War within a breath

The storms that are continuously brewing in North Africa and the Middle East are unbelievable to me. I simply cannot believe the number of countries that are rebelling against their government. It makes me think back to when I was really into Rage Against the Machine. I would listen to their lyrics that incite rebellion and plant the desire for revolution.

"So make your move and plead the 5th, cuz you can't plead the 1st."

"Americanize, Americanize, few the world through american eyes."

"So called facts are fraud
They want us to allege and pledge
And bow down to their God
Lost the culture, the culture lost
Spun our minds and through time
Ignorance has taken over
Yo, we gotta take the power back!

Bam! Here's the plan
Motherfuck Uncle Sam
Step back, I know who I am
Raise up your ear, I'll drop the style and clear
It's the beats and the lyrics they fear
The rage is relentless
We need a movement with a quickness
You are the witness of change
And to counteract
We gotta take the power back"

YES! Bring on the revolution, grab your gun, close your eyes, and make a fist! Take the power back citizens, revolt against those that oppress you! Take it from their corrupt bloody hands...

Now, I get a different feeling when I see or hear of war. I don't know if I'm just getting older, but the more I read about all the stories poring in from all these places, the more it saddens me. I see neighborhoods that have become war zones. The only thing more broken than the buildings and streets are the families of the martyrs, those loyal to those in power, and the poor innocents caught in between. I hear that in Bahrain the government is taking physicians and other medical personnel captive who treat wounded protesters that come into hospitals. I see the millions of refugees that are leaving their homes fleeing the violence. I see the price of war over and over in the photos from this wounded part of the world.

I want to help these people, but I don't know how. No power will keep them safe, money will not buy them safety. Mothers and Fathers will try to sleep tonight without their children, and get no rest. Children will wonder what to do now that their parents are dead. This is happening now as I type this. The world is much different that my life in the USA. I want to see it. Will it be safe for me?

No more bombs, no more broken promises of change, no more Predator Drones raining hellfire missiles, no more guns, no more violent (guilty or innocent) death. No more broken families, no more starving, no more corrupt leaders stealing the breath of their people only to watch them struggle under the crippling hypoxia…
...just peace
                someday maybe

...Reason #87 why I'm liking religion less and less: It gets people to burn books. Reason #88: It gets people to murder innocent people. Reason #89...

Sad story about the deaths of innocent victims of religious intolerance. Here is a recent NY Times article about more escalating violence.

Mormon Stance of Evolution

     For those who don't know, I was raised LDS (pronounced marmon in missoura). I even went on an LDS mission. I was at one point I was"in full faith and fellowship with (The LDS church), a duly ordained minister of the gospel, and as such has authority to preach the principles of the gospel and to administer the ordinances thereof," according to the white bible (the missionary handbook). When I became interested in evolution, I wondered how scientists could think that all animals descended from others, and an even more unbelievable claim, that mankind descended from other animals.

     It became clear after examining the evidence (and a lot of evidence at that, it took literally years to overcome the falsehoods taught to me in the various church educational systems and church about the origin of species and in particular, humans) that evolution is the best explanation for the array of facts we observe in animals. It accounts for the incredible diversity of life in all of its forms, it accounts for the origin of species, and for the curious facts of biogeography. There are loads of others but, the most life changing for me was much more personal. I gave me insight as to our place in nature. It tells us we are a part of nature; in-fact, that we are nature. We share ancestry will all animals, fungi, and plants (in order of relatedness actually, yet another interesting find from research in evolutionary biology). I'll have to post some posts on evolution in the future.

     The real reason for this post is a particular problem I have with church doctrine. Trying to pin down what counts as doctrine to a mormon is like nailing jello to a tree. Usually the conversations go like this: “Only the prophet delivers church doctrine,” and then I show them something the embarrassing or obviously wrong prophet has said and then, “well, the prophet is just a man, he has opinions too,” but he is speaking as a prophet, officially representing the church, (enter fall back answer)“well, all I know is that the church is true, and if you trust...” blah blah close your minds and open your heart stuff.

     Often I ask mormons what they think about evolution. ALL, and I do mean every, LDS person I remember talking to who didn't attend college say that they don't believe it. Those that have a college education or better, their beliefs become as smoke, both tricky and shifty. Most believe that animals can adapt to their environment but don't accept the idea of speciation, or that new species arise. Some come to accept that animals evolve, but think that humans share no ancestry with animals. On very few occasions, they actually accept the entire theory including the animal origins of humans. Almost all say that “The church has no official stance on evolution,” and I think they are wrong!

     What is the highest form of doctrine in the church? Scripture right? Well, how about modern scripture, as in the Ensign. What if I said the first presidency of the church produced a document signed by each member of the presidency, including the prophet. That's as high as I can think. In 1909 (consequently the 50th anniversary of Charles Darwin's book The Origin of Species, and the 100th anniversary of his birth) the first presidency published an article in the Improvement Era, Nov. 1909, 75–81 titled The Origin of Man by the First Presidency of the Church. It was reprinted as in the Ensign "The Origin of Man", Feb. 2002, 26. It lays out the official church doctrine about the creation of the earth and humans, man's place in nature, and evolution.

“In the early 1900s, questions concerning the Creation of the earth and the theories of evolution became the subject of much public discussion. In the midst of these controversies, the First Presidency issued the following in 1909, which expresses the Church’s doctrinal position on these matters. A reprinting of this important First Presidency statement will be helpful as members of the Church study the Old Testament this year.”

     The prophet and his two councilors wrote, signed as representatives of the church, and published it as an official church publication, how can it not considered church doctrine?! If it isn't, then the words of modern prophets can be meaningless.

      Most of the article is quoting scripture. But it does get to something very interesting:

“It is held by some that Adam was not the first man upon this earth and that the original human being was a development from lower orders of the animal creation. These, however, are the theories of men.” 
 

      Boom. Evolution is among the “theories of men,” which is a particularly potent phrase to mormons, (especially when it is mingled with scripture).

“True it is that the body of man enters upon its career as a tiny germ embryo, which becomes an infant, quickened at a certain stage by the spirit whose tabernacle it is, and the child, after being born, develops into a man. There is nothing in this, however, to indicate that the original man, the first of our race, began life as anything less than a man, or less than the human germ or embryo that becomes a man.”

     There are many other instances where the church published unfavorable things about evolution. Read the older version of the old testament study manual, it has 4 full pages of anti-evolution/creationism drivel. Bruce R. McConkie, a member of the Quorum of the Twelve, in Mormon Doctrine which is a encyclopedic book about various mormon doctrine topics, tries for 10 pages (pp. 247-256) to dismantle the many points of evolution that conflict with LDS doctrine. It culminates in 

 

“There is no harmony between the truths of revealed religion and the theories of organic evolution.”

      BYU, a church owned school, does in fact teach evolution, and I must say quite well. It actually has a very respectable evolutionary biology research program.They were one of the most represented schools at Evolution 2009, the professional evolutionary biology conference I went to. This seems to conflict with many of the members beliefs though.

      This creates problems for people that believe that books and/or people can literally speak for God or literally contain his words. This is yet another example of science moving triumphantly forward discovering the once mysteries of nature, and religion hanging on desperately to archaic dogma. The theories of “God” are becoming more and more kookie, and our understanding is pushing these theories into the camps of mythology, as it should be.

      For a more through discussion see http://en.wikipedia.org/wiki/Mormonism_and_evolution.

Update, Aims and Rational for My Research

Dr. Kondrashov's laboratory is primarily concerned with discovering more about the diversity and evolutionary history of animal life. Documentation of the diversity of life is accomplished by describing the anatomy of animals and the evolutionary history is addressed by performing phylogenetic analyses. These specific aspects are studied in the laboratory by: i) describing newly discovered fossils, which provides dates as to when the animal existed and documents the anatomical characters at that time in history; and ii) inferring the phylogenetic relationships of animals based on their anatomical characteristics. With this knowledge a picture of how animals have changed through time can be pieced together. It shows where and when in history unique animal features evolved. It also allows groups of related animals to be constructed. This organizes the bewildering array of characters found in nature into hierarchical groups.

The focus of this project is to better understand the phylogenetic relationships of animals grouped in the superorder Xenathra. Every species in Xenarthra need not be included in the study. Only animals that represent each of the major evolutionary lineages in this group should be included. Anatomical characters will be used to infer the phylogenetic relationships among Xenathrans. We will be using established cladistic methodology it infer phylogenetic history from the subject animal’s anatomy. These methods have been verified by the long history of used in the field of systematics and phylogenetics.

Specific Aim 1 Monophyletic lineages or clades are the desired outcomes of phylogenetics. They are groupings of animals based solely on their evolutionary relatedness. I wish to determine if i) Xenathra is in fact a clade and ii) if each of the three major clades in Xenathra that are repeatedly found in more recent phylogenetic studies emerge using different anatomical data. Every study by necessity uses an incomplete set of anatomical characters for analysis. The inclusion of all data is impossible. The inclusion of different or additional data often results in different conclusions. Further studies that include different sets of characters allow more and more data to be analyzed. This will decrease assumptions and ensure more correct conclusions.
Specific Aim 2 The addition of taxa may alter the topology of a phylogenetic tree and thereby alter our understanding of phylogenetic relationships. Additional taxa, in particular extinct taxa, make the sample size more representative of what is or was found in nature and thus brings us closer to knowing how changes in animals has happened through time. Current phylogenetic analyses based on nucleic acid and amino acid sequence data are blind to extinct taxa. This is why morphological analyses are vital to understanding the full diversity and evolutionary history of animal life. The addition of novel taxa, including extinct taxa, will be utilized to realize these benefits.

Xenarthra is an ancient lineage of Eutheria or commonly called placental mammals. They are one of the first major clades that evolved in the Mesozoic era, over 100 million years ago. This unique place in placental mammal evolution means their phylogenetic history is vital to the correct interpretation of phylogenetic history of all placental mammals. This is of particular importance humans and Xenathrans are both grouped in Eutheria meaning they are important to our understanding of our own ancestry.

Review of "Girl With a Dragon Tattoo"

This book was originally published under the Swedish title Män Som Hatar Kvinnor which means Men Who Hate Women by Swedish author Stieg Larsson. The Swedish title is quite telling of the repeated subject of violence against women in the book. This was a roller coaster thriller for me. In parts the pace of the book was entirely too slow, with vast amounts of history and detail to wade through before getting to some action. It seemed like every time a new character was introduced there had to be a two page history accompanying even very minor characters. But in other spots I was simply unable to put it down. It's a big story so it takes time to put it together, but when it does, buckle up. Perhaps you should schedule arriving at the middle of this book when you've got some time on your hands, and not during the week of a test (blush).

USA Today reviewed this book as “Mesmerizing...Imagine the movies of Ingmar Bergman crossed with The Silence of the Lambs.” Having never heard of Ingmar Bergman but have read several books by Thomas Harris (Red Dragon, Hannibal Rising), I was a little excited about the possibility of having a character similar to the scariest character in my experience of fiction, the Dr. Hannible “the cannibal” Lecter. Here I was disappointed. The book does have dark parts that are designed to make one cringe in disgust, but the main evil character is nothing compared to Lecter. The author adds statistics about the abuse of women in Sweden on each chapter title page, so perhaps the dark parts are to raise awareness by describing a scenario of abuse so one can experience it vicariously.

The Girl with a Dragon Tattoo is categorized as a crime novel, and honestly it is probably my first. I'm more of a science/spy/monster kinda guy. If you're not into crime like me take heart, the crime stuff just peppers the story. The real draw for me was the interesting Characters. Getting into the mind of a unique troubled young woman called Lisbeth was what made the story have that dark allure that is so inviting. She is a no-nonsense, anti-social, young skinny punk who once commonly victimized but transforms to a person who takes charge and revenge, and no longer allows herself to be a victim.

I would totally recommend this book.

Stop what you're doing and watch this!

I just watched one of the best programs about evolution that I've ever seen! It expresses the majesty and sparks the curiosity I feel when I learn more about how and why animals are the way they are. It inspires the passion that one can feel when one wonders how all animals are connected and shows how and why the answers are so gratifying. It's produced by Sean B. Carroll, one of the best new evolutionary biologists today.
Stop what you're doing and watch.

This is Nova's great site about evolution too.

Kondrashov and Cladistics

            One area of research in Dr. Kondrashov's lab is the phylogenetic reconstruction and the systematics of various animal fauna. Being a paleontologist by training, Dr. Kondrashov is not only interested in the phylogenies of extant or living animals, he is also interested in the phylogenies of extinct animals and uses them to help us understand how the modern animals came to be. One of his recent papers describes a fossil found on an expedition to New Mexico of a Tetraclaenodon. Tetraclaenodon is the most primitive genus of the family Phenacodontidae, and as such it is paramount to the phylogenetic reconstruction of the family. As a Paleontologist, Dr. Kondrashov uses anatomy to infer relationships and to properly classify living and extinct animals (Kondrashov and Lucas, submitted 2010). Much of what I did in this lab rotation was learn anatomy and the methods and rational of morphological based phylogenetic reconstruction.

          Sense the onset of evolutionary theory, specifically the idea that animals are descended from ancestral populations, scientists have been interested in reconstructing the one true evolutionary history of all life. The difficult part is that evolution happened in the past, and as such, what truly happened must be inferred by evidence. Similar to a crime scene investigator, evolutionary biologists use clues or evidence that gives away what actually happened. The techniques for doing this are both interesting and technical.

            The branch of science interested in the diversification of life and the relationships among living things is called Systematics. Methodology in systematics in the 1960's began to change a with the advent of Phylogenetic Systematics in the 1960's by an German entomologist Willi Hennig. Phylogenetic Systematics was later coined Cladistics and is concerned with grouping animals based on their evolutionary history. Cladistics utilizes specific methodology to remove the subjectivity of its predecessors, namely Phenetics, and also to infer the most parsimonious phylogeny. Basically, they create a character matrix which logs character states among different taxa of interest, then use computers to analyze the matrix and group the animals based on the number of similarities shared between taxa. This helps remove investigator bias and makes the methodology more transparent. Dr. Kondrashov used Cladistics in his Tetraclaenodon paper, and will be the method used in my project in his lab.

            The difference between Cladistics and Phenetics is demonstrated by the examination of three groups of animals namely Lepidosaurs (snakes, lizards, etc), Crocodilians, and Birds. Overall, Crocodilians seem to have more in common with Lepidosaurs than Birds. Thus in phenetics, they and other similar organisms are grouped within the Reptiles. Phylogenetic systematists have come to a different conclusion however. Studies employing cladistic analysis on these and other similar animals reveal that Crocodilians and Birds are more closely related than both are to Lepidosaurs (Benton, 1985). This is interesting because Crocodilians and Birds seem like very different animals.

          The rationale behind grouping these seemingly dissimilar groups together is that they share many derived characters or synapomorphies that are thought to have originated in their common ancestor. These animals share an antorbital fenestration, an orbit that is shaped like an inverted triangle, and a muscular gizzard (Hickman et al. 2006). Birds and Crocodilians are thus grouped together under the name Archosauria. Archosaurs share common traits with Lepidosaurs as well, but the common ancestor connecting them with Archosaurs is earlier in history than the Archosaurian common ancestor and as such, Birds and Crocodilians are more closely related to each other than either is related to Lepidosaurs.

           Cladistics is not only reserved for morphological studies. Cladistics is well suited for molecular analysis of nucleic acids or amino acid sequences in order to infer phylogenies. Cladistic analysis will reveal shared derived molecular anomalies and group organisms based on nucleic acid or amino acid sequence similarity. This has become much more prominent with the increase in popularity of molecular biology and computer assisted cladogenesis.

            Dr. Kondrashov had an idea for a project when I arrived. The relationship between major groups of vertebrates are quite resolved with both molecular and morphological data (Janvier 1997), but the relationships of animals within those major groups is sometimes not as resolved. The relationship of Mammals to the other major vertebrate groups (“fishes,” Amphibians, “reptiles” and Birds) is not hotly debated. Even the three subgroups of Mammals namely Monotremes, Marsupials, and Placentals, are highly resolved. However, their have been mixed results in finding the Placental tree root meaning the most basal or ancient group that is the sister taxa to all other Placentals, and also the interrelationships between the various orders within Mammalia.

          I began by reviewing the literature on Placental Mammal phylogenetics. There have been many recent molecular studies on the infraordial relationships of Mammals (Delsuc et al. 2001, Delsuc et al. 2002, Hallström et al. 2007, Wildman et al. 2007, and Murphy et al. 2007) all with differing trees and roots based on the methods and nucleic acid sequences used. There have also been several morphological studies done on the various Placental mammal groups (Fu-Guo et al. 2001, Asher et al. 2003, Asher 2007, and Asher et al. 2008) with similar results. Our project is to study the relationships of the Xenarthrans using morphological data. We will also include several extinct animals that represent a better picture of Xenarthran diversity.

           Asher 2007 provided an online database of the morphological characters used in his study (http://people.pwf.cam.ac.uk/rja58/database/morphsite_bmc07.html). This is extremely helpful because it provides me many meaningful characters (potential synapomorphies) that I could include in my project. I spent much of my time in Dr. Kondrashov's lab learning the anatomy of all of these characters (there are 185 characters with several character states each). I will also have to learn the characters specifically in the animals that I will include in my project.

References

Asher, R.J.; et al. “Relationships of Endemic Aftican Mammals and Their Fossil Relatives Based on Morphologiccal and Molecular Evidence.” Journal of Mammalian Evolution. 10 (2003) 131-142.

Asher, R.J. “A databast of Morphological Characters and a Combined-Data Reanalysis of Placental Mammal Phylogeny. BMC Evolutionary Biology. 7 (2007) 108.

Asher, R.J.; et al. “Morphology, Paleontology, and Placental Mammal Phylogeny.” Systematic Biology. 57 (2008) 2:311-317.

Benton, M.J. “Classification and Phylogeny of the Diapsid Reptiles.” Zoological Journal of the Linnean Society. 84 (1985), 2:97-164.

Delsuc, F.; et al. “The Evolution of Armadillos, Anteaters, and Sloths Depicted by Nuclear and Mitochondraial Phylogenies” Implication For the Status of the Enigmantic Fossil Eurotamandua.” Proceding of the Royal Society of London. 268 (2001) :1605-1615.

Delsuc, F.; et al. “Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling of the Placental Tree Rooting.” Molecular Biology and Evolution. 19 (2002) 10:1656-1671.

Fu-Guo, R.L.; et al. “Molecular and Morphological Supertrees for Eutherian (Placental) Mammals.” Science. 291 (2001) 1786-1789.

Hickman, C.P.; et al. Integrated Principles of Zoology, Thirteenth Edition. New York: McGraw Hill, 2006.

Hallstrom, B.M.; et al. “Phylogenomic Data Analyses Provide Evidence that Zenarthra and Afrotheria Are Sister Groups.” Molecular Biology and Evolution. 24 (2007) 9:2059-2068.

Janvier, Philippe. Vertebrata. Animals with backbones. Version 01 January 1997 . <http://tolweb.org/Vertebrata/14829/1997.01.01> in The Tree of Life Web Project,<http://tolweb.org/>

Kondrashov, P; Lucas, S. “A Nearly Complete Skeleton Of Tetraclaenodon (Mammalia, Phenacodontidae) From the Early Paleocene of New Mexico: Morpho-Functiona Analysis.” Journal of Vertebrate Paleontology. Submitted June 29 2010.

Murphy, W.J.; et al. “Using Genomic Data to UnRavel the Root of the Placental Mammal Phylogeny.” Genome Research. 17 (2007):413- 421.

Wildman, D.E.; et al. “Genomics, biogeography, and the Diversification of Placental Mammals.” Procedings of the National Academies of Sciences of the USA. 104 (2007) 36:14395-14400.