|User’s votes are weighted by their contribution to the site (log10 contribution). In addition, the user who created the observation gets an extra vote.|
|I’d Call It That||3.0||19.31||4||(Byrain,Pulk,Claude Kaufholtz-Couture,...)|
sum(score * weight) /
(total weight + 1)
|User’s votes are weighted by their contribution to the site (log10 contribution). In addition, the user who created the observation gets an extra vote.|
|I’d Call It That||3.0||0.00||0|
|Could Be||1.0||14.34||3||(Pulk,Claude Kaufholtz-Couture,Mycowalt)|
|As If!||-3.0||5.72||1||(Alan Rockefeller)|
sum(score * weight) /
(total weight + 1)
Now with bootstrap values.
Good to see the data on this collection!
Do you Coprinellus truncorum species in your area ?
Alan Rockefeller requested specimens from this collection, so I sent them today by priority mail. They should arrive wednesday.
Looking forward to your updates Alan!
Calflora and Bugguide have submissions which are checked for correctness, if you look at Eschscholzia californica observations on Calflora they are going to be trustworthy, but Agaricus campestris observations on MO are not necessarily so since there is no standard level of identification quality here. They both also have many professionals contributing to the data set while MO has only a fraction of the number of trained mycologists and selling the site to others is an embarrassing and tedious task. I’m not really familiar with how Calflora works, I just know that its the go to site for botanists in CA and is recommended by actual botonists. Bugguide only allows editors and the person who submitted the photo(s) to move photos from name to name. Anyone else can submit corrections through comments, contacting the person that maintains the group, or posting on their forum. Regardless they seem to have a conservative stance on naming things and often defer to expert opinions which are either contributors themselves or acquainted with someone that is. Here at MO we have many more or less knowledgeable citizen scientists that don’t really agree upon very much, have widely variable views on simple things as voting and naming and aren’t able to sort the various issues with confidence, consistency and usefulness. Only genera like Amanita have managed to overcome this thanks to the generous help from users like ret.
Continuing the what-might-improve MO thread, but maybe we need a discussion thread for this.
I believe Calflora is more the “Cathedral” model; that is, it is centrally controlled and administered, but maybe I mis-understand how it works, while MO is crowd sourced both for observations and for voting.
Bugguide allows others to offer a name, but only as a comment. How is that an improvement over a voting system? Or is it that the original poster can give it a name or not and then put it in a category for ID request and this is a better model than “I have a guess how about you?”.
Does “the mob” really overwhelm a scientist or two voting on a name? I hardly see more than 4 or 5 votes on a mushroom, but maybe that’s me.
Hi Walt. Glad I could help.
I’m not sure how big of a problem discordance will end up being for phylogenetic sorting and naming, but on my view, the wicked forest of gene trees represents the true topology of the genealogical nexus, as do reticulations from horizontal gene transfer between lineages. It is a mistake on my view to dismiss these complexities of evolutionary history as “noise” to be averaged out in search of a true phylogenetic tree.
Some parts of the genealogical nexus seem to be more tree-like than others, so it might be that phylogeneticly based names will work for some kinds of organisms and not for others.
The professional vs. amateur is less important than someone informed about the latest research and understands where the tricky issues are.
I thought voting on [MO] gets weighted toward those that vote (contribute more otherwise?). Such a weight then is a rough proxy for more experience.
" the admins don’t seem very interested in improving it outside of technical site issues"
Or they are not funded to have the time.
mycologists (i.e., those with degrees and/or occupations in the field) to amateur mycophiles (that would include all non-professionals no matter the length of time spent collecting and studying fungi) on MO? Is that something that Nathan or Jason could determine from their available data?
Adolf, I have had similar issues when showing MO to professional mycologists/biologists. I have heard it described as a mere blog and stories of all the imageless observations have been received with disapproval. Also the voting system is rather flawed, inconsistent and lacks confidence in the way Calflora or Bugguide are able to achieve which are both supported by professionals. Recently the incident where it was shown how easy it is to repeatedly delete and recreate proposals just to remove contrary votes was extremely silly. I agree, MO is a good site and it has potential, but the admins don’t seem very interested in improving it outside of technical site issues. Thankfully its an free/open source project and if this continues it will be forked eventually, it would be too much of a loss to not have a mycologically based site that can be relied upon by professionals as well as beginners.
Thanks for this term Dan. I now have a name for DNA discordance!
Check our profile and you will see that we posted MO observations from over 190 locations: http://mushroomobserver.org/observer/map_observations?q=2Xz08
That compares well with your close to 80 sites.
For our contribution to Haida Gwaii (Queen Charlotte Islands) mushrooms see
Our “single location” is not the best site to beef up one’s MO “Life List”.
It has only one major mycorrhizal tree, i.e., Douglas-fir and its relatively dry forest would not have too many fungi. We selected this site for our long term survey because it is relatively undisturbed and close to our home. Nevertheless, we did find some interesting mushrooms there:
I am happy with MO regardless its idiosyncrasies. I got used to them and I am thankful to the MO designers for such a wonderful website. I would also like if professional mycologists would use MO for documenting their collections, but they would not like to fight with Consensus and similar oddities. MO is full of them. – Adolf
P.S. I spoke with one professional mycologist, specialist in several difficult groups, who is lurking in MO and she complained, "Whenever I see a misidentification in MO and point it out, the “Consensus” beats me, since I don’t have enough “votes”." I cannot “sell” MO to professional mycologists in the state it is today.
“I believe, however that with more and more DNA sequences, you will get a nice continuum and you will be reach a dead end again.”
I believe you are right about this. Take any given specimen and run your tree generating software using different DNA sequences, and you will find discordance between the trees. Phylogenetic trees generated from different genes in the same organisms will not match, and discordance is once again found at the level of the organism, the population, and the species. Some philosophers of biology call this phenomenon the “wicked forest”.
Degnan and Rosenberg (2009) is a good place to start for this, here is their abstract:
The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome. Recent advances in genealogical modeling suggest that resolving close species relationships is not quite as simple as applying more data to the problem. Here we discuss the complexities of genealogical discordance and review the issues that new methods for multilocus species tree inference will need to address to account successfully for naturally occurring genomic variability in evolutionary histories.
If the history of evolution does not follow a tree-like pattern (or more precisely if the history of evolution follows multiple overlapping discordant tree-like patterns), then names based off gene trees inferred from one or a few loci will not reflect the history of evolution.
The wicked forest is a metaphysical problem for phylogenetic nomenclature, but the endeavor is also afflicted with epistemic concerns. Should we use maximum parsimony methods, maximum likelihood methods, or Bayesian methods for generating trees? Each of these methods will generate different phylogenetic trees using the same data. What about our model of evolution? We end up with different trees depending on how we assign mutation rates to the various nucleotides.
So, I agree molecular data + phylogenetic inference is not going to yield the definite answer to taxonomy that many thought it would just a few years ago.
I do not think that I’m asking too many questions, though perhaps you are right that these are too many questions to ask at once. But this comes back to my original claim about different research programs. What counts as valuable data depends on the questions one seeks to answer.
I suppose my overall point is to counsel a bit of humility. I see too many mycologists laboring under unexamined species concepts, placing too much confidence in phylogenetic trees produced by a single method using a limited number of loci, or worse, still thinking of species as classes defined by essenses. I have encountered mycologists who think that minor variations in color are taxonomically significant, and yet these same mycologists are completely unaware of the literature on color science. For those that think essentialism is a viable research program – it’s not.
The question of how names attach themselves to referents is another elephant in the mycologist’s living room. On a casual theory of reference, it does not make sense to even ask how many characters make a taxon, because evolutionary lineages cannot in principle be defined.
I’ve said enough here.
TLDR: Check for gaps, unsupported assumptions, and anomalies in your own research program before telling others they are doing it the wrong way.
Research without the specimens is not a research:
Look at e.g., Amanita pantherina. You can make a list of sites where you have seen it, until somebody comes and says, " Amanita pantherina is a complex of small isolated taxa."
The DNA sequences are the motto of the day. Today it’s a nice tool to separate all the microtaxa. I believe, however that with more and more DNA sequences, you will get a nice continuum and you will be reach a dead end again. “How many characters you need to define a species?” As German pedologist Kubiena said about soil classification, “It is the same, as if you would ask, how many hairs a man has to loose to become bald.”
Naming vs. identification. How often I had the MO observation name changed just in order to go with the newest “taxonomical innovation”?
Those name changes will mess up our records and destroy the link between the MO observations and our collections. Here I am beating the dead horse again.
Thank you gentlemen for the stimulating discussion.
The mushrooms in this observation are sitting on my desk if anybody wants them, but I don’t plan to hang onto them forever. There will be more up in the same spot next year.
Whether one finds value in a given observation depends entirely on one’s research program.
O@A, Thank you for the link to the Cripps (2014) article. I understand from your arguments that within your research program an observation without a voucher specimen is not valuable – it is data that you simply cannot use. Am I understanding this correctly? Can you explain why this is the case?
In other research programs, of course, voucher specimens might be less important. It all depends on what questions you are trying to answer. As I have noted before, any time spent collecting and preserving specimens is time not spent searching for and photographing specimens. I like to see and photograph lots of mushrooms, and I let other people direct me toward what might be worth collecting. That is when I make it out into the woods, which is not often these days.
You might notice that I am a student of philosophy of biology. I’m interested in your claim that the naming convention here at MO is merely that – a naming convention – while you deny that it is an identification convention. I’m sure that you can see how tensions might arise if one group of users thought they were playing a naming game while another group thought they were playing an identification game.
Of course I’m not sure how you can tease the two questions apart in a clean way. This is philosophy of language territory here. Do you think that mushroom names have meanings, such that the name refers to a group of mushrooms with a given set of morphological, microscopic, and molecular properties? Or instead does a mushroom name rigidly designate an individual evolutionary lineage(causal theory of referent)?
If we are playing the identification game, then we have to assume that mushroom names have meanings (even if this meaning is merely a useful fiction); otherwise we would have no way of affixing the same name to two distinct mushrooms.
If we are merely playing the naming game, then we collect type specimens, point at them, and say, “I name you thus and such”, and henceforth the name attaches to the specimen. I don’t see why a specimen under the causal theory of naming can’t be a photograph – the name attaches to the photo instead of to a dried piece of fungus. Is a photograph of a mushroom necessarily a photograph of that mushroom’s species? Is the photo representative of the species?
Preserved type specimens serve as the physical referent of a mushroom species name; the type specimen necessarily belongs to its species. But given a lack of consensus regarding what a species is, the type specimen can’t be used to identify what other mushrooms also belong to the species.
I’m curious about your species concept as well. Do you countenance a single species concept? Are you a pluralist about species? Are species real?
I think that somebody has to consider many questions like these in order to say something meaningful about the value of a given observation.
Although I see that MO isn’t quite a perfect resource for professional mycologists, distinguishing the vouchered obses gets it as close as it could, without the entire direction of the site being pointed at that purpose.
Similarly, re: the observer’s preferred name, MO does distinguish it with that big-eyes graphic, and the herbarium page features the “Original Herbarium Label” column with the names “untainted” by the public’s votes.
(and thanks for the compliment, O&A! :)
MO programmers did exactly this option for us. We get posting notifications for several genera (Cortinarius, Inocybe etc.) and we are getting the notification only for MO observations with herbarium specimens.
Several users suggested that I would use something else for storing my photos. Why? I am happy with MO and our MO observations seem to be well appreciated by the MO community. From our postings, nobody can tell that we have some problems with MO. We really don’t have any problems with other MO users, unless we are caught in the MO naming game and unless we try to communicate with other mycologists outside the MO universe (linking our MO observations with our specimens, or asking the specialists for identification).
As for the MO Lists, they are excellent and we use them all the time. However, they are “dynamic” and they are created anew from the MO observation names, whenever you ask for the particular list. We are lucky that with some genera (e.g., Inocybe) there are not too many changes done by the MO self-invited experts.
“My problem is that I cannot use our MO observations for communication with professional mycologists.”
I have a suggestion that doesn’t require anyone insulting what they don’t want.
It sounds as if you need a checkbox when searching that limits the search to ONLY samples with herbarium specimens. I didn’t see this in advanced search.
If you created the list yourself, why would your list become effected by the other 83%? I would think it would be a fine list. I’m curious why the other scientist can’t use it.
I, like Dan, have posted field observations with photos here which lead to professionals asking me about them which resulted in specimens sent to real herbariums (not just saved at my house). If other scientists ignore good observations that are well identified, because there are other observations with bad ids, no photos, or poor photos or they happen to need specimens that seems to be a problem with the scientist not a website full of various observations and any “social game” that gets played on it.
Mushroom Observer is great in that that everybody can use it the way he/she considers it suitable. We are using it for documenting our collections and we are trying to have a voucher specimen for every MO observation. From the MO point of view, our observations are not any different from observations without any herbarium specimens or even without any images. Each of us, MO users, can use MO its own way. My problem is that I cannot use our MO observations for communication with professional mycologists. They see a game in MO, where pictures without any further documentations are just pawns in a social game. I created several MO lists of some critical genera or groups (Cortinarius, Hebeloma, Inocybe, Ramaria, Russula, etc.) and our professional contacts ignore them, just because they see those about 87% (“useless”, as I called them) MO observations without any voucher specimens.
Use MO the way you are using it! My calls for improvement of MO refers only to those 17% of MO observations that are documented by voucher collections. By the way, I like your MO observation photos.
Observations without herbarium specimens are useful for
- sharing finds (“enjoyment”)
- learning what you’ve found
- learning how to identify mushrooms macroscopically
- understanding species better by seeing everyone else’s specimens
- and reading their location, date, smell, taste, texture, growth habit, and habitat.
- enabling identification practice (and enjoyment!) when field access is undesirable or impossible
- sharing art
- informing us of a subset of biodiversity
- (potentially?) facilitating publishable research by indicating species distributions
- housing, in the comments, interesting and helpful conversation about anything in mushroom science
- learning which specimens to collect for herbaria
- learning where to look for specimens for, e.g., herbaria. Not all of us are as lucky as you are to have a single location that provides all the mushrooms we’d like.
- observations without specimens can sometimes be seen to be likely the same taxon as an obs with a specimen, providing new indirect information about the latter.
I hope not only that this demonstrates that specimen-free observations can have worth, but also that demonstrating it wasn’t necessary.
If you don’t like MO, perhaps you can simply not use it, or create your own website and database, or start coding for the admins.
A&O, notice that NO definition of “science”, much less “useful”, is going to say anything about direct use for publishable research.
Photographs are proof of fungus occurences.
Not all publications require voucher specimens for photographs.
MO already distinguishes (IN BOLD) observations that have herbarium specimens.
After reading your obtusely dismissive comments about observations without specimens, and cringing, over and over and over and over, I have to make a request: please at least use true statements to argue your “point”.
and they are really outstanding. However, they are good as photographs, not as a proof of fungus occurrences. I have also supplied photos of fungi to various publications, but for the professional mycological publication the authors required only those photos that were supported by voucher specimens. I am not a mycologist and I as a partner to one, I take photos only of those specimens which my wife-mycologist is going to collect and preserve.
I joined MO in 2011 and ever since then I have been suggesting to MO creators to make a separate MO section that would cater only for those MO observations supported by voucher specimens. Never mind, they too found my suggestions offensive.
If you guys are asking for specimens, then I’ll be happy to send some your way.
Accusations of “worthless observations” are a bit offensive. I receive very frequent requests for use of my photos in fields guides, academic journals, government publications, etc. My photos are featured in biology text books, encyclopedias, and I even had a few displayed in a museum the one time a friend convinced me to enter some photos in an art contest. All this without specimens.
I make collections when folks think an observation is interesting enough to have a closer look, and then I collect the mushrooms and send them along.
There is more than one way to contribute to the mushroom science game. It’s okay to say “Yay for me; my way is the best!”, but there is no need to insult other people by calling their work “worthless”, especially considering that such a claim is demonstrably false.
Remember that MO observations without supporting collections are useless. See the article “VIRTUAL MUSHROOMS OR VOUCHERS: TO DEPOSIT OR NOT TO DEPOSIT, THAT IS THE QUESTION” by Cathy Cripps in BEN #482
I.e., over 87% MO observations are virtually garbage and cannot be used for mycofloristics. Yes, the users can get their photos identified (actually only “named”) to some degree, but that the end.
You can test how good a collector you are, if you download your observation in Adolf’s format: the last column has an “x” for those observations for which you have a specimen. Oluna and I (user # 2873) have voucher specimens for over 90% of our observations. (On the other hand, we have only about 20% of all our collections posted on MO as MO observations.) How difficult is it to put the specimens into a desiccator once you brought them home for microscopic examination? Adolf
P.S. I do understand that with Coprinellus, this is quite a challenge! :-)
As per Byrain’s request I collected and dried quite a few of these. If anybody would like some specimens I can send them your way.
Please save as many specimens for microscopy and DNA as possible, maybe some of the European mycologists that work with Psathyrellaceae will know what to do with them. The biggest problem is no one is really working with this group in North America and all we have to go on is an obviously incomplete European key and guesswork. Also most of the people that have experience with these seem to be in Europe…
I just walked up the road and collected some young specimens from this patch. I’m making spore-prints and I have a few drying over a lamp right now. I’ll Post updates in due course.
Any chance you collected some of these and could check some microscopic features?
Nice photos, as always.
The web page you gave us is OUTSTANDING. Who is the author? What is FAN6?
This new combination is not valid though, unless the author published it somewhere else. In order to be valid, electronic publications have to be published in a journal which has an International Standard Serial Number (ISSN) and is distributed in the PDF format.
Article 29.1 of The Code says:
29.1. Publication is effected, under this Code, by distribution of printed matter (through sale, exchange, or gift) to the general public or at least to scientific institutions with generally accessible libraries. Publication is also effected by distribution on or after 1 January 2012 of electronic material in Portable Document Format (PDF; see also Art. 29.3 and Rec. 29A.1) in an online publication with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN).
For examples see:
Best info I can find is here – http://www.vielepilze.de/coprinus/sections/micacei.html
The name is adapted from FAN6, if you have a better suggestion for the same group please feel free to provide the correction. :)
Also, just for any uninformed readers, I am most certainly NOT a reference for this being called Coprinellus micaceus despite Alan’s recent extremely lame trolling.
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