|
Sunday, July 31, 2005
Seething Unease Shaped British Bombers' Newfound Zeal.
Related: Profile of Salafi jihadists.... Update: A British Jihadist. Update II: This part of the article from The Prospect (an interview with a gleeful radical) is interesting:
The above is why I have mooted the idea of a new historically contextualized view of the Koran as being an option for some "Muslims." Right now this is a discounted view, and so you have to push the argument over to one of interpretation on the next level. If you read the interview above though, note how sly some of the redefinitions of terms of the radical are. Note: Value added comments appreciated!
Saturday, July 30, 2005
Dienekes reports on recent extractions of mtDNA from remains in the Iberian peninsula1...not surprisingly (to me at least) there is continuity between the ancient populations and modern ones. This is relevant to debates about replacement of various aspects of the identity of one people by another. In places like Hungary, Spain or France it seems like there was elite replacement of the substrate language and culture (though not alleles). In contrast, in places like Bulgaria or Assam the substrate absorbed the elite. But, a problem crops up when people try and extend these particular cases to the whole world as if they hold true like a scientific law. For example, the recent story that "Britains have changed little since Ice Age" is a bit too neat, and fits into an archealogical bias that is part of the backlash against excessive typological thinking about "nations" before 1950. That is, the English nation were a volk of one tongue and one blood, which replaced the British ethnos in the 6th century, as hinted in Gildas' writings ("The barbarians drive us to the sea"). Rather, the archealogical and historical paradigms now tend to presume that the replacement of the British by the English was one of elite cultural imposition. If you read the old post Celts and Anglo-Saxons you will find that the "truth" as suggested by the genetic data that is emerging in the last 5 years is more complex than either replacement or acculturation.2 Strictly speaking the assertion that the peoples of the United Kingdom are descended from Ice Age Northern Europeans is probably correct, because even if there was an influx of alleles from Germany in the 5th and 6th centuries the two populations were not particularly distinct (well, at least in comparison to "Neolithic farmers" from the "Near East").
Since islands are relatively simple systems (migration is often constrained to choke points) I leave you with a post Japanese origins. 1 - I assume the reference to "Iberians" implies the peoples of the southern half of the peninsula, who in pre-Roman times spoke their own languages unrelated to Celtiberian and possibly distant from the Basque dialects. The people of Tartessos are the most prominent representatives of this cultural complex. 2 - I have read recently that the transition from a Celtic to an Anglo-Saxon peasantry was marked by a shift in the layouts of field and village in much of the east of England. Such changes could be triggered by cultural diffusion, but since the change wasn't functionally that important it suggests to me that there was some replacement of a Celtic peasantry by Germanic settlers who brought their own traditions and customs.
This poll is directed at regular readers....
Results from past reader surveys below.... Political Orientation Far Right 11% 24 Moderate Right 26% 56 Centrist 8% 18 Moderate Left 15% 33 Far Left 3% 6 Libertarian 26% 56 Other 9% 20 Questions about God (sort of) I believe in a personal God 17% 35 I bellieve in a impersonal God 8% 17 I believe in a supernatural force 8% 16 Am skeptical of supernatural entities 25% 51 Really don't believe in that kind of thing 43% 88 What is your religon? Protestant 14% 29 Catholic 10% 21 Orthodox 1% 3 Other Christian 2% 5 Jew 4% 9 Muslim 2% 5 Hindu 4% 9 Buddhist 1% 3 Other religion 3% 6 No religion 57% 119 Who are you voting for (if American) Kerry 33% 54 Bush 26% 43 Nader 3% 5 Libertarian guy 9% 15 Other 5% 9 None 23% 38 Results so far.... How did you find this web site? Search engine 19% 43 Word of mouth (includes email) 5% 11 Instapundit 6% 13 Steve Sailer 38% 85 Blogroll of a weblog (besides Instapundit or Steve Sailer) 13% 28 A link in a post on another weblog (besides Instapundit or Steve Sailer) 14% 31 Discussion forum 1% 3 Comment of GNXP poster on another weblog 4% 8 222 votes total
Thursday, July 28, 2005
On many measures, identical (monozygotic, MZ) twins are not in fact "identical", despite the fact that they share essentially identical DNA and highly similar family environments. Indeed, for some traits, such as personality, all non-genetic effects appear to be of the kind that makes siblings different than one another. Peer socialization is one plausible source of this non-shared environment, but stochastic biological events probably play a role as well.
These stochastic effects are seen prominently in studies of aging in the worm C. elegans. Even when genes and environment are held constant[1], there is considerable variation in lifespan (time of death) within a population. (Almost as much variation in relative lifespan as the human population of the US.) A paper published this week in Nature Genetics (ironic) reports that chance variation in the level of induction of a stress-induced reporter predicts (to some extent) variation in lifespan. When both genotype and environment are held constant, 'chance' variation in the lifespan of individuals in a population is still quite large. Using isogenic populations of the nematode Caenorhabditis elegans, we show that, on the first day of adult life, chance variation in the level of induction of a green fluorescent protein (GFP) reporter coupled to a promoter from the gene hsp-16.2 predicts as much as a fourfold variation in subsequent survival. The same reporter is also a predictor of ability to withstand a subsequent lethal thermal stress. The level of induction of GFP is not heritable, and GFP expression levels in other reporter constructs are not associated with differences in longevity. HSP-16.2 itself is probably not responsible for the observed differences in survival but instead probably reflects a hidden, heterogeneous, but now quantifiable, physiological state that dictates the ability of an organism to deal with the rigors of living. The astonishing implication is that similar reporters could be found that predict the chance variation in human lifespan (or other dimensions of human biodiversity). How did they do this research? First, they created a strain of worm which fluoresces in response to exposure to high temperatures ("heat shock") (panel "a" below). The "heat-shock gene" hsp-16.2 is expressed when worms are heat shocked. The promoter of hsp-16.2 was joined with the protein coding sequence of green fluorescent protein (GFP) and this construct was integrated into the worm's genome. The intensity of GFP expression (measured by fluorescent intensity) is variable within an isogenic population (panel e). For their experiments, young adult worms were exposed to a heat shock (panel b) and then some time later they the worms were sorted into high, medium and low GFP subpopulations (panels f-h). The level of GFP expression becomes more variable at later times (panels c-d). The GFP expression level is not heritable: the progeny of worms from the high and low groups are indistinguishable when tested for GFP induction.  After sorting into three subpopulations, worms were tested for lifespan (panels a-c) or thermotolerance (i.e., lifespan at high temperature; panels d-f).  Numerous controls follow. The biggest problem for their study is that heat shock is known to cause increased lifespan on its own. They don't claim to have overcome this confounding effect, and so it seems to me that differential GFP expression may actually be a marker for this effect. 1 - C. elegans has two sexes: male and hermaphrodite. Hermaphrodites are self-fertilizing. Selfing allows for the production of genetically homogenous populations (except random mutations). Worms are grown on solid media in Petri dishes ("plates") or in liquid cultures. Worms living on the same plate are essentially experiencing the same environment, but undetected variation may exist between different plates or within different regions of the same plate.
Drudge says that Bill Frist will back stem cell research funding.
I'm conflicted, Discovering functional relationships: biochemistry versus genetics:
I've cut & pasted the text below, it works out in the end. Introduction For more than ten years, Doug, a retired biochemist, and Bill, a retired geneticist, have lived on a hill overlooking a car factory, debating their strategies for reverse engineering a car (see: http://www2.biology.ualberta.ca/locke.hp/dougandbill.htm). Doug advocated rolling up his sleeves, getting under the hood and determining how the parts fit together. Bill preferred tying the hands of a different car-factory worker each morning, then relaxing with a cup of coffee and later examining the cars that emerged from the factory. One day, Doug and Bill strolled over the next hill. In the midst of debate, they encountered Sharyl, a graduate student in computational genomics. Having overheard their debate, she interjected, ‘I don't know much about cars, but I detect an analogy to biochemistry and genetics. I'm trying to discover functional relationships between genes and proteins in yeast and I wonder which of your strategies would work best.’ Differing approaches to determining gene function To discover functional relationships, Doug would ask, ‘Which proteins physically interact with my favorite protein?’ By contrast, Bill would perturb the DNA sequence of a gene and observe the consequences in vivo, asking ‘What are the genetic interaction partners of my favorite gene?’ In other words, ‘Which genes produce surprising phenotypes if mutated in combination with my favorite gene?’ Sharyl described how the fields of biochemistry and genetics had ‘gone genomic,’ scaling up their classical approaches to discover functional relationships with ever-greater efficiency. Their resulting systematic studies offered a playing field on which to assess Doug and Bill's dilemma. Sharyl then wondered, ‘Which type of interaction – protein or genetic – is better at revealing functional relationships?’ She pulled out her laptop computer and set to work (Figure 1). Protein versus genetic interactions in predicting functional relationships Because ‘gene function’ is vaguely defined, Sharyl used the Gene Ontology (GO) vocabulary, which describes gene products in terms of biological process, cellular component and molecular function (http://www.geneontology.org/) 1 and 2. She defined three measures of functional relatedness for a pair of genes: (i) shared GO biological process (shared process); (ii) shared GO cellular component (shared component); and (iii) shared GO molecular function (shared function). For example, if two genes were assigned to the same GO biological process category, Sharyl considered the gene pair to have a ‘shared process’. To avoid associations between genes in broadly defined categories, she considered only specific GO categories – those to which 200 or fewer genes (out of not, vert, similar6000 total yeast genes) were assigned, including genes assigned to more specific daughter categories. To represent the biochemists, she chose a high-confidence protein-interaction data set based on affinity purification followed by mass spectrometry (APMS) [3]. For the geneticists, she fielded a recent systematic genetic-interaction data set [4] (Tables 1 and 2 in the supplementary data online; Box 1). Protein and genetic-interaction screens Synthetic genetic array (SGA) analysis is a high-throughput method that assesses pairs of genes for genetic interaction 4 and 19. A strain carrying a mutated query gene is crossed to an array of not, vert, similar4700 strains, each mutated in a different non-essential yeast gene. The resulting double mutants are then assessed for fitness. Slow growth or lethality relative to each of the single-mutant strains is declared synthetic sickness or lethality. In the SGA data set used here, 159 query genes were crossed to the array, resulting in not, vert, similar730 000 gene pairs tested for genetic interaction. Based on this data set, the genetic network is between two and 54 times more dense than the protein-interaction network. Affinity purification followed by mass spectrometry (APMS) is used for high-throughput discovery of physical protein interactions. A ‘bait’ protein is precipitated in a complex with its interacting proteins. Members of this ‘pulled-down’ complex are then identified by mass spectrometry. The two large APMS studies in yeast are known as the tandem affinity purification (TAP) [3] and high-throughput mass spectrometric protein complex identification (HMS-PCI) [6] studies. In both studies, the data can be interpreted in two ways. The spoke interpretation defines an interaction between a bait protein and each protein it pulls down. The matrix interpretation, however, counts interactions between all pairs of proteins pulled down by a bait. In the TAP study, bait constructs were integrated into the yeast genome and expression was controlled by an endogenous promoter. In the HMS-PCI study, however, the bait construct was plamid-borne and expression was controlled by a robust exogenous promoter. Thus, the TAP data set is more likely to be physiologically relevant, although the HMS-PCI study could detect interactions between gene products not normally expressed in the condition examined. The TAP and HMS-PCI data sets employed 1167 and 725 baits, respectively. A gene pair was considered assessed for protein interaction, if at least one gene of the pair was a bait and the other was not filtered out as a ‘promiscuous prey’ [6]. Yeast-two-hybrid (Y2H) is a high-throughput method for assessing direct physical interaction between two proteins (although indirect ‘bridged’ interactions can also be detected). Here our Y2H data set consisted of the union of the interactions reported by Uetz et al. [18] and the ‘core’ version (corresponding to interactions detected at least three times) of the data set produced by Ito et al. [17]. To level the playing field, she considered only the 104 409 gene pairs (the ‘arena’) assessed by both approaches and for which both genes in each pair had a GO annotation. In this arena, the number of gene pairs sharing a specific GO process, component or function was 3841, 1803 and 1139, respectively. The arena contained 48 biochemical interactions and 729 genetic interactions, derived primarily from screens involving the 17 genes used both as baits in the protein-interaction screens and as query genes crossed to 4500 mutants in synthetic genetic array (SGA) analysis. Interestingly, there was no overlap between the protein and genetic interactions (Table 3, supplementary data online). A previous related study [5] did not consider whether gene pairs had been assessed for both types of interaction and used literature-derived interaction data, which are subject to inspection bias. With a few taps on her keyboard, Sharyl let the games begin. Two proteins exhibiting a protein interaction had a shared process, component or function 42% (P=2e-17), 31% (P=2e-15) and 29% (P=1e-16) of the time, respectively. Genetic interactions were uniformly less-accurate indicators of shared function, with corresponding rates of 19% (P=2e-63), 15% (P=2e-66) and 8% (P=2e-28). However, genetic interactions detected gene pairs with shared function with much higher sensitivity (4–6%) than biochemical interactions (0.5–1.2%; Table 4 in the supplementary data online). When considering different physical-interaction data sets 3 and 6 (Box 1), genetic interactions were consistently more sensitive and sometimes more accurate (see Glossary; Table 4, supplementary data online). Thus, it was difficult to declare a clear winner. Combining genetic and protein interactions with other data Are genetic interactions combined with other types of evidence more informative than protein interactions combined with other evidence? Rather than considering each type of interaction in isolation, several groups have previously combined heterogeneous data, using machine learning approaches to predict some property of a gene pair or to predict gene function 7, 8, 9, 10, 11 and 12. Therefore, Sharyl combined multiple types of evidence [11] – including co-localization [13], sequence homology [14], correlated mRNA expression 15 and 16 and chromosomal distance (Table 5, supplementary data online) – to predict shared function. She chose a previously described probabilistic-decision tree approach [12] and compared performance with and without the benefit of protein and/or genetic-interaction data. For each of shared process, component, and function and for each choice of input data, she performed cross-validation: she randomized all gene pairs in the arena into four groups, and successively scored each group using a model trained on the remaining three. She then compared the prediction score of each gene pair with its corresponding shared process, function or component status. A plot of true- versus false-positive rates revealed that genetic and protein interactions were comparable at low sensitivities; however, as sensitivity increased, genetic-interaction data enhanced performance more than protein-interaction data. This trend was observed for shared process (Figure 2), component (Figure 1a, supplementary data online) and function (Figure 1b, supplementary data online). Doug, the biochemist, began to despair. Before Bill could begin to gloat, however, Sharyl showed that genetic- and protein-interaction data together gave markedly better results than either alone, suggesting that each offers distinctly different types of information. Although protein interactions can represent associations between genes in the same complex or physically connected pathway, genetic interactions can additionally reflect relationships between genes in physically non-interacting pathways. She repeated this analysis with another APMS protein-interaction data set [6] and then with the union of two yeast-two-hybrid (Y2H) data sets 17 and 18 (Tables 1 and 3, and Figures 2 and 3 in the supplementary data online), altering the arena appropriately. In each case, genetics beat biochemistry by a slim margin, but the combination of these complementary interaction types outperformed either alone. Sharyl's results convinced Doug and Bill to shake hands and head back over the hill … until new data or new technology call for a rematch.
Seems like there is some intellectual cannibalism going on over on the Left. The Savage Minds anthropology weblog is being stomped on from all angles of the Progressosphere because they dared to point a sharp object at Jared Diamond. Kerim has the round up. He pointed to us back when Greg & Henry's paper broke and I appreciate that, but my experience on that weblog is that it has a pretty standard liberal slant, so I'm sure this episode of being broadsided by big names in the Progressosphere must be somewhat surreal. Anyway, the original post that started this actually referenced Guns, Germs and Gonads, you know, to show the racist perspective. Also check out Henry Farrell's post. I think I agree with him that Ozma does throw around the term "racist" in a cavalier fashion. Shit gets complicated when you are trying to stay on the politically correct side all the time.
Addendum: Since I've been a bit priggish about concepts, categories and precision recently, I will admit I probably elided over great differences within what I termed the "Progressosphere" because I'm not too political and my own inclinations are pretty orthogonal to the center to Left axis. So yeah, they aren't all Muguloos.
Here is a profile of a researcher who has been on the Cajun beat for a while now. If you are a member of a small relatively homogenous group which has weird diseases and keeps decent records, well, expect more of this sort of thing.
The article, The Christian Paradox is making the rounds. It starts:
Perhaps the readers of Harper's believe that Christianity is something you find in the Gospels (sola scriptura writ large), but if you are an unbelieving anthropologist you would say that a religion is lived by the people who profess it, and it is out here, not in there. This is relevant to the thread below where we discuss the future of (North) American Islam. If you are a believer in religion X, you are going to assent to creedal assertions a, b, c..., and the intersection of those assertions help define what a religion is fundamentally. But, if you are not a believer a religion is nothing fundamentally except for what the people who espouse it say it is, and to make that judgement you need to weight various semantical nuances in their proper context, ascertaining the character of a religion is not an act of faith but a cognitive process of category creation. Apropos of this, in the first chapter of Knowledge, Concepts, and Categories  I learned that:
I think the last is a problem in light of public policy disputes because we no longer live in bands of 100 people, we exist in a world where macroscale constructs which exhibit flux and continuity are the norm. 10,000 years ago there might have been 50 Muguloo tribesmen, and you could make pretty robust generalizations of those Muguloos, to the point where a distribution-population way of thinking was unnecessary. Today, you have 12 million Jews, or 1.2 billion Muslims, tens of millions of liberals and conservatives...but we still talk as if they were just a band of Muguloos.1 Additionally, the disjunctive tendency of categories (trait A OR trait B OR trait C) also causes confusions because people disagree about the particulars but never make their axioms explicit so that it is often the norm to just talk past each other. More later.... 1 - The closer a category or concept comes to one's own self-reference the more nuanced, precise and qualified one will get about defining it. Muguloos be damned!
Wednesday, July 27, 2005
One of the main reasons this site is around is to make basic genetic knowledge a casual background feature of the data bases of people who would otherwise not know much about this important science (another reason, at least for me, is to dump a lot of historical and non-science data out there to a scientifically literate audience so they can better form models which influence their view of public policy). So in that spirit, check out Using Karyotypes to Predict Genetic Disorders (it has some neat interactive movies, though if you know genetics, don't worry about it, but if you have been skipping the science posts for lack of a basic background, I advise you check out the link). Remember, to the first approximation it all starts out on basic Mendelian principles.
Przewalski's Horse:
Related to this, FISH analysis comparing genome organization in the domestic horse (Equus caballus) to that of the Mongolian wild horse (E. przewalskii):
Also, Invasive honeysuckle opens door for new hybrid insect species:
"Hybrid" speciation is pretty common in plants from what I know, but the issues surrounding animals are sketchier.... Related: Breakin' free of biology?
In Genesis 6:3 God states "...My spirit shall not always strive with man, for that he also is flesh: yet his days shall be an hundred and twenty years." And yet if you keep reading you note that many people do live beyond 120 year in the Bible. And in the past century people have lived past 120 years. Something is off. In a comment below one individual asserts that "religion - no matter what the denomination is, and always has been a logical absurdity." I believe when viewed as a system of axioms religious beliefs fall flat on their face due to an internal lack of coherency, and yet they persist.
But just because religion fails as a system of formalized knowledge about the world does not mean that we should chalk it up to historical forces (opium of the masses), abstracted psychological yearnings (wish fulfillment) or an inexplicable irrationality (mass hysteria). I have stated that the religious need seems to be rather lacking in my own person, but, two personal points should get across what I want to communicate: 1) I can still repeat Surah Fatihah, the opening passage of the Koran and the preamble to the daily prayers, when called upon to (in a language foreign to me, and without any ability to break the passage into "chunks"). 2) When I hear a call to prayer I have a difficult time expressing in words the peculiar chill that runs down my spine. One must keep in context the following facts: 1) I never really believed. 2) My Islamic education was minimal at best. 3) I have never lived in an area with many Muslims. If I could "delete" my knowledge of the Surah Fatihah, I surely would if that meant I could free up "space" for something far more interesting. But somehow it persists in my memory.1 Humans often live under the illusion that we govern ourselves fully consciously, but a moment of reflection on what you've done in the past hour would surely disabuse you of that notion if you still hold to it. You might have taken a shower, locked the door or turned the oven off with barely a recollection of the details, these chores have become "instincts." Many aspects of our nature are delegated to subroutines or helper programs, and we don't really have conscious access to what's going on down there. In theory we can issue a chain of commands, but don't expect the help to oblige you if they are of one mind. It recalls an acquaintance of mine who was raised a Born Again Christian, and though a vocal atheist now, he still listens to Christian music. Though he didn't believe in the message, the melodies and themes were familiar to him and still aroused an emotional response that he sought out. The importance of indepdent cognitive subroutines and emotional associations are just two of the facts that I believe make religion explicable. For whatever reason a minority of any given population tends to dissent from the dominant supernatural narrative of its locale, but unfortunately many of these individuals project their own peculiar psychology on to the rest of the population. I believe a good portion of this minority even verbally assents to the general supernatural narrative but recreates it so that it is intelligible in its own language (ie; theology). I suspect an understanding of religious process is possible, but we need to move beyond assuming that it is either a formal system of thought or that it is at its core irrational, and will never be accessible to systematic inquiry. 1 - Some Muslims would offer this as evidence of the miraculous nature of the Koran, but I could give other examples of things I can't forget that I would like to.
Tuesday, July 26, 2005
In 1998 the C. elegans genome was complete. Two years later we had the draft of the human genome. The connection between these two events is the "hook" for Andrew Brown's In the Beginning Was the Worm: Finding the Secrets of Life in a Tiny Hermaphrodite
 (also author of the The Darwin Wars, which focuses on the life of George Price and his influence on seminal figures in evolutionary biology like J.M. Smith and W.D. Hamilton). I actually didn't find the last part of the book that interesting because the topic has been pretty well done. Who wants anymore anecdotes on the toothy Jim Watson? Rather, the first 150 pages (out of some 200) which chronicled the persistence of the brilliant Sydney Brenner1 and the team of researchers that he gathered around him in the late 1960s and 1970s before the worm was "hot" is an interesting anecdote laced analysis of the sociology and psychology of science. This isn't surprising, Brown has a background as a religion reporter, which showed in The Darwin Wars, and here he goes out of his way to note the quirky socio-religious backgrounds of many of the early wormers (Quakers, Jews and other assorted nonconformists).There is scientific detail in the book, the simple anatomy of the worm is sketched out (~1000 cells, eukaryotic and multicellular, but not too much!), the benefits of selfing hermaphroditism is highlighted (recessives can be snatched out as one out of four self-crosses are homozygous on the two alleles which produce a non-dominant phenotype) as well as the utility of the rare males in swapping alleles between the lineages. I felt Brown spent way too much time ruminating on Brenner doing Assembly coding back ~1970, it boggles the mind.2 But the meat of the book is the sociology, personality and philosophy. Some of the anecdotes are really bizarre...who would have guessed that the first "picks" were actually toothpicks! The researchers would spend an hour each morning sharpening them and discarding their pile throughout the day. When one of them got the bright idea of sticking a platinum filament to a tong-handle Brenner disapproved, suggesting that brilliance doesn't forbid obstinacy. But there are also the "big picture" questions. How far can reductionism go? What is the worth of a model organism? Is there any real point in the Human Genome Project beyond the "It was there" aspect? The book only really gives a good answer on the last question, chalking up Sydney Brenner's skepticism of the enterprise to age and ego (Brown was gentler, but that's what he was saying). There are many golden roads, but many dark and thankless ditches in science, and I think the fact that for every winner (as the worm people were) there are innumerable losers. That's how lab science works, it isn't measured in individuals as much as man hours many times (the mapping of the worm nervous system for example seemed to be a chore of herculean tedium). The decisions people make aren't always justifiable, but some of the times their hunches hit paydirt. The good angel on your right shoulder and the bad angel on your left shoulder both give a skewed view of who you are to God on the day of judgement, but summed together they hit the proper mark. Science is filled with good angels and bad angels, and the God of Spinoza judges fairly in the end. Addendum: Non-science types might find the bitchness of the "fly" (Drosophila) people to the worm people pretty funny. I wonder though, do astrophysicists who study black holes look down on those who model neutron stars??? Update Rikurzhen: Most of the tools are now in place to dissect worm biology from a systems level down to molecules. If there is a logical limitation to reductionism, work on the worm will soon the bumping into it. The genome is complete and feature annotation is greatly simpler in a 100MB genome (worms) than a 3000MB genome (mammals). Reverse genetics using RNAi is ridiculously easy to do (>80% of known genes have been assayed by RNAi for many, many phenotypes). Worms can be grown to population sizes unimaginable for other multicellular model organisms, and many phenotypes can now be assayed with automation. But obviously the most important question is whether this model organism can keep producing new insights into (human) biology. I anticipate that "$1000 genome" sequencing technologies are going to accelerate work on new/existing model organisms just as much as they will human genetics. 1 - Brenner's father was an illiterate. He, on the other hand, matriculated as an undergraduate at the age of 14. 2 - I recall that back in the 1990s the WordPerfect guys were forced to write the app in Assembly so that they could be closer to machine language and optimize performance. Of course, soon enough Word blew them out of the water, partly because Microsoft could push it via its Office Suite, but also because they were coming out with new versions slapped together (I assume) in a human friendly VB IDE at a much faster clip.
In Razib's post Patents, genes and Jews some commentators raised concerns about the patents granted, so I thought I'd expound a bit on this particular issue.
There is a long legal debate underlying the patentability of claims that many critics feel should be classified as being within the Common Heritage of Mankind. I get the sense that many objections that we're going to see on gene patents in the coming years are going to be framed from such a perspective. We can go back to the 1600's and the writings of Hugo Grotius in Mare Liberum where he wrote about that the ownership of goods that were created by nature for common use should be forbidden and that common use is viable as long as the object can be used without loss to anyone else. He was at the time writing specifically about the laws of the sea, but many in the years that followed took these principles of international law to apply to to other realms, such as outer space and agriculture. Twenty-five years ago when Diamond vs. Chakrabarty was decided it brought the issue of patents for life forms front and center into conflict with with the principle of Common Heritage. The ruling set about a flurry of debate regarding plant life and how the gene poor but industrial West was robbing the poor, but gene-rich, Third World of their genetic resources with as much as 95% of world food crops originating in the developing world. If you're interested in the views of a defender of Indigenous Peoples who isn't as hysteric as the persecutors of the Human Genome Diversity Project, you might find this page to be of interest. The author doesn't begrudge the right of those scientists who add value to genetic material to profit from their work but champions the position of Indigenous Peoples so that they too may also profit from the seed material that is collected from their territory. He notes, afterall, that:
Does anyone else see the parallels to the genetic information that is being mined from Jewish, Finnish, and Icelandic peoples with most of the benefits flowing to the researchers? I wouldn't be surprised to see the same arguments flare-up as human gene patents more frequently find their way into the marketplace. If such a replay does come to pass, it might help to keep in mind how it played out with plant genetics. The effort to redress the situation resulted in a UN Agency, the Food and Agriculture Organization, at it's 22nd biennial meeting in 1983 to come forth with a resolution 8/83 that stated "plant genetic resources are a heritage of mankind and consequently should be available without restriction." This resolution, especially Article 2.1 (a) (v) in the Annex to Resolution 8/83, which read "special genetic stocks (including elite and current breeders’ lines and mutants);" put the FAO Undertaking in direct conflict with Diamond vs. Chakrabarty. Now politics being what it is, and especially UN-centric politics, I happen to think that the FAO undertaking had more to do with advancing the dead horse of the New International Economic Order than it really did with settling the issues of intellectual property law, the prinicples of CHM and International law. The developed nations were opposed to the FAO undertaking and its attack on IP law and property rights and their position had three main pillars: 1.) A price can't be assigned to raw germplasm because, while there may contain useful genes, until those genes are evaluated and traits identified, the germplasm is an unknown quantity. 2.) The collection of germplasm doesn't deprive a country of a good or benefit. If utility isn't lost, then there is no claim for compensation. 3.) The FAO undertaking was inconsistent with Intellectual Property rights. The FAO Undertaking would have had to overturn quite a number of patents, and and for the expired patents, their history and reasoning, such as that found in patent #141072 granted to Louis Pasteur for claiming "yeast, free from organic germs of disease, as an article of manufacture" and precedents established in cases such as Argoudelis, Feldman v. Aunstrup, and a host of other rulings. What we're seeing with the BRCA2 gene is the gene has existed in certain populations but there was little that could be done medically with regards to its effects until BCRA2 was evaluated and it's traits identified, and therefore it remained an unknown quantity. Myriad Genetics has though their work in identification and evalution brought value to the identification of the gene, therefore the test for the presence of the gene is their intellectual property. The fact that it is targeted predominantly at Jewish populations who provided the "raw material" for study doesn't unfairly target them, nor does it exploit them, for without the research performed by Myriad Genetics the presence, and identification, of BCRA2 within the population wouldn't by itself create any value. The study of Jewish genes doesn't deprive the community of any goods or benefits and as a community they don't lose any utility of those genes, so it's difficult to base a claim of exploitation when a test for BCRA2 is offered to the commmunity.
Slate has an interesting piece up that highlights the controversy with patenting aspects of the BRCA2 gene. Of course the article focuses on the specific case of Jews, but as far as the ultimate issues of intellectual rights relating to genetic sequences and the methods to ascertain their identity, this is the tip of the iceberg. Today we are squabbling over music and film, but in the near future I suspect that we are going to focus less on such trivialities.
Monday, July 25, 2005
Randall has a long post up where he highlights a book titled The Impossibility of Religious Freedom, which addresses the legal implications of religious pluralism. There are many complicated issues here, and I simply ask readers to check out the facts for themselves, but not get too caught up in the details. From the introduction:
I have read a fair amount about the Reformation as well as the history of Northern Europe in the 16th and 17th century and I support one of the contentions of the author that something rather peculiar happened in places like England1 and The Netherlands during this period, and the full flower of that process can be found in the United States, a nation that gives expression to Christianities, but no support for one state church. Of course, there isn't a sharp dichotomy between the "Protestant model" and everything else, there is after all a difference between 16th century Spain or 21st century Saudi Arabia and traditional Chinese or Indian attitudes toward pluralism of faith.2 Also, note that one reason I believe Roman Catholicism has been such a success in the United States is that operationally it has become a Protestant religion here, when I listened to Catholics being interviewed on television after the priest scandals talking about how "they cared more about their relationship to Jesus" than "the edicts of the Church" it really struck home. Many Jews also mock the Reform as (in the words of John Stewart) "Christians with curly hair," but again, the introduction of organs and other Protestant motifs and the popularity of personal "spirituality" as opposed to adherence to the norms of halakah suggests to me a definite inward Protestantization of that faith as well. Will Herberg's Protestant-Catholic-Jew triumvirate was possible in large part, I believe, because the latter two were fast renorming themselves to adhere to mainline Protestant mores. 1 - Please note that there were multiple Reformations (including a Catholic one, what is termed the "Counter Reformation"). To say that the Protestant Reformation resulted in the trend toward disestablishmentarianism is to ignore the reality that in much of Germany and Scandinavia Lutheranism was closely identified with the temporal powers that be, that in Geneva and Scotland Calvinism became the state church (with some bumps in the road in the latter case). Rather, the road to disestablishmentarianism was seeded by the intransigence of groups like Baptists, Quakers and other assorted "Free Thinkers" who simply could not or would not submit themselves to the religious establishment and had abandoned any pretense of universal societal salvation. The difference between the Roman Catholic and Protestant models was not their mode or median, that is, as a whole Protestantism was not more or less predisposed to disestablishmentarianism than Roman Catholicism, but there was far greater variation because of the nature of Protestantism. It could be argued that in many parts of the Roman Catholic world the church was more separate from the state than in parts of the Protestant world (ie; Scandinavia), but for every Denmark you had a Holland. 2 - Many Hindus take pride in the fact that religious minorities like Jews and Parsis came to India to escape persecution, and rightfully so.
It seems that the lads in Iraq can find some free time to make an absolutely hilarious music video entitled "Is this the way to Armadillo?"
Click here to watch "Is this the way to Armadillo" UPDATE: Here is the version done by Dutch troops stationed in Afghanistan. Here is the original version that the soldiers are spoofing. Here is the BBC story on how the demand for this video crashed military servers.
RAPID EVOLUTIONARY ESCAPE BY LARGE POPULATIONS FROM LOCAL FITNESS PEAKS IS LIKELY IN NATURE:
|
