Like the male members of many species, male beetles fight over female beetles. And, like male deer and antelope, many male beetles sport formidable (for a beetle, anyway) horns, spines, and mandibles, which they use to intimidate (if not outright harm) other males. In the February 6 issue of Science, Rowland and Emlen report that some male beetles take a different tack: instead of fighting over the ladies, they pull an Achilles and "dress" like them.
Rowland and Emlen conducted statistical analyses of body size and horn, mandible, or spine length for several different species of beetles. Most previous analyses had assumed only two main male phenotypes for each species (e.g., big horns and small horns, with hornless males being classified in the "small horns" phenotype). Rowland and Emlen, however, found that several species of beetles actually show facultative male trimorphism--that is, the males actually demonstrate three distinct phenotypes (alpha, beta, and gamma). Alpha males have large bodies and large horns (or mandibles, or spines). Beta males have smaller bodies and smaller horns (mandibles/spines). Gamma males have the smallest bodies and no horns (you get the idea).
The differences in phenotype are facultative because they don't seem to be related specifically to genotype. Instead, the main factor determining whether a male is alpha, beta, or gamma seems to be his body size at maturity--beetles that get lots of food and good living conditions end up as alpha males (big bodies = big horns), while beetles that get less food and are smaller at maturity end up as betas or gammas.
Alpha, beta, and gamma males also seem to employ somewhat different mating strategies. Alpha males have the typical pissing contests for access to mates--for example, some alpha males will guard the burrows where the ladies are living, and fight off all comers. Beta or gamma males, though, are sneakier: they might dig side tunnels into the burrows and cuckold the alphas without ever having to fight them. In some other species (e.g., cuttlefish), "gamma"-type males actually get in with the ladies by "cross-dressing"--for example, some male cuttlefish can change color to mimic female cuttlefish, thus allowing them to get in close enough to mate with the females while the other males are busy showing off.
According to Rowland and Emlen, previous studies (and phenotypic analysis methods) have assumed that the majority of beetles display male dimorphism, rather than trimorphism. They suggest that alternative analyses may be necessary to detect trimorphisms--apparently, some of the traditional analyses did not detect all three male morphs in the beetles they studied.
I suppose the moral of the story is, if you're an alpha male, you might want to check the skirts of the ladies in your harem!
Rowland, J. Mark, and Douglas J. Emlen, 2009. "Two thresholds, three male forms result in facultative male trimorphism in beetles." Science 323: 773-776. doi 10.1126/science.1167345
Wednesday, February 18, 2009
Thursday, February 12, 2009
Darwin in Context
I've been trying to figure out what to write about for my Blog for Darwin entry. I've been reading Origin, but I haven't finished it yet (the last few chapters are not nearly as interesting as the first few). Even so, as I've been reading, I haven't really been struck with any brilliant insights or profound thoughts. One thing that has occurred to me a lot, however, is just how much we've learned since Darwin's time. So, I thought that for my BfD contribution, I would outline what was going on in science while Darwin was doing his thing. I'm hoping it might give some insight into what Darwin did and didn't know, and how his ideas may have been influenced by what was going on around him.
Disclaimer: I am not a historian; the summary below is not intended to be exhaustive. I'm mainly going to focus on the big ideas and events; if you're interested in the gory details, there are a plethora of excellent books out there to satisfy you, I'm sure. Also, please note that I've done my best to verify all of the information below, but I'm not an expert in this stuff. Any errors are solely my responsibility. If you find any, please let me know!
Chemistry
By the 1800s, the study of chemistry was becoming modernized. In the 1600s and 1700s, naturalists began to discover general laws that govern natural processes. Both Boyle's law and Charles's law (on the properties of gases) had been discovered by the early 1800s; a number of gaseous elements and compounds (including oxygen, nitrogen, and nitrous oxide) had been isolated and described.
John Dalton proposed his atomic theory in the early 1800s; although his concept of the atom (i.e., hard, solid, indivisible sphere) has since been replaced, his work on the conservation of mass and the law of definite proportions still underlies much of modern chemistry. His law describing the partial pressures of gases in a mixture is still used today.
The early 1800s also saw the publication of Avogadro's hypothesis (i.e., that equal volumes of gases at the same temperature and pressure contain the same number of molecules).
In the mid 1800s, Lord Kelvin proposed the idea of absolute zero and an absolute temperature scale.
What Darwin didn't know: Most elements were not identified or isolated until after the 1860s. Electrons were not discovered until the late 1800s; the concept of the atom as we know it today (i.e., nucleus of protons and neutrons surrounded by electrons) was not developed until the twentieth century. The nature of chemical bonding was also unknown in Darwin's time, as was the periodic table and the notion of periodic properties.
Physics
Electricity and magnetism were the order of the day in eighteenth and early nineteenth century physics. Franklin "discovered" electricity in the late 1700s; Ohm's law was proposed in the 1820s; Oersted discovered evidence of a magnetic field around a current-carrying wire in 1820; Faraday discovered electromagnetic induction in the 1830s; Joule and Helmholtz proposed the law of conservation of energy in the 1840s.
Newtonian mechanics were well established by the 1800s.
What Darwin didn't know: Radioactivity, quantum physics, relativity, and nuclear physics were decades to centuries away in Darwin's time.
Biology
As Origin does a pretty decent job of summarizing what was going on in evolutionary biology (such as it was) at the time it was written, I won't spend space on that here. In the mid-1800s, the idea that all living things are made of cells was just beginning to take hold; spontaneous generation was beginning to be discredited. Taxonomy was becoming more rigorous. Paleontology was starting to become a well-established field; most naturalists accepted that the majority of the fossils being unearthed around the world represented organisms that no longer exist.
What Darwin didn't know: Genetics and the theories of inheritance had not been discovered when Darwin did his work; a story I've heard (which I have not verified) is that Darwin had Mendel's papers on his desk when he died. Molecular biology, most of microbiology, and, of course, genomics were completely unknown. The germ theory was still a few years off, as was the discovery of many disease-causing microorganisms.
Earth Science
Naturalists were just beginning to come to grips with Earth's immense age during the late 1700s and early 1800s. The best consensus was that Earth was a few hundred million years old at most; these estimates were based on rates of physical processes (such as sedimentation and cooling). Radioactivity was unknown, so both a method for accurate dating and a mechanism for keeping Earth "warm" for long periods of time were lacking.
However, the principle of uniformitarianism was pretty well accepted, having been proposed in the late 1700s. As I mentioned above, paleontology was becoming more rigorous and "scientific," although some of the interpretations of fossils--especially dinosaurs--were rather interesting.
The idea of a global geologic column or time scale was becoming increasingly popular. Indeed, Darwin makes many references to the accepted contemporary time scale (although the time scale of the mid-nineteenth century bears little resemblance to our modern one).
What Darwin didn't know: The theory of plate tectonics was still about a century away. Radiometric dating (and an understanding of how radioactive decay has heated the planet) wouldn't be developed for quite a while, so Earth's true age was unknown to Darwin. In addition, research into the fossils and strata of the planet was generally restricted to Europe and North America, so Darwin's (and everyone else's) ideas about geologic history (and paleontology) were accordingly limited.
Well, there you have it: the two-bit tour of the state of science in the 1860s. I hope this is helpful to someone. If I had time, I'd go into more detail...yet another item to add to my "things to do when I win the lottery" list!
Disclaimer: I am not a historian; the summary below is not intended to be exhaustive. I'm mainly going to focus on the big ideas and events; if you're interested in the gory details, there are a plethora of excellent books out there to satisfy you, I'm sure. Also, please note that I've done my best to verify all of the information below, but I'm not an expert in this stuff. Any errors are solely my responsibility. If you find any, please let me know!
Chemistry
By the 1800s, the study of chemistry was becoming modernized. In the 1600s and 1700s, naturalists began to discover general laws that govern natural processes. Both Boyle's law and Charles's law (on the properties of gases) had been discovered by the early 1800s; a number of gaseous elements and compounds (including oxygen, nitrogen, and nitrous oxide) had been isolated and described.
John Dalton proposed his atomic theory in the early 1800s; although his concept of the atom (i.e., hard, solid, indivisible sphere) has since been replaced, his work on the conservation of mass and the law of definite proportions still underlies much of modern chemistry. His law describing the partial pressures of gases in a mixture is still used today.
The early 1800s also saw the publication of Avogadro's hypothesis (i.e., that equal volumes of gases at the same temperature and pressure contain the same number of molecules).
In the mid 1800s, Lord Kelvin proposed the idea of absolute zero and an absolute temperature scale.
What Darwin didn't know: Most elements were not identified or isolated until after the 1860s. Electrons were not discovered until the late 1800s; the concept of the atom as we know it today (i.e., nucleus of protons and neutrons surrounded by electrons) was not developed until the twentieth century. The nature of chemical bonding was also unknown in Darwin's time, as was the periodic table and the notion of periodic properties.
Physics
Electricity and magnetism were the order of the day in eighteenth and early nineteenth century physics. Franklin "discovered" electricity in the late 1700s; Ohm's law was proposed in the 1820s; Oersted discovered evidence of a magnetic field around a current-carrying wire in 1820; Faraday discovered electromagnetic induction in the 1830s; Joule and Helmholtz proposed the law of conservation of energy in the 1840s.
Newtonian mechanics were well established by the 1800s.
What Darwin didn't know: Radioactivity, quantum physics, relativity, and nuclear physics were decades to centuries away in Darwin's time.
Biology
As Origin does a pretty decent job of summarizing what was going on in evolutionary biology (such as it was) at the time it was written, I won't spend space on that here. In the mid-1800s, the idea that all living things are made of cells was just beginning to take hold; spontaneous generation was beginning to be discredited. Taxonomy was becoming more rigorous. Paleontology was starting to become a well-established field; most naturalists accepted that the majority of the fossils being unearthed around the world represented organisms that no longer exist.
What Darwin didn't know: Genetics and the theories of inheritance had not been discovered when Darwin did his work; a story I've heard (which I have not verified) is that Darwin had Mendel's papers on his desk when he died. Molecular biology, most of microbiology, and, of course, genomics were completely unknown. The germ theory was still a few years off, as was the discovery of many disease-causing microorganisms.
Earth Science
Naturalists were just beginning to come to grips with Earth's immense age during the late 1700s and early 1800s. The best consensus was that Earth was a few hundred million years old at most; these estimates were based on rates of physical processes (such as sedimentation and cooling). Radioactivity was unknown, so both a method for accurate dating and a mechanism for keeping Earth "warm" for long periods of time were lacking.
However, the principle of uniformitarianism was pretty well accepted, having been proposed in the late 1700s. As I mentioned above, paleontology was becoming more rigorous and "scientific," although some of the interpretations of fossils--especially dinosaurs--were rather interesting.
The idea of a global geologic column or time scale was becoming increasingly popular. Indeed, Darwin makes many references to the accepted contemporary time scale (although the time scale of the mid-nineteenth century bears little resemblance to our modern one).
What Darwin didn't know: The theory of plate tectonics was still about a century away. Radiometric dating (and an understanding of how radioactive decay has heated the planet) wouldn't be developed for quite a while, so Earth's true age was unknown to Darwin. In addition, research into the fossils and strata of the planet was generally restricted to Europe and North America, so Darwin's (and everyone else's) ideas about geologic history (and paleontology) were accordingly limited.
Well, there you have it: the two-bit tour of the state of science in the 1860s. I hope this is helpful to someone. If I had time, I'd go into more detail...yet another item to add to my "things to do when I win the lottery" list!
Tuesday, February 10, 2009
If the Egyptians had only known...
According to legend, one of the way the Egyptians were punished in the time of Moses was with a swarm of locusts.
Locusts are insects that look a bit like big grasshoppers. They're a classic example of what's called phenotypic plasticity. An organism's phenotype is basically its observable characteristics--behavior, color, size, etc. (Phenotype is the outward expression of genotype; genotype is the specific group of alleles that an organism has. Most--all? I'm not sure--genes have at least two alleles, or "flavors." The classic example is, of course, Mendel's peas; the gene that controls flower color in pea plants has two alleles, purple and white. A pea plant's flower-color genotype is the particular combination of alleles that it has; its flower-color phenotype is the particular color of flower it produces.)
Organisms such as locusts that demonstrate phenotypic plasticity can undergo significant changes in behavior, appearance, etc due to changes in their surrounding environment. Locusts are a classic case because the change is so dramatic. If you take two locusts and put them in a box, they will pretty much avoid each other--that is, assuming they're demonstrating the "solitarious" phenotype. This is pretty much the default position for locusts; most of the time, they hang out by themselves (not a lot of singles bars in their neighborhoods, I guess).
Now if you had put, say, 20 or 30 solitarious locusts in that box and shut them in for a couple of hours, they would be quite changed when you opened the box. They would be swarming together, and they would have changed in appearance (from kind of boring and green to a rather striking, Steelers-like combination of yellow/tan and black...sorry, couldn't help it). They would be demonstrating the "gregarious" phenotype.
Solitarious (top) and gregarious (bottom) desert locusts. Image from Dr. Tim Matheson, University of Leicester
Locusts in the gregarious phase are the stuff of legend. These are the critters that mow crops down to the roots and blacken the skies. (Presumably, the Egyptians crowded their locusts.)
The cause of the transition from solitarious to gregarious has been known for a while, at least in broad strokes: being in the presence of lots of other locusts makes a locust more gregarious. In a recent article in Science, Anstey et al identify the mechanism that triggers the transformation.
There are two different sets of stimuli that can make a locust more friendly: mechanical and "cephalic." Mechanical stimulation involves being jostled by other locusts; in contrast to most humans, most locusts become more friendly when strangers stroke their legs. Cephalic stimulation involves the sight and smell of other locusts; locusts apparently have really great makeup and cologne. Both types of stimuli cause the locust's central nervous system (CNS) to produce (what else?) serotonin. (Yes, that serotonin.)
Previous researchers established that serotonin levels are higher in locusts undergoing the solitarious-to-gregarious transition. Anstey et al set out to determine the limits of this relationship. They did four main experiments: first, they figured out whether artificial stimulation of the individual sensory pathways could stimulate serotonin production and gregariousness. Then, they tested whether serotonin antagonists (i.e., chemicals that block the action of serotonin) could prevent the onset of gregarious behavior. Third, they determined whether artificially increasing serotonin levels was enough to induce gregariousness. Finally, they determined whether giving the locusts a serotonin precursor (i.e., a chemical that is easily converted to serotonin) increased their sensitivity to environmental stimuli.
In the first experiment, the researchers either stroked the hind legs of solitarious locusts, stimulated the nerve connecting the legs to the CNS directly, or put the locusts in a cage that allowed them to see and smell (but not touch) other locusts. In all cases, the locusts switched from solitarious to gregarious, and serotonin levels increased, suggesting that either type of stimulation is sufficient to induce gregariousness.
Next, they injected some of the locusts with serotonin antagonists (they also, of course, injected others with just saline--this was the control group). After the injections, the treated locusts (the ones that received the antagonist) were significantly less responsive to stimuli than the control locusts; treated locusts did not become gregarious, even when exposed to stimuli that caused the control locusts to boogie down. This relationship showed that inhibiting the action of serotonin prevents the "phase change."
In the third experiment, Anstey et al applied serotonin directly to the locusts' nerves (again, they also used a control group that received just saline). They also injected a third group of locusts with a serotonin agonist (i.e., a chemical that increases the activity of serotonin--the opposite of an antagonist). The treated locusts became much more friendly, but the control locusts remained aloof. In other words, just increasing serotonin levels (without actual stimuli) can make solitarious locusts more gregarious.
In their final experiment, the researchers determined whether increasing the ability of the locusts to produce serotonin would cause them to become more gregarious after only a small amount of stimulation. Typically, a solitarious locust has to hang out with other locusts for a couple of hours before putting on its party shoes. However, when solitarious locusts were injected with a serotonin precursor, 30 minutes of exposure was enough to get them dancing.
There's some hope that these results might lead to new possibilities for locust control. Individually (i.e., in the solitarious phase), locusts aren't too much of a problem--no more so than, say, grasshoppers, really. It's only when they start to swarm that they become economically disastrous. If a way could be found to prevent locusts from become gregarious, even when crowded, then locust swarms could be controlled. (Too late for Rameses, of course.) Such possibilities are still in the future--currently, there is no locust-specific serotonin antagonist that can be applied appropriately--but it does give some hope.
Until then, there is one thing we can definitely conclude: keep the locusts away from the Prozac!
Anstey, Michael L., Stephen M. Rogers, Swidbert R. Ott, Malcolm Burrows, and Stephen J. Simpson, 2009. "Serotonin mediates behavioral gregarization underlying swarm formation in desert locusts." Science 323: 627-630. doi 10.1126/science.1165939
Stevenson, P.A., 2009. "The key to Pandora's box." Science 323: 594-595. doi 10.1126/science.1169280
(Yes, I know this isn't quite 1,000 words. But it's pretty darned close!)
Locusts are insects that look a bit like big grasshoppers. They're a classic example of what's called phenotypic plasticity. An organism's phenotype is basically its observable characteristics--behavior, color, size, etc. (Phenotype is the outward expression of genotype; genotype is the specific group of alleles that an organism has. Most--all? I'm not sure--genes have at least two alleles, or "flavors." The classic example is, of course, Mendel's peas; the gene that controls flower color in pea plants has two alleles, purple and white. A pea plant's flower-color genotype is the particular combination of alleles that it has; its flower-color phenotype is the particular color of flower it produces.)
Organisms such as locusts that demonstrate phenotypic plasticity can undergo significant changes in behavior, appearance, etc due to changes in their surrounding environment. Locusts are a classic case because the change is so dramatic. If you take two locusts and put them in a box, they will pretty much avoid each other--that is, assuming they're demonstrating the "solitarious" phenotype. This is pretty much the default position for locusts; most of the time, they hang out by themselves (not a lot of singles bars in their neighborhoods, I guess).
Now if you had put, say, 20 or 30 solitarious locusts in that box and shut them in for a couple of hours, they would be quite changed when you opened the box. They would be swarming together, and they would have changed in appearance (from kind of boring and green to a rather striking, Steelers-like combination of yellow/tan and black...sorry, couldn't help it). They would be demonstrating the "gregarious" phenotype.
Solitarious (top) and gregarious (bottom) desert locusts. Image from Dr. Tim Matheson, University of Leicester
Locusts in the gregarious phase are the stuff of legend. These are the critters that mow crops down to the roots and blacken the skies. (Presumably, the Egyptians crowded their locusts.)
The cause of the transition from solitarious to gregarious has been known for a while, at least in broad strokes: being in the presence of lots of other locusts makes a locust more gregarious. In a recent article in Science, Anstey et al identify the mechanism that triggers the transformation.
There are two different sets of stimuli that can make a locust more friendly: mechanical and "cephalic." Mechanical stimulation involves being jostled by other locusts; in contrast to most humans, most locusts become more friendly when strangers stroke their legs. Cephalic stimulation involves the sight and smell of other locusts; locusts apparently have really great makeup and cologne. Both types of stimuli cause the locust's central nervous system (CNS) to produce (what else?) serotonin. (Yes, that serotonin.)
Previous researchers established that serotonin levels are higher in locusts undergoing the solitarious-to-gregarious transition. Anstey et al set out to determine the limits of this relationship. They did four main experiments: first, they figured out whether artificial stimulation of the individual sensory pathways could stimulate serotonin production and gregariousness. Then, they tested whether serotonin antagonists (i.e., chemicals that block the action of serotonin) could prevent the onset of gregarious behavior. Third, they determined whether artificially increasing serotonin levels was enough to induce gregariousness. Finally, they determined whether giving the locusts a serotonin precursor (i.e., a chemical that is easily converted to serotonin) increased their sensitivity to environmental stimuli.
In the first experiment, the researchers either stroked the hind legs of solitarious locusts, stimulated the nerve connecting the legs to the CNS directly, or put the locusts in a cage that allowed them to see and smell (but not touch) other locusts. In all cases, the locusts switched from solitarious to gregarious, and serotonin levels increased, suggesting that either type of stimulation is sufficient to induce gregariousness.
Next, they injected some of the locusts with serotonin antagonists (they also, of course, injected others with just saline--this was the control group). After the injections, the treated locusts (the ones that received the antagonist) were significantly less responsive to stimuli than the control locusts; treated locusts did not become gregarious, even when exposed to stimuli that caused the control locusts to boogie down. This relationship showed that inhibiting the action of serotonin prevents the "phase change."
In the third experiment, Anstey et al applied serotonin directly to the locusts' nerves (again, they also used a control group that received just saline). They also injected a third group of locusts with a serotonin agonist (i.e., a chemical that increases the activity of serotonin--the opposite of an antagonist). The treated locusts became much more friendly, but the control locusts remained aloof. In other words, just increasing serotonin levels (without actual stimuli) can make solitarious locusts more gregarious.
In their final experiment, the researchers determined whether increasing the ability of the locusts to produce serotonin would cause them to become more gregarious after only a small amount of stimulation. Typically, a solitarious locust has to hang out with other locusts for a couple of hours before putting on its party shoes. However, when solitarious locusts were injected with a serotonin precursor, 30 minutes of exposure was enough to get them dancing.
There's some hope that these results might lead to new possibilities for locust control. Individually (i.e., in the solitarious phase), locusts aren't too much of a problem--no more so than, say, grasshoppers, really. It's only when they start to swarm that they become economically disastrous. If a way could be found to prevent locusts from become gregarious, even when crowded, then locust swarms could be controlled. (Too late for Rameses, of course.) Such possibilities are still in the future--currently, there is no locust-specific serotonin antagonist that can be applied appropriately--but it does give some hope.
Until then, there is one thing we can definitely conclude: keep the locusts away from the Prozac!
Anstey, Michael L., Stephen M. Rogers, Swidbert R. Ott, Malcolm Burrows, and Stephen J. Simpson, 2009. "Serotonin mediates behavioral gregarization underlying swarm formation in desert locusts." Science 323: 627-630. doi 10.1126/science.1165939
Stevenson, P.A., 2009. "The key to Pandora's box." Science 323: 594-595. doi 10.1126/science.1169280
(Yes, I know this isn't quite 1,000 words. But it's pretty darned close!)
Blogging for Darwin
I joined the Blog for Darwin blog swarm (which means I have to actually finish Origin soon, so I have something to write about). Check it out--it's pretty cool.
I haven't decided yet what to write about; I'm having a hard time coming up with anything super profound. I'll wait and see if any inspiration strikes as I keep reading.
Thanks to Newton's Ocean for the link.
I haven't decided yet what to write about; I'm having a hard time coming up with anything super profound. I'll wait and see if any inspiration strikes as I keep reading.
Thanks to Newton's Ocean for the link.
Thursday, February 5, 2009
From opposite ends of the spectrum
Apparently, the downturn in the economy is causing some of us to become a bit too obsessed with language.
On the other hand, some are just giving up in disgust (or despair?).
And some are robbing stores with bat'leths.
(Thanks to Lou for the first link, erv for the second, and Gwynne for the third.)
On the other hand, some are just giving up in disgust (or despair?).
And some are robbing stores with bat'leths.
(Thanks to Lou for the first link, erv for the second, and Gwynne for the third.)
Friday, January 23, 2009
You would think...
...that in 200 years, the anti-science crowd would have come up with some new objections to evolution. Apparently not: Check out this quote from Origin.
These questions, of course, have many parallels in the standard litany of "problems" with the theory of evolution often spouted by creationists and intelligent design proponents. Is this yet another example of Darwin's apparent prescience? Or is it more accurate to say that Darwin's statements echo those of modern-day denialists because they are building on the "work" of those who came before, who undoubtedly read Darwin? If the latter, it's really a shame they didn't read the whole book. Even if they'd read a few pages further on, they would have come across this beauty:
Perhaps it might be better said that Vox populi, vox veritas "cannot be trusted in science." But the sentiment still holds: Just because most people think it's so, doesn't make it so. The fact that so many people argue that we should teach the Bible as science because "most Americans believe in God" speaks to a fundamental lack of understanding of the way science is done. But I'm not the first to make that statement, nor will I be the last.
Long before the reader has arrived at this part of my work, a crowd of difficulties will have occurred to him...These difficulties and objections may be classed under the following heads:--First, why, if species have descended from other species by fine gradations, do we not everywhere see innumerable transitional forms?...
Secondly, is it possible that an animal having, for instance, the structure and habits of a bat, could have been formed by the modification of some other animal with widely-different habits and structure? Can we believe that natural selection could produce, on the one hand, an organ of trifling importance, such as the tail of a giraffe...and, on the other hand, an organ so wonderful as the eye?
Thirdly, can instincts be acquired and modified through natural selection? What shall we say to the instinct which leads the bee to make cells, and which has practically anticipated the discoveries of profound mathematicians?
These questions, of course, have many parallels in the standard litany of "problems" with the theory of evolution often spouted by creationists and intelligent design proponents. Is this yet another example of Darwin's apparent prescience? Or is it more accurate to say that Darwin's statements echo those of modern-day denialists because they are building on the "work" of those who came before, who undoubtedly read Darwin? If the latter, it's really a shame they didn't read the whole book. Even if they'd read a few pages further on, they would have come across this beauty:
When it was first said that the sun stood still and the world turned round, the common sense of mankind declared the doctrine false; but the old saying of Vox populi, vox Dei, as every philosopher knows, cannot be trusted in science.
Perhaps it might be better said that Vox populi, vox veritas "cannot be trusted in science." But the sentiment still holds: Just because most people think it's so, doesn't make it so. The fact that so many people argue that we should teach the Bible as science because "most Americans believe in God" speaks to a fundamental lack of understanding of the way science is done. But I'm not the first to make that statement, nor will I be the last.
Friday, January 16, 2009
Self-catalytic RNA enzymes
GumbyTheCat recently posted about a study in which researchers created self-replicated RNA enzymes. There was a bit of discussion in the comments about what those enzymes are all about and whether they are, indeed, "true" enzymes (i.e., proteins).
As I have access to Science magazine online, I was able to read the actual article (Gumby's post was based only on the abstract, I think), and so I can now answer the question of what, exactly, an RNA enzyme is, and how the research group got it to replicate itself.
An RNA enzyme, it turns out, is not a true enzyme. That is, it isn't a protein made up of amino acids. It's actually a strand of RNA. The particular RNA enzymes this group made look kind of like a capital T with one side of the crossbar a lot longer than the other. Like all RNA, they're made up of nucleotides (a nucleotide is a molecule consisting of a sugar molecule--ribose, in the case of RNA--a phosphate group, and a nitrogenous base). (I am forced to conclude that the "RNA" in "RNA enzyme" is an adjectival form, rather than a description of what the enzyme catalyzes.)
To understand how the enzyme works, you first need to know a bit about bonding in nucleic acids (DNA and RNA). What follows is a brief discussion; details can be found in any introductory biology textbook.
A single strand of a nucleic acid is a polymer (a really big molecule made up of a lot of similar, smaller subunits called monomers). As mentioned above, the monomers in nucleic acids are nucleotides. When nucleotides join together to form a nucleic acid, the sugars and phosphates bond together to form a "backbone." The nitrogenous bases stick off one side of the backbone. There are five nitrogenous bases that can form nucleotides: thymine, adenine, uracil, guanine, and cytosine. They are abbreviated T, A, U, G, and C, respectively. A, T, G, and C are found in DNA; RNA contains A, U, G, and C. So, a single strand of RNA looks kind of like half a ladder; the rungs are A, U, C, and G molecules. A double-stranded nucleotide (such as DNA) looks like a full ladder; the base in each "rung" is bonded to another base on a rung on the other side of the ladder. The bonded bases form a full rung. (Of course, a DNA molecule really looks like a twisted ladder, but the physics of why it twists isn't important for our purposes here.)
These bases aren't just any random molecules, though. As it turns out, their molecular structures force them to bond together in specific ways: A can bind only with T or U, and G can bind only with C (and vice versa, in each case). In a double-stranded nucleotide, therefore, each rung is made up of either a C-G pair or an A-T (or A-U if it's RNA) pair. You can probably see the beauty of this arrangement: it means that if you have one half of a double strand of RNA or DNA, you can construct the other half.
As I mentioned before, the RNA enzymes in this study look like lopsided Ts. The stem of the T is actually a double strand of RNA: part of the RNA molecule has bonded to itself. (A similar structure is found in some kinds of RNA that take part in transcription and translation in eukaryotic cells.) The crossbars of the T are single strands of RNA.
Each enzyme forms from two smaller pieces of RNA: a straight piece (called "B") and a piece that looks like a regular (i.e., not lopsided) T (called "A"). The straight piece binds to one of the crossbars of the T-shaped piece to form the lopsided T (which the researchers refer to as "E", for enzyme).
Each enzyme (and each sub-enzyme piece) actually exists in two "mirror-image" forms (i.e., E and E', A and A', and B and B'). The mirror-image forms can bind to each other because of the way the bases pair. However, A doesn't bind to A', or B to B'. Instead, A binds to B', and B bonds to A'. The A-B' combination forms E; the A'-B combination forms E'. [EDIT: the previous sentences should read "Instead, A binds to B, and B' binds to A'. The A-B combination forms E; the A'-B' combination forms E'."] The drawing below shows my lame attempt to summarize.
Essentially, when the researchers put some E into a mixture of A, B, A', and B', the A' and B' pieces bonded to the E to form molecules of E'. Once there was some E' in the mixture, the A and B molecules could bond to it to form new E molecules, and Presto! self-replicating RNA.
Of course, it wasn't really that simple. And actually, the not-simple part is kind of cool: The original E that the researchers used wasn't very efficient at catalyzing its own formation. So, basically, the researchers evolved it. They generated new A and B with mutations--variations in the sequences of bases on the backbone--and selected the ones that formed E that could replicate itself most quickly.
Because they have groovy tools (such as polymerase chain reaction machines) and computer to do the analysis, they were able to try a whole lot of different combinations in order to find the set of A and B that produced the most efficient E.
All in all, a really groovy little study!
Lincoln, Tracey A., and Gerald F. Joyce, 2009. "Self-sustained replication of an RNA enzyme." Sciencexpress. published online 8 January 2009; 10.1126/science.1167856.
As I have access to Science magazine online, I was able to read the actual article (Gumby's post was based only on the abstract, I think), and so I can now answer the question of what, exactly, an RNA enzyme is, and how the research group got it to replicate itself.
An RNA enzyme, it turns out, is not a true enzyme. That is, it isn't a protein made up of amino acids. It's actually a strand of RNA. The particular RNA enzymes this group made look kind of like a capital T with one side of the crossbar a lot longer than the other. Like all RNA, they're made up of nucleotides (a nucleotide is a molecule consisting of a sugar molecule--ribose, in the case of RNA--a phosphate group, and a nitrogenous base). (I am forced to conclude that the "RNA" in "RNA enzyme" is an adjectival form, rather than a description of what the enzyme catalyzes.)
To understand how the enzyme works, you first need to know a bit about bonding in nucleic acids (DNA and RNA). What follows is a brief discussion; details can be found in any introductory biology textbook.
A single strand of a nucleic acid is a polymer (a really big molecule made up of a lot of similar, smaller subunits called monomers). As mentioned above, the monomers in nucleic acids are nucleotides. When nucleotides join together to form a nucleic acid, the sugars and phosphates bond together to form a "backbone." The nitrogenous bases stick off one side of the backbone. There are five nitrogenous bases that can form nucleotides: thymine, adenine, uracil, guanine, and cytosine. They are abbreviated T, A, U, G, and C, respectively. A, T, G, and C are found in DNA; RNA contains A, U, G, and C. So, a single strand of RNA looks kind of like half a ladder; the rungs are A, U, C, and G molecules. A double-stranded nucleotide (such as DNA) looks like a full ladder; the base in each "rung" is bonded to another base on a rung on the other side of the ladder. The bonded bases form a full rung. (Of course, a DNA molecule really looks like a twisted ladder, but the physics of why it twists isn't important for our purposes here.)
These bases aren't just any random molecules, though. As it turns out, their molecular structures force them to bond together in specific ways: A can bind only with T or U, and G can bind only with C (and vice versa, in each case). In a double-stranded nucleotide, therefore, each rung is made up of either a C-G pair or an A-T (or A-U if it's RNA) pair. You can probably see the beauty of this arrangement: it means that if you have one half of a double strand of RNA or DNA, you can construct the other half.
As I mentioned before, the RNA enzymes in this study look like lopsided Ts. The stem of the T is actually a double strand of RNA: part of the RNA molecule has bonded to itself. (A similar structure is found in some kinds of RNA that take part in transcription and translation in eukaryotic cells.) The crossbars of the T are single strands of RNA.
Each enzyme forms from two smaller pieces of RNA: a straight piece (called "B") and a piece that looks like a regular (i.e., not lopsided) T (called "A"). The straight piece binds to one of the crossbars of the T-shaped piece to form the lopsided T (which the researchers refer to as "E", for enzyme).
Each enzyme (and each sub-enzyme piece) actually exists in two "mirror-image" forms (i.e., E and E', A and A', and B and B'). The mirror-image forms can bind to each other because of the way the bases pair. However, A doesn't bind to A', or B to B'. Instead, A binds to B', and B bonds to A'. The A-B' combination forms E; the A'-B combination forms E'. [EDIT: the previous sentences should read "Instead, A binds to B, and B' binds to A'. The A-B combination forms E; the A'-B' combination forms E'."] The drawing below shows my lame attempt to summarize.
Essentially, when the researchers put some E into a mixture of A, B, A', and B', the A' and B' pieces bonded to the E to form molecules of E'. Once there was some E' in the mixture, the A and B molecules could bond to it to form new E molecules, and Presto! self-replicating RNA.Of course, it wasn't really that simple. And actually, the not-simple part is kind of cool: The original E that the researchers used wasn't very efficient at catalyzing its own formation. So, basically, the researchers evolved it. They generated new A and B with mutations--variations in the sequences of bases on the backbone--and selected the ones that formed E that could replicate itself most quickly.
Because they have groovy tools (such as polymerase chain reaction machines) and computer to do the analysis, they were able to try a whole lot of different combinations in order to find the set of A and B that produced the most efficient E.
All in all, a really groovy little study!
Lincoln, Tracey A., and Gerald F. Joyce, 2009. "Self-sustained replication of an RNA enzyme." Sciencexpress. published online 8 January 2009; 10.1126/science.1167856.
Subscribe to:
Posts (Atom)