PSYCHOLOGICAL FACTORS IN THE IDENTIFICATION OF MUSHROOMS, PART III: IS DNA ANALYSIS THE ANSWER? 

Bill Bakaitis  Feb 2010

In the first installment I tried to show that through various psychological/biological processes we create internal mental symbols – names - from the flux of sensory constellations gathered from the external world. This process is so automatic and well greased that we can easily forget that these symbols, mushroom names in this case, have been abstracted from the reality from which they spring.  This understanding was first applied to subjective naturalistic observations and then extended into the realm of more 'objective' taxonomies. 

In the second installment, I described the cognitive end of the perceptual-cognitive continuum: memory and meaning in the identification process, the role of operational definitions in establishing specific referents for the precise meanings of our conceptual constructs, and the role of language in mediating our notions of reality. That investigation ended with the observation that our ideas of what constitute a 'specie' are fraught with philosophical questions that cannot be settled by empirical evidence. The arrival of DNA technology upon the scene has been suggested as a way around these philosophical, linguistic, and 'artificial' taxonomies of the past.

In this, the third and final part, of this long article I shall attempt a look at the claims that this branch of science can offer us a taxonomy that is 'real and final' in our search for the perfect mushroom taxonomy.  Wish me luck.

Let me first confess that the specific details of DNA technology lie far beyond my ability to understand. I will not/cannot therefore comment in detail upon the quite substantial discussions, critiques, and controversies about the technology.  Some launch point, however, is in order. (Two readable sources are Krukonis & Barr 2008 and Carroll 2006)

Cladograms, bootstraps, and the Tree of Life

Suffice it to say that credible articles published within the field suggest that the primary merits of Cladistic analysis lies in creating a robust, yet parsimonious template (usually visualized as a Cladogram) of the hypothetical reality of the Phylogenetic Tree, often referred to as The Tree of Life..http://en.wikipedia.org/wiki/Clade

Cladograms graphically plot the results of DNA analyses of variations both within and between the materials sampled. Restrictive enzymes are used to clip snippets of the genetic code thought to be indicative of change. These are then subject to PCR amplification, electrophoresis, bar coding and analysis by complex computer programs which robotically decipher these coded proteins and arrange them in logical sequences capable of demonstrating where the evolutionary lines have diverged. (For more, see Nicholson, et. al.  DNA Fingerprinting in Fungi: A Primer Fungi Vol2:4Fall 2009 p 49 following)

Where the sample size is small (say a single specimen) certain mathematical models (called Bootstrapping) http://en.wikipedia.org/wiki/Bootstrapping_(statistics) allow continual resampling of the numbers to 'bulk up' the data and create a finding that may be more reliable concerning the sample, but is thought to be overly optimistic when applied to the larger population from which the sample was drawn.  From this analysis, different lines of descent and modification can be demonstrated, with some lines branching unabated to the present.













This Cladogram of the Evolutionary Relationships of Fungi was presented at the 2007 NEMF Foray.

A Taxonomy of Taxons:

Three classification schemes (or taxons) can be viewed from this vantage which may be though of as indicating the relative degree of congruence between classical taxonomies of surface morphology, or actual mating characteristics and the presumed underlying genetic factors. These are: ( Seehttp://www.ucmp.berkeley.edu/glossary/gloss1/phyly.html for a graphic representation of these terms.)

1. Monophyletic taxons which include an ancestor and all descendants. This is called a Clade, (from the Greek term klados, for 'branching'). There is complete congruence in this taxon giving great validity to the surface groupings.

2. Paraphyletic taxons which include some, but not all recent descendents of the ancestor.  Congruence here could vary from slight to major.  Some of the species bounded by the surface taxonomy would be presumed to be genetically valid, others the product of convergent evolution.

3. Some taxons group together organisms which have similar characteristics derived from quite different evolutionary lines. This is called a Polyphyletic taxon and represents an artificial classification system. 

For example, warm blooded dinosaurs (what we call 'birds') and warm blooded mammals (cows) both developed this condition independently, modified by their environment through convergent evolution. A classification system which groups together all warm blooded animals is therefore 'artificial'  (Polyphyletic) and not based upon the evolution of the family tree demonstrated by the genetic analysis described above,  even though it may  be valid from another perspective. Biological considerations of the chemistry of warm blooded fishes such as Tuna , the investigation of antifreeze compounds in organisms as diverse as fishes, animals, plants, and algae, the spread of diseases across kingdoms,  may, in each case involve genetic similarities which arrived in the surface species independently.  

Horizontal Gene Transfer

Alternatively, genetic similarities may exist from packets of genetic material which dislodge and migrate horizontally from place to place upon the chromosome, between chromosomes within the same genome, or from genome to genome, even across biological kingdoms. This type of genetic exchange falls outside of the Darwinian "descent with modification" model upon which the Cladistic scheme depends and results in viable genetic characteristics which seem to defy the branching family tree rules specified by the computer programs responsible for the generation of the Cladistic tree.

Some of these 'jumping genes' involved in horizontal transfer of genetic information are referred to as 'transposons'. They are thought to be transmitted by plasmid exchange, among other genetic mechanisms, and seem to occur quite frequently in living organisms, from once every few months to once every few years in species studied.  Once migrated, these transposons can apparently force their way through the entire species population in a few decades, and can come to represent considerable portions of the genome of that species. Half of the genome of Maze (corn) for example is thought to have come from transposons. (For this and much more see http://en.wikipedia.org/wiki/Transposons for a brief overview of the processes involved and summary of findings.) 

Deep Structure Vs Surface Variability

Commentators from within the field note that the nature of Cladistic analysis is not particularly well suited to recognizing the differences separating 'species' as much as it can show commonalities which delineate heritage.   The patterns revealed are shown to be fractals, each level, from the surface to the deep, showing abstract geometric similarity with the other.  One also reads that the Cladistic method does not differentiate between surface species and deep ancestors, and would also be unable to detect even the presence of primal ancestor (should that organism actually be present in the data base). A relatively clear description with straightforward comparison of both the Cladistic and Linnaean systems can be found athttp://en.wikipedia.org/wiki/Cladistics.

There are significant and divergent viewpoints within this field, a factor which emphasizes that the entire enterprise is based upon powerful, but also powerfully abstract symbolic manipulation. In light of the arguments presented earlier in this article, note that every single aspect of the process described above relies upon procedures completely mediated by symbolic systems, each with their attendant frameworks and assumptions. (see for example Species Concepts and Phylogenetic Theory: A Debate - Quentin Wheeler, Rudolf Meier)

Given the axiomatic position "everything is connected to everything else" it follows that hypotheses come 'bundled' and that anytime we test one hypothesis, we are at the same time, testing the assumptions of  auxiliary hypotheses. For more see  http://undsci.berkeley.edu/article/bundle

As one commentator within the field sated when attempting to parse the meaning of a particularly dense tangle into which he had ventured  " Clade (X in A) as an apomorph-based definition meaning 'the first species to possess character X synapmorphic with that in A, together with all its descendants.   Whatever the hell that means." http://www.miketaylor.org.uk/dino/faq/s-class/phyletic/

A SIDEBAR FROM WIKIPEDIA

Summary of advantages of cladistics

Proponents of cladistics enumerate key distinctions between cladistics and Linnaean taxonomy as follows:[33]

Cladistics

Handles arbitrarily deep trees.

Discourages naming or use of groups that are not monophyletic

Primary goal is to reflect actual process of evolution

Assumes that the shape of the tree will change frequently, with new discoveries

Linnaean Taxonomy

Often must invent new level names (such as superorder, suborder, infraorder, parvorder, magnorder)              to accommodate new discoveries. Biased towards trees about 4 to 12 levels deep.

Acceptable to name and use paraphyletic groups

Primary goal is to group species based on morphological similarities

New discoveries often require renaming or releveling of Classes, Orders, and Kingdoms

Summary of criticisms of cladistics

Critics of cladistics include Ashlock,[34] Mayr,[35] Williams.[36] Some of their criticisms include:

Cladistics

Limited to entities related by evolution or ancestry

Does not include a process for naming species

Ignores sensible, clearly defined paraphyletic groups such as reptiles 

Difficult to understand the essence of a clade, because clade definitions emphasize ancestry at the expense of meaningful characteristics

Difficult to determine if a given species is in a clade or not (e.g. if clade X is defined as "most recent common ancestor of A and B along with its descendants", then the only way to determine if species Y is in the clade is to perform a complex evolutionary analysis)

Limited to organisms that evolved by inherited traits; not applicable to organisms that evolved via complex gene sharing or lateral transfer

Linnaean Taxonomy

Supports groupings without reference to evolution or ancestry

Includes a process for giving unique names to species

Taxa definitions based on tangible characteristics

Permits clearly defined groups such as reptiles

Straightforward process to determine if a given species is in a taxon or not

Applicable to all organisms, regardless of evolutionary mechanism

from http://en.wikipedia.org/wiki/Cladistics

The Cladistic Baker: an analogy: Here is an analogy from my career as a baker: let's see if this helps.

As a teenager and in my early 20's I worked in and on occasion, by myself, ran a small bakery in Washington Pennsylvania: Orban's Bakery for those few readers who were alive then and there.

Every night, around midnight I would begin the daily baking. We had several large mixing machines and the first order of business would be to mix up the various batches of dough from which the goods displayed in the front of the store would be baked. Each night I made doughnuts, sweet rolls, pastries, cookies, breads, rolls, and cakes.

We sold four types of bread: white, high-gluten, whole grain, and rye, and each was staged to be ready for baking when space in the huge revolving oven would be available. Once begun, work progressed quickly as time and economic constraints placed their demands upon our production. To deal with some of these constraints, a huge steam box was available for proofing the products, hastening the activity of the yeast, and large refrigerators could be used to retard the dough.  

Consider these constraints and gadgets as environmental factors shaping the 'descent with modification' of the dough.

As the dough rose in the mixing bowls a first baking would be pinched off as it overfilled the bowl and began creeping down the side. This first dough was processed into loaves which fit into square pans, placed into the proof box, then subsequently baked. The remainder of the dough was punched down and allowed to rise a second and then a third time, each time being pinched off and made into loaves of other shapes and textures as the yeast continued to digest the sugars and starches in the mix, producing a dough with different characteristics. In addition some of these loaves were given longer, some shorter proofing times.  

By five in the morning, on the cooling rack, all of the bread so produced from the 'white bread' mix could be considered to have come from the same ancestral dough. Similar lineages of other doughs were also produced, each in turn from their own ancestral mix, the pinching off process analogous to the nodes of a branching cladogram.

Later that morning, in the store, displayed alongside one another on the shelves and in the cases would be the goods arranged by shape, texture, and durability: There were the square, soft pan loaves, the long Italian loaves with their crusty split tops, the flaky crusted Boules, the braided and seeded Twists, the small Hard Rolls, Sandwich Buns, and butter-creased Clover Leaf Rolls, and next to them the various pastries, doughnuts, cookies and cakes.

The customers could choose from a large array of sizes, shapes, textures and tastes but if one were to follow the development of the end products with a branching diagram, all could, if desired, be traced to their original ancestral mixing bowl.

So, on Day One; So far, so good as far as the Cladistic model might show.. But what happens as time goes on? What becomes, for example, of the day-old or otherwise damaged products? Some would be sold at 'day-old' discounted prices, some were given to the needy, and some to the hog farmer who made his daily rounds.

Some, however, as dictated by the economics of survival, were returned to the back of the store where they were ground up and added to the mixes which would be incorporated into the ancestry of tomorrow's baked goods, with the composition of the items available to the customer becoming accordingly scrambled...  At this point it simply becomes less and less relevant to ask about the ancestral heritage of the products in the store and of the purity implied by a Cladistic 'descent with modification' model.

I remember the morning a woman came to the side door, before the store was opened, and asked to purchase some day old goods. She was obviously poor and not in the best of health. She explained that she needed something without cinnamon as she was deathly allergic to it. I went back and asked Willie, the owner and long time master baker.  He replied in a panic…."What's she talking about. It's ALL got cinnamon in it", he said, waving his hands in an arc wide enough to encompass all of the surfaces, covered with the dust of flours, spices, and other ingredients, the common tools, machines, and ferment of activity, our aprons caked with the day's detritus. I knew in a flash that he was correct.

Making this analogy all the more compelling is the fact that while cinnamon is more or less inert, transposons are active, capable of reproducing and amplifying their effect and increasing the likelihood of non-parental genetic modification of the mushrooms we come to sample in the store called reality.  End of Analogy.

A Phenomenology of Grouping:

From the perspectives described earlier in this article it seems obvious that mycologists who favor a field or biological (breeding) approach have built their classification systems upon grouping together of the tangible end products of the evolutionary lines.  From the perspective of Cladistics the groupings are of their tangible bar-coded diagrams created by computerized mathematical models.

The former progresses primarily by the grouping of visible characteristics into 'species', 'families' 'orders' 'phylum': the latter mostly by cleaving into lines which have diverged cleanly from the ancestor. 

These are not only 'different strokes for different folks' reflecting differences in temperament, but also represent different ways we come to frame and view 'reality'. From a psychological/philosophical point of view they flow from different operational definitions of  the presumed composition and structure of that reality. 

The gestalt principles of grouping described in Part I of this article retain their significance, but the items which are grouped differ radically.  For the field mycologist the perceptions which are squeezed through their sensory portals are elements of gross morphology - color, shape, texture, etc.  For those who conduct genetic analysis, that which gets squeezed through their doors of perception are barcodes and such, which have been created, assembled and arranged by the hand of man. This does not deny any underlying reality to genetic analysis but focuses squarely upon the psychological factors present in the observation of the phenomena perceived, grouped, and then processed by the mind of the observer.

The various explorations below stem from understandings related to the discussion presented in Part II in this series of three articles.

Words are not things, Snippets are not the whole, and Biases can easily be buried by synthetic constructions... 

Recall the seven postulates of Korzybski. [appended to the end] These postulates are paraphrased and encapsulated here as: Nature is all of a piece, best described symbolically as the dynamic interrelationship of discrete multidimensional events separated by the insensible gradations of unlimited characteristics.  Or recall Dr. Both’s discussion of Gastroboletus lariscinus, “a recent [form] of Suillus grevillei, genetically identical with it… [but containing]… a number of macro- and microscopic differences which warrant [maintaining] it as an autonomous species.” 

We should not underestimate the strength and power of DNA technology. But it is not the end-all and be-all of taxonomy. It is true, for example, that a complete genome sequencing of the material from a single individual renders a unique genetic blueprint. But that is not what Montcalvo et al. offer when they sequence a snippet or two of DNA material from “A. farinosa”.

If we assume that the snippet of material comes from a single specimen, the questions then arise, “Which specimen?” “Who identified that specimen?”  And, “What concept of “farinosa” did they use for their identification?” Any ambiguity in that concept, misidentification of that specimen, or opinion of the identifier would just be buried at a deeper level by DNA sequencing of that particular specimen. This appears to be the reason why Michael Kuo proposes starting from scratch in the process of describing Leccinum species which would then be used for DNA analysis. http://www.mushroomexpert.com/leccinum.html  as "even the Gen Bank sequences" would be subject to this problem.

An analogy from my own field of study (Psychology and The Philosophy of Science) might apply here; the attempt to correlate a person’s Stanford Binet IQ score with a certain pattern of brain activity. Such a correlation could easily be done, but would only bury the various cultural biases of that (or any) verbal test at a deeper biological level. The patterns of brain activity might seem “real” and “more scientific” to the layperson, but that is clearly not the case. Recently brain scientist Steven Pinker has elaborated on similar issues as they relate to his understanding of bits of his own genome as revealed by DNA analysis. (Pinker, Steven;' My Genome, My Self: The New York Times Magazine 1/11/09)

It is important to remember that the DNA bar code given for “farinosa” is not of the entire organism. It is not a genome, but a snippet. The snippets, have, of course, been standardized, and clipped with the aid of enzymes easily available from commercial sources, but different snippets, cut with differing restrictive enzymes, would render different orderings, with different meanings.  Those snippets actually chosen are ones which are cheap and easy to work with and which are thought to best demonstrate common or discriminate ancestry for the particular species being investigated. (See, for example Carroll, S.B. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution p 98-102)

Structure or relationships?

Another issue can be forcibly put by the following question: “Is it the structure of the gene that determines the form of the organism, or is it the relationship of the genes to one another?”  

Indo-European languages (with their noun-verb syntax) are said to be biased for structure and, therefore for a reductionistic determinism. This view would lead to the conclusion that the floristic “farinosa” which we “see” in the field can be reduced to a genetic sequence.  

An alternative view, advanced by General Systems Theory, has been well summarized by the theoretical physicist, Fritjof Capra (1996). He argues that it is not the structure that matters so much as the relationship, a rule that he sees operating at every level of organization within the universe.

As applied here, this view raises the “relationship question” of the effect of one gene upon the many others within the genome. The received wisdom is that although genetics loads the gun, it is the environment that pulls the trigger. And the internal environments – of the chromosome, the nucleus, the cell, and the organism itself – are all environments one would expect to be capable of “pulling the trigger.” Consequently genes may or may not fire, and if they do fire it is not guaranteed that they will have the same effect. Some 'epistatic' genes require interactions with others to produce protein. Alternately, the same protein can be produced by different genetic arrangements via 'triplet' alternations.  Also,. proteins created from what were once thought to be 'junk' DNA are known to be capable of altering the phenotype – the shape, morphology and functioning of “genetically identical” organisms. It has been suggested that these interactive protein paths are likely to become increasingly important with the next generation of genetic analyses. (Carmichael, Mary; A Changing Portrait of DNA Newsweek 12/10/07) 

Increasingly one finds references to diseases that vary depending upon which parent the identical gene came from. (see Kolata, Gina NYT 7/16/91 Biologists Stumble Across New Pattern of Inheritance or Wade, Nicholas NYT 12/19/09 Disease risk depends upon which parent a DNA variant is inherited from) 

And, for fungi, remember that the mycelial matt from which the fruiting body springs, has not two parents, but hundreds, perhaps thousands or more spore generated hyphal 'parents'.  One rather remarkable feature of morels is the genetic variability and fluidity within a given mycelial colony. As described in a recent report, each morel may be "composed of a variable mixture of mono-, di-, multi, or heterokaryotic hyphae and the pairing of haploid nuclei can occur anywhere."  Such colonies should be considered populations of nuclei or genes [rather than as individual morels]. As one geneticist reported, no two morels she has ever analyzed were genetically identical, even if they were growing in a cluster arising from a common mycelium. This inherent genetic diversity can apparently be augmented by the incorporation of new genetic material on a seasonal basis into an already established colony. (see Ecology and Management of Morels Harvested From the Forests of Western North America   USDA General Technical Report PNW GTR 710http://www.fs.fed.us/pnw/publications/gtr710/pnw_gtr710c.pdf )

And, as Pinker reminds us, to the basic nature-nurture relationship process must be added another factor, that of  'brute chance'. "Even in the simplest organisms, genes are not turned on and off like clockwork but are subject to a lot of random noise, which is [one reason] why genetically identical fruit flies bred in controlled laboratory conditions can end up with unpredictable differences in their anatomy."

As the semanticist might say; Nature works in dynamic processes, with insensible gradations and unlimited characteristics. Or to put it in terms of the German psychologists who first studied perception: 'the whole is more than the sum of its parts'.  The organism we call “farinosa” is larger than any description or gestalt of it we may create.

A Deck of Cards:

Two final analogies may help make the point. In the first consider classification in a deck of playing cards. In this case we know with certainty the identity of every one of the 52 cards of the deck spread out on the table, quite unlike the fungi which are but the fruits of unseen mycelial networks.

Each of the 52 playing cards is unique. There is only one Queen of Spades. Does she go with the other Three Queens? Or with the other face cards? Perhaps she goes with the family facing left: She, the King, Jack of Spades and the Jack of Clubs. Or do we divide the deck so that she goes only with the Spades, or only with the Black Cards? 

Shuffle the deck and deal out a hand of five to a few players, and suddenly whole new possibilities suggest themselves. She might go with any one of the other Three Queens to form a class known as “a Pair,” among which there are other hierarchical arrangements. Or she could also be a member of a class known as a Full House, a Straight, a Flush, or a Royal Straight Flush. Her value is determined to a great extent by her relationship to the other cards, which cards are in play, and which are not. 

Assume now that there are only 52 mushrooms in the world. Even if we could know with absolute certainty the genetic descriptions of each of these mushrooms, we would be in much the same situation as with the deck of cards. We would arrange them by their relationships as seen by the perceptual-cognitive framework of the individual players.  

And even players of the same game, playing, as it were, by the same rules would be interested in aspects “unseen” by the other players. A dealer of cards for example would likely be interested in the plastic coating on the cards. Do they slide, shuffle, deal more easily. Some players might consciously look for subtle differences in how the backs of the cards took the oil from their fingers or impressions from their fingernails as they handled the cards, or perhaps ever yet more subtleties of small “imperfections” of the designs on the backs of the cards be they put there by Nature (the designer and/or printing press) or by environmental forces (random wear and tear or systematic handling). The more I think about the possibilities (and I am not a card player) the more I see. 

For our all but forgotten Dear Reader I could finally inject Freud into this discussion and hypothesize that if we hold a Hot Queen in our hand for a long period of time would she not reflect that caress on her backside? Considerable perceptual research indicates that we can pluck from our Sensory Store items that do not muster the strength of full awareness. We call these “hunches,” “subliminal perceptions,” or behaviors reflecting “unconscious” thought processes.

Of course in the card game analogy the relationships are tautological – true by definition. In the real world we would expect that the genetic material and its biological output, proteins for example, would have an inherent integrity that would transcend the human thought process. I would not deny this but simply point out that within our individual and cultural system of referents there are very important differences that at the same time transcend the genetic reality.

The Folly of Reductionistic Thinking

Consider an argument made by Michael Pollan (2007) about the scientifically isolated nutrients in our food. He points out the problems created by this reductionism. “Eat food,” he says if you want to be healthy. However, “If you’re concerned about your health, you should probably avoid food products that make health claims. Why? Because a health claim on a food product is a good indication that it’s not really food and food is what you want to eat.”  

The result of reducing the operational definitions of “food” to “nutrients,” he offers, has led to a vast array of conflicting dietary advice within the literature, some quite harmful. Why do we do it?  In part because… “A nutrient bias is built into the way science is done: scientists need individual variables they can isolate. Yet even the simplest food is a hopelessly complex thing to study, a virtual wilderness of chemical compounds, many of which exist in complex and dynamic relation to one another, and all of which together are in the process of changing from one state to another. So if you’re a nutritional scientist, you do the only thing you can do, given the tools at your disposal: break the thing down into its component parts and study those one by one, even if that means ignoring complex interactions and contexts, as well as the fact that the whole may be more than, or just different from, the sum of its parts. This is what we mean by reductionist science.” It is a powerful tool, but encourages us to take a mechanistic view of complex biological interactions.

The Grape in Everyday Life

The addition of psychological and cultural variables to the matrix leads to even greater complexity. Follow, the grape for example, as it becomes raisin, juice, jam, jelly, wine, communion, vinegar or compost. Many of the “nutrients” would be similar or identical. Presumably the DNA retained in some of these states would be identical. Yet even with identical DNA we recognize the importance of maintaining different conceptual identities for these states – differences based upon different properties.

A similar example could be given with H20. Important structural differences exist in its gaseous, liquid, and solid forms – clouds, rain, and snow. And the aboriginal Eskimo, we recall, had many names for snow, each name reflecting differences important to the ability of their culture to survive the long arctic night.

A classical case in mycology is the maintenance of separate binomials for the anamorph and telomorph states of certain genetically identical fungi: Curvularia intermedia, for example is the conidial stage of the ascomycete Cochliobolus intermedius (Moore-Landecker, 1982). Here presumably identical genes produce dramatically different morphological structures.

And finally, when we examine the claim that DNA sequencing will settle, for once and for all, the problem of identifying our mushrooms for us, we come smack up against the issue of flux, raised by horizontal gene transfer –  “jumping genes” and plasmid exchange of genetic material or the chance reappearance of previously extinguished genetic material. Mix well with environmental stressors and competition for scarce resources and, contrary to popular assumptions, you end up with measurable and rapid changes in the genetic composition of species. 

As Jonathan Weiner puts it in The Beak of the Finch, “The [genetic] borders between species are as fluid and adaptable, as sensitive to changes in pressure, as the heaving waves in a high sea.” Whereas, the conventional “version of the tree of life was plain, neat, stark; this view is softer messier, more tangled, and more alive.” Darwin’s Finches, studied in precise detail, over decades by teams of scientists on the Galapagos Islands “pass invisible messages back and forth, swapping genes as casually as good neighbors exchange recipes, tools, or limericks. Their lines come together and come apart, and in this way the birds are created and re-created, again and again.” The organisms “cannot stand still” in the face of a dynamic world. 

As the author of one of our most widely used field guides has been known on occasion to quip, “You know, the more I think about it, the more I come to the same conclusion. It’s all one mushroom!"(1)

[(1.) In 1991 Geoffrey Pullam used his self-described  'humorous essay'  "The Great Eskimo Vocabulary Hoax" as the title of the collection of essays of the same name, establishing the meme which rapidly spread throughout much of our popular culture. An examination of the boundaries of this 'Hoax" may be found at  http://en.wikipedia.org/wiki/Eskimo_words_for_snow .    Linguist Anthony Woodbury illustrates some of the complexity involved, along with a list of lexemes from just one dialect athttp://www.ecst.csuchico.edu/~atman/Misc/eskimo-snow-words.html. , and Pullham himself offers comment upon "the extremely complex truth" of this infinitely reflexive, infinitely rich, infinitely complex language system on his 2004 blog post http://itre.cis.upenn.edu/~myl/languagelog/archives/000405.html  For those who might be interested, the word meme, is often defined as the cultural equivalent of a gene, transmissible from one mind to another, but also subject to cultural modification along the way.]

The Luddite Within

How do we deal with all of this in the field as we go about our pleasures of collecting the natural fruits of the genetic tree of life? In Mexico recently, a team of ornithologists looked at a subset of the recognized species of birds in a restricted geographical region and subjected them to the genetic analysis from which the Cladistic tree was assembled. .

Their analysis produced a plethora of new 'species' as 'the continual re-creation' of birds studied in the Galapagos would suggest. They conclude: "The biological species concept (BSC) and its inclusion of diagnosably distinct populations as subspecies remain dominant in ornithology. This may be attributable, in part, to the seemingly infinitely fine divisions possible under phylogenetic species concepts (PSC)—which, among other things, could strain public credulity over what constitutes a species." (Winkler et al.)

In a similar way, when I walk in the sea of mushrooms which confront me in the forest and field, or when I am called upon to identify a mushroom involved in a suspected toxic event, the best tools I have at my disposal to process, name, and reference that which I see is the mental map of reality that I carry buried in the tissue of my brain. Here the robust parsimony of the past serves not only to frame the present but also to preview the future.

Until we have portable DNA probes that can be plunged into the tissue of the fruiting bodies that I hold in my hand, the best taxonomic models available to me will be those built upon morphological similarities and differences, which I can see and from which reasonably accurate cognitive templates can be assembled. I need to be able to know in a flash, or at least in a reasonably short time, what it is I am looking at or collecting. The deep evolutionary proposals may be ever so interesting, completely valid as a scientific tool and technologically feasible but are simply irrelevant to most of what I do.

For those of us in the field, sometimes simpler is better, and if it works reasonably well, we would be foolish to fix it. Call this psychological parsimony, the tendency to retain that which works. It is why I am much more interested in the new field guide/vernacular monograph on 'Milk Mushrooms' (Bessette. et.al. 2009) than I am in the 'Species delimitation and phylogenetic relationships in Lactarius section Deliciosi ' ( Nuytinck,J.and Verbekena, A. Mycological research V 111, Issue 11 , November 2007, Pages 1285-1297 )  It is also why, at best, I am but an amateur mycologist.

The spark for this very long three-part article came to me one morning during a short drive a few years ago. The ideas sprang effortlessly to mind, the outline fully drawn during the duration of Nikhil Banerjee's rendition of Raag Chandra Kauns. I thought it would take only a day or two to commit the ideas to script, but a myriad of unrelated events conspired to keep this raga going. So hugs galore to Dianna Smith for the tambour of her kindness, encouragement and support as these events played out. She has become such an important player in Northeastern Mycology it is hard to remember what it was like without her participation.

ACKNOWLEDGMENTS

I would like to thank John Haines, my mentor at the New York State Museum during a sabbatical several years ago, for reviewing earlier drafts of this paper and offering helpful comments and corrections. I would also like to remember Peter Katsaros, my collecting partner of a quarter century, for the wonderful hours of discussion during which many of the ideas presented here germinated and grew. Thanks too, to Britt Bunyard who provided valuable comments during earlier versions of this manuscript, and to Leon Shernoff for his assistance in shaping the present evolution of the piece…     That said, all the goofs, gaffs and outrageous statements are mine.

REFERENCES CITED

Bessette, A.E. Harris, D.B. and Bessette, A.R.2009 Milk Mushrooms of North America: A Field Identification Guide to the Genus Lactarius. Syracuse University Press, Syracuse New York, 2009 

Bessette, A. E., Roody, W.C. and Bessette, A.R.  2000. North American Boletes: A Color Guide to the Fleshy Pores Mushrooms. Syracuse University Press, Syracuse, NY.

Both, E. 1993. The Boletes of North America: A Compendium. Buffalo Museum of Science, Buffalo, NY.

Capra, F. 1996. The Web of Life; A new Scientific Understanding of Living Systems. Anchor Books, Random House, NY. 

Carroll, S.B. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution Norton 2006

Carmichael, M. A Changing Portrait of DNA Newsweek 12/10/07)

Gilbertson, R. L. and L. Ryvarden. 1986. North American Polypores. Fungiflora Oslo Norway 

Gregory, R. L. 1997. Eye and Brain: the Psychology of Seeing, 5th ed., Princeton University Press, Princeton, NJ.

Groopman, J. 2007. How Doctors Think. Houghton Mifflin, Boston, MA.

Grund, D.W. and A. K. Harrison. 1976. Nova Scotian Boletes. Bibliotheca Mycologica Vol. 47.  

Jenkins, D. 1986. Amanita of North America. Mad River Press. Eureka, CA. 

Kolata, G. NYT 7/16/91 Biologists Stumble Across New Pattern of Inheritance

Krukonis G. and Barr, T. Evolution for Dummies Wiley Publishing 2008

Kuo, M. (2007, May). The genus Leccinum. Retrieved from the MushroomExpert.Com Web site:http://www.mushroomexpert.com/leccinum.html

Largent, D., D. Johnson, and R. Watling. 1977. How To Identify Mushrooms To Genus III: Microscopic Features. Mad River Press; Eureka, CA. 

Leonardi, L. and J. Haines. in ms. “The Mycological Work of Homer House”. 

Lincoff, G. H. 1981. The Audubon Society Field Guide to North American Mushrooms. Alfred A. Knopf, New York.

McKnight, K. H. 1977. “A note on the ISCC-NBS Centroid Color Charts”. McIlvainea 3 (1): 4-11.

Miller, O. K. and H. H. Miller. 2006. North American Mushrooms: A Field Guide to Edible and Inedible Fungi. A Falcon Guide Guilford, CT.

Moore-Landecker, E. 1982. Fundamentals of the Fungi, 2nd. ed. Prentice-Hall Englewood Cliffs, NJ.

Nicholson, et. al.  DNA Fingerprinting in Fungi: A Primer Fungi Vol2:4Fall 2009 p 49 following

Nuytinck,J.and Verbekena,A. Species delimitation and phylogenetic relationships in Lactarius section Deliciosi in Europe. Mycological research V 111, Issue 11 , November 2007, Pages 1285-1297 )  

Overholts, L. O. and J. L. Howe. 1953. The Polyporaceae of the United States, Alaska and Canada. University of Michigan Press, Ann Arbor, MI.

Pigliucci, M. (2003). "Species as family resemblance concepts: the (dis-)solution of the species problem?" BioEssays 25: 596-602

Pinker, S.'  My Genome, My Self: The New York Times Magazine 1/11/09

Pollan, M. 2007. “Unhappy Meals”. New York Times Magazine, Jan. 28, 2007.

Robbins, J. 2007. “Out West, with the buffalo, roam some strands of undesirable DNA”. The New York Times, Jan. 9, 2007. 

Smith, A. H. and H. D. Thiers. 1971. The Boletes of Michigan. The University of Michigan Press, Ann Arbor, MI.  

Snell, W. H. and E. A. Dick. 1970. The Boleti of Northeastern North America. Verlag von J. Cramer, Lehre, Germany. 

USDA General Technical Report PNW GTR 710  Ecology and Management of Morels Harvested From the Forests of Western North America  ( also athttp://www.fs.fed.us/pnw/publications/gtr710/pnw_gtr710c.pdf )

Wade, Nicholas,  NYT 12/19/09 Disease risk depends upon which parent a DNA variant is inherited from, 

Weber, N. S. 1972. “The Genus Helvella in Michigan”. The Michigan Botanist 11

Weber, N. S. 1988.  A Morel Hunter’s Companion:  A Guide to the True and False Morels of Michigan. Two Peninsula Press. Lansing, MI. 

Weiner, J. 1994. The Beak of the Finch: A Story of Evolution in Our Time. Vintage Books Random House, NY.

Winker, K., Rocque, D.A., Braile, T.M.,. and Pruetti,  C.L. Vainly Beating the Air: Species-Concept Debates need not Impede Progress in Science or Conservation Ornithological Monographs Volume (2007), No. 63, 30–44  (also athttp://www.uaf.edu/museum/bird/personnel/KWinker/Winker%20et%20al.%202007%20Vainly%20beating%20the%20air%20(species%20concepts)%20OM63.pdf)

Wood, S. E. and E. G. Wood. 1996. The World of Psychology, 2nd ed.  Allyn and Bacon, Needham Heights, MA.

Korzybski referent; from Language and the Structure of Reality  in Part 2 of this article.

A good summary of this “Tyranny of Words” is given by Stuart Chase in his book of the same name.  In it he summarizes these first seven semantic postulates of Alfred Korzybski’s Science and Sanity (website reference #8):

1. No two events in nature are identical. This proposition is accepted by modern scientists. It runs counter to the "is of identity" in Indo-European languages, and to the "A is A" of formal logic. 

2. Nature works in dynamic processes. Accepted by modern scientists and by some schools of philosophy. It disagrees with the linear, cause-and-effect structure of our language. 

3. Events flow into one another in nature by "insensible gradations." Nature is all of a piece, though our language tends to separate it into classes. 

4. Nature is best understood in terms of structure, order, relationships. Einstein helped to establish this through the principles of relativity. Indo-European languages, with substantives, entities, absolutes, are at odds with the proposition. 

5. Events in nature are four-dimensional. Modern physicists think in terms of space-time. Indo-European languages are structured for three dimensions, and those who speak them have great difficulty with the concept of time. 

6. Events have unlimited characteristics. Our languages leave many of them out and thus often distort a judgment. 

7. There is no simultaneity in nature. Western languages assume it as a matter of course.