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Everything posted by GDG

  1. Well, in my dictionary there was no other "part" of the definition. If you are going to communicate an idea, you must perforce use terms in a way that will be understood by the receiver. If you do not know the receiver that well, you had best use terms according to their commonly-accepted definitions. As a moderator, you should be well aware of this concept. Fields of endeavor often develop their own terms ("terms of art"), which usually have specific meanings known to people in that field, but generally unknown to the lay public. For example, in law we often use the term "constructive", as in "constructive notice" or "constructive trust". The meaning of "constructive X" in law does not mean "helpful" or "creative", but instead means that X did not in fact occur, but will be treated as if it did. For example, "constructive notice" means that a party did not actually receive notice, but for legal reasons will be treated as if he or she had received notice. You appear to be using "design" in a similar fashion, as a term of art in some subset of the field of biology (or perhaps philosophy), without regard for the common definitions of the term. This argument is posted on a public forum, frequented both by people with scientific training, and those with little or none. Thus, you cannot assume that your audience is familiar with terms of art peculiar to your field. The most common definitions of the term "design" all indicate the action of intelligence: I've italicized a few words in the definitions that specifically suggest intelligence or consciousness, as you seem to have trouble noticing them. Note that you don't get away from intelligence until the sixth definition of the noun (and not at all for the verb). And again, for the umpteenth time, I am not proposing that evolution is the work of intelligence: I am saying that "design" is a particularly poor choice of terms because evolution is not the work of intelligence. There may be perfectly valid philosphical or biological reasons for using the term "design" as a term of art in this case, but if you use the term with lay people and fail to explain that you are not using it in its common and accepted sense, you are not communicating. When your use of the term implies the opposite of the common meanings, failure to explain nearly guarantees that you will be misunderstood. When I talk to lawyers, I know I can use the term "constructive" in the legal sense and be understood: if I am talking to non-lawyers, or to someone whose knowledge of law is unknown, I know I have to explain what "constructive" means or use other terms in order to be understood. I'd bet that if you look at how "design" is used in the field, it is either explained (perhaps as "unintelligent design" or something similar), or is being used in a context where its use as a term of art can be assumed. You can continue asserting that "When I use a word, it means just what I choose it to mean -- neither more nor less" like Humpty Dumpty in Through the Looking Glass, or you can choose to be understandable. Then I take it that Dawkins cares about being understood. So far, I am not impressed with "Darwin's Dangerous Idea". Perhaps my opinion will improve when I've read more, but it strikes me as an odd choice of authority. I am interested in seeing what Gould and Orr criticized so much. His analogy based on patent law strikes me as fundamentally inaccurate. He says: To start, copyright is not part of patent law; each covers non-overlapping fields (with the exception of design patents), and has decidedly different rules and principles. Copyright admits that "independent creation" (his words, I assume not in the religious sense) can and does occur. For example, if you photograph the Empire State Building, you automatically have copyrights in your photograph. However, somebody standing right next to you can photograph the ESB at the same time, and have copyrights in his or her photograph, despite the fact that it is indistinguishable from yours. Thus, in copyright infringement litigation, it is not sufficient just to show similarity: one must also show that there was access to the "original". I assume that by "industrial espionage" he really means patent infringement, as the interior of a marketed device cannot be considered "secret", or require spying to copy. In patent law, it does not matter if you have copied the device or not: just making, selling, or using the device constitutes infringement. The plaintiff need only prove that the accused device meets all of the claim limitations in the asserted patent (i.e., that it falls within the legal description of the patented invention). Innocent independent invention of the same device is not a defense, although if you can prove that you invented the device prior to the patentee's date of invention, you win by invalidating the patent itself. These "cosmic coincidences" do happen -- often enough that the US Patent Office has a special procedure (called "Interference") for determining which of two or more applicants was the first to invent.
  2. From Merriam-Webster: "Devise: 1 : invent, 2: plot". You are postulating that a non-conscious entity can "devise", and that evolution has a "specific function or end." I think you are stretching the definitions of terms past their breaking point. We cannot have communication through language unless you and I can each understand a word to have a particular meaning, and to agree on that meaning. You keep insisting on using terms that, at least to me (and I think to most others here) imply the action of an intelligence. To design (v) requires planning, a consciously thought-out series of steps. A design (n) is the result of designing. Natural selection is a natural process, incapable of planning, goals, or design. NS results in structures, but not designs. To me, the word "design" necessarily implies a conscious, intelligent "designer". You seem intent on insisting otherwise, and I am baffled as to why. You are conflating "design" with structure. Sedimentary rocks have structure. Crystals have structure. They do not, in general, have design, and we do not talk, for example, of a river having "designed" a bed of sedimentary rocks by delivering silt of differing compositions. Similarly, although we humans can program a genetic algorithm and use an analog of natural selection (by definition, it is artificial selection) to design an end result, it is the fact that a conscious, presumably intelligent human is using selection as a tool that justifies use of the verb "design." The algorithm itself does not "design", although it may generate useful structure. Considering the abominable percentage of the population that believes in Ignorant Drivel, I think it is foolish to ignore them. How many politicians espouse fundamentalist/ID views? How many have influence over how much is spent for research, and in what fields? I think it is a very bad idea to adopt the terms that IDers use, while giving them different meanings. Much better to adopt clearly different terms, and clearly distinguish what you mean. Otherwise, you are misleading those who read this forum and have not yet learned to think clearly about the mechanisms of evolution. Far from it. I reject your misleading use of the term "design", not the fact of evolution and natural selection. Natural selection results in structure, not design. Most of us, both scientists and general population, consider the term "design" to require planning and intelligence. As far as I can tell, you alone want to redefine it. I can't agree that your redefinition of "design" is useful, and think it leads to a great deal of misunderstanding and miscommunication. If Dennet thinks we should call this "design", I'll have to disagree with him too. Just because he is published does not make him correct. Or to put it another way, I am insisting on ascribing the accepted definitions to the words I use. You haven't shown me any common definition that supports your reformulation of the terms. You cannot tell what "fitness" is until you look at the success of a particular phenotype in the population. For example, animal X may have a mutation that causes it to bear 4X the wild type number of offspring. Is that fit? You cannot tell: it may be that the resulting offspring do not survive to maturity, or that the mother is so taxed that she expires instead of bearing several more litters. And the mutation may be far more subtle: perhaps the ability to metabolize lactose in adulthood, which may not confer a benefit until food supplies run scarce, and those that can drink milk have a benefit. "Fitness" is what worked. They are structures that evolved. They are not "designs": they were not "designed." Genetic drift is not natural selection, true: instead of selection based upon survival/reproductive fitness, you have selection based on random chance. It is still an evolutionary process. Technically, NS by itself does not produce eyes, blood clotting systems, etc. either: for that, you need descent with variation. Yep, positive. Considering who is pushing "design" here, and who objects, I think it clear that the stealth IDer is not me. Take another look at what you are mis-quoting. I did not say that NS was a tautology: I said that "individuals with a useful variation benefit" is a tautology. The variation is useful because they benefit: they benefit because it was useful. If they did not benefit, it would not have been a useful variation, and vice versa. The problem is that not all variations are obviously "useful". If the variation does not have an effect on reproductive success, it will not be selected. Other than that, the bottom line is that it does not much matter what the variation is. Whether or not it was beneficial can really be determined only in retrospect. Again, I suggest that the term "design" carries conotations that are the opposite of what we intend. Thus, the term "design" is poorly selected. The problem is not in the way that evolution and natural selection work: it is in your insistence on using terms that imply the action of an intelligence, like "design", "purpose", and "goal."
  3. I'm not sure we can extrapolate from the peripheral nerve axon diameters to the CNS neuron sizes. Smaller animals probably have a smaller number of brain neurons. Intelligence may be more a matter of how they are connected.
  4. I do a fair amount of literature and patent searching as part of my job. In terms of search strategy, I first try to think of terms that are "characteristic" or specific to the topic you're trying to retrieve. Start by determining if you have a "term of art", i.e., a name or phrase that is used specifically (and, ideally, only) by the professionals in the field you are searching. I suspect that both "feedback" and "intervention" are widely used terms, across numerous fields. For example, if you google "feedback", you'll get references to (I assume) acoustics, music, circuitry, biofeedback, automation, counseling, etc. To narrow your search down from a billion to something relevant, try to think of a term that would be used in your field that is not used commonly in the others. Like, you might expect the term "gestalt" to appear pretty much only in your field, and not in circuit design or acoustics, etc. (I'm not saying that "gestalt" will help in this particular search: just trying to think of a term that might be semi-unique to psych.) Not knowing any psych databases, I would start with PubMed. Think of all of the available/searchable literature as forming a set, which you are going to filter down to a target subset of a size that can be examined by inspection. Your first filter is to figure out the terms that should appear in your target subset. If your terms are pretty much unique to your inquiry, you may be done at this point. Let's assume that the first filter narrowed the set down to something like 10^5 articles. Your second filter should be designed to eliminate those articles that likely have nothing to do with your inquiry (e.g., carving out all the circuits, acoustics, etc.). If you are being swamped by only one or 2 other fields (e.g., if circuit design frequently used "feedback intervention", and most of the search results involved circuits), you might try excluding a common circuit design term. Probably not "resistance", as that might also exclude relevant articles, but perhaps something like "voltage" or "microphone" would serve. Alternatively, you add a search term that is pretty specific to your field (if not to the subject of the inquiry). Perhaps "pedagogy" or something of the sort. You should have good results after the second filter. Obviously, if you end up with zero, you need to relax the filter a bit (or check the spelling of your search terms ). If you managed to narrow it down to articles mainly in the correct field, but still have too many to inspect, try to find the review articles in the bunch, and start tracking down the footnote references. Hope this helps
  5. I think the term "design" by definition presupposes a conscious designer. Considering the recent (and continuing) idiocy regarding "intelligent design", I prefer to avoid use of the term "design" when talking about anything other than the actions of intelligent, conscious beings. Thus, I would not say that river rocks are "designed" by the river, or that clouds are "designed" by the wind and atmosphere. Similarly, I will not say that organisms are "designed" by evolution. If you want to redefine the term idiosyncratically, you can deal with the confusion and misattribution that results. NS is no more an "entity" than the quadratic equation, unless you are considering abstractions to be entities. I cannot agree that either is an entity that is capable of design. The point you are missing is that "fitting" also implies a conscious design, as if NS were a being that deliberately caused particular variations to occur, in order to actively adapt a species to its environment. Your tailor does "fitting". NS does not. "Fitness" in the evolutionary sense is a shorthand for "degree of relative reproductive success as a species", which in turn refers to the ability of a species (or group within a species) to out-compete its competitors for resources and reproduce most effectively. But it doesn't. There is no designing. If you drop the word "entity", we agree. Are you suggesting that evolution cannot occur by genetic drift? I have no problem with the quote: it means only that where there is a "useful" variation, individuals with that variation benefit -- which is what "useful" means in this context. It is a tautology. However, I can't agree that Darwin in any way implied a design. They reproduce more successfully only because we have defined "useful" to mean that, and that all the other "non-useful" variations (which still occur) do not confer any such benefit. No, there is no short term purpose. I'm not sure what parameters you are referring to, but in any population you will have diversity due to random mutation. Yes, random. The environment also changes, due to changes in climate, erosion, insolation, and the activities of other organisms, etc. If your random mutation is lethal, you die, and your mutation is not passed on. If your random mutation is not lethal, but not beneficial, it may persist for generations, but will not come to dominate. If your random mutation is beneficial, or the environment changes in such a way that suddenly the mutation is beneficial, then the percentage of the population carrying that mutation will increase, and come to dominate. But none of that requires "purpose" or "design". The environment can change in such a way that none of the animals survive: more species have gone extinct than exist today. I don't see Aristotle using the term "purpose". "Cause", as in "cause and effect", yes. "Purpose", no. To the contrary, I suggest that you discard these terms, as your use of them makes it sound like you expect the universe to be full of purpose and design, anthropocentric. I think anthropomorphizing evolution and natural selection is pointless and misleading. Think of NS as a mathematical algorithm, and you will be right much more often.
  6. Dr. Syntax, you may want to take a look at the Wikipedia entry on phases of ice before you run off to the USPTO.
  7. Here are a few more references: T.A. Iudna et al., "Cell biology and life cycle of the testate amoeba Corythion delamarei" Tsitologiia (2000) 42(7):613-23 (finding that C. delamarei undergoes sexual reproduction); and P. Pernin et al., "Genetic structure of natural populations of the free-living amoeba, Naegleria lovaniensis. Evidence for sexual reproduction", Heredity (1992) 68:173-81 (finding evidence for sexual reproduction in N. lovaniensis) Don't know if they're considered social or not. You are correct that most of the literature states (or assumes) asexual reproduction for most amoeba.
  8. Just as a point of clarification, homeopathy is not the same as traditional medicine. Homeopathy was invented in 1790 by someone who took the medieval idea of treating "like with like", i.e., that if your illness was characterized by particular symptoms, you should administer a substance that produces the same symptoms. Of course, those substances are often noxious, so they are diluted to an extreme degree. When I say "an extreme degree", I mean that the substance is serially diluted so many times that there is only a very small chance that even a single molecule remains in the formulation. In other words, homeopathy is pure bunk. Traditional or herbal medicine, on the other hand, is generally based on, well, tradition, and usually involves administering or applying some form of plant preparation. The plant preparations may have components that actually do have a pharmacological effect (although, apparently not all preparation do). Whether the traditional herb is selected for a religious reason, or based on lore handed down from practitioner to practitioner, it at least has a chance of having some effect. Homeopathy has none (unless you are treating dehydration).
  9. See H. Urushihara, "Cultivation, spore production, and mating" Methods Mol Bio (2006) 346:113-24, which mentions sexual reproduction in Dictyostelium (the slime mold amoeba); and H. Urushihara et al., "Genes involved in Dictyostelium discoideum sexual reproduction" Eur J Cell Biol (2006) 85:961-68.
  10. Duh, from Bose-Einstein statistics.
  11. 1. Antibodies are fairly large proteins, and are not typically internalized by cells (although this does occur in certain disorders). Why can't cells make their membranes permeable? Making the membrane permeable enough for antibodies would probably be enough to kill the cell (after all, this is how complement kills cells): most large proteins that are internalized are taken in by specific mechanisms. Typically, the virus-infected cell may no longer be in control of its "operating machinery", because it has been hijacked by the virus, so defenses that require the cell to change somehow would be subject to failure. 2. This is not perfectly understood, but is thought to be regulated by T cells. B cells (which produce antibodies) need activation by T cells in the context of the antigen. When T cells are maturing, T cells that react strongly to "self" antigens are weeded out, thus eliminating the T cells that would activate B cells to make "self" Abs. When this fails, you can get autoimmune diseases, like lupus. 3. It can take a few weeks, from first exposure to an antigen to effectively fighting it off. Much of this time is spent "selecting" the best Abs and T cells, and then further refining them.* Then, the selected immune cells need to divide again and again in order to build up a sufficient population to challenge the invading pathogens. In contrast, the memory cells represent immune cells that are already optimized, and ready to crank out plasma cells and Tc cells immediately. *When I say "select", this just means that cells that produce Abs that bind well are stimulated to divide, while those that don't aren't. 4. White blood cells (lymphocytes) are produced mainly in the bone marrow. They differentiate from stem cells called hematopoietic stem cells. See Hematopoiesis.
  12. IIRC, both. Epithelium lines the insides of lumens (like the inside of the intestine) and the outside of organs. Your skin is a form of epithelium.
  13. Not exactly: as long as you have reproduction with variation, and selection based upon reproductive success, you will have evolution. Consider microorganisms that reproduce by division: does the "parent" die? Of course, having your ancestors continue to hang around, competing for resources, may not benefit offspring. As for "why" we didn't evolve immortality, the question supposes that there is a reason. It just didn't happen.
  14. No, just the distance between the genes. Imagine a chromosome: ----*------------------------*------------------- I've flagged two genes at random (*) for purposes of illustration. Assume that crossing-over can occur at any point (-) on the chromosome. In the illustration above, there are 24 units (arbitrarily assigned) between the two flagged genes. If crossing-over happens in between the two *'s, they get separated: otherwise, they are inherited together. If crossing-over happens to the left of the first one, or to the right of the second one, they get inherited together. Now consider this chromosome: ----&--&----------------------------------------- Between these two flagged genes (&), there are only 2 units. Clearly, there are many fewer opportunities to cross-over in between these two genes -- 1/12th the number of the genes in the first chromosome. All else being equal, the two **'s will be separated 12 times as often as the two &&'s.
  15. Fermions are particles that have a spin of N/2, where N is an odd number. Electrons, quarks, protons, and neutrons are all spin 1/2 fermions. In other words, all of the fundamental particles that make up matter are fermions. The other category is "baryons", which are particles that have 0 spin or an integer spin N, where N is an integer. Photons are baryons.
  16. ... and are less likely to be inbred...
  17. Except that the actual OP was directed toward that physical difference. Just saying that there must be some evolutionary reason for the difference does not explain the mechanism that implements the difference.
  18. It is: this is what makes the Sun shine. Hydrogen is fused to make helium, and a small amount of the mass is converted into energy. The total amount of mass and energy together is conserved.
  19. Who says no one is doing that? A number of current drugs on the market originated from folk medicines or natural products (like digitalis). There was a pharmaceutical company that based its entire approach on that (Shaman Pharmaceuticals -- it went bust in 1999). But lets look at the difficulties in trying everything. First off, how many different species of plant, fungus, bacteria, and insect are there? The number is astronomical. There is no way that any company has the resources to test every living thing for possible therapeutics, even if you only needed to run one test per organism. Second, you're going to have to fractionate those critters somehow: you can't just stuff a whole caterpillar into a test tube and see if it has any pharmaceutical activity. If it does have an active component, and the component is a small molecule (typical drug size), you may be able to separate it out by chromatography. However, if the active component is a protein or other large molecule, the act of separation may denature it, destroying its activity. It is not easy to separate components, while preserving their activity, when you don't know what those components actually are. For each component, you'll need to test a range of different concentrations, several different concentrations for each different activity you're looking for. OK, so maybe we concentrate on only those organisms that are actually used in traditional medicine today. It would help if we could focus just on the traditional medicines that actually seem to help. Which ones are they? Here, the problem is that you just cannot tell if a traditional medicine does anything helpful, because no research was done, and there is no control group. Some have been found to be pretty harmful -- like the ones that contain lead OK, so say you've found a traditional treatment that seem to be effective. Now you have to take it apart, because until you know what causes the beneficial effect, there is no way to manufacture it. You can't just package portions of "wonder root", because the amount of active component can vary from plant to plant, and from day to day, depending on its environmental conditions. You can't establish an effective dose if you don't know how strong your root is. So you have to narrow it down to the specific compound or compounds that are responsible for the activity. Then, you have to hope that the active component is something you can synthesize. Many natural products are very, very complex and difficult to synthesize. It is not uncommon to see someone earn their PhD in synthetic chemistry by being the first to synthesize a microscopic amount of a natural product, taking 25 synthetic steps and 4-6 years. It is a lot of work!
  20. Wegener's granulomatosis is associated with the presence of classical anti-neutrophil cytoplasmic antibodies (c-ANCA, found scattered throughout the cytoplasm), while Churg-Strauss is associated with the presence of perinuclear or protoplasmic ANCA (p-ANCA, found mainly near the nuclear membrane). The antigen in WG is typically proteinase 3, while in CS it is usually myeloperoxidase. They otherwise have extremely similar symptoms.
  21. I don't know if this is the article you are looking for, but here is a 1999 paper about gender selection using a "swim up" procedure. The procedure is based on the theory that Y sperm (because they are less massive) swim faster than X sperm. In this study, 86.7% of those seeking a girl were successful, and 89.2% of those seeking a boy were successful. M.A. Khatamee et al., "A controlled study for gender selection using swim-up separation" Gynecol Obstet Invest (1999) 48(1):7-13.
  22. 1. The short answer is "the 2nd law of thermodynamics". For an explanation of why, you have to read up on statistical mechanics. 2. The particles move from high to low because they already have the energy, whether that energy is potential or kinetic (which is what makes them "high"). Think of the high energy particles colliding with low energy particles: the high energy particle loses some energy, while the low energy particle gains some. Since, between any two particles that collide, the high energy particle loses while the low energy particle gains (heat doesn't flow from the colder to the hotter), the population of particles averages out, and you end up with a collection of particles having a distribution of energies centered on the average.
  23. A mutation will survive quite a while, as long as it does not prevent reproduction. A mildly detrimental mutation will be passed on to one's descendents, and not die out for generations. (A mutation that drastically reduced reproduction would not be "mild" by definition.) Even pretty bad mutations like hemophilia can survive many generations. How would you explain the fact that humans have many inherited diseases, most of which are not new this generation? No, simply automatic. By definition, a "good" mutation is one that increases the organism's fitness in its environment, and results in its eventual predominance due to reproductive success. It is a mathematical fact, not an intelligent design.
  24. The Wikipedia entry on Transduction should answer your questions in detail.
  25. How about just looking up "neuron" in Wikipedia? Fortunately, our DNA polymerases are very accurate, and correct their errors (really!). You do find the odd mutation here or there, but many mutations are selected against. If you have a population with a predominant sequence, and a few mutants that occur at frequencies like 1:1000, how many individuals do you have to sequence to find more variants? As for the second part, you can try Wikipedia again... The mRNA from a gene can be spliced in different ways, so that in some cases you can have several distinct proteins encoded by the same gene. If that was all that sleep deprivation did, possibly. However, it is more likely that sleep deprivation also affects the expression of many other genes: the net result could easily cancel out the upregulation of A. I have yet to meet someone who thinks that they are smarter after they've been deprived of sleep... The system is a bit more complicated than that. For one thing, it is rare to find a disorder that affects only a single gene, for which modulating the gene activity alleviates the disorder. And sometimes the disorder is not the result of differential expression, but of a mutation in the gene that affects (or eliminates) the function of the encoded protein. For example, if you have cystic fibrosis because both copies of the relevant chloride channel gene are defective, no amount of gene modulation is going to help. Just about every environmental factor alters the expression of some gene somewhere in the body. Even thinking! If you rehearse something mentally, for example memorizing your part in a play, the neural activity causes the affected neurons to strengthen their synapses -- which requires protein expression -- which requires gene expression. The regulation state probably changes constantly (although the expression of individual genes may vary only within a narrow range). As for the last question, hard to say. As mentioned above, "thinking" by itself changes the regulatory state of several genes, which directly affects the neurons doing the thinking, which changes the regulatory state again, which ... However, the system (brain, this time) is complex enough that your genes cannot fully determine what (or how) you think.
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