Saturday, February 06, 2016

A DNA quiz

Jerry Coyne discovered a Quiz on DNA. He calls is a so-so quiz on DNA. He says that one question is really, really, dumb. I disagree, I think there are several dumb questions.

I tried it and got a score of 19/19 in just under four minutes. This is misleading since you have to get every question right before continuing on to the next question. I had to anticipate what the authors wanted in order to proceed.

Try the quiz yourself before reading any further. There are spoilers below!

This quiz is harder than the average quiz. You have to know quite a bit about DNA in order to get all the answers correct. It seems to be aimed at college students although I suppose there are high school students who could answer all the questions.

The first thing I noticed about this website is that the structure of the DNA molecule in the image is wrong. It's a left-handed helix when it should be right-handed [see On the handedness of DNA]. That does not inspire confidence.

The very first question is, "What is the shape of a DNA molecule?" The correct answer is, "DNA is a long skinny molecule." The answer they wanted was the answer to a different question; namely, "What is the shape of double-stranded DNA (two molecules)." (See the questions and required answers in the table below.)

The really, really, dumb question is #2. "What is the purpose of DNA?" There are many correct answers but the answer they want is definitely wrong, or at best incomplete. It ignores genes for noncoding functional RNAs and it ignores regulatory regions that control gene expression.

For Question #9 ("What is one of the component of a nucleotide?") the only acceptable answers are sugar, phosphate, and base. "Nucleoside" is not an acceptable answer even though nucleotides are just phosphorylated nucleosides. (Ribose is not acceptable either so if you are being picky the question should have asked about deoxyribonucleotides.)

Many prokaryotic genomes are circular but "circle" is not an acceptable answer for Question #12. You have to say "ring." Some prokaryotic genomes are linear; this has been common textbook knowledge for over 30 years. The answer is not correct.

"When DNA replicates, what enzyme unzips the parent strand?" I don't know what a "parent strand" is. What I do know is that unwinding at the replication fork is assisted by one of the subunits of the replication complex. This subunit has helicase activity. I suppose it's not wrong to say that DNA has to be "unzipped" by DNA helicase but it's not how I would word the question.

According to the authors of the quiz, there is only one acceptable answer to "DNA directly codes for which type of RNA?" It's not ribosomal RNA and it's not tRNA. Now I suppose you could quibble about the word "code" and assume that this only refers to protein-encoding genes but that's a stretch. It looks to me like the authors of the question don't know about any information content other than protein-coding genes.

The last three questions require you to have memorized two names (Chargaff and Okazaki) and to remember that DNA polymerase can only work in the 5′→3′ direction. That's asking a lot.

Is a quiz like this the best we can do to educate the general public and promote scientific literacy? Who made the quiz? Was it created by people who knew all the problems that I addressed above but decided that they should be ignored for simplicity? Or was it made by people who actually didn't know the correct answers but thought they did? It seems to me that the second possibility is more likely since there are lots of other examples of misleading scientific information being spread by amateurs on the internet—especially about evolution.


46 comments :

  1. A few more incorrect questions:

    3) Where in the (eukaryote) cell does DNA reside?

    A: nucleus
    Correct answer: nucleus, mitochondria, chloroplasts, nucleomorphs

    6) What is the other nucleic acid?
    A: RNA
    Correct answer: RNA is the other commonly found in nature nucleic acid, but there are also many synthetic analogs

    10) What is one of the four nitrogen bases found in DNA
    A; A,G,C,T
    Correct answer: A,G,C,T are common to all life, but there are a number of additional variants unique to certain contexts (say, base J in kinetoplastids)

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    Replies
    1. Hi Georgi,

      re:
      3) Where in the (eukaryote) cell does DNA reside?

      What is your opinion of the flagella basal bodies having their own DNA - or least used to have their own DNA ???

      Delete
    2. Lynn Margulis also was guilty of hype?

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  2. I guessed the intentions of the testmaker for the first 16 questions, though I had to rephrase some of the answer several times before they were accepted: "stores hereditary information?" wrong (#2); "circle, circular? loop? -- ah, ring!" (#12), and it was clear that some of the "passing" answers had to be slightly wrong. Then I got stuck -- I couldn't recall Chargaff's name. I checked that up and tried again. I knew the answer to #18, but had to give up on #19 (Okazaki fragments).

    It's a rather silly test, though I have seen worse:

    Solve 5x3

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  3. Apparently some issues (like not detecting "circle" in q#12) are due to the js code not picking those properly. Here's what the code should accept:

    q#1: A double helixa double helixdouble helixtwisted laddertwisted staircasestaircaseladder
    q#2: Serves as genetic code for protein synthesisserves as genetic code for protein synthesismake proteinsgenetic codegeneticgenecodeprotein synthesisproteininformation
    q#3: In the nucleusin the nucleusnucleus
    q#4: 23 pairs23 pairs46twentythree paristwenty three pairsforty sixfortysix
    q#5: Nucleic acidnucleic acid
    q#6: RNArnaribonucleic acid
    q#7: Deoxyribonucleic aciddeoxyribonucleic aciddeoxyribo nucleic acid
    q#8: Nucleotidesnucleotidesnucleotide
    q#9: Deoxyribose sugar nitrogenous base and phosphate groupdeoxyribose sugar nitrogenous base and phosphate groupsugardeoxyribosenitrogen basebasephosphate
    q#10: Adenine guanine cytosine and thymineadenine guanine cytosine and thymineadenineguaninecytosinethymineadenosine
    q#11: Hydrogen bondshydrogen bondshydrogen
    q#12: A ringa ringringloopcircleoval
    q#13: Deoxyribose sugar and phosphate groups alternatingdeoxyribose sugar and phosphate groups alternatingsugarphosphatephosphate and sugarsugar and phosphate
    q#14: DNA helicasedna helicasehelicase
    q#15: DNA polymerasedna polymerasepolymerase
    q#16: Messenger RNAmessenger rnamrnammessengerm
    q#17: Chargaffchargaffchagraffchagaff
    q#18: 33three33number 3
    q#19: Okazaki fragmentsokazaki fragmentsokazaki

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  4. I failed at question #2, "What is the purpose of DNA?" Aside from the question of whether "purpose" is appropriate, I tried things like inheritance, reproduction, genetic, but failed because it didn't occur to me to limit my answer to coding for proteins. So I'm a failure. Sigh.

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    1. I struggled with it for quite a while, trying to find an answer that would please the damn thing. I think something like "genetic code" worked at last. I don't like the word "purpose" in the question, by the way.

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    2. I think "gene" worked. But the issue with sporcle quizzes is that you have to list answers (and unless you mess with the setting it ends up case sensitive and cares about punctuation - still mad about the one that asked for Rick Astleys greatest hit and didn't accept "gonna", but wanted "going to" and I've also run across one that wanted George Michaels band as "Wham!" and one that asked me to by tiral and error figure out that they wanted "AC-/-DC", because obviously that's how you translate that bolt into ASCII). I.e. it's a platform with great potential to annoy you even when it's only about pop music...

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    3. Speaking as a high school teacher here - I think the authors of this quiz were fixated on a particular misconception of the Central Dogma (as Larry has addressed on many occasions)

      Junior High students are taught there are three basics categories of transcripts: mRNA, tRNA & rRNA. Others exist but leave that for high school.

      High School students are taught the Lac Operon before rushing on to "Eukaryotic gene regulation" (which still irks me - given every supposed method of eukaryotic gene regulation had its antecedents first in Prokaryotes) meaning the purpose of DNA is not always "coding" (well Junior High students already knew that), but can also be regulatory. Meanwhile, transcripts come in many more varieties such as RNAi (for example).

      Any high school student following a current Biology curriculum would have been frustrated by this "quiz"

      Its not clear to me whether the authors of this quiz know the difference between nucleoside and nucleotide... but now I am niggling.

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    4. The purpose of DNA is to assimilate or eliminate in its Borg-like plot for world domination.

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    5. @ Allan

      LOL

      BTW - I attempted to fire you an email which may have hit your spam folder...

      Did you get it? are you "at"csulb.edu ??

      best

      Delete
  5. Somewhat irritating as one had to guess at what the authors were driving at. Like the answer for the structure of bacterial DNA which was ultimately "a ring" yet circular was not accepted. Ugh.

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    Replies
    1. ... and in any case there are examples of linear bacterial chromosomes.

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    2. oh shit, just read the rest of Larry's post in which he addressed this very issue.

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    3. Yes, dredged up circular from memory banks. Not accepted.

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  6. Is Jarry Coyne any relation to Jerry Coyne?

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  7. It was like a college exam, where you are expected to regurgitate the exact phrasing of the professor who taught you, rather than demonstrate comprehension. I was exiled to a state university for a semester for misbehavior, and the tests were exactly like this.

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  8. Try this one:
    http://www.sporcle.com/games/drakemilleriii/biology-dnarna
    it's even worse

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    Replies
    1. Whoah that one was just straight up painful. "Is DNA single stranded or double stranded?" Well, when it's single-stranded it's single-stranded. Amazing.

      Delete
    2. On a more positive note:
      http://www.sporcle.com/games/Scuadrado/climb-the-tree-of-life
      that one is done very well.

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    3. Hi Simon,

      Maybe we should continue this offline, as I do not want to highjack this thread.

      But on the subject of the Tree of Life: I am really flummoxed by the hype surrounding Xenoturbella rooting the Bilateran Tree as just published in Nature.

      New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

      I question the authors' explanation; to wit...

      The sister group relationship between Nephrozoa and Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa.


      My problem is their placement of Ctenophora on their own phylogenetic tree as a "more primitive out-group" (for lackof better words).

      Myself, I always considered Ctenophora and Cnidaria as bilateral (I never could wrap my head around textbook orthodoxy proposing "bilateral radial symmetry")

      IMHO Ctenophorees should root the bilateran tree as their own diagram suggests... which of course begs more than one question upon rereading their analysis.

      Delete
    4. Hey Georgi - any enlightenment you could provide regarding my question posed to Simon, would be greatly appreciated!

      С най-добри пожелания

      Delete
    5. Хе-хе :)

      Unfortunately, I am stuck with something really painful that I need to finish right now (and yes, that means I should not be procrastinating here), so I put the Xenoturbella papers in the ``to read later when there is time'' pile when they came out. And they will be there for a few more days :(

      Delete
    6. Hi Georgi - no problem

      It's just that I think the authors are guilty of hubris as well.

      As I mentioned, my problem is their placement of Ctenophora on their own phylogenetic tree as a "more primitive out-group". Myself, I always considered Ctenophora and Cnidaria as bilateral - in this case more primitively bilateral which IMHO should root the bilateran tree... which of course begs more than one question upon rereading their analysis.

      OK OK... I realize that textbook orthodoxy bandies terms such as "Bilateral Radia Synmetry", but "biltaeral" by any other name is still "bilateral"!

      In any case, the sea anemone Nematostella vectensis, clearly exhibits bilateral symmetry, if this paper is to be believed! (check the diagram on page 96)

      http://www.ncbi.nlm.nih.gov/pubmed/15131263

      Can anybody help me out? ... or refer this to an expert who can help me out? What were the authors (or the reviewers for that matter) thinking?

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    7. ... I must be missing something here.

      Delete
    8. Tom,

      Re your question about Ctenophores that's old news. Several years ago a very large sequencing effort came up with the very courter-intuitive result that Ctenophores are the outgroup. The implications of this is that sponges are either secondarily simplified or that Ctenophores put their tissues together in a fundamentally different way than other animals. I think there was mild support for the latter..then a few months ago I group supposedly refuted the original result and sponges are the outgroup again

      Delete
    9. Well, it's worth noting that in the analysis presented in the science paper there is an unresolved trichotomy at the base with Porifera, Ctenophora and the rest. So this analysis is equivocal on whether it's (P,(C,O)),(O,(P,C)) or (C,(P,O)). But the key finding here is that Xenoturbella is sister to the Nephrozoa. A key apomorphy of the bilateria (which wasn't soley based on the symmetry) is the presence of protonephridiae, i.e. excretory organis with a particular cytology. These remain as an apormorphy of the Nephrozoa, but the idea that they had been reduced in Xenacoelomorpha, making them sister to Deuterostomia is rejected in the new analysis.

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    10. Thank you for your responses. Let's see if I have this all correct.

      What seems clear is that all Pre-Cambrian fauna representing basal acoelomates or pseudo-coelomates (other than singular esoteric exceptions such as Xenoturbella) may have all gone extinct. All modern eumetazoan (whatever that is now supposed to mean)acoelomates or pseudo-coelomates may all be derived from a triploblastic ancestor, that according to the rules of parsimony was possibly if not probably, coelomate.

      OK... that last sentence is pure speculation. It still is possible that tribloblasty arose before Cnidaria emerged, whereas coelomy occured after Cnidaria emerged. That both occured prior to the emergence of Cnidaria is considered likely according to Volker Schmidt's followers but less than likely acccording to Volker Schmidt's detractors.

      Meanwhile, while some textbooks still consider Ctenophores and Cnidaria as diploblastic, other texts have classed both as triploblastic, in deference to sort of muscles that everywhere else are of mesoderm derivation.

      Bottom Line: Current textbook orthodoxy requires radical revision.

      Delete
    11. I need to confess that I owe much to others who conjecture along similar lines. I draw your attention to Jordi Garcia-Fernàndez and his great review discussing

      ...in fact, the simplest bilaterian metazoans, having a single or only a few Hox-like genes and several NK genes. This would imply that no basal non-bilaterian animals currently exist. An intriguing exception might be the placozoans...

      http://www.nature.com/nrg/journal/v6/n12/full/nrg1723.html

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    12. @ Lantog

      re your
      I think there was mild support for the latter..then a few months ago I group supposedly refuted the original result and sponges are the outgroup again

      Could you please provide the reference which pretty well destroys much of my line of speculation...

      Delete
    13. @ lantog

      OK - I found it
      http://www.pnas.org/content/112/50/15402.abstract

      and a review thereto

      https://medium.com/@caseywdunn/who-is-our-most-distant-animal-relative-4309b9fe4e48#.87fi1bxq8

      Clearly the jury is still out, but to my dilatant eye, I would bet on Ctenophores & not Porifera

      Delete
    14. Here is a three day old post:

      http://mprous.blogspot.ca/2016/02/xenoturbella-and-xenacoelomorpha.html

      Salient quote:
      In conclusion, I think it is too early to exclude deuterostome affinity of Xenacoelomorpha.

      Now that is interesting!!!

      In any case, lantog's dismissal of my original query:

      ...Re your question about Ctenophores that's old news....

      ... missed the point altogether. I was questioning the hubris and what I perceived to be the hype of the Xenoturbella paper where the authors placed the Ctenophore lineage as ancestral to Xenoturbella all the while claiming Xenoturbella rooted the Bilateran Tree.

      This is the part I do not get... whey aren't Ctenophores and Cnidaria commonly recognized as Bilateral?

      I would appreciate any help in this matter.

      best regards to one and all...

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    15. Whether any taxon is bilateral in morphology has nothing to do with whether they are members of Bilateria.

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    16. If bilateral morphology has nothing to do with being members of Bilateria, then why are the members labeled as Bilateria?

      Aren't all Bilateria bilateral in at least one life stage,. e.g. embryonic, larval, and/or adult?

      Delete
    17. The bilateria are defined by a number of apomorphic characters. When they were named bilateral symmetry was one of the apomorphies listed. As long as bilateria remain a monophylum the name remains valid and this is irrespective of whether bilateral symmetry is actually a synapomorphy for that clade - it might well be a plesiomorphic trait.

      Delete
    18. Bilateria, as all taxa, is defined phylogenetically, as a node or branch on the tree and all its descendants. Names are given for various reasons, but etymology doesn't determine meaning. That's why Basilosaurus is a whale, not a lizard.

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    19. Two questions:

      Why don't textboos recognize Cnideria as bilateral?
      http://www.ncbi.nlm.nih.gov/pubmed/14756328

      ditto Ctenophores:

      http://www.nature.com/nrg/journal/v6/n12/full/nrg1723.html

      According to Jordi Garcia-Fernandez:

      ...in fact, the simplest bilaterian metazoans, having a single or only a few Hox-like genes and several NK genes. This would imply that no basal non-bilaterian animals currently exist. An intriguing exception might be the placozoans...


      I remain perplexed.

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    20. @ John Harshman
      re

      Names are given for various reasons, but etymology doesn't determine meaning.

      Cute!

      The problem remains that the authors of the Xenoturbella paper are making attention-drawing claims of re-rooting the Bilaterian Tree.

      Is it correct to presume they are guilty of hype?

      Delete
    21. BTW - big thanks to P Z Myers for his exemplary altruism!

      Were it not for him - I never would have twigged on to this fascinating digression

      http://scienceblogs.com/pharyngula/2006/05/08/hox-genesis/

      Delete
  9. "Complementary", goldangit (q. 11).

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  10. These quizzes demonstrate how far we have to go to get truly accurate machine graded responses. (If we want to go that route.) The questions are typical of ones that I have seen in the publisher-supplied quizzes that accompany many textbooks. And also the quizzes in some of the MOOC I've sampled. Most profs construct test questions off the top of their heads and seldom or never do any validation of them. But at least they can recognize a correct, but unexpected response.

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    Replies
    1. Reminds me of a class I taught many years ago. I don't use publisher-supplied tests wholesale, but I do mine them for questions. The test in this book had multiple choice tests with no right answer, two right answers, incomprehensible questions, etc. I contacted the publisher with a scathing review, and actually got paid a few (very few) hundred dollars to correct the test.

      Multiple choice tests have problems, but they're obviously better than the "fill in the blank but only exactly the way I expect" tests like we're discussing here.

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  11. I have to thank Larry for providing a graphic that finally allowed me to learn right from left. I've had some kind of dyslexia problem with this. I have mixed dominance, if that makes any difference. I always blocked when trying to remember how DNA is labeled.

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