Lecture 25 12/2/09 Writing and the big finish

Course evaluations   Please let them know : How I was as a professor If this was a good topic for a class If you liked having a small class

MondayMondayMondayMonday #WhoTopic 1AminahIon transporter 2ChloeOlfaction 3SohanBat echolocation 4LibbyElectroreception 5UzairSweet taste 6JamieAutism and senses 7KarenFPR receptors 8Shewa*Bat vision 9Robin*Bitter taste 10Samiha*Nocturnal color vision

WednesdayWednesdayWednesdayWednesday #WhoTopic 1BobakPheromones 2SonalUmami taste 3ZanBat vision 4NadiaSweet taste 5JohnUV vision in birds 6LaureneBarn owl hearing 7ChrisSpicy taste 8NidalCat taste 9Eric*Insect hearing 10Jessica*Deep sea vision 11Naomi*Umami taste

Writing  Most important thing that you do as a scientist  Do it often Strive to improve it

Once you’ve written something  Getting your first version done is just the first step  Edit, edit, edit  Simplify, simplify, simplify

Goal of writing  Making an argument as simple as possible - stating your case  Explaining something  Clarifies the authors thinking  Transfer of information - stating results

Writing  If a tree falls in the woods and no one is there, does it make a sound?  If an author writes a paper and no one understands it, did they make a contribution?

Writing to sound right  If you write scientifically to sound like what you think science should sound like - DON’T  Likely you are modeling bad writing  Write to make things as clear as possible

Premise  As readers, we have certain expectations as to how writing is arranged  If the writer meets those expectations, the reader is more likely to understand the science They can find the meaning without having to fight the structure

Structure informs meaning T(time)=15’ T(temp)=32°; t=0’ T=25°; t=6’ T=29°; t=3’ T=27°; t=12’ T=32°; t=9’ T=31°

Temperature as a function of time time (min)Temp (°C)

The reverse is not as obvious? Temp (°C)time (min)

Writing also has expectations  Large scale form Intro Methods Results Discussion If find results in the intro or methods in the discussion, the paper is confusing

Writing expectations  Also occur on smaller scale Paragraphs Sentences  We rely on structure to guide our understanding

0. Paragraphs  Usually the first sentence is the topic sentence Tells what the paragraph is about

0. Paragraphs  Usually the first sentence is the topic sentence Tells what the paragraph is about  You can list the topic sentences from each paragraph and get a summary of the paper

Exp1. Subject and verb occur close together  Avoid long phrases separating subject and verb “Darwin, a leader of 19th century thought and the developer of the theory of natural selection, was trained at Cambridge.”

Exp1. Subject and verb occur close together  Avoid long phrases separating subject and verb Darwin was trained “Darwin, a leader of 19th century thought and the developer of the theory of natural selection, was trained at Cambridge.” These make reader wait and suspend attention

Exp1. Subject and verb occur close together  Avoid long phrases separating subject and verb Darwin “Darwin, a leader of 19th century thought and the developer of the theory of natural selection, was trained at Cambridge.” “Darwin was a leader of 19th century thought and the developer of the theory of natural selection. He trained at Cambridge”

Exp1. Subject and verb occur close together  Avoid long phrases separating subject and verb Darwin “Darwin, a leader of 19th century thought and the developer of the theory of natural selection, was trained at Cambridge.” “Darwin was trained at Cambridge. He was a leader of 19th century thought and the developer of the theory of natural selection. “

Example 1. Gopen and Swan  URF passage  Simplified version  Sentence 1 What is most important? If parenthetical phrase is unimportant - LEAVE IT OUT

Exp2. New info comes at end of sentence  End of sentence is “stress position”  Start with old and move to the new Save the best for last  Reader assumes what comes at end is the important information

Exp 3. Sentences flow from old to new  Subject at beginning should link to prior knowledge  Sentence should end with new information - stress position  New info is then familiar and so becomes old. Next sentence then starts with old and links to next new idea  Old  new. Old  new. Old  new.  A  B. B  C. C  D.

 Large earthquakes along a given fault segment do not occur at random intervals because it takes time to accumulate the strain energy for the rupture. The rates at which tectonic plates move and accumulate strain at their boundaries are approximately uniform. Therefore, in first approximation, one may expect that large ruptures of the same fault segment will occur at approximately constant time intervals. If subsequent main shocks have different amounts of slip across the fault, then the recurrence time may vary, and the basic idea of periodic mainshocks must be modified.

Problems  Old info keeps coming at end  Confuses the reader  Burdens reader to carry new info till connect with old info  Reader wastes lots of energy just dealing with prose and not in getting ideas

 Large earthquakes along a given fault segment do not occur at random intervals because it takes time to accumulate the strain energy for the rupture. The rates at which tectonic plates move and accumulate strain at their boundaries are roughly uniform. Therefore, nearly constant time intervals (at first approximation) would be expected between large ruptures of the same fault segment. If subsequent main shocks have different amounts of slip across the fault, then the recurrence time may vary, and the basic idea of periodic mainshocks must be modified.

Gopen and Swan 1990

Perceiving logic gaps The enthalpy of hydrogen bond formation between the nucleoside bases 2’deoxyguanosine (dG) and 2’deoxycytidine (dC) has been determined by direct measurement. dG and dC were derivatized at the 5’ and 3’ hydroxyls with triisopropylsilyl groups to obtain solubility of the nucleosides in non-aqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. From isoperibolic titration measurements, the enthalpy of dC:dG base pair formation is ± 0.32 kcal/mol.

Perceiving logic gaps The enthalpy of hydrogen bond formation between the nucleoside bases 2’deoxyguanosine (dG) and 2’deoxycytidine (dC) has been determined by direct measurement. dG and dC were derivatized at the 5’ and 3’ hydroxyls with triisopropylsilyl groups to obtain solubility of the nucleosides in non-aqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. From isoperibolic titration measurements, the enthalpy of dC:dG base pair formation is ± 0.32 kcal/mol.

Perceiving logic gaps We have directly measured the enthalpy of hydrogen bond formation between the nucleoside bases 2’deoxyguanosine (dG) and 2’deoxycytidine (dC). dG and dC were derivatized at the 5’ and 3’ hydroxyls with triisopropylsilyl groups to obtain solubility of the nucleosides in non-aqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. From isoperibolic titration measurements, the enthalpy of dC:dG base pair formation is ± 0.32 kcal/mol.

Perceiving logic gaps We have directly measured the enthalpy of hydrogen bond formation between the nucleoside bases 2’deoxyguanosine (dG) and 2’deoxycytidine (dC). dG and dC were derivatized at the 5’ and 3’ hydroxyls with triisopropylsilyl groups; these groups serve both to solubilize the nucleosides in non- aqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. From isoperibolic titration measurements, the enthalpy of dC:dG base pair formation is ±0.32 kcal/mol.

Perceiving logic gaps We have directly measured the enthalpy of hydrogen bond formation between the nucleoside bases 2’deoxyguanosine (dG) and 2’deoxycytidine (dC). dG and dC were derivatized at the 5’ and 3’ hydroxyls with triisopropylsilyl groups; these groups serve both to solubilize the nucleosides in non-aqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. Consequently when the derivatized nucleosides are dissolved in non-aqueous solvents, hydrogen bonds form almost exclusively between the bases. Since the interbase hydrogen bonds are the only bonds to form upon mixing, their enthalpy of formation can be determined by measuring the enthalpy of mixing. From our isoperibolic titration measurements, the enthalpy of dC:dG base pair formation is -6.65±0.32 kcal/mol.

Gopen and Swan - Write with reader in mind 1. Keep verb close to subject 2. Put new information in stress position 3. Put subject in topic position 4. Topics are “old info” which links back 5. Use verbs which indicate the action 6. Give reader context before introducing new info

Approaches to writing  Ways to start

What to do when you get stuck  Deal with subunits Does each paragraph hang together Topic sentence  Outline paper based on topic sentences Test organization  Have other people read it

History of Carleton et al 2008  Submit MBE March 2003rejected (not evolutionary enough)  Submit JEBApril 2003didn’t want to review rejected Added new MSP data Reframe w/ heterochrony  Submit PNASAug 2007not sent for review  Submit PLOS BioDec 2007not sent for review  Submit PLOS GenDec 2007not sent for review  Submit BMC Evol Bio Jan 2008reviews required extensive revisions  Submit revisionsMarch 2008accepted accepted for BMC Biology

What did we learn this semester  Similarity of genes (receptors + transduction pathways)  Commonality across organisms  You can contribute to an understanding of the senses

What did we learn this semester

The top ten things I learned this semester

10. Receptors for different senses are similar

9. All students can learn phylogenetics

8. We would be nowhere without GFP and Calcium imaging

7. Scientists can be inspiring  Nobel prize for Chemistry 2003 Roderick Mackinnon, Rockefeller Univ

6. Duplications can change genes

5. Duplications can make diverse receptors capsaici n Heat>52C Heat Heat Cold <32C

Zfish - 98 / 35 Puffer - 40 / 54 Frog / 478 Chicken - 78 / 476 Human / well actually A LOT of receptors

…and entire new pathways Vertebrate rod and cone photo- transduction

4. Evolution reuses / rearranges pathways Olfaction Vision

3. There are a ton of things we have no clue about 2 mice Along pit axis In front of snake

2. We might all get a personal view of our senses

#1 This is a sensitive class of students who all work hard. Each of you has a lot of potential. Be sure to make a difference in the world!