Friday, March 25, 2016

Teaching about genomes using Nessa Carey's book: Junk DNA

Nessa Carey's book about junk DNA is an embarrassment to the scientific community [Nessa Carey doesn't understand junk DNA] [The "Insulation Theory of Junk DNA"].

Today, while searching for articles on junk DNA, I came across a review of Nessa Carey's book published in The American Biology Teacher: DNA. The review was written by teacher in Colorado and she liked the book very much. Here's the opening paragraph,
The term junk DNA has been used to describe DNA that does not code for proteins or polypeptides. Recent research has made this term obsolete, and Nessa Carey elaborates on a wide spectrum of examples of ways in which DNA contributes to cell function in addition to coding for proteins. As in her earlier book, The Epigenetics Revolution (reviewed by ABT in 2013), Carey uses analogies and diagrams to relate complicated information. Although she unavoidably uses some jargon, she provides the necessary background for the nonbiologist.
The author of the review does not question or challenge the opinions of Nessa Carey and, if you think about it, that's understandable. The average biology teacher will assume that a book written by a scientist must be basically correct or it wouldn't have been published.

That's not true, as most Sandwalk readers know. You would think that biology educators should know this and exercise a little skepticism when reviewing books. Ideally, the book reviews should be written by experts who can evaluate the material in the book.

Now we have a problem. The way to correct false information about genomes and junk DNA is to teach it correctly in high school and university courses. But that means we first have to teach the teachers. Here's a case where professional teachers have been bamboozled by a bad book and that's going of make it even more difficult to correct the problem.

The last paragraph of the review shows us what influence a bad book can have,
As a biology teacher who enjoys sharing with students some details that go beyond the textbook or that challenge dogma, I enthusiastically read multiple chapters at each sitting, making note of what I cannot wait to add to class discussions. “Junk DNA” may be a misnomer, but Junk DNA is an excellent way of finding out why.
Oh dear. It's going to be hard to re-educate those students once their misconceptions have been reinforced by a teacher they respect.


31 comments :

  1. That book is such a total cringe-inducing disaster on almost every page, yet I think I saw another positive review in a different journal so that makes it two.

    Sigh...

    ReplyDelete
  2. Scientific American published a review that is rather horrifying:

    http://www.scientificamerican.com/article/book-review-junk-dna/

    "When the human genome was first sequenced, 98 percent of it was dismissed as “junk” because it did not code for proteins and thus seemingly lacked purpose. Yet in recent years researchers have realized that these stretches of DNA are also important: for one thing, changes to them can lead to serious diseases. In chronicling what we know and what we wonder about junk DNA, biologist Carey makes an apt comparison to dark matter. Just as the universe appears to contain mass that we cannot see or understand and yet nonetheless exerts a pull on normal matter, the mysterious parts of our genome have a vital effect on the workings of more straightforward elements of DNA. In fact, far from being useless, genetic rubbish may be what differentiates humans from less advanced species."

    ReplyDelete
    Replies
    1. The rise and fall of orthodoxy is always painful.

      Delete
    2. The rise and fall of orthodoxy is always painful.

      Well, as a religious person and a creationist, you are at long last commenting on an issue you know something about.

      Delete
  3. Does it seem at all odd that "the genome is entirely functional" is always accompanied by "we used to think that all DNA that didn't code for proteins was junk, and in fact 'non-coding' was the very definition of junk"? After all, there's no necessary logical connection between them. There clearly is a connection, but what is it?

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    Replies
    1. Hi John

      Looking at bits and pieces of Carey's book as permitted by Amazon.com preview, I too am appalled at Carey's attempt to dumb down the concepts for the lay public and meanwhile get the story completely wrong!

      Nessa Carrey's definition of "junk" DNA is "one that doesn't code for protein" (p87)

      Yikes!

      Carey's treatment of Epigenetics makes me cringe... but lets look at that article written by my colleague and fellow AP Biology teacher

      I just want to point out that AP Bio teachers do a better job in the classroom than Carey! We have to! We needed to submit an audited syllabus.

      According to the latest AP Biology Curriculum Framework document:


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

      a. Both DNA regulatory sequences, regulatory genes, and small regulatory RNAs are involved in gene expression.
      1. Regulatory sequences are stretches of DNA that interact with regulatory proteins [& RNAs!] to control transcription.
      2. A regulatory gene is a sequence of DNA encoding a regulatory protein or RNA.


      Meanwhile, the AP Biology curriculum goes on to mention regulatory RNA in broader terms including specific mention of RNAi, and I could go on but leave it there.

      The AP Curriculum Framework document is readily available online.

      I think the issue here is one of poor choice of vocabulary no differently than my earlier defense of another Damsel in Distress

      http://sandwalk.blogspot.ca/2016/01/bryony-graham-another-scientist-who.html?showComment=1453525226235#c4810232411037933960

      ITMT - Larry has access to the AP Biology teachers' community forum where he will confirm that he is referenced frequently in grateful and appreciative tones, specifically for highlighting common misconceptions that require correction.

      ITMT - corrective warnings about the ENCODE bandwagon and the controversy of "junk" DNA has been frequently highlighted, and in no small part to participants deferring to this blogsite.

      All that said - I concede Larry makes a valid point!

      Unfortunate oversimplification of vocabulary such as equating "junk" with "non-coding" must be avoided, especially when Biology teachers go on to specifically teach otherwise. We must learn to parse our words more carefully in the classroom when mentioning for example the "Central Dogma". I think most heed the curriculum document as written, not as we remembered been taught. Careful attention to the CF document keeps us honest in any case, if for no other reason than preparing our young charges for the immanent exam.

      I think much of all this is a hold-over from less than adequate textbooks past resulting in some bad habits (ie choice of words) that need urgent fixing. For that - AP teachers continue to be in debt of gadflys (in the good and Socratic sense of the word)like Larry.

      ITMT - I agree Carey's book should be avoided. Yes sometimes she writes eloquently and manages to passionately ignite excitement with what hitherto had been boiler-plate textbook orthodoxy - kernels of wheat amongst too much chaff... But invoking Primum non nocere obliges cooler heads to forewarn others less expert to avoid this book. But hey that's just my opinion, for what it's worth.

      ever best & grateful regards to all present.

      Delete
    2. Almost everyone in this game, that is, both scientists and science journalists/popular writers, has to attract attention, or they don't survive for too long.

      It is difficult to attract attention unless you make bombastic overhyped claims, there is too much stuff coming out every day and nobody has the time to sift through carefully hedged statements, pick out the important bits of information, weigh the evidence and update his assessment of what is likely to be true and what not. And the premium has always been on the "paradigm shifting" revolutionary discoveries, even before the current dysfunctional system developed. Over time that leads to a culture that accepts hyping things up as the standard practice.

      The problem is that there is a chain of transmission of information and if at each step of it, there is overhyping, then we get compound overhyping that can lead to truly grotesque distortions of the science. Which is what that book is a perfect example of.

      It's a truly sad situation...

      Here is what I had to say on subject:

      http://link.springer.com/article/10.1186/s12052-015-0050-7

      Delete
    3. a) nature is too parsimonious to permit vast amounts of non-functional DNA
      b) there must be considerable hidden functionality within DNA that explains our extraordinary complexity (meaning brain function I suppose).
      c) recent discoveries (whether actually recent or not) of functionality in non-protein coding sequences is viewed as the "break in the log-jam" blazing the path to the discovery of vast amounts of functionality in non-protein coding DNA
      d) the claims (or interpretations) of ENCODE output that indeed suggests functionality in most of the genome.

      I know researchers who are knowledgable enough re: mol biology and quite understand that no one ever believed that functional only meant protein coding yet seem today to be smirking at the concept that most of the genome is junk.

      I would attribute that mostly to (d) followed by (c) with various contributions from points (a) and (b).

      Delete
    4. @SRM...

      ... let me see if I have learned anything by a more than patient John Harshman:

      To you I reply: lungfish and pufferfish and an emphatic handful of various onions all with different c-values; from both fishes and from each other...

      Basta!

      Delete
    5. @Tom Mueller

      I'm not sure I understand the intent of your comment. I am not defending the points I raised, I am saying these ideas underlay the belief of some people that the genome likely has vast undiscovered function, and is possibly mostly functional.

      Delete
    6. @SRM

      There are couple of factors that affect the genome size evolution: the ratio of insertions vs deletions, and the efficiency of selection to promote or get rid of those changes. When insertions are more common than deletions and the effective population size is small, you end up accumulating junk DNA.

      RNA polymerases have a small chance to initiate transcription from a random sequence of DNA, although they strongly favor promoters. When you have junk DNA, you quite likely have junk RNAs. With ENCODE's definition of function, those RNAs and the junk DNA coding them are functional just because they exist.

      Delete
    7. Georgi

      Apropos your comment above, I just read your review of Carey and Parrington's books in Evolution: Education and Outreach. Very nice, and spot on! Larry, you should highlight this review.

      Delete
    8. @SRM

      Sorry! I didn't catch that.

      Delete
  4. Don't forget that we're probably the ones who taught the teachers.

    ReplyDelete
    Replies
    1. Don't get me started... Our province's curriculum documents are no where as in the same league as AP Biology!

      Curriculum Committees are generally silver haired elders regurgitating what they were taught and continue to teach. I don't think our documents have been revisited for 15 years and I know our text is over 10 years old!

      Check out this diagram from our current textbook currently in use:
      http://www.cpalms.org/Uploads/resources/45851/Assessment/SummativeAssessment/graphics/animal%20cladogram.png

      I remember Georgi mentioning that his old Soviet texts he needed to use in Bulgaria in the 90s were better.

      Last year our local campus reported the average high school mark of university students entering Freshman Biology was in the 90s.

      The average mark on the final exam (after many had already dropped out) was in the high 50s!

      A travesty really!

      The powers that be in university need to get the word out to ministers of education to fix the problem and have curriculum written by current experts and that all text and resources must similarly be current.

      The beauty of a current textbook - students keep the teacher honest, again another advantage of AP Biology which mandates current resources and texts.

      Delete
    2. @Rosie

      Don't remind me!

      My colleagues who teach introductory biochemistry courses make all kinds of mistakes in their classes.

      Delete
    3. I need to changed my mind, retract one of my last points and, perhaps respectfully disagree with Larry Moran.

      After looking some more through the amazon.com search feature of the book's preview; I think a savvy teacher could justify purchase of Carey's book in order to inspire and enhance some digressionary classroom discussion.

      I agree with Larry that Carey is guilty of hubris and hype, and damn it all, Carey gets the history wrong a more than a few facts backwards!

      already discussed here:
      http://sandwalk.blogspot.ca/2016/01/bryony-graham-another-scientist-who.html?showComment=1453525226235#c4810232411037933960

      Just the same - there are kernels among the chaff which could be gleaned to advantage. Students could be impressed that recent discoveries have indeed unleashed an alphabet soup of RNA molecules with a variety of bizarre functions never imagined back in the days the Central Dogma was first proposed.

      Meanwhile, a savvy teacher could also provide selective snippets and challenge the class if they perceive any errors.

      Good meta-lessons could be learned thereby, especially caution when reading popular literature on science.

      I don't want to beat this to death...

      Delete
    4. Students could be impressed that recent discoveries have indeed unleashed an alphabet soup of RNA molecules with a variety of bizarre functions never imagined back in the days the Central Dogma was first proposed.

      If you were teaching this, how would you describe that "alphabet soup" and what do you mean by "recent"? If "recent" is over two decades ago, then how would you explain to your students that you didn't know anything about it until you read Nessa Carey's book? How would you explain your lack of knowledge of snRNAs, regulatory RNAs, antisense RNAs, and a host of other RNAs that have been in the textbooks for thirty years including one for which a Nobel Prize was awarded in 1989?

      How would you describe the Central Dogma of Molecular Biology? Why is it relevant to the discovery of "an alphabet soup of RNA molecules" when Crick knew all about genes for ribosomal RNAs and transfer RNAs when he published his 1970 paper defending the Central Dogma?

      Delete
    5. @Tom Mueller,

      Jonathan Wells wrote a book in 2011 called The Myth of Junk DNA. It has a lot more real science in it than Nessa Carey's book and it contains a lot of information about strange functional RNAs.

      Would you recommend it to your students and have them study it in order to learn about these RNAs?

      Why, or why not?

      Delete
    6. Hi Larry,

      You and I agree far more than we disagree! But before continuing I ask you to remember – this exchange between the two of us is NOT an exchange between equals! I am but a humble aging high school Biology teacher hopelessly non-current and grateful for your corrective exclamations.

      Please note I said above:

      I too am appalled at Carey's attempt to dumb down the concepts for the lay public and meanwhile get the story completely wrong!

      Regarding your question:
      If you were teaching this, how would you describe that "alphabet soup" and what do you mean by "recent"? If "recent" is over two decades ago, then how would you explain to your students that you didn't know anything about it until you read Nessa Carey's book?

      I wonder if perhaps you may be jumping to unfair conclusions here. Indeed any high school student would know that Jacob and Monod elucidated the Operator region in the Lac Operon back in the 60s, for crying out loud. And that rRNA & tRNA don’t “code” for Protein like mRNA.

      I agree with you, Carey’s presentation of the revolutionary advances made by the Cold Spring Harbor Phage Group (for example) is a travesty of history that screams to the heavens! In any case, Carey is not alone and teachers can be somewhat excused. I believe we already discussed this paper on an earlier occasion.

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051107/

      ITMT, I think you misunderstand me! I probably did not explain myself clearly. For example, I direct my students to this website

      http://www.pbs.org/wgbh/nova/body/rnai.html

      specifically here:

      http://www.pbs.org/wgbh/nova/next/body/rnai/

      … where it is clearly explained that RNAi was first observed in the 1980s and more clearly elucidated in the 1990s.

      But your point is well taken. Antisense RNA was written in textbooks before then! I just pulled out my old copy of Ursula Goodenough’s still great text Genetics from 1984! It was pure joy to look through that text again!

      Allow me to share a snippet from one of my worksheets I throw at my own students. I hope you approve and confirm that my exuberance does not constitute misplaced hubris.

      ”When the Jews were expelled from Spain in 1492, a majority went to the Ottoman Empire where they settled. There was an apocryphal anecdote that the Ottoman sultan, Bayezit II was heard to remark: “How can you call Ferdinand of Aragon a wise king, the same Ferdinand who impoverished his own land and enriched ours?”

      History repeated itself as Europe’s best scientific minds sought refuge in America during the Nazi years. Forgive me for going on a tangent here – but I strongly feel that modern texts and curricula are missing something important here!

      Today’s Geneticists and today’s Molecular Biologists are standing on the shoulders of intellectual giants (the epicenter was Cold Spring Harbor) whose work remains forgotten because modern textbooks cannot dumb-down their intellectual tours des forces! Intergenic Recombination, Genetic Complementation, Intragenic Recombination and gene regulation were all figured out FIRST in VIRUS systems … “


      Like I said, I think you and I agree more than we disagree. FTR – Mark Ptashe has always been a hero of mine. I think his work on Lambda rocks!

      Delete
    7. con't:

      On another worksheet, I ask my students to refer to this link:

      http://tinyurl.com/8wm65cg

      Here is the question I ask later on:

      Let’s return to Eukaryotic RNAi. On the first page of this exercise, we defined translational control, mRNA stability control, post-translational control, processing control and transcriptional control. Let’s find examples for each. Here is a word bank that may help you out. You will need to access this search engine to find out the functions of these various RNA transcripts.

      short non-coding RNAs: snRNA, snoRNA, miRNA, siRNA
      and lncRNA

      That should leave one spot empty on your list on page 1 of this exercise.

      Using that same search engine, explain how Protease Inhibitors work as a treatment for AIDS/HIV:


      Of course technically RNAi is restricted to post-transcriptional control, but hey… I don’t think the damage is irreparable.

      Of course, I then ask my students to promptly forget these acronyms, because I was just trying to make a point.

      Again, I hope my efforts meet your approval.

      So, I think I am whittling down your criticisms to your approval – I hope so.

      Back to Carey’s book and my “alphabet soup” remark you take issue with:

      siRNA was only discovered in 1999

      Yes, the first miRNA was discovered in 1993, but it really didn’t hit the radar until 2004

      http://www.the-scientist.com/?articles.view/articleNo/23890/title/MicroRNAs-assume-a-developmental-role/

      piRNAs in 2006

      http://mobile.the-scientist.com/article/24024/new-class-of-small-rnas-found

      The elucidation of snoRNA was even more recent:

      http://jbiol.biomedcentral.com/articles/10.1186/jbiol211

      The real problem with Carey’s book is that it is already out of date and fails to mention even more recent acronyms such as CRISPR and its latest RNA equivalent

      http://science.sciencemag.org/content/351/6276/920

      Your point regarding our need to do a better job of teaching the Central Dogma is well taken – again you and I agree far more than we disagree! I do have one question. I always thought the Central Dogma had at first been called the Jacob-Monod Hypothesis and I remain unclear on how Crick’s contribution eclipsed theirs.

      http://www.bookrags.com/research/jacob-monod-hypothesis-wob/#gsc.tab=0

      Any help you could give me on the matter would be appreciated. Thanks in advance.

      Again thanks for recommending Wells’ book. I will pick it up. BTW – have you finished your book? How does one obtain an autographed copy?

      best

      Delete
    8. Tom,

      You said,

      I need to change my mind, retract one of my last points and, perhaps respectfully disagree with Larry Moran.

      After looking some more through the amazon.com search feature of the book's preview; I think a savvy teacher could justify purchase of Carey's book in order to inspire and enhance some digressionary classroom discussion.

      ... Just the same - there are kernels among the chaff which could be gleaned to advantage. Students could be impressed that recent discoveries have indeed unleashed an alphabet soup of RNA molecules with a variety of bizarre functions never imagined back in the days the Central Dogma was first proposed.


      I asked you to explain the "kernels" that would justify giving Nessa Carey's book to your students and you responded by saying, essentially, that there are none. You already teach your students that there is an "alphabet soup of RNA molecules" and furthermore, you already teach them that this has been known for decades.

      So, you want to give them Nessa Carey's book to show that a practicing scientist doesn't understand what a typical high school student should know? Is that why you want to assign the book?

      Your comment also made it clear that you don't understand the Central Dogma in spite of our earlier discussions. Your question (below) makes this clear ...

      I do have one question. I always thought the Central Dogma had at first been called the Jacob-Monod Hypothesis and I remain unclear on how Crick’s contribution eclipsed theirs.

      Delete
    9. Again thanks for recommending Wells’ book. I will pick it up.

      Larry, you have to be more careful how you say things when talking to Tom.

      Delete
    10. @ Larry Moran,

      I think I need to repeat myself here before proceeding :

      You and I agree far more than we disagree! But before continuing I ask you to remember – this exchange between the two of us is NOT an exchange between equals! I am but a humble aging high school Biology teacher hopelessly non-current and grateful for your corrective exclamations.

      Please understand, gene regulation may take maybe two weeks tops, in a typical Introductory Course in Biology. So I do not see any high school Biology teacher assigning the book. There isn’t any time.

      ITMT – I am on public record on the AP Biology teachers’ forum (just this January) in response to a different teacher’s recommendation of the book:

      I just want to provide a heads’ up that the term “Junk DNA” is a hot-button topic and AP bio teachers should beware and hesitate before employing that term in class.

      You may find this blog interesting:

      Sandwalk: Nessa Carey doesn't understand junk DNA

      This topic happens to be the bailiwick of Laurence Moran who takes great issue with uninformed and naïve musings of those who should know the subject better.


      There are other instances where I attempt to correct my colleagues' often naïve suggestions that the term "junk DNA is obsolete", but let's move on. I did say I did not want to beat this to death.

      You also say:

      I asked you to explain the "kernels" that would justify giving Nessa Carey's book to your students and you responded by saying, essentially, that there are none.

      I already answered that. I apologize, I could have made myself clearer when I said:

      Students could be impressed that recent discoveries have indeed unleashed an alphabet soup of RNA molecules with a variety of bizarre functions never imagined back in the days the Central Dogma was first proposed.

      Perusing the online amazon.com preview of Carey’s book, she eloquently and passionately explains some interesting details of the so-called “alphabet soup” that have not yet made it to introductory textbooks. A savvy teacher could liven up interest by making the briefest (remember the time constraints) of mention to how some of these short non-coding RNAs do their job.

      That’s all I meant, nothing more!!! My antipathy to Carey’s book has already been explained.

      Indeed some (not all) of these discoveries (at least in mammalian systems) are indeed recent. Meanwhile some discoveries are so recent that they didn’t even make it into Carey’s book. I presume all that is alright since you did not correct me on any of that.

      ITMT you ask:


      So, you want to give them Nessa Carey's book to show that a practicing scientist doesn't understand what a typical high school student should know? Is that why you want to assign the book?


      I already answered that! Of course, I would never assign the book! That said, note I did say above:

      Meanwhile, a savvy teacher could also provide selective snippets and challenge the class if they perceive any errors.

      Good meta-lessons could be learned thereby, especially caution when reading popular literature on science.


      Like I said – I think we agree far more than we disagree. I was merely coming to the aid of a damsel in distress whom I thought was being pilloried a little unfairly.

      Delete
    11. Let's try this again:

      con't

      ITMT you say:

      Your comment also made it clear that you don't understand the Central Dogma in spite of our earlier discussions. Your question (below) makes this clear ...

      Oops, you are correct, I was guilty of a brain-fart. Of course, I meant to say Watson and not Crick.

      I have carefully read what you have to offer on a more correct teaching of the Central Dogma and I agree.

      I appreciate what you are saying about Crick’s flow of information paradigm but frankly (as far as high school teachers are concerned) this is may need to be one subtlety that can be “corrected” in university. Good Luck with that BTW. It would appear that far too may textbooks are persisting with an orthodoxy that will be a long time in correcting.

      As you yourself said and I will quote you one more time:

      My colleagues who teach introductory biochemistry courses make all kinds of mistakes in their classes.

      ITMT - I still do not understand why Jacob & Monod do not get their due. Did not their insight precede Watson”s? That was the thrust of my previous question.

      I really need to take issue with your criticism of me when elsewhere you said:

      …another high school teacher reveals his confusion about the subject in the comments to my post

      If you believe I remain in any confused – I welcome correction.

      Thanks in advance. I mean that sincerely. I am eager to do a better job by my students.

      ITMT – I really would like an autographed copy of your book.

      Delete
    12. @ John Harshman,

      re: Wells' book

      Larry, you have to be more careful how you say things when talking to Tom.

      ... apparently! Embarrassed am I!

      I completely missed Larry's sarcasm. I had presumed the thesis of Wells' book was entirely the contrary and that his title was ironic.

      BTW - I really do hope you and I meet in person so I can purchase that promised beer.. I owe you big time on the help you provided me on phylogenomics.

      grateful regards

      Delete
    13. Last word to Larry Moran.

      Larry - I am taking a deferred year off teaching and one of my tasks is to correct previous years' worksheets. I am chagrined at how big the task is proving to be.

      I have to say that I am in your debt - big time!

      Frankly, I am embarrassed at the great number of howling errors and misconceptions that require fixing. Lurking on your blog has been a great benefit to me and my unknowing students are deep in your debt.

      I hope my conciliatory explanations meet your satisfaction.

      Like I said, I was jumping to the defense of a colleague who clearly is dedicated and prepared to go the extra mile to inspire her students.

      That prompted me to "change my mind and retract" albeit with caveats.

      Thinking this over, I have to admit, some of what I said was disingenuous.

      You clobbered me and I need to admit I took it on the chin with your last remarks - I deserved them. That said, I hope I am not "confused" and my explanation of AP Bio quality control meets your approval.

      as I mentioned at the outset:

      AP teachers continue to be in debt of gadflys (in the good and Socratic sense of the word)like [you]

      best and grateful regards

      Delete