tag:blogger.com,1999:blog-37148773.post2934267340817417501..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: My molecular evolution midterm testLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger37125tag:blogger.com,1999:blog-37148773.post-6545569701972994842014-02-27T06:40:37.986-05:002014-02-27T06:40:37.986-05:00@ Larry
I would love to have been one of your stu...@ Larry<br /><br />I would love to have been one of your students!<br /><br />Clearly you are moving up Bloom's Taxonomy and see yourself less as "sage-on-the-stage" but more as "guide-on-the-side"<br /><br />What is also clear, is that it is very difficult to evaluate your evaluation without knowing what happened in your class not to mention examining your marking rubric.<br /><br />I would have phrased some of your questions differently - but that is a matter of style. As students accustom to your style and understand where you are coming from, the thrust of these questions would become more obvious to them than to those who do not know you so well.<br /><br />As the mists of time erase the memories of university experiences, your students will surely remember you and your classes.<br /><br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35637065859061366222014-02-27T06:31:14.178-05:002014-02-27T06:31:14.178-05:00@The Brummell
Impressive!
re: Question #5 - I su...@The Brummell<br /><br />Impressive!<br /><br />re: Question #5 - I suspect that Larry discussed at great length Ford Doolittle's c-value paradox blasting ENCODE ... as a matter of fact, I could not imagine Larry failing to blast ENCODE in class, making this a "gimme" question for his students.<br /><br />To follow up on question #5, I am still scratching my head over this post<br />http://sandwalk.blogspot.ca/2014/01/can-some-genomes-evolve-more-slowly.html<br /><br />How is it that molecular clocks across lineages (even considering identical proteins) click at slower rates depending on which lineage is examined?<br /><br />I can think of several possible answers, but hesitate to embarass myself in public.Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69705849441815563212014-02-27T05:42:31.617-05:002014-02-27T05:42:31.617-05:00Now I understand where you are coming from. You ex...Now I understand where you are coming from. You expect me to teach a technology course and not fundamental principles and concepts of evolution at the molecular level. Undergraduate students do not need to memorize substitution models for maximum liklihood algoriithms. That's a good illustration of what's wrong with undergraduate education.<br /><br />Essays give students an opportunity to demonstrate their critical thinking skills and show that they can learn on their own. They also allow me to access their ability to communicate and that's an important part of education. The students choose their own topics, but I have to approve. <br /><br />Some of the topics are: junk DNA, the role of recombination in evolution, whether the rate of human evolution has changed recently, whether epigenetics is important in evolution, what molecular evolution tells us about the Cambrian explosion, and whether the molecular clock ticks at a constant rate in most lineages. <br /><br />I don't think it's the least bit "odd" for undergraduates to be writing essays on such topics but I'm not surprised that you find this kind of teaching very strange. I think my course is much more "rigorous" than the kind of course you would teach. You seem to think that "rigorous" requires memorizing mathematical formulae whereas I think that "rigorous" means teaching students how to think for themselves. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77367635632533431232014-02-26T22:48:07.578-05:002014-02-26T22:48:07.578-05:00Fine. If its been witnessed its just witnessing a ...Fine. If its been witnessed its just witnessing a very common mutationism in something in biology. however evolutionism is about mutation monsters creating the glory of biological reality.<br />Its NOT been witnessed and is completely speculation.<br />Even if true it would still be lucky speculation.<br />you make the case that creationists demand about scientific evidence before claims of conclusions are said to be from science.<br />evolutionism has mutated logic to its aims .Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71855463941118193102014-02-26T21:53:45.007-05:002014-02-26T21:53:45.007-05:00Well, I don't know what you actually teach in ...Well, I don't know what you actually teach in the course, and it may be more rigorous than it looks from this test, but your choice of questions seems rather fuzzier and less mathematical than I would except in a molecular evolution course. Do you cover things like substitution models for maximum likelihood phylogeny later on? And you apparently have an *essay* for a molecular evolution course, which seems rather odd outside the humanities or maybe the "physics for poets" style science courses for non-majors. Jonathan Badgerhttps://www.blogger.com/profile/04921990886076027719noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17167120889930602062014-02-26T21:30:54.403-05:002014-02-26T21:30:54.403-05:00Jonathan,
What's the point of your comment? H...Jonathan,<br /><br />What's the point of your comment? Have you ever seen any evidence that science education is going in the direction you suggest? Are you implying that my course is like that because that's what it seems like to me?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87358515479920068352014-02-26T19:43:07.121-05:002014-02-26T19:43:07.121-05:00We have got to stop teaching the "memorize an...<em> We have got to stop teaching the "memorize and regurgitate" style of course.</em><br />Maybe. But the other extreme which is just as bad if not worse is the humanities-style free-style response where there are no objectively right or wrong answers -- just answers the professor/TA likes or not. One of the reasons I became I scientist is that I was deeply unimpressed with the rigor and lack of objectivity in the humanities, and I wouldn't want to see science education go that way.Jonathan Badgerhttps://www.blogger.com/profile/04921990886076027719noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59055447839204046992014-02-26T16:57:00.013-05:002014-02-26T16:57:00.013-05:00Part the third:
5. Hmmm... "best" implie...Part the third:<br />5. Hmmm... "best" implies a single, most-correct answer that was probably discussed at some length in class. I could talk about the abundance of inactive transposable elements in the human genome (without looking up the relevant posts here at Sandwalk, they're something like 40% of the genome? I think?). Or I suppose I could talk about Dr. Gregory's "Onion Test" that challenges any argument for majority function in the human genome with the question (paraphrasing, with apologies for errors and poor writing) "why do onions require so much DNA in their cells, if the proposed function for human non-coding DNA is true? Are onions that much more complex / protected by dilution from mutations / evolutionary potential mumblemumblemumble (I don't understand the "evolutionary potential" arguments)".<br />Where was I? Oh, right, a test. Um... I'll just go with: We have looked and looked, and there has never been any evidence of function of great swathes of the human genome, such that a fair description of at least 80% of the DNA in each human cell is "junk", as in, having no known function. Evidence of absence is available in this case, because many predictions about function for bulk DNA or for particular segments / sequences / motifs have been tested and failed.<br /><br />6. Earlier comments describe a class exercise and discussion about these issues. Not having attended that discussion, I'll bow out of this one and accept a lower grade on this test.<br /><br /><br />How'd I do?TheBrummellhttps://www.blogger.com/profile/08973380652057861796noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2692805395793744172014-02-26T16:56:30.774-05:002014-02-26T16:56:30.774-05:00Part the second:
3. Part of this apparent mismatch...Part the second:<br />3. Part of this apparent mismatch in priorities - working biologists believe evolutionary biology is fundamental to all aspects of biology, yet core concepts in evolutionary biology are taught relatively late in many biology cirricula - may stem from historical inertia (course structures take a long time to change in many university departments) and may stem from a perceived heirarchy of concepts.<br />It may be that some concepts, such as the main tenets of cell biology (cells come from cells, living organisms are made of cells, all the cells in a multicellular individual have the same genome*) or of ecology (food chains, food webs, nutrient cycles, succession, responses to disturbance, keystone species) are easier to teach to individuals with little or no former trainining in biology. However, I am not aware of thorough tests of this idea that some important biological concepts are inherently more difficult for people to grasp, or that some "background" information is necessary before it becomes worthwhile to discuss ideas such as selection vs. drift. Many of the key concepts of population genetics are simply applied statistics, such that the only necessary prerequisite might be a course in probability and statistics. On the other hand, I personally found it an "aha!" moment when I finally realized *why* most mutations (in coding sequences) are negative - and the answer has to do with allele dominance, protein synthesis and function, and development in multicellular eukaryotes, concepts that may be divided among introductory biology courses in genetics, physiology, and developmental biology**.<br />I think population genetics is a necessary key concept (or set of concepts) in evolutionary biology, and its relegation to late (and often optional) courses in undergraduate biology training may reflect historical forces in academic departments, a path of building knowledge upon earlier foundations through a 3- or 4-year degree program, and on acceptance of a compromise position among professors that may wish to devote their teaching time to some courses or subdisciplines at the expense of others.<br />* with modifications in some specialized tissues, such as the highly duplicated chromosomes of Drosophilid salivary gland cells<br />** Come to think of it, I suspect developmental biology is almost always a 3rd or 4th year course in biology departments.<br /><br />4. Again, because I have not taken Dr. Moran's Molecular Evolution course, I might be working with a different definition of the word "gene". Rather than tackle this question (we get a choice to omit one, right?), I"ll be facetious and say "get new friends, anybody who threatens violence during a discussion of one's preferences or strategies for finding long-term romantic love is clearly a deranged individual and best avoided."TheBrummellhttps://www.blogger.com/profile/08973380652057861796noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67093981952522328242014-02-26T16:55:37.631-05:002014-02-26T16:55:37.631-05:00"How would you do?"
1. I haven't tak..."How would you do?"<br />1. I haven't taken the class, and I indeed I've never taken a class titled "Molecular Evolution" or something similar. I have, however, taken classes titled "Molecular Biology" and "Evolutionary Biology", though that was a while ago. I remember being surprised by some facts that were presented in those classes, so I'll answer with one of those: The most important new thing I learned was the range of potential sources of error one has to take into account when building phylogenies using datasets of mixed molecular (e.g. gene sequence, protein sequence) and morphological data. Beyond the obvious quesions regarding how to compare "traits" as diverse as an A->G mutation in a third codon position and a doubling of some morphological ratio (e.g. beak length to beak thickness), there are layers of concerns and pitfalls around issues such as molecular clock calibration against fossils, population size changes through time and the effects on neutral evolution, and uncertainties about phylogenetic trees, and how those uncertainties affect overall estimates of things like time-since-divergence based on which nodes are well supported and which are not. And then there are the statistical problems, such as appropriate analytical methods for building phylogenies (e.g. neighbour joining alone seems to have very situation dependent pros and cons) and how to interpret the methods section of a paper that presents a new phylogeny of some group of organisms. Much of this discussion was new to me when I encountered it in Molecular Biology and in Evolutionary Biology, and I found it very interesting.<br /><br />2. As a quick stab at this one: different proteins experience different amounts of purifying or stabilizing selection because different proportions of their total amino-acid sequence will be under relaxed or stringent selection. To clarify, imagine a short protein with an active site (we'll assume this protein is an enzyme) and some other sequence that's mostly just spacer between critically-important residues. Mutations in that sequence that affect the active site are strongly selected against because the function of that protein is changed, but most mutations in the spacer amino acids are neutral or near-neutral and can accumulate through time in different lineages carrying that protein. Another protein might be very long and have relatively few amino acid positions that are under strong selection, and great chunks of that sequence may be free to accumulate many neutral mutations.<br />In addition, amino acids are encoded by different numbers of codons - some by only one, others by as many as six different 3-base RNA codons. This means some amino acid substitutions will be caused by a single DNA mutation, while others will be silent as regards the amino acid composition (with the caveat that tRNA abundances and ratios are probably important for determining the maximum rate of protein production in at least some cells). <br />I'm going to leave alone the idea that some proteins (the whole molecule) are under more intense purifying selection than others and that many proteins may actually be evolving entirely by drift in many lineages.<br />Short version: proteins have many differences that mean a constant genome-wide mutation rate will lead to different rates of fixation of mutations within the sequences of individual genes, due to differences in selection intensity across the length of each protein's sequence.<br /><br /><br />...Google won't allow really long comments. Apologies for the length, continued in next comment...TheBrummellhttps://www.blogger.com/profile/08973380652057861796noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87376884506282024662014-02-26T15:08:29.812-05:002014-02-26T15:08:29.812-05:00Read: Mutation to see all my post on mutation and ...Read: <a href="http://sandwalk.blogspot.ca/2013/01/theme-mutation.html" rel="nofollow">Mutation</a> to see all my post on mutation and <a href="http://sandwalk.blogspot.ca/2013/03/estimating-human-human-mutatin-rate.html" rel="nofollow">Estimating the Human Mutation Rate: Biochemical Method</a> to see the specific example of calculating mutation rate from a knowledge of biochemistry.<br /><br />The most common errors are: (1) not taking into account the error rate of DNA repair, (2) not knowing the correct size of the haploid genome, (3) not knowing the number of cell divisions between zygote and formation of gametes, and (4) not considering the separate contributions of sperm and eggs. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45738555787794913732014-02-26T10:09:17.929-05:002014-02-26T10:09:17.929-05:00You're saying that morphology is unimportant t...You're saying that morphology is unimportant to evolution? Is it really necessary to leave out the finch beaks just because you also bring in molecular evolution?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69551895220890103542014-02-26T10:08:17.707-05:002014-02-26T10:08:17.707-05:00I would have thought #6 was a strictly empirical q...I would have thought #6 was a strictly empirical question. How do you get a mutation rate from your knowledge of biochemistry? Also, I'm interested in the answer. It would be handy to know just what mistakes a student is likely to make.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51954446012878198432014-02-26T09:39:55.633-05:002014-02-26T09:39:55.633-05:00" Their choice of "sufficient" can ..." Their choice of "sufficient" can be completely arbitrary except that some choices won't pass muster, so they have to guess what would please the examiner."<br /><br />Jesus Christ, it's like you've never taken a written test before. I'm flabbergasted at how strung up over semantics you get. I agree that the question is needlessly wordy, but come on, most questions have an unwritten but implied component of "you must explain or describe ____ sufficiently".<br /><br />It's like you get a written test on history and are told to give a comprehensive description of a certain event, and you whine to the teacher how "comprehensive" is arbitrary and would also take too much ink. For crying out loud, what's wrong with you?Uncivilized Elkhttps://www.blogger.com/profile/17216440898113949568noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2709216091970472472014-02-26T09:33:57.510-05:002014-02-26T09:33:57.510-05:00For fuck's sake, I have never taken Larry'...For fuck's sake, I have never taken Larry's course and I can tell what he is trying to get at. It's not fucking difficult; these people are supposed to be in college. <br /><br />And while I think the following statement is complete and utter horseshit (yes, I'm sure people are super duper delighted to be calling out white guys perpetuating the same harmful tropes they have been for fucking ages instead of annoyed and exhausted):<br />"That's correct. There are a bunch of politically correct students and faculty at my university who are completely humorless. They delight in exposing examples of everthing they think is improper behavior. They are classic examples of the exact opposite of the kind of critical thinking I'm trying to teach."<br /><br />if that statement actually WAS written in a journal, it's that group of douchebags being sexist in how they phrase "I want an intelligent partner", Larry isn't endorsing it or anything. Though like I said, I find that comment I quoted goddamn ridiculous. "Oh, haha, you feel oppressed and hurt by the constant blindness of the privileged in society. How uncritical of you!"Uncivilized Elkhttps://www.blogger.com/profile/17216440898113949568noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81674708548676929582014-02-26T09:24:37.896-05:002014-02-26T09:24:37.896-05:00What exactly is bad about "subjective" q...What exactly is bad about "subjective" questions? They usually prompt much more explanation and thought. I also see nothing arbitrary other than maybe including that quote from the journal in the gene question.Uncivilized Elkhttps://www.blogger.com/profile/17216440898113949568noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8468621892825854262014-02-26T09:19:48.873-05:002014-02-26T09:19:48.873-05:00"And of course your students know they won..."And of course your students know they won't get credit for answers that are honest and correct"<br /><br />I don't think the word honesty means what you think it means. If you know what your instructor is trying to get at (which one should if they attended classes), yet you purposefully answer the question by adhering strictly to the way it was written while ignoring all context and the contingency of the course you took, you're not being honest. You're being a dick who will probably fail their exam.Uncivilized Elkhttps://www.blogger.com/profile/17216440898113949568noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10084481503526438932014-02-26T07:49:58.985-05:002014-02-26T07:49:58.985-05:00Question 2 is one we give in our first-year biolog...Question 2 is one we give in our first-year biology course at Western. Molecular evolution in first year that's how to teach evolution...no more finches beaks!Anonymoushttps://www.blogger.com/profile/17637910546080343435noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51875050544545296262014-02-26T03:47:06.771-05:002014-02-26T03:47:06.771-05:00Mutation rates is pure speculation unless its been...<i>Mutation rates is pure speculation unless its been witnessed(tested) over past amounts of time where mutations actually took place and perhpas produce results. otherwise its all poor sampling from presumptions.</i><br /><br />Fortunately, we have been doing precisely that for quite a long time. For example, we can trace the geographical spread of a bacterial or viral disease by analizing mutations starting from an outbreak. It's routine work in molecular epidemiology. It's also easy to set up in a microbiology lab. An there are many indirect ways to get extimations too. Nailing down exact mutation rates, specially for complex eukaryotes is more difficult, but it's not like we're dealing with estimation errors of orders of magnitude.Pedro A B Pereirahttps://www.blogger.com/profile/15195139833344839287noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63103440753209033182014-02-25T21:47:25.630-05:002014-02-25T21:47:25.630-05:00BTW, we did the same thing for the question "...BTW, we did the same thing for the question "What is a gene?" After the discussion was over I gave out references to several papers and posts on the issue so the students could see that there were several different legitimate answers. I described my preferred definition and explained to the students that whenever I use the word "gene" that's what I mean. <br /><br />I forgot to mention that two weeks before the test I handed out a list of 30 questions, including the six ones you see above, and I told the students that all the questions on the test would be taken from the list.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63271362669261464122014-02-25T21:36:45.121-05:002014-02-25T21:36:45.121-05:00I'm committed to trying this style of teaching...I'm committed to trying this style of teaching since I strongly believe it's the right way to go. We have got to stop teaching the "memorize and regurgitate" style of course. <br /><br />But you've put your finger on the tough part. It's hard to assign grades to the middle part of the class. Students also have to submit an essay on a topic of their choice. Fortunately, the essay grades and the test scores show a strong correlation so it looks like subjective grading is pretty fair.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40607782384803889252014-02-25T20:46:13.684-05:002014-02-25T20:46:13.684-05:00I read those questions and wondered if I'm gla...I read those questions and wondered if I'm glad I never took a class from Larry Moran, or sorry I didn't! Assuming that he provided enough background, as apparently he did for #6, those questions would be thought-provoking. They suggest the whole class would be an interesting challenge. <br /><br />I'd hate to grade such questions, though. With open-ended questions like these it's surprisingly easy to tell who knows the material (and may make some errors) and who doesn't get it (though relevant correct vocabulary might be thrown at the answer). It's harder for me to decide how to grade the failures that have correct bits in them. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40946060261036381312014-02-25T20:29:07.934-05:002014-02-25T20:29:07.934-05:00The story definitely changes the question (unless ...The story definitely changes the question (unless we imagine a student who would only select a partner who can repeat their preferred definition verbatim - and if I were marking it I would fail such students as a matter of principle :-) ).<br /><br />Instead of giving a single definition, the students are being asked what would make a definition acceptable or unacceptable, i.e. to specify the entire set of potential definitions that, in their opinion, would convey a sufficient understanding of what a gene is. This presents some problems:<br /><br />1) Their choice of "sufficient" can be completely arbitrary except that some choices won't pass muster, so they have to guess what would please the examiner. <br /><br />2) It is not clear that such a question can be sensibly answered under realistic time and ink constraints. <br /><br />3) It is even less clear that the question tests anything worth testing.<br />Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27008070892487604112014-02-25T20:11:10.857-05:002014-02-25T20:11:10.857-05:00I can just picture it:
"7. Whether and what ...I can just picture it:<br /><br />"7. Whether and what is the scientific molecular evidence that present DNA is a accurate model to make past molecular associations demonstrating common descent and this by evolution."Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60633533634431604592014-02-25T19:01:48.643-05:002014-02-25T19:01:48.643-05:00Well, education is a two way street, but that incl...Well, education is a two way street, but that includes the professor putting a bit of thought into the questions...<br /><br />As for 4), I just don't see how the story serves any purpose other than confusing the issue and possibly offending some people. Asking students for their definition of a gene and their justification for it is all good and well -- why not leave it at that? Jonathan Badgerhttps://www.blogger.com/profile/04921990886076027719noreply@blogger.com