I have yet to read this article, but it looks interesting. I figured I’d offer something up until I can get to it, what with my lack of posting recently.
Filed under: Evidence, Evolution, Misc | Leave a comment »
Only in the light of evolution
Posted on May 10, 2009 by Michael
Now that finals are over, I can devote more time to my dear, neglected blog. I begin with a series:
I am following a specific chapter in Jerry Coyne’s Why Evolution is True.
The fossil record: We should see fossils in a certain order if evolution is correct. They should go from simple to more complex overall, and the fossils we see in the most recent strata should resemble extant life much more than the fossils we see in old strata.
We should also see changes within lineages. We should be able to observe instances of gradual change in species that eventually leads up to either current species or at least to the time of extinction for these species.
Here’s a simple timeline of life’s history. Click it.
What the evidence shows is gradual change. First we find simple bacteria which survived off energy from the Sun, then we see more complicated cells known as eukaryotes arise. (You are a eukaryote.) Next we see a slew of multi-cellular animals arise. They’re still simple, but much more complex than the original bacteria. A few million years later more complicated life arrives. Early (and simple) plants begin to take hold. Soon the fossil record begins to show more plant complexity with low-lying shrub such as ferns, then conifers, then deciduous trees, and finally flowering plants. Gradual changes occur in the oceans and fresh waters which lead to fish and then tetrapods (Tiktaalik comes to mind).
One of my favorite fossils is trilobites. They’re extremely common due to their hard bodies. In fact, even their eyes are well-preserved because of their hard mineral make-up. I personally recall entering touristy-stores seeing countless fossils of these guys in the mid-west to the west (which, unsurprisingly, was once a shallow sea). This image shows the different lineages of this organism. Studies show that the ‘rib’ count has changed over time in each individual species, often without regard to how the other species changed. Going back further, there is less and less divergence in each species. Eventually, as evolution predicts, they all meet at a common ancestor.
So naturally the next step is to find fossils which show more significant changes. Let’s take birds and reptiles. They hold similarities between each other, both morphologically (certain shapes and structures) and phylogenetically (genetic sequence). A good hypothesis is that they came from one common ancestor. If this is true, the links between birds and its ancestors and reptiles and its ancestors should lead to the same point. They do. Dinosaurs are the ancestors of both. The links between birds and dinosaurs are so incredibly well established that I’d prefer to not go over them in detail. But for starters, some dinosaurs sported feathers and claws and had the same proteins for the feather-making process as extant birds. The links between reptiles and dinosaurs is easier just on intuition, so I’ll leave it at that for now.
Other transitional fossils include the already mentioned Tiktaalik. A view of the history of life can be see here. This shows the change in head and neck structure. Recent research on long-ago discovered Tiktaalik fossils has shown the importance in the gradual bone changes in the neck. These changes – a hallmark of evolution – were important to the ability to turn its head. This is a hallmark because natural selection only modifies what already exists. This is precisely what happened.
Going further with this example, evolution makes predictions as to how early fish evolved to survive on land. If there were lobe-finned fish 390 million years ago and obviously terrestrial organisms 360 million years ago (which is what the fossil record shows), then if scientists are to find transitional fossils, they should date in between that time frame. There should be an animal that shows both features of lobe-finned fish and terrestrial animals. Tiktaalik is that animal. It has fins, scales, and gills, but it also has a flat, salamander-like head with nostrils on top of its nose. This is a good indication that it could breathe air. Its eyes were also placed there, indicating that it swam in shallow waters. Furthermore, it was lobe-finned, but shows bones (which eventually evolved into the arm bones you used to get out of bed today) that were able to support its weight to prop itself up. And of course, it dates to 375 million years ago.
Next, evolution says the fossil record should show recent fossils being more closely related to extant species than are early fossils. This is precisely what happens. Sixty million years ago there were no whales. Fossils resembling modern whales only show up 30 million years ago. So, again, evolution makes a predication: if transitional fossils are to be found, they will be within this gap. And so it is.
We begin with Indohyus. It was an artiodactyl. This is important because extant whales have vestigial bones which indicate that they came from this order: scientists expected to find this because, again, evolution predicted it. It should be of no surprise that this fossil dates to about 48 million years ago, right in the predicted gap. From here there is a gradual evolution shown in the fossil record which leads up to modern whales.
Filed under: Evidence, Evolution | Tagged: Eukaryote, Evolution, Fossil record, Fossils, Indohyus, Jerry Coyne, Morphology, natural selection, Neil Shubin, Phylogenetics, tiktaalik, Trilobites, Whales, Why Evolution is True | 1 Comment »
The uncanniness of Darwin
Posted on April 23, 2009 by Michael
Scientists make an otter-like fossil discovery.
They named the creature Puijila darwini (“pew-YEE-lah dar-WIN-eye”). That combines an Inuit word for “young sea mammal,” often a seal, with an homage to Charles Darwin. The famed naturalist had written that a land animal “by occasionally hunting for food in shallow water, then in streams or lakes, might at last be converted into an animal so thoroughly aquatic as to brave the open ocean.”
Filed under: Evidence | Leave a comment »
What science is all about
Posted on April 6, 2009 by Michael
All which is between “~~~” is from Jerry Coyne.
~~~
I have sometimes written that evolutionary biology doesn’t have much practical value in medicine or other areas impinging on humanity’s material well being. Here is one example of what I’ve said. However, my friend and colleague David Hillis at The University of Texas in Austin — who played a big role in trying to make the Texas State Board of Education teach real science – has taken exception to my view. I asked him to let me know how he thought that evolutionary biology had been of use in medicine, and he wrote me an email with his answer, which he’s given me permission to post. He’d wants to emphasize that it’s an off-the-cuff response rather than a comprehensive reply, which of course I appreciate; but I think it’s worth posting:
OK, here are just a few examples from the thousands that are in the literature, off the top of my head:
Using positive selection to identify the pathogenic mechanisms of HIV in humans: PNAS 102:2832-2837 (one of many such studies that are now appearing and are using positive selection in pathogens to identify pathogenic mechanisms).
Using phylogenies and positive selection to predict which currently circulating strains of influenza are most likely to be closely related to future flu epidemics: Science 286: 1921-1925.
Using evolutionary analyses to track epidemics in human populations: many examples that have wider health implications, but our study of transmission in a forensic case was an interesting example with a specific legal application; PNAS 99:14292-14297.
Using evolutionary analyses to identify new disease outbreaks: new examples in every single issue of Emerging Infectious Diseases.
Using phylogenetic analyses to identify whether polio outbreaks are from native circulating viruses or from reverted, escaped vaccines (which tells health workers which vaccines to use in these areas to eradicate disease): see review in Bulletin of the World Health Organization, Vol. 82, No. 1.
Identifying changes in sodium channel genes that are under positive selection for TTX resistance, which has led to understanding the function of human diseases that are caused by the corresponding substitutions in human sodium channel genes: Mol. Biol. Evol. 25(6):1016–1024. (I included this one to show that all of the examples are not from virus work; this is the original evolutionary work from Manda Jost and Harold Zakon, with our collaboration, but there has been follow-up on the understanding of human diseases that are produced from these same mutations, now that they have been replicated by in vitro mutagenesis)
This just scratches the surface. I think there are now more papers that use evolutionary methods and analyses in the human health literature than all other areas of biology combined. I think it is crazy to not acknowledge the numerous and important human health applications of evolutionary theory and methods.
David
Well, this is good enough for me–I gladly retract my earlier opinion that evolutionary biology hasn’t been of much use in medicine. Thanks, David.
~~~
Imagine a creationist making the claim that evolution doesn’t have much practical value in medicine (something with which I am hugely surprised Jerry Coyne ever said) and then retracting it when presented with counter-evidence. It would never happen. Creationism rejects all principles of science.
Filed under: Evidence, Evolution | Tagged: Creationism, David Hillis, Jerry Coyne, Medicine | 7 Comments »
Cancer
Posted on March 25, 2009 by Michael
I’ll post more on this later, but the jist of it is an improved way of treating cancer.
The team’s goal is to successfully treat 10 dogs with NO-Cbl and slingshot the drug into human use as soon as possible. Because of the genetic similarity between dogs and humans, Bauer says his approach should have a much better chance of getting through the FDA’s strict drug approval chain.
Whoa! “Genetic similarity”? Now, let’s back up this gravy train. It’s clear that dogs and humans were magically created at separate times, no lineages attached to their genes. Any similarities are pure coincidence. Afterall, science is conducted through dogmatic declaration, right?
Thank goodness creationism doesn’t drive medicine. We’d still be (uselessly) praying for an end to The Plague.
Filed under: Evidence, Evolution, Science | Tagged: cancer | Leave a comment »
Our morality is rooted in evolution
Posted on February 17, 2009 by Michael
Duh.
MONKEYS and apes have a sense of morality and the rudimentary ability to tell right from wrong, according to new research.
In a series of studies scientists have found that monkeys and apes can make judgments about fairness, offer altruistic help and empathise when a fellow animal is ill or in difficulties. They even appear to have consciences and the ability to remember obligations.
The research implies that morality is not a uniquely human quality and suggests it arose through evolution. That could mean the strength of our consciences is partly determined by our genes.
This isn’t exactly news, though I suppose the studies are recent. As expected, they go to confirm that “evolution could not have evolved” is a patently stupid statement made without basis. It’s a favorite of creationists and is just a variation on the God of the Gaps argument – “It’s soooo complicated! I can’t explain it and I’ve insolated myself from all forms of science because it is SATAN so I don’t know about any evidence, so it couldn’t have evolved! It just couldn’t have! LA LA LA LA!”
Anyway, off the creationists and on the science:
The animals were asked to perform a set of simple tasks and then rewarded with food or affection. The rewards were varied, seemingly at random. De Waal found the animals had an acute sense of fairness and objected strongly when others were rewarded more than themselves for the same task, often sulking and refusing to take part any further.
Another study looked at altruism in chimps – and found they were often willing to help others even when there was no obvious reward. “Chimpanzees spontaneously help both humans and each other in carefully controlled tests,” said de Waal.
Other researchers, said de Waal, have found the same qualities in capuchin monkeys, which also show “spontaneous prosocial tendencies”, meaning they are keen to share food and other gifts with other monkeys, for the pleasure of giving.
“Everything else being equal, they prefer to reward a companion together with themselves rather than just themselves,” he said. “The research suggests that giving is self-rewarding for monkeys.”
Filed under: Creationism, Evidence, Evolution | Tagged: AAAS, American Association for the Advancement of Science, Capuchin monkeys, Chimpanzees, Christopher Boehm, Emory University, Evolution, Frans de Waal, Jane Goodall Research Center, morality, University of Southern California | 1 Comment »
Schinderhannes bartelsi
Posted on February 7, 2009 by Michael
The title just grabs you, doesn’t it? It’s okay if it doesn’t; this organism did enough grabbing in its day anyway.
S. bartelsi was recently discovered in a piece of slate in Germany. The fossil offers some clues as to the origin of the claws of scorpions and horseshoe crabs.
“With a head like the giant Cambrian aquatic predator Anomalocaris and a body like a modern arthropod, the specimen is the only known example of this unusual creature,” said Derek Briggs, director of Yale’s Peabody Museum of Natural History and an author of the paper appearing in the journal Science.
Scientists have puzzled over the origins of the paired grasping appendages found on the heads of scorpions and horseshoe crabs. The researchers suggest that Schinderhannes gives a hint. Their appendages may be an equivalent to those found in the ancient predatory ancestor, Anomalocaris — even though creatures with those head structures were thought to have become extinct by the middle of the Cambrian Period, 100 million years before Schinderhannes lived.
Recognizing the rarity of this find, Briggs references Anomalocaris (also a rare find). This organism was a proto-arthropod, but came some time before S. bartelsi. Its appendages are basically precursors to pedipalps, or the grasping claws present in scorpions and horseshoe crabs. They’ve proved to be quite durable, especially in horseshoe crabs, which have maintained their body ‘plan’ for a few hundred million years. These claws have proved quite useful for the horseshoe crab niche. Scorpions, on the other hand, have varied a bit more, but their claws are still likely homologous to this new fossil and thus also good evidence for the durability of this appendage.
Filed under: Evidence | Tagged: Anomalocaris, Derek Briggs, Eureka, Hunsrück Slate, Schinderhannes bartelsi | Leave a comment »
Great fossil find
Posted on February 5, 2009 by Michael
Maiacetus inuus is a a four-legged creature ancestral to modern whales that was recently discovered. Two adult fossils were found in in Pakistan dating close to 50 million years old. One of these fossils are carrying a fetus. The interesting thing is that the fetus was faced head first. This likely means it was born on land, not water – it does an oxygen breathing animal no good to be born head first in water if it needs to get to some air quickly. Modern whales are borned tail first. This conveniently prevents drowning before they are fully born.
This ancestral whale was far smaller than its modern day lineage. It weighed roughly 600-850 lbs and came in near 9 feet long. This makes sense if the animal was to give birth on land (dragging one’s self is more consistent with laying eggs).
Here’s kind of a crappy idea of what it looked like.
Filed under: Evidence, Evolution | Tagged: B. Holly Smith, Eocene, Habib Rahi Formation, Iyad S. Zalmout, Maiacetus inuus, Mineralogie und Paläontologie, Munir ul-Haq, Museum of Anthropology, Museum of Paleontology, Philip D. Gingerich, Protocetidae, Steinmann-Institut für Geologie, Universität Bonn, University of Michigan, Wighart von Koenigswald, William J. Sanders | Leave a comment »
Ancestral environments and reverse evolution
Posted on January 14, 2009 by Michael
There’s been a long debate regarding whether evolution can be reversed or not. The general trend has been that it can not. The idea goes that once one evolutionary pathway has been crossed, it cannot be retraced back to its origins. It turns out that is not entirely true.
Says [researcher] Henrique, ‘In 2001 we showed that evolution is reversible in as far as phenotypes are concerned, but even then, only to a point. Indeed, not all the characteristics evolved back to the ancestral state. Furthermore, some characteristics reverse-evolved rapidly, while others took longer. Reverse evolution seems to stop when the populations of flies achieve adaptation to the ancestral environment, which may not coincide with the ancestral state.
What the researchers did was subject fruit flies to various selection pressure for multiple decades, i.e., they changed their environment over and over. The ‘end’ result was fruit flies that were markedly different in their traits as compared to the original specimens. That’s evolution. Children should understand that. What happened next was the researchers mimicked the original environment of the fruit flies from decades gone by. In response, the fruit flies adapted to those environments, possessing many of the same allele frequencies they originally had. What I find particularly interesting is that they did not evolve exactly the same, but they still evolved in a way that was similar to the original phenotypes. This helps to explain why sharks and horseshoe crabs remain so similar for so long: the gene pool of the population centers around certain allele frequencies because, well, they work. Change may happen – in fact, it certainly does – but ancestral pheno- and genotypes can evolve to such similar future counterparts as to make little difference in show, even though we know there to actually be differences, at least in contigency. It’s a bit like how two people of very different backgrounds and even different alleles can come to have the similar tones to their skin. Their evolutionary contigency, or histories, are different, but the result is virtually the same.
Another point of note here is that evolution can produce similar things, but it will almost never produce the exact same thing. The history of life, if rerun, would be much, much different in all likelihood. When exolife is discovered, we’ll have indirect confirmation of this. Until then, it should be important for people to realize that nothing in biology is inevitable – including humans.
Filed under: Evidence, Evolution | Tagged: Ana Godinho, Drosophila melanogaster, Evolution, fruit flies, Fundação para a Ciência e a Tecnologia, Henrique Teotónio, Historical contigency, Instituto Gulbenkian de Ciência, natural selection, Nature Genetics | 1 Comment »
Examples of evolution
Posted on December 31, 2008 by Michael
Here are some basic examples of evolution for those zealots who still reject good science in favor of their unfounded belief in magic.
Filed under: Evidence, Evolution | Tagged: Evidence for evolution, Nature | Leave a comment »
For the Sake of Science 
