Alpha taxonomic drought & molecular meanderings

From: botanist at malesiana.com (Peter Boyce) on 2008.07.17 at 05:33:35(18185) Dear Leland, Well, where I live unless there is a change in education policy to imbue those few (and it is FEW) students with some botanical aptitude, to gain knowledge of the basic building blocks of botany, notably comparative morphology, ecology & geomorphology, the spectre of no wide-experience field botanists, already a fact in many parts of Asia, will become a region-wide problem. In fact the whole of taxonomy, let alone systematics, is in danger of slipping off the curriculum in universities throughout the region such that only the minute hard-core (essentially botanically hard-wired) folks will make it through and continue. The problem then will be that there are increasingly fewer jobs that call for taxonomic expertise such that those few that wish to remain in the field usually end up earning a living doing something at the best only tangentially associated with their passion. Of course the irony is that there has never been a greater need for taxonomic expertise in order to make the rational decisions requir ed to protect the remaining tropical habitats. Curiously, I am not anywhere near as doubtful or indeed pessimistic about the increasing use of molecular data and also don't altogether agree with the total genome argument. Regarding the function of various parts of the molecular code, in recent years there has been made enormous strides in understanding what various coding regions 'do' such that the link with this and evo-devo is now a well established area of scientific exploration. Of course some of these areas are ferociously expensive but with molecular extraction methodologies and analyses programmes increasingly simplified costs are dropping such that even quite sophisticated extraction and analyses methodologies are well within the budget of even quite modest research establishments. Regarding the usefulness of molecular data, especially vis-a-vis the ability of the molecular practitioners to actually identify the organisms they are studying, yes, I agree, that still far too many molecular research outputs are the product of lab rats without any practical field training and worse are oftentimes undertaken without or with only minimal taxonomic cross fertilization. However, that situation is fast becoming history as more and more multi-author research outputs based on sound alpha-taxonomy, with the molecular toolbox being opened only once a decent 'traditional' taxonomy is established and is testable. This is much the approach we are using, with a multi-stranded project that is investigating alpha-tax. and then phylogentics and then using the phylogenies to investigate spatial evolution, etc. We have been very fotunate to find good students who are willing to spend the necessary field time as part of their molecular-based research and as a result have a much more complete biological resea rch toolbox. Cheers Peter +More -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gizmoworks.com/mailman/private/aroid-l/attachments/20080717/1108e619/attachment-0001.htm

From: crogers at ecoanalysts.com (Christopher Rogers) on 2008.07.21 at 23:38:28(18209) This is a really important issue. The same thing is happening in the zoological realm as well. There is a big misconception that genes are all you need. Taxonomy and systematics is being forced into purely molecular based research, ignoring the ecological and morphological aspects. Genes are but one tool (and a very good tool) in the tool box for identifying organisms. The problems are as follows: 1. Less than one tenth of one percent of the species of the world have had their genes sequenced. So, this makes it difficult to define taxa. 2. Morphological identifications are used to identify the organisms before they are sequenced, so despite what some genetic only proponents say, you still need morphology to have a starting point. 3. It is a very rare thing that any more than one or two individuals from a population are sequenced. This often results in two or more populations called out as separate species, when no one really knows what the inherit genetic variability of the species is in the first place. This is painfully obvious in groups like the naked mole rats of Africa and the Middle east which are morphologically indistinguishable, yet molecularly can be separated into two or three species up to 50% genetically different, verses the Hawaiian fruit flies which morphologically, behaviorally, and ecologically can be separated into several well reproductively isolated species (they literally cannot eat the same food, cannot live in the same humidity, are sexually active at different times of the year, and live at different altitudes), yet genetically they are less than 1% different. 4. I am an associate editor for an international zoological journal, and I am always receiving and rejecting genetic papers where the researcher(s) did not deposit any specimens. One of the tenants of the scientific method is reproducibility. Anyone should be able to reproduce the results of someone else?s experiment. It amazes me how often some genetics type will revise a genus, family, or species group, but does not deposit any specimens in a museum. If I cannot go to the museum, find their material and recreate their work, it is not science. 5. Genetic barcoding and Phylocode are also problematic. The vast majority of my professional work and the work of my colleagues is bioassessment, in which we use invertebrate community structure as a meter stick of habitat health functionality. This type of habitat assessment is far more accurate and precise at measuring habitat functionality then chemical testing, because you are gauging the suitability and health of the habitat using the organisms that are actually using the habitat: organisms that are adapted to a given habitat or niche. I conduct this work in aquatic and terrestrial habitats. What does this have to do with the classification debate? The traditional Linnaean classifications provide us with the means of understanding the ecology of the habitats we study. Certain orders, families, genera and species in my quantitative samples have certain ecological meaning. I can take a one square meter sample from a river, for example, and depending on what taxa are there, I can tell you what metals and pollutants are present, what nutrients, what the dissolved oxygen levels are, what the flow regime is, how long an impacted site will take to recover, or if a restored habitat is beginning to function naturally, how clean the water is, etcetera. Different species, genera, and families of invertebrates mean very different things ecologically. I could give dozens of general, and hundreds of specific examples. Certain subfamilies of flies in the family Dixidae will tell you different things than others. Different mayfly genera will give you different information concerning heavy metals. Different midge genera will tell you what type of nutrient loading (if any) is occurring in a given site. My beloved crustaceans at order level can tell me about pesticide contamination in certain areas. Most larval insects cannot be identified beyond family or genus level, yet they are important ecological indicators of water quality! Furthermore, I need dichotomous keys to orders, families, genera and species to identify the organisms in my samples, and some of these samples may harbor more than 10,000 individual organisms. I need taxonomical hierarchy to identify my specimens. There is an international bioassessment industry (I work all over the world), borne of the desire for clean water, clean soil and clean air, as well as natural and restored wildlife habitat, that relies on Linnaean taxonomy. Therefore, to those of us who work in this field much of phyllocode, barcoding and least inclusive taxonomic units are of little use, and to some of us in this industry represent "ivory tower thinking". Organisms are a function of their environment. Their taxonomy, in terms of their biology and ecology, are of far greater significance to the general public who wants clean water, clean air, and a healthy environment. If you take an organism out of its environment, and reduce it to a mere terminus on a line, you may risk losing everything that made it what it is. Just my two cents worth! I hope that I have not strayed! But why do we collect these amazing plant? For their genes or to appreciate their beauty and complexity? Happy days, Christopher +More D. Christopher Rogers Senior Invertebrate Ecologist/ Taxonomist ((,///////////=======< EcoAnalysts, Inc. 1.530.756.4481 1.530. 383.4798 (cell) 1307 "L" Street Davis, CA 95616 USA ?Invertebrate Taxonomy ?Endangered Species ?Ecological Studies ?Bioassessment ?Invasive Species ?Plankton ?Phycology Moscow, Idaho ? Bozeman, Montana ? Davis, California ? Joplin, Missouri Selinsgrove, Pennsylvania ecoanalysts.com From: aroid-l-bounces at gizmoworks.com [mailto:aroid-l-bounces at gizmoworks.com] On Behalf Of Peter Boyce Sent: Wednesday, July 16, 2008 10:34 PM To: Discussion of aroids Subject: [Aroid-l] Alpha taxonomic drought & molecular meanderings Dear Leland, Well, where I live unless there is a change in education policy to imbue those few (and it is FEW) students with some botanical aptitude, to gain knowledge of the basic building blocks of botany, notably comparative morphology, ecology & geomorphology, the spectre of no wide-experience field botanists, already a fact in many parts of Asia, will become a region-wide problem. In fact the whole of taxonomy, let alone systematics, is in danger of slipping off the curriculum in universities throughout the region such that only the minute hard-core (essentially botanically hard-wired) folks will make it through and continue. The problem then will be that there are increasingly fewer jobs that call for taxonomic expertise such that those few that wish to remain in the field usually end up earning a living doing something at the best only tangentially associated with their passion. Of course the irony is that there has never been a greater need for taxonomic expertise in order to make the rational decisions required to protect the remaining tropical habitats. Curiously, I am not anywhere near as doubtful or indeed pessimistic about the increasing use of molecular data and also don't altogether agree with the total genome argument. Regarding the function of various parts of the molecular code, in recent years there has been made enormous strides in understanding what various coding regions 'do' such that the link with this and evo-devo is now a well established area of scientific exploration. Of course some of these areas are ferociously expensive but with molecular extraction methodologies and analyses programmes increasingly simplified costs are dropping such that even quite sophisticated extraction and analyses methodologies are well within the budget of even quite modest research establishments. Regarding the usefulness of molecular data, especially vis-a-vis the ability of the molecular practitioners to actually identify the organisms they are studying, yes, I agree, that still far too many molecular research outputs are the product of lab rats without any practical field training and worse are oftentimes undertaken without or with only minimal taxonomic cross fertilization. However, that situation is fast becoming history as more and more multi-author research outputs based on sound alpha-taxonomy, with the molecular toolbox being opened only once a decent 'traditional' taxonomy is established and is testable. This is much the approach we are using, with a multi-stranded project that is investigating alpha-tax. and then phylogentics and then using the phylogenies to investigate spatial evolution, etc. We have been very fotunate to find good students who are willing to spend the necessary field time as part of their molecular-based research and as a result have a much more complete biological research toolbox. Cheers Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gizmoworks.com/mailman/private/aroid-l/attachments/20080721/7f610bc6/attachment-0001.htm

From: lbmkjm at yahoo.com (brian lee) on 2008.07.22 at 12:38:29(18215) Dear Christopher, Pete, Tom, and all concerned, Aloha. Priceless...I got my two cents worth. Your email reminds me of epigenetics and the underappreciated and unknown implications of this emerging field. I agree that genetic research is just one aspect in the toolbox of understanding. I simply do not want to see this alpha taxonomic drought becoming a crisis. Aloha, Leland +More --- On Mon, 7/21/08, Christopher Rogers wrote: > From: Christopher Rogers > Subject: Re: [Aroid-l] Alpha taxonomic drought & molecular meanderings > To: "'Discussion of aroids'" > Date: Monday, July 21, 2008, 1:38 PM > This is a really important issue. The same thing is > happening in the > zoological realm as well. There is a big misconception that > genes are all > you need. Taxonomy and systematics is being forced into > purely molecular > based research, ignoring the ecological and morphological > aspects. Genes are > but one tool (and a very good tool) in the tool box for > identifying > organisms. The problems are as follows: > > > > 1. Less than one tenth of one percent of the species > of the world have > had their genes sequenced. So, this makes it difficult to > define taxa. > > 2. Morphological identifications are used to identify > the organisms > before they are sequenced, so despite what some genetic > only proponents say, > you still need morphology to have a starting point. > > 3. It is a very rare thing that any more than one or > two individuals > from a population are sequenced. This often results in two > or more > populations called out as separate species, when no one > really knows what > the inherit genetic variability of the species is in the > first place. This > is painfully obvious in groups like the naked mole rats of > Africa and the > Middle east which are morphologically indistinguishable, > yet molecularly can > be separated into two or three species up to 50% > genetically different, > verses the Hawaiian fruit flies which morphologically, > behaviorally, and > ecologically can be separated into several well > reproductively isolated > species (they literally cannot eat the same food, cannot > live in the same > humidity, are sexually active at different times of the > year, and live at > different altitudes), yet genetically they are less than 1% > different. > > 4. I am an associate editor for an international > zoological journal, > and I am always receiving and rejecting genetic papers > where the > researcher(s) did not deposit any specimens. One of the > tenants of the > scientific method is reproducibility. Anyone should be able > to reproduce the > results of someone else?s experiment. It amazes me how > often some genetics > type will revise a genus, family, or species group, but > does not deposit any > specimens in a museum. If I cannot go to the museum, find > their material and > recreate their work, it is not science. > > 5. Genetic barcoding and Phylocode are > also problematic. > The vast majority of my professional work and the work of > my colleagues is > bioassessment, in which we use invertebrate community > structure as a meter > stick of habitat health functionality. This type of habitat > assessment is > far more accurate and precise at measuring habitat > functionality then > chemical testing, because you are gauging the suitability > and health of the > habitat using the organisms that are actually using the > habitat: organisms > that are adapted to a given habitat or niche. I conduct > this work in aquatic > and terrestrial habitats. What does this have to do with > the classification > debate? The traditional Linnaean classifications provide us > with the means > of understanding the ecology of the habitats we study. > Certain orders, > families, genera and species in my quantitative samples > have certain > ecological meaning. I can take a one square meter sample > from a river, for > example, and depending on what taxa are there, I can tell > you what metals > and pollutants are present, what nutrients, what the > dissolved oxygen levels > are, what the flow regime is, how long an impacted site > will take to > recover, or if a restored habitat is beginning to function > naturally, how > clean the water is, etcetera. Different species, genera, > and families of > invertebrates mean very different things ecologically. I > could give dozens > of general, and hundreds of specific examples. Certain > subfamilies of flies > in the family Dixidae will tell you different things than > others. Different > mayfly genera will give you different information > concerning heavy metals. > Different midge genera will tell you what type of nutrient > loading (if any) > is occurring in a given site. My beloved crustaceans at > order level can tell > me about pesticide contamination in certain areas. Most > larval insects > cannot be identified beyond family or genus level, yet they > are important > ecological indicators of water quality! Furthermore, I need > dichotomous keys > to orders, families, genera and species to identify the > organisms in my > samples, and some of these samples may harbor more than > 10,000 individual > organisms. I need taxonomical hierarchy to identify my > specimens. There is > an international bioassessment industry (I work all over > the world), borne > of the desire for clean water, clean soil and clean air, as > well as natural > and restored wildlife habitat, that relies on Linnaean > taxonomy. Therefore, > to those of us who work in this field much of phyllocode, > barcoding and > least inclusive taxonomic units are of little use, and to > some of us in this > industry represent "ivory tower thinking". > Organisms are a function of their > environment. Their taxonomy, in terms of their biology and > ecology, are of > far greater significance to the general public who wants > clean water, clean > air, and a healthy environment. If you take an organism out > of its > environment, and reduce it to a mere terminus on a line, > you may risk losing > everything that made it what it is. > > > > Just my two cents worth! I hope that I have not strayed! > But why do we > collect these amazing plant? For their genes or to > appreciate their beauty > and complexity? > > > > Happy days, > > Christopher > > > > > > D. Christopher Rogers > > Senior Invertebrate Ecologist/ Taxonomist > > ((,///////////=======< > > > > EcoAnalysts, Inc. > > 1.530.756.4481 > > 1.530. 383.4798 (cell) > > 1307 "L" Street > > Davis, CA 95616 > > USA > > > > ?Invertebrate Taxonomy > > ?Endangered Species > > ?Ecological Studies > > ?Bioassessment > > ?Invasive Species > > ?Plankton > > ?Phycology > > > > Moscow, Idaho ? Bozeman, Montana ? Davis, California ? > Joplin, Missouri > > Selinsgrove, Pennsylvania > > ecoanalysts.com > > > > From: aroid-l-bounces at gizmoworks.com > [mailto:aroid-l-bounces at gizmoworks.com] > On Behalf Of Peter Boyce > Sent: Wednesday, July 16, 2008 10:34 PM > To: Discussion of aroids > Subject: [Aroid-l] Alpha taxonomic drought & molecular > meanderings > > > > Dear Leland, > > > > Well, where I live unless there is a change in education > policy to imbue > those few (and it is FEW) students with some botanical > aptitude, to gain > knowledge of the basic building blocks of botany, notably > comparative > morphology, ecology & geomorphology, the spectre of no > wide-experience field > botanists, already a fact in many parts of Asia, will > become a region-wide > problem. In fact the whole of taxonomy, let alone > systematics, is in danger > of slipping off the curriculum in universities throughout > the region such > that only the minute hard-core (essentially botanically > hard-wired) folks > will make it through and continue. The problem then will be > that there are > increasingly fewer jobs that call for taxonomic expertise > such that those > few that wish to remain in the field usually end up earning > a living doing > something at the best only tangentially associated with > their passion. Of > course the irony is that there has never been a greater > need for taxonomic > expertise in order to make the rational decisions required > to protect the > remaining tropical habitats. > > > > Curiously, I am not anywhere near as doubtful or indeed > pessimistic about > the increasing use of molecular data and also don't > altogether agree with > the total genome argument. Regarding the function of > various parts of the > molecular code, in recent years there has been made > enormous strides in > understanding what various coding regions 'do' such > that the link with this > and evo-devo is now a well established area of scientific > exploration. Of > course some of these areas are ferociously expensive but > with molecular > extraction methodologies and analyses programmes > increasingly simplified > costs are dropping such that even quite sophisticated > extraction and > analyses methodologies are well within the budget of even > quite modest > research establishments. > > > > Regarding the usefulness of molecular data, especially > vis-a-vis the ability > of the molecular practitioners to actually identify the > organisms they are > studying, yes, I agree, that still far too many molecular > research outputs > are the product of lab rats without any practical field > training and worse > are oftentimes undertaken without or with only minimal > taxonomic cross > fertilization. However, that situation is fast becoming > history as more and > more multi-author research outputs based on sound > alpha-taxonomy, with the > molecular toolbox being opened only once a decent > 'traditional' taxonomy is > established and is testable. This is much the approach we > are using, with a > multi-stranded project that is investigating alpha-tax. and > then > phylogentics and then using the phylogenies to investigate > spatial > evolution, etc. We have been very fotunate to find good > students who are > willing to spend the necessary field time as part of their > molecular-based > research and as a result have a much more complete > biological research > toolbox. > > > > Cheers > > > > Peter_______________________________________________ > Aroid-L mailing list > Aroid-L at www.gizmoworks.com > http://www.gizmoworks.com/mailman/listinfo/aroid-l

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