Sunday, November 22, 2009

Publishing a paper

I wanted to share an email exchange I had earlier this year. I thought that I had sent an email to Paul Peterson, a colleague who I was writing a paper with (but have never actually met in person), when in fact I sent it to Jeff Peterson, a friend from Ithaca who is an anthropologist turned librarian. I also actually addressed the letter to Jeff in mistake.

My original letter is in blue, and Jeff's comments are in light green. (If you are bored by 'science' then stop reading now).

Jerry and Jeff,

I have made some revisions to the paper as suggested. I have also had another read through and made some other changes. Attached is a document describing revisions – if you could take a read through my responses and suggest any other changes I would appreciate it. The original uploaded paper with line references is also attached.


Hey, I know nothing about this, but that sure hasn't stopped me before. I'm far from a classic Renaissance man, but as a librarian I like to think of myself as somewhat well-rounded. But I must have oversold myself somehow if you were thinking I would be a great contributor here. Still, I would be happy to make up some stuff for you. See below.

The only outstanding matters which I would like your comments on are:

1) ‘Describe the type of grinder used (Wiley or cyclone or ??).’
Jerry – do you think this is necessary to include? Do you have a sentence already?

I like the idea of the cyclone one. It sounds cool.

2) (3, 6-8) ‘This statement needs a reference. It is too broad--some would argue for other constituents under specific conditions. What type/class of livestock is being referred to? Dairy cattle?’
Jerry – can you provide a reference for NDF as the principal forage quality characteristic of concern? What about livestock class?

Here you are getting into the natural kinds debate. You need to slow this down. It's important to understand that species and types are not rigid categories. There aren't any really good rigid definitions of species that work in real world situations. Rather than representing discrete chunks, species boundaries are fuzzy. Take the fox in the circum-polar region. Foxes that are adjacent to one another around this circuit can mate and produce viable offspring with each other. But if you were to mate two foxes that came from sufficiently distant points in the circum-polar region, then you would find that they are unable to produce offspring. So when you ask "what type/class of livestock is being referred to" you aren't acknowledging the nuances here and may be asking the wrong question. See John Dupre's "Natural Kinds and Biological Taxa" in The Philosophical Review Vol. 90, No. 1. and Richard Boyd's "Kinds as the 'Workmanship of Men': Realism, Constructivism, and Natural Kinds".

3) (8, 49) ‘Do you have statistics to back up this statement? It is relatively simple to compare statistical differences among linear slopes.’
‘Either add some statistics to indicate whether slopes were truly different from each other, or avoid making statements that speculate on such differences.’
I still haven’t decided what to do here. It is relatively simple to compare the differences between 2 slopes, but not so simple when you have more than 2. Here are some web articles on it:
The problem is that the methods I have read about work okay for either comparing 2 slopes or using orthogonal contrasts to compare more than 2 slopes. Because we want to compare each slope with every other slope we can’t use orthogonal contrasts, and we can’t use the 2 slope method because of the potential compounding of errors. We need a multiple comparison procedure, like Tukey’s test but for slopes, and I am not aware of anything available. The stats guy here is not around so I haven’t been able to ask anyone about it. Maybe the simplest think is to just cut back on the interpretation.

Look, I don't use statistics. This is too positivist. In the classical world rather than being wowed by numbers people were really suspicious when they were used because they thought they were trying to trick you. Just talk about what all of this means to you.

Good luck,


That’s all for the moment. We don’t have too much more time on this but if you send me your comments I will make some changes and re-submit it.


So I replied to Jeff:

Hi Jeff,

Sorry I sent you the message earlier which obviously wasn't for you. I chose the wrong Peterson! Hope all is well. All the best for 2009.


And Jeff replied:

"obviously" wasn't for me? I'm hurt by the word obviously. I was really hoping to sneak my name onto your paper. I could have kept going with that.
I could use this on my cv. Oh well.

But hey, even though my information is ridiculous in the context of your paper, I should say that I really didn't make any of it up (it's all true, except for the part about it being over the top to use any stats at all. I don't really think that). And just for fun, I actually do recommend reading the two papers I mentioned. I think the Boyd paper is potentially helpful for just about anyone.


And here's my final response to Jeff, with his comments inserted:

Hi Jeff,

Sorry I haven’t replied earlier. Busy times!

Thanks for the reply. I assume you are pretty busy. I'm thrilled to know that I have made a contribution to Agronomy. This makes me feel like a real Renaissance person, and I can consider this to be one more box checked off on my to do list before I die.

I would like to read about the fuzzy species boundary at some stage, it sounds interesting.

...but probably not very practical. But yes it is interesting and I think I think it is worth reading about. John Dupre's "Natural Kinds and Biological Taxa" in The Philosophical Review Vol. 90, No. 1. is a real paper that I recommend. And as I mentioned I really do recommend the Boyd paper for just about anyone. Categories are important in most disciplines. You never know how things might apply. I actually drafted a section in my EQ notes on the Godhead (if you still are on the list) that connected to this discussion on categories and natural kinds. I was going to talk about the criticism that is sometimes offered against the Bible: the Law of Moses classifies the bat with birds. I am not sure who it is that really fires off these kinds of criticisms; they seem kind of puerile to me. At any rate, I think Dupre and Boyd's papers help us to understand (if we need the help) why I don't think this is really a "problem". And I wanted to tie this open understanding about categories into the discussion on the Godhead. I can't tell if this is all obvious or not, but since people seem[?] to have trouble speaking about the Father, Son, and Holy Spirit as one God, I thought this might help. But then I scrapped it because it seemed like too much. But you just never know how things are going to be connected.

I appreciate your contribution and will add it to the acknowledgements – I was thinking : ‘The authors would like to thank the three anonymous reviewers for their valuable comments and suggestions, and also Jeff Peterson for encouraging us to publish in the Journal of Experiential Agronomy. All statistics were omitted on Jeff’s advice.’

:-) I like it.
(comedy aside for a moment, I'm actually not one of those anthropologists who completely stays away from numbers. I'm all for using both qualitative and quantitative data).

I’ll try and send future papers your way. At least you responded a lot quicker than everyone else!

Regards, David


I would be happy to see any papers that you are working on, although I can't promise any helpful comments



In the true spirit of Jeff, he always manages to find something interesting in what other people have to say. I'll have to collaborate with him on a paper one day...


  1. Ah, you witty academics. I have always wanted to be credited in a scientific paper because I too am a renaissance man. I was thinking about providing you with a legal perspective. For instance, as a teaser, in providing statistical information, you should always include prominently a disclaimer stating that "Past performance is not necessarily indicative of future results". You don't want to get sued! Other disclaimers would need to be included based upon the manner in which you selected or obtained the data being referred to. Just let me know.

  2. I will admit is over my head Dave..and i did read ond ponder the presentation..
    so give me cooking anyday...
    but the fact you sent it to the wrong Jeff and he responded ..
    well that is funny....