Spanish hunter-gatherer had blue eyes and dark skin

Jan 26, 2014
La Braña 1, the name used to baptize a 7,000-year-old individual from the Mesolithic Period, had blue eyes and dark skin. Credit: Spanish National Research Council

La Braña 1, name used to baptize a 7,000 years old individual from the Mesolithic Period, whose remains were recovered at La Braña-Arintero site in Valdelugueros (León, Spain) had blue eyes and dark skin. These details are the result of a study conducted by Carles Lalueza-Fox, researcher from the Spanish National Research Council (CSIC), in collaboration with the Centre for GeoGenetics (Denmark). La Braña 1 represents the first recovered genome of an European hunter-gatherer. The research is published in Nature.

The Mesolithic, a period that lasted from 10,000 to 5,000 years ago (between the Paleolithic and the Neolithic), ends with the advent of agriculture and livestock farming, coming from the Middle-East. The arrival of the Neolithic, with a carbohydrate-based diet and new pathogens transmitted by domesticated animals, entailed metabolic and immunological challenges that were reflected in genetic adaptations of post-Mesolithic populations. Among these is the ability to digest lactose, which La Braña individual could not do.

Lalueza-Fox states: "However, the biggest surprise was to discover that this individual possessed African versions in the genes that determine the light pigmentation of the current Europeans, which indicates that he had dark skin, although we can not know the exact shade".

CSIC researcher, who works at the Institute of Evolutionary Biology (a joint centre of CSIC and the University Pompeu Fabra (UPF), located in Barcelona, adds: "Even more surprising was to find that he possessed the genetic variations that produce blue eyes in current Europeans, resulting in a unique phenotype in a genome that is otherwise clearly northern European".

The skeleton of La Braña 1, as it was discovered in 2006. Credit: J.M. Vidal Encina

The study of the genome suggests that current populations nearest to La Braña 1 are in northern Europe, such as Sweden and Finland. In addition, the work points out that La Braña 1 has a common ancestor with the settlers of the Upper Paleolithic site of Mal'ta, located in Lake Baikal (Siberia), whose genome was recovered a few months ago. Lalueza-Fox concludes: "These data indicate that there is genetic continuity in the populations of central and western Eurasia. In fact, these data are consistent with the archeological remains, as in other excavations in Europe and Russia, including the site of Mal'ta, anthropomorphic figures –called Paleolithic Venus– have been recovered and they are very similar to each other".

DNA with an "exceptional" preservation

La Braña-Arintero site was discovered by chance in 2006 and excavated by Julio Manuel Vidal Encinas, archeologist of the Council of Castilla y León. The cave, located in a cold mountainous area with a steady temperature and 1,500 meters below the sea level, contributed to the "exceptional" preservation of the DNA from two individuals found inside, and they were called La Braña 1 and La Braña 2.

Frontal view of the La Braña 1 skull. Credit: J.M. Vidal Encina

According to Iñigo Olalde, lead author of the study, "the intention of the team is to try to recover the genome of the individual called La Braña 2, which is worse preserved, in order to keep obtaining information about the genetic characteristics of these early Europeans".

Explore further: Genetic study pushes back timeline for first significant human population expansion

More information: Paper: dx.doi.org/10.1038/nature12960

Journal reference: Nature search and more info website

Provided by Spanish National Research Council

4.8 /5 (34 votes)

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The Shootist
5 / 5 (3) Jan 26, 2014
Caucasian: a general physical type of some or all of the people of Europe, North Africa, the Horn of Africa, Western, Central, and South Asia. This term was used in biological anthropology for to describe the many peoples from these regions, usually without regard to skin tone.

Dark skin - blue eyes. Like the Afghanistani girl in the famous NatGeo photo. .
JVK
1.7 / 5 (6) Jan 26, 2014
Journal article abstract excerpt: "The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet."

See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.socioa...53/27989

In that recent review, I detailed how nutrient-dependent epigenetically-effected alternative splicings in pre-mRNA led to amino acid substitutions and chromosomal rearrangements manifested in the species-specific cell types of different individuals in different species with specific morphological and behavioral phenotypes.

As has since exemplified in published works on birds and bees, mutation-driven evolution is no longer considered to be ecologically valid or biologically plausible, since ecological adaptations are clearly nutrient-dependent and pheromone-controlled in species from microbes to man.
Whydening Gyre
2.5 / 5 (4) Jan 27, 2014
I detailed how nutrient-dependent epigenetically-effected alternative splicings in pre-mRNA led to amino acid substitutions and chromosomal rearrangements manifested in the species-specific cell types of different individuals in different species with specific morphological and behavioral phenotypes.

Nicely described. Agree.
As has since exemplified in published works on birds and bees, mutation-driven evolution is no longer considered to be ecologically valid or biologically plausible, since ecological adaptations are clearly nutrient-dependent and pheromone-controlled in species from microbes to man.

Again, agree.
I believe previous disagreements on the subject were a misunderstanding of your more inclusive (therefore refined) definition of mutation, on my part. I now see this in a larger context and where you are going with it.
However, keep in mind... your level of understanding and therefore clarity are not readily available to others not in your field.
JVK
1.8 / 5 (5) Jan 27, 2014
Thanks. My "level of understanding and therefore clarity are"... "readily available to others not in" my field who are willing to read my published works, beginning with book publication for a general (albeit educated) audience in 1995. Note, for example, a corrected problem with word use "affect" vs "effect" to more accurately portray "biological embedding," which is actually epigenetic imprinting. http://www.pnas.o....2.short http://www.pnas.o...1.2.full

It's a simple as that! Correct the problem for people who don't know the difference between epigenetic effect and affects on behavior and move on.

If Nei and Nozawa had not dispensed with ecological factors, more would be known about the molecular mechanisms of speciation sans mutations http://gbe.oxford...abstract
Instead, theorists continue to believe in their well-established nonsense as if their belief in effects of mutations made the nonsense any less nonsensical.
Hot Rod
4 / 5 (2) Jan 27, 2014
Supplementary figure 6 seems to show a close relatedness between La Braña 1 and the Chinese. If the Basque are the last survivors of the Palaeolithic population, this might strengthen the theory that the Basque are (linguistically) related to the Chinese.
PS. I assume the cave is 1500 m ABOVE sea level - not BELOW. :-)
Torbjorn_Larsson_OM
4.2 / 5 (5) Jan 27, 2014
It is really nice that genetics are accessible and interesting for laymen. They also add value to the papers, as they can add and analyze with open data. For example, I learned that swedes (my area) have as much WHG (the hunter population) as neighboring finns, but there is a split between EEF ("Sardinian") and ANE (north-east asian, I believe): http://www.anthro...ost25390 .

Not so nice is to go to a science site and see the pheromone spamming. (It tries to sell 'pheromones' through a web site, despite that humans seems to be insensitive.)
JVK
1.8 / 5 (5) Jan 27, 2014
Insensitivity to human pheromones??? See "The Scent of Disease: Human Body Odor Contains an Early Chemosensory Cue of Sickness" http://pss.sagepu...abstract

Torbjorn has repeated the same claims about me in other posts across a variety topics, but never addressed the content of my published works, including award-winning published works in 2001 and 2006. With the clarity of evidence in this report, it is long past time for others to comment on biological facts; admit they were formerly unaware of them; and apologize for antagonizing people like me with their ignorance.

There is simply no excuse to continue to make ignorant comments when experimental evidence can be discussed. However, has anyone ever heard about academic who has admitted to being wrong throughout a career of touting nonsense? Is that why some people so clearly despise fools like Larsson?
JVK
2.3 / 5 (3) Jan 28, 2014
See: "Table 1 | Mesolithic genome allelic state at 10 nonsynonymous variants recently selected in Europeans"

It lists the nutrient-dependent SNPs; amino acid substitutions; and function(s), which in my model are epigenetically-effected by the metabolism of nutrients to pheromones that control the physiology of reproduction in species from microbes to man.

Now, wait for Torbjorn or any other evolutionary theorist to say something intelligent about any aspect of these results.

"Olfactory-Based Fat Discrimination in Humans" links fat detection and nutrient uptake from the bottom up via conserved molecular mechanisms. http://dx.doi.org....0085977

Our sensitivity to human body odors links them to the pheromone-controlled physiology of reproduction via the same signaling pathway found in yeasts. (see our 1996 Hormones and Behavior review: http://www.hawaii...on.html)

Ecological adaptation or evolution?

JVK
2.3 / 5 (3) Jan 28, 2014
http://www.hawaii...ion.html

Title: From Fertilization to Adult Sexual Behavior

Authors: Milton Diamond Ph.D., Teresa Binstock, and James V. Kohl

Published in: Hormones and Behaviour, 30, 333-353 (1996)

"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. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes."

Sexual differentiation appears to involves ecological variation that also results in chromosomal rearrangements. If it involves mutations, Larsson may tell us whether the males or the females of different species are mutant conspecifics (if he's not intelligent enough to acknowledge his ignorance).
Captain Stumpy
3 / 5 (2) Jan 28, 2014
@jvk
effected alternative splicings in pre-mRNA l

in other words, there was a MUTATION

In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element. Mutations result from unrepaired damage to DNA or to RNA genomes (typically caused by radiation or chemical mutagens), errors in the process of replication, or from the insertion or deletion of segments of DNA by mobile genetic elements.[1][2][3]


https://en.wikipe...Mutation

therefore your statement
mutation-driven evolution is no longer considered to be ecologically valid or biologically plausible

is blatantly wrong
Captain Stumpy
3.7 / 5 (3) Jan 28, 2014
@Whydening Gyre
before you get sucked into the whole JVK anti-mutation pheromone hypothesis, PLEASE read the following link, written BY A BIOLOGIST who is well versed and understands just what is being said... read the link first then make an informed decision!!!!

http://freethough...-page-1/

the above link describes what JVK says and refutes the basis of his argument using easy to understand language by a professional in the field.

we have argued with JVK about mutation before (i am sure you remember) but mostly all this posting he does above is about his pheromone sprays and his PSEUDOSCIENCE hack CRACKPOT hypothesis etc

RealScience
4.2 / 5 (5) Jan 28, 2014
@Whydening:
JVK thinks that nature never makes use of mutations, so JVK has a RESTRICTIVE view of what nature does.
I suggest that you read through the comments in:
http://phys.org/n...ene.html
It's rather long, but it shows clearly the fallacy of JVK's position (and it saves retyping the same comments in this thread).


@Captain:
While JVK is totally wrong about nature using mutations, he is not totally wrong on everything. Mutations are not the whole story - genomes do quite a bit of adapting based on which existing genes and splicings they activate at which times.

Unfortunately JVK's refusal to address the reality that nature does select for some mutations means that almost everyone ignores his valid point that genomes have remarkable homeostasis mechanisms based on genome expression and splicing that provide a great deal of adaptability even without DNA sequence changes.
JVK
2.3 / 5 (3) Jan 28, 2014
The theorists who defamed me on PZ Myers (the biology teacher's) blog do not realize that their theory is not biologically plausible or ecologically valid. Besides, my model has nothing to do with an anti-mutation hypothesis. See: "Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era" http://gbe.oxford...abstract

"...will not consider geographical and ecological factors because of space limitation. Our primary purpose is to clarify the roles of mutation and selection..." That's an anti-ecological variation hypothesis.

PZ Myers and his under informed minions won't consider ecological factors because they prefer the nonsense of theory to biological facts that link food odors and pheromones to ecological adaptations in species from microbes to man. Clearly, if you must remove ecological varlation to clarify anything about mutation and selection, you are only clarifying that you prefer theory to facts.
RealScience
3.7 / 5 (3) Jan 28, 2014
my model has nothing to do with an anti-mutation hypothesis.


@JVK - in a recent thread you posted:
I stand amazed by the fact that bird watchers still have not considered the primary role of ecological variation (e.g., nutrient availability) in morphological changes due to single amino acid substitutions, which are controlled via their epigenetic effect on the physiology of reproduction.


Does that mean that you now acknowledge that single amino acid substitutions are sometimes selected for in evolution? Even if it is a secondary role?

If so, do you hold that all single-amino-acid substitutions are deliberately made by the cell?
Or have you changed your mind about mutations?
Captain Stumpy
3.7 / 5 (3) Jan 28, 2014
@RealScience
While JVK is totally wrong about nature using mutations, he is not totally wrong on everything

yes, and i am fully aware of this
i just wanted WGyre to be more aware of what jvk was up to.

Thank you for posting that link above... going through it now

as for the rest (last paragraph - jvk's refusal, etc)
Good point. and pretty true as well...
JVK
2 / 5 (4) Jan 28, 2014
Now the anonymous RealScience wants to tell everyone about my RESTRICTIVE VIEW of what nature does, after Horton et al (2014) showed what nature does and how nature does it -- via chromosomal rearrangements, which is what we detailed in our 1996 review.

http://www.pnas.o...abstract

Excerpt: "The evolution of behavior relies on changes at the level of the genome; yet the ability to attribute a behavioral change to a specific, naturally occurring genetic change is rare in vertebrates. In the white-throated sparrow (Zonotrichia albicollis), a chromosomal polymorphism (ZAL2/2m) is known to segregate with a behavioral phenotype. Individuals with the ZAL2m haplotype engage in more territorial aggression and less parental behavior than individuals without it. These behaviors are thought to be mediated by sensitivity to sex steroids, and the chromosomal rearrangement... [sans mutations as in every other species on the planet]
JVK
1 / 5 (1) Jan 28, 2014
Before these anonymous fools take this further, I will add that my participation on PZ Myers nonsensical blog, occurred because he called me a crank, akin to another crank who touted the role of chromosomal rearrangements in speciation.

I had discussed Horton's poster presentation with him at the annual SBN meeting in June 2013, since I have followed Donna Maney's work for several years. I already knew that her group had detailed the role of chromosomal rearrangements in speciation (see the link above) before the debate on PZ Myers' blog, which degraded when more and more anonymous fools joined in to support Myers in his ignorant attack on the obviousness of ecological variation and its role in chromosomal rearrangements and speciation sans mutations.

As we've already seen, however, these anonymous fools are as relentless with their attacks as their leader: PZ Myers, and they are equally uninformed but they refuse to inform themselves -- as does Myers.
RealScience
5 / 5 (3) Jan 28, 2014
Do you now agree that natural selection can select FOR mutations?


No. (JVK Feb 8 2013)


Do you still think that natural selection never selects FOR a mutation?
If so, your view is still restrictive.

JVK
1 / 5 (2) Jan 28, 2014
My view is restricted to the biological facts. I have detailed every step involved in the ecological adaptations that are represented here as skin pigmentation and eye color in the article that is the topic of discussion.

If you think these differences somehow arose due to natural selection for mutations instead of via nutrient-dependent pheromone-controlled biologically-based epigenetic cause and effect, which includes epigenetic effects on morphological and behavioral phenotypes detailed in Horton et al (2014), tell us what experimental evidence supports your ridiculous belief in a nonsensical theory, and we can proceed to discuss it -- not here, and not on PZ Myer's idiotic blog, but somewhere else that other intelligent people might be found instead of anonymous fools.

Try my blog at Pheromones.com, for example or my Facebook page https://www.faceb...Research
RealScience
5 / 5 (3) Jan 28, 2014
If you think these differences somehow arose due to natural selection for mutations instead of via nutrient-dependent pheromone-controlled biologically-based epigenetic cause and effect

As I have said repeatedly, IN ADDITION TO rather than "instead of".

When evidence that natural selection sometimes selects for a mutation has been pointed out in real-world examples (and even in references you have cited), you have repeatedly failed to refute it (any reader can see this in:
http://phys.org/n...ces.html

You have said:
I can throw out results that appear to attest to mutations as the cause of adaptive evolution because no evidence suggests that is possible.


That selection for mutations happens is evidence that it is possible. So you throw out evidence that it is possible, and justify this because no evidence suggests it is possible.

Open your mind!
JVK
1 / 5 (2) Jan 28, 2014
What kind of idiot writes things like this? "That selection for mutations happens is evidence that it is possible." That was a rhetorical question.

You are a confused student who will probably never realize that the null model of speciation that you believe in -- because you were taught to believe in it -- is based on nothing and it has not been ecologically validated because it is not biologically plausible.

"Dobzhansky [8] and Muller [9], partially preceded by Bateson [3,7,10] proposed that hybrid sterility and inviability are caused by incompatible alleles alternatively fixed in two previously isolated populations (BDM model). The BDM model is so straightforward that it became the null model of speciation [7]..."

http://linkinghub...10001795

The BDM model is clearly the answer for those teaching "evolution for dummies" and for the dummies that are taught to believe in mutation-driven evolution.
RealScience
5 / 5 (2) Jan 31, 2014
What kind of idiot writes things like this? "That selection for mutations happens is evidence that it is possible."


@JVK, if you can't see that something happening is evidence that it is possible for that thing to happen, it is pretty obvious that you have blinders on.

Open your eyes and open your mind to what nature DOES use, rather than trying to tell nature what it can and cannot use.
JVK
not rated yet Jan 31, 2014
@JVK, if you can't see that something happening is evidence that it is possible for that thing to happen, it is pretty obvious that you have blinders on.


What's interesting here is the fact that you do not address the experimental evidence that might support what you think you see. You address the automagical nonsense of the BDM proposal, which ignores conserved molecular mechanisms and focuses on observation-based beliefs.

Why not simply say: "If I think it happens; it happens, because I thought I saw it happening!" ?
RealScience
5 / 5 (2) Jan 31, 2014
What's interesting here is the fact that you do not address the experimental evidence that might support what you think you see.


I already cited such evidence for you months ago (in threads that I linked to above).
For example: http://www.plospa....1002158

I have also pointed out evidence that it occurs in natural selection itself, rather than just in laboratory experiments. For example:
http://www.nature...-8756219

which ... focuses on observation-based beliefs.

Since you refuse to see evidence that disagrees with your preconceived ideas, it is not surprising that you would reject observation of what nature actually does.

Quit trying to tell nature not to use mutations - nature doesn't listen to you.
Open your eyes instead, and look at what nature actually does use.
JVK
not rated yet Jan 31, 2014
We have an example of someone who believes that the ecological adaptations of hemoglobinopathies and antibiotic resistance occur via mutation-initiated natural selection, when no experimental evidence supports that ridiculous assumption. There are currently 1180 different hemoglobin variants in different populations and in all animals these variants are clearly linked to ecological variants, including the altitude at which hummingbirds live in the Andes.

Gene duplication is clearly nutrient-dependent in cases where antibiotic resistance develops which links it to aerobic glycolysis, amino acid substitutions, and chromosomal remodeling associated with the hemoglobin variants in birds. Thus, we have someone who is not capable of understanding a systems biology approach. This fool would be very likely to tell us that because sodium explodes in water and chlorine is a poisonous gas that NaCl cannot possibly be linked across species to ecological adaptations or human deaths via CVAs.
Whydening Gyre
5 / 5 (3) Jan 31, 2014
epigenetic adaptation due to ecological/nutrient variation result in transcription changes which PRODUCE a DNA "mutation" which can then be "selected". The "mutation" that survives - wins.
Will that work?
RealScience
5 / 5 (2) Jan 31, 2014
We have an example of someone who believes that the ecological adaptations of hemoglobinopathies and antibiotic resistance occur via mutation-initiated natural selection


As do the authors, or did you miss prominent heading "Mutant Beta-globin Leads to Positive Natural Selection" in the article?

You are an example of someone who refuses to see any evidence that disagrees with your preconceived ideas.

I asked you months ago to explain where the multiple sickle-cell variations in human hemoglobin come from if not from mutations, and you failed to do so (http://phys.org/n...e.html).
Even the paper YOU referenced (http://www.ncbi.n...622298/) last exchange ascribes the variation in gene sequences to mutation, that some variants provide malarial resistance, and that these variant are most common in areas where malaria is endemic.
RealScience
5 / 5 (2) Jan 31, 2014
epigenetic adaptation due to ecological/nutrient variation result in transcription changes which PRODUCE a DNA "mutation" which can then be "selected". The "mutation" that survives - wins.
Will that work?


Certainly - many species will, when stressed, undergo much higher mutation rates. Mutations are also far from random - occurring less often and being fixed more rapidly in critical areas of the genome, and being tolerated (or even encouraged) in areas where recent variety has proved beneficial.
JVK
not rated yet Feb 01, 2014
No experimental evidence suggests mutations are ever fixed in the DNA of any organized genome in any organism.

An experimental test on the probability of extinction of new genetic variants http://www.nature...417.html

"Ivo Chelo explains: "Our data suggests that the value a new allele brings to the individuals is not fixed." http://www.scienc...5804.htm

The "mutation" that survives - wins. Will that work?


Of course not! But thanks for asking. The amino acid substitutions that contribute to organism-level thermoregulation survive, because that works. That's also why the different cell types with the hemoglobin variants work, and realistically it's how everything in life works.

Perhaps, organism-level thermoregulation is like a Law of Biology, since protein folding is perturbed in some organisms at different temperatures. Does anyone here understand biophysical constraints, like fever and death?
RealScience
5 / 5 (1) Feb 01, 2014
Did you read the paper of your first link?
It says: "Haldane reasoned that the probability of fixation of new beneficial alleles is twice their fitness effect... Our study CONFIRMS the key results from classical population genetics"
The Chelo paper discusses the probability of fixation in the case where an allele is beneficial regardless of frequency, and shows the expected probability of fixation over 100 and 1000 generations. The expected probability of fixation is quite high even for a 15% benefit, although this experiment was not run long enough to confirm the model.

Thus even YOUR reference SUPPORTS that fixation of beneficial alleles can occur with high probability (see graphs 2b and 4a), although it was not run long enough to prove it.

As for the second reference, 'not fixed' in the phrase you quote means 'not constant', rather than 'does not become fixed in the genome' (the allele's value was positive when the allele was rare and negative when the allele was common).

RealScience
5 / 5 (1) Feb 01, 2014
The amino acid substitutions that contribute to organism-level thermoregulation survive, because that works.


Great- it may be more productive to start with something we agree on.

To be sure, please confirm that:
1) You agree that amino acid substitutions can produce beneficial changes?
2) You agree that these beneficial changes can be selected for by natural selection?
JVK
not rated yet Feb 01, 2014
I agree that you are too ignorant to read my most recent published review and ask me about how I linked the common molecular mechanisms of speciation from microbes to man without incorporating mutations theory.

http://www.socioa...53/27989

I used the C. elegans model organism as an example of how ecological and social niche construction are manifested in neurogenic niche construction due to ecological variations sans mutations.
JVK
not rated yet Feb 01, 2014
Adaptive Capacity to Bacterial Diet Modulates Aging in C. elegans.
http://www.ncbi.n...24440036

Of course, anonymous fools like "RealScience" will attribute the dietary modulation of aging to beneficial mutations and to deleterious mutations, and the idiots on PZ Myers blog will jump in and cheer for the anonymous fools until they reach their inevitable end, which is when they crawl back into the woodwork like the insignificant little "roaches" they are.

Not that there's anything wrong with that. We need the insignificant little roaches to exemplify nutrient-dependent pheromone-controlled ecological adaptations, that have obviously not occurred in their human counterparts, like "Captain Stumpy" and his conspecifics who believe that all roach-like creatures and all other creatures have mutated into existence after being naturally selected to exist.

JVK
not rated yet Feb 01, 2014
http://comments.s...6170.471

These results appear to conflict with previous reports of biologically plausible non-random experience-dependent receptor-mediated species divergence due to ecological variation and adaptations. At least two of those reports were co-authored by Dr. Akey.

The adaptations show up in nutrient-dependent pheromone-controlled differences in cell types, which appear to be due to alternative splicings of pre-mRNA and amino acid substitutions, and the adaptations also show up in chromosomal rearrangements like those recently reported in sparrows with different morphological and behavioral phenotypes (see Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes).

The differences in sparrows appear to be consistent with vertebrate-wide nutrient-dependent pheromone-controlled adaptations like those in the mouse-to-human example detailed in Kamberov et al (2013) and Grossman et al (2013) where...
RealScience
5 / 5 (1) Feb 01, 2014
You didn't answer, so I'll repeat in case you didn't understand:

You said:
The amino acid substitutions that contribute to organism-level thermoregulation survive, because that works. That's also why the different cell types with the hemoglobin variants work, and realistically it's how everything in life works.


Do you agree that amino acid substitutions can produce beneficial changes?
Do you agree that these beneficial changes can be selected for by natural selection?
Captain Stumpy
5 / 5 (1) Feb 01, 2014
that have obviously not occurred in their human counterparts, like "Captain Stumpy" and his conspecifics who believe that all roach-like creatures and all other creatures have mutated into existence after being naturally selected to exist

@jvk
nice to see that you are exemplifying the arguments in the article about pseudoscience and supporting my arguments about you. thanks!

secondly: even YOUR hypothesis requires MUTATION
again... please refer to the definition used by BIOLOGISTS in the field
this link is pretty close to spot on

https://en.wikipe...Mutation

also... try to answer Real Science, as he seems to be refuting you quite nicely

by the way... PZ Meyers is a REAL BIOLOGIST working in the field, whereas you are, by your own admission, nothing more than a glorified lab tech with a Mensa membership (as if this was special?) who is trying to sell pheromone perfume.

not that there is a problem with selling perfume...
but sell the crackpot stuff elsewhere.

JVK
not rated yet Feb 01, 2014
From Fertilization to Adult Sexual Behavior (1996)
http://www.hawaii...ion.html

"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..."

With details on the conserverd molecular mechanisms of epigenetic effects, we linked nutrient-dependent pheromone-controlled ecological adaptations involving amino acid substitutions and chromosomal rearrangement in sex chromosomes at the advent of sexual reproduction in yeasts via a common signaling pathway in vertebrates (Horton et al., http://www.pnas.o...bstract) and invertebrates (Maleszka et al http://bfg.oxford...bstract)

Not one evolutionary theorist has addressed any of the data in any of these three published works.
Captain Stumpy
not rated yet Feb 01, 2014
@jvk
Not one evolutionary theorist has addressed any of the data in any of these three published works


you cant get your theory recognized by real scientists so you come here to argue?
WHAT IS YOUR POINT?
do you really think that if you get Bob the local plumber to say "you are right" that this is going to make all the other Biologists/researchers in the field come running to your side and pat you on the back and say "good job"????

you keep coming here to argue your point...
this only reinforces the above assessments of your lack of validity

it appears to me that your lack of ability to "prove to the world" that you are correct is the simple and resounding fact that
you are pushing pseudoscience and it is NOT REAL SCIENCE!

therefore, even YOUR Mensa brain should register that your efforts are futile as your science must meet specific requirements and be addressed by SCIENTISTS

like THIS PUBLISHED scientist:

PZ MEYERS

JVK
not rated yet Feb 01, 2014
http://rationalwi...PZ_Myers

"Paul Zachary "PZ" Myers is one of the most popular atheist bloggers on the Internet, a biology professor well-known for his smack-downs of creationism, popularization of science, and love of cephalopods."

The fact that he has viciously attacked anyone who has every supported the claims for speciation via chromosomal rearrangements with experimental evidence attests to his ignorance and bias, especially now that we have seen the accumulation of evidence that supports the claims for ecological adaptations via chromosomal rearrangements.

Also, for someone who loves cephalopods to not realize the focus of my model on gonadotropin releasing hormone links all of nutrient-dependent pheromone-controlled ecological adaptations from yeasts to humans attests to his ignorance. He is a fool with foolish followers.

Oxytocin/vasopressin and gonadotropin-releasing hormone from cephalopods to vertebrates
http://dx.doi.org....05569.x
Captain Stumpy
5 / 5 (1) Feb 01, 2014
Also, for someone who loves cephalopods to not realize the focus of my model on gonadotropin releasing hormone links all of nutrient-dependent pheromone-controlled ecological adaptations from yeasts to humans attests to his ignorance. He is a fool with foolish followers

@jvk
so... because you cannot get a real scientist to understand your gobbledy-goop this is justification for you to come here and flounce around touting your pseudoscience?

i guess you MISSED my point
i will use smaller words:
IF you cannot get REAL SCIENTISTS
actually IN THE FIELD in which you are participating
to acknowledge you or support your claims
AND
scientists REFUTE your claims with REAL SCIENCE
it is RIDICULOUS to assume that coming to a layperson pop-sci site is going to bolster your arguments
AND
as it is refuted already, it is considered PSEUDOSCIENCE
especially given the historical reference!

http://freethough...s-place/
JVK
not rated yet Feb 01, 2014
http://www.amazon...99737673

In his book, linked above: Neuroanatomist Simon LeVay wrote:

" James Kohl, an independent researcher who also markets "human pheromones" to the general public, believes that pheromones may have a primary influence in setting up a person's basic sexual orientation. Other, more consciously perceived aspects of attractiveness, such as facial appearance, are attached to a person's basic orientation through a process of association during early postnatal life, according to Kohl.

This model is attractive in that it solves the "binding problem" of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as..." see p210
RealScience
5 / 5 (2) Feb 01, 2014
@JVK - I don't disagree with you on nutrient-driven epigenetic changes being INVOLVED in adaptation to new environments, or on humans reacting to pheromones through conserved pathways, so quit trying to change the subject.

I'll repeat again - you have said:
The amino acid substitutions that contribute to organism-level thermoregulation survive, because that works. That's also why the different cell types with the hemoglobin variants work, and realistically it's how everything in life works.


Do you agree that amino acid substitutions can produce beneficial changes?
Do you agree that these beneficial changes can be selected for by natural selection?
JVK
not rated yet Feb 01, 2014
It is the natural selection of nutrients that allows the epigenetic landscape to become the physical landscape of DNA in the organized genomes of species from microbes to man, and I have provided examples of that fact in my review article.

http://www.socioa...53/27989

It is probably clear to every intelligent researcher that "Ecological variation is the raw material by which natural selection can drive evolutionary divergence." http://rspb.royal...abstract

What idiots can't seem to grasp is the biological fact that natural selection drives evolutionary divergence via food choice as I showed in every one of my published works since 1995. Twenty years of stupidity and you ask:

Do you agree that amino acid substitutions can produce beneficial changes?
Do you agree that these beneficial changes can be selected for by natural selection?
--so you can drag me into discussion of mutations
RealScience
5 / 5 (2) Feb 01, 2014
@JVK - YOU dragged yourself into a discussion on mutations in your first two comments:

As has since exemplified in published works on birds and bees, mutation-driven evolution is no longer considered to be ecologically valid or biologically plausible


Instead, theorists continue to believe in their well-established nonsense as if their belief in effects of mutations made the nonsense any less nonsensical.


So quit trying to change the subject that YOU dragged yourself into.

You have said:
The amino acid substitutions that contribute to organism-level thermoregulation survive, because that works. That's also why the different cell types with the hemoglobin variants work, and realistically it's how everything in life works.


Do you agree that amino acid substitutions can produce beneficial changes?
Do you agree that these beneficial changes can be selected for by natural selection?
JVK
not rated yet Feb 02, 2014
State your case for attempting to make the amino acid substitutions equate with mutations so others can dismiss your nonsense as I have repeatedly shown they MUST do before attempting to understand the scientific progress that has already been made and ignored by ignorant theorists like you in the context of what is known about the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to man.

My model is a refutation of mutation-initiated natural selection (explained in less than 5.5 minutes in the video from my most recent poster presentation).

http://www.youtub...youtu.be

I'm not going to address your nonsense unless you are willing to address the biological facts.
RealScience
5 / 5 (1) Feb 02, 2014
State your case for attempting to make the amino acid substitutions equate with mutations.


Standard genetics terminology includes ALL amino acid substitutions as a class of mutations, so the onus is on you to explain why they DON'T equate with mutations.

However I think that the standard terminology goes too far, and I do NOT equate ALL such substitutions with mutations - the genome has evolved to be clever enough that it wouldn't surprise me at all if RNAs would in some cases controllably make amino-acid substitutions in the DNA. You hint at that at 1:50 into your video; I've been watching the literature for evidence of such and haven't seen any yet, so if you have any experimental evidence to support that it would be a significant contribution to the field.

On the other hand there is a big difference between ALL and NEVER.
Do you claim that amino acid substitutions are NEVER the result of mutations?
JVK
not rated yet Feb 02, 2014
Thanks.

Mutations perturb protein folding; amino acid substitutions stabilize it. Biophysical constraints on protein folding prevent fixation of mutation-caused amino acid substitutions that stabilize protein folding in the cell types of organisms of different species, which is why ecological variation must be the cause of amino acid substitutions that stabilize intracellular signaling, intermolecular interactions, stochastic experience-dependent receptor-mediated de novo gene creation, and chromosomal rearrangements in yeasts at the advent of sexual reproduction, and in all other species that sexually reproduce via nutrient-dependent pheromone-controlled ecological adaptations sans mutation-driven evolution, which is a ridiculous theory.

Thus, as I've told you before, and explained why: fixed amino acid substitutions are NEVER the result of mutations. If they were, there would be someone who had by now provided experimental evidence to support the ridiculous claims of theorists.
JVK
1 / 5 (1) Feb 02, 2014
State your case for attempting to make the amino acid substitutions equate with mutations.


Standard genetics terminology includes ALL amino acid substitutions as a class of mutations, so the onus is on you to explain why they DON'T equate with mutations.


I forgot to note how much I appreciate the fact that your case is based on standard genetics terminology. Didn't I mention the problem with the standard?

"...we will not consider geographical and ecological factors because of space limitation. Our primary purpose is to clarify the roles of mutation and selection..."
http://gbe.oxford...abstract

Clarifying anything by exclusion of some factors, such as ECOLOGICAL VARIATION is one way to support a nonsensical theory that has not been supported by experimental evidence, so that the nonsense becomes a part of standard genetics terminology (e.g, for dummies).

It's only a problem for serious scientists who can't dismiss any factors.

RealScience
5 / 5 (1) Feb 03, 2014
The standard terminology is misleading, with all genetic changes other than from crossovers during recombination being termed 'mutations'. While this SHOULD merely be a matter of semantics, it gets coupled with the archaic thinking that all mutations are random.

Nature is seldom so simple. Even radiation-induced mutations are far from random because the genome has evolve to be more mutation resistant in critical regions, and also to fix mutations faster in critical regions, so such regions have far fewer mutations for natural selection to act on.
And other mutations are less random still. For example, in dms4-mutants of A. thaliana Sasaki et al document 35x to 150x amplification of mutations of the dms4 gene that restore its function, without a higher mutation rate in the rest of the genome (http://www.ncbi.n...023006).
However the restoration event is far from predictable, so it falls between a relatively random mutation and a controlled alteration. – continued -
RealScience
5 / 5 (1) Feb 03, 2014
What I'm looking for is experimental evidence of a whole range of control on the non-randomness of alterations to DNA, especially when RNA is involved (RNA editing not just of epigenetic tags, but of the DNA sequence itself). Lolle et all appeared to have found quasi-controlled editing about a decade ago, but those results since appear to be explained by outcrossing. There is also some fairly controlled editing in the suppression of transposons, but that is a very special case.

But I'm not sure why you said 'thanks'. I said that IF you had experimental evidence of RNAs controllably making amino-acid substitutions, it would be a significant contribution, and so far I have not seen experimental evidence of this.
RealScience
5 / 5 (2) Feb 03, 2014
I forgot to note how much I appreciate the fact that your case is based on standard genetics terminology. Didn't I mention the problem with the standard?


No.

(And if your argument is based on non-standard terminology, and you don't explain that terminology, you really shouldn't insult people who respond as you were using standard terminology.)

So what is the definition of a mutation that you are using?

JVK
1 / 5 (2) Feb 03, 2014
Terms are understood when they are used, if used properly. I'll try it again -- only to see you ignore this:

Mutations perturb protein folding; amino acid substitutions stabilize it. Biophysical constraints on protein folding prevent fixation of mutation-caused amino acid substitutions that stabilize protein folding in the cell types of organisms of different species, which is why ecological variation must be the cause of amino acid substitutions that stabilize intracellular signaling, intermolecular interactions, stochastic experience-dependent receptor-mediated de novo gene creation, and chromosomal rearrangements in yeasts at the advent of sexual reproduction, and in all other species that sexually reproduce via nutrient-dependent pheromone-controlled ecological adaptations sans mutation-driven evolution, which is a ridiculous theory.

JVK
1 / 5 (1) Feb 03, 2014
What I'm looking for is experimental evidence of a whole range of control on the non-randomness of alterations to DNA, especially when RNA is involved (RNA editing not just of epigenetic tags, but of the DNA sequence itself).


No you're not! You're ignoring the evidence. http://jonlieffmd...volution


But I'm not sure why you said 'thanks'. I said that IF you had experimental evidence of RNAs controllably making amino-acid substitutions, it would be a significant contribution, and so far I have not seen experimental evidence of this.


I provided examples across species in http://www.socioa...53/27989
RealScience
5 / 5 (1) Feb 03, 2014
Mutations perturb protein folding; amino acid substitutions stabilize it. Biophysical constraints on protein folding prevent fixation of mutation-caused amino acid substitutions that stabilize protein folding in the cell types of organisms of different species, which is why ecological variation must be the cause of amino acid substitutions that stabilize intracellular signaling


That doesn't make it clear how what you mean by mutations differs from the standard definition. If you are using non-standard terminology and don't clearly state what you mean by the terms, you can hardly blame people if they write you off as a crank.

Furthermore it appears to acknowledge that mutations can cause amino-acid substitutions that stabilize proteins (although your wording is somewhat ambiguous). If so, what biophysical constraints would prevent their fixation while allowing fixation of ecological-variation-induced substitutions?
RealScience
5 / 5 (1) Feb 03, 2014
No you're not! You're ignoring the evidence


Neither of those links addresses mutations in the genetic sequence.

As I have said before:
I don't disagree with your comments when you ascribe a role for nutrients and epigenetics in adaptation. In the short term (up to thousands or even tens of thousands year for humans) I believe that these dominate over mutations. Over the mid-term things like copy-number variations dominate; some would call these mutations, and others wouldn't.

However in the long term (hundreds of thousands to millions of generations), I think that mutations play an important role. Therefore I disagree with is what I UNDERSTAND to be your opinion that mutants in the genetic sequence itself are NEVER selected for by natural selection.


You insist that mutations CANNOT become fixed in the genome, but the only 'evidence' you have presented to support this is to claim that two simultaneous mutations would be needed, and that was shown to be false.
JVK
1 / 5 (1) Feb 03, 2014
You insist that mutations CANNOT become fixed in the genome, but the only 'evidence' you have presented to support this is to claim that two simultaneous mutations would be needed, and that was shown to be false


How many times have I provided this link to the research that says mutations are not fixed in the genome, only to have you come back and say I haven't presented any evidence?

An experimental test on the probability of extinction of new genetic variants
http://www.nature...417.html

You should long ago have realized that you don't understand the experimental evidence because you need to keep believing in a ridiculous theory -- and you can't do both. That's why theorists always say there is no evidence. They simply can't accept it since it makes them look like the idiots they are.
JVK
1 / 5 (1) Feb 03, 2014
The molecular basis of food choice imprinting associated with conserved ion and amino acid transporters, protein biogenesis, synaptic transmission and epistasis (e.g., from atoms to ecosystems) in C. elegans is due to be reported soon -- as everyone knows who is not an evolutionary theorist.

I mention this only because the next response from RealScience is predictable. It will be something like this: "Nuh uh" that's not what Chelo et al showed -- their experiments showed beneficial mutations might somehow be fixed and that means they could be somehow naturally selected.
RealScience
5 / 5 (2) Feb 03, 2014
Of course I'll say that, because I read and understood the paper.

How many times have I provided this link to the research that says mutations are not fixed in the genome, only to have you come back and say I haven't presented any evidence?


As I have pointed out, the paper says: "Haldane reasoned that the probability of fixation of new beneficial alleles is twice their fitness effect... Our study CONFIRMS the key results from classical population genetics"

The paper discusses the probability of fixation in the case where an allele is beneficial regardless of frequency, and shows the expected probability of fixation over 100 and 1000 generations. The expected probability of fixation is quite high even for a 15% benefit, although this experiment was not run long enough to confirm the model.

Thus the reference that you keep citing as 'evidence against fixation' SUPPORTS that FIXATION of beneficial alleles can occur with HIGH PROBABILITY(see graphs 2b and 4a).
RealScience
5 / 5 (2) Feb 03, 2014
And I have already I sent you a link to an experiment that demonstrated de novo mutations being selected for: http://www.plospa....1002158

And a 10,000 generation experiment already showed just that ~20 years ago:
www.pnas.org/cont...l.pdf‎

So natural selection FOR mutations IS shown in experiments.

You are the one who keeps ignoring the evidence, and saying "Nuh uh it doesn't happen, because it is impossible, and since it is impossible I can ignore evidence that it happens because I know it is impossible."

JVK
1 / 5 (2) Feb 04, 2014
Does anyone else not realize that population genetics ignores ecological variations and adaptations every step of the way in attempts to explain how mutation-initiated natural selection might be possible -- even thought it isn't. Lenski's experiments exemplify how nutrient-dependent pheromone-controlled amino acid substitutions differentiate cell types, and even if the links above don't work, so do the other works this student has cited in the past.

I'll try this again: "Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era"

"...we will not consider geographical and ecological factors because of space limitation. Our primary purpose is to clarify the roles of mutation and selection in the evolution of reproductive isolation..." http://gbe.oxford...abstract

Ecological adaptations show up in eye color and skin pigmentation in this study, which does not exemplify mutation-driven evolution because it doesn't exist.
RealScience
5 / 5 (2) Feb 05, 2014
The Nei article is specifically on how mutations and selection from gene conflicts is sufficient to create new species. Far from ignoring ecological variations, the authors acknowledge that "The occurrence of speciation ALSO depends on the reproductive system, population size, bottleneck effects, and environmental factors, such as temperature and day length."

As Lenski's experiments, if the changes that enables citrate metabolism were "nutrient-dependent pheromone-controlled amino acid substitutions", they wouldn't take tens of thousands of generations to occur, and they would occur in all populations. In contrast, at the population size of Lenski's experiment, tens of thousands of generations is roughly how long it takes for any given simple mutation to randomly occur, so Lenski's results perfectly match nutrient-controlled selection FOR mutation.

So again an experiment that YOU cite is evidence FOR mutation-driven evolution.
JVK
1 / 5 (3) Feb 06, 2014
They ignored availability of nutrients, the ecological factor that determines everything else they (and you) attribute to mutations. Inform yourself, you idiot!

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors
http://www.socioa...38/20758

Excerpt:
Just as the influence of diet and pheromones can be in the larval stages or in other developmental stages of insects, it can also be in the pre- and postconception stages of mammals, including humans... For example, pheromones and nutrition could alter levels of maternal hormones, gestational events, and postnatal outcomes via their direct effect on maternal GnRH and the placenta. The outcomes might not always be positive, which means the possible effects should not be ignored. That would be like ignoring the likely effects of docosahexaenoic acid in the maternal and postnatal diet on LH and on neuronal development ...
JVK
1 / 5 (3) Feb 06, 2014
No matter how many times I say that Nei has excluded the ecological factor of nutrient uptake in an attempt to keep people focused on the ridiculous idea of mutation-driven evolution, we will have people like RealScience who dispute any version of reality known to serious scientists.

The evolutionary theorists must have fools continue to believe that mutations cause differences in morphology and behavior lest they all be recognized for the years of pseudoscience that teachers and students have convinced others to believe.

Monkeys that eat omega-3 rich diet show more developed brain networks
February 5th, 2014
http://medicalxpr...ain.html

Journal article excerpt from: http://www.jneuro...abstract
"Docosahexaenoic acid (DHA), a long-chain ω-3FA, is the most abundant polyunsaturated fatty acid in membranes of the mammalian retina and cerebral gray matter..."

But evolution is mutation-driven if you're an idiot!
RealScience
5 / 5 (2) Feb 06, 2014
They ignored availability of nutrients, the ecological factor that determines everything else they (and you) attribute to mutations.


Lenski's experiment FOCUSES on the availability a nutrient (citrate).
Lenski's experimental results are NOT consistent with controlled amino acid substitutions (whether nutrient-driven/pheromone-controlled or any other type of control.
However Lenski's experimental results ARE consistent with nutrient-driven SELECTION for mutations.

That's doesn't exclude other mechanisms also existing, but it does mean that an experiment that YOU cite REFUTES your claim that there is no experimental evidence that mutations are EVER selected for.
RealScience
5 / 5 (2) Feb 06, 2014
No matter how many times I say that Nei has excluded the ecological factor of nutrient uptake in an attempt to keep people focused on the ridiculous idea of mutation-driven evolution, we will have people like RealScience who dispute any version of reality known to serious scientists.


So you believe that no serious scientists agree with Nei, and that there is some deliberate plot to hide any factors other than nutation?

Nei shows that (and how) selection for mutations alone is sufficient to drive speciation.
If Nei were trying to hide other factors, he wouldn't mention them at all or would dismiss them as non-existent rather than acknowledging them and saying that they are excluded for lack of space.

But evolution is mutation-driven if you're an idiot!

Evolution is SELECTION-driven.
Mutations CONTRIBUTE to evolution by contributing variety for selection to act on.
And this happens whether or not you continue to deny the evidence for it.

RealScience
5 / 5 (2) Feb 06, 2014
Monkeys that eat omega-3 rich diet show more developed brain networks


That nutrition has a role in brain development has been known for centuries, and no comment on this thread has argued with it.
Do you think that nutrition having a role means that no other factors can have a role?
Or are you stating the obvious to try to hide the roles of other factors?

JVK
1 / 5 (3) Feb 06, 2014
I'm stating the obvious because Darwin's 'conditions of life' are obviously nutrient-dependent and pheromone-controlled, which means ecological variation is the first thing that must be considered in the context of adaptations sans mutations.

That fact is not obvious to the most ignorant person I have ever encountered: the biology teacher, PZ Myers, and it is not obvious to you. Did he teach you to believe in mutation-driven evolution?

If not, who convinced you to believe that natural selection of nutrients was not responsible for ecological adaptations and that mutation-initiated natural selection was the cause of species diversity?

I ask because I am compiling a list of idiots who are biology teachers and a list of their idiot minions so that others can quickly recognize them when they encounter one. See for examples:

http://freethough...s-place/

Please join them in their discussions of social pseudoscience.
Captain Stumpy
5 / 5 (4) Feb 06, 2014
It is a rather fascinating and propitious occurrence that whenever JVK is directly refuted, she resorts to aspersions against the scientific community, the author of said refute (in this case, RealScience), people in general (for not believing in her proclamations) as well as subtle threats.
I ask because I am compiling a list of idiots ...and a list of their idiot minions so that others can quickly recognize them when they encounter one

and so you will only create a following of ignorance based upon the fallacy of your claims
She also lashes out with proclamations that only she is intelligent enough to understand, which can be a sign of mental affliction.

JVK cannot accept logical refute, as proven here and on Myers blog, therefore it would be best if she took up something more to her capabilities.
Stick with the perfume
JVK
1 / 5 (4) Feb 06, 2014
Darwin: "...the greater variability of species having wider ranges than of those with restricted ranges, lead to the conclusion that variability is generally related to the conditions of life to which each species has been exposed during several successive generations."

Darwin: "When a variation is of the slightest use to any being, we cannot tell how much to attribute to the accumulative action of natural selection, and how much to the definite action of the conditions of life."

Darwin: "Instances could be given of similar varieties being produced from the same species under external conditions of life as different as can well be conceived..."

Darwin: "IF under changing conditions of life organic beings present individual differences in almost every part of their structure, and this cannot be disputed..."

PZ Myers and his idiot minions: Mutations somehow cause evolution via natural selection for something! Forget 'conditions of life.'

The Roach King knows more than Darwin.
JVK
1 / 5 (4) Feb 06, 2014
A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution (2013)

http://www.plefa....fulltext

"The preservation of DHA in neural signalling systems for 500–600 million years occurred despite enormous genomic changes since the beginning of animal evolution."

What kind of idiot repeatedly shows up to claim that PZ Myers has proved anything, or that he has proved anything by repeatedly mentioning what PZ Myers proved?

That was a rhetorical question. I would consider Captain Stumpy to be a bigger idiot than PZ Myers except for the fact that an idiot minion cannot be a bigger idiot than the biology teacher that taught him to be an idiot minion and ignore Darwin's work and every biological fact introduced in the context of experimental evidence.
RealScience
5 / 5 (3) Feb 06, 2014
@JVK - That you can confuse a role for nutrients in brain development with no role for mutation in evolution, in spite of having the difference pointed out, shows that you do not think rationally about mutations.

Multiple causes can have similar effects, so that nutrients can contribute to evolution does NOT mean that other factors cannot contribute.

For example, that your lack of rational thinking could be caused by a DHA deficiency in your youth does not mean that that is the only possible cause. It could also caused by toxins (did you eating lead paint flakes?), by sociological conditions (were you told that mutations being selected for would disprove god?), by pheromones (did some hot chick tell you not to believe in mutations?), or by mutations (you could have a de novo mutation that negatively affects brain function).

(If you are so sensitive to Myers' negative comments about, you shouldn't start slinging insults at others.)
JVK
1 / 5 (4) Feb 06, 2014
If you think I am not exhibiting rational thinking when I repeatedly tell you that mutation-driven evolution is neither a biologically plausible nor ecologically valid proposal, and that it is instead merely a ridiculous idea that has never been supported by experimental evidence, all you need to do is provide experimental evidence to support the ridiculous theory.

That's what did not happen on PZ Myers' blog, or anywhere else I've entered discussion. And the lack of experimental evidence is why I sling insults back at the people who don't realize they have no experimental evidence to support their ridiculous beliefs. Like you, they simply believe what they were taught to believe, and keep regurgitating whatever they think it is that will make others consider them to be intelligent beings, instead of idiot minions.

All that aside; How might a "de novo mutation that negatively affects brain function" result in natural selection in the context of mutation-driven evolution?
RealScience
5 / 5 (2) Feb 06, 2014
all you need to do is provide experimental evidence ...
That's what did not happen on PZ Myers' blog, or anywhere else I've entered discussion.

I have no idea on PZ Myers blog (I hadn't never heard of him before this thread) or anywhere else.
But if phys.org is any indication, you have ignored evidence presented to you while repeating your claim and insulting anyone who disagreed with you.
For example, I have already pointed out NEI and Charo as evidence that mutations CAN become fixed in genomes. and Lenski, Gullbeg and Gabriel as evidence that mutations ARE selected for, and yet you continue to CLAIM that there is no evidence.

All that aside; How might a "de novo mutation that negatively affects brain function" result in natural selection in the context of mutation-driven evolution?


The impact would be minimal these days since one does not have to think rationally to survive or reproduce. It might even be selected for, like enjoying consuming alcohol.
JVK
1 / 5 (2) Feb 06, 2014
What Nei did was eliminate ecological factors and reported beneficial fixed mutations that Chelo et al reported did not occur in C. elegans at the same time they reported the lack of any experimental evidence that suggested beneficial mutations were fixed in any other species.

I've already told you about the problems with what you call evidence of mutation-driven evolution, and told you about the ridiculous misrepresentations that Lenski has repeatedly made, Nevertheless, you continue to tell me that your evidence is biologically plausible and ecologically valid despite the fact that it is not evidence from any model organism, and I have provided evidence across species in my published works of nutrient-dependent pheromone-controlled ecological adaptations.

Now you say the impact of a de novo mutation on brain function would be minimal after de novo mutations in the brain and every other tissue have been linked to cancer. You're not very bright, are you?
RealScience
5 / 5 (2) Feb 06, 2014
@JVK - since you didn't understand, I'll spell it out more clearly:

The natural selection result of a de novo mutation that affects only rational thinking (the context in which the hypothetical mutation was mentioned) would be minimal because even those who do not think rationally survive and reproduce in the modern world. Such a mutation might even be selected FOR -for example, alcohol consumption impairs rational thinking thinking, and yet enjoying drinking is selected for because impaired rationality leads to unprotected sex which leads to pregnancy.

You seem not to understand the difference between SOME and ALL.
That SOME de novo mutations are linked to cancer does not mean that ALL de novo mutations are linked to cancer.
RealScience
5 / 5 (3) Feb 06, 2014
...beneficial fixed mutations that Chelo et al reported did not occur in C. elegans at the same time they reported the lack of any experimental evidence that suggested beneficial mutations were fixed in any other species.


Your Chelo reference does NOT say that there is no experiment evidence for fixation of mutations.
Chelo says: "There is no experimental test of Haldane's insight that new beneficial alleles are LOST with high probability".
Chelo then tests whether fixation of a beneficial allele SOMETIMES fails rather than being ALWAYS fixed, and concludes that beneficial alleles are NOT ALWAYS fixed.

You appear to be confusing 'are not always fixed' with 'are always not fixed'.
These are different - think about it if you don't understand the difference at first!

Chelo tested Haldane's reasoning that the probability of fixation of new beneficial alleles is twice their fitness effect. Chelo says "Our study confirms the key results from classical population genetics".
Captain Stumpy
5 / 5 (4) Feb 06, 2014
...never been supported by experimental evidence, ... provide experimental evidence ...

@jvk
had you been paying attention above, you would have seen ample evidence in the links and refute to your hypothesis
guess Mensa aitn what it used to be

@RealScience
here is the link

http://freethough...s-place/

I recommend reading it as Myers gives a logical and well written article about Kohl (aka JVK)
...what Kohl has described is a limited subset of the processes in development and that no one in their right mind thinks that development somehow refutes the contribution of other sources of variation to evolution

also points out thus:
It was Van Valen who said in 1973 that "Evolution is the control of development by ecology…" That's pretty much the mainstream view, so there's nothing novel in what Kohl wrote
Captain Stumpy
5 / 5 (4) Feb 06, 2014
crashes into a thread full of lay people and then lords it over them with his abuse of jargon. And he does it over and over again, and you can see the responses: most of the other commenters are more or less stunned, they don't know how to deal with all the specific buzzwords he throws at them, and they have these doubts…maybe he's saying something I should know about. No, he's not. He's babbling in scientese

@RealScience
from the link I mentioned above
I think that last part and the above is what incenses jvk the most. She is essentially claiming that a part of the process of evolution is actually the only possible force in evolution but she is wrong, as pointed out by the scientific community. This makes her so mad that she comes to these comments to egest bilious pseudoscience and lord over others with lesser vocabularies, when, in all actuality, she is simply another underpaid lab tech with a pheromone obsession and a pseudoscience hypothesis.
JVK
1 / 5 (4) Feb 06, 2014
http://www.scienc...6171/624

Excerpt: "Similar dynamics may occur in the natural setting, resulting from signaling networks built around the same core secrete-and-sense regulatory motif."

My comment: That was detailed in "Signaling Crosstalk: Integrating Nutrient Availability and Sex."

The author noted: "The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response."

In mammals, that signaling pathway is exemplified by the gonadotropin releasing hormone (GnRH) neuronal system. It links food odors and social odors called pheromones from the epigenetic landscape to the physical landscape of DNA via subtle changes in GnRH pulse frequency and amplitude.

The molecular epigenetics of biologically-based cause and effect are conserved in all species, which refutes the biologically implausible theory of mutation-driven evolution touted by PZ Myers and his idiot minions.
JVK
1 / 5 (4) Feb 06, 2014
http://www.scienc...abstract

"By integrating simple mathematical models, measurements on single cells and whole populations, and a bottom-up synthetic biology approach, we revealed a diverse repertoire of biological functions that secrete-and-sense cells can achieve. Crucially, this integrated approach uncovered design principles that enable the circuit to tune the balance between self-communication and neighbor communication among cells—a crucial mechanism for achieving myriad cellular behaviors and an important general issue in biology."

The more general issue is one of ignorance of biologically based cause and effect--exemplified by evolutionary theorists. The molecular epigenetics of biologically-based cause and effect are conserved in all species, which refutes the biologically implausible theory of mutation-driven evolution.

Experimental evidence arrives daily and it will be ignored by PZ Myers and his idiot minions.
JVK
1 / 5 (4) Feb 07, 2014
The following quote will mean nothing to PZ Myers or his idiot minions. It may pique the interest of others in learning about biologically based cause and effect.

In the context of Lenski's experiments and the interpretations by evolutionary theorists who have been taught "evolution for dummies":

"At the RNA level, each cell in what was thought to be a rather homogeneous population shows differential expression of transcripts across the genome [2-4]. Indeed, at a recent meeting, one presenter studying a gene whose allelic forms show strong quantitative expression variation at the RNA level (eQTL) in cell populations concluded that genetics don't determine expression at the individual cell level. This was the interpretation of the data even though summing expression from each allele over many individual cells gave the same biased distribution of expression as seen using bulk populations... "

Only an idiot would tell others that results from bulk populations are meaningful here.
RealScience
5 / 5 (3) Feb 07, 2014
The molecular epigenetics of biologically-based cause and effect are conserved in all species, which refutes the biologically implausible theory of mutation-driven evolution


@JVK - once again you are confusing epigenetics (WHEN genes are expressed, and even which portions of genes are expressed) with genetics (the sequences of those genes themselves, and thus the sequences that the expressed portions translate into).

Your Youk reference is on epigenetics and doesn't even mention gene sequences let alone modifications to the sequences.

While the epigenetic Youk paper you reference is mute on mutations, Youk himself disagrees with you: in NatureNV2010_Youk, Youk states "Bacterial resistance to an antibiotic arises when mutations in the DNA of a few cells in a bacterial population enable them to fend off the harmful effects of the antibiotic."
RealScience
5 / 5 (2) Feb 07, 2014
"At the RNA level, each cell in what was thought to be a rather homogeneous population shows differential expression of transcripts across the genome [2-4]. Indeed, at a recent meeting, one presenter studying a gene whose allelic forms show strong quantitative expression variation at the RNA level (eQTL) in cell populations concluded that genetics don't determine expression at the individual cell level.


Another confusion between epigenetics (in this case, control of expression) and genetics (DNA sequence).

You consistently make the error of confusing epigenetics and genetics, and you consistently make the error of confusing showing that something happens with proving that other things don't happen.
RealScience
5 / 5 (3) Feb 07, 2014
crashes into a thread full of lay people and then lords it over them with his abuse of jargon. ... He's babbling in scientese

@RealScience
She is essentially claiming that a part of the process of evolution is actually the only possible force in evolution but she is wrong, as pointed out by the scientific community. This makes her so mad that she comes to these comments to egest bilious pseudoscience and lord over others with lesser vocabularies

Which is why I take the time to point out JVK's errors (although JVK makes so many errors that I can't address them all).

However even a blind chicken sometimes finds a corn, and JVK is obsessed enough that he might find a stronger example of the non-randomness of mutations than the 35x to 150x dms4 mutation amplification that I cited, so I also try to push him into finding something useful.
JVK
1 / 5 (3) Feb 07, 2014
"... at a recent meeting, one presenter... concluded that genetics don't determine expression at the individual cell level.


Another confusion between epigenetics (in this case, control of expression) and genetics (DNA sequence).

You consistently make the error of confusing epigenetics and genetics, and you consistently make the error of confusing showing that something happens with proving that other things don't happen.


Given my publications and the linked information in a recent published work (above), what level of comparable expertise gives you the ability to report the errors that you claim I have made?

See for example: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors
http://www.socioa...38/20758

Please tell me more about my errors by referencing where they occur in my published works or anywhere else.

Are you one of Lenski's idiot minions?
JVK
1 / 5 (2) Feb 07, 2014
While the epigenetic Youk paper you reference is mute on mutations, Youk himself disagrees with you: in NatureNV2010_Youk, Youk states "Bacterial resistance to an antibiotic arises when mutations in the DNA of a few cells in a bacterial population enable them to fend off the harmful effects of the antibiotic."


Thanks. As others know, that perspective ignores biophysical constraints on mutations.

Unlike social pseudoscientists, serious scientists have learned not to cling tightly to ridiculous theories after they've been repeatedly refuted. When it becomes clear that mutations cannot cause evolution, they simply no longer pretend that it does.

They make scientific progress via experimental evidence of how ecological variation causes adaptations and speciation. Why would Youk do the experiment and put it together with a mathematical model of cause and effect if anyone still believed that Lenski's results exemplify mutation-driven evolution?

You're not very bright, are you?
RealScience
5 / 5 (3) Feb 07, 2014
Are you one of Lenski's idiot minions?


You claimed:

Lenski's experiments exemplify how nutrient-dependent pheromone-controlled amino acid substitutions differentiate cell types


After I pointed out that:
Lenski's experiment FOCUSES on the availability a nutrient (citrate).
Lenski's experimental results are NOT consistent with controlled amino acid substitutions (whether nutrient-driven/pheromone-controlled or any other type of control.
However Lenski's experimental results ARE consistent with nutrient-driven SELECTION for mutations.


Now anyone who supports Lenski has become a minion!

RealScience
5 / 5 (2) Feb 07, 2014
You consistently make the error of confusing epigenetics and genetics…

...
Please tell me more about my errors by referencing where they occur in my published works or anywhere else.

Example:

Why would Youk do the experiment and put it together with a mathematical model of cause and effect if anyone still believed that Lenski's results exemplify mutation-driven evolution?


Youk's experiment is on epigenetics and doesn't even mention gene sequences let alone modifications to the sequences. Yet you cite it as if it were evidence that Youk doubts the role of mutations in evolution.

RealScience
5 / 5 (2) Feb 07, 2014
… you consistently make the error of confusing showing that something happens with proving that other things don't happen

...
Please tell me more about my errors by referencing where they occur in my published works or anywhere else.

Example:

The evolutionary theorists must have fools continue to believe that mutations cause differences in morphology and behavior lest they all be recognized for the years of pseudoscience that teachers and students have convinced others to believe.

Monkeys that eat omega-3 rich diet show more developed brain networks


You cite diet influencing morphology as if it meant that mutations don't influence morphology.
anonymous_9001
5 / 5 (3) Feb 07, 2014
James has a long history of making complete non sequitur interpretations of studies. Chelo et al's confirmation of Haldane's fitness effect hypothesis certainly does not mean that mutations are never fixed. I even emailed Chelo to confirm that. Apparently James knows more about Chelo's research than Chelo himself does. After all, he's just an "idiot evolutionary theorist". As for Lenski, Realscience covered it pretty well here-

"As Lenski's experiments, if the changes that enables citrate metabolism were "nutrient-dependent pheromone-controlled amino acid substitutions", they wouldn't take tens of thousands of generations to occur, and they would occur in all populations. In contrast, at the population size of Lenski's experiment, tens of thousands of generations is roughly how long it takes for any given simple mutation to randomly occur, so Lenski's results perfectly match nutrient-controlled selection FOR mutation."
anonymous_9001
5 / 5 (2) Feb 07, 2014
Which I believe is similar to something I probably told you on Yahoo. If the evolution of citrate metabolism were causally linked to the presence of citrate, ALL of Lenski's populations should have evolved it in a timely manner. It wouldn't appear to be by chance. They should have all had the same physiologic response.