http://phys.org/news/2015-01-perspective-snake-evolution.html
Nature Journal
January 5, 2015
Jason Head's and P. David Polly's recent study of the snake skeleton has revealed new information on how they may have evolved. We previously believed that snakes evolved from their lizard ancestors to a more simplified form. Now, it is becoming considered that other animals and lizards gained a more complex skeleton instead. This is due to the finding of distinctions among vertebral bones in the snake's skeleton identical to those of four-legged lizards. This ties to the function of Hox genes in the snakes. Hox genes regulate growth of the neck, trunk, lumbar, sacral and tail regions of limbed animals. Before, it was thought that the function of these genes was disrupted in snakes, resulting in no limbs and a simplified skeleton. It was then thought that the absence of limbs resulted in the loss of the distinction between the shape of the vertebrae in their backbones and neck, trunk, and lumbar regions. However, Head's and Polly's study revealed distinctions in the snake skeleton's vertebrae similar to the ones in lizards and mice. If the Hox genes were really disrupted in snakes, then their vertebrae would all be similar shapes and sizes, but they were not. Further investigation showed that the regions with Hox genes in snakes matched those in lizards, revealing that these genes in snakes simply control more simple and gradient changes in shape instead of the complex patterned ones in mice and lizard skeletons. It isn't that snakes simplified, it's that mammals and birds have gained more complex skeletal and Hox regions. This completely contrasts what was originally believed about snake evolution.
This new discovery is very important to science and directly relates to what we have been learning in the evolution unit. Scientists now have a better understanding of how reptiles may have evolved, which could lead to further investigation and discovery of the evolution of different animals and/or species. Although their evolution isn't what we had expected and originally predicted, snakes did change over the course of a long time from their lizard ancestors. This evolution was likely due to the need to survive in a different environment from the one lizards lived in. This new body shape for the snakes could help them catch food, escape predators, and blend in to different surroundings, and has evidently been working for them, as they have thrived in many areas. This also relates to how the study of bones and fossils can lead to great evolutionary discoveries, as we have learned in class. Overall, it is a great new point of view that helps us as students as well as other scientists learn more about evolution.
Wednesday, January 7, 2015
Cancer-Preventing GM Potato Approved
Genetically Modified Potato Approved Anna Rychlik P6
Link: http://www.nytimes.com/2014/11/08/business/genetically-modified-potato-from-simplot-approved-by-usda.html?_r=0
Date: November 7, 2014
Author: Andrew Pollack
This article is explaining that a new variety of genetically modified potato has been approved by the U.S.D.A. This potato has been altered so that when it is fried, poteientally dangerous amounts of a (cancer causing) chemical called acrylamide, are not created by the potato. In addition, this new type of potato can also resist bruising. Later in the article, it is questioned wether or not these new potatoes will actually sell. It is argued that in the past, GM potatoes have caused great contraversy with consumers in the US, but these GM potatoes could potentially flourish because of the fact that they are genetically modified to not only help the growers, but the people eating them.
This relates to what we have been learning in class in the GMO lab we did and the report we wrote up after. This also relates directly to the video we watched about how GM potatoes were not recived well by the general public.
Monday, January 5, 2015
A Second Miller-Urry Experiment
Article: The Origins of Life, by Helen Fields. Published by Smithsonian Magazine
http://www.smithsonianmag.com/science-nature/the-origins-of-life-60437133/?all
The Miller-Urry experiment was widely hailed as a milestone in origin of life research, for it showed a verifiable way for the generation of amino acids and other required biological building blocks to be generated by natural phenomena. However, the two assumed energy sources, ultraviolet light and lightning, only act on the surface of the planet, which, at the time life evolved, was most likely not a hospitable place. Due to the lack of free oxygen, there was no ozone layer to prevent the damaging ultraviolet rays from making it to the surface and smashing up the slowly accumulating (or so is hypothesized) fragile complex organic molecules. However, this article presents an alternative way: the building blocks of life could have been formed at the high heats and pressures around geothermal vents, deep under the ocean, protected from ultraviolet radiation (and the asteroids of the LHB) by kilometers of water. With a much less volatile environment, the complex molecules would have had a chance to form protected.
The article also gives insights into how those basic molecules could have bumped into each other enough to form the polymers of life. The prebiotic soup that was the starting point of life could not have been very concentrated, so much so that randomly floating monomers forming polymers has been described as "infinitesimally small." However, if the molecules were sliding along a surface, all of a sudden this becomes a two-dimensional instead of three-dimensional problem, making an interaction much more likely. It would also reduce the amount of space the molecules had to work in from the whole ocean to just the surface itself, reducing the search space. These researchers are investigating to see if certain rocks might have been able to do that with amino acids or other monomers. If so, that's another lot of improbability in the origin of life accounted for.
Yet, like all articles on the origin of life I have seen, it does not address the real issue with the RNA world hypothesis, the one currently accepted by most researchers. Despite there being plausible hypothesis for the generation of basic biological monomers, there remains the problem: How do we get this first replicating molecule? According to this article: http://www.nature.com/nature/journal/v515/n7527/pdf/nature13900.pdf, the best that has been done that had a limited capacity to self-replicate when given the proper starting components (those components is another moderately improbable "if"), is 83 bases in length. It requires 1 ribozyme (enzyme made of RNA) and 1 template strand, which is the same thing as the enzyme. Probability-wise, if there are 8 possible bases (U, A, G, C in both left-handed and right-handed forms http://en.wikipedia.org/wiki/Chirality), and a specific sequence of 83 bases to follow, the number of possible sequences is 8^83, which is approximately 10^75. Taking in mind that we need 2 of these, one as ribozyme and one as template, we need to multiply again for the two sequences: 10^75*10^75=10^150. This is the same as the number of actions the universe could have taken in its entire lifetime, (http://en.wikipedia.org/wiki/Universal_probability_bound) of 10^150 possible actions. In other words, if the whole universe attempted to find, by random processes, two specific sequences of 83 bases each, it could, if if every possible action it took searched one possible combination. Note that this is, of course, a wild overestimation on the probabilistic resources that could be brought to bear on the problem of the origin of life, and the estimate of 10^150 possible actions assumes a search time of about 1 billion times longer that the age of the universe. That, it seems to me, is the real problem with our current understanding of the origin of life.
http://www.smithsonianmag.com/science-nature/the-origins-of-life-60437133/?all
The Miller-Urry experiment was widely hailed as a milestone in origin of life research, for it showed a verifiable way for the generation of amino acids and other required biological building blocks to be generated by natural phenomena. However, the two assumed energy sources, ultraviolet light and lightning, only act on the surface of the planet, which, at the time life evolved, was most likely not a hospitable place. Due to the lack of free oxygen, there was no ozone layer to prevent the damaging ultraviolet rays from making it to the surface and smashing up the slowly accumulating (or so is hypothesized) fragile complex organic molecules. However, this article presents an alternative way: the building blocks of life could have been formed at the high heats and pressures around geothermal vents, deep under the ocean, protected from ultraviolet radiation (and the asteroids of the LHB) by kilometers of water. With a much less volatile environment, the complex molecules would have had a chance to form protected.
The article also gives insights into how those basic molecules could have bumped into each other enough to form the polymers of life. The prebiotic soup that was the starting point of life could not have been very concentrated, so much so that randomly floating monomers forming polymers has been described as "infinitesimally small." However, if the molecules were sliding along a surface, all of a sudden this becomes a two-dimensional instead of three-dimensional problem, making an interaction much more likely. It would also reduce the amount of space the molecules had to work in from the whole ocean to just the surface itself, reducing the search space. These researchers are investigating to see if certain rocks might have been able to do that with amino acids or other monomers. If so, that's another lot of improbability in the origin of life accounted for.
Yet, like all articles on the origin of life I have seen, it does not address the real issue with the RNA world hypothesis, the one currently accepted by most researchers. Despite there being plausible hypothesis for the generation of basic biological monomers, there remains the problem: How do we get this first replicating molecule? According to this article: http://www.nature.com/nature/journal/v515/n7527/pdf/nature13900.pdf, the best that has been done that had a limited capacity to self-replicate when given the proper starting components (those components is another moderately improbable "if"), is 83 bases in length. It requires 1 ribozyme (enzyme made of RNA) and 1 template strand, which is the same thing as the enzyme. Probability-wise, if there are 8 possible bases (U, A, G, C in both left-handed and right-handed forms http://en.wikipedia.org/wiki/Chirality), and a specific sequence of 83 bases to follow, the number of possible sequences is 8^83, which is approximately 10^75. Taking in mind that we need 2 of these, one as ribozyme and one as template, we need to multiply again for the two sequences: 10^75*10^75=10^150. This is the same as the number of actions the universe could have taken in its entire lifetime, (http://en.wikipedia.org/wiki/Universal_probability_bound) of 10^150 possible actions. In other words, if the whole universe attempted to find, by random processes, two specific sequences of 83 bases each, it could, if if every possible action it took searched one possible combination. Note that this is, of course, a wild overestimation on the probabilistic resources that could be brought to bear on the problem of the origin of life, and the estimate of 10^150 possible actions assumes a search time of about 1 billion times longer that the age of the universe. That, it seems to me, is the real problem with our current understanding of the origin of life.
Thursday, November 6, 2014
Discovery of an Enzyme May Help Create Better Biofuel
Article: http://www.news.wisc.edu/22033
Aug. 15, 2013
This article describes how people thought they understood how plants created lignin, a compound that helps plants have structure. Researchers discovered a gene in plants that helps create an enzyme that is key to lignin synthesis, or putting together lignin compounds. John Ralph, a professor of biochemistry and biological
systems engineering, said "This is the first new gene in the [lignin] pathway that's been discovered in ten years." The enzyme caffeoyl, shikimate, esterase, or CSE that the gene produces is important in the creation of lignin. When scientists grew mutant plants without the gene, the amount of lignin dropped by 36%. If the plant has less lignin, then it would be easier to break down and therefore be a better biofuel. By manipulating this gene, scientists will most likely be able to create a better biofuel than before.
This relates to biology class because it shows how enzymes affect living organisms-- what we studied.
Sunday, November 2, 2014
Energy for Runnning
Author: Owen Barder
Source: Running for Fitness Blog
Date: Dec 2013
This article explains how your body breaks down/burns energy for extended periods of strenuous exercise, like, in the case of the article the running a marathon.
Barder explains how, as we learned in class, our energy comes from three major macromolecules: carbohydrates, lipids, and sometimes proteins. Running, which is an aerobic activity, burns mostly carbohydrates and lipids. Low intensity running begins by burning mostly fat, but as the intensity goes up, so does the amount of carbohydrates burned. These two macromolecules do not store/burn energy in the same way though, which has led runners to develop strategy for storing and relaeasing energy in the most efficient way possible.
Throughout the post, Barder discusses tips and strategies like “carbo-loading" which is where runners eat a lot of carbohydrates the night before a marathon so their stores of carbohydrates. He also explains the importance long, slow training runs which teach the body to rely on lipids for a longer period time of exercise instead of glycogen (a carbohydrate), a more limited source. He also discusses how and when to get energy during long runs in the context of the carbohydrate capacity of the blood. By using Barder's scientific strategies, runners can perform their best.
ribozymes
http://exploringorigins.org/ribozymes.html
This Article is about ribozymes. In class we have been studying enzymes and their application in the human body. Enzymes act as a catalyst. It allows for 2 substances to mix easier without affecting the output materials. There are tons of different types of enzymes and each one breaks down a different substance. The one similarity? They are all proteins. Proteins are building blocks in your body. They are the stuff that does stuff. Not all proteins are enzymes. Some proteins are muscles, or bones, or other organs. For a long time, scientists thought that proteins were the only thing that did applications in your body, but they were debunked by 2 scientists named Sidney Altman and Thomas Cech. These two proposed that ribosomes could break down other materials as well as proteins. These scientists found that some RNA as catalytic properties and can act like an enzyme. These were called Ribozymes.
Ribozymes aren't more powerful or more common than normal enzymes, but it's interesting how a ribosome, which is used to make proteins, actually can do some of the same stuff.
This Article is about ribozymes. In class we have been studying enzymes and their application in the human body. Enzymes act as a catalyst. It allows for 2 substances to mix easier without affecting the output materials. There are tons of different types of enzymes and each one breaks down a different substance. The one similarity? They are all proteins. Proteins are building blocks in your body. They are the stuff that does stuff. Not all proteins are enzymes. Some proteins are muscles, or bones, or other organs. For a long time, scientists thought that proteins were the only thing that did applications in your body, but they were debunked by 2 scientists named Sidney Altman and Thomas Cech. These two proposed that ribosomes could break down other materials as well as proteins. These scientists found that some RNA as catalytic properties and can act like an enzyme. These were called Ribozymes.
Ribozymes aren't more powerful or more common than normal enzymes, but it's interesting how a ribosome, which is used to make proteins, actually can do some of the same stuff.
Saturday, November 1, 2014
Cellular self-destruct has deep roots through evolution
http://www.sciencedaily.com/releases/2014/10/141016192824.htm
Date: October 16th 2014
Source: Molecular Biology and Evolution (Oxford University Press)
This article explains the importance of the the protein caspase-8, a protein responsible for triggering the death of a cell in a process known as apoptosis.
The researchers had taken the protein and triggered it in a variety of animals, the protein had triggered the elaborate death pattern in all of the tests, mammals and non-mammals The protein can be triggered in any animal in the animal kingdom. This shows how the protein functions universally through the evolutionary pathway. It turns out that this protein is important in evolution because it allowed animals to get rid of sick, inefficient or dangerous cells, It also reacts with another protein called FADD. The key protein reaction produced can be observed throughout the animal kingdom too.
This relates to what we learned in class by covering how animal cells evolved to work the way they do, and shows more detail on how animal cells function.
Date: October 16th 2014
Source: Molecular Biology and Evolution (Oxford University Press)
This article explains the importance of the the protein caspase-8, a protein responsible for triggering the death of a cell in a process known as apoptosis.
The researchers had taken the protein and triggered it in a variety of animals, the protein had triggered the elaborate death pattern in all of the tests, mammals and non-mammals The protein can be triggered in any animal in the animal kingdom. This shows how the protein functions universally through the evolutionary pathway. It turns out that this protein is important in evolution because it allowed animals to get rid of sick, inefficient or dangerous cells, It also reacts with another protein called FADD. The key protein reaction produced can be observed throughout the animal kingdom too.
This relates to what we learned in class by covering how animal cells evolved to work the way they do, and shows more detail on how animal cells function.
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