Wednesday, February 13, 2013

Is it really "Taxonomic Exuberance" or "Phenotypic Plasticity" ?

Credit: Charley Murphy"Charlie Murphy’s glass sculptures 
delicate ‘stamen’ series celebrates
the extraordinarily expressive
features of plant life"
 
Back in January of 2013 (last month), there was an article in the online publication - smithsonianmag.com - "How the Tree Frog has redefined our view of Biology". It's an interesting and fascinating look at these Tree Frog's Egg responses to environmental changes. This is actually known as 'phenotypic plasticity' which is merely the ability of any living organism to modify it's behavior or shape in response to changes in the environment. Now in the past, this is where Researchers took liberties at what is called "taxonomic exuberance" (a rush to label something a new species) , when in reality, it was nothing more than "phenotypic plasticty" for no other reason than, "Well it looks different from the rest of it's other companions in other geographical locations". While referring to this article, I'm not so much pointing to the amazing ability of this organism to change behavior as I'm blown away by quotes in the article like, " . . redefined our view of biology" and  " . . a phenomena that is transforming biology" or even hailing this as " . . a revolutionary new concept". Seriously ? Are they kidding ? Anyone who has ever had an interest and love for studying or growing plants has always known about this unique fascinating phenomena. This really isn't rocket science. This has actually been around for a very long time now. There is no real surprise here that evolutionary biologists are astonished and amazed about the "revolutionary concept" called "phenotypic plasticity". Many are motivated by the fame, glitter and glory associated with new species discoveries which can often muddled the truth of the actual findings. I highly doubt many of today's University Professors and/or their graduate students spend much time outdoors anymore as they use to view how nature really worked years ago. Why should they, electronic gadgetry, the Internet and Computer Models in Labs have made all of that old archaic way of accomplishing things totally unnecessary. Taking only a few field trips outdoors to make it look legit. But nobody seems to live in the outdoors anymore when it comes to research like the old days. 

Photo by Sanguin-lupus

Horticulturalists, Botanists, Foresters, Landscapers, Gardeners all have an incredible amount of hands-on outdoor experience when it comes to understanding a plants ability to respond to different environmental variables. I've written about this here before. Grow a pine tree within the context of other pines and shrubs where  competition for light is much greater and they will grow straight and tall. Even deciduous trees growing within a forest canopy will have bigger leaves inside and smaller ones on the outer layers of the tree canopy. The question is why ? What happens within a garden or an urban landscape when the desired result is to have tall slender trees ? The gardener has to artificially perform the pruning task that Nature would have done in the wild in a more cramped competitive scenario. This is also what we see with your typical industrial forestry plantation which is actually what they are looking and selecting for. 


photo: Mine (2013)
However, grow the same exact species of pine tree out in the open in full sunlight and they will in the beginning exhibit more shrubby branching characteristics than the ones grown in the shade. The tree simply takes full advantage of the sun's energy and produces more branches and needles which act a major factory for photosynthesis. However, they often times won't stretch as high towards the sky as those within a forest tree canopy. These three trees in the photo above left are Jeffrey and one Coulter Pine. Before I sold my land in in 2002, there were among Chaparral shrubs called Redshank or Ribbonwood (Adenostoma sparsifolium) for which I established them by means of a Nurse Plant relationship. Also the deep rooted chaparral acted as a means of hydraulic life and redistribution of underground water during drier months. Out in the open on cleared land, they would have required irrigation and this is a major reason many US Forest Service transplanted on vegetation stripped land has ended in failure in this region. But I also was interested in the phenotypc plasticity influence from which the old growth chaparral would have helped develop these trees for a more slender lower trunk with later branching outgrowth higher up the trunk as they pushed through the Elfin-Forest canopy. But the new property owners back then, like most people, mistakenly believe that the chaparral was competition and strangling the poor trees. This was untrue. Nevertheless they were shaped into more of an open bush-like structural pattern. Their continued survival now is facilitated by the several species of mycorrhizal fungal spores I injected though inoculation into the soil around the feeder root regions. Still, the environmental features & the reasons behind them are what have shaped these trees as you see them presently when I photographed this in Spring 2013 in the above photograph.


You should see my Prickly Pear Cactus which I took from the chaparral plant community of Tenerife in the Canary Islands for which I've previously written about here on these blogs before. The beavertail cutting I took was placed in a pot last spring. Through this past summer 2012, it grew another beavertail on top of that older one. Of course I left it outside & the Spanish Slugs tore holes in that new growth, but it had healed and survived. I finally brought it indoors and placed it on our dining room in late October when the first frosts were present outside. Two weeks later it started to put on newer growth even though technically it wasn't even close to Springtime or in it's home range. Though I have two huge picture windows next to the dining room table, it's is mostly darkness here outside in Swedish winter. After the new year, we start to get 10 minutes of sun shining on that Cactus, then 15, 20 and so on over the next weeks. But the growth is not beavertail-like, it's more like one of those holiday Christmas Cactus sold at stores. Now, could I technically call this seemingly evolving Cactus a brand new species ? Of course not, it's still the same cactus responding to an odd environmental circumstance. Trust me I know. And yet, for years many an ambitious researcher has employed "taxonomic exuberance" by observing just this same thing with other organisms. Admittedly, this phenomena of "phenotypic plasticity" makes it a challenge in data collection for many field researchers, but a good plant specialist will understand the difference. 


So simple, even a Child gets this!
Yesterday this same subject came up when I wrote about the native Tule Elk of California. In comparing Tule Elk with Roosevelt Elk or even Rocky Mountain Elk, it was noted that these later two are much more larger than the California Tule Elk, and yet someone did transport some California Tule Elk to an area of northern Oregon which environmental conditions are exacting for the much large Roosevelt elk and the Tule Elk bulls grew close to the same size and weight as the Roosevelt bulls. Clearly they are the same species of animal, just a variation depending on environmental cues. On this subject of "taxonomic exuberance" I found this term in a book called "Mammals of the National Parks" by John H. Burde & George A. Feldhamer, where they specifically address the issue and question of what constitutes a species (a word whose definition is often fuzzy and muddled) and what the subspecies were with regards Grizzly Bears. Here's a paragraph quote from page 167:
"Biologists in the early 1900s had a difficult time determining the number of species and sub-species of Grizzly Bears. Resulting 'taxonomic exuberance' produced over a hundred named taxa. Some confusion remains today regarding common names. Grizzly, Brown and Kodiak bears are all the same species, although there are noticeable size differences associated with location, habitat and diet of different populations. Biologists now recognize five distinct genetic groups (clades) of Grizzly Bears throughout the world, but again, only one species." 
image: Resilient Earth
Related to this subject, when I was writing my post on the weather phenomena of  'lake effect rain' which has implications in climate influences hundreds of miles away, I was mostly interested in the subject of the ancient Lake Cahuilla which it today is a mere puddle when we compare it to the present Salton Sea. It was anything but salty, mostly freshwater, or at worst it was brackish water. Nevertheless, in the Cahuilla Indian Fish Traps found along the ancient shoreline around La Quinta, they have found the bones of fish known to be native only to the Colorado River which once flowed into this ancient sea basin. The fish of the Colorado that were found there are Bonytail Chubs and Razorback or Humpback Sucker. These fish of the Colorado have a unique body design for very swift river life where massive flooding periods are common. But I wonder what the same species of fish looked like in the fresh waters of ancient Lake Cahuilla (today's Salton Sea) ? Interestingly, the physical change features are noted in other fish species native to rivers and when they suddenly find themselves trapped in isolated still waters of lakes. Take a look at the example I've placed in this paragraph above here what happened to fish in swift rivers and those trapped in Lagoons. One has to wonder what changes occurred to river populations once trapped inside this vast Lake Cahuilla as compared to those still in the Colorado River ? 

Another very interesting and actually surprising usage of this terminology called "taxonomic exuberance" came from a source I never ever expected. On February 4th, 2013, Current Biology released a paper written by Tim White of UC Berkeley who works in the department of Human Evolution Research Center. This part of science has never been my favourite for no other reason than the fables, myths and stories created by the embellishments and exaggerations of the fossil findings and Anthropologist. Tim White agrees. Here is a link to this paper which was originally behind a pay-wall and now published on a PDF. Very interesting read and I'll post some pertinent quotes from this paper below this link:
UC Berkeley, Tim White: Paleoanthropology: Five’s a Crowd in Our Family Tree
Veteran Researcher, Tim White, reveals through a kind of critical sarcasm the problems within his specific scientific field which he considers unregulated, undisciplined and where most of his fellow  Paleoanthropologists are bent on self-promotion, where making things up as they go along are common place. In so many fields of scientific discipline, there is a rush to fame, glitter or glory and that has the tendency to colour research results. Interesting paper and very bold in it's criticism for which many in this field can find themselves losing a job or black balled in other ways in exposing errors or flaws in such an often ideologically driven subject as Tim White did.
"The unilineal depiction of human evolution popularized by the familiar iconography of an evolutionary ‘march to modern man’ has been proven wrong for more than 60 years. However, the cartoon continues to provide a popular straw man for scientists, writers and editors alike." 
What Tim White is referring to are the religious iconography still found in many of the scientific textbooks which are still in use today. And he condemns this use of such depictions which are continually used in those school boy biology textbooks which have yet to be corrected, no doubt for ideological reasons. There's no denying it, we've all seen it and it's provided great creativity fodder for Hollywood's Sci-Fi motion pictures. Unfortunately the depiction's end result is always the same. A big studly white man leads the pack. Somewhere between the Chimp and that white man, there are any number of countless mythical [half Ape - half Human] beast species and this is what Tim White was condemning. Categorizing today's human races as different species by some over exuberant researchers is yet another nail in the coffin of humankind ever coming together in unity. For you who may disagree with me, put yourself in the position of someone of African heritage on the outside looking in and you'll understand what I mean.      


"Do most of these species labels reflect real, biologically distinct lineages? Or have the alleged species proliferated merely as a result of 'taxonomic exuberance' misapplied to within-species variation (idiosyncratic, geographic, sexual, and/or ontogenetic)? The sequence of prominent paleoanthropological publications across the last decades reveals a pattern of diversity promotion."  
Paleoanthropology’s ecosystem of publishing, access, fundraising, career advancement, media promotion and celebrity seems squarely aligned against the field’s ability to self regulate, a condition exacerbated by the limited fossil resources available. There is ample and obvious motivation for authors to generate ‘new’ species names in this environment. Readers should, therefore, beware of attendant species diversity claims. Illegitimate names have become part and parcel of the symbiosis itself. 
Furthermore, ‘chronospecies’ are merely artificial segments of evolving species lineages, rather than truly separate species. Such assertions of biological species diversity via taxonomic hyperbole are questionable representations of the real paleobiology of our ancestors and their few close, now extinct biological relatives."

Image - Rob Horne - creekbed.org
These very problems and issues Tim White himself has been criticized from within his own unregulated field of research as he put it, but I find this to be a common problem within many areas of modern science, not just his. I often find this rewriting of history when it comes to  plant identification which I find very annoying. For example, how many times does the Cuyamaca Cypress of San Diego County have to be scientifically renamed ? Look up all the named references lately in the past couple of years, I think there have been five changes or attempts at change by private individuals looking for acknowledgement. And I have to tell you, I love this last sentence in the quote of Tim White's article. He said, "Despite the branch waving, our family tree still looks like a Saguaro Cactus more  than a Creosote Bush" - Tim WhiteIf nothing else, I'm a desert rat by heart and can relate to this very illustrative and beautifully expressed conclusion he made here.

So, "taxonomic exuberance", "phenotypic plasticity", "species" ? These words/terms are quite often muddled and murky depending on the circumstance used, person using them and the ideological concerns motivating such usage. I've truly never found a topic more fuzzied than this one often gets into. Sometimes by accident and other times more deliberate depending on the researcher's philosophical religious priory. I can understand natural excitement of finding something not seen before, as I also have to admit, that when I've been out in the field looking for specific plants, that just perhaps I would stumble upon some as yet unknown species or at least variation of plant I'm searching for. So much so because I quite often will be deliberately looking for something in a location geographically which I already know will have or hold specific traits engineered into it's genetic code for survival within this specific area for which may have practical value in the urban landscape. That's why when collecting seed for native plant nurseries, I was ever so careful to list details on where the seed source was located. It's this "phenotypic plasticity" which many foresters are looking for in seed source collection to replant within a specific region destroyed by fire and in need of replanting. I could care less about self-promotion or public recognition for anything I may stumble upon. My personal view is, if I have something that I've found to be important, I share it with others, then that knowledge becomes their property to share as well. But our world is defined by promoting self and this hinders any type of unity which in turn stifles any goal of true peace and security. Many people today are indoctrinated into trusting anything and everything that spews from a Scientists mouth or dripping ink of his/her pen. We often forget they are also human beings just like us with the same faults and flaws common to imperfect human beings. Look at the mess our natural world is in and it's this world's failed leadership or authority which got us here. Evolutionary Biologist, Austin L. Hughes from the University of South Carolina wrote a great piece in the online journal, "The New Atlantis" called The Folly of Scientism . It's a great well written article, not slamming science, but rather the modern day practice of blindly giving it's researchers a passing grade even when they fail horribly. He also wrote a couple of years ago in 2011, something incredible about this very same subject I'm writing about with "phenotypic plasticity" which was published in PNAS and called  The origin of adaptive phenotypes . Take a long look at some important quotes of Austin Hughes.
“Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations.”
“Contrary to a widespread impression, natural selection does not leave any unambiguous “signature” on the genome, certainly not one that is still detectable after tens or hundreds of millions of years. To biologists schooled in Neo-Darwinian thought processes, it is virtually axiomatic that any adaptive change must have been fixed as a result of natural selection.  But it is important to remember that reality can be more complicated than simplistic textbook scenarios.”
“In recent years the literature of evolutionary biology has been glutted with extravagant claims of positive selection on the basis of computational analyses alone, including both codon-based methods and other questionable methods such as the McDonald-Kreitman test.  This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science.” 


Austin's observations, comments, and reflections almost mirror what the Berkeley Paleoanthropologist Tim White said in his article about his colleagues rush to label supposedly new fossil finds as a new found species. Nature behaves far differently in the field than what many of the outdated textbooks in a university lab say. Not everything out there can be attributed to Darwinian mechanisms as Austin Hughes mentions. An organism's encoded information & sophisticated communication systems within it's DNA and the nano-machinery they control & operate along with a plethora of Switches and Sensors in what we know as epigenetics can accomplish whatever it takes for adaptability within reasonable environmental changes. [Pay very close attention to this new field of Epigenetics, it too is going to outrage the present Scientific Orthodoxy, I kid you not] Otherwise if organisms cannot adapt, then they completely fail. And that right now is what scares me. Lately science has come out with a series studies which are showing that our natural world may not be capable of repairing itself and certainly has reached the limits of it's adaptability despite the painting of rosy pictures by some researchers on climate change adaptability in hopes in allaying people's fears and panic. In other words, lulling them to sleep to prevent panic. Well, they should be panicked. Some of the content and subject matter of the papers almost make me sick because I don't really see any so-called eco-green innovations way out of any of this mess. Things I've seen for decades working in nature are no longer doing so in many areas I am familiar with. Things I've seen over a decade ago and warned about to friends are just now being revealed as truth in research papers. Most of my personal experiences were local to the Anza, California area, but now even more widespread, even globally.

What people should do is think before you blindly except or put faith in something stated from a self-appointed Authority. I'm not talking about some Hollywood cliche from X-Files like "Trust no one agent Mulder". There's enough of those conspiracies theories running rampant around the globe as it is. But you should find out and test out a statement when it's authors promote it as an irrefutable fact. It may turn out to be actually Factoidal as opposed to an actual FACT. Get yourself outdoors into the field, learn how nature really works. Drag your kids along too, they desperately need it if you're going to cure them of their "Nature Deficit Disorder". Do it for their own good. It's an education that becomes etched and burned into memories and not easily lost or forgotten. Now is it "taxonomic exuberance" or "phenotypic plasticity" ? Teach them the real difference between something being a different species or a variety of the same species. Armed with this new knowledge, you decide! There is a great old Proverb which even those claiming to be religious among mankind don't even take to heart.
Proverbs 14:15
"Only a simpleton believes everything he’s told! A prudent man understands the need for proof."
I hope you at least found this subject very interesting as I did and take it to heart the real reasons for the differences in many things in the normally orderly well arranged natural world around us. Please also understand that this world and it's long historical well ordered complexity are breaking down and disintegrating as a result of human ignorance. Generally by the very leadership who insist they are the leading intellectuals in the field. Take this post for how it was originally purposed, to instill deep appreciation for Nature. There is far more to this story than the few tidbits I've given here. There is growing science of Epigenetics which is revealing actual sophisticated complex mechanisms within the genetic code called Epigenetics which allow for multiple change and variation, but in a controlled manner. This is specific science discipline with the study of Genetics is proving to be a refreshing departure from an old outdated Victorian Era belief in random mutations (copying errors) which are firther chosen by a blind unguided mystic force no one can accurately explain other than a default term called, "Natural Selection." I'll continue to provide updates down here as time progresses. Stay Tuned.
Update - April 19, 2016
Just a post on the subject of Random Mutations so happily wedded to it's buddy Natural Selection in mutating life by accident. The problem with such dogma is that it has held actual viable scientific understanding of our natural world and therefore our working with it sustainably with regards to technological innovation. 
Random Mutations-Natural Selection & it's Copying Errors Legacy Illustrated
Update - April 26, 2016
This is a post continuing down the line of illustrating hidden mechanisms of changes gene expession not by dumb luck or guided forces, but of sophisticated epigenetic mechanisms influenced by varying changes from outside Environmental Cues which trigger 'on' or 'off' various 'switches' (think punctuation within a paragraph) within a gene which works within the context of other genes which in turn cause a different reading of the same informational content of an organism's DNA. This is what gives our natural world such beauty in variety and interest.  
Epigenetic Mechanisms Defined & Illustrated
Update - September 7, 2016
This is a beautiful article written about the incredible epigenetic mechanisms which allow for great variety in adaptation and variation within the same kind of organism. These are things we can actualy grab onto and hold, taste, smell and feel. As opposed to the mystic forces of random mutatio & natural selection which cannot accurate account for anything but the ignorance of past intellectuals from the Victorian Era. Here is one beautiful quote from the author:
“Many of the key players orchestrating DNA methylation had previously been characterized, but what we didn’t fully realize before this study is that they all work together in an elegant way,” said Scott Rothbart, Ph.D.,
This is a far cry from the promotion of "evolution is messy" dogma. Seriously, without going further here with this, google "evolution is messy" for yourself. Enjoy the article.
Van Andel Institute: "The whole of epigenetic regulation may be greater than the sum of its parts"






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