I recognize this is a very niche topic, but I was wondering what the best approach is to observations of bacteria identified by MALDI mass spectrometry. For those who are unfamiliar, this is a method of identifying microorganisms by their unique chemical fingerprint that allows species-level ID, which has been revolutionary in medical microbiology. I’ve noticed many observations of bacteria ID’d by MALDI reaching research grade. But what troubles me is that there is no way to confirm the ID from the posted observation itself, which is often a microscopy image. Don’t get me wrong, these observations are very cool, I absolutely want to encourage them. But I’m not sure if these observations can qualify for research grade because other users can’t independently confirm the ID. In other taxa, when species can’t be determined from photos alone (insects requiring dissection come to mind) is a comment explaining that the observer took the necessary ID steps (i.e. dissection) enough to reach research grade? I’m sure this question has come up in other taxa, and I’m curious what the community thinks.
My area of interest (lichen) often has observations with spot tests (that are critical to id) written in a comment instead of photographed. Often the reactions are faint or temporary so photographing isn’t always practical.
I’m of the opinion that there’s a level of trust that has to be maintained with the observer. There’s no way to tell photos haven’t been manipulated or faked, so why assume a comment is false? Allowing photo-less observations to be RG would be a step too far, but a good faith and otherwise high quality observation with some additional info in the comments or other fields should be allowed IMO. That all said I don’t know if this is really “inat policy.”
How is this chemical fingerprint represented when people are recording lab results or writing papers about it? How are they presenting it in observations? As “verified by mass spectrometry test as X species” or more specifically, e.g. details of the chemical composition of the results. I would not consider the first of these notes to be verifiable information, but the second one likely would be.
It seems to me that this is similar to DNA sequencing; there is no way to visually represent this, but people can include the string of characters that represents the DNA barcode (in a note or observation field). I don’t know much about the process of associating barcodes with species names, but in principle the barcode represents a form of information that is verifiable and can be checked for plausibility and whether it matches what is expected for the species, even if it isn’t possible to check the conditions that led to the test result.
A range of opinions were expressed on this subject in this thread recently (and in another thread linked a few replies down): ID based on observer notes
Personally I don’t think it’s consistent with iNaturalist’s standards of evidence to accept comments as sufficient to confirm an observation as RG. Otherwise there are plenty of observations which have no media which should be eligible for RG if they have a sufficiently detailed description of what was observed. But in pure text it’s more difficult to tell how experienced or honest the observer is. What if they misinterpreted the features in a dissection, or misread the graph indicating the chemical results?
For bat identification people will upload a spectrogram of the bat calls; I think here uploading an image of the results of the spectrometry would be analogous?
Another example is that a photo of a positive result on a Covid test strip has generally been considered acceptable evidence.
I agree. Even in more charismatic taxa like birds, a description of the bird’s vocalization can work alongside a photo to allow for a specific ID, even if the vocalization wasn’t recorded. Behaviors like “tail-bobbing” can be described and help with an ID even if they weren’t recorded.
I get that we’re only supposed to provide IDs that we can “independently verify” based on the evidence provided, but field notes, reports of tests performed, etc. still count as “evidence”. If one were to take the “verification” idea to a literal extreme, then nothing could ever reach research grade. How can I independently verify that the location is correct? That the photo wasn’t manipulated? That the field notes aren’t lies? The official iNat policy is that you have to be able to arrive at the identity on your own from the evidence provided. So in my mind, that means “trust me I saw it, it was this species!!” is not grounds for agreement, but “I made the following observations/did the following test” can be taken into account.
Thanks for the great discussion, I agree with basically all that has been said. I wanted to just add two clarifying points to the discussion. The observations I had in mind do not typically include any photo of the actual MALDI output, analogous to a positive covid test or a bat spectrogram image. I agree that including an image of the results is probably the best practice here.
My approach to this question was not at all to doubt the trustworthiness of these observations, but more to ask myself if I were to identify this observation, what am I actually saying or adding? Ideally I’m saying “I also conclude the evidence shown is X species”. In an observation like these, I feel that I’m saying… sort of nothing? It feels like I’m just duplicating the identification already present, not adding another identification. That being said, I liked what has been said about taking additional information into account as an identifier, which includes date, location, and commented information (ex. behavior). I won’t beat this topic to death given the aforementioned threads which already discuss this concept generally. Thanks for the interesting discussion points!