I don’t know if it’s a common problem, but I have found that many times I have been unable to connect to Blogger, either to write posts or to read comments. It loads the blog page most of the time, but it refuses to connect to the sign in features. As you can see it is really starting to get on my nerves.
A student who would be my teacher.
There was some discussion recently regarding the usefulness (or not) of student evaluations of instructors. Some argued that they are not particularly informative, some (like me) suggested that some approaches to soliciting feedback can be productive, and others suggested that anonymous evaluations at least might be not much more than a means of getting back at instructors.
I’d like to contrast my school’s only-signed-comments-count-in-annual-review approach* with the anything-can-be-said-on-teh-interweb format. I am talking about the notorious RateMyProfessors.com, which apparently some students consult for insights about potential instructors of courses they are considering taking. I already noted that I think that voluntary, signed comments are useful, though not perfect — but what about the other?
I won’t go into what the official student evaluations of my course are, except to note that a substantial fraction of students complete them and they are positive. But I recently saw what is written on RateMyProfessors by less than a dozen students out of about 475 students that I have taught to date. This one specifically stood out:
he is arrogant and its a distraction from teaching. he needs a lesson on making effective lecture slides and teaching. and i’d give it to him because i could do a better job with no prior understanding of the material!I fell asleep on the uncomfortable desks EVERY class. run far far away if you dont need to take this class. you wont learn anything!
The problem I have with this is not that it is negative. Anyone is entitled to their opinion, and I learned early that you can not make everybody happy. No, the problem is that he or she did not provide any means for me to accept the invitation to show me how to teach a course!
Dear student, if you are reading this, my office is SCIE 1450. Please come by at your convenience to enlighten me on the proper method of teaching the material. Also, please let me know which lecture(s) I can pencil you in for as a guest presenter next semester.
I wonder: do any students really take RateMyProfessors seriously, or do they simply ask their friends who have taken a course what it’s like?
* In particular, students are asked to fill out an online survey, which consists of both a questionnaire with numerical scales and a choice of also leaving comments, either signed or unsigned. The questionnaire and signed comments are used by the department, but unsigned comments are shown only to the instructor and the chair. So, students can still make their evaluation using only the questionnaire if they want to remain anonymous but have their opinion seen.
Blogroll amnesty day.
Both Sandwalk and Pharyngula — two of the big boys, and among my own favourite blogs — make note that this is Blogroll amnesty day. The idea is to add some blogs that receive fewer visits than one’s own to help them gain exposure.
Well, Genomicron is no Sandwalk or Pharyngula. My own take on this will be slightly different from that of the major blogs. What I want to do is single out a particular group of bloggers: graduate students. As long as blogging isn’t interfering with their studies/research, I am all for seeing students starting early with communicating to nonspecialists. Of course, several of these are (or, I suspect, will be) on ScienceBlogs, and most probably receive more visits than Genomicron, but nonetheless here is my non-exhaustive list:
- Laelaps (ok, an undergrad)
- ERV (soon to be a ScienceBlogs star?)
- Evolgen
- Fish Feet (also Fish Feet)
- Catalogue of Organisms
- Retrospectacle
- My Biotech Life
- Scienceroll
A great mix of topics from both male and female students and well worth reading if you don’t already.
Evidence of design in a genome.
There is some buzz at the moment about the latest cool-but-kinda-controversial output of Craig Venter’s research group. Specifically, they assembled a synthetic Mycoplasma genitalium genome from scratch. Hidden inside the artificial DNA sequence were sequences of codons that had been arranged to spell out messages once the initials for the amino acids that they specify were deciphered. (See here for more about the genetic code and amino acid initials — 20 letters are represented, but there is no B, J, O, U, X, or Z). The short messages were:
CRAIGVENTER
HAMSMITH
CINDIANDCLYDE
GLASSANDCLYDE
As Wired reports,
Three of the five watermarks have obvious referents as authors from the original paper (Craig Venter, Hamilton Smith, John Glass, Clyde Hutchison). In fact, the only mystery left is the reference to “Cindi” but that could be a reference to Cindi Pfannkoch, who was (is?) in the employ of Hamilton Smith, according to this New Yorker article.
If you’re wondering about the “v” in “Institvte” that’s because no amino acid correlates to the letter U, so the Venter Institute (undeterred, as always) reached back to medieval times, when orthography was less settled and U and V were interchangeable.
But what about natural genomes? Carl Zimmer has suggested a little game of word search using the BLAST engine at NCBI. Carl thinks it’s a game, but I know this has real scientific and philosophical importance: in fact, I am prepared to state that it provides the absolute best evidence ever proposed for design in a genome.
Here is what happened when I searched for DESIGN in the protein database. I have not altered the output of the query in any way. Be warned, the result is staggering.
ORIGIN
1 pisgiysnme dltigyqhfs kyrhylkwvp kyiahklgkv rdykelfylv npemlcllav
61 neklnynfrq ntgslmtlfk dvnyysdldt demvsfysal gihssmhmrs lsyfilnirn
121 eyylrlynip aylsdinvsn nfpffnyikn npickhvpdh nlgqfisfvn eiinydqkpk
181 pyipnryvyk npklshfvlp tnmsdktytp havigsgrtn lllytydvyr nvsrkqased
241 nvltsdvlfe yegdplifyn wlsyigdqnd mkrrnfmqki ylysdninin vvdnlinafs
301 tthytkffif dknhpvdahk hlhrtlnnfs ipiqivsfsv gnkkkitfpi lntpkidrde
361 aiayeyinry tnflqnhvir nsfytttdhn yilthktfkg yqqkavdrlr dqikvvknfi
421 nshktfnemk kalrdsfnih gtapintdny inhelgdles fveenypnpi gldegvsndd
481 ssqydlsyyd nyngtyllvn sdlklrsvyk ymlkyskiyk ntkyiefvmk nemrgdvhdq
541 lvnvengssc lfdfndnirv syiidycnyd kksyflfyke ykskniysvp sqdlcesaey
601 sylklcqnms llkkfftktl dtqlseihkd emkrmtkikn aiednidfkn ilsisndslv
661 siihdknegi ttfdinacft vsakltlgni fnvnsqidpe tartninnsi fctpvsvpva
721 vnrpimrsin dvyiraifni mkdqqfreym ripvnsnpyh sfiyffdkya yvykkrkwyk
781 nmnhvkmfip pqtikwnmfy yllrnnsqts ynnemflydf fygkksadik alsrnimkpf
841 lshftlffyl ykvdesign
That’s right. There is DESIGN found in the sequence of amino acids in this “hypothetical protein PC001346.02.0”. And not just anywhere. Right at the end, obvious for everyone to observe.
Also, I should point out that I did not search the complete database. No, this needed to be a strict test. Therefore, only one genus was searched: Plasmodium.
Junk from Thomson Scientific.
I like Web of Science a great deal. Nearly every paper published in at least the last 20 years is listed, and there are several extremely helpful tools like links to papers cited in and by any given article, total citation numbers, and citation alerts sent via email. It’s incredible.
I dislike scientific junk mail a great deal. It comes in two varieties, as with regular junk mail: electronic and snail. Jonathan Eisen has registered his frustration about the growing flood of solicitations, most of which, as I also have noted, are completely useless. It’s irritating.
Thomson Scientific is behind Web of Science — and, evidently, a lot of the junk mail.
I reprint here an email that went around this morning on the EvolDir, from Steve Jordan of Bucknell University:
Dear Colleagues,
A few years ago I began to receive many email and paper mail advertisements at my work addresses from companies selling scientific products. Most of these messages were of no interest to me, and their numbers have increased to the point of becoming a nuisance.
It turns out that Thomson Scientific (the Web of Science and Science Citation Index people) may be behind this flood of spam and junk mail that many of us receive. Thomson offers a product called “Scientific Direct” that harvests author contact information from the papers that we publish and sells it to marketers.
Here is a description from their website:
The Process is Simple. First, you consult with one of our list selection experts to create highly focused profiles. These profiles are then run against the multidisciplinary Thomson Scientific database. The resulting names are sent to you in the form of postal addresses or e-mail addresses, chosen carefully from the more than 500,000 international authors who have published papers in the top scientific, peer-reviewed journals.
I was disappointed to read this. I have never provided my contact information in a scientific paper with the goal of it being used to send me spam or thousands of pages of worthless and wasteful paper catalogues.
If you wish to contact Thomson about this practice, I suggest beginning here:
http://scientific.thomson.com/press/mediacontacts/
or here: customsales@thomson.com
Please let me know if you get a reply.
Modern Synthesis dead?
There seems to be new interest in the blogosphere regarding what Stephen Jay Gould had to say about evolution, invigorated, at least in part, by Jerry Coyne’s post on The Loom. This appears to have grown into the creation of a “ScienceBlogs Book Club” which will discuss Gould’s massive book, The Structure of Evolutionary Theory. I read it when it came out. I am certain that Larry Moran has read it. But we’re not on ScienceBlogs (he declined, and I was never approached). I also am fairly sure that PZ Myers has read it, so maybe he can provide some perspective.
My last post dealt briefly with one aspect of this discussion, namely a misinterpretation of punctuated equilibria as representing a saltatationist mechanism. In no small part, this has been based on cherry picking quotes from Gould’s diverse writings, which did indeed cover mutations of substantial effect in addition to patterns of speciation in geological timescales.
This time I want to revisit one of Gould’s most famous quotes, and certainly his most infamous. The version that is most familiar, I believe, is the one cited in Charlesworth et al. (1982), who quote Gould thus:
I have been watching it [neo-Darwinism] slowly unravel as a universal description of evolution … I have been reluctant to admit it … but … that theory, as a general proposition, is effectively dead, despite its persistence as a text-book orthodoxy.
Strong claims, to be sure. But evolutionary biologists, I should hope, are always wary of ellipses, and that passage has several.
Here is Gould’s (1980) quote in full (emphasis added):
I well remember how the synthetic theory beguiled me with its unifying power when I was a graduate student in the mid-1960’s. Since then I have been watching it slowly unravel as a universal description of evolution. The molecular assault came first, followed quickly by renewed attention to unorthodox theories of speciation and by challenges at the level of macroevolution itself. I have been reluctant to admit it — since beguiling is often forever — but if Mayr’s characterization of the synthetic theory is accurate, then that theory, as a general proposition, is effectively dead, despite its persistence as textbook orthodoxy.
The question is, what was Mayr’s characterization that Gould considered effectively dead as a general proposition?
Ernst Mayr (1963) (emphasis added):
The proponents of the synthetic theory maintain that all evolution is due to the accumulation of small genetic changes, guided by natural selection, and that transspecific evolution is nothing but an extrapolation and magnification of the events that take place within populations and species.
Polyploidy. Genetic drift. Mass extinction. Gould said many controversial things, but his claim, without ellipses, that the modern synthesis so defined had perished was pretty neutral.
_____________
References
Charlesworth, B., R. Lande, and M. Slatkin. 1982. A neo-Darwinian commentary on macroevolution. Evolution 36: 474-498.
Gould, S.J. 1980. Is a new and general theory of evolution emerging? Paleobiology 6: 119-130.
Mayr, E. 1963. Animal Species and Evolution. Harvard University Press, Cambridge, MA.
Punctuated equilibria is not saltationism.
If I get more time, I may weigh in on the debate that has erupted of late on several blogs, namely regarding saltationism in evolution. This was sparked by Olivia Judson’s post, and fanned by Jerry Coyne’s guest critique on Carl Zimmer’s blog, The Loom.
For the moment, I will sidestep the issue of small mutations of large effect (and the additional issue of large mutations, like genome duplications) and will focus briefly on the claim that Coyne makes in the post and in various articles that Eldredge and Gould’s idea of punctuated equilibria is, or at least was, saltationist in mechanism.
It isn’t. It never was. Gould did maintain an interest in macromutations in his discussion of development in the 1970s and 80s, but this was separate from punk eek. Linking them just because the same author discussed them would be like calling natural selection a Lamarckian theory because Darwin considered the inheritance of acquired characteristics in the Origin.
I am pleased to note that Niles Eldredge will provide an article entitled “The early evolution of punctuated equilibria” as his Editor’s Corner of the forthcoming issue of Evolution: Education and Outreach, so look for that in the spring and for additional discussions in future issues of the journal.
You can also consult Gould’s The Structure of Evolutionary Theory, or the chapter on the topic that was published alone as Punctuated Equilibrium.
Meanwhile, I will simply direct you to the summary of punctuated equilbria by Bruce Lieberman and Niles Eldredge at Scholarpedia:
Punctuated equilibria actually comprises several different and related observations. These include:
- the fossil record contains a rich source of data useful for developing important evolutionary hypotheses;
- speciation typically happens allopatrically, in narrow and geographically restricted populations containing relatively few individuals;
- species are not slowly and gradually adapting and evolving over long stretches of geological time;
- species lineages that show stasis – or an absence of morphological change – dominate the fossil record and provide useful information about the tempo and mode of evolution;
- the first appearance of a new species in the fossil record usually does not represent its point of evolutionary origin but rather the migration of a new geographically isolated species back into its ancestral range, with concomitant expansion in abundance; and
- speciation typically takes on the order of 5,000 to 50,000 years to occur – far shorter than the average duration of species in the fossil record.
This is, in essence, an extrapolation into deep evolutionary time, of Ernst Mayr’s ideas regarding allopatric speciation. Mayr himself thought so:
I believe I was the first author to develop a detailed model of the connection between speciation, evolutionary rates, and macroevolution (Mayr, 1954). Although long ignored, my new theory of the importance of peripatric speciation in macroevolution is now widely recognized. “Mayr’s hypothesis of peripheral isolates and genetic revolution must of necessity be a centerpiece of the punctuated equilibria theory; it is the theory, for all practical purposes” (Levinton, 1983:113). I once more presented my theory in great detail (Mayr, 1963:527-555). Under these circumstances it is most curious that the theory was completely ignored by paleontologists until brought to light by Eldredge and Gould (1972).
Mayr, E. 1992. Speciational evolution or punctuated equilibria. In: The Dynamics of Evolution (eds. A. Somit and S.A. Peterson), pp. 21-53. Cornell University Press, Ithaca, NY.
Indeed, here is what he said in the 1954 paper:
…rapidly evolving peripherally isolated populations may be the place of origin of many evolutionary novelties. Their isolation and comparatively small size may explain phenomena of rapid evolution and lack of documentation in the fossil record, hitherto puzzling to the palaeontologist.
Mayr, E. 1954. Change of genetic environment and evolution. In: Evolution as a Process (eds. J.S. Huxley A.C. Hardy, and E.B. Ford), pp. 157-180. George Allen & Unwin, London.
Several bloggers have discussed Coyne’s critique, and you can find summaries here and here. The one to which I most enthusiastically direct you is by Larry Moran. Larry puts it clearly, and points out that even one of Gould’s major detractors agreed that Gould never proposed punctuated equilibria as a saltationist process. Incidentally, I am not the only person to endorse that post. As Niles Eldredge told me when I mentioned the blog discussions, “PS: Larry Moran says it all!”.
Welcome Pharyngulanchers.
I see PZ has linked here in a discussion of yet more IDist nonsense regarding junk DNA. To help you find what you’re after, here is a list of relevant posts on the subject:
- Function, non-function, some function: a brief history of junk DNA
- Junk DNA: let me say it one more time
- An opportunity for ID to be scientific
- “Fx of Junk DNA” or “Mondo hackitude-o-rama”
- Junk DNA and ID redux
- Is most of the human genome functional?
- The onion test
- A word about “junk DNA”
1,000 genomes on the way (sort of).
ScienceNOW and ScienceDaily are reporting the announcement of the 1000 Genomes Project, which will be supported by agencies in the UK, China, the US, and elsewhere. It will include analyses of the genomes of 1000 individual humans, and will build upon the International HapMap Project.
ScienceDaily describes the early phases of the project:
In the first phase of the 1000 Genomes Project, lasting about a year, researchers will conduct three pilots. The results of the pilots will be used to decide how to most efficiently and cost effectively produce the project’s detailed map of human genetic variation.
The first pilot will involve sequencing the genomes of two nuclear families (both parents and an adult child) at deep coverage that averages 20 passes of each genome. This will provide a comprehensive dataset from six people that will help the project figure out how to identify variants using the new sequencing platforms, and serve as a basis for comparison for other parts of the effort.
The second pilot will involve sequencing the genomes of 180 people at low coverage that averages two passes of each genome. This will test the ability to use low-coverage data from new sequencing platforms to identify sequence variants and to put them in their genomic context.
The third pilot will involve sequencing the coding regions, called exons, of about 1,000 genes in about 1,000 people. This is aimed at exploring how best to obtain an even more detailed catalog in the approximately 2 percent of the genome that is comprised of protein-coding genes.
So, it’s really six “complete” sequences like those available for Jim Watson and Craig Venter, plus low-redundancy coverage for 180 additional people. Then the rest are subsets of genes (1,000 of around 20,000) from 1,000 people, or about 0.075% of the genome.
Though it isn’t 1000 genomes sensu stricto, it is definitely a very exciting project.
A quick shot of the thrill of science.
PZ has posted this video, and I liked it so much that I thought I would share it as well. It is meant to contrast “biblical science” with science, but really this is a minor point. The more relevant aspect is the, quite frankly, thrilling tour of a tiny portion of what science has achieved.

