While I like open source as much as anyone, I have to agree that it's kind of silly to say that closed source software has no place in science. Should scientists be disallowed from using Windows? If you are doing processing of the sequence (e.g. A multiple sequence alignment) then it's important to know the math that goes into it, but it doesn't really matter if they don't tell you the way that they render the graphical drawings of a plasmid.
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I think that equating "It just pastes sequences together" to "I just extracted teh DNA" to be flawed logic. Saying "the cloning was simulated with snapgene 3.1.2" is just about as good as saying "the DNA was extracted with the Qiagen miniprep kit", in which the latter is sufficient for a user to go and find out how the protocol was done (and vice versa).
When a miniprep is done with 2 different kits, the outcome can be very different.
All else being equal, I'd say say open source deserves to be a gold standard for scientific applications. Saying that writing and using applications under other licenses has 'no place in science' is hyperbole, I'll give you that, but along the same dimension I think that using harder-than-necessary terms to encourage preferred practices under scientific ideals falls some distance short of 'exaggerated entitlement and bigotry'.
Don't forget to include things like diagrams of their heating and lighting systems, lighting frequency, color temp., mechanical details of every cog and wheel in any timing devices used, and so forth (obviously source code for any digital devices). You might find it hard to get details on the etching masks for every IC used in these devices, but you certainly can't publish something without these details. The ICs could be discontinued and you'd have to etch exact replacements to have any hope of the perfect replicability we are now demanding. Perhaps with special permission and unanimous consent of the review board you could allow logic diagrams to substitute in certain cases, as long as the complete datasheet is included and the functionality has been independently verified.