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bubonic plague essay intro

bubonic plague essay introBubonic plague essay intro -The others are the major forms of molecular evolution observed by biologists, phrased in terms of parts.The mechanical and manufacturing analogies so influential in Behe's thinking miss the flexibility of living things.At first the duplicate genes make the same protein, but these genes may evolve to make slightly different proteins that depend on each other.The nearer ones are first affected and slowly bend towards the centre, and then those farther off, until at last all become closely inflected over the object.When a protein is deployed out of its usual context, it may be co-opted for a different function.IC refers to an organism doing something (the function) in such a way that the system (that portion of the organism that directly performs the function) has no more parts than are strictly necessary. Organisms don't come with parts, functions and systems labeled, nor are 'part', 'system' and 'function' technical terms in biology. We might say, for instance, that the function of a leg is to walk, and call legs walking systems. If we divide a leg into three major parts, removal of any part results in loss of the function. On the other hand, if we count each bone as a part then several parts, even a whole toe, may be removed and we still have a walking system. As a mental exercise, try before reading on to formulate an argument to prove that IC systems cannot evolve.A fourth noteworthy possibility is that brand new parts are created.This may be accomplished by redefining 'direct' or 'IC', or (best, I think) by defining Behe's expression 'be produced' which he uses in place of 'evolve'. This illustrates yet another important facet of evolution: not only single mutations, but even large organs may begin more or less accidentally.At this point, what is left of PCP is well on its way to being food for the bacterium. In fact the first and third enzymes were used for this.We will see later that Behe's treatment of cilia and flagella follows this pattern. IC is supposed to be the biochemical challenge to evolution, and thus the case when the parts are molecules, usually proteins, is the important case.Behe's parts are usually whole proteins or even larger. What difference does this make, compared to saying that proteins evolve?The chlorines and the ring structure are both problems for bacteria. chlorophenolica uses three enzymes in succession to break it down, as follows: the first one replaces one chlorine with OH.Then it holds the oxygen until the surrounding oxygen concentration is quite low, which happens in our tissues.Then the parts may coevolve to do something better, but in a codependent manner so that all are required, without further change in the number of parts. It has a ferocious looking tooth-edged trap for unwary creatures.With evolving parts, nature can create a snap-trap after all.We always have the genes for it, but only make it at the right time. Lampreys and hagfish, which don't have jaws, also don't have the alpha and beta varieties of hemoglobin.There are some problems: How can one construct a valid argument that IC cannot be produced directly? Yet it's easy (and left as an exercise for the reader) once you realize that a valid argument from definitions requires carefully defining the terms so that the argument becomes a tautology. As a consequence, this back end, and muscular extensions of it, could also be used to help the animal move.Interestingly, these diverse functions depend critically on when and where the protein is deployed.As a manufactured item the mousetrap neatly illustrates his definition, but with its static parts it cannot model evolution.Introduction The Argument That Irreducible Complexity Cannot Evolve How Might Irreducible Complexity Evolve?bubonic plague essay introGene duplication and changes in protein deployment may introduce a new protein 'part' into a system. It is time to look at living examples and let nature decide. But since a mousetrap is not alive, it doesn't tell us much about whether or how living IC systems might evolve. The Venus' flytrap, Dionaea muscipula, is a small flowering plant which grows naturally in acidic wetlands in North and South Carolina.It is now recognized as a dangerous pollutant that we need to dispose of. And conveniently for us, they do it in an irreducibly complex way.Hemoglobin is a wonderful protein that picks up oxygen in our lungs and delivers it to the rest of our cells.Darwin, whose book If a small organic or inorganic object be placed on the glands in the centre of a leaf, these transmit a motor impulse to the marginal tentacles.This typically comes from gene duplication, which is well known in biology.Here is the crux of it: "Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect, circuitous route.It traps and digests insects to make up for the lack of nitrogen in the soils of its habitat. When an insect brushes against the trigger hairs in the center, the lobes snap most of the way shut with surprising speed.If a good sized bug is caught it is digested over the next few days as the trap closes the rest of the way. A trap can only be fully closed about 4 times, so it must be used sparingly. We must specify a function and all the parts needed to carry it out (and no extra parts).Even more interestingly, the trap was able to evolve because the parts evolved.He makes no special connection between indirect evolution and IC. Since evolution does not aim at anything in advance, the longer the history, the more circuitous it may be.They occur in plants and bacteria as well as in animals, and have diverse functions including oxygen transport, oxygen storage, scavenging oxygen to protect some metabolic processes from it, and electron transfer.And his very limited meaning of 'direct' renders much indirect that is not circuitous at all.The PCP molecule is a six carbon ring with five chlorine atoms and one hydroxyl (OH) group attached.This takes place in from one hour to four or five or more hours. rotundifolia with a fly; Makoto Honda (3) shows the action with a faster species, D. Recent genetic research confirms that Venus's flytrap and the waterwheel plant Aldrovanda are related and are in the sundew family Droseraceae, and that snap-traps very likely evolved from flypaper traps (4) as Darwin thought: CONCLUDING REMARKS ON THE DROSERACEAE.The second enzyme (called Pcp C) is the most interesting one; the cell produces it in sufficient quantity to be effective all the time instead of just when it is needed in its normal metabolic role.Losing a part means losing all copies of it, or at least so many that the function is effectively lost.The term was defined by Michael Behe in 1996 in his book (1).Thanks to this unusual situation Pcp C is available when it is needed to help eat PCP.They can lead to new protein functions, sometimes slowly and sometimes, especially when parts are redeployed, abruptly.Irreducible complexity (also denoted IC) has gained prominence as the evidence for the intelligent design (ID) movement, which argues that life is so complicated that it must be the work of an intelligent designer (aka God) rather than the result of evolution. bubonic plague essay intro There are two each of two different chains called alpha and beta hemoglobin.A protein is made up of hundreds of smaller parts called amino acids, of which twenty different kinds may be used. If you think about it, each protein that your body makes is made at just the right time, in just the right place and in just the right amount.Commenting on this in his article "The Evolution of Hemoglobin", Ross Hardison says "This suggests that the creation of new protein functions arises as much from changes in regulation as from changes in structure." (8, p 126).So far as biologists can tell, a recent mutation that changed the deployment of this enzyme is what made PCP degradation possible for this bacterium.The chemistry and probable evolution of this system are explained in much greater detail in Shelly Copley's article "Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach" in Trends in Biochemical Sciences (5).When finally one oxygen is released, the next is released faster and so on.Let's take a look at the definition of IC, and then see if we can figure out its relation to evolution, and why scientists are so unimpressed.If a small insect is caught, it may escape between the teeth, and then the trap reopens without fully closing.chlorophenolica that use Pcp C only in its normal role, but not nearly as well as would be expected for an old, well adapted system.The resulting compound, while still bad, is much easier to deal with, and the third enzyme is able to break the ring open. First of all, bacteria of this type could already metabolize some milder chlorophenols which occur naturally in small amounts.It also happens that both Pcp C and the first enzyme in the process are now slightly optimized for dealing with PCP; they handle it better than the corresponding enzymes in strains of S.This essay will, I hope, prove helpful to any school teachers, boards of education, legislators and members of the press who may be wondering about it.The function of interest is trapping insects for food in a manner that brings the plant more benefit than the cost of the trap.So it is surprising to read, on page 40, Behe's argument against indirect evolution of IC systems.The hemoglobins (globular proteins incorporating a heme group, which in turn cradles an atom of iron) turn out to be a widespread protein family with a long history.This brings up another point: the parts themselves evolve.Irreducible Complexity in Nature Venus' Flytrap How to Eat Pentachlorophenol Hemoglobin for the Active Life The Blood Clotting System: is it IC?And even short term evolution can be indirect in Behe's terms.Oxygen binds to hemoglobin very quickly in our lungs and stays bound.IC, ID, and Creationism Conclusions References new term, irreducibly complex, (IC) has been introduced into public discussions of evolution. bubonic plague essay intro So of course there may be multiple copies of a part.As a result the cell is triggered to produce them in the presence of chlorophenols.Or the parts may become co-adapted to perform even better, but become unable to perform the specified function at all without each other.The resulting compound is toxic, but not quite as bad as PCP itself.This makes a striking contrast with the mousetrap which Behe has repeatedly presented to illustrate why IC cannot evolve.The trap started out as a Drosera-like leaf, and the parts of the leaf were progressively changed.The long term evolution of most features of life has not been what Behe, or indeed most people, would call direct.The best known of these bacteria is called Sphingomonas chlorophenolica (also called Sphingobium chlorophenolicum).The inefficient regulation of Pcp C is evidently the key to the whole process.These factors, combined with the fact that PCP is not known to occur naturally, make a strong circumstantial case that this system has evolved very recently.As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously." (page 40) He simply asserts that evolution of irreducible complexity by an indirect route is so improbable as to be virtually out of the question, except in simple cases. Actually, a more complex system probably has a long evolutionary history.The argument from IC to ID is simply: This article just looks at the first part, the argument that irreducibly complex systems cannot be produced by evolution, either because they just can't evolve, or because their evolution is so improbable that the possibility can be ignored.We can summarize these four possibilities this way: The first of these only comes up if we are looking for IC.The complex binds reversibly to oxygen, one O molecule per each subunit.Pentachlorophenol (PCP) is a highly toxic chemical, not known to occur naturally, that has been used as a wood preservative since the 1930's. A few soil bacteria have already worked out a way to break it down and even eat it.The argument against 'direct' evolution of IC is contained in this long sentence right after the definition: "An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional." The last part of the sentence, "...because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional." is why we should agree to the rest of the sentence. Going back still farther, some very early animals started to have two distinct ends; one end for food intake (with sense organs for locating food) and the other end for excretions.A precursor to IC lacking a part can have any functions except the specified one, which brings us to 'indirect' evolution. So far as I know, the main thing a cow uses its tail for is to swat flies. It also illustrates that biological functions evolve. It may not even make sense to expect a precursor to have had the same function.Swimming Systems The Eukaryote Cilium The Archaeal Flagellum The Bacterial Flagellum IC Cores How Does Irreducible Complexity Get Its Charm?Then an 'extra' part may be lost, leaving an IC system.He finds that direct evolution of IC is logically impossible, and indirect evolution of IC is too improbable. bubonic plague essay intro At first the duplicate genes make the same protein, but these genes may evolve to make slightly different proteins that depend on each other. bubonic plague essay intro




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