Ardern, Swamidass, Gauger, and Overlapping Genes

[glipsnort (Steve Schaffner)]

@Zachary_Ardern

I said if you go to google scholar and type in overlapping genes overprinting that nearly all of the top hits on this topic use overprinting in the way I have described. It is in numerous paper titles. Overprinting refers to the mechanism of gene origin, and “overlapping gene” as the result.

In a quick survey of google scholar results, I found 8 cases of ‘overprinting’ referring to the mechanism of gene creation and 1 that treated it as a description of the resulting state. So points to @Zachary_Ardern for correctness (but work on your diplomatic skills.)

[swamidass (S. Joshua Swamidass)]

I agree that overprinting is proposed as as a de novo gene mechanism. The understanding I had was that overlapping genes in alternate reading frames is, by definition, an example of overprinting. The term does not only apply to that mechanism.

There are many papers that define it just I did here. Is the usage in the papers inconsistent with that definition? I’m not sure.

This came up because it was suggested overprinting is a loaded term to avoid using with ID advocates questioning de novo gene origins in the first place. I don’t think it’s such a loaded term as it is also used in other ways.

Or at least that is how I understand it. As I’ve repeatedly said, perhaps I am wrong. Perhaps there is two definitions to the term. Whatecer the case, when I have used the term it is not to stack the deck in conversation with ID.

[Zachary_Ardern]

@Zachary_Ardern

Also references using “overlapping genes” to refer to something other than genes in alternative reading frames would be interesting - though again I am quite sure that the standard meaning of “overlapping” is genes in alternative reading frames.

Thank you for reporting what you observed and for the advice. I understand that I have not been diplomatic in this discussion. Perhaps some may appreciate that it is difficult to be diplomatic when a bunch of senior scientists are not regulating their own tone towards me, a junior scientist trying to clear up some perceived inaccuracies and unfairness towards someone I consider a friend, and Josh is accusing me of “many” errors, misreading, etc in a field I am very familiar with.

[T.j_Runyon]

@Zachary_Ardern

Thank you for reporting what you observed and for the advice. I understand that I have not been diplomatic in this discussion. Perhaps some may appreciate that it is difficult to be diplomatic when a bunch of senior scientists are not regulating their own tone towards me, a junior scientist trying to clear up some perceived inaccuracies and unfairness towards someone I consider a friend, and Josh is accusing me of “many” errors, misreading, etc in a field I am very familiar with.

This is completely outside my knowledge range so I can’t judge who is and who isn’t correct but in this case Zach you came in swinging and gave the conversation a negative tone. Maybe Josh did misrepresent her but you came in really aggressive

[glipsnort (Steve Schaffner)]

@Zachary_Ardern

I understand that I have not been diplomatic in this discussion. Perhaps some may appreciate that it is difficult to be diplomatic when a bunch of senior scientists are not regulating their own tone towards me, a junior scientist trying to clear up some perceived inaccuracies and unfairness towards someone I consider a friend, and Josh is accusing me of “many” errors, misreading, etc in a field I am very familiar with.

Sure, but (going off topic), diplomacy isn’t about being pleasant. It’s about behaving in ways that help you achieve your aims in a complex social environment without resorting to open warfare. That sometimes includes behaving pleasantly even when you’re legitimately annoyed by the behavior of others. Successfully jockeying for status (which includes getting people to take you seriously enough to attend to your views) is sometimes obvious but seldom overt.

To be specific. . . Academics(*) are a pretty touchy and status-conscious lot: you’re generally better off impressing them by displaying expertise than by stating your expert status.

(*) Speaking as someone in the penumbra of academia.

[DaleCutler]

@glipsnort

…the penumbra of academia.

Interesting choice of metaphor – one inference could be that academia is shadowy. (Many YECs have bought into that. )

[glipsnort (Steve Schaffner)]

@DaleCutler

Interesting choice of metaphor – one inference could be that academia is shadowy. (Many YECs have bought into that. )

There’s plenty of darkness in academia.

[DaleCutler]

Yes, I’ve seen some. (You’ll find it wherever there are people, for the most part.) It’s just not the broad conspiracy that many YECs envision that is synonymous with mainstream science.