new science, check out this article by Darren Naish.
Other problems this page has is the description of some dinosaurs being as small as birds. Yes, because birds are dinosaurs. That was known then, but was not as widely accepted as it is now. So the statement “there hasn’t been a dinosaur around for 65 million years” is not accurate. We also have a much better, if not completely understood, idea of why they became extinct.
The next part of the book talks about people finding fossils and a bit of early dinosaur paleontology history. There is a good, dynamic description of what fossils are and how they form. One complaint here is that paleontology is limited to the study of the fossils, a problem that runs throughout the book. The book does discuss many different jobs needed to collect fossils, but they all focus on collecting, preparing, and studying the fossils. If that were true, we would know very little indeed. Fortunately, study by people throughout the sciences, especially the study of modern organisms, help inform us about dinosaurs and tell us much more than the bones ever could by themselves.
The book continues with a description of finding fossils, what it takes to collect them, and get them back to the museum. Most fossils don’t actually go to museums, but the emphasis here is on the fossils that people see in museums, so we can skip over that detail. These pages illustrate a lot of the back-breaking work involved in digging up a dinosaur. The book also illustrates some of the problems that must be carefully considered during the process, such as getting fragile fossils out of the rock and shipping them to the museum without further damage, and some of the ways those problems are solved.
Once at the museum, there is much work studying the fossils to figure out what they are, which is displayed mostly by scientists looking at a fossil and proclaiming what it is. Sadly, that is exactly what a lot of people think, ignoring the hard work and real science that goes on before any proclamations are made and they are rarely made so definitively as presented. To be fair, the text explains more of the process and makes it much less like arrogant scientists making guesses. The illustrations do not do the words justice.
Photo by Kyle Davies. Baby Apatosaurus bone cast made at the Sam Noble Museum. http://samnoblemuseum.tumblr.com/post/45998762660/how-to-build-a-baby-apatosaurus
The book ends with noting that molds are made from the bones from the better specimens, so that copies can be made. These fiberglass (or plastic) copies are what is seen on display in most museums, but they look just like the original. This is an important point. Many people assume that if it isn’t the real bone, it is “fake”. Unfortunately, they use fake for both a copy of an original and something that is not real, and they usually confuse the two meanings. To be clear, these copies are NOT fake. They are more appropriately termed replicas. They are not the actual bone, but they look just the same. Because this is such a common mistake, it is great to see the actual process described here.
The other thing shown here, which makes this last part the best part of the entire book, is an illustration of a discussion among some scientists in the background. They are talking about new ideas and discoveries and make the important comment that if the ideas are confirmed, they will have to change their model. Changing what we think in the face of new evidence is the essential ingredient in science. This illustration not only shows the benefits of the fiberglass copies, but it shows real science in action.
Dinosaurs Are Different
by Aliki Brandenberg
Publication Date: 1985
Harper Collins Publishers. ISBN: 0-690-04456-9, 0-06-445056-2 (pbk)
AR Book Level: 3.6
Dinosaurs Are Different introduces the diversity of dinosaurs to kids, breaking up a nebulous, homogeneous concept of “dinosaur” into an array of different types. It does a good job of showing different types of dinosaurs. It also nicely shows pterosaurs as being related to, but not actually being dinosaurs. The book, to its credit, gives a clear and succinct of the characteristics that scientists use to categorize the dinosaurs. So at this level, the book succeeds well. There are some problems in the details, though, because the science has moved on.
The biggest problem this book has, as in the previous book, is the illustrations that show the dinosaurs in a woefully antiquated style. The postures retain the slow, ponderous, tail-dragging poses that were popular before the 70s when we started learning more about dinosaurs. John Ostrom‘s work on Deinonychus began the revival of the idea that birds evolved from dinosaurs and, along with it, the view that dinosaurs were not the slow reptiles of yore, but active, dynamic animals. The more active view really became widely accepted when Jurassic Park hit the movie screens (although Jurassic Park committed the faux-paus of bunny hands and fatherless raptors as well). Since then, even more changes have covered more and more dinosaurs in feathers. As a result, the illustrations look painfully anachronistic. On the plus side, she still draws kids talking about related things and they are well worth reading.
The book starts with a brief discussion of observations on the skeletons that the teeth indicated diet, nicely done for little kids. It then talks about differences in hip structure. This is the chief characteristic separating the two main groups of dinosaurs and she does a great job of explaining the hip types and how they are used to categorize the dinosaurs into saurischians (lizard-hipped) and ornithischians (bird-hipped). She talks about how both dinosaur groups, along with crocodilians, are part of the group called archosaurs, the “ruling reptiles”. So far, so good. I like this discussion because it shows some of the steps scientists really use to figure out relationships in fossils.
But then some problems arise. Thecodonts are described as the ancestors of both groups of dinosaurs, crocodilians and pterosaurs. In the illustration (and text), she properly indicates that pterosaurs are not dinosaurs like they are often shown. However, she makes it appear that the different groups of dinosaurs are no more closely related to each other than they are to pterosaurs and crocodilians. We now know that “thecodonts” did not constitute a real group, meaning that it contained many animals that were not really related to each other and so it is no longer recognized; it holds no place in modern discussions. All archosaurs arose from a small group within what was traditionally called thecodonts and moreover, all share a common ancestor. From that ancestor, the crocodilians split off, then the pterosaurs, leaving the dinosaurs, which only then split into the two groups.
Egg-laying mammals
There is a page in here that hits a particular sore point with me. It is a discussion between a boy and a girl talking about what dinosaurs are. They talk about dinosaurs being reptiles and then lists several characteristics reptiles have. This is a problem because not all reptiles have these characteristics and because scientifically, animals are generally not defined by superficial characteristics like this. If at all possible, organisms are classified according to their relationships as far as we know them. A platypus lays eggs, but that does not make it a reptile. Many lizards bear live young (there is even a frog that does this), but they are still reptiles. Nevertheless, it continues to be a major challenge getting people to understand this, that organisms can not be properly classified according to what they look like.
The second half of the discussion is much better as it moves into how reptiles are broadly categorized by the type of skull they have. This is a sophisticated point for a book geared to kids and she handles it well, considering her target audience. Sadly, she makes a blunder. She calls synapsids reptiles. When the book was published, it was still common (and sadly, is still such in some circles) to call synapsids “mammal-like reptiles.” There is only one small problem. They weren’t reptiles. Amniotes, animals that lay eggs capable of surviving on land, are split into two main groups: the synapsids and the reptiles (often called Sauropsida because of all the baggage that comes with the term reptile). You may guess by that split that mammals are synapsids and you would be right. Now at the earliest stages, would you have been able to tell them apart? Not really. They both would have looked much like reptiles. But there were important changes that sent them careening off onto very different evolutionary paths.
Moving on, we get to really good parts of the book. The predentary, a bone at the front of the lower jaw, as a characteristic of ornithischians and its relationship with herbivory is well discussed. As the book goes into the saurischians, the differences between the two main groups, the sauropods and theropods are shown well.
Unfortunately, time once again rears its ugly head as progressed marched on. The simplistic definition of coelurosaurs and carnosaurs as little theropods and big theropods, respectively, is completely wrong today. We now know that theropods changed sizes radically several times. It is no longer possible to split them up by size anymore that makes any evolutionary sense. It is also no longer true that all theropods ate meat as we now know some that were herbivores, most notably the therizinosaurs, which admittedly, were not really known when the book was written. It however, can be said that MOST theropods were carnivores.
Giant coelurosaurs. Artist unknown, if you do, please contact me.
The relationships within the Ornithischia are now very different than what is described in this book. The book describes four major groups: ornithopods, ceratopsians, stegosaurs, and ankylosaurs. There is a good discussion of hadrosaurs as ornithopods. However, unlike the book states, psittacosaurs and pachycephalosaurs are not ornithopods. Psittacosaurs are considered to be one of the earliest ceratopsians, the lineage that includes Triceratops. Pachycephalosaurs, the bone-headed dinosaurs, are also placed in a group with ceratopsians called marginocephalians. Ornithopods are are completely separate group of ornithischians. Stegosaurs and ankylosaurs are also now thought to be more closely related to each other than to the rest of the Ornithischians. New fossils have also told us how the plates on Stegosaurus were positioned (up in two rows). We also have a much better understanding for why they had them, which applies to all the rest of the groups as well. The numerous and fancy head ornaments, plates, and spikes were most likely primarily as sexual displays. They may have had secondary uses in defense, offense, or cooling, but they were primarily display structures.
The last page is a list of the different types of dinosaurs and their diet. Time and new discoveries has made this list far more diverse than Aliki could have imagined 30 years ago.
In conclusion, would I recommend the books? Yes, despite their flaws. They cover several concepts well. Digging Up Dinosaurs holds up a bit better, but both suffer from outmoded drawings and advances in our understandings of dinosaur relationships. But these flaws, if recognized, can be usefully used as valuable teaching moments to talk about how science is a dynamic field, how what we know is constantly being reevaluated based on new evidence, helping us to test and refine our ideas. Comparing the book to a more modern book would make an interesting and informative educational experience.
Happy New Year!
Happy New Year and welcome to 2015! I know it is after January 1st, but this is the first workday of the new year for many people. It is the time that we are putting aside holiday treats and adding to our productivity rather than our waistlines. Paleoaerie is returning after the holidays to supply more dinosaur and evolution fun facts and educational materials.
This is just a short post to get things rolling for the new year. The next post later this week will have the second half of the Aliki books. Next week will kick off another round of Mystery Monday fossils. After that, there will be many a topic to discuss. If you have anything in particular you would like to have discussed or would like to contribute as a post, please feel free to let me know. let’s make this year one of increased collaboration and sharing, exponentially increasing the fun and learning.
paleoaerie 
