Research practice

Define research topic

Prepare research plan

Conducting the research

Research practice

Define research topic

Prepare research plan

Conducting the research

Research practice

Define research topic

Often part of a larger scheme

State specific, testable hypotheses

an exercise in logic

Research practicePrepare research plan

Updated review of the literature (existing grant proposal may be outdated)

an academic exercise

Types of sources

peer reviewed journals

non-peer reviewed journals

published reports

internet

To: shafir@agri.huji.ac.ilSubject: reviewing BES-04-0168?Message-ID: <20040506093409.MCnarnia6469299@gemini.scholarone.com>From: giurfa@cict.fr Cc:Date: Thu, 6 May 2004 09:34:09 -0400 (EDT)

Dear Sharoni

Would you be interested in reviewing for Behavioral Ecology and Sociobiology the following manuscript:

…

If you would like to read the Abstract of this manuscript before committing yourself, you will find it pasted in further below.

Please let me know whether or not you are willing to review this manuscript, by replying to my above email address.

If you agree, I'll email you how to access the full manuscript.

Looking forward to hearing from you soon,

With best wishes,

Martin GiurfaAssociate Editor for BES

Request to review

From: sksakal@ilstu.eduSubject: RE: Review for Ethology ms ETH-05-0075Date: October 24, 2005 4:34:13 PM ISTTo: shafir@agri.huji.ac.il

Great! Thanks Sharoni - details to follow shortly.

Scott SakalukProfessor Phone: 309-438-2161Department of Biological Sciences Fax: 309-438-3722Illinois State University email:

sksakal@ilstu.eduNormal, IL 61790-4120

http://www.bio.ilstu.edu/sakaluk

Thank you!From: giurfa@cict.frSubject: Re: Review for BES-04-0332Date: October 12, 2004 2:39:43 PM ISTTo: shafir@agri.huji.ac.il

Thanks Sharoni!

MartinFrom: courant@avignon.inra.frSubject: AR:comments on manuscript (E1441)Date: April 15, 2004 10:09:38 AM IDTTo: shafir@agri.huji.ac.il

Dear Sharoni,

Thanks a lot for your fast review of that manuscript. Best regards,

Christiane --------------------------------------------------------------------- Christiane Courant Managing editor of Apidologie UMR INRA-UAPV "Ecologie des Invertébrés" Site Agroparc F-84914 Avignon cedex 9 Christiane.Courant@avignon.inra.fr Tél: +33 (0)4 32 72 26 19 ; Fax: +33 (0)4 32 72 26 02 Apidologie on line: http://www.edpsciences.org/apido

From: Editor@abs.animalbehavior.orgSubject: Your Submission to Animal Behaviour [7977]Date: January 30, 2004 11:32:49 AM ISTTo: shafir@agri.huji.ac.il

Dear Dr. Shafir

Caste-specific differences in risk-sensitivity in honey bees (Apis mellifera)

Thank you for submitting your manuscript to Animal Behaviour. We have given it the number 7977 which should be quoted in all correspondence. The manuscript will now be assigned to an Editor and reviewed by at least two reviewers. We shall be in contact again when we have reached a decision. This usually takes about 8 weeks but please bear in mind that this may be longer during conference and holiday periods.

Best RegardsFrom the Editors of Animal Behaviour

Submission

From: Editor@abs.animalbehavior.orgSubject: Your Submission to Animal Behaviour [7977]Date: March 19, 2004 10:58:06 AM ISTTo: shafir@agri.huji.ac.il

Dear Dr. Shafir7977 Caste-specific differences in risk-sensitivity in honey bees (Apis mellifera)

I am happy to inform you that your manuscript is acceptable for publication in Animal Behaviour, subject to suitable revision in line with the comments given below. The reviewers raise important issues, but I would like you to pay particular attention to reviewer 1's point suggesting that it is variation-sensitivity, rather than risk-sensitivity, that your study measures, and also that a stepwise procedure should be avoided in the regression analyses that you perform. I also agree with reviewer 1 that the inclusion of the process-based explanantion using Weber's law does not really add anything to the argument presented, and that removing this would help to shorten a rather lengthy paper. However, if you feel this information is essential, perhaps you could provide more justification for doing so, so that its relevance is made clear. Please also include in the Methods section the ethical information provided to Dr Turner by email.

When you revise your paper, you should prepare a detailed explanation of how you have dealt with all of the reviewers' and Editor's comments. Refer to the Instructions for Authors (on the main menu of Editorial Manager at http://anbeh.edmgr.com and in the back of the latest issue of Animal Behaviour) for details of our house style and for a list of file types that are acceptable for revised papers. Log in to Editorial Manager as an Author to submit your response to the comments and your revised paper. Changes in the revised paper should be highlighted; you can use Track Changes, then Highlight Changes in Word or just underline your changes.

The revised paper will be edited and further changes may be necessary then. Final acceptance for publication depends on the date when the manuscript has been edited and all queries have been resolved.

We should like to receive the revised paper within 120 days. If you think you will be unable to revise your manuscript in that time please let the appropriate Editorial Office know (justine.fox@nottingham.ac.uk for UK papers). Please do not reply directly to this email.

Yours sincerelyLouise BarrettEditor

Response

Reviewer #1: This well-written manuscript continues the use of a promising experimental paradigm (proboscis extension response) to explore a novel question: do castes differ in risk-sensitivity? The integration both functional and mechanistic approaches is commendable. The experiments seem carefully conceived and well executed. The results are of general interest, and fit nicely with predictions.

I two major quibbles with the work, some minor quibbles, and a few editorial questions, as follows:Major

1. It's not risk-sensitivity.What the authors claim to be risk-sensitivity strikes me instead as "variation sensitivity". Unlike the approach used by Shafir et al. (1999), where bees experienced a random sequence of rewards each time they selected the variable option, these bees experienced deterministic sequences (description begins on line 231). That is, they got "1-0-0-1-0-0-1-0-0-1-0-0-...." (for the low variance) or "1-0-0-0-1-0-0-0-1-0-0-0-1-....." (for the high variance). This is a problem, because the deterministic sequences ensure that there is no risk, only variation. While I agree that the authors may have shown a response to these treatments, it cannot be called "risk-sensitivity". No research in risk-sensitivity that I'm aware of used such strongly deterministic sequences to simulate a "risky" state. There's a big difference between 0-1-0-1-0-1-0.... and a random string of equi-probable 0's & 1's in terms of how organisms might perceive risk, and in the functional consequences ofrisky choices. A forager feeding at what Shafir et al. call low or high risk would experience IDENTICAL foraging gains after some period of foraging. There's no shortfall-minimization reason to be risk-sensitive, and there's no risk.

2. Stepwise models are flawed.All of the logistic regressions presented here are stepwise models. There is a lot of theory out there about why stepwise models are to be avoided when one is making inferences about variables (as opposed to finding an optimal subset of variables for the purpose of prediction, which is not the point of this research). Some of it's reviewed at: www.gseis.ucla.edu/courses/ed230bc1/notes4/swprobs.html. It strikes me that if the authors wish to test hypotheses about the importance (or non-importance) of different variables, then all of them should be in the "final" model. That is, a priori decide what variables to examine/control, then run the model with all of them in. Don't build an potential inferential "house of cards".

It's true that each variable in the logistic multiple regression is assessed for its contribution to maximizing the likelihood of the observed data by comparing the model fit with and without it in the model. This sounds like a stepwise procedure, but it isn't. The other variables in the model are statistically controlled when the focal variable is assessed for its contribution to model fit.

The choice of stepwise models makes me doubt the overall conclusions. That said, I suspect that the conclusions of Tables 3-5 and Figures 1-4 would not be seriously altered if the analysis is performed properly.

MinorIn a few places (lines 310-311, 328-331) non-significant results are presented incorrectly. Bees did NOT show faster learning of the high reward relative to the low reward. Mean preference for the high reward was NOT greater in the 0-.4 condition than the .4-1.2 condition.

I don't see the value of using precious journal space to present trial-level data, as done in Figs 1 to 4. This is particularly true when there aren't any obvious temporal trends of interest. Instead, any significant trend (Fig. 4) can be described in the appropriate Table.

Tables 3 through 5 can also be made more informative (and not just by presenting full model fits, rather than stepwise-selected subsets of variables). In particular, the direction (sign) of each significant effect should be provided, along with an indication of what state (e.g., 0 or 1) was associated with what preference (e.g., low or high variance). This way, one could support previously unsupported statements like (line 318):"When bees extended their proboscis, they showed significant preferences for the high rewards, with a significant difference between conditions".

lines 359-364. It's unclear to me whether this analysis (including Figure 6) is worth presenting. Why do we need to know that hungry bees ate more than less hungry ones?

I'm not convinced that the "process-based explanation" using Weber's Law adds much to the study (other than 3 manuscript pages of discussion and a figure). This may simply reflect my "functional" bias (and "process" ignorance), but if there is a compelling reason for this lengthy discussion, it's not obvious to me. Note, however, that the other mechanistic approach (CV) strikes me as clearly relevant.

Editorialline 86: remove extra bracket before "Rescorla".

Methods. No information about number of honey bee colonies is provided. The authors note how many bees were used, but these are social animals, so number of colonies is also critical.

line 131. What proportion of bees didn't extend their proboscis? Answers the nagging question: is this a tiny subset of bees that was tested?

line 137. What proportion of bees didn't extend their proboscis?

lines 214, 216, 219, 220. Add the word "discrimination" before "experiment", or it gets very confusing.

line 269. US not previously defined.

line 308. the meaning of "generalization" in this context is unclear.

line 316. No statistical test provided to support the hypothesis of random choice.

Research practicePrepare research plan

Updated review of the (peer-reviewed) literature

Databases

ejournals

Types of sources

peer reviewed journals

Impact factor? Rank?

non-peer reviewed journals

published reports

internet

“All the thinking, all the textual analysis, all the experiments and the data-gathering aren’t anything until we write them up.”

“In the world of scholarship we are what we write.”

“It is a truism that an experiment is not done until it is published.”

Donald KennedyAcademic Duty

Publishing

New and recommended

Research practice

Prepare research plan

Updated review of the (peer-reviewed) literature

Reformulate specific hypotheses

Design an experiment to address each specific hypothesis

Experimental design

“Nothing is as simple as it may first appear ...”

Experimental design

Decisions, decisions, decisions ...

Type of data to collect

Size of sampling unit

Number of replications

Statistical analyses

Experimental design

“Spend a lot of time planning -- it will save you

a lot of time.”

Experimental design

Ergonomics

Experimental design

Automation

Experimental design

“Nothing is random”

Haphazard

Random

Pseudorandom

tests: means and runs

Experimental design

Real-world vs simulation

Real-world

smaller sample size

“less random”

Simulation

larger sample size (but with limits!)

“more random” (but with limits!)

Experimental design

Micro

write precise experimental protocol

prepare charts of protocol

Macro

prepare chart of full experiment

“Plan everything in advance -- during the experiment don’t

think”

Experimental design

Costs

Labor

Equipment

Time

Seasons

Other ...

Constraints