Genomics of sensory systems - University Of Maryland

Genomics of sensory systems - University Of Maryland

Lecture 25 12/2/09 Writing and the big finish Course evaluations www.CourseEvalUM.umd.edu 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 M o n d a y # 1 2

3 4 5 6 7 8 9 10 Who Aminah Chloe Sohan

Libby Uzair Jamie Karen Shewa* Robin* Samiha* Topic Ion transporter Olfaction Bat echolocation Electroreception

Sweet taste Autism and senses FPR receptors Bat vision Bitter taste Nocturnal color vision W e d n e

s d a y # 1 2 3 4 5 6 7

8 9 10 11 Who Bobak Sonal Zan Nadia John Laurene Chris

Nidal Eric* Jessica* Naomi* Topic Pheromones Umami taste Bat vision Sweet taste UV vision in birds Barn owl hearing Spicy taste

Cat taste Insect hearing Deep sea vision Umami taste Writing Most important thing that you do as a scientist

Do it often Strive to improve it Once youve 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 DONT 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) 0 3 6 9 12

15 Temp (C) 25 27 29 31 32 32 The reverse is not as obvious? Temp (C)

25 27 29 31 32 32 time (min) 0 3 6 9 12

15 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, 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 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.

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 2deoxyguanosine (dG) and 2deoxycytidine (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 gaps The enthalpy of hydrogen bond formation between the nucleoside bases 2deoxyguanosine (dG) and 2deoxycytidine (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 gaps We have directly measured the enthalpy of hydrogen bond formation between the nucleoside bases 2deoxyguanosine (dG) and 2deoxycytidine (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 gaps We have directly measured the enthalpy of hydrogen bond formation between the nucleoside bases 2deoxyguanosine (dG) and 2deoxycytidine (dC). dG and dC were derivatized at the 5 and 3 hydroxyls with triisopropylsilyl groups; these groups serve both to solubilize the nucleosides in nonaqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. From isoperibolic titration measurements, the

enthalpy of dC:dG base pair formation is 6.650.32 kcal/mol. Perceiving logic gaps We have directly measured the enthalpy of hydrogen bond formation between the nucleoside bases 2deoxyguanosine (dG) and 2deoxycytidine (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 -6.650.32 kcal/mol. Gopen and Swan - Write with reader in mind 1. 2. 3. 4.

5. 6. Keep verb close to subject Put new information in stress position Put subject in topic position Topics are old info which links back Use verbs which indicate the action 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 2003 rejected (not evolutionary enough) Submit JEBApril 2003 didnt want to review rejected

Added new MSP data Reframe 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 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

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

Cold <32C capsaici n Heat>52C Heat 32-39 Heat 27-24 .. well actually A LOT of receptors Zfish - 98 / 35

Puffer - 40 / 54 Frog - 410 / 478 Chicken - 78 / 476 Human - 388 / 414 and entire new pathways Vertebrate rod and cone phototransductio n 4. Evolution reuses / rearranges pathways

Olfaction Vision 2 mice Along pit axis In front of snake

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

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