(Re-posted from Genomicron 2.0)

In one of my snarkier moments, I coined the term “Dog’s Ass Plot” (DAP) in reference to

A graphical representation of data in any field that, through a lack of clear axis labels, selective inclusion/exclusion of data, visual presentation style, and/or other questionable characteristics, generates a misleading interpretation of the data in the viewer, especially by implying an illusory pattern that is not supported by the available data.

This was based on a figure that purported to demonstrate a relationship between non-coding DNA and complexity.

As I noted,

The sloping of the bars within taxa suggests that this is meant to imply a relationship between genome size and complexity within groups as well, with the largest genomes (i.e., the most non-coding DNA) found in the most complex organisms. This would negate the goal of placing humans at the extreme, as our genome is average for a mammal and at the lower end of the vertebrate spectrum (some salamanders have 20x more DNA than humans). Indeed, the human datum would accurately be placed roughly below the dog’s ass in this figure if it included a proper sampling of diversity.

Now, GraphJam has posted a figure that is not only a superb DAP (i.e., the presentation implies a pattern that extends beyond the data themselves), but a Human’s Ass Plot, or a HAP DAP:

Shedding light on Darwin.

Apparently shedding light on Darwin (for photography) is difficult.

Not enough:

Too much:

Incidentally, this statue of Darwin is located next to a small cafe at the back end of the first floor at the Natural History Museum in London. In the main hall, halfway up the central staircase and overlooking the reconstruction of Dippy (Diplodocus carnegii), is a bronze statue of Richard Owen. It seems the Natural History Museum forgot to expel this vocal opponent of “Darwinism”. I suppose the fact that he did real research and founded a real museum (namely, the NHM) had something to do with it.

No DAPs, but still pretty funny.

Readers may recall that I coined the term Dog’s Ass Plot (DAP) in reference to

A graphical representation of data in any field that, through a lack of clear axis labels, selective inclusion/exclusion of data, visual presentation style, and/or other questionable characteristics, generates a misleading interpretation of the data in the viewer, especially by implying an illusory pattern that is not supported by the available data.

Well, a new website called GraphJam (which borrows its general modus operandi from LOLcats), showcases user-generated graphs designed not to mislead but to amuse. Current content is limited, but here are two that I thought were chuckle-worthy.

HT: Of Two Minds

The Irish might drive on the right side.

Reuters is reporting that a senior politician in Ireland suggests that they make the switch from driving on the left side of the road to right-side driving, in light of the dumb tourists from North America and continental Europe who cause accidents.

I don’t know what the Irish think about this, but I recommend phasing it in gradually like they did in Newfoundland in 1947, starting with just the large trucks.


In a follow up to my last post about funny lines, here are some more funny lines.

Some of these are borrowed from comedians (though I don’t remember who), and quite a few are, I think, original (by me or my brother). If you want to double check, feel free to do so. If you don’t find them attributed to anyone else, you can link to this list. 😀

  • Despite the rising cost of living, have you noticed how popular it remains?
  • I intend to live forever. So far, so good!
  • I run sometimes. But only if it’s raining really hard and my car is parked way down the street.
  • The only substitute for good manners is fast reflexes.
  • The way to a man’s heart is through his ribcage.
  • He who laughs last thinks slowest.
  • Nostalgia isn’t what it used to be.
  • There are three types of people in the world: those who can count, and those who can’t.
  • 5 out of 4 people have a problem with fractions.
  • 43% of all statistics are made up on the spot, and 69% of people can use statistics to prove whatever they want.
  • A day without sunshine is like, night.
  • If at first you don’t succeed, then skydiving isn’t for you.
  • The early bird gets the worm, but the second mouse gets the cheese.
  • You always find something in the last place you look. But then, who keeps looking for something once they’ve found it?
  • I’m only photogenic in person.
  • Wake me up when I’m not so tired.
  • I thought I was wrong once, but it turns out I wasn’t.
  • I’m not conceited. But I should be.
  • Enough about me, what do you think of me?
  • That’s like the Rolls Royce of clichés.
  • Guns don’t kill people, bullets do.
  • The squeaky wheel makes the noise.
  • Most “common knowledge” it false. Everyone knows that.
  • Is it just me, or am I all alone here?

Let’s get biological about stupidity!

Over on Sandwalk, Larry reposts a list of euphemisms for stupidity (“Not the sharpest knife in the drawer”, “One neuron short of a synapse”, so on).

There are some on the list that are biological, but I think we could benefit from more. I will start things off with one of my own:

He’s not the brightest bioluminescent bacterium in the photophore.




For some reason, one that my brother sometimes says (with a requisite straight face) cracks me up:

He’s not the smartest guy in the world, if you know what I’m saying.

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.

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:


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.

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.

Science spam.

A few weeks ago, Jonathan Eisen vented some frustration at science spam on his blog [Biotechnology spam getting worse and worse]. Like many other researchers, I am inundated with irritating spam from science companies, usually selling reagents or equipment that I don’t use. They just end up in the spam filter with the rest of the aggravating, time-wasting solicitations that we all receive.

This one struck me as particularly amusing, however, so I thought I would share it. Next time you’re thinking of writing a paper about macroevolutionary theory in a paleontology journal, be sure to order your monoclonal antibodies from these folks.

Hi Dr. Gregory,

We’ve learned of your research with TWIST from the journal article titled Macroevolution, hierarchy theory, and the C-value enigma. MyBioSource is currently has the TWIST monoclonal antibody in our catalog products. Please click on the link below to view the datasheet of TWIST antibody.

TWIST Monoclonal Antibody (Datasheet: http://www.mybiosource.com/datasheet.php?products_id=120163
Other TWIST Antibody or Protein (Products Listing: https://www.mybiosource.com/advanced_search_result.php?keywords=TWIST&Submit=SEARCH&search_from_header=on

Additionally, we have over 12,000 monoclonal, polyclonal antibodies, recombinant proteins and peptides. Please spend a few minutes to browse our catalog offering.

Please visit MyBioSource.com and get started: http://www.mybiosource.com

Best regards,

MBS Sales Team
Tel: 619-795-6727
Fax: 619-512-4535

Funny picture place holder.

I must apologize — it has been a long time since I have posted, despite there being all sorts of interesting new things to talk about with regard to genomics and evolution. It’s teaching and grant season, which means I will probably continue to be a part-time blogger at most for another couple of weeks. I have lots to write about [1], but no time — so please bear with me.

One item of note, I have been invited to contribute regularly to Scitizen. I may also reconsider being a featured blogger at Scientific Blogging once things calm down later in the semester. In any event, it is nice to see that Genomicron is being appreciated.

Some of my fellow science bloggers (for me, that’s a small s / small b since I have not been called up to the big leagues by Seed!) are working on a paper to discuss the role of blogging for scientists. I can say that blogs have turned out to be useful for all three major components of a prof’s job, namely service (as public outreach), research (as a source of discussions of and links to interesting papers), and teaching. An example of the latter happened this morning. I was checking out Retrospectacle [2] and came across the picture below. When I stopped laughing, I decided to add it to the lecture I will be giving on kin selection today, which includes a section on sibling conflict and parent-offspring conflict. Sometimes a picture is worth 1,000 words, evn if teh words iz spelld all rong. Enjoy.


1) This includes finally responding to a meme, namely the one on the evolution of Genomicron as tagged by Sandwalk.

2) Shelley Batts needs votes to get a scholarship — help her out, won’t you?