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Everything posted by Biochemist

  1. To all the Buffy admirers: The only problem with chatting with her is that the individual responses get longer, and longer, and longer. I apologize if we are either monopolizing the thread or boring the sock off of others. But it is nice to chat with you, Buff. Bio
  2. I saw that eventually. Nice to be back for a bit. Actually, I am probably a little bit more this direction than you are. More on that below. Agreed. Although I don't know Shannon and Kolmo. .I think we are still in the pretending-to-understand-this phase on this particular topic (Ubiquitin tagging). This tagging system is 1) incredibly complex, and 2) incredibly efficient. Nothing "foreign" gets past it. It is a bit of a stretch to suggest that all of the "genetic engineering" you discuss below would automatically be recognized as native protein. But it is. Hmmm. I plan to l
  3. FYI, it really is great to chat with Buffy again, after a multi-year hiatus. Amazing woman, really. Bio
  4. I am note sure that "required for passage" even makes it meaningful. That just means it was a close vote. Any close vote has all kinds of stuff in it to get it passed (e.g., Obamacare). I don't think that means that the elements were even important, other than as horse-trading. It is a bit of a stretch to call the IPAB just advisory. It has regulatory authority to preclude specific procedures. This is a LOT different than the independent advisory boards that many private health plans have. Because if you preclude it nationally, it is actually precluded universally. I don't believe a b
  5. Nice, CD. This is pretty close to what I do: "Sense" an interesting chord sequence Write the lyrics Write the song Arrange the song. BUT (please comment!): This really only works on acoustic pianos. I have a nice keyboard with a nice synthesizer, but my piano is a 7'5" 1972 Grotrian Steinweg. I think of my piano as my "largest" child (and by far the heaviest). I almost never (perhaps absolutely never) compose at an electronic keyboard. Acoustic noise is just so much more connective. Anyone relate to this? Bio
  6. Thanks for the hello!! I really didn't mean to misdirect; I just disagree. I think the primary issues were federalism and defense. The fact that some southern states had other priorities is relevant, but I don't think it was primary to the documents. The impression I got from your link is that the author was saying it was the primary driver. I just don't think that is the case. Agreed. But I think this supports my point that federalism was pretty key to the Constitution. I think the fraction of people that were racist was higher then, and it reflected itself in the document, yes.
  7. Shucks. I was really hoping for a "welcome back" after a couple years. I missed you folks. Oh, well. Not sure what you are talking about here. I have always been a PE advocate. Still am. Nothing in the junk DNA mechanism gets around the probabilistic issues. We will have to accept that the vast majority of small changes to a set of genes result in dysfunction. And any new protein will be scavenged by the various internal cell police (e.g., the ubiquitin tagging system) to remove new proteins. I am OK with this point of view, but it is a faith position. You can't suggest that th
  8. This deserved it own response. I think it is more than a little disingenuous to tie Bob Bennett to Lee Atwater. I think Bob Bennett actually meant what he said: Some policy presriptives are ludicrous, but it does highlight that the end does not justify the means. Bob Bennett is a pretty good (i.e., moral) guy. I think we could find lots of folks on the right that would not make that claim about Lee Atwater. I am a healthcare guy. I am pretty deep in analytics that relate to cost and quality in large populations. I have occasionally said (to make a point) that if we legislated that no
  9. Hmmm. Now there is a powerful statistical argument. :) These number appear roughly correct, but I think they actually apply to AFDC (that is, the program that ended in 1996). I think that TANF is even better than this, but I can't figure out your link. It is dated 2012, but TANF replaces AFDC in 1996. I am a little confused about this data. Bio
  10. Please tell me: this was tongue-in-cheek? I assume we recall that a large well-armed country with a large navy tended to arrive and suddenly land troops. That circumstance was of interest to all colonials, not just the southern states. Preserving the right of the states to maintain militias also supported defense of the state, don't you think? Bio
  11. Nice to read you again, Buff. Wouldn't it have been more accurate to have said that this characteristic of DNA is "consistent" with PE, not that it "explains" it? The mechanism of action of (misnomer) "junk" DNA is indeed consistent with PE, but frankly was not even necessary. We could have already "explained" PE by the arithmetically increased likelihood of expression of recessive alleles in small, sequestered populations. It is easy (and likely) to suggest that significant environmental changes during those rare PE episodes drove small populations to be separated from larger ones. We c
  12. All true, and a good point. I still am surprised (and it seems somewhat counterintuitive) that after "carving into stone" so much of the standardized cell infrastructure, that we could generate such a remarkable diversity in body plans without significant alteration to the standardized machinery. My opinion on this (completely unsubstantiated, of course) is that the tendency toward life (in fact toward the tree of life that we see) is intrinsic in the fundamental molecular structure of the basic molecules. That is, development of life is similar to the order created when solids crystallize
  13. Nice point, Riper. Darwin should probably have said something like "survival of the most opportune variant in the niche", but it doesn't quite roll off of the tongue as well.
  14. This is a really interesting development, MA. Your point is valid, but since the retrotransposon activity is embryonic, it also suggests that genetic changes that would result in death of a fertilized ovum now will only result in death of an early embryo cell. Essentially, it raises the probability of embryonic survival, and increases the probability off a functional cell mosaic (whether good or bad). Really interesting. Also, I never saw the numbers (noted in the summary) that L1 retrotransposons are 17% of the human genome. This is roughly six times the portion that transcribes prote
  15. This is undeniably true. Very likely to be true. And your argument above that higher phyla are less likely to branch is a strong one as well. Absolutely agree. But the core of the scientific method is prediction and falsifiability. If we posit gradualism based on serial incrementalism, we should either defend (or question) the predictions, modify the hypothesis, or throw it out. I continue to think the argument for gradualism is weak. We have strong examples of genetic drift, but these seem to be cases of selection of recessive alleles. There is just so much assumption about how those
  16. Gradualism does not require (or even imply) species or phyla need to go extinct slowy. Only that they accrue slowly. And the slow growth should be "reasonably" consistent (e.g., generally logarithmic) over long time horizons. I know you were joking on this, but it is true that new phyla actually may have shown up, and we missed them. This is a valid hypothesis, but it feels more like a postulate. It is a little tought to falsify. Further, we are accepting that speciation occured regularly over the last 500 million years, but no phylogenation. This alone seems to argue against the postul
  17. Hmmm. I didn't mean to be particularly contentious here. I was merely suggesting that if the number of phyla went form 3 to 70 to 30 in roughly equal LONG time periods (3 about a 750 million years ago, 70 about 500 million years ago and 30 now) this is not particularly consistent with gradualism. Yes. All true, Pyro (thanks) but not really my point. No one was requiring that all new phyla only come from more complex species. There would be nothing stopping the existing lower forms (or, more succinctly, the lower forms 500 million years ago) from creating additional new primitive branc
  18. Nice post, and nice perspective, Pyro. I think it is worthwhile to summarize the core issues that (one could argue) remain open, while, at the same time, noting those that are closed. On the closed front: 1) The tree of life (for higher phyla) is incontrovertible. Those of us who still had questions in the '80s (mostly due to the incomplete nature of the fossil record) have had the TOL confirmed by the proliferation of genetic maps of species. 2) Relatedly, common descent (at least back to the early eukaryotes) is a given Still open: 1) the primary mechanism for speciation (any
  19. This seems to equate religious activity with any fad or partisan opinion. It is certainly true that political partisanship (for example) does indeed have familial tendencies. Last I heard, something approaching 70% of voters vote the same as their parents did. But if you look at the drift in political party positioning, it moves much faster that religious position. And there are really a relatively small number of religions that have stood in substantially the same form for extended periods (discounting the atomistic spirituality of tribal peoples). So, something about this does not qu
  20. Well, I have to admit I am tickled that you could decipher my post. The only (potential) disagreement we have is around the character of the illusion. My suggestion is that the environment that ended up creating life was not only possible, it is likely. We look at this massive amount of biochemical complexity and think (credibly) that most of the actions are not random because earlier states minimize or bound many of the options. Ergo, given these constraints, we surmise that life developed because of an aggregation of increasingly complex states that minimized the options for sequential
  21. Agreed. I prefer to think of science as that body of information that can be characterized by the scientific method. This leaves out large bodies of information and experience (e.g., relationships, art, etc) but focuses on demonstrability. This definition is a little open to attack, since some academic disciplines don't lend themselves to testability in the classic sense (e.g., paleontology), but I like it because it essentially outlines the degree to which a particular discipline is "science". In this vein, science isn't either open or closed-minded. It just is. A more relevant ques
  22. Well, not really. I have worked on this post for over 2 hours, and I don't think it is particularly clear. But let me give it a shot.... Merging together data from two of your recent posts, the mutation rate attachment above demonstrated that E Coli generated resistance to the T1 phage at a rate of about 10^-10. Given that the E Coli genome is about 5 million base pairs, this means that roughly every 200th replication has a genomic alteration. Hence 199 little beggars get through unscathed for every genomic change. More intriguing, however, is that (apparently) a single nucleotide mutat
  23. I give up. You are now trying to correct me for things that I agree with. I must be unable to make my point. But thanks, sincerely, for trying to respond. Bio
  24. Sure. As a general rule, I don't discuss much about scriptural interpretation of anything before Genesis 12, since the stuff is so very very very old. It is also true that standard, conservative hermeneutic principles (interpretive rules) of the Bible allow for: 1) Poetry 2) Allegory 3) Hyperbole 4) Simile or metaphor 5) Parable 6) Normal usage, normal usage, normal usage That is, there is no such thing as "literal" in Genesis 1, or the other scriptural references to it. "Inspired" makes some sense, but "literal" is not a word that ought to be used for Genesis 1 (or any of the poetic pa
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