Saturday, April 19, 2014

Core concepts in genetics

I stumbled across an article in Science & Education that caught my eye. The authors discuss the way genetics is taught in introductory university courses (McElhinny et al. 2014). They quote several sources that define the core concepts of genetics that students must learn.

Here's the list ...
  1. DNA is the universal information molecule in living organisms, encoding genes and allowing for genetic variation within and genetic continuity between generations (DNA);
  2. Mendelian patterns of inheritance are directly related to the mechanisms of meiosis (MENDELIAN);
  3. Traits result from the expression of one or more genes working alone or together, with the environment, often in unpredictable ways (GENE EXPRESSION);
  4. The activities of genes and the environment regulate all developmental processes (GENES + ENVIRONMENT);
  5. Genetic variation underlies variation in traits, which is the basis for the differential survival and reproduction that allow populations to evolve (VARIATION); and
  6. The ability to analyze and manipulate genetic information raises a variety of complex issues for individuals and society (GENES + SOCIETY).
These six concepts for genetic literacy will hereafter be referred to as the core genetics concepts.
This is a strange list. Let me explain why.
  1. The structure of DNA and how it is expressed should be covered in other mandatory courses, including introductory biology and biochemistry. You should not have to spend any time at all on these topics in a genetics course. (P.S. DNA does not "encode genes.") You may want to spend some time on the biochemistry of recombination if it's not covered elsewhere. Students should understand Holliday junctions and how they are resolved.
  2. Mendelian genetics is important. Students should learn and understand the three laws he discovered. They should also learn about meiosis and sex. However, it's important for students to understand that simple transmission genetics is not limited to diploid eukaryotes. Bacteria also do genetics.
  3. Traits (phenotype) are due to information in DNA (not just genes) but most of those traits have very little to do with the external environment.
  4. Of course the activities of genes regulate development. They also regulate the citric acid cycle, photosynthesis, and protein synthesis. Surely you don't want undergraduates to think that development is the only thing that's important in genetics?
  5. It's important for students to understand that populations contain genetic variation. That means they have to learn about MUTATION and how it happens. They also have to learn why there's so much variation in populations—one of the most important discoveries in genetics in the last century. The answer is Neutral Theory and random genetic drift. No genetics course should leave out this important concept, especially because so few students will have never heard of it before enrolling in the course.
  6. Discussions about cloning, GM foods, and personal genomes are interesting but, unfortunately, there are very few scientists who can handle those issues in a genetics course. The important core concept is to get the science right and make sure students understand that getting the science right is absolutely essential whenever you discuss controversial issues.
  7. POPULATION GENETICS is an essential core concept in an introductory genetics course. You can't teach students about the genetics of EVOLUTION without it.
The authors discovered that only the first three "core concepts" were taught in every genetics course. Variation and mutation were taught in only 88% of the courses they surveyed. Only 63% covered GENES + ENVIRONMENT and only 9% covered GENES + SOCIETY.

McElhinn et al. (2014) discuss one possible change in the curriculum. It's a suggestion originally made by Dougherty (2009) and echoed by Redfield (2012). The idea is to "invert" genetics courses by beginning with coverage of poplations, variation, and complex traits. I strongly disagree with Rosie Redfield's proposal [see Questions for Genetics Students] but what surprises me in the McElhinny et al (2014) paper is that they can seriously list those core concepts without mentioning mutation and population genetics.


McElhinny, T.L., Dougherty, M.J., Bowling, B.V., and Libarkin, J.C. (2014) The Status of Genetics Curriculum in Higher Education in the United States: Goals and Assessment. Science and Education 23:445-464.
[doi: 10.1007/s11191-012-9566-1]

Redfield, R. J. (2012) "Why do we have to learn this stuff?’’—A new genetics for 21st century students. PLoS Biology, 10, e1001356 [doi: 10.1371/journal.pbio.1001356]

60 comments :

  1. Now why am I not surprised? For decades people in my department (and obviously in lots of others) have carefully placed the population genetics week last in their genetics course schedule. Then of course they run a bit late and don't have time to get to it. So they tell the class "Well, I haven't had time to cover population genetics, but it will be covered on the exam, so read the chapter on that in the textbook." And that's all the coverage it often got.

    In this case it actually fell all the way off the questionnaire.

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    1. Hi Joe,

      It would appear that great minds do think alike. Allow me to direct your attention to the latest incarnation of the AP Biology Curriculum Framework document. Its designers were very intelligent indeed and clearly concur with your way of thinking.
      http://media.collegeboard.com/digitalServices/pdf/ap/10b_2727_AP_Biology_CF_WEB_110128.pdf


      Enduring understanding 1.A : Change in the genetic makeup
      of a population over time is evolution.

      Essential knowledge 1.A.1: Natural selection is a major
      mechanism of evolution.

      Essential knowledge 1.A.2: Natural selection acts on
      phenotypic variations in populations.

      Essential knowledge 1.A.3: Evolutionary change is also
      driven by random processes.

      Essential knowledge 1.A.4: Biological evolution is
      supported by scientific evidence from many disciplines,
      including mathematics.

      OK – I will not bore you with all the details – so let’s skip ahead to

      Enduring understanding 3.A: Heritable information
      provides for continuity of life.

      Essential knowledge 3.A.1: DNA, and in some cases RNA,
      is the primary source of heritable information.

      Essential knowledge 3.A.2: In eukaryotes, heritable
      information is passed to the next generation via processes
      that include the cell cycle and mitosis or meiosis plus
      fertilization.

      Essential knowledge 3.A.3: The chromosomal basis of
      inheritance provides an understanding of the pattern of
      passage (transmission) of genes from parent to offspring.

      Essential knowledge 3.A.4: The inheritance pattern of many
      traits cannot (emphasis mine) : be explained by simple Mendelian genetics.

      Enduring understanding 3.B: Expression of genetic
      information involves cellular and molecular mechanisms.

      Essential knowledge 3.B.1: Gene regulation results in
      differential gene expression, leading to cell specialization.

      Essential knowledge 3.B.2: A variety of intercellular and
      intracellular signal transmissions mediate gene expression.

      Enduring understanding 3.C: The processing of genetic
      information is imperfect and is a source of genetic variation.

      Essential knowledge 3.C.1: Changes in genotype can result
      in changes in phenotype.

      Essential knowledge 3.C.2: Biological systems have
      multiple processes that increase genetic variation.

      Essential knowledge 3.C.3: Viral replication results in
      genetic variation, and viral infection can introduce genetic
      variation into the hosts.

      In due time, the effects of this new curriculum document should work itself through the educational system nationwide. Intellectual osmosis as it were.

      Before Larry jumps all over this - I want to remind everybody that this outline is designed to be a highschool student's first introduction to Biology before continuing on to university. So in other words - not at all bad!!! Quite good as a matter of fact,especially compared to precedent (IMHO)

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    2. @Tom

      That curriculum looks pretty impressive to me. What's the point of teacing "AP" biology in Canada?

      Delete
    3. @Larry: I do not understand your comment. "AP" courses in high school prepare you for an "AP" exam which gets you out of some elementary college courses. Are you saying this is unnecessary in Canada?

      @Tom: I'm glad to hear that the AP guidelines cover these topics. Does Common Core cover them as well? There is a lot of pushback from the crazier part of the right wing against Common Core because it allegedly leads to dictatorship simply by being a Federal program. (Except it isn't a Federal program but is a common set of guidlelines adopted by individual states). If the objectors had their ways they have their states never mention evolution in their K-12 courses except to "diss" it.

      Larry's original point, and mine, is that here McIlhenny et al. have bought into the omission of evolution. They have done so not out of creationism, but out of buying into the mindset of many molecular biologists, which does not consider evolutionary biology as ian important part of a molecular biologist's education.

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    4. Hi Larry – to answer your question:
      What's the point of teaching "AP" biology in Canada?

      Canada is the only country in the OECD that neither sets national standards nor has a coherent national education policy.

      I have taught Biology in three provinces and have come to the conclusion that aging and hopelessly out-of-date senior teachers must meet together to set curriculum in order that Biology can continue to be taught as it was 30 years ago when they were in university.

      That explains my need to frequent cyber-fora (such as your excellent site when it focuses on matters scientific).

      AP Biology is the only curriculum document in Biology available in Canada that merits consideration at a high school level. IB takes a distant second. Why distant? AP Biology is a student-centred inquiry-based discipline – ("discipline" I do not use the term lightly). AP does more than impart knowledge, it also fosters skills. Check out this relevant section of the curriculum framework document I list below.

      Last year was the first official year I actually taught AP Biology. My top student was just awarded an NSERC scholarship in his freshman year! He credits the rigor of the AP program. My remaining students are all near or at the top of their classes in a variety of universities.

      FTR – and by way of clarification, an AP course simultaneously represents two entities:

      1 - Completion of the course (without writing the exam) constitutes an advanced high school course credit. The AP designation on the report card is of paramount importance. An AP credit carries great prestige and influences the award of scholarships.

      2 - Successful completion of the AP exam constitutes a university credit. Whether or not a transfer credit is accorded is completely up to the discretion of the university. Not all students who complete an AP course in fact write the exam.

      3- Students who successfully complete the AP exam often do not exercise the option of a obtaining a university course credit. The experience of preparing for and writing the exam will better prepare students for the rigors of university and provide more academic students the greater academic challenge they deserve.

      Science Practices for AP® Biology starting at page 81

      http://media.collegeboard.com/digitalServices/pdf/ap/10b_2727_AP_Biology_CF_WEB_110128.pdf


      Science Practice 1: The student can use representations and
      models to communicate scientific phenomena and solve
      scientific problems.

      Science Practice 2: The student can use mathematics
      appropriately.

      Science Practice 3: The student can engage in scientific
      questioning to extend thinking or to guide investigations
      within the context of the AP course.

      Science Practice 4: The student can plan and implement
      data collection strategies appropriate to a particular
      scientific question.

      Science Practice 5: The student can perform data analysis
      and evaluation of evidence.

      Science Practice 6: The student can work with scientific
      explanations and theories.

      Science Practice 7: The student is able to connect and
      relate knowledge across various scales, concepts and
      representations in and across domains.

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    5. @Joe Felsenstein

      I do not understand your comment. "AP" courses in high school prepare you for an "AP" exam which gets you out of some elementary college courses. Are you saying this is unnecessary in Canada?

      Yes. In order to get into the University of Toronto and take first year courses, all you need are the standard high school courses. American students need a bunch of AP courses to get admitted to Canadian universities.

      As far as I know, the USA is the only country that has an "AP" system that lets high school students skip some university courses.

      Delete
    6. Tom Mueller says,

      Canada is the only country in the OECD that neither sets national standards nor has a coherent national education policy.

      I didn't know that. There are 34 countries in the OECD including some countries like Australia, USA, and others with strong regional governments. I'm surprised that they all have national education policies.

      Delete
    7. @ Joe

      Larry's original point, and mine, is that here McIlhenny et al. have bought into the omission of evolution. They have done so not out of creationism, but out of buying into the mindset of many molecular biologists, which does not consider evolutionary biology as an important part of a molecular biologist's education.

      ?!...

      Excuse me? How could that be possible in the 21st Century?

      What about the convergent evolution a variety of enzymes - Lysozyme for example?!

      And on the other hand what about the physiologically important differential tissue distribution of a variety of alloenzymes?

      Then again - Riboswitches also immediately jump to mind.

      Seriously? You gotta be kidding me!

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    8. @ Larry - I think you misconstrued Joe

      If I understand Joe correctly when he said:

      "AP" courses in high school prepare you for an "AP" exam which gets you out of some elementary college courses. Are you saying this is unnecessary in Canada?

      I think Joe was referring to the OPTION available in SOME universities to pass over freshman university courses and proceed directly to second year.

      My understanding is that this OPTION is available in both Canadian and American Universities SOME of the time at the university's discretion.

      My understanding is that most students would prefer not to exercise this option, preferring instead the higher marks of essentially taking an equivalent course the second time around and garnering the accrued benefits such as scholarships.

      I also understood that American students could enter Canadian universities such as UofT with the appropriate IB certification.

      Failing that - a third option would be an acceptable SAT/ACT score...

      http://discover.utoronto.ca/wp-content/uploads/2011/11/Int-Admission-Bulletin-2012-13.pdf

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    9. @ Larry

      re: Canada is the only country in the OECD that neither sets national standards nor has a coherent national education policy.

      LM I didn't know that. There are 34 countries in the OECD including some countries like Australia, USA, and others with strong regional governments. I'm surprised that they all have national education policies.

      That was my understanding... apparently even Turkey is ahead of Canada on this score!

      http://www.oecd.org/canada/educationataglance2013-countrynotesandkeyfacttables.htm

      Delete
    10. @Larry: I made use of the AP system myself, so I'm not against it. In secondary school ("high school") in the 1950s I had an elementary calculus course taught by two teachers in my school, Bernie Warshaw and Clyde Schock. There was no AP exam system then but when I got to the University of Wisconsin I was told I could ask for advanced placement and skip the first year of calculus. I went to the math department and asked the secretaries there, and they sent me up to the office of Dr. Joshua Chover. I had my pencil with me and fully expected him to give me some long exam.

      Instead, once he knew what I was asking for, he just said "What's the Mean Value Theorem?" I got a little rattled and explained Rolle's Theorem to him. It's a special case of the Mean Value Theorem. He said, "Well, that's Rolle's Theorem but that's close enough" and he sent me back downstairs to tell the secretaries that I had passed the exam.

      It was a good thing to get that advanced placement, as I did fine in third-semester calculus, and was able to move ahead in math without repeating old material.

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    11. @Joe

      I don't know very much about teaching math so I suppose it may be okay to let some very bright students skip calculus if they have had special instruction in high school.

      I don't see how, or why, this should work in other disciplines. In biology, for example, we assume that all students have had the basics in high school so we offer two specialized half courses in first year. One on cell biology/molecular biology and another on evolution and ecology.

      The material in those courses is designed to prepare students for second year courses and it's designed (not very well) to integrate with other first year courses. There are labs and exercises that no high school student will have ever encountered and, in theory, teaching methods that are different from high school.

      University education is not supposed to be just a glorified high school. If that's true then allowing students to skip first year courses should do them a great deal of harm—in an ideal university.

      We used to allow IB students to skip some first year courses but that didn't work out very well. Many of them did quite poorly in my second year biochemistry course, for example. We started to advise them to take the first year chemistry and biology courses. (I don't know if we are stll doing this.)

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    12. Hi Larry

      Re: “We used to allow IB students to skip some first year courses but that didn't work out very well.”

      No surprises from my end… From participation on other fora, I understand that AP Biology students consider the IB final exam somewhat of a joke.

      Not all IB courses are created equal. Remember there are two versions of IB – the standard high school diploma as well as the more rigorous equivalent to an european abitur; a high school qualifying exit exam granting entrance into an European university. The AP exam is designed as a university challenge exam, a deliberately higher challenge than either of the two IB versions.

      FTR – the new AP Biology curriculum (just started last year) is quite revolutionary and I suspect would do a better job of preparing students for second year University than most freshman university courses.

      On the subject of mathematics:

      I direct your attention to the very impressive AP Biology Quantitative Skills Guide

      http://media.collegeboard.com/digitalServices/pdf/ap/AP_Bio_Quantitative_Skills_Guide-2ndPrinting_lkd.pdf

      Found on this very informative link:

      http://apcentral.collegeboard.com/apc/public/courses/teachers_corner/2117.html

      I remind everyone that AP Biology is a stand-alone 2 semester high school course intended to be a high school student’s first and only encounter with Biology before moving on to university.

      I suspect as more AP Biology students come on stream in university that professors will take notice. My students report they are easily a standard deviation ahead of the pack… due to the rigors of AP I may add and not at all to do with my skill at teaching.

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    13. Hi again Larry - Your comment on Australia and New Zealand prompted more investigation on my part.

      Australia and New Zealand have federal ministries of education. Both countries have recently devolved some responsibilities to regional governments. That said, some cursory google-whacking confirms both still have National Ministries of Education that still set policy and national standards.

      Whereas Canada is quite different

      Paul Cappon, former president of Canadian Council on Learning and a senior fellow at the University of Ottawa’s graduate school of international and public policy commenting on Canada’s Results from the OECD’s Programme for International Student Assessment (PISA):

      “Every federal state worthy of the name has ongoing discussions and joint planning between federal government and the state or provincial governments collectively. Canada has nothing of the kind.”

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    14. @Tom and Larry and Joe
      I'd like to throw my hat in the ring a little. I'll agree with Joe that the AP curriculum has take a great adjustment to its syllabus. I won't say curriculum since technically how it is taught is not specifically dictated and still at the teachers discretion. However, AP has specifically adjusted its testing and Labs to demand student inquiry and design. I'll respectfully disagree with Tom that the IB does not do this. The IB like the AP has a philosophy and AP has actually moved towards this philosophy. The IB also stresses inquiry [in fact moreso until the AP changes two years ago]. However, how the instructor designs the curriculum to meet the syllabus has huge implications. Similar to the older AP, the IB CAN be taught as primarily content memorization. I specifically attempt to avoid this situation and demand all lab work to have significant, it not totally be student inquiry based. Also, paper 2 and 3 of the IB exam contain significant data analysis questions. These are always different from year to year but provide students with real data and scenarios that require students to interpret/analyze the data and come to conclusions. It always connects to the syllabus in a number of divergent ways. Funnily, the IB biology syllabus also underwent a review and is more open and less strict towards its examples, diagrams and expectations. The new syllabus begins this coming fall. The design/inquiry is maintained. Command terms SEEM removed. The expectations much less specific. Large focus on nature of science. No one knows what the exam will really look like. Time will tell. IMO the AP and IB look more and more alike over time.
      @Joe. Their is technically no 'common core' in the US. The AAAS, NAS, NSTA gathered together under the guise of a team names AERO. AERO was developing a set of science standards to be an equivalent to the common core but not CALLED common core. The AERO group merged [If I remember properly] with the AAAS/NSTA/NAS group to create the Next Generation Science Standards. These are not a curriculum. They are performance expectations about what students need to be able to do. These expectations have been adopted by my school and we begin implementation next year. They are focused on three foci - core content, practices, cross cutting concepts. All equally important. A large number of states supported their development. Last I heard about 10 states adopted. Many states do not like the evolution focus. I'll stop here but there is much to discuss about it.
      @all? For credit AP are often accepted depending on the student score and institution. IB is similar but many of my students attend school in Singapore or Great Britain or Hong Kong which favour the IB and often accept them for credit depending on score.
      I think thats all I wanted to say.

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    15. Linzel – I owe you an apology.

      I liken this discussion to asking the question which of the martial arts is superior, Kung Fu or Karate? The correct answer is “yes” depending on locale. If our neighborhood master teaching Kung Fu is more adept than the Karate master – then Kung Fu is the better choice and vice versa.

      Ditto – IB and AP. Teacher quality trumps all other considerations.
      From what you write – I would eagerly and gladly send my own children to your IB classes

      Let’s be clear here – both IB and AP exceed the expectations of typical Canadian high school curricula.

      That said – not all IB courses are created equally. For example, Mathematics and the Core Sciences can be taught at either the Higher Level (HL) or the Standard Level (SL). The Higher Level courses are equivalent to an “abitur” or entrance into European universities, the lower level courses are not.

      AP is supposed (emphasis on “supposed”) to be a higher level high school course if the AP teacher (emphasis on the word “if”) adheres to the syllabus and secondarily a university credit (even in some international universities) if the student successfully scores a high enough mark on the AP exam (at the universities discretion).

      As I understand it – this is not the case with IB. Acceptance into university is not identical to permission to skip First Year University. I can categorically state that I know of one private school which was obliged to abandon the AP program and embrace instead the IB program because AP was too rigorous in comparison.

      That may be "old news".

      Your detailed response intrigues me. It would appear that we are witnessing an evolution of pedagogy – some Hegelian progression of "thesis-antithesis-synthesis" as AP and IB co-evolve.

      Letting a hundred flowers blossom and a hundred schools of thought contend is the policy for promoting the progress of the arts and the sciences and a flourishing culture in our land.
      Mao Zedong

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  2. I agree, genetics should be taught after students understand population genetics (evolution). Once the concepts of mutation, variation, and natural selection (as well as neutral theory) are understood, students can then appreciate the significance of asexual reproduction vs meiosis and sexual reproduction.
    I applaud you for your reminder that bacteria also do genetics. One of my favorite topics in class deals with conjugation and plasmids. Bacteria do not receive their proper recognition in most biology classrooms.

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    1. re: "Bacteria do not receive their proper recognition in most biology classrooms."

      AMEN!

      Neither Bacterial nor Viral Genetics if I may be permitted to put my Canadian 5 cents worth in...

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  3. Isn't #4 referring to evolution? In an adaptationist program out of Dawkins, the developmental process of natural selection regulates all developmental processes like protein synthesis, as well as cellular differentiation. And isn't it why #1 is deemed a novel essential. Instead of a prerequisite? DNA-->gene is the selfish gene, the unit of selection.

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  4. I think saying population genetics requires developmental processes, and therefore #4 covers it, is like saying that it also requires atoms, and therefore physics covers all of genetics. Which sounds like saying that physics courses should therefore include genetics, or that studying physics is sufficient and we don't need genetics courses.

    Also, single-celled organisms, which have lots of evolution and lots of population genetics, don't have development.

    No, the survey really did leave population genetics out.

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    Replies
    1. @ Joe

      re: Also, single-celled organisms, which have lots of evolution and lots of population genetics, don't have development.

      Hmmm... Bacteria do possess "quorum sensing"

      ditto slime molds which present a very exciting model to examine the evolutionary origins of cell differentiation

      John Bonner is one of my heroes! check out the video on slime molds... exciting stuff

      http://www.princeton.edu/main/news/archive/S26/40/89S11/index.xml?section=featured

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    2. For a contrary point of view, as Rosie Redfield about quorum=sensing.

      Slime molds are unicellular (except when they aren't, and that is when they most have development.

      I like John Tyler Bonner too -- first met him in 1966 or 1967 when I visited Princeton and heard from him about the slime mold story.

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    3. Tom, I doubt that quorum sensing counts as anything remotely like multicellularity. Kin selection is frequently invoked, as nearby cells will be more closely related than distant ones, but what marks out 'true' multicellularity is actually the presence of the haploid/diploid alternation. It is the relationship of 'somatic' cells to the gametes that stabilises the multicellular colony, not the relation of a cell to its neighbour. A clone has no kin-derived 'interest' in its neighbour - 100% relatedness alone is insufficient for the stability of an 'altruistic' behaviour.

      Delete
    4. I don't think #4 covers population genetics either, nor did I mean to imply I thought any such thing. I also agree that the core concepts omit "population genetics," though I suspect that needs to be broken down a little more to be very useful.

      I thought genetic regulation of "citric acid cycle, photosynthesis and protein synthesis" are meant to be covered in #3, and the whole point of #4 is to emphasize that genes are adaptive, i.e., more or less directly disagrees that "most...traits have very little to do with the external environment."

      Or to rephrase, it seems to me that if you view genetics in a selfish gene light, the core concepts are rather good, except possibly for the omission of population genetics. That omission seems to be a conscious decision that population genetics is not introductory, but more advanced.

      As we all know, attacks on selfish gene thinking are only driven by self-interest, or even baser impulses.

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    5. In regard to bacterial development there's also the dimorphic prosthecate bacteria like Caulobacter (and Hyphomonas). In these organisms there are non-motile mother cells that "give birth" to motile daughter cells that swim away to become mothers themselves. Lucy Shapiro got herself into the National Academy for her studies of the molecular mechanisms of how this happens.

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  5. Mendelian Genetics? Things that make you go hmmm….

    One of the best articles I ever read that discussed the limitations of Mendelian Genetics was penned by PZ Myers

    Steve Pinker’s hair and the muscles of worms

    IMHO – high school students should be taught that Mendel’s Laws were serendipitous exceptions to the rule - exceptions that eventually proved the rule, as it were.

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    1. … following up – IMHO this link is outstanding when directing students’ attention to the limitations of Mendelian Genetics. Exceptions to Simple Inheritance

      …even if it does not match the eloquence and depth of PZ Myers’ excellent appraisal.

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  6. As a creationist i would just say.
    Within the DNA there surely is mechanisms to bring sudden cxhanges in creatures.
    Therefore mutationism is not needed where there is proven changes in bodies etc.
    Evolutionism is entirely dependent on mutationism and time.
    This is what goes against common sense or uncommon sense after careful thinking on these matters.
    Genetics is just a language for the biology we see. Its not explaining origins by studying living DNA.

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  7. Hi Allan

    Thank you for your reply. I welcome any opportunity to rein in hubris and hyperbole on my part.

    Let me see if I got this right...

    Quorum sensing includes switches to different modes of growth representing a phenotypic shift in behavior during which large suites of genes are DIFFERENTIALLY regulated. (eg bacterial biofilm)

    OK - the entire population is responding identically meaning “quorum sensing” does not present a prima facie case for a model representing a putative transition to multi-cellularity and cell differentiation in the strictest sense of the word. As you point out, these signal molecules oblige the WHOLE population to initiate a concerted action once a critical concentration (corresponding to a particular population density) of the signal has been reached.

    Or is it really that simple?

    The quorate population is not as homogenous as would appear at first glance.

    In Pseudomonas aeruginosa researchers have discovered quorum sensing “cheater” mutants that don't make public goods in response to increasing population density.

    http://www.sciencedaily.com/releases/2012/10/121011141435.htm

    Meanwhile, E. coli and Salmonella enterica do NOT produce AHL signals commonly found in other Gram-negative bacteria. However, they have a receptor that detects AHLs from other bacteria and change their gene expression in accordance with the presence of other "quorate" populations of Gram-negative bacteria.

    To my naïve eyes, this is beginning to sound a lot like tentative transitional evolutionary steps to some version of cell differentiation required of multi-cellularity.

    Meanwhile, I am fascinated that yet again we witness a paradigm of cell signalling that invokes “positive feedback” (along the lines of classical genetics) contradicting yet again current textbook orthodoxy erroneously “positive feedback” always accelerates to some terminal event. Jacob and Monod long ago suggested that “positive feedback” could represent commitment steps shifting one lineage of cells from one “mode” of operation to another.

    Look no further than the shift mechanism of Lambda phage lysogeny to lysis.

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    1. Tom,

      We might wonder why, despite 100% relatedness, clonal cells and organisms don't display marked kin selection. And prokaryotes have had 4 billion years to get to multicellularity, and haven't yet. There may be mechanistic reasons for this (cell walls getting in the way, perhaps), But I think a significant driver is the presence of a haploid exit. (There are haploid somas; I'll ignore that). If there is benefit to a conglomerate germ-plus-soma configuration, that benefit can only be passed on through the gametes. Somatic cells could 'rebel', and replicate on their own account (like detachable cancers), but they lose the conglomerate benefit, unless they can somehow reset the program. The program is linked to the zygote-zygote cycle: multicellularity, whatever its other benefits, is a way of amplifying genomes.

      If, however, every cell is reproductively competent and there is no sexual cycle, there is less (or no) reason for genes in a cell to help copies of themselves instead of replicating on their own account. The formation of a zygote, and the derivation of both somatic and germ line cells from it, gives a rationale for cohesiveness which is absent in a community of free-living haploid cells, even if some kind of clumping and differentiation could be envisaged. Sex and multicellularity are interlinked (asexual multicellular forms being all derived).

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    2. @Allan Miller

      I'm not sure if I understand your point. Could you rephrase it using plants or fungus as an example of complex multicellular species? In those species there isn't a distinctive germ cell lineage. Does that fit with what you were trying to say?

      As a matter of fact, in many fungi the haploid stage is a pretty complex multicellular organism, if I remember my biology correctly.

      Let's not forget that there are quite a few examples of multicellularity in bacteria although none of them as as complex as flowering plants or mushrooms. Let's also not forget that most eukaryotic species are unicellular and it took eukaryotes more than a billion years to evolve complex multicellular species.

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    3. I’m not sure if I understand your point. Could you rephrase it using plants or fungus as an example of complex multicellular species? In those species there isn't a distinctive germ cell lineage. Does that fit with what you were trying to say?

      Plants have a germ line, according to many authors. They just don’t have stem cells. Of course they can propagate vegetatively. A piece of leaf can grow roots and shoots and, ultimately, flowers. But this is little different, conceptually, from aphids. The zygote-zygote interval simply covers several distinguishable individuals. (I am aware that many plants never produce gametes. But they are always derived from multicellular ancestors that did). It remains the case that one lineage of cells connects each gamete to the zygote, and all other lineages suffer the ‘somatic’ fate – a dead end for genes, and the only reason for them to accept that fate is if the 'germline' copy is favoured.

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    4. As a matter of fact, in many fungi the haploid stage is a pretty complex multicellular organism, if I remember my biology correctly.

      That’s right (though I tried to head this one off – “There are haploid somas; I'll ignore that”!). I’m not saying it’s essential that multicellularity be associated with diploidy. My point, though, is its association with the cycle - the sexual cycle. This cycle consists of haploidy (with optional haploid mitosis) and diploidy (with optional diploid mitosis). No organism dispenses with mitosis in both phases, but many do in one or the other. Most dispense with the haploid version. The point remains that the mitotic phase serves a dual purpose – it builds a soma (which itself can fulfil many functions) and it amplifies the gametes. It is the association with gamete-amplification that I am emphasising. If any cell can, at any moment, reproduce on its own account, what would persuade it to suffer a somatic fate? It is only through the funnelling of genetic futures through a distinct bottleneck – meiosis and syngamy – that ‘true’ multicellularity can be stabilised (IMO). Simple kinship is not enough

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    5. Let's not forget that there are quite a few examples of multicellularity in bacteria although none of them as as complex as flowering plants or mushrooms.

      A semantic point, like calling bacterial conjugation ‘sex’. I don’t think anything bacteria do qualifies as multicellular. It is properly attributed to a very distinctive and controlled series, starting with one zygote and ending with the next. Organisms that don’t have zygotes don’t evolve multicellularity (although many asexual forms dispense with outcrossing, generating pseudo-zygotes instead, but following the ancestral program.).

      Let's also not forget that most eukaryotic species are unicellular and it took eukaryotes more than a billion years to evolve complex multicellular species

      Well as I say, prokaryotes have had 4 billion years, and candidates for genuinely multicellular behaviour are few IMO. Multicellularity is not compulsory, but it does appear to have been arrived at independently about 16 times in sexual eukaryotes.

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    6. Hi Allan – I think we need to define our terms here. I suggest you may be betraying a very decidedly zoopocentric Point of View.

      I also believe you may be conflating the terms “sex” and “reproduction”

      Is it possible to have one without the other?

      Yes! How about bacterial conjugation, the acme of sex unlinked to reproduction. You start out with two conjugating bacteria and finish with two bacteria.

      Sex occurred – i.e. the genetic shuffling of information generating new genotypes, but no reproduction occurred during sex.

      Meanwhile - I believe we may be underestimating the “multi-cellularity” of prokaryotes.

      http://blogs.scientificamerican.com/lab-rat/2011/11/16/bacteria-with-bodies-multicellular-prokaryotes/

      Bacterial multi-cellularity may not be “complex”, but prokaryotic multi-cellularity would appear very real.

      Meanwhile, your concept of germlines in plants leaves me scratching my head in bewilderment.

      To push the argument even further – One could explain “germline” along the lines of … “a chicken is one haploid egg’s way of producing more haploid eggs”. There exists a linear lineage of one egg to the next – diploid chickens remain expendable dead-end epiphenomena in this on-going saga of egg production. (tip of the hat to Professor Bud Ruth for first explaining that to me).

      That said, whenever an organism does not experience senescence by succumbing to some version of a Hayflick limit, such subtleties of distinction (germline vs. somatic lineages) are rendered moot? … especially when any germline identity is determined by environmental influence and not by cell lineage.

      Here is an interesting reappraisal of germlines in plants:
      https://www.sciencemag.org/content/337/6092/301.summary

      As far as I can tell - Larry’s original rebuttal remains standing.

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    7. Allan – I think we need to define our terms here. I suggest you may be betraying a very decidedly zoopocentric Point of View.

      Absolutely not. I believe I clarified this issue in my response to Prof Moran.

      I also believe you may be conflating the terms “sex” and “reproduction”

      Is it possible to have one without the other?

      Yes! How about bacterial conjugation, the acme of sex unlinked to reproduction. You start out with two conjugating bacteria and finish with two bacteria.

      Sex occurred – i.e. the genetic shuffling of information generating new genotypes, but no reproduction occurred during


      Obviously, it depends how you define them. I say, emphatically, NO. Bacterial ‘sexual’ mechanisms start and finish with conjugation, which is two cells doing something that’s a bit like something multicellular animals do. Transduction and transformation are about as much ‘sex’ as me catching a cold off you! It is you, I suggest, that is being ‘zoopocentric’!

      Ultimately, definitions are a sideline. We know what the other means, and could waste hours persuading each other what we ought to call it. I define 'sex' as cyclic syngamy and reduction. Reciprocal recombination may or may not take place between homologues as part of the process. That involves genes that (naturally enough) are also involved in recombination during general DNA management, including the mechanisms that integrate fragmentary DNA in prokaryotes.

      As far as I can tell, Larry's original rebuttal remains standing

      Yes, I'm aware that you agree that 'sex' means gene shuffling, 'multicellularity' means contextual variation in the genetic program of colonial cells, and 'germline' means the thing that animals sequester. It's a 'rebuttal' inasmuch as my definitions are not yours, and doesn't go near my actual point re: kin selection.

      You may have a pedagological rationale for calling all those things ’sex’, or ‘multicellularity’ something that also happens in diffuse colonies, but to me it’s just a semantic sideline, and taken too far can lead to confusion of analogous processes with homologous ones.

      I was inviting you to consider why 100% relatedness does not lead to extensive co-operation among prokaryotes, whereas somatic cells in sexual ‘organisms’ are quite common. Interesting as bacterial sociality may be, I think there is a vital distinction, and that distinction is the eukoryotic life cycle, centered upon (what I call) sex.

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    8. Hi again Allan

      Re: “I define 'sex' as cyclic syngamy and reduction.”

      According to your restricted definition; paramecia do not engage in sexual reproduction – or if they do, then E coli Hfr+ “males” that can transfer an entire chromosome in about 100 minutes to F- E coli “females”are engaging in sex no less than Paramecia.

      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441268/pdf/bactrev00145-0029.pdf

      Allan, I need to thank you for expanding my horizons and focusing my thinking on these subtle questions.

      On the subject of “Prokaryotic Co-operation”, I draw your attention to


      In order to be considered a multicellular creature, an organism must fulfil certain criteria:
      • Cells must stick together! This sounds fairly obvious but it does involve mechanisms for cellular adhesion
      • Cells must be able to communicate. In an multicellular body the cells must remain in communication, and change in response to conditions that affect the whole body
      • Dependency. Cells must be dependent on the surrounding cells for survival, otherwise the body is just a large colony.
      • Differentiation. The cells of the body specialise at different tasks. In most cases this is terminal differentiation – i.e once the cell has specialised it cannot return to it’s unspecialise state.



      There are bacteria that can do all of that!

      http://blogs.scientificamerican.com/lab-rat/2011/11/16/bacteria-with-bodies-multicellular-prokaryotes/

      Regarding Larry’s citation of haploid fungi and plants – when all is said and done, I still have to disagree with your contention that it is only about “meiosis and syngamy”.

      Even when considering your preferred animal phyla, I remind you that many populations that meet your criterion of “clonal” in fact engage in “sexual reproduction”.

      We broached this very difficult topic on an earlier occasion:
      http://sandwalk.blogspot.ca/2014/03/what-did-joe-felsenstein-say-about-sex.html

      best regards

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    9. Ah, it's the old wood-and-trees thing! ;) Biology has an exception to just about every rule. And ciliates are just plain weird!

      According to your restricted definition; paramecia do not engage in sexual reproduction – or if they do, then E coli Hfr+ “males” that can transfer an entire chromosome in about 100 minutes to F- E coli “females”are engaging in sex no less than Paramecia.

      To which I can only say 'meh'! If the F plasmid becomes integrated into the chromosome it drags the whole thing along with it, yes. But this isn't cyclic syngamy and reduction. If paramecia alternate haploidy and diploidy, they are sexual in my terms. If they don't they aren't.

      But I'm not going to fight unduly over it. (What I call) sex is essentially a synapomorphy in eukaryotes. The capacity has been lost in many asexual eukaryotes, but characteristic meiosis genes are found throughout the kingdom (indicating the general youth of non-extinct asexual lines, rotifers notwithstanding). Autogamous species are a borderline case - they reduce to gametes which immediately re-fuse. It seems like an attempted 'gotcha!' to bring them up. I'm happy to accept exceptions, just as I'd be happy to accept that every species concept is flawed by the general continuity of the underlying parent-child series.

      The important thing, particularly when considering the inception of a phenomenon, is to expose its central theme. The central theme of eukaryotic sex IS syngamy and reduction, with at least one crossover typically to ensure correct disjunction on reduction. Plants and fungi (I don't 'prefer' animals!) don't do anything outrageous, though they play with ploidy a bit more, triploid endosperm, haploid somas, transient diploidy, vegetative generations, and all that.

      Likewise, the stable multicellularity found in eukaryotes is fundamentally tied to the sexual cycle, albeit with many variations. Bodies - plant, animal, fungus and seaweed - are gamete amplification machines, albeit with other roles as well.

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    10. Allan Miller says,

      I don’t think anything bacteria do qualifies as multicellular. It is properly attributed to a very distinctive and controlled series, starting with one zygote and ending with the next.

      The examples I use are cyanobacteria [see Multicellular Bacteria and Bacteria with bodies – multicellular prokaryotes]. I also talk about sporulation in gram positive bacteria where the mother cell pumps nutrients into the spore cell.

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    11. @ Larry - I love that link by PZ Myers on Choanoflagellates - I was reviewingit again just the other day.

      I have a very naive question for you:

      The striking resemblances between choanoflagellates and the choanocytes of Sponges could possibly be best understood that neither are “outgroups” to eumetazoa but both in fact both had a multicellular eumetazoan ancestor not dissimilar to modern Ctenophores.

      http://www.aaas.org/news/science-jelly-not-sponge-base-animal-family-tree

      Your thoughts?

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    12. Allan - I think we are arguing at cross-purposes:

      Before we can agree on WHAT sex is – we first need to agree on WHY sex evolved.

      Presuming we agree on what Joe calls the two great classes of models: the Fisher/Muller and the Sturtevant/Mather... then the rest remains ancillary detail. The HOW of sex becomes incidental. A variety of HOW mechanisms (other than your precious syngamy & meiosis) could conceivalbly accommodate a unifying WHAT/WHY.

      We are rehashing: http://sandwalk.blogspot.ca/2014/03/what-did-joe-felsenstein-say-about-sex.html

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    13. Larry,

      I accept that many prokaryotes are colonial, but they do not form 'organisms'. You can call it multicellular, because there are many cells, but the distinction is due to the absence of a reproductive bottleneck of specialised cells with all other cells relegated to a genetic dead-end role.

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    14. Before we can agree on WHAT sex is – we first need to agree on WHY sex evolved.

      That seems completely wrong-ways-about to me.

      Presuming we agree on what Joe calls the two great classes of models: the Fisher/Muller and the Sturtevant/Mather... then the rest remains ancillary detail.

      There are many factors to consider. But the prime one (if one accepts, which you seem reluctant to do, 'minimal sex' as cyclic syngamy/reduction) is how to explain cyclic syngamy and reduction. Fisher-Muller and many others are recombinational theories. I think recombination is a side-effect, probably due to the need to generate Holliday junctions to ensure proper disjunction. The fact that crossover resolution products are 50% recombinant may well be incidental (but has wide-reaching consequences).

      Sturtevant-Mather is cyclic selection, which is possible but incomplete as a driver for the cycle.

      So no, I don't agree on these as the ideas from which I must make my choice. The primary benefit of syngamy is likely to be due to increase in size and/or hybrid vigour. This creates temporary diploidy. There are several possible reasons for return of the haploid. One is that the cell cycle is pushed towards the end of G2 - the mitotic machinery doesn't know it isn't dealing with mechanically separated replicated sisters. It would be triggered to divide. Another possibility is replicative competence in the diploid phase. It is possible that the capacity to replicate a diploid chromosome set was not available, and hence the only possible mitosis was haploid.

      These are speculative, and probably untestable, but my point is that the core of sex is the most fundamental thing about it - this stable, symmetric association of haploids in binary organisms followed by their release (shaken and stirred by recombination). What you refer to as my 'precious' syngamy/meiosis is the heart of the matter. All the dynamics that govern we 'higher' organisms derive from this perennial arm-wrestle between the haploid partners, neither of which can gain the upper hand.

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    15. Hi Allan

      I really appreciate this exchange as it obliges me to focus my thoughts.

      To cite Dobzhansky yet again – Nothing in Biology makes sense except in the light of Evolution!

      Ditto – sexual reproduction.

      Sexual reproduction short-cuts Muller’s ratchet. E.g. two individuals each with one copy of some deleterious mutation will produce offspring that are free of either mutation 25% of the time. Furthermore, sexual reproduction permits organisms to shed themselves of deleterious gene combinations faster than by reverse mutation (the only asexual option available)

      But your take on Holliday Structures etc is well taken… prior exaptations to our current understanding of sex perhaps.

      I understand Zygospores as quiescent resting bodies awaiting environmental conditions to return to "normal" ...

      or alternatively...

      ...allow recombination resulting in novel variable offspring, some of which can to adapt to the “new normal”.

      I imagine the original emergence of zygospores as some evolutionary quiescent exaptation that eventually gave rise to sexual reproduction… the exaptation possibly being DNA repair (including Holiday Structures)

      Why is sex beneficial? Parent’s chances of producing offspring that can survive competition are greatly enhanced, remembering that each generation produces far more progeny than can possibly survive.

      If syngamy and meiosis evolved as mechanisms to escape Muller’s ratchet

      And

      If different mechanisms also evolved to escape Muller’s ratchet

      Then

      These various mechanisms are essentially of the same category… i.e. there is more than one way to engage in sex.

      Segue to Paramecia and Hfr E coli.

      I think we may not really be disagreeing with each other all that much.

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    16. Tom, I appreciate your comments. I really ought to finish off some jottings I've been working on, which would present my argument in a more coherent manner than blog commentary allows!

      I encounter a lot of 'organism-centricity' from biologists, and a strong tendency to focus on the primacy of recombination. From the organism's point of view, sex makes little sense, while most benefits of recombination are somewhat long-range. Which is why I try the inversion: to look at it from the perspective of the haploid, whose immediate benefit must arise from partnership. Each is minced by serial diploidy but still retains an identity in us binary organisms.

      As to Muller's Ratchet, I'm doubtful of its primacy. It requires the evolution of outcrossing syngamy, two-step meiosis and crossover, just to get 25% of its offspring clean (and only then if the crossover's in the right place!). The assumption that we start with a scruffy, barely competent asexual organism that is ratcheting mutations like mad doesn't seem like a promising start point for the evolution of this elaborate strategy. Rather than longer-range effects, I think direct organismal factors are likely to be key - complementation of deleterious alleles in the diploid phase, for example, is an immediate benefit of syngamy. Of course, one immediately finds oneself having to explain reduction, which just throws the benefit away. I suggested two possibilities above, but another is that the benefit is time-limited. Gene conversion will gradually increase homozygosity, so it does not pay to remain diploid eternally.

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    17. Larry - I may need to walk back my objection. MTB's seem to have a fair case for the rank of 'organism', rather than mere 'colony'

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  8. @ Joe -

    Hi Joe - I wish I had read your post before reading Allan's!

    Rosie Redfeld does indeed pose very provocative rebutal to conventional wisdom regarding Quorum Sensing...

    http://rrresearch.fieldofscience.com/2007/11/ive-never-posted-about-quorum-sensing.html

    My cursory read of this blog and its comments is that one particular Nature paper is indeed guilty of hubris and hyperbole but Quorum Sensing as a bona fide biological phenomenon is not necessarily refuted.

    However, the ubiquity and scope of Quroum Sensing in bacteria would appear more limited than I initially surmised.

    I am going to need to reexamine Rosie Redfeld's paper with the the due diligence it deserves.

    Thanks for directing attention this way... I remain in your debt.

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    1. Hi again Joe - and thanks again.

      I found an interesting review paper discussing the distinction between Quorum sensing and Diffusion Sensing.

      Quorum sensing and the confusion about diffusion

      Redfield's skepticism apparently provoked quite the reaction amoung her peers. From what I gather, most of her initial objections have been successfully dealt with by the champions of QS.

      After a little google-whacking and mulling it over, I have to agree with the thrust of this review paper. At a minimum, DS could be considered an exaptation to QS. Meanwhile, the evidence for QS as a "social trait" seems pretty solid.

      Your thoughts?

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    2. My thoughts are that I haven't really read any of that literature. I have heard Rosie present her views, which was great fun to hear.

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    3. Joe,

      Did I ask you for some kind of direction as to how we can scientifically check were and how we have come for apes...?Forgive me if I'm repeating myself.... You are my hero in the population genetics, if that gives you any comfort from a moron who has no home and is publicly spanked by both ends of the spectrum....(that is me just in case you are wondering) ...

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    4. You asked, so I asked, right here and here in that thread, what evidence you would conceivable accept. Fossil birth certificates? Movies of the whole process? You had somewhat mysteriously said "there is only one" [one what?]

      Now if you're a silly troll you will move on to baiting others. If you are on a serious Quest for knowledge, you will discuss that issue so I can figure out what evidence might be meaningful to you.

      So far, you have moved on to baiting others.

      I'm waiting for your answer, but hearing nothing but crickets chirping.

      ...[chirp, chirp, chirp]

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    5. Typo: ...would conceivably accept ..."

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    6. Hi Joe - that is twice now on just this one thread you have made me green with envy.

      First your encounter with John Bonner and then again with Rosie Redfield...

      ... consider me jealous.

      I thank you for your patient interventions. I always learn a lot and remain in your debt.

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  9. I just have a minor point to make. You stated that:

    "Traits (phenotype) are due to information in DNA (not just genes) but most of those traits have very little to do with the external environment."

    However, it was always my understanding that the "environment" referred to here includes both the external and internal environment. Surely how most traits are expressed will be affected by this.

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  10. Hi,

    Sorry for a slightly off-topic post...

    But could anyone recommend a book on population genetics for someone with a reasonably good background in maths and evolutionary biology?

    Something reasonably self-contained and suitable for self-studying, that starts from the basics, but covers most of the important stuff? I know Gillespie's 'Population genetics: a concise guide'. And Felsenstein's free book online.

    What do you think of those two? Any other recommendations? Thanks for any tips!

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    1. I think highly of Felsenstein's free online book.

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  11. Thanks, I appreciate the unbiased opinion!

    Seriously though, I did browse it and it looks very good. Are there any big philosophical differences between these books (e.g. Giellespie's and yours)?

    I was also browsing Charlesworth's 'Evolution in age-structured populations' at the university library. Where does that fit in? Given that I don't think I would even be able to give a definition for population genetics, a lot of Charlesworth's book looks like population genetics to me. But I assume I would be learning something quite different from that book?

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    1. There are no "philosophiocal" differences between my text and Gillespie's, it is just that his is written more for an undergraduate audience, and mine goes into a lot more obsessive detail and is written for a graduate course in theory.

      Brian Charlesworth's monograph is that -- a careful and well-thought-out treatment of the theory for overlapping generations. It is not intended as a general textbook for population genetics theory, so one would miss many topics if one used it as a text.

      Take a look also at Rasmus Nielsen's and Monty Slatkin's book "An intoduction to Population Genetics: Theory and Applications" which is very recent and well done.

      None of these books will disagree with each other on any topic where they overlap.

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    2. Thanks again, very helpful!

      I now have both your and Gillespie's book. Someone else had got to Nielsen&Slatkin at our library first, so I'll start with these two.

      I'm already wishing I'd done this earlier. After reading the first few pages, some very basic things which I didn't get in lectures now make perfect sense.

      PS Are there any online discussion forums for this sort of thing? Or are there not enough theoretical biologists to make one worthwhile?

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