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Interactions in biology: it’s binding all the way down

Source: http://imgur.com/PE07XGM

We use a several terms in IntroBio that all mean the same thing, but may mean little to students in the classroom–‘binding’, ‘specific interaction’, ‘interacts with’, ‘recognizes’. This is particularly dangerous with ‘recognizes’, because newcomers can envision a police line-up: targets appear and we visually choose one. Alternatively, we risk students imagining a somewhat mystical, or at least poorly-defined ‘way’ that molecules have that is beyond their ken. Nothing could be further from the truth; in some ways one of the easiest things to understand is why two molecules ‘stick to’ one another and overcome the force of Brownian motion, at least for a little while.

(Image source:  http://imgur.com/PE07XGM)

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AP Biology Structure/Function What's important about... | Bruce | | Leave a comment

Teaching majors biology better: think non-majors biology

Is teaching majors biology just brain-jamming?

In my own little sphere, I’ve been fascinated by some of the contrasts between design and delivery of majors vs. non-majors biology courses. Non-majors courses are subjected to thoughtful cherry-picking: “What is most relevant to student lives or futures?”, “What has ties to society and their interests”, “What can we successfully convey in the allotted time?”. On the other hand, in teaching majors biology, I think there is a lot of pressure for the ‘kitchen sink through a fire hose’ approach: ‘everything’ must be force-fed to students at whatever pace necessary to get it ‘into their heads’, and there simply isn’t time for the extravagance of relevance or interest. I propose that teaching majors biology more along the lines of non-majors biology can make our students more interested and provide them with more  knowledge and understanding when we’re done.

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Lecture modules What's important about... | Bruce | | Leave a comment

Pull yourself together! Self-assembly in biology

Double stranded DNA moleculeLists of the ‘characteristics of life’ are a common element in introductory biology early lectures. Generally, these focus on movement, energy conversion, organization, etc.–all legitimate concepts. But the role of self-assembly in biology must not be underestimated; it’s a key feature of the flow of information in the Central Dogma (through the specific partnering of bases), folding of proteins from linear strings of amino acids (readily specified by linear structure of nucleic acids) gives rise to the functioning machines at the heart of almost all cellular work and action, and even membranes, while not members of the Central Dogma club, have function that relies critically on aspects of self-assembly. Without these properties, life would not only be impossible–they’re prerequisites for life to evolve from non-life.

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AP Biology Sense of things Structure/Function What's important about... | Bruce | | 1 Comment

Molecule display in introductory biology

Molecule display of guanine as it 'feels'Teaching the world of molecules to relative newcomers is challenging because it’s an invisible world with ‘rules’ that don’t always have a 1-to-1 correspondence with the macroscopic world (looking at you, hydrophobicity). A second issue is that while the molecules themselves are concrete things, we discuss them using their labels–A or adenine or glucose or ‘protein’. Too often, students end up with vague notions (or none at all) about these entities. Given that everything in the cell is made of and run by molecules, student success in thinking and understanding is critically dependent on what they’re picturing as molecules. I think care in and improvements of molecule display can go a long way towards making their lives easier and their understandings richer.

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AP Biology Sense of things Structure/Function What's important about... | Bruce | | Leave a comment

Amino acid building blocks: components for life’s machines

Generic amino acidUnderstanding the cellular roles of DNA and protein is challenging because they are, in important and meaningful ways, not analogous to anything in the macroscopic world. Proteins are a fascinating study: while cars, watches and houses are built by specialized builders, a single master factory, the ribosome, strings together all cellular proteins. And in a richly meaningful sense, that string then assembles itself (folds) into its final form. And the machines of the cell are almost unimaginably diverse in their forms and functions, the latter of which derive once again from within: the amino acid building blocks and precisely where they come to rest in the final three dimensional structure.

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AP Biology Lecture modules Sense of things Structure/Function What's important about... | Bruce | | Leave a comment

Plea for pedigrees: pedigree deduction in Introductory Biology

Pedigree symbolic family imagePedigree-solving can be perceived as passé in an era in which every single nucleotide of an individual’s genome can be learned (relatively) affordably, parents be damned. But I don’t think that’s the value in teaching pedigree deduction; indeed, I question whether it ever should have been. As with many exercises in Introductory Biology, I think we need to make careful distinctions between means and ends. Pedigree deduction can be employed as one of a class of near-perfect problem-solving opportunities, employing limited, easy-to-grasp tools, reflecting core biology (meiosis, randomness), and representing an unforgiving series of clear deductions. To my mind, the question should be how do we make sure these aspects are represented in tasks and assessments involving pedigrees.

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AP Biology Genetics Problem solving strategies What's important about... | Bruce | | Leave a comment