Organismal biologists needed to interpret new trees of life

Jul 16, 2014

Rapidly accumulating data on the molecular sequences of animal genes are overturning some standard zoological narratives about how major animal groups evolved. The turmoil means that biologists should adopt guidelines to ensure that their evolutionary scenarios remain consistent with new information—which a surprising number of scenarios are not, according to a critical overview article to be published in the August issue of BioScience and now available with Advance Access.

The article, by Ronald A Jenner of the Natural History Museum in London, describes how evolutionary trees inferred from genomic information have overtaken and even displaced traditional studies of animal forms. The traditional studies sought explanations for how the body plans of the three dozen or so major most likely evolved, but molecular data provide strong evidence about genealogical relationships without yielding explanations. So even though data are accumulating as researchers study more and more , there remain severe limits on researchers' ability to construct satisfying accounts of how diverse animal forms evolved.

The difficulty arises because the major evolutionary changes that established the principal animal groups occurred in the remote past, and there are too few surviving intermediate forms to infer evolution's steps in detail. This has sometimes led zoologists to give imagination too free a rein when they devise their hypotheses, Jenner argues. In other cases, new data have forced biologists to accept accounts they had previously found unimaginable. Imagination will remain important in evolutionary studies, Jenner stresses, but biologists will best advance science if they ensure their proposals are consistent with evolutionary trees that are well supported by molecular data, if they look for incompatible evidence and obvious difficulties, and if they evaluate alternative scenarios, as well as their preferred ones. They should also examine the basis of their intuitions and build their ideas of the broadest possible base of evidence, including, for example, that from newly discovered fossils and from new anatomical information. New fields of inquiry offer hope that progress will be made, but "we desperately need" well-funded organismal biologists to achieve it, according to Jenner, not just bioinformaticians and molecular evolutionists.

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Vietvet
5 / 5 (3) Jul 16, 2014
And here comes verkle in -----1----2---3

Torbjorn_Larsson_OM
4 / 5 (4) Jul 18, 2014
Indeed. Science progression means creationist digression. After millenniums of religious magic unwarranted privilege it doesn't know how to wither and die with honor. Ergo verkle.
JVK
1 / 5 (4) Jul 22, 2014
Why do ..."we desperately need" well-funded organismal biologists...?

With no funding our 1996 model of cell type differentiation via alternative splicings of pre-mRNA and amino acid substitutions attests to the ignorance of biologically-based facts that is touted in the context of mutation-initiated natural selection and the evolution of biodiversity.

Evolutionary theorists seem unable to recognize the fact that ecological variation must be linked to ecological adaptations via cell type differentiation before what they think is "natural selection" occurs. What we need is for evolutionary theorists to educate themselves and accept the biological facts that link conserved molecular mechanisms in species from microbes to man.

From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
http://www.ncbi.n...24693353
JohnGee
5 / 5 (4) Jul 22, 2014
Damn almost got in before JVK.
cjn
5 / 5 (4) Jul 22, 2014
I've seen how genomics is having a radical impact in bacterial cladistics, so it makes sense that it would have a similar impact on "higher" animal clade formation. I feel like this shift in approach is analogous mental jump of targeting the transcriptome of an organism rather than the genome to truly determine what drives phenotypic expression. I'm excited to see where our phenotypic cladistics have masked the "true" genomic and evolutionary history of life.
JVK
1 / 5 (4) Jul 22, 2014
There is no evolutionary history of life. Ecological variation results in ecological adaptations that exemplify the biodiversity of nutrient-dependent pheromone-controlled reproduction, which occurs via conserved molecular mechanisms in species from microbes to man.

Those who insist on using terms associated with mutation-initiated natural selection and the EVOLUTION of biodiversity have failed to provide experimental evidence of biologically based cause and effect, which I detailed in a series of publications.

Note: Israeli middle-school education recently changed. They now teach the theory of evolution to show the difference it makes in the context of what is known about ecology. Simply put, ecological facts eliminate evolutionary theory from any further consideration whatsoever. The Israelis obviously want students to be informed, not misinformed by theorists.

http://www.educat...olution/
JVK
1 / 5 (4) Jul 22, 2014
Science progression means creationist digression.


"I am a creationist and an evolutionist." Dobzhansky (1973) in "Nothing in Biology Makes Any Sense Except in the Light of Evolution" Link opens pdf: http://img.signal...nsky.pdf

What is currently known about amino acid substitutions that differentiate cell types revises Dobzhansky's title.

Nothing about molecular biology makes sense in the light of evolution. Biodiversity is clearly nutrient-dependent and pheromone-controlled. It is not the result of mutations and natural selection. Dobzhansky could not have known that, but the facts continue to be ignored by those who should know what Dobzhansky did. Amino acid substitutions, not mutations, differentiate cell types in primates and all other species. Life is biophysically constrained; it did not arise via mutations and mutations cannot cause biodiversity because they perturb protein folding.
anonymous_9001
5 / 5 (4) Jul 22, 2014
mutations cannot cause biodiversity because they perturb protein folding


This is directly refuted by induced mutagenesis experiments. Not all mutations have drastic negative effects.
Whydening Gyre
5 / 5 (3) Jul 22, 2014
It is clear JVK wishes to revise the definitions of some words and meanings in the English language...
cjn
5 / 5 (4) Jul 22, 2014
There is no evolutionary history of life. Ecological variation results in ecological adaptations that exemplify the biodiversity of nutrient-dependent pheromone-controlled reproduction, which occurs via conserved molecular mechanisms in species from microbes to man.


So let me get this straight: If I were to take an undifferentiated cell from a feline embryo (assume the first initial cell fertilized) and implant it into a dog -assuming that it was possible-, then the product would be a dog at birth? You know, since the cells were exposed to the same nutrients and pheromones.
Whydening Gyre
5 / 5 (3) Jul 22, 2014
mutations cannot cause biodiversity because they perturb protein folding


This is directly refuted by induced mutagenesis experiments. Not all mutations have drastic negative effects.

Correct. Given that, if a mutation does not immediately kill an organism, the epigenetics of that organism have a chance to "adapt" and pass that adaptation on to the next generation. So, apparently, mutation IS a driver. Not the only one, to be sure...
CJN - it would more likely be a dot or a cog...
JVK
1 / 5 (4) Jul 22, 2014
It is clear JVK wishes to revise the definitions of some words and meanings in the English language...


I'm not revising definitions; I'm eliminating them along with their use in invented theories that others were taught to believe in.

"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... No, it wasn't dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact."

http://www.huffin...211.html

Simply put, I'm replacing pseudoscientific nonsense with facts. http://youtu.be/DbH_Rj9U524
JVK
1 / 5 (3) Jul 22, 2014
So let me get this straight:...


This may help:
The epigenetic effects of nutrients on intercellular signaling and stochastic gene expression appear to enable adaptive evolution of tightly controlled organism-level thermoregulation in mammals. Nutrient-dependent single amino acid substitutions and de novo protein biosynthesis exemplify the involvement of the seemingly futile thermodynamic control of intercellular and intrarmolecular interactions in microbes that result in stochastic gene expression.

Thermodynamically "futile" cycles of RNA transcription and degradation (Yap & Makeyev, 2013) may also be responsible for changes in pheromone production that enable accelerated changes in nutrient-dependent adaptive evolution controlled by the microRNA/messenger RNA (miRNA/mRNA) balance (see for review Meunier et al., 2013). Environmental cues, like those that signal the availability of glucose, appear to cause changes in the miRNA/mRNA balance that enable gene expression...
Whydening Gyre
5 / 5 (1) Jul 22, 2014
You are being too contextually confined.
I don't think anyone here is saying that the mutations themselves are what survives. Just that mutation drives adaptation.
JVK
1 / 5 (4) Jul 22, 2014
...induced mutagenesis experiments. Not all mutations have drastic negative effects.


Which mutations contribute to evolution of increased organismal complexity and biodiversity?

How can anyone be so ignorant as to claim that "Not all mutations have drastic negative effects." What difference does the effect of a neutral mutation make in the context of the evolution of biodiversity?

I have modeled how ecological variation leads to ecological adaptations in species from microbes to man, and the anonymous fool (i.e., Andrew Jones) with his BA from a liberal arts college challenges the model by saying "Nuh-uh."

http://www.ncbi.n...4049134/
JVK
1 / 5 (4) Jul 22, 2014
mutation drives adaptation


How? Can you compare what you think mutations do to what ecological variation enables via the conserved molecular mechanisms that lead to morphological and behavioral phenotypes in ecologically-adapted species from microbes to man (e.g., in my model)?

If not, I think you are confused about the differences between theory and biological facts.

JohnGee
5 / 5 (4) Jul 22, 2014
Quit spamming the comments with your nonsense JVK.
anonymous_9001
5 / 5 (3) Jul 22, 2014
challenges the model by saying "Nuh-uh."


You forgot the part where I got a manuscript criticizing yours published in the very same journal yours is published in plus just as many unpublished criticisms plus verifiable accounts from your own coauthors and authors of papers you've misrepresented.

And you still cannot account for non-eukaryotic evolution since your model is based on splicing.
JVK
1 / 5 (4) Jul 22, 2014
You forgot the part where I got a manuscript criticizing yours published in the very same journal...


I provided the link to your comments (above). It would be great for others to see your ignorance expressed without anonymity. For example: "Allele changes are not epigenetic and I know of no mechanism that makes deterministic gene sequence changes prompted by epigenetic alterations."

"Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans" http://www.cell.c...)00806-X and "The common marmoset genome provides insight into primate biology and evolution" http://dx.doi.org.../ng.3042 are among the most recent articles that link nutrient-dependent changes in the microRNA/messenger RNA balance to amino acid substitutions that differentiate the cell types of species from microbes to man via their pheromone-controlled physiology of reproduction.

My model incorporates conserved molecular mechanisms, which include details from 1996
JVK
1 / 5 (4) Jul 22, 2014
"Molecular epigenetics
Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called "chromo domain" proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988)...."
anonymous_9001
5 / 5 (3) Jul 22, 2014
Transcription modification and silencing do not change the DNA sequence.
JVK
1 / 5 (4) Jul 22, 2014
And you still cannot account for non-eukaryotic evolution...


What example of a prokaryote that evolved into another prokaryote are you using as an example of mutation-driven evolution? You are correct that I cannot account for non-eukaryotic evolution, but that's because no experimental evidence of biologically based cause and effects suggests that evolution occurs. All experimental evidence shows that ecological variation results in ecological adaptations manifested in morphological and behavioral phenotypes via amino acid substitutions that differentiated cell types.
JVK
1 / 5 (4) Jul 22, 2014
Transcription modification and silencing do not change the DNA sequence.


What kind of idiot minion of a biology teacher like PZ Myers or anonymous fool like Andrew Jones does not understand that "Effects of starvation can be passed to future generations, through small RNAs apparently without DNA involvement" http://www.scienc...4600.htm

That was a rhetorical question.

Andrew Jones wrote: " A multitude of misconceptions and misunderstandings can be seen in his comments on Dr. PZ Myers' blog, Pharyngula (Kohl, 2014b)." http://www.ncbi.n...4049134/

Compare the comments at http://freethough...-page-1/ to the factual representations at http://www.thethi...ion.com/

Does anyone else think that PZ Myers has a better understanding of biologically-based cause and effect than those who have abandoned neo-Darwinism?
Arties
1 / 5 (1) Jul 22, 2014
Science progression means creationist digression
This is a big simplification. The panspermia hypothesis is still waiting and lurking in shadows in similar way, like the dark matter and aether model for general relativity. In similar way, like the expansion of scope of view at the water surface gradually reveals the hidden dual scope of emergent reality, we may get a new surprises in paradigm of evolution too. After all, this process already started with reveal of hidden role of horizontal gene transfer and "junk" DNA. Not every progress is evolution is driven with phylogenetic tree.
JVK
1 / 5 (4) Jul 22, 2014
'...nematodes have concentration-dependent odor-sensing mechanisms that are segregated at the olfactory receptor and sensory neuron levels."

http://stke.scien...abstract

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. http://www.ncbi.n...24693349

"Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000)."

C. elegans and P. pacificus represent differences in nutrient-dependent pheromone-controlled biodiversity in a grazing nematode compared to a predatory nematode with teeth.
Arties
1 / 5 (1) Jul 22, 2014
For example, I can imagine, that at the beginning the organic life at the Earth evolved as a single huge multiorganism. The well distinguished branches of evolutionary tree, which we are observing by now were merged into continuum similar to foam. The same molecular mechanisms evolved and were stored in junk DNA again and again and reused in different connections. This mechanism of evolution has still counterpart in evolution of marine viruses. Being a proponent of steady state Universe, I can imagine that the primitive forms of life travel across the space and seed new planets continuously, which may resemble the action of intelligent designer. After all, the occasional terraformation visits of extraterrestrial intelligence can be still excluded neither. So that the creationism could have some merit at both ends of complexity spectrum - the terrestrial evolution of life at the Earth may be connected with the rest of Universe via both simplest both most complex organisms in subtle way.
JVK
1 / 5 (4) Jul 22, 2014
Receptor-mediated learning and memory link the epigenetic effects of food odors and pheromones in species from nematodes to humans in this accurate representation of biologically based cause and effect.

Role of synaptic phosphatidylinositol 3-kinase in a behavioral learning response in C. elegans http://stke.scien...abstract

Does anyone know how evolutionary theorists link atoms to ecosystems in their theories about mutation-initiated natural selection and the evolution of biodiversity?

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
http://figshare.c...s/994281
Captain Stumpy
5 / 5 (3) Jul 22, 2014
I'm not revising definitions; I'm eliminating them along with their use in invented theories that others were taught to believe in.
@jk
Nope, sorry... you want to completely redefine the whole lexicon because you never learned it correctly in the first place, and THAT can be proven WITH YOUR OWN WORDS. we shall start here: You say
mutations cannot cause biodiversity because they perturb protein folding
and then say that the ANSWER is your model
Nutrient-dependent/pheromone-controlled adaptive evolution: a model
the only problem is... YOUR MODEL CREATES MUTATIONS! remember.. I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
THIS IS THE DEFINITION OF MUTATION- to which you answered
YES!
--Thanks for asking
SO ANYTHING you push here is based upon a FALLACY and the fact that YOU DON'T KNOW WHAT YOU ARE TALKING ABOUT

PROVEN IN YOUR OWN WORDS

Captain Stumpy
5 / 5 (4) Jul 22, 2014
How can anyone be so ignorant as to claim that "Not all mutations have drastic negative effects."
@JK
Well WHY DON'T YOU ANSWER THIS FOR EVERYONE, JK? because, by YOU supporting your model publicly, then saying
mutations cannot cause biodiversity because they perturb protein folding
then BY DEFINITION you are saying that YOUR OWN MODEL CANNOT CAUSE BIODIVERSITY
YOU are also IGNORANTLY CLAIMING THAT NOT ALL MUTATIONS HAVE DRASTIC EFFECTS, because YOU claim that YOUR MODEL supports biodiversity... and EVERYONE KNOWS your model causes mutations, EVEN YOU! (do I REALLY have to re-post it again?)

and YOU can't even see the blatant fallacy behind your own words posted here!
anonymous_9001
5 / 5 (6) Jul 22, 2014
Genetic changes occur alongside epigenetic changes and nothing in your model can explain those genetic changes because all your model consists of is alternative splicing, which doesn't make changes to the genome and doesn't occur in non-eukaryotic organisms. These are huge flaws in your model.

Add that to your ignorance of what proteasomes do and the means by which Lenski's bacteria adapted to use citrate (hint: it wasn't splicing) and you've shown that you know next to nothing about the most basic biological concepts.

Simple question: What molecular mechanism makes new genes?
JVK
1 / 5 (4) Jul 22, 2014
all your model consists of is alternative splicing


All your comments attest to your ignorance!

"Aminoacyl tRNA synthetases (AARSs) establish the genetic code by esterifying specific amino acids to the 3′ ends of their cognate tRNAs (1–5) and have adaptations of this reaction for specific physiological responses (6). A few literature examples show that natural proteolysis or alternative splicing of AARS can reveal previously unknown AARS proteins (7, 8) with new functions (9–11)." http://stke.scien...abstract
Small [nutrient-dependent] intranuclear proteins participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species and probably contribute to cell type differentiation in all cells of all multicellular species that sexually reproduce.But, even in bacteria, reproduction is nutrient-dependent and pheromone-controlled.

JVK
1 / 5 (4) Jul 22, 2014
http://dx.doi.org....1003802 Cause and effect can be addressed in the context of antigenic properties of the human influenza virus, which are determined by a single amino acid substitution. Mathematical models frame this in the context of mutations theory, but no evidence suggests mutations enable adaptive morphologies. Instead, mutations are typically edited out via nutrient uptake and alternative splicings. They are allowed to remain if they do not perturb intercellular signaling that leads to adaptations. However, it has become apparent that under conditions of nutrient stress or social stress mutations can accumulate and cause diseases and disorders associated with changes in morphology. The mutations clearly represent stress linked accumulation of amino acid changes which are manifested in atypical morphology.
JVK
1 / 5 (4) Jul 22, 2014
The authors use E. coli to exemplify mutation-driven evolution via inclusion of a mathematical model, but they are actually exemplifying how organisms react to the combination of nutrient stress and social stress that parallels heat stress at the molecular level of hydrogen bonds.

The hydrogen bonds are actually typically altered to benefit organism-level thermoregulation via nutrient uptake and amino acid substitutions that link the epigenetic landscape to the physical landscape of DNA in the organized genome of species from microbes to man. For example, ecological variation includes variation in essential vitamins that benefit human immune system function because they facilitate receptor-mediated uptake of other nutrients into the cell.

Thus vitamins and other essential nutrients, when available, allow the differentiation of cell types, individuals, and organisms via amino acid substitutions that are chemically controlled (via species-specific pheromones).
JVK
1 / 5 (4) Jul 22, 2014
Protein folding is based upon the amino acid sequence. "It now appears that alternative splicing is, perhaps, the most critical evolutionary factor determining the differences between human beings and other creatures." http://jonlieffmd...volution

In my model alternative splicings of pre-mRNA and protein folding are nutrient dependent, which links amino acid substitutions from ecological variation in the nutrient supply to ecological adaptations manifested in morphological and behavioral diversity. There is no need to view this in terms associated with any aspect of evolution. Indeed, no aspect of mutation-initiated natural selection has ever been supported with experimental evidence of biologically based cause and effect.

Those who believe they can continue to tout the pseudoscientific nonsense of evolutionary theory when faced with biological facts about protein folding are anonymous fools and the idiot minions of biology teachers like PZ Myers.
JVK
1 / 5 (4) Jul 22, 2014
"...tRNAs also perform additional functions in both prokaryotes and eukaryotes for example in regulating gene expression." Excerpted from:

"Transfer RNAs (tRNA) are best known for their role as adaptors during translation of the genetic code. Beyond their canonical role during protein biosynthesis, tRNAs also perform additional functions in both prokaryotes and eukaryotes for example in regulating gene expression. Aminoacylated tRNAs have also been implicated as substrates for non-ribosomal peptide bond formation, post-translational protein labeling, modification of phospholipids in the cell membrane, and antibiotic biosyntheses. Most recently tRNA fragments, or tRFs, have also been recognized to play regulatory roles. Here, we examine in more detail some of the new functions emerging for tRNA in a variety of cellular processes outside of protein synthesis." http://www.fronti...14.00171
anonymous_9001
5 / 5 (4) Jul 22, 2014
None of that addressed my questions or contradicted anything I said. I'd expect nothing less. Go back and carefully reread my previous post.
JVK
1 / 5 (4) Jul 23, 2014
http://www.cell.c...)00751-9
Compositional homogeneity in all of the amino acids and taxa included was addressed in the context of morphological similarities and behavioral diversities that link differences in the behavior of spiders to nutrient-dependent pheromone-controlled amino acid substitutions and cell type differentiation manifested in in the morphology and receptor-mediated behavior of white-throated sparrows.

This "...novel and radical hypothesis of spider evolution..." does more than simply "...set the roadmap toward an until-now elusive spider tree of life." It reasserts a fact that evolutionary theorists refuse to accept. "Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000)." http://www.ncbi.n...24693349

Who else is addressing facts about the tree of life?
JVK
1 / 5 (4) Jul 23, 2014
Go back and carefully reread my previous post.


"Organismal biologists needed to interpret new trees of life" is the title of this report. My model and examples from model organisms assists organismal biologists. Understanding the model differentiates serious scientists from social scientists who insist on framing everything in the context of theories that have been unsubstantiated by experimental evidence of biologically based cause and effect.

The fact that Andrew Jones (anonymous_9001), with his BA from a liberal arts college, wants me to reread anything he has written attests to his failure to present any evidence whatsoever to support his ridiculous claims that I have misrepresented what is currently known about the "tree of life."

Clearly, life is nutrient-dependent and ecological speciation via adaptation is the outcome attributed to ecological variation in spiders, birds, and all other species on this planet.
JohnGee
5 / 5 (3) Jul 23, 2014
No one reads your posts JVK.

Did you get in trouble for posting your snake oil website? I see you don't post links to it anymore.
cjn
5 / 5 (4) Jul 23, 2014
JVK, for your model to be accurate, it would have to assumed that all instances of life have had interaction with or are pre-programmed to interact with all "nutrient" or "pheromone," with specific cellular behavior (BP/AA substitutions, splicing, etc...) attributable to each stimuli. In doing so, the genome would be forced to retain inordinate amounts of sections which code for nothing useful in the vast preponderance of instances, but must be maintained with absolute accuracy. That is not something that is observed, nor is it something that practical for an organism to maintain.
anonymous_9001
5 / 5 (4) Jul 23, 2014
And he still cannot explain how his model is supposed to account for non-eukaryotic adaptation (if he's going to object to using the word "evolution" for no apparent reason) when they're not capable of splicing.

with his BA from a liberal arts college


Is this supposed to be some sort of insult? James, with his high school diploma (which in Georgia probably means even less than nothing) thinks I should be ashamed of my college education.
JVK
1 / 5 (4) Jul 23, 2014
Re: "... the genome would be forced to retain inordinate amounts of sections which code for nothing useful in the vast preponderance of instances, but must be maintained with absolute accuracy."

Epigenetic effects of nutrients and their metabolism to pheromones link the epigenetic landscape to the physical landscape of DNA in organized genomes. They eliminate the need for maintained sections of code.

There is no need to assume that this is the case because it is exemplified in organisms from microbes to man in my model of cell type differentiation via amino acid substitutions. Comments like yours exemplify ignorance that extends to not even reading about the model before commenting that assumptions of its accuracy must be made.

Assumptions are for social scientists (and liberal arts majors), facts are presented by serious scientists. I am a medical laboratory scientist.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353
JVK
1 / 5 (4) Jul 23, 2014
... thinks I should be ashamed of my college education.


No. You should be ashamed that you wasted someone's money and are now attempting to discuss biological facts with someone who has a history of published works, including two award-winning works, that extends back to 1995 book publication with co-author Dr. Robert T. Francoeur.

If you were not ashamed, you would not need to continue posting as if you were like all the other anonymous fools and idiot minions that congregate here.

Kudos, however, for the magnificent display of your ignorance published as Andrew Jones.

The display is unparalleled given the extent of my publications and your ignorance of biologically based cause and effect.

I hope others read what you wrote http://www.ncbi.n...4049134/ in response to my conclusion:

"Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'."
JohnGee
5 / 5 (3) Jul 23, 2014
I think the snake oil salesman should be ashamed, but alas you have no shame.
JVK
1 / 5 (4) Jul 23, 2014
"Trained in embryology, evolution, theology, and the humanities, Francoeur's main work was to synthesize and integrate the findings of primary sexological researchers. He is the author of twenty-two books, contributor to seventy-eight textbooks, handbooks, and encyclopedias, and the author of fifty-eight technical papers on various aspects of sexuality. His books include The Scent of Eros: Mysteries of Odor in Human Sexuality (1995)..."
http://en.wikiped...rancoeur

See also the information on co-author Milton Diamond
http://en.wikiped..._Diamond

and the link to a 2001 award-winning review at http://en.wikiped...heromone

"Furthermore it has been suggested that in the evolution of unicellular prokaryotes to multicellular eukaryotes, primordial pheromone signaling between individuals may have evolved to paracrine and endocrine signaling within individual organisms.[23]"
JVK
1 / 5 (4) Jul 23, 2014
"The evolution of the C4 pathway requires many changes. These include the recruitment of multiple enzymes into new biochemical functions, massive shifts in the spatial distribution of proteins and organelles, and a set of anatomical modifications to cell size and structure. It is complex, and it is also highly effective: C4 plants include many of our most important and productive crops (maize, sorghum, sugarcane, millet) and are responsible for around 25% of global terrestrial photosynthesis (Still et al., 2003)."

http://elifescien...3/e03702

The ecological variation that led to ecological adaptations via amino acid substitutions should be viewed in the context of light-induced amino acid substitutions that link nutrient-dependent plant life to nutrient-dependent pheromone-controlled animal life via the example of light induced amino acid substitution in algae.

http://www.pnas.o...abstract
JohnGee
5 / 5 (3) Jul 23, 2014
JVK sells refined human semen as a love potion. Snake oil, lol.
anonymous_9001
5 / 5 (4) Jul 23, 2014
Assumptions are for social scientists (and liberal arts majors)


My school is classified as a liberal arts school, but I did not major in any sort of liberal arts. My major was biology. I did independent research in plant physiology amd microbiology and now I have my own history of published works with my peer reviewed letter to the editor.
JVK
1 / 5 (4) Jul 23, 2014
http://elifescien...3/e03702
"Insights often stem from experimental lab studies that manipulate systems under 'directed evolution' (Weinreich et al., 2006; Blount et al., 2012; Finnigan et al., 2012). However, complex traits that have evolved many times over in independent lineages present a different—yet equally powerful—opportunity to infer the evolutionary trajectories of novel traits."

Blount et al., 2012 (above), is a citation to work with Lenski that has confused anonymous fools and idiot minions of biology teachers like PZ Myers. A three-step process—in which potentiation makes a trait possible, actualization makes the trait manifest, and refinement makes it effective—is probably typical of many new functions, but the biophysical constraints that make the trait effective are not linked from ecological variation to ecological adaptation.

Thus, uninformed social scientists continue to attribute multi-step processes to mutations, natural selection, and evolution.
JVK
1 / 5 (4) Jul 23, 2014
...now I have my own history of published works with my peer reviewed letter to the editor.


Did you minor in comic relief? In response to my detailed model of cell type differentiation via amino acid substitutions that was based on my history of published works, you wrote a letter that said "Nuh-uh."

I think it was published as a joke, albeit one that was necessary since many others may share your ignorance of biologically-based cause and effect. One way to bring attention to accurate factual representations is for anonymous fools and idiot minions to comment on published works. Thank you for doing so.

Did you stop to think about why no serious scientist commented -- one of my former co-authors, perhaps? Or anyone who perceived flawed logic that the reviewers missed?

Do you think biophysical constraints that prevent mutation-initiated natural selection are the reason Israeli middle schools now teach evolutionary theory as a joke -compared to what is known about ecology?
JohnGee
5 / 5 (3) Jul 23, 2014
JVK literally sells semen for men to wear on dates.
cjn
5 / 5 (4) Jul 23, 2014
JVK: ... In response to my detailed model of cell type differentiation via amino acid substitutions...


If all that was needed to alter the phenotypic expression of an individual within a species was to allow "nutrients" and "pheromones" to influence transcription and splicing changes (and thus AA's for proteins), then why does each species have a unique genome? That would be unnecessary in your model, correct?
anonymous_9001
5 / 5 (4) Jul 23, 2014
In response to my detailed model of cell type differentiation via amino acid substitutions that was based on my history of published works, you wrote a letter that said "Nuh-uh."


Instead of going through my fully cited letter and refuting my refutations, all you've been able to say is this.

Did you stop to think about why no serious scientist commented -- one of my former co-authors, perhaps?


Having short term memory problems? Need I bring up my correspondences with Fink or Chelo again?
Captain Stumpy
5 / 5 (3) Jul 23, 2014
No. You should be ashamed that you wasted someone's money and are now attempting to discuss biological facts with someone who has a history of published works, including two award-winning works, that extends back to 1995 book publication with co-author Dr.
@jk
this is the appeal to authority. the only problem is... you are NOT an authority. just some glorified lab tech hanger on... your "publications" and awards mean NOTHING... especially given that you have NO IDEA who you are talking to.
You commented on some posts of mine with serious derogatory remarks, except that the information came from a PhD with FAR MORE AWARD WINNING POSTS than even you...
Then there is the fact that I've published more frequently... so what. there is NO argument against logic and empirical data
YOU cannot even get your own field lexicon correct and you want to correct everyone else on biology? that's like hiring a non-citizen who only speaks Korean to grade spelling and grammar
JVK
1 / 5 (4) Jul 23, 2014
Need I bring up my correspondences with Fink or Chelo again?


Yes, thanks for asking. Why didn't you cite personal correspondence in your ridiculous criticisms? Why didn't you cite their published works? Why did you provide a link to the atheist blogger PZ Myers site where he challenged the concept of chromosomal rearrangements within weeks of a publication that detailed their predictable effects outside the ridiculous concepts of mutations and natural selection?

Why did you not address anything about the experimental evidence that links amino acid substitutions to the thermodynamics of organism-level thermoregulation and genomic stability?

For example, a single nucleotide substitution between G--> A results in an amino acid change from valine to methionine at codon 158. The A or Met allele is associated with lower enzymatic activity (due to thermoinstability), with exploratory behaviour and cell type differentiation in the hippocampus.
Captain Stumpy
5 / 5 (3) Jul 23, 2014
You should be ashamed that you wasted someone's money and are now attempting to discuss biological facts with someone
@jk
LETS DISCUSS this shame thing...
WHICH is more shameful:
A FACTUAL POST that is denied by some pseudoscience crackpot like you?
or a person who ATTEMPTS to explain a biological series of studies who cannot even get the definitions of his own field used terminology correct?
I would say that the FAILED DROPOUT glorified lab-tech that cannot get his lexicon correct is the bigger failure and shamed one... especially when you CONTINUALLY argue against MUTATION when YOUR OWN MODEL CAUSES MUTATION!
That is the mark of a truly pseudo-scientific idiot who does NOT know what is really going on!

By all means, continue to post. YOU ONLY UNDERMINE YOUR OWN ARGUMENT WITH YOUR OBVIOUS IGNORANCE.

You have a FAITH not supported by empirical evidence. you call it your model. Your model is already a small part of EVOLUTION theory supporting MUTATIONS, you moron!

EPIC FAILURE
Captain Stumpy
5 / 5 (3) Jul 23, 2014
Why did you provide a link to the atheist blogger PZ Myers site where he challenged the concept of chromosomal rearrangements within weeks of a publication that detailed their predictable effects outside the ridiculous concepts of mutations and natural selection?
@jk
and on THAT note... let it ALSO BE KNOWN that YOU HAVE YET TO REFUTE PZ MYERS and his comments on your stupidity and known PSEUDOSCIENCE

WHY IS THAT?

I would say that Myers had your number and described you QUITE WELL!
http://freethough...-page-2/

EVEN YOU cannot refute EMPIRICAL DATA
and EMPIRICAL DATA PROVES that you dont know what you are talking about... after all, YOUR OWN MODEL IS USED TO PROVE AND SUPPORT EVOLUTION USING MUTATION BECAUSE, IN YOUR OWN WORDS, YOUR MODEL CAUSES MUTATIONS!

shall I prove that AGAIN? link all the pages where I proved it already?

you are an epic failure in pushing your pseudoscience
JVK
1 / 5 (4) Jul 23, 2014
http://www.jneuro...abstract

The link is to an open access article and some discussion of the nutrient-dependent amino acid substitution associated with lower enzymatic activity (due to thermoinstability), with exploratory behaviour, and with cell type differentiation in the hippocampus.

Cell type differentiation is obviously nutrient-dependent and it is controlled by social odors in mammals, which is how nutrient stress and social stress are linked via epigenetic effects on hormones to affect hormone-driven changes in behavior.

"Notably, these effects were driven by both recent and childhood events, suggesting that environmental effects on hippocampal volume occur throughout life and probably last for years (Teicher et al., 2012; Gray et al., 2013)."

Anyone unable to think in terms of epigenetically-effected alternative splicings of pre-mRNA and amino acid substitutions that differentiate cell types is destined to remain horribly under informed.
JVK
1 / 5 (4) Jul 23, 2014
If all that was needed to alter the phenotypic expression of an individual within a species was to allow "nutrients" and "pheromones" to influence transcription and splicing changes (and thus AA's for proteins), then why does each species have a unique genome? That would be unnecessary in your model, correct?


We've been through this before. Read what I've published and ask questions about the representations based on what you don't understand. Do not trouble me with open ended questions based on your assumptions of what I have included in the model.

"...why does each species have a unique genome?"

Biodiversity is nutrient-dependent and pheromone-controlled, because species-specific pheromones control the nutrient-dependent physiology of reproduction.
JVK
1 / 5 (4) Jul 23, 2014
Unless someone with more intelligence than those who already have commented enters discussion of the topic: "Organismal biologists needed to interpret new trees of life" intelligent others can follow scientific progress via my blog posts at Pheromones.com or on my Facebook page: https://www.faceb...bookmark
Captain Stumpy
5 / 5 (3) Jul 23, 2014
Unless someone with more intelligence than those who already have commented enters discussion of the topic
@jk
so you can't refute logic or legitimate empirical data with your pseudoscience so you are going to run away?
WHY POST AT ALL if you will not PROVE YOUR POINT?
is it because REAL SCIENTISTS like MYERS keep proving you an idiot? or because YOU YOURSELF continually prove yourself an idiot by NOT KNOWING what you are talking about and by LYING?
intelligent others can follow scientific progress via my blog posts at Pheromones.com or on my Facebook page: https://www.faceb...bookmark
SPAM AND TROLLING PAGES
also reported for being SPAM AND TROLLING PAGES

these are KNOWN pseudoscience sites!
KNOWN FOR PUSHING PSEUDOSCIENCE because the poster here cannot validate his claims, and because the claims are debunked with valid empirical data.

run away tiny jim, this is a SCIENCE SITE, and pseudoscience and lies are NOT welcome
JVK
1 / 5 (2) Jul 24, 2014
Refutations of evolutionary theorists illogical claims were published in a special issue of the Journal of Physiology on June 1, 2014. http://jp.physoc....2/11.toc

From what I see in the abstracts, the authors may have separately covered many of the topics and experimental evidence that I integrated in an invited review on nutritional epigenetics. When reviewers refused to review it, I published it to figshare.com because I knew that the information reviewers would rather not see was forthcoming (e.g., in bits and pieces that are not integrated into any model). See for example this 5.5 minute video presentation of my model. http://youtu.be/DbH_Rj9U524

I added more details to the submission that went unreviewed, which is here. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

http://figshare.c...s/994281

Let me know if I missed anything.
JohnGee
not rated yet Jul 24, 2014
I thought you took your ball home JVK? Please leave and stop spamming the website you gross immoral semen salesman.