# Why molecular taxonomy is pure bullshit....



## Roth (Jun 10, 2011)

If you look here:


http://images.wikia.com/orchids/en/images/b/b8/Genetic_relationship_and_differentiation_of_Paphiopedilum_and_Phragmepedium_based_on_RAPD_analysis.pdf

Some molecular taxonomists are happy that their 'RAPD analysis results' were in agreement with the morphology of the studied plants. Joyce Hasegawa close to callosum, very far from emersonii and malipoense, besseae hybrids further than besseae is from pearcei... paph rothschildianum close to phrag sargentianum...

What I really LOVE is paphiopedilum emersonii, malipoense and Hamana Wave ( a maudiae hybrid) 'show similar leaf morphology. Really ?

The original Paphiopedilum taxonomy using molecular technics by Cox and Chase looked very similar. During the proof reading, a paph grower had to teach them that it was absolutely crazy, so they reworked their copy...


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## John Boy (Jun 10, 2011)

This is truly great scientific reasoning! Congratulations!!!


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## TyroneGenade (Jun 10, 2011)

Surely this paper has been retracted? It is total BS.


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## Shiva (Jun 10, 2011)

Not all scientists are good scientists as there are bad and good judges and so on. That said it's so stupid it brings a smile to my face.

Their methodology is obviously wrong, perhaps like mixing hybrids and species in their study. Hybrids have already had their genes modified and the machines might interpret that as relations that don't really exist. Something like mixing apples and oranges at the molecular level. Or as we used to say in the early days of computing: ''garbage in; garbage out''

Michel


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## valenzino (Jun 10, 2011)

:rollhappy:


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## Ernie (Jun 10, 2011)

Hmm. This isn't really a systematics/taxonomy paper. Most systematists these days rely on either parsimony or liklihood analyses to elucidate interrelationships. They use a cluster analysis which is one of many multivariate statistics (UPGMA is unweighted pair group method, arithmetic mean- just one version of a cluster). Yes, it does tell us something about _similarities_, but not the best choice from a _taxonomy _standpoint. And it's heavily laden with assumptions that the user can dictate. I probably could've used the same data matrix and got a more reasonable dendrogram ('similarity-gram', versus a cladogram= (hopefully) a 'relationship-gram'). 

As far as the example of the leaves being similar between some barbata hybrid and a Parvi hybrid, it's all in how you CODE the character!!! I'd love to see their coding scheme and data matrix!!! If they simply coded leaves as maybe two or three characters, something like...
*leaves mottled above (yes, no)
*leaves burgundy underneath (yes, no)
YES, these two _will_ show up as being similar, Duh!!! If they were intelligent and added characters for leaf surface structure, these would've separated nicely. 

If they wanted to know a TON about leaf morphology, they could've use TPS (thin plate spline) decomposition, now that's CRAZY morphology analysis. 

Also, RAPD was shown to work for other genera, and they mention Goodyera. It is well known that different molecules are good/bad for different genera/groups/taxonomic levels. The fact that it successfully separated Paphs from Phrags, but not anything below the generic level tells us clearly that RAPD is NOT a good molecule to discern slippers at the species/hybrid/cultivar level. DUH! I'd say the species of slippers are therefore evolving at a different rate than Goodyera and the comparison is null!!! Double Duh! I wouldn't have published this paper until I found a more logical molecule, this is a "crappy background knowledge paper" that leads to something hopefully better???


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## Heather (Jun 10, 2011)

Interesting that so many names are spieled incorrectly, as well. I realize that is a minor issue comparatively but clearly not a carefully written article.


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## Ernie (Jun 10, 2011)

Heather said:


> Interesting that so many names are spieled incorrectly, as well. I realize that is a minor issue comparatively but clearly not a carefully written article.



Yes!!! That drove me crazy!!! Any taxonomist/systematist worth their salt is so crazy insane over such details. It's like hearing fingernails on a chalkboard to read such errors!!!


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## Marc (Jun 10, 2011)

I'm not an expert but I briefly scanned through the file and it is a big bunch of crap if you ask me. And don't get me started about the "names".

Looking forward to see Guido's contribution to this topic.


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## Ernie (Jun 10, 2011)

Read it a little more closely. They didn't actually use morphology in the data matrix, just made inferences back to it. Still, character coding will always be a major point of discussion. Even pretty clear cut things like AGCT for DNA (an example of a multistate character since there are more than two choices)- seems like there are four choices, right? Well, should one weight them based on the probability of one occurring next to another? Richness of one or more in a genome? 

Also found it odd in that they said material of Paph delenatii (a parent of Joyce Hasegawa) was not available. Say what? They couldn't get plant material of one of the most commonly grown Paph species??? 

Authors like these give decent systematists a bad rap! 

I'd have to guess that their granting agency (an ag research center if Korea) demanded they publish one or more papers to prove they used the money (wisely???). This is fairly common. If I were that agency, I'd ask for my money back! Curious how many "real" systematics journals declined it before it got to this horticultural journal?


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## NYEric (Jun 10, 2011)

Forget what the article says, how do I get some of the phrags!? 
Taxonomy by DNA information alone is useless, Any knowledgable slipper grower working with this data could have helped them make some sense.


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## labskaus (Jun 10, 2011)

I feel sorry for the Ag Research Center that wasted their grant money. I also feel sorry for the editors of a this crappy journal which were desperate enough to print this. I feel ashamed for the referees who let ths thru for publishing. And I hope the authors are still in a pretty early state of their learning curve.


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## Braem (Jun 10, 2011)

John Boy said:


> This is truly great scientific reasoning! Congratulations!!!


I have scientifically rebuked the Cox et all article in several publications, and in the mean time specialists in statistics have shown that the method simply is wrong. Also Cox et al just leave characteristics away that does not fit in their "argument". It is a fact that "molecular taxonomy" (which has nothing to do with taxonomy because it is a purely mathematical technique" gives irratical species level and any level thereunder. And as I have said before ... when I need a lab to differentiate between a Cattley and a Phalaenopsis, or between a blonde and a redhead ... I will quit doing biology.


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## Braem (Jun 10, 2011)

labskaus said:


> I feel sorry for the Ag Research Center that wasted their grant money. I also feel sorry for the editors of a this crappy journal which were desperate enough to print this. I feel ashamed for the referees who let ths thru for publishing. And I hope the authors are still in a pretty early state of their learning curve.


The problem is that all those "molecular freaks" got to be professors in the early nineties and got zillions of dollars to do reserach (also from the AOS) ... they are still getting their big salaries by writing the nonsense ... see Chase, Pridgeon and their croonies,


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## Braem (Jun 10, 2011)

TyroneGenade said:


> Surely this paper has been retracted? It is total BS.


No, the paper has not been retracted, and Cox openly slandered me for rebuking it .... so did Pridgeon and Chase ....


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## Ernie (Jun 10, 2011)

Braem said:


> when I need a lab to differentiate between a Cattley and a Phalaenopsis, or between a blonde and a redhead...



Um, sign me up as a CoI for the blonde/redhead study! I think we should throw in brunettes just to be complete. I think this need serious scientific consideration. And we could do a cluster [email protected]#$ analysis just to make it publishable.


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## Braem (Jun 10, 2011)

Ernie said:


> Um, sign me up as a CoI for the blonde/redhead study! I think we should throw in brunettes just to be complete. I think this need serious scientific consideration. And we could do a cluster [email protected]#$ analysis just to make it publishable.


Definitely, you are on .... and we must differentiate between natural blondes and chemistry blonds ... but again, we need no molecular analysis for that, we just got to seduce them and have a look ..... Maybe there is some grant money about for that ???


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## likespaphs (Jun 10, 2011)

may i sign up for redhead research?
i mean....


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## Heather (Jun 10, 2011)

:rollhappy:


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## Candace (Jun 11, 2011)

Any published paper that has spelling errors, loses immediate credibility.


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## Braem (Jun 11, 2011)

YES ... if one writes about plants ... anywhere, one should at least bother to have the spelling wright .... and diferentiata between species and hybdrids and even between man-made hybrids and natural hybrids ... If one does not have the correct name "ready" on can ask, and if one is not sure what one has, one should not write about it.

This is alos one of the things that makes me a bit nervous about an open forum like this. If the forum is to be considered serious, there should be some editing and I am willing to answer all questions about names, taxonomy, etc. etc.


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## quietaustralian (Jun 11, 2011)

You can nominate the researchers for an Ig Nobel Prize but there is always a lot of competition.

http://improbable.com/ig

Mick


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## chrismende (Jun 11, 2011)

ahem...


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## chrismende (Jun 11, 2011)

hysterical!


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## Heather (Jun 11, 2011)

Braem said:


> This is alos one of the things that makes me a bit nervous about an open forum like this. If the forum is to be considered serious, there should be some editing and I am willing to answer all questions about names, taxonomy, etc. etc.



Hrm…sorry Guido - we try to leave that up to the posters - edit yourselves, no one else will be doing it here...


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## SlipperFan (Jun 11, 2011)

Actually, I've been pretty impressed with the posts here. Yes, there are some grammar and spelling errors, but those can be excused for a number of reasons. The vast majority of posts are coherent and minus the shortcuts one sees in texting. I think it's great!


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## Braem (Jun 12, 2011)

Heather said:


> Hrm…sorry Guido - we try to leave that up to the posters - edit yourselves, no one else will be doing it here...


THat is Ok ... typos are fine ... we all have them ... but at least the names of the plants should be correct


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## NYEric (Jun 12, 2011)

Refering only to STF, is this a scientific endeavor or an information sharing site?


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## emydura (Jun 12, 2011)

NYEric said:


> Refering only to STF, is this a scientific endeavor or an information sharing site?



To me it is the latter with scientific endeavour just one aspect of the information we share.

David


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## NYEric (Jun 12, 2011)

I agree, therefore I question the thought of having to spell plant names exactly here.


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## Heather (Jun 12, 2011)

I personally think it is also an educational site and we owe it to folks new to the hobby to be careful and knowledgeable about the correct way to spell things. I had people correct me when I was wrong when I first started and it helped me learn a great deal.


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## ohio-guy (Jun 12, 2011)

Getting back to the title of this thread....I don't think one should completely invalidate an area of study, (ie molecular taxonomy) just because a particular paper is very bad or has incorrect information. Just because something is published, even if in a reputable Journal, does not mean it has been well reasoned or correctly evaluated. The writers may not know what they are doing, or may not truly understand the methods they are using. Just because an under-educated person manages to get a paper published, which is subsequently shown to be wrong, does not invalidate the entire branch of study itself. 

One well known case is of a paper that appeared over a decade ago in a major British Medical Journal that tried to show a link between Autism and Vaccines, based on a very limited number of test subjects ( I think it was less than 20 or 30 subjects, if I remember correctly.) The paper was soon shown to be full of errors in the design of the tests, in reasoning, and incorrect in the conclusions it drew. (Even so, it was not retracted until just recently I think, after it was finally shown the the investigator had falsified much of his data. Retractions can take ages sometimes.) 
And yet, who hasn't at least heard of the concerns of the general public that vaccines may still be somehow related to Autism. And in the ensuing years, we have see a rise in the communicable diseases that the vaccines are supposed to protect against, sometimes resulting in serious illness or even death. 
All this due to a bad paper that was published years ago, and whose claims have never been able to be replicated in another well designed study, whose methods were shown to be shoddy and the data of which was at least in part falsified.
There are many well designed subsequent studies, with published results, involving thousands of subjects, that show no relationship between vaccines and Autism. The methods or research can be used well or poorly, but it does not make the methodology itself the problem.


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## Braem (Jun 13, 2011)

Heather said:


> I personally think it is also an educational site and we owe it to folks new to the hobby to be careful and knowledgeable about the correct way to spell things. I had people correct me when I was wrong when I first started and it helped me learn a great deal.


Yes ... but some people take offence and immediately start writing sarcastic messages when corrected


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## Braem (Jun 13, 2011)

No-one invalidates the method because one single paper is nonense. In the mean time, it has been scientifically proven (not only by us alpha-taxonomists, but also by statistics people and mathematicians, that the method is nonsense.
The methodology is WRONG, and therefore the resulsts CAN not be rational.


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## quietaustralian (Jun 13, 2011)

Heather said:


> I personally think it is also an educational site and we owe it to folks new to the hobby to be careful and knowledgeable about the correct way to spell things. I had people correct me when I was wrong when I first started and it helped me learn a great deal.



I agree! I’m more than happy to be corrected on plant names, taxonomy etc. 

Regards, Mick


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## TyroneGenade (Jun 13, 2011)

quietaustralian said:


> You can nominate the researchers for an Ig Nobel Prize but there is always a lot of competition.
> 
> http://improbable.com/ig



Ig Nobel Prizes are for work which actually makes sense and the results are useful, just not main stream.

The article in question is plain BS (even before the method was invalidated). It should have been obvious that something fishy was going on when the plants grouped so unexpectedly. Instead, the authors then cherry-picked morphological characters to back up their DNA tree. This couldn't a better example of pseudoscience.

I can't image how in a rational world this article is still up there.


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## NYEric (Jun 13, 2011)

ohio-guy said:


> Getting back to the title of this thread....I don't think one should completely invalidate an area of study, (ie molecular taxonomy) just because a particular paper is very bad or has incorrect information.


I agree and hope in the future more (and better) studies are done which use research on the molecular level to confirm taxonomic research and help distinguish or trace evolutionary similarities and/or distinctions between species.


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