Sure, I get what he's trying to say. It's the intolerance, attitude, and level of review that I think is inappropriate. What he's demanding goes beyond the details of how the data is manipulated, even beyond the exact bitwise manipulations of the data. He thinks that the entire source is required, or else it should be prohibited from scientific use altogether. This is analogous to demanding the details of the cogs and gears involved in a mechanical timer. I could tell you that one revolution is equivalent to 60 min. +/- 3 sec.. But that's not what he's asking for. He's asking for the exact details of how that result is accomplished, and that is what makes his argument absurd and deserving of sarcastic rebuke.
On Monday, April 18, 2016 at 3:34:41 PM UTC-7, Koeng wrote:
-- This entire argument has no place in science because there's one side that has no empirical support. Closed source software is routinely used in science at all levels, and I am unaware of any instance where replication failed, or an invalid conclusion was reached, because of poison in the secret sauce, insufficient details of the algorithms used, or anything along those lines.
Any good scientist will use all the tools at his disposal, and valid solutions reached by any means can't be disregarded simply because of intolerance towards the means used to obtain them.
On Monday, April 18, 2016 at 3:34:41 PM UTC-7, Koeng wrote:
I think that he's simply pointing out the hypocrisy that everything experimental is peer reviewed while software is usually not. That is not a ridiculous thing to ask, what is ridiculous is to strawman this simple argument to the point of sarcasm.Anyway, this should be topical to the original poster's desires. So far, it doesn't look like there is any software which meets all qualifications. Are there any open source plasmid editors that are locally run? I tend to trust these more than browser based.-KoengOn Monday, April 18, 2016 at 2:44:59 PM UTC-7, Jake wrote:> You literally just described peer review.Maybe you should start your own journal and appoint yourself chairman of the peer review committee. Then you can demand the firmware source of every thermocycler, timer, transilluminator, imaging system, thermostat, etc.. In a few years, when you've accumulated a few 800 page papers that meet your standard, you can publish your first issue. I'm sure it will be a big hit. ;)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.Perhaps with your strong leadership on this issue we can get rid of all these garbage papers with poisoned secret sauce that are currently being published.
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