In a recent article that has been making its rounds in layman news media, Duesberg et al. (2011) have been proposing that carcinogenesis should be considered speciation. In other words, this means that cancers should be considered new species and that the formation of cancers are, in fact, the creation of new species. This paper is both intriguing and shameful at the same time.
Showing posts with label Random thought. Show all posts
Showing posts with label Random thought. Show all posts
Friday, July 29, 2011
Tuesday, June 7, 2011
Random Thought: Genetics, Evolution, & Eugenics
A recent slew of articles in Science caught my attention. All the papers highlight the effect of epistatic interactions between beneficial mutations can cause a decline in the rate of increase of fitness of the population1,2,3.
A little background first. Evolution is the process by which a population changes in order to adapt to some selective pressure. This usually occurs by the weeding out of individuals who are not as fit as the others. As this occurs the fitness of the population as a whole increases.
In the lab we can study evolution in bacteria. We expose bacteria to a selective pressure and see how they adapt and evolve. With gene sequences we can tell exactly which genes have been altered/selected. The researchers of these papers did exactly this. In the one paper, researchers took, the bacteria and exposed it to low glucose (main food source) environment and looked at the adaptations that resulted2. The saw that there were five mutations that were being incorporated into the bacteria. They showed that the decreases in the increases in the fitness could be attributed to negative epistatic (gene-gene interactions) effects between the beneficial. While I did read the paper I didn't really understand, it seems they did some math magic and some other stuff (not an evolutionary biologist, didn't really get everything they were talking about).
Anyways, this got me thinking about the current state of human evolution. In my opinion, humans are currently in a state of evolutionary limbo. Our technology, medicine (courtesy of our intellect) have overcome any environmental stimulus in place of any biological adaptations.People of all shapes, sizes, intellects, colours, dispositions, et cetera are breeding without regard to the increasing fitness of the human population (some breed merely for the concept of 'love'). There could, of course, be selective pressures that I am not taking into account (irony will probably have radio waves or some such man-made thing become our next selective pressure). Some have presented the solution to this problem: artificial selection.
Eugenics is process by which humans select traits that they wish future populations to have and breed accordingly. Eugenics also includes the selective breeding out of certain traits/diseases. Using this, we could theoretically, artificially evolve humanity. This is an impractical method though, for all of humanity would have to abide by the eugenics program (or at least one large enough to branch off into its own species). I'm of two minds on this topic.
On one hand, I wouldn't mind humanity evolving into a bunch of beautiful genius olympic-level athletes. By doing this we could accelerate our technological advancements as well as increase our physical preparedness for disaster. One of my fears is that our brains will become a limiting factor in our technological development. What happens when to advance the current state of science we have to study for 40 or 50 years just to get caught up. What happens when the 'basics' are beyond the capacity of the human brain. If we do not either become more intelligent and have higher brain capacity, eventually our technological development may not grow either. We could also rid ourselves of a number of genetic diseases, securing the medical future of our race.
On the other hand, I fear the repercussions. Evolution itself requires that there be variability in a population. Eugenics, is in essence a program in which we decrease the variability of our population. We remove those traits that we dislike or find unattractive and we keep only those that we like. Should we take this too far, we may face the same problems that our monoculture crops currently face. If a disease or other selective pressure comes in the future and we've removed so much variability in our species that no one individual has an immunity, we will have caused our own extinction. Furthermore, I don't believe we have enough knowledge of our bodies that we can make educated assumptions about what traits are truly beneficial. On its face, sickle cell anemia is a very detrimental disease, whereby red blood cells are deformed. This causes poor oxygen transport, which leads to a wide variety of symptoms. However, it does confer upon the individual an increased immunity to malaria. What if, in some future we discover that a gene that increases the risk of leukemia actually grants protection against HIV (or some other disease), but we've eliminated it from our population. We'd have lost a valuable, yet seemingly negative trait.
The obvious solution to this would be genetic engineering (another way we could artificially evolve). We keep track of all current traits and their various genetic permutations, and when we find one we want tor bring back, we just engineer it into our populations again. I didn't mention gene therapy/engineering in the same breath as eugenics due to the fact that the technology just isn't on par. We can and are (sperm/ova banks) implementing eugenics, but gene therapy for the purposes of evolution are far beyond our current capabilities. Setting aside the moral dilemmas that eugenics might create, I think we should hold off until we require it, or until we have a near complete understanding of the human body at a molecular level (all pathways mapped).
A little background first. Evolution is the process by which a population changes in order to adapt to some selective pressure. This usually occurs by the weeding out of individuals who are not as fit as the others. As this occurs the fitness of the population as a whole increases.
In the lab we can study evolution in bacteria. We expose bacteria to a selective pressure and see how they adapt and evolve. With gene sequences we can tell exactly which genes have been altered/selected. The researchers of these papers did exactly this. In the one paper, researchers took, the bacteria and exposed it to low glucose (main food source) environment and looked at the adaptations that resulted2. The saw that there were five mutations that were being incorporated into the bacteria. They showed that the decreases in the increases in the fitness could be attributed to negative epistatic (gene-gene interactions) effects between the beneficial. While I did read the paper I didn't really understand, it seems they did some math magic and some other stuff (not an evolutionary biologist, didn't really get everything they were talking about).
Anyways, this got me thinking about the current state of human evolution. In my opinion, humans are currently in a state of evolutionary limbo. Our technology, medicine (courtesy of our intellect) have overcome any environmental stimulus in place of any biological adaptations.People of all shapes, sizes, intellects, colours, dispositions, et cetera are breeding without regard to the increasing fitness of the human population (some breed merely for the concept of 'love'). There could, of course, be selective pressures that I am not taking into account (irony will probably have radio waves or some such man-made thing become our next selective pressure). Some have presented the solution to this problem: artificial selection.
Eugenics is process by which humans select traits that they wish future populations to have and breed accordingly. Eugenics also includes the selective breeding out of certain traits/diseases. Using this, we could theoretically, artificially evolve humanity. This is an impractical method though, for all of humanity would have to abide by the eugenics program (or at least one large enough to branch off into its own species). I'm of two minds on this topic.
On one hand, I wouldn't mind humanity evolving into a bunch of beautiful genius olympic-level athletes. By doing this we could accelerate our technological advancements as well as increase our physical preparedness for disaster. One of my fears is that our brains will become a limiting factor in our technological development. What happens when to advance the current state of science we have to study for 40 or 50 years just to get caught up. What happens when the 'basics' are beyond the capacity of the human brain. If we do not either become more intelligent and have higher brain capacity, eventually our technological development may not grow either. We could also rid ourselves of a number of genetic diseases, securing the medical future of our race.
On the other hand, I fear the repercussions. Evolution itself requires that there be variability in a population. Eugenics, is in essence a program in which we decrease the variability of our population. We remove those traits that we dislike or find unattractive and we keep only those that we like. Should we take this too far, we may face the same problems that our monoculture crops currently face. If a disease or other selective pressure comes in the future and we've removed so much variability in our species that no one individual has an immunity, we will have caused our own extinction. Furthermore, I don't believe we have enough knowledge of our bodies that we can make educated assumptions about what traits are truly beneficial. On its face, sickle cell anemia is a very detrimental disease, whereby red blood cells are deformed. This causes poor oxygen transport, which leads to a wide variety of symptoms. However, it does confer upon the individual an increased immunity to malaria. What if, in some future we discover that a gene that increases the risk of leukemia actually grants protection against HIV (or some other disease), but we've eliminated it from our population. We'd have lost a valuable, yet seemingly negative trait.
The obvious solution to this would be genetic engineering (another way we could artificially evolve). We keep track of all current traits and their various genetic permutations, and when we find one we want tor bring back, we just engineer it into our populations again. I didn't mention gene therapy/engineering in the same breath as eugenics due to the fact that the technology just isn't on par. We can and are (sperm/ova banks) implementing eugenics, but gene therapy for the purposes of evolution are far beyond our current capabilities. Setting aside the moral dilemmas that eugenics might create, I think we should hold off until we require it, or until we have a near complete understanding of the human body at a molecular level (all pathways mapped).
- 1. Kryazhimskiy, S; Draghi, JA; and Plotkin, JB. 2011. In Evolution, the Sum is Less than its Parts. Science. 322:1160-1161
- 2.Chou, HH; Chui, HC; Delaney, NF; Segre, D; and Marx, CJ. 2011. Diminishing Returns Among Beneficial Mutations Decelerates Adaptation. Science. 322:1190-1192
- 3. Khan, AI; Dinh, DM; Schneider, D; Lenski, RE; Cooper, TF. 2011. Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population. Science. 322:1193-1196
Wednesday, April 6, 2011
Random Thought: Statistics in science
I was conversing with a friend of mine about the research project that she was doing and we both came to an agreement. Statistics should not be done by the researcher. There are two main reasons why I think that statistics on a set of data should not be done by the researcher who gathered the data.
Sunday, March 27, 2011
Random thought: Greenhouse effect and solar energy
Comparing the effects of greenhouse effect and solar energy. I was thinking and I came to an odd thought: is it hypocritical/counter-intuitive to use solar energy to combat greenhouse effect.
Primer: The greenhouse effect that some believe is contributing climate change. Light penetrates the glass and heats the interior of the greenhouse (heating the surfaces it touches upon), the heat is then radiated into the air. Rather than letting it pass through the heat is absorbed into the greenhouse gases and then re-radiated outwards, sometimes back into the surface. End result is that the greenhouse is warmer than expected. More of the sun's energy remains upon the Earth rather than being reflected/radiated back into space.
The basis for solar energy is capturing sunlight and converting it into electricity. I know of two methods that they do this. The first is through photovoltaicism (probably spelled that wrong), whereby photons are absorbed by a metal and a current is generated. This is what you see on lawn lights and calculators. The second I know heats up a medium and then converts the heat energy into electricity, in much the same way as conventional electricity generation. This method uses mirrors instead of panels, to focus, rather than collect, the sunlight onto one spot. This spot is usually inhabited by something with a high specific heat capacity. something like molten salts. This way the energy is stored long after the sun has gone down. The heat is then used in some sort of engine to drive a turbine or otherwise generate electricity.
Overly simplistic thought: Greenhouse gases (CO2, CH4, etc.) trap the sun's energy and convert it into heat. Solar power traps the sun's energy and converts it into heat, and then into electricity or directly into electricity. This electricity will likely be used and will, eventually produce heat. So Is using solar power contributing to the problem rather than helping it.
The other green power sources don't run into this problem. Wind, geothermal,and tidal utilize energy already absorbed by the planet. This energy comes from within the earth, from the movement of the earth, from the movement of the moon around the earth, and from the sun (only the energy that would have originally been absorbed by the earth)
So, is solar power adding to the problem rather than solving it?
Edit/Update: Something I forgot to mention. A relatively recent solar power idea that I've read about is to beam energy collected from space down to earth. This would likely be done from a geostationary satellite that gathers the sun's rays and transmits them down to a receiver platform on earth via laser or microwave. This is, in many ways worse than conventional solar power with regards to this article as solar energy that would have normally passed the Earth by would then be transmitted to the planet.
Primer: The greenhouse effect that some believe is contributing climate change. Light penetrates the glass and heats the interior of the greenhouse (heating the surfaces it touches upon), the heat is then radiated into the air. Rather than letting it pass through the heat is absorbed into the greenhouse gases and then re-radiated outwards, sometimes back into the surface. End result is that the greenhouse is warmer than expected. More of the sun's energy remains upon the Earth rather than being reflected/radiated back into space.
The basis for solar energy is capturing sunlight and converting it into electricity. I know of two methods that they do this. The first is through photovoltaicism (probably spelled that wrong), whereby photons are absorbed by a metal and a current is generated. This is what you see on lawn lights and calculators. The second I know heats up a medium and then converts the heat energy into electricity, in much the same way as conventional electricity generation. This method uses mirrors instead of panels, to focus, rather than collect, the sunlight onto one spot. This spot is usually inhabited by something with a high specific heat capacity. something like molten salts. This way the energy is stored long after the sun has gone down. The heat is then used in some sort of engine to drive a turbine or otherwise generate electricity.
Overly simplistic thought: Greenhouse gases (CO2, CH4, etc.) trap the sun's energy and convert it into heat. Solar power traps the sun's energy and converts it into heat, and then into electricity or directly into electricity. This electricity will likely be used and will, eventually produce heat. So Is using solar power contributing to the problem rather than helping it.
The other green power sources don't run into this problem. Wind, geothermal,and tidal utilize energy already absorbed by the planet. This energy comes from within the earth, from the movement of the earth, from the movement of the moon around the earth, and from the sun (only the energy that would have originally been absorbed by the earth)
So, is solar power adding to the problem rather than solving it?
Edit/Update: Something I forgot to mention. A relatively recent solar power idea that I've read about is to beam energy collected from space down to earth. This would likely be done from a geostationary satellite that gathers the sun's rays and transmits them down to a receiver platform on earth via laser or microwave. This is, in many ways worse than conventional solar power with regards to this article as solar energy that would have normally passed the Earth by would then be transmitted to the planet.
Wednesday, March 9, 2011
Evolution of Scientific Theory/Hypothesis: Lamarckian? (Ironic or just amusing?)
Random thought of the day (may or may not become a daily occurrence):
For those of you without a biological background, a primer. Evolution is the study of the development of new species from older species (ex. from ape-like beings to humans). During the development of evolutionary theory there were two competing theories. Both theories involve the transfer of traits from the parent generation to the next. Both theories also state that the accumulation of these changes/traits will eventually lead to the formation of new species. The two theories differed in where the traits came from. The first theory, largely discredited now, states that these new traits arose from an organisms own ability to change itself. A famous example of this would be the giraffe gaining its long neck via stretching. Giraffe-ancestors would not be able to reach foliage in high up places (they were vertically challenged), so they would stretch their necks. This self-inflicted change would be passed on to their offspring, eventually leading to the creation of giraffes. This theory was labelled as Lamarckian evolution. The second theory states that these traits originated among the population already and that environmental pressures would give individuals with certain traits an advantage and these traits would be passed on. While a famous example of this would be moths in Europe during the Industrial Revolution, I prefer to look at the evolution of antibiotic resistance in microbes. Many species of bacteria are susceptible to penicillin. If we take a large population of a species of bacteria and expose them to penicillin, you'll find that some of the bacteria will survive and form new colonies. In this case, the environmental pressure would be the antibiotics and the trait would be the resistance. This theory would be called Darwinian evolution.
Okay primer over, back to my story. I was reading an article about cancer and the article mentioned HeLa cells. I remembered what HeLa cells were, but I was curious as to any new research on them. Ironically, I came across a fairly old article (1991) that proposed that the HeLa cells had evolved into a new microbial species. This then made me think about evolution, and then about science itself when I came to the conclusion that scientific theories evolve in a Lamarkian manner.
Take a fictional scientific theory stating that liquid water makes aliens explode. With each new discovery the theory changes a little bit. At first it becomes liquid water makes aliens explode because they are made of lithium. In the end you have a theory about how alien physiology created a new flexible lithium. Now inspecting how this theory/hypothesis evolved, you see that with new challenges to the theory, the theory adjusts itself, becoming a new, slightly different explanation.
Looking into this further we are aware that sometimes there are competing theories that try to explain the same phenomenon. There are two outcomes to this. One, the theories merge and become a new theory (this would be akin to two species evolving into a single species [I can't think of a biological equivalent]). The second outcome would be that one of the theories is discredited. One could argue that this is textbook natural selection, but I disagree. In this case the theories adjusted themselves in different directions. The key here isn't the survival of the fittest concept but rather the origin of the differences in the theories. The theories may have started the same but they diverged by changing themselves. If the theories didn't start the same it is more akin to two different species competing for the same ecological niche.
Anyways, I'm not expecting, or even wanting the current scientific method to change. I was just amused by how scientific theories evolve in a way that is not parallel to biological evolution.
For those of you without a biological background, a primer. Evolution is the study of the development of new species from older species (ex. from ape-like beings to humans). During the development of evolutionary theory there were two competing theories. Both theories involve the transfer of traits from the parent generation to the next. Both theories also state that the accumulation of these changes/traits will eventually lead to the formation of new species. The two theories differed in where the traits came from. The first theory, largely discredited now, states that these new traits arose from an organisms own ability to change itself. A famous example of this would be the giraffe gaining its long neck via stretching. Giraffe-ancestors would not be able to reach foliage in high up places (they were vertically challenged), so they would stretch their necks. This self-inflicted change would be passed on to their offspring, eventually leading to the creation of giraffes. This theory was labelled as Lamarckian evolution. The second theory states that these traits originated among the population already and that environmental pressures would give individuals with certain traits an advantage and these traits would be passed on. While a famous example of this would be moths in Europe during the Industrial Revolution, I prefer to look at the evolution of antibiotic resistance in microbes. Many species of bacteria are susceptible to penicillin. If we take a large population of a species of bacteria and expose them to penicillin, you'll find that some of the bacteria will survive and form new colonies. In this case, the environmental pressure would be the antibiotics and the trait would be the resistance. This theory would be called Darwinian evolution.
Okay primer over, back to my story. I was reading an article about cancer and the article mentioned HeLa cells. I remembered what HeLa cells were, but I was curious as to any new research on them. Ironically, I came across a fairly old article (1991) that proposed that the HeLa cells had evolved into a new microbial species. This then made me think about evolution, and then about science itself when I came to the conclusion that scientific theories evolve in a Lamarkian manner.
Take a fictional scientific theory stating that liquid water makes aliens explode. With each new discovery the theory changes a little bit. At first it becomes liquid water makes aliens explode because they are made of lithium. In the end you have a theory about how alien physiology created a new flexible lithium. Now inspecting how this theory/hypothesis evolved, you see that with new challenges to the theory, the theory adjusts itself, becoming a new, slightly different explanation.
Looking into this further we are aware that sometimes there are competing theories that try to explain the same phenomenon. There are two outcomes to this. One, the theories merge and become a new theory (this would be akin to two species evolving into a single species [I can't think of a biological equivalent]). The second outcome would be that one of the theories is discredited. One could argue that this is textbook natural selection, but I disagree. In this case the theories adjusted themselves in different directions. The key here isn't the survival of the fittest concept but rather the origin of the differences in the theories. The theories may have started the same but they diverged by changing themselves. If the theories didn't start the same it is more akin to two different species competing for the same ecological niche.
Anyways, I'm not expecting, or even wanting the current scientific method to change. I was just amused by how scientific theories evolve in a way that is not parallel to biological evolution.
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