Philosophy, DNA, Morphology and Taxonomy

[raglanroad]

They're wonderful people.

"Doing the best they can", sounds like there is some room to wiggle ! I like it when the they say "Just do the best you can".

The Sea Serpent hunters will be pleased to hear this.

bottle or no bottle, locale or no locale.

You make it sound like ichthyologists are a bunch of incompetents . It is simply not realistic to describe a species based on 500 specimens collected from surveys of the whole geographical range. The overwhelming majority (if not all) of modern studies in peer-reviewed journals are of excellent quality and more than adequately test the hypotheses proposed. It is unfortunate that Heok Hee (a taxonomist) no longer contributes in this forum, as I am sure he would have something to say on the matter. Sure, historically there were some less than ideal practices, but we learn from that and correct mistakes in the future.

that's the rationale behind keeping a jar..but is it the code ?

You can find the online copy of the ICZN code here.

uhh, if the name was never used as binomial - rejected- would it be available in the circumstances you describe ?

The name was deemed to be available by Ready et al., as they found Lyons' description to fulfill the requirements of the code. The disagreements with Bleher seem to revolve around this, as well as the various publication dates and obscure papers/books.

I am not in a position to state who is correct here, as I don't have the time to do the research.

If they locate Nessie, the bastards must kill her ?

I'm sure there are exceptions for very rare and endangered creatures. It will be in the Code. Have a read.

thanks, but I'm not the one who made the declarations about it. I'm questioning answers. I'm pretty sure Svendl double-checked for "Tarzoo". You have to know the history of the particular namings, as well as the rules, to make sense of it.

and yes, exceptions are allowed, aren't they ? If David Suzuki had an encounter while out with his 5 kids trout overfishing , had his camera...and BigFoOt was measured and filmed by them, perhaps bodily fluids collected...just maybe !

Suddenly Barcoding is not on the hot seat, once we take a little look behind the curtain. Leeway and laxity - "Relax, we only do as best we can - what with funding as it is, and with consideration given to the practical constraints".

sounds good. but makes previous criticism of Barcoding sound hollow. In fact, the jar system is at fault here. David Suzuki says it's not sustainable in view of the great number of organisms, and hampers any community involvement, restricting investigations, as the purview of The Ivory Tower Brigade.
http://www.rense.com/general48/badjoke.htm

[racoll]

thanks, but I'm not the one who made the declarations about it. I'm questioning answers.

and yes, exceptions are allowed, aren't they ? If David Suzuki had an encounter while out with his 5 kids trout overfishing , had his camera...and BigFoOt was measured and filmed by them, perhaps bodily fluids collected...just maybe !

Suddenly Barcoding is not on the hot seat, once we take a little look behind the curtain. Leeway and laxity - "Relax, we only do as best we can - what with funding as it is, and with consideration given to the practical constraints".

sounds good. but makes previous criticism of Barcoding sound hollow. In fact, the jar system is at fault here. David Suzuki says it's not sustainable in view of the great number of organisms, and hampers any community involvement, restricting investigations, as the purview of The Ivory Tower Brigade.

I'm struggling to understand some of the points you are trying to get across raglanroad, if indeed you are actually are trying to make some points, and not just troll the thread.

Please be more clear.

[raglanroad]

could you be more clear about which points you would like expanded or cleaned up ? sorry, but I edited while you were posting, so it is a bit more explanatory now. I added this

I'm pretty sure Svendl double-checked for "Tarzoo". You have to know the history of the particular namings, as well as the rules, to make sense of it.

, saying that Kullander probably did find a way to use the name, though it's validity might be dependent on proper procedure in the rest of the work.

But my question about the necessity of having a preserved specimen was answered to the affirmative - "since 1999". However, I think it's not "set in stone".
And similarly, but more mundane...the question about GPS or coordinates of collection site for establishing a specimen as holotype...absolutely necessary or not ?

[raglanroad]

I'm struggling to understand some of the points you are trying to get across raglanroad, if indeed you are actually are trying to make some points, and not just troll the thread.

are the two states mutually exclusive ? Troll my own thread....good ideas

Author a Troll Thread...hmmmm...could be...but a Troll Thread as your best thread going, on Planet ?

[raglanroad]

Searching the Cat-eLog for "market" in the "type locality" shows several fish that are indeed from "____ Market ____".


Mats

Thanks for that, Mats. I think the relevance of my Trolly Questions is starting to sink in. I'm just exploring my preconceptions .

[Suckermouth]

Not quite correct in my opinion. How much do you think an experienced taxonomist charges per hour for biodiversity assessment work? For a large sample, it will also likely require a team of experts all trained in many different groups a long time to accurately identify everything. Even if a parataxonomist wanted to carry out the work, often keys do not exist, or literature too obscure to access.

I guess I didn't have a complete view... I was looking at it from the point of view simply from doing the species description work. DNA barcoding will indeed be useful for identification in species it has been shown to work.

After further reading the ICZN code, I think if no type material for a species described before 2000 exists, than a neotype can be preserved to serve this purpose, assuming you can confirm that it is of the same species as this previously described species.

[racoll]

are the two states mutually exclusive ?

No, but stick to making points clear and pertinent, otherwise nobody will bother to contribute.

But my question about the necessity of having a preserved specimen was answered to the affirmative - "since 1999". However, I think it's not "set in stone".
And similarly, but more mundane...the question about GPS or coordinates of collection site for establishing a specimen as holotype...absolutely necessary or not ?

I don't know, but its all written in the code, provided in the link I posted.

The code is not particularly stringent, but if you want to publish in a peer-review scientific journal (which you should) you will need much better quality of data.

As I keep saying, the overwhelming majority of studies published in the last 50 years have this information.

[raglanroad]

so, what the deal with Cryptoheros , Morphology, DNA and Barcoding.
Q/ any ideas of what mechanism is responsible for what was seen ? what that might be called ?
how is it an example of failure of anything , rather than failure of everything ?

[raglanroad]

are the two states mutually exclusive ?

No, but stick to making points clear and pertinent, otherwise nobody will bother to contribute.

I do not believe this has been evidenced, thus far.

But my question about the necessity of having a preserved specimen was answered to the affirmative - "since 1999". However, I think it's not "set in stone".
And similarly, but more mundane...the question about GPS or coordinates of collection site for establishing a specimen as holotype...absolutely necessary or not ?

I don't know, but its all written in the code, provided in the link I posted.

Yes, but my question was in response to an assertion. It's customary, on fora, I think, for one making assertions to supply what they already know.

The code is not particularly stringent, but if you want to publish in a peer-review scientific journal (which you should) you will need much better quality of data.

Thanks, don't want to climb the scrotum poles in the Ivory Tower. It needs to go down. Better to just follow whatr is absolutely necessary, and do the barcoding better ( through getting proper capture locale fish )than other analyses that have been done. Not perfect, just better.

As I keep saying, the overwhelming majority of studies published in the last 50 years have this information.

yes. majorities.

[racoll]

I guess I didn't have a complete view... I was looking at it from the point of view simply from doing the species description work.

I think this confusion is part of the reason for the initial hostility towards barcoding. It was being touted as a way to "discover species", which many interpreted as new species being delineated on the basis of a say 2% sequence divergence, which they were, correctly I think, opposed to.

What was actually really meant was that barcodes could be used to screen large samples of potentially undescribed species, creating hypotheses that could be tested with morphological and further genetic data.

So, yes it can discover putative species, but should not be used to delineate them, exclusive of other information.

so, what the deal with Cryptoheros , Morphology, DNA and Barcoding.

Which study is this? Have you got a reference?

Yes, but my question was in response to an assertion. It's customary, on fora, I think, for one making assertions to supply what they already know.

What assertion?

[raglanroad]

What assertion?

this assertion

And what happens in case of a very very rare creature ? do you need one in a bottle in an institution in order to get a binomial ?

It's a rule that there must be a holotype for species descriptions after 1999, yes.

[raglanroad]

Which study is this? Have you got a reference?

this Cryptoheros situation described as something that gives reason for discounting any DNA work .
And I was wondering if anyone had the explanation for the event, or why it shows failure of any DNA system of investigation.

In central America, we used to have a genus of smaller c*****ds, Cryptoheros. This contains the convict c*****d, and a few related species

In genetic research, a group of Cr septemfesciatus popped up within the group of convicts. septenfesciatus are a specis of reddish brown fishes, with blue eyes, and golden scales on the sides of the females - something completely different from a convict, in fact nobody would mistake one for the other. Not even the fish do, I never heard of hybrids between these (which does so a lot, in CA everything seems to hybrid)

Now we have Cr myrnae, to cope twith this problem. But they are as good as identical to Cr septemfasciatus

I am a chemist, but to me the above is better seen as proof of the wrongness of DNA studies to do taxonomy than something else

[racoll]

this Cryptoheros situation described as something that gives reason for discounting any DNA work .

Without seeing the paper I can't comment. It may not even be a DNA barcoding study. The technique is relatively new (since 2003).

[raglanroad]

this Cryptoheros situation described as something that gives reason for discounting any DNA work .

Without seeing the paper I can't comment. It may not even be a DNA barcoding study. The technique is relatively new (since 2003).

that's all I could get out of them. wondering if Bas or Larry could say why the event shows a failure of tests, and if anyone had offered explanation for the event.

[Mike_Noren]

The overwhelming majority (if not all) of modern studies in peer-reviewed journals are of excellent quality and more than adequately test the hypotheses proposed.

Uhhhh... Majority, yes.

Suddenly Barcoding is not on the hot seat, once we take a little look behind the curtain. Leeway and laxity - "Relax, we only do as best we can - what with funding as it is, and with consideration given to the practical constraints".

Sorry, but your argument appear to be 'because sometimes the locality data is not exact, the system of using types is useless', which a) is a taxonomic argument irrelevant to the use of barcoding, and b) does not make sense.
Corydoras hastatus was originally described from apparently captive specimens in a pond in Manaus, its real distribution is thousands of miles to the south, in southern Brazil to Argentina - does that make the species invalid?

sounds good. but makes previous criticism of Barcoding sound hollow. In fact, the jar system is at fault here. David Suzuki says it's not sustainable in view of the great number of organisms, and hampers any community involvement, restricting investigations

Sorry, but that is bullshit. It is also disingenious, as the biggest problem barcoding faces is maintaining the connection between the sequence and the individual. Once the DNA is extracted it is anonymous, and it's not rare for contamination or mix-ups of test tubes to give "unexpected" results, and unless you have voucher specimens deposited at a museum, you're just SOL and your sequence useless.

[Bas Pels]

I'm very sorry for being unable to answer the above questions.

I did read it somewhere, but did not write down where. After all, I'm not a scientist.

However, regarding the barcoding - I never commented barcoding. I did explain what it was, but I did not say barcoding has certain problems. I think doing DNA studies has risks of messing things up, regardless what studies.

I think the only exception would be if one would sequence a certain area, and than would find out what this area does - so one could concentrate on those areas which are real non-sense areas.

To explain what I mean, in all multicellular organisms large parts of the DNA is - as far as we now know - without function, the non-sense areas. The genes can (and normally do) include large parts of these areas, together with areas which are decoded (sense areas). Somehow the decoding mechanism is able to know what to decode and what not

However, if one does taxonomy on sense parts, the problem is, the sense parts are vunarable to selection: the decoded protein enhances survival, or it doesn't - thus change is the result of environmental influences

Thus, one would use non-sense parts. However, nature does not waste much. Before we can say a part is non-sense, we should firstly find out whether it is real non-sense or not. It might have a function still, without being decoded, such as a storage for decoding equipment, or an achoring place or so. A lot of work in this field has been done, but a lot more still needs to be done

Currently somehow a chunk of DNA is selected, and than measurings take place. But noone knows what exactly is measured. That could explain strange results

[racoll]

Currently somehow a chunk of DNA is selected, and than measurings take place. But noone knows what exactly is measured. That could explain strange results

Not really in the case of barcoding, as it is well known what the gene does; it codes for an enzyme in the respiratory electron transport chain of the mitochondrion. Most substitutions are silent and selectively neutral, as they do not change the amino acid code.

The causes of poor resolution or conflicting results in barcoding are mostly well known and I present some here in approximate order of importance:

1. Initial morphological misidentification of specimens
2. Species too young to have a differences in the COI sequence
2. Shared haplotypes caused by incomplete lineage sorting and retention of ancestral polymorphisms - again young species
3. Shared haplotypes due to introgession - i.e. hybridisation
4. Species taxonomically oversplit or undersplit (not to say that the taxonomy is wrong - just a cause of data conflict)
5. Sequencing of nuclear mitochondrial pseudogenes - (numts)
6. Contamination

[raglanroad]

The overwhelming majority (if not all) of modern studies in peer-reviewed journals are of excellent quality and more than adequately test the hypotheses proposed.

Uhhhh... Majority, yes.

racoll wrote that, though. I answered as you did.

Suddenly Barcoding is not on the hot seat, once we take a little look behind the curtain. Leeway and laxity - "Relax, we only do as best we can - what with funding as it is, and with consideration given to the practical constraints".

Sorry, but your argument appear to be 'because sometimes the locality data is not exact, the system of using types is useless', which a) is a taxonomic argument irrelevant to the use of barcoding, and b) does not make sense.

well then, I'm happy to say that your apprehension of my argument is faulty.

Corydoras hastatus was originally described from apparently captive specimens in a pond in Manaus, its real distribution is thousands of miles to the south, in southern Brazil to Argentina - does that make the species invalid?

Well, no, not IMO. Whether or not the captive is considered domesticated ( under any of several definitions) there may not even be ancestral forms of the domesticated form still extant. In fact, domesticated creatures should be investigated too, with "capture" locale possibly being irrelevant, but not certainly being irrelevant.

sounds good. but makes previous criticism of Barcoding sound hollow. In fact, the jar system is at fault here. David Suzuki says it's not sustainable in view of the great number of organisms, and hampers any community involvement, restricting investigations

Sorry, but that is bullshit. It is also disingenious, as the biggest problem barcoding faces is maintaining the connection between the sequence and the individual. Once the DNA is extracted it is anonymous, and it's not rare for contamination or mix-ups of test tubes to give "unexpected" results, and unless you have voucher specimens deposited at a museum, you're just SOL and your sequence useless.

In this case, as with beauty, "bullshit" is in the eye of the beholder, and disingenuity is in the mind.

In this age, sampling and imaging data in many ways can replace the jar. The institutional jar requirement is a major stumbling block. What gets vouchered possibly depends ONLY on what some dink in an institution wants or deems necessary ...regardless of where chain of possesion started, or what supplementary information is available. Pity it's sport designed exclusively for the elite.
Now there's nothing wrong with having a jar specimen in institution, that is preferable in fact. It's the illusory compelling regulation, not adhered to in the past ( pre 1999) and not adhered to now; that is the problem. The compelling regulation was brought in just slightly before the possible success of a WIKI approach became evident.

[MatsP]

In this age, sampling and imaging data in many ways can replace the jar. The institutional jar requirement is a major stumbling block. What gets vouchered is ONLY what some dink in an institution wants or deems necessary ...regardless of where chain of possesion started, or what supplementary information is available. Pity it's sport designed exclusively for the elite.
Now there's nothing wrong with having a jar specimen in institution, that is preferable in fact. It's the illusory compelling regulation, not adhered to in the past ( pre 1999) and not adhered to now; that is the problem. The compelling regulation was brought in just slightly before the possible success of a WIKI approach became evident.

Can you describe why it's a major stumbling block - surely there is no strict requirement to stuff fish in a jar isn't that difficult - it just makes it more likely that someone else can come back and look at those samples AGAIN in the future, and not have to use some images that may not show what was wanted - say someone wants to look at a certain bone-structure which isn't apparent in any of the photos? I can assure you, no matter how many different images and samples you take, someone will come up with something else to look for/at. Retaining the original specimen will ensure this is possible. If you do not do that, you'd have to then capture the same species again - and how do you know it's actually the same species?

--
Mats

[raglanroad]

Yes, Mats. I did edit to say "possibly" depends on the insitutionary dink's desires.
You see, suppose I want to barcode Pterophyllum, and so must ascertain that for my barcoding of Pterophyllum, the correct holotype collection locale is used for my investigation....a trip to the museum shows they have a wrongly ID'd fish masquerading as altum.
And there is no original available for testing. So I want them to take a real altum, voucher it, and then my barcoding is "a go". But the curator doesn't understand that a fish from the market he has is not altum, and he has no space for more jars of freshwater angelfish.
You're "deemed' out of an opportunity to study, as you are not of the elite.

[MatsP]

Or you find a different museum that has the right specimen, and ask them to lend it to you - or get a photo + sample sent over.

Or donate your specimen to another museum and then use that for your research!

--
Mats

[raglanroad]

Or you find a different museum that has the right specimen, and ask them to lend it to you - or get a photo + sample sent over.

Or donate your specimen to another museum and then use that for your research!

--
Mats

As Heiko and others have noted, many or most museums have mislabeled fish as altum. so as you say, one must hunt through museums and curators to find a real altum and coinciding with that, a non-dink who has a brain. That sucks. It's an impediment. Do you suppose the dinks send their specimens to any old requesting members from the great unwashed public ?

So doing a proper barcoding becomes, in practical terms, a project dependant upon the whims of a possible dink who has the wrong fish in his collection.
as an "off the top" example; Without pausing for a breath, "Dink" would grab a legally imported for the Ornamental Trade Panaque suttonorum corpse and voucher it (chain of possession out the window). But not an altum. That's the problem.

[MatsP]

I think this problem happens in all sorts of different areas where hobbyists and experts "meet". (experts in italic to indicate that I mean this in the sense that they are supposed to know more than the hobbyist - not that they actually do - some do, some don't, I'd say). It is usually caused by what you call dinks - people who can't think for themselves, have fairly little knowledge/understanding of the subject itself, but know how to follow the rules they've been given.

Misidentified samples are probably fairly widespread in many species - especially those that aren't that easy to ID.

Here's an idea: Start your own museum! I'm not joking - I mean, set up the tests, store the samples in your house, and publish the results. Anyone questioning it can come to your house for a loan of the sample, just like if they went to the Natural History Museum in London, England, or anywhere else.

--
Mats

[raglanroad]

I think they mean vouchered by reps of "public institutions".The elite dinks have grasped de facto control over study efforts.

[MatsP]

I think they mean vouchered by reps of "public institutions".The elite dinks have grasped de facto control over study efforts.

But how did those institutions become "public"....

--
Mats

[raglanroad]

Oh, you mean by having good connections for thieved articles ? Mind you, not all museums are built of it. http://www.greenpeace.org/international ... azon-destr

http://www.czeglediartlaw.ca/Documents/ ... ture_2.pdf
They have a "Crimes Against Culture" presentation...but

http://www.blogto.com/arts/2008/01/were ... es_stolen/ their biggest treasures are stolen articles piped to them , by the good Bishop White, whose name they glorify.

[Mike_Noren]

Well, no, not IMO. Whether or not the captive is considered domesticated ( under any of several definitions) there may not even be ancestral forms of the domesticated form still extant. In fact, domesticated creatures should be investigated too, with "capture" locale possibly being irrelevant, but not certainly being irrelevant.

What's domestication got to do with anything? The capture locality is inaccurate, the species does not live there. Wasn't your argument that this somehow invalidated the species?

Sorry, but that is bullshit. It is also disingenious, as the biggest problem barcoding faces is maintaining the connection between the sequence and the individual. Once the DNA is extracted it is anonymous, and it's not rare for contamination or mix-ups of test tubes to give "unexpected" results, and unless you have voucher specimens deposited at a museum, you're just SOL and your sequence useless.

In this case, as with beauty, "bullshit" is in the eye of the beholder, and disingenuity is in the mind.
In this age, sampling and imaging data in many ways can replace the jar. The institutional jar requirement is a major stumbling block.

When you can x-ray the image to investigate the skull, do electron microscopy on it, unfold the fin of the fish in the photo and count the finrays, zoom in and count the scales, flip the fish over and count the scales on the other side because some are missing on this side, and you can guarantee that the picture is displayable in 200 years time... then maybe. Until then photos remain nice supplementary information to go with the specimen. Yeah, it is usually possible to get by without a holotype - thankfully, since many holotypes have been destroyed, e.g. during WW2 bombings - but that's not really an argument to not provide one when it is possible.

EDIT: Also in the field it's actually far easier to collect a specimen than to take a good photo. Trust me on this.

What gets vouchered possibly depends ONLY on what some dink in an institution wants or deems necessary ...regardless of where chain of possesion started, or what supplementary information is available. Pity it's sport designed exclusively for the elite.
Now there's nothing wrong with having a jar specimen in institution, that is preferable in fact. It's the illusory compelling regulation, not adhered to in the past ( pre 1999) and not adhered to now; that is the problem. The compelling regulation was brought in just slightly before the possible success of a WIKI approach became evident.

So your argument now is that it is too much work to collect specimens, and museums too restrictive with what material they accept? Didn't you just ridicule lazy researchers who bought their material at the market?

Oh, you mean by having good connections for thieved articles ?

And now you claim museums are too indiscriminate about what objects they accept. Your arguments are all over the place.

[raglanroad]

Well, no, not IMO. Whether or not the captive is considered domesticated ( under any of several definitions) there may not even be ancestral forms of the domesticated form still extant. In fact, domesticated creatures should be investigated too, with "capture" locale possibly being irrelevant, but not certainly being irrelevant.

What's domestication got to do with anything?

It may no longer be the same as the wild species

The capture locality is inaccurate, the species does not live there. Wasn't your argument that this somehow invalidated the species?

the capture locale was accurate if it was truthful. and no, it doesn't invalidate the species - it might invalidate that specimen.

Mike Noren: Sorry, but that is bullshit. It is also disingenious, as the biggest problem barcoding faces is maintaining the connection between the sequence and the individual. Once the DNA is extracted it is anonymous, and it's not rare for contamination or mix-ups of test tubes to give "unexpected" results, and unless you have voucher specimens deposited at a museum, you're just SOL and your sequence useless.

raglanroad: In this case, as with beauty, "bullshit" is in the eye of the beholder, and disingenuity is in the mind.
In this age, sampling and imaging data in many ways can replace the jar. The institutional jar requirement is a major stumbling block.

Mike Noren: When you can x-ray the image to investigate the skull, do electron microscopy on it, unfold the fin of the fish in the photo and count the finrays, zoom in and count the scales, flip the fish over and count the scales on the other side because some are missing on this side, and you can guarantee that the picture is displayable in 200 years time... then maybe. Until then photos remain nice supplementary information to go with the specimen. Yeah, it is usually possible to get by without a holotype - thankfully, since many holotypes have been destroyed, e.g. during WW2 bombings - but that's not really an argument to not provide one when it is possible.

didn't say it was

raglanroad: What gets vouchered possibly depends ONLY on what some dink in an institution wants or deems necessary ...regardless of where chain of possesion started, or what supplementary information is available. Pity it's sport designed exclusively for the elite.
Now there's nothing wrong with having a jar specimen in institution, that is preferable in fact. It's the illusory compelling regulation, not adhered to in the past ( pre 1999) and not adhered to now; that is the problem. The compelling regulation was brought in just slightly before the possible success of a WIKI approach became evident.

So your argument now is that it is too much work to collect specimens

no

and museums too restrictive with what material they accept?

no

Didn't you just ridicule lazy researchers who bought their material at the market?

did I ?

raglanroad wrote:Oh, you mean by having good connections for thieved articles ?

And now you claim museums are too indiscriminate about what objects they accept.

no

Your arguments are all over the place

easy for you to say after you reword them with your own oversimplifications and inaccuracies, and then leave them strewn about.

[Mike_Noren]

easy for you to say after you reword them with your own oversimplifications and inaccuracies, and then leave them strewn about.

Yes it is easy for me to say, because I have no fricking clue what your point is, or even if you have one. Do you?

[raglanroad]

perhaps. here's one:

Museums function as warehouses and showrooms for illegally gained articles.
like this

http://www.uruknet.info/?p=57101

and their main treasures

http://www.theglobeandmail.com/news/wor ... 660929.ece

but they are fussy , they may not want a legally-gained article merely because it is not so glamorous, not glamorous at all compared to their stolen treasures.
putting the future of study done by private individuals in the hands of disreputable, elitist scoundrels, is a bad move.

http://www.thestar.com/comment/columnis ... cle/655930

We can talk about it at cocktail parties.