Lecture 25Lecture 25

12/2/09Writing and the big finish

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Please let them know :How I was as a professorIf this was a good topic for a classIf you liked having a small class

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# Who Topic

1 Aminah Ion transporter

2 Chloe Olfaction

3 Sohan Bat echolocation

4 Libby Electroreception

5 Uzair Sweet taste

6 Jamie Autism and senses

7 Karen FPR receptors

8 Shewa* Bat vision

9 Robin* Bitter taste

10 Samiha* Nocturnal color vision

WWeeddnneessddaayy

# Who Topic

1 Bobak Pheromones

2 Sonal Umami taste

3 Zan Bat vision

4 Nadia Sweet taste

5 John UV vision in birds

6 Laurene Barn owl hearing

7 Chris Spicy taste

8 Nidal Cat taste

9 Eric* Insect hearing

10 Jessica* Deep sea vision

11 Naomi* Umami taste

WritingWriting

Most important thing that you do as a scientist

Do it oftenStrive to improve it

Once you’ve written Once you’ve written somethingsomething

Getting your first version done is just the first step

Edit, edit, edit

Simplify, simplify, simplify

Goal of writingGoal of writing

Making an argument as simple as possible - stating your case

Explaining something Clarifies the authors thinking Transfer of information - stating

results

WritingWriting

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 rightWriting 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

PremisePremise

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 scienceThey can find the meaning without

having to fight the structure

Structure informs meaningStructure 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 Temperature as a function of timetime

time (min) Temp (°C)0 253 276 299 3112 3215 32

The reverse is not as The reverse is not as obvious?obvious?

Temp (°C) time (min)25 027 329 631 932 1232 15

Writing also has Writing also has expectationsexpectations

Large scale formIntroMethodsResultsDiscussionIf find results in the intro or methods

in the discussion, the paper is confusing

Writing expectationsWriting expectations

Also occur on smaller scaleParagraphsSentences

We rely on structure to guide our understanding

0. Paragraphs0. Paragraphs

Usually the first sentence is the topic sentenceTells what the paragraph is about

0. Paragraphs0. Paragraphs

Usually the first sentence is the topic sentenceTells 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 Exp1. Subject and verb occur close togetheroccur 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 Exp1. Subject and verb occur close togetheroccur close together

Avoid long phrases separating subject and verb

“DarwinDarwin, a leader of 19th century thought and the developer of the theory of natural selection, was was trainedtrained at Cambridge.”

These make reader wait and suspend attention

Exp1. Subject and verb Exp1. Subject and verb occur close togetheroccur close together

Avoid long phrases separating subject and verb

“DarwinDarwin, 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 Exp1. Subject and verb occur close togetheroccur close together

Avoid long phrases separating subject and verb

“DarwinDarwin, 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 SwanExample 1. Gopen and Swan

URF passage

Simplified version

Sentence 1What is most important?If parenthetical phrase is unimportant

- LEAVE IT OUT

Exp2. New info comes at end Exp2. New info comes at end of sentenceof sentence

End of sentence is “stress position”

Start with old and move to the newSave the best for last

Reader assumes what comes at end is the important information

Exp 3. Sentences flow from Exp 3. Sentences flow from old to newold 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

Oldnew. Oldnew. Oldnew. 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.

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.

ProblemsProblems

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 1990Gopen and Swan 1990

Perceiving logic gapsPerceiving 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 -6.65 ± 0.32 kcal/mol.

Perceiving logic gapsPerceiving 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 -6.65 ± 0.32 kcal/mol.

Perceiving logic gapsPerceiving 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 -6.65 ± 0.32 kcal/mol.

Perceiving logic gapsPerceiving 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 -6.65±0.32 kcal/mol.

Perceiving logic gapsPerceiving logic gapsWe 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 Gopen and Swan - Write with reader in mind reader in mind

1. Keep verb close to subject2. Put new information in stress position3. Put subject in topic position4. Topics are “old info” which links back 5. Use verbs which indicate the action6. Give reader context before

introducing new info

Approaches to writingApproaches to writing

Ways to start

What to do when you get What to do when you get stuckstuck

Deal with subunitsDoes each paragraph hang togetherTopic sentence

Outline paper based on topic sentencesTest organization

Have other people read it

History of Carleton et al History of Carleton et al 20082008

Submit MBE March 2003 rejected (not evolutionary enough)

Submit JEB April 2003 didn’t want to reviewrejected

Added new MSP dataReframe w/ heterochrony

Submit PNAS Aug 2007 not sent for review Submit PLOS Bio Dec 2007 not sent for review Submit PLOS Gen Dec 2007 not sent for review Submit BMC Evol Bio Jan 2008 reviews required

extensive revisions Submit revisions March 2008 accepted

accepted for BMC Biology

What did we learn this What did we learn this semestersemester

Similarity of genes (receptors + transduction pathways)

Commonality across organisms You can contribute to an

understanding of the senses

What did we learn this What did we learn this semestersemester

What did we learn this What did we learn this semestersemester

The top ten things I learned this semester

10. Receptors for 10. Receptors for different senses different senses

are similarare similar

9. All students can learn phylogenetics9. All students can learn phylogenetics

8. We would be nowhere without 8. We would be nowhere without GFP and Calcium imagingGFP and Calcium imaging

7. Scientists can be inspiring7. Scientists can be inspiring

Nobel prize for Chemistry 2003Roderick Mackinnon, Rockefeller Univ

6. Duplications can change genes6. Duplications can change genes

5. Duplications can make diverse 5. Duplications can make diverse receptorsreceptors

capsaicinHeat>52C

Heat 32-39Heat 27-24

Cold <32C

Zfish - 98 / 35

Puffer - 40 / 54

Frog - 410 / 478

Chicken - 78 / 476

Human - 388 / 414

.. well actually A LOT of receptors

……and entire new pathwaysand entire new pathways

Vertebrate rod and cone photo-transduction

4. Evolution reuses / 4. Evolution reuses / rearranges pathwaysrearranges pathways

Olfaction

Vision

3. There are a 3. There are a ton of things we ton of things we have no clue have no clue aboutabout

2 mice

Along pit axis

In front of snake

2. We might all get a personal view of our senses2. We might all get a personal view of our senses

#1#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!