Posts with Comments by Mike McKeown

IQ and “conventional wisdom”

  • "Fuse your gametes with someone intelligent!" 
     
    It worked for me. Now if only the F1 would start showing some interest in gamete fusion.
  • The Wisdom of Repugnance

  • Chargaff also said (from memory), re Watson and Crick, "That midgets such as these cast long shadows only shows that it is late in the day." (Heraclitean Fire)
  • IQ and Higher Education

  • Razib is correct that the tails are raised for IQ. I don't know about other traits. My decidedly PC Psych 1 prof taught me this and attributed it to assortative mating, unintentionally admitting heritability (possibly leaving environment in play). 
     
    In any case, using the Razib Heritability/Regression to the Mean Application is useful, as long as we recognize that it may, because of raised tails, UNDER represent the degree to which parents at the extremes of the scale may be represented at that level by their children (i.e. their kids will be above (top end) or below (bottom end) the statistically predicted level). The error favors Dr. Charlton's argument.
  • There is a very useful application relevant to this discussion on Razib's SciBlogs. 
     
    This is written to calculate predicted heights of offspring given parental height, but it is flexible so you can change the parameters and instead of getting height you get the trait that interests you. Substitute any metric you like for height, use reasonable parameters for average and SD on that metric, and calculate what your kids, or somebody else's, will be. 
     
    Relevant to this post, this can serve as an IQ predictor (e.g. make avg for both parents 100, SD=15, heritability 0.5). For two parents at 145 (+3 SD above population average) the expect IQ is 122.5 = +1.5 SD >population average. Only about 2.25% of children will be above 137.5 (+2.5 SD above pop average).
  • When Histories Collide: The Development and Impact of Individualistic Capitalism

  • The quote "The milk, which weights roughly 1 lbs. per gallon," 
     
    has to be a typo, both because a gallon is 8 pints, which for water is 8 pounds, and because the back of the envelope calculation uses 10, not 1. 
     
    8 vs 10 lowers the yield number by 20%, but milk still beats meat by about an order of magnitude. OTOH - half the calves are male, and cows have to be kept close to home to be milked, so there should be a niche for free-ranging the males. Also, I seem to remember that milk is low in iron, which would be found in the dry food. This is true, perhaps more so, in places not amenable to larger scale farming.
  • Pleiotropy in melanocortin receptors

  • You have just given a great idea to sci fi writers, and I am sure The Next Generation will feature striped, spotted, etc. humanoids of many colors.  
     
    A colleague of mine has considered how things might be if tyrosinase were encoded by a gene on the human X chromosome. Think pinto ponies.
  • SNPs don’t lie

  • Diseases listed in the article, in just one sentence: 
     
    "A sample of Gaucher disease patients show a startling occupational spectrum of high IQ jobs, and several other Ashkenazi disorders, idiopathic torsion dystonia and non-classical adrenal hyperplasia, are known to elevate IQ."
  • Hypotheses are overrated

  • Genomic association studies seem formally similar to genetic screens for mutations that alter a specific biological function of interest (e.g. embryonic body plan in Drosophila). Both hinge on the idea that there are indeed genes controlling the process. If they succeed, then the genes identified are candidates for deeper, hypothesis-based study. The genetically identified genes have the advantage that we know they actually contribute to the normal process at some level. 
     
    Human diseases are more problematic as the mapping is harder and the mutations are catch-as-catch-can. For these, association with particular SNPs is a powerful way to localize candidate genes, especially with a sufficient pool of genomes to scan. Even in the case of implicated SNPs, I'm willing to bet that if there is a nearby gene with a series of well defined motifs, and one that is lacking or short of well defined domains of known function, all the action will go to the gene that looks like something we already know. 
     
    By this logic, association studies, like large screens for new mutations, are the beginning of the process, not the end. For human traits, Association is a powerful way to search for candidate genes and should be used well and often. As with genetic screens, some loci will, for various reasons, seem better candidates for initial study. In the case of associations, the stronger the association with the trait (which already requires a substantial data set on the phenotypes of people in the study), the more worthy of immediate study. In any case, from that point on, this is still Popper in action. 
     
    One final comment. Those who do genomic/proteomic/computational studies often introduce their talks by touting their methods over hypothesis test approaches, and then proudly describe what they do as ?Discovery Research.? For those in the audience who have been making discoveries for some time without calling their research ?Discovery Research,? this is irritating arrogance. This feeling is compounded at the end of many of these seminars by the paucity of any meaningful conclusions or take home messages other than, ?well, we have some genes that might be involved?, or ?some potential regulatory sites?, or ?some genes are expressed more and some are expressed less.?
  • Scientific American: Summers makes a fine strawman

  • In a way not directly related to this posting, Scientific American has been deteriorating for the last 10 years, at least. Indeed, each month, I feel that SA has become more of a clone of Discovery. 
     
    More and more articles written by science writers rather than scientists. More and more articles specifically chosen because of their topical nature. More and more political advocacy and more and more emphasis on public policy and not on basic science. Lamer and lamer columnists (Martin Gardner how I miss you). 
     
    As a kid I read SA because my Dad picked it up at the newsstand every month. We flew SA airplane contest winners, and had soma cubes. I fondly remember Dr. IJ Matrix and his daughter Eva, and knew about split brain baboons, as well as continental drift. In college, one of the main texts for the first quarter of the Bio Core was a collection of SA articles on molecular biology. I bough GEB based on a Martin Gardner review, Phil Morrisons? book reviews were great.  
     
    Now we get ever less intelligible string theory summaries and a PC columnist on third world issues.
  • GNXP survey

  • Looks like a real advertising opportunity at GNXP for the well-off, highly-educated, non-believing, largely libertarian market.  
     
    With a market that size, imagine the money just waiting to be made.
  • Math Test

  • All OK 
     
    Intel iMac Safari 
     
    10.4.10
  • Evolution by mutations of large effect…or not?

  • Drosophila naming conventions are not as simplified as nematode naming systems, nor as arcane as the numerous names given to the same mammalian protein or protein-like activity. They are simply based on the mutant phenotype of the early alleles recovered.  
     
    White mutants have white eyes. Wingless reflects the phenotype of the first homozygous viable allele, rather than the stronger phenotypes of null alleles. OTOH, it turns out to be substantially important across phyla. Notch reflects the dominant phenotype of the first allele, a notch in the wings. Aceate and scute (both reflecting a lack of bristles) are key bHLH proteins involved in cell type determination downstream of notch. Hedgehog may be initially named after the larval mutant phenotype (nulls have a lawn of 'deniticles' (hair-like cuticular protuberances normally found in limited areas of the ventral portion of each segment)) leading to the name, but the mammalian versions were given names associated with a video game. 
     
    Shavenbaby describes an embryonic lethal mutation that removes the hair like structures (tricomes) on embryonic larvae. In this context, the name makes sense, particularly since this describes a loss-of-function phenotype of sufficient severity to be lethal. All of this developed in the context lacking molecular data. Nematodeologists use a similar system, but with a simplified set of nameable phenotypes: Uncoordinated (unc), sickly short and maybe fat (dumpy, dpy), lethal (let), etc., each followed by a number indicating isolation order. (Is it easier to remember acheate, scute and notch or Let 13 26 and 30?) 
     
    Human gene names are either based on a single biochemical assay or a disease, neither of which are more informative than either worm or fly names. Since the fly community and worm community spotted so many of the key genes first, the MDs are now worried about unPC names and are trying to develop a seemingly meaningless nomenclature that won't irritate patients (trying to avoid the Far-Side-cartoon scenario of saying to a patient, "Mr. Farnsworth, I'm sorry, but you have cows." 
     
    BTW, if building a functioning body is compared to building a house, the mutants people who work on worms and flies generally concentrate on are the things involved in making solid foundations, building walls, floors, roofs and critical aspects of plumbing, heating and insulation. What human genetics finds are all the add ons that happen after those key events have happened. The things that people of who study flies and worms fined would generally be lethal in humans. Human diseases, or variants, occur in 'animals' in which the more fundamental things went very well.
  • New GRE cancelled – the cost of attempted gap-reduction?

  • Re the need to have means and SDs by sex (or in other cases, race). This info is available for a number of past years for both verbal and math SAT. ONE can't necessarily accurately compare male and female means because substantially more females took the test, which is usually an indication of an increase in weaker students. OTOH, the math scores from 2004 above 600 are male biased, with boys above750 outnumbering girls about 21K to 9 K. 
     
    The desire of elite universities to make the SAT match the world as they want it to be is certainly real. One can argue that Dick Atkinson (former Chancellor for the whole University of California system, and a former psych prof at Stanford) was the driving force against verbal analogies. His public complaint was that kids in private schools and elite public schools were practicing them in school, making this artificial and directly $ biased. 
     
    Atkinson further argued, only slightly more subtly than I will present it, that the SAT I (verbal and math) is an IQ test and not a test of what a student can really accomplish or what he or she has learned. Thus, it is obviously not as important as something that tests what a student has learned. Thus, UC has downgraded the weight it gives to the SAT I and made up for it with heavier weighting on the SAT II (subject tests). They have also pestered the SAT people to make the SAT I more a test of learned material than of intelligence. One might infer from Agnostic's post that Atkinson was was using one prevarication (questions of bias resulting from socioeconomic status etc and the test) to hide a second unstated problem, sexual dimorphism. 
     
    The great irony in this is that the SAT I was originally designed by the elites to open up top universities by identifying students who had real intellectual potential but did not have the background (either social or via access to top K-12 schooling(socially loaded as well)) to necessarily stand out. Now, they want to get rid of the 'real' SAT since it probably does spot talent, but not of the diverse mix wanted. 
     
    One point not mentioned about the GRE: It has already been weakened. Years ago, it was just Verbal and Math. Then somewhere along the line, they added an 'Analytical' test, which I gather was based on logic problems. This came with clear 200-800 scores. Recently this has been changed to 'Analytical Writing'. This is certainly not the same as a logic problem test and obviously has a major subjective grading component, with grades in half unit increments from 1-6.
  • Swappable DNA Module in Bacteria Gives Light Harnessing Ability

  • This seems like really old news to me. We have been aware of bacterial rhodopsin for at least 30 years and knew that it acts as a proton pump allowing production of ATP in the usual electron transport way.  
     
    This has been all over the news, but it seems that all they did was add one such gene to E.coli and find Ta DA!! A proton gradient. 
     
    Did I miss something?
  • Emma Darwin, novelist (again)

  • She writes, "The Darwin writing DNA, as it were, is recorded in innumerable books and their indexes."  
     
    Aside from Darwin family inbreeding, she is substantially reduced in Darwin's genes.
  • The Economist

  • Three generations of my family feel that The Economist is the best news magazine in America.
  • Arc-o-mania

  • I have long been amused by the way multiple different groups can all independently find the same thing in time to be published in the same 'Cool' press journal (or competing Natural Coolish Science press journals) on the same date. 
     
    It makes one marvel at the originality of basic research. 
     
    Rather reminds me of the 'simultaneous' discovery of reverse transcriptase, or the dictum of my youth, "Autoclave all correspondence."
  • Rushton

  • The College Board makes lots of information of this kind available to those with web connections.  
     
    I have in front of me the report on the SAT class of 2004. It has recentered scores going back to 1972. The male-female split in average math score holds constant at ~35 points. One SD is about 114 pts for 2004. For verbal scores, the male scores are higher at all years, but average about 5-10 points with an SD of 112. 
     
    In recent years the number of women taking the exam exceeds the number of men taking the exam, perhaps confounding the interpretation of average scores, as one expects that an increase or decrease of test takers happens mostly at the lower range of scores. 
     
    For 2004, the distribution in bins of 50 points (e.g. 750-800, 500-549) is given for Males and Females. 660,270 males took the test, 758,737 females. On the math test, 21,507 males were above 750, with 9,800 females above 750. Males exceed females in all bins above 600, and trail in all bins below 600. In the verbal test, males barely exceed females in the bins above 700, and trail in all bins below 700. 
     
    For those interested, the means and SDs for males and females in various self reported racial/ethnic groups are given as well. In general, the 30 pt difference in math scores holds across groups, as does the 5-10 pt difference in verbal scores. 
     
    Not surprisingly, scores increase with parental income and parental education. 
     
    If interested, go to http://www.collegeboard.com/sat/cbsenior/yr1996/nat/cbs1996.html for links to reports from 2006 back to 1996.
  • Green pigs and journalist’s scientific illiteracy

  • GFP does not glow green except in response to stimulation with UV light. Unless you want green pigs in the haunted house at DisneyLand, the green pig is just for show. 
     
    On the other hand, the use of animals having a mix of GFP expressing cells and non-expressing cells (produced in any one of a number of ways) is an extremely powerful way of marking cell lineages in a number of different organisms. Except for the most external of structures, e.g. skin, or the smallest, clear animals (e.g. nematodes, zebra fish, sometimes fly larvae), little information can be gathered about internal structures without dissection.
  • 10 questions for Ken Miller

  • Re EvoDevo 
     
    Since the discovery that homeo domains are conserved across vast evolutionary distances, and the ever increasing number of gene sequences available, the principle of conserved function across phyla has been a major aspect of modern biology. 
     
    Indeed, my perception is that for a number of years the fastest way to make progress in mammalian embryology and pattern formation was find out the most recent results from Drosophila and nematodes and see if the same genes are present in mammals. This was, and still is, a highly effective strategy. 
     
    In addition, comparisons between closely related species that differ in specific aspects of development and differentiation has been quite informative as to mechanism of change between lineages. The example of sex-specific changes in expression of brick-a-brack resulting from changes in transcription factor binding sites serves as clear paradigm for evolutionary changes between species and phyla unrelated to changes in the protein coding sequnce.
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