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Wednesday, January 23, 2013

Teaching Developmental Biology

PZ Myers posted some lecture notes from his developmental biology course [What I taught today: molecular genetics and basic concepts ]. Here's part of what he said ...
Think about that. In the early days of developmental biology, we didn’t even know whether there was differential gene activity or not; it was considered a reasonable possibility that all the genes were just doing their work, whatever it was, all the time in every cell, and that differences between cells emerged farther downstream, in biochemical interactions. But they knew this was an important question. They knew that we had to look at the activity of individual genes…they just didn’t have the tools yet. So it was back to hacking up embryos and trying to infer causes from aberrations.

The change emerged gradually, but there were a couple of watershed moments where everyone looked up and noticed that hey, we do have ways of looking at genes directly. One was the work of Ed Lewis, a most excellent geneticist who used the tools of genetics to look directly at mutations that caused changes in fly morphology, in the 1960s. This was amazing stuff — the papers he wrote were beautiful and complex and very, very genetical — but it was written in a language that most developmental biologists of the day were unprepared to read. They were genetics papers. But I think they laid a foundation: if you want to do development, you’d better learn about genetics.

The second big event was the saturation mutagenesis screen of Christiane Nusslein-Volhard and Eric Wieschaus, about 20 years later. This work was also built on an understanding of genetics, but also used the tools of molecular biology. It was another lesson: if you want to do development, you’d better learn about molecular biology.
I used to teach this stuff in the 1980s and I certainly agree with PZ that you need to understand molecular biology and gene expression.

When it came time to write my first textbook I incorporated the examples I had used in class. The first ones I described were: the early to late switch in gene expression in bacteriophage T4, sporulation in Bacillus subtilis, and the genetic switch in bacteriophage lambda. These were well-studied examples from experiments carried out in the 1970s. They teach fundamental concepts in developmental biology and they have an additional advantage; namely, they get students thinking about species that aren't animals.

These are still excellent examples that are well-understood at the molecular level. They are much easier to understand than Drosophila or plants. Unfortunately, we've educated an entire generation of developmental biologists who have never heard of these elegant examples.

Is this a good thing or a bad thing? Do students need to know the real history of developmental gene expression as worked out by scientists who studied phage and bacteria?


  1. Hacking up embryos and studying aberrations.
    Seems like it was all just lines of reasoning and not actual hands on investigation.

    This is indeed, to this YEC, just what genetic research is.
    There is no research done to figure out a history of biological origins.
    All that is done is lines of reasoning.
    There is no evidence for man being biologically related to primatesw for example.
    Even if true our genetics relatedness would still be only evidence of relatedness.
    Thats all it is.
    Then a line of reasoning fills in the pieces.
    Always evolutionists have told me my dna sameness with my dad equal mans sameness with apes.
    It doesn't. Even if true.
    Its just very alike DNA.
    So just introducing another line of reasoning as to why man/primate dna can be alike but without biological breeding heritage instantly eliminates any reason to see dna as a trail.

  2. "Do students need to know the real history of developmental gene expression as worked out by scientists who studied phage and bacteria?"

    Define the fundamental concepts in the field and use whatever examples you want. But you might assist future research scientists more if your examples familiarize them with current trends and models.

    1. But you might assist future research scientists more if your examples familiarize them with current trends and models.

      I have to respectfully disagree. Without a good grounding in the basics and the history of the field, you really are not ready to enter the research field. You end up riding the trends and looking ignorant of the past. Look at Ewan Birney and the recent fun that his mis-understanding of the history of our understanding of the genome is causing.

    2. "Without a good grounding in the basics..."

      Which is what is meant by "fundamental concepts."

      Larry Moran raised a likely false dichotomy when he asked if students need to know the history. The question was not whether students should be equally familiar with historical as well as contemporary research. So you still haven't explained why knowing the history of a field trumps a more inclusive pedagogy. The alleged mishaps of Ewan Birney have been overdramatized in the blogosphere and have greatly overshadowed the benefits of the research.

    3. Re: Birney - This is the perfect example of the problem from my original comment. Either A) he does not know the history of Junk DNA and seems to not hear that he is incorrect or B) he is spinning an incorrect story for his own benefit. I'm giving him the benefit of the doubt and going for A). Either way, it is a problem.

      Why we think what we do is as important as the fact. 60-80% of the genome is probably "junk" is arrived at by a large number of observation, not intellectual laziness, as the story goes.

      From Comings in 1972 “Why should the disturbing possibility that some of the DNA of our genome is relatively useless junk even be considered? There are several reasons: (1) Some organisms have an unreasonable excess of DNA, clearly more than they require. (2) Reasonable estimates of the number of genes necessary to run a eukaryote seem significantly less than the amount of DNA available. (3) The mutational load would be too great to allow survival if all the DNA of most eukaryotes carry was composed of essential genes. (4) Some junk DNA, such as mouse satellite, clearly exists.”

      Also read SR Eddy (2012) Current Biology, Volume 22, Issue 21, R898-R899

      And for your "over dramatized" claim - he has been given every opportunity to correct the error above. But he keeps saying "we are sooo complex - we need sooooo much DNA!. When a scientist makes a factually incorrect claim, they are usually asked to clarify it, or correct it. If they are not, we are heading down an unpleasant path. Lysenkoism anyone?

    4. I can't understand your case-resting logic. Care to elaborate?

      Stalin liked Lysenko's ideas - they fit the "trend", the social script of the time. So they were embraced because of a dislike of that "idealist" Mendelian stuff. The data was irrelevant.

      Extreme example? Yes. But born in the same environment of "spin" over facts.

    5. comparing what Birney said to an antiscientific apparatchik ideology culpable in the deaths of millions is the overdramatized irony-free reaction to which I referred upthread.

    6. Isn't his continual statement that "all that DNA that we didn't know the function of was dismissed as junk DNA" anti-scientific? Many people have pointed out the error, and he keeps repeating it.

  3. It is definitely a bad thing, students have a shocking ignorance of the earlier work in molecular biology.

    I've had conversations that went something like this:

    Me: "How did we come to know that DNA was the genetic material?"

    Fellow student: "Hershey and Chase."

    Me: "Can you explain the experiments they performed?"

    Fellow student: "Something with viruses."

    Me: "Indeed, something with viruses..."

  4. Here's a study that confirmed that DNA was indeed the genetic information. It all began with Frederick Griffith. Griffith studied two strains of bacteria, a virulent form of the disease, or provocation, and a non-virulent or causing non-disease. His research found two seemingly harmless strains of bacteria were fatal due to the transformation, a process in which bacteria making foreign DNA.


    Sarrah @ Bergey's Manual of Determinative Bacteriology