Darwin 2.0: Scientists shed new light on how species diverge

Darwin 2.0
Macaws flying over the rainforest canopy at dawn. The study found that bird lineages that inhabit the forest canopy, such as these macaws, accumulate fewer species over evolutionary time than do bird lineages that inhabit the forest understory. Credit: Mike Hankey.

Birds that are related, such as Darwin's finches, but that vary in beak size and behavior specially evolved to their habitat are examples of a process called speciation. It has long been thought that dramatic changes in a landscape like the formation of the Andes Mountain range or the Amazon River is the main driver that initiates species to diverge. However, a recent study shows that speciation occurred much later than these dramatic geographical changes. Researchers from LSU's Museum of Natural Science have found that time and a species' ability to move play greater parts in the process of speciation. This research was published today in the print edition of Nature.

"The extraordinary diversity of birds in South America is usually attributed to big changes in the landscape over geological time, but our study suggests that prolonged periods of landscape stability are more important," said Robb Brumfield, LSU Museum of Natural Science director and Roy Paul Daniels professor in the Department of Biological Sciences, one of the lead authors.

Brumfield and his colleagues examined the genealogy of 27 species of birds in the most bio-diverse region in the world, the Neotropics, which extends from southern Mexico through Central America to southern Brazil and includes the Amazon rainforest.

"By using detailed sampling of many bird lineages, we were able to get a clearer and larger picture of when and how species formed within those lineages," Brumfield said.

The genetic data showed multiple accounts of species divergence, from nine to 29 different instances across the Andes Mountains that varied over time. This shows that rather than being the primary cause of speciation, the formation of the Andes Mountains had an indirect effect on diversification as a semi-permeable barrier.

The researchers then investigated how the history and ecology affected speciation among the 27 lineages of birds. They discovered the longer length of time a species can inhabit an area, the more likely it will disperse and diverge. Also, the less mobility a species has, the more likely it will diverge as well. For example, birds restricted to the forest floor showed significantly higher species diversity than birds that inhabited the forest's open canopy. These findings have conservation ramifications. If a species cannot inhabit the same area for an extended time, it will not have the opportunity to evolve and continue.

"Our results suggest that human alterations of the landscape can effectively kill the process," Brumfield said.


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Research identifies drivers of rich bird biodiversity in Neotropics

Journal information: Nature

Citation: Darwin 2.0: Scientists shed new light on how species diverge (2014, November 20) retrieved 17 August 2019 from https://phys.org/news/2014-11-darwin-scientists-species-diverge.html
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JVK
Nov 20, 2014
Excerpt: "The researchers then investigated how the history and ecology affected speciation among the 27 lineages of birds."

What happened to mutations, natural selection, and the evolution of biodiversity? Can we finally dispense with that pseudoscientific nonsense?

Are they saying that ecological variation leads to ecological adaptations via conserved molecular mechanisms in species from microbes to man, or just in some birds?

Is it Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

or, Species coexistence and the dynamics of phenotypic evolution in adaptive radiation
http://www.nature...874.html

Nov 20, 2014
What happened to mutations, natural selection, and the evolution of biodiversity?
Nothing much.

It's just that everybody else in biology isn't a nutjob and *expects* mutations, natural selection, and the evolution of biodiversity. It's kind of like how pilots expect gravity, or sailors expect water.

JVK
Nov 20, 2014
Does anyone realize how ridiculous it is to report this in terms of evolution AND speciation after publication of Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes http://www.pnas.o...abstract

It's like admitting that they never knew anything about how the epigenetic landscape is linked to the physical landscape of DNA in species from microbes to man via nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types of all individuals of all species via their pheromone-controlled physiology of reproduction.

Now, instead of mutation-driven evolution or other ridiculous evolutionary inferences it's "specially evolved" speciation -- another ridiculous inference.

JVK
Nov 20, 2014
...pilots expect gravity, or sailors expect water.


That's consistent with what is known about physics, chemistry, and molecular biology (except for not knowing where the gravity came from).

Evolutionary theory ignores physics, chemistry, and molecular biology and idiot minions of biology teachers tell us that species evolved because that's what they were taught to believe.

Nov 20, 2014
Evolutionary theory ignores physics, chemistry, and molecular biology


Wrong.

http://www.nature...672.html

We then advance a biophysical model of protein evolution that helps us to understand phenomena that range from the dynamics of molecular adaptation to the clock-like rate of protein evolution.


http://www.cell.c...901268-8

Our results illustrate common biophysical mechanisms for occurrences of positive and negative epistasis.


This one is actually exactly what you're looking for:
http://rsif.royal...19?rss=1

http://faculty.ch...ications

JVK
Nov 21, 2014
Claims that proteins evolve ignore the fact that theromodynamic cycles of protein biosynthesis and degradation begin with metabolism and end when nutrient-dependent amino acid substitutions stabilize the DNA in the organized genomes of species from microbes to man.

We've been through this so many times that I have concluded you are one of the most ignorant people I will ever encounter.

http://www.nature...306.html

"We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms."

How do you think proteins evolve their amino acid compositions?

Nov 21, 2014
9001 seems to have covered the part about it not being proper physics or science or whatever. I'll take this one:

idiot minions of biology teachers tell us that species evolved because that's what they were taught to believe.
This is incorrect.

Biology teachers tell you species evolved because there's an enormous amount of evidence that species evolved. Start with fossils. Then go look up ring species.

Do you know the actual biological definition of "evolution?" Here you go:
Its strict biological definition is "a change in allele frequencies over time."
That this happens today is a known well-proven fact, and that it generates new species is also a known well-proven fact. (Remember I told you to look up ring species.)

Oh, and BTW you forgot sex. Sex mixes the genes around, by the genetic recombination which occurs during meiosis; thus, a mutation in so-called "junk DNA" can get held there for generations, until its turn finally comes up through recombination.

Nov 21, 2014
BTW, evolution and religion are compatible. Read here:
http://talkorigin...god.html

So basically, the so-called "Christians" who are "against" evolution are nothing but religious bigots, no different than those who claim Buddhists or Muslims are "going to hell."

I don't know whether I believe Jesus lived or not; it's not important to me. But if he did, I know from reading the Gospel that he'd seek to convert bigots and persuade them to stop being bigoted. And I know he'd never lie, if what's said in the Gospels is true (as you all say you believe). So this bigotry is distinctly un-Christian.

cjn
Nov 21, 2014
JVK:
http://www.nature.com/nature/journal/v433/n7026/full/nature03306.html

"We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms."


Its almost like you don't read or don't understand the articles you post. From the 2005 Nature Article:
"Gainers (or losers) do not seem to be unusually similar to each other in terms of their physico-chemical properties, metabolic pathways, or codon assignments. However, a loser-rich and gainer-poor amino acid composition of primordial proteins may be explained historically by the order in which amino acids were recruited into the genetic code...."

Nov 21, 2014
Finegrained evolution. We have come a long way...

@DaSchneib: I don't think a science source like TalkOrigins should make theological claims. They are thus bad references, even if they would be correct in details. Do we ask scientists for astrological claims, if Virgo is the better sign say?

That site is wrong in details, unfortunately. By their own words in practice religion, or other forms of unsupported superstition, is always in conflict with facts. 99.9+ % of religions are creationist magic agency based, making up the "[Some] religious beliefs do make predictions" part.

And of course we know from 19th century thermodynamics and on, that magic is wrong. There isn't any, and we know this.

cjn
Nov 21, 2014
^Cont
"...All four strong losers (but only one of the five strong gainers, Ser) are among the ten amino acids produced in spark experiments imitating conditions for pre-biotic synthesis. All strong losers, but none of the strong gainers, are among the eight amino acids found in the Murchison meteorite and thought to be abiogenic."

What the authors are saying is that there are more "new" proteins as they require biology to evolve, and do not occur naturally in an abiotic environment. No magic necessary, just new proteins (enabled by the new AA's) slowly replacing the ones the original ones. Think of it like renovating an old colonial house, you'll have to install new electrical wiring and fixtures, new plumbing, new insulation, etc..., but you'll still have artifacts of the old house, like the foundation and exterior.

Nov 21, 2014
@cjn: That troll is a spammer. (Has, or had, a pheromone selling site.)

Nov 21, 2014
Its almost like you don't read or don't understand the articles you post.


He does that thing a lot. The only articles he postums up that agree with him is the one (yeah the same ONE over and over) he wrote back in 1995. All the rest he puts up tell how he is wrong. He's one of those silly couyons that put them up there thinking nobody will look at what they say.

He also thinks every single article on the physorg is about stinky love potions and is an invitation to him to come on in and peddle his wares.

That's why the physorg makes him put on that silly looking pointy cap he's always got on that weird looking head of his. Have you seen his picture on the profile page? That is one ugly Texan him. Looks like somebody is tickling his toes off camera.

Nov 21, 2014
@DaSchneib: I don't think a science source like TalkOrigins should make theological claims. They are thus bad references, even if they would be correct in details. Do we ask scientists for astrological claims, if Virgo is the better sign say?
Bad analogy. It's more like we point out that astrology doesn't conflict with evolution; talking about astrological signs (mine is "Stop," heh) is outside the scope of the intent.

That site is wrong in details, unfortunately.
Where, precisely? Can you link and quote it?

By their own words in practice religion, or other forms of unsupported superstition, is always in conflict with facts. 99.9+ % of religions are creationist magic agency based, making up the "[Some] religious beliefs do make predictions" part.
Only for literalists. The normal religious folk who aren't nutjob bigots would have no problem with it if they understood. The Catholics don't. The Buddhists don't either.

contd

Nov 21, 2014
And of course we know from 19th century thermodynamics and on, that magic is wrong. There isn't any, and we know this.
So? Religion, when not practiced by crazy fundies, is not incompatible with evolution. Why does this bother you? I'm an atheist and the son of atheists. It doesn't bother me. If people need an imaginary super magic sky daddy, they can have one, as long as they don't start denying reality.

Minor update to the previous post: the Catholics and Buddhists don't have a problem with evolution, was what I meant to say.

Nov 21, 2014
Are they saying that ecological variation leads to ecological adaptations via conserved molecular mechanisms in species from microbes to man, or just in some birds?


I think that no matter what "driver" you're talking about (natural selection, environment, nutrients, etc) you are ALWAYS talking about mutation. If the genetic code doesn't change, then neither does the organism...

JVK
Nov 21, 2014
Illuminating the Interactome

http://www.the-sc...ractome/

See also: everything currently known about RNA-mediated events, which occur in the context of thermodynamic cycles of protein biosynthesis and degradation that link nutrient stress and social stress to epigenetic changes in the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms.

Thanks again to Ren82 for his intelligent comment in the midst of all the pseudoscientific nonsense:

Diversity in the living world is due to the built in mechanisms in DNA for recombination of genes from the gene pool of the species and expression or supression of different genes (alleles).


http://perfumingt...mit.y=23
Search Results for: RNA-mediated Number of Results: 145

JVK
Nov 21, 2014
Religion, when not practiced by crazy fundies, is not incompatible with evolution.


If that was true, they would not have changed from mutations and natural selection to
...specially evolved... examples of a process called speciation.


They just admitted that evolution via mutations is not compatible with anything known about the conserved molecular mechanisms that link nutrient-dependent species-specific pheromone-production to the control of reproduction and ecological speciation.

What kind of idiot doesn't realize that "Darwin 2.0" is a refutation of everything they were taught to believe about population genetics?

That was a rhetorical question.

The answer is: All idiots who don't understand enough about the laws of physics; the chemistry of protein folding; and the conserved molecular mechanisms that link nutrient-dependent pheromone-controlled ecological speciation via cell type differentiation in all species.

JVK
Nov 21, 2014
Are you one of the idiots who was taught to believe in the pseudoscientific nonsense about mutations, natural selection, and the evolution of biodiversity?

If so, please add your quotes and citations to a list that can be used to exemplify how pervasive ridiculous theories can be. There is no reason to raise another generation to believe in nonsense, but it will take a collective effort to prevent that from happening.

I'll start:
http://publicatio...er1.html
"Over time, mutations supply the raw material from which new life forms evolve (see Chapter 3, "Life's Genetic Tree")." [This page last reviewed on June 9, 2011]

http://www.nature...tion-441 "...mutations provide the "raw material" upon which the mechanisms of natural selection can act."

JVK
Nov 21, 2014
no matter what "driver" you're talking about (natural selection, environment, nutrients, etc) you are ALWAYS talking about mutation.


I'm talking about nutrient uptake as one of Darwin's 'conditions of life' and successful nutrient-dependent reproduction as the driver of ecological speciation. So is this article.

What makes you think that Darwin 2.0 is talking about mutation as a driver, when they claim "behavior specially evolved" in the context of "examples of a process called speciation."?

How could mutations drive "specially evolved" behaviors that lead to speciation?

How can you not recognize the fact that you are one of the idiots who has been taught to believe in the pseudoscientific nonsense, which you have incorporated into your ridiculous behavior associated with your comment?

Nov 21, 2014
How can you not recognize...
the claim of every religious creationist as well as every pseudoscience acolyte like jk
How could mutations drive "specially evolved" behaviors
perhaps you should explain how your anti mutation model actually causes mutations first
remember when 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 what we see from you is confusion over the nomenclature/lexicon as well as blatant stupidity regarding biology
So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
[sic] (Dr. Extavour in a private email asking to explain her work vs jk's "interpretation" ) that you are simply coming from a religious creationist stand point

Nov 21, 2014

How can you not recognize the fact that you are one of the idiots who has been taught to believe in the pseudoscientific nonsense, which you have incorporated into your ridiculous behavior associated with your comment?


I know that DNA is the blueprint for ANY living organism.

How is it that you don't know that if DNA doesn't change or isn't different then you have only one organism? This is VERY BASIC stuff. You have to have changes to the genetic code (mutation) to have more than one organism on the planet. That we obviously have more than one organism (blueprint) goes beyond speculation or theory...it's actually INCONTROVERTIBLE evidence of mutation. Unless you believe a sky fairy just made everything exactly the way it is wholecloth and nothing in nature ever changes...

....if you DO believe that, well good luck with it. I'm not going to engage in a puerile discussion about the color of the sky...

cheers :)

Nov 21, 2014
They just admitted that evolution via mutations is not compatible with anything known about the conserved molecular mechanisms
this is your delusion, and your interpretation because you see the world colored by your faith and creationist belief system

this is why you intentionally ignore evidence that refutes your claims about mutations always being negative: like the following
http://myxo.css.m...dex.html

you continually "interpret" exactly what you want to believe in a study as well... as evidenced in your claims about Dr. Cassandra Extavour et al's work
WHen i sent your interpretation and mine, her response was (again)
So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
i used your words verbatim when i quoted, and linked the site/comments section to avoid misinterpretation from me as well

show us what else you misinterpret, kohl-slaw
you pseudoscience hack

JVK
Nov 21, 2014
INCONTROVERTIBLE evidence of mutation.


We need experimental evidence to support any claim that mutations lead to the evolution of biodiversity manifested in nutrient-dependent pheromone-controlled morphological and behavioral phenotypes with increasing organismal complexity. What you've been taught is akin to the simple-minded approach of population geneticists who looked at differences in morphology and claimed OF COURSE, THEY EVOLVED via accumulated mutations.

Nutrient-dependent changes in hemoglobin vary with altitude in hummingbirds and humans and other human hemoglobin variants also vary with ecological variation of geographic regions. Attributing the variants to mutations instead of nutrient-dependent amino acid substitutions and the pheromone-controlled physiology of reproduction is something only a brain-dead theorist, like Captain (SSgt) Stumpy -- tragically injured in an explosion -- would continue to do.

Nov 21, 2014
We need experimental evidence to support any claim that mutations lead to the evolution of biodiversity


ok
start here: http://myxo.css.m...dex.html
Supported by work being done now my Dr. Cassandra Extavour, et al
Attributing the variants to mutations instead of
perhaps you "forgot" this little tid-bit? remember when 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
and as for
a brain-dead theorist, like Captain (SSgt) Stumpy
I am neither brain dead, a SSgt, nor a theorist
and a FAR more educated person than you are
plus i can comprehend the nomenclature/lexicon used by biologists etc
Something that you and your "mensa" brain can't wrap yourself around yet

epic fail for "kohl-slaw" and his traveling word salad

Nov 21, 2014
Attributing the variants to mutations instead of nutrient-dependent amino acid substitutions and the pheromone-controlled physiology of reproduction is something only a brain-dead theorist, like Captain (SSgt) Stumpy -- tragically injured in an explosion -- would continue to do
and here is another really funny part... SO DO YOU, perfume boy
again, i reiterate... your model causes mutations
you admitted this
your promote your model
therefore logically, YOU PROMOTE MUTATIONS
this does NOT take mensa brains to figure out

and continuing to misquote and blatantly lie about what people are saying is not helping either
like your misinterpretations of Dr. Extavour
which i shall post separately (again)

Nov 21, 2014
" If a species cannot inhabit the same area for an extended time, it will not have the opportunity to evolve and continue."
---------------------------------------------

Perhaps they meant to say " . . . it will have less opportunity to evolve and continue."

And perhaps being able to find more advantageous living areas elsewhere, they do not have to mutate to survive.

Nov 21, 2014
remember when you claimed
This is the kind of question not asked by idiot minions of biology teachers...who teach others to believe in mutation-driven evolution
and you inferred this link supported your anti-mutation stance here? http://phys.org/n...firstCmt
I asked the SOURCE
I can clarify that although our work does, we hope, provide an example of how nutrition/ecology could affect the evolution of potentially adaptive traits, you [Captain Stumpy-CS] are right that we in no way claim that mutations in the heritable genome play no role in evolution. Indeed, as you [CS] correctly state, just because we provide evidence that nutritional conditions play a role, this does not negate a role for mutations. Indeed, in that very same paper, we provide evidence that heritable differences in the genome sequences between Drosophila species, in other words, mutations, ALSO play a role in the evolution of the trait we are studying.

Nov 21, 2014
so when you make the claim
We need experimental evidence to support any claim that mutations lead to the evolution of biodiversity
when Lenski, et al as well as Extavour and more ( http://www.oeb.ha...oeb.html ) have given you empirical evidence as well as experimental evidence in their studies...what do we learn?

that , in the words of the good Dr...
So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
we also learn how someone can be so blinded by a religion and desire to alter data to force a specific conclusion that he would IGNORE reality

we also learn that kohl is a PSEUDOSCIENCE CRACKPOT

my POV is altered by the introduction of evidence, as is best for someone with a scientists perspective
jk is a creationist, and therefore incapable of seeing reality, so decides before hand

epic fail for jk

JVK
Nov 21, 2014
For intelligent discussion, see Illuminating the Interactome
A massive screen yields the most comprehensive map of binary human protein interactions to date. By Molly Sharlach | November 20, 2014

http://www.the-sc...ractome/

The brain-damaged Captain (SSgt) Stumpy seems to represent the best efforts of moderators here to encourage discussion of pseudoscientific nonsense.


Nov 21, 2014
Dashneib, if you believe the words youve typed, your existence is hypocritical
Why? And you can save yourself some typing and just call me "Schneib."

Nov 21, 2014
Thanks for taking care of perfume boi for me, Cap'n.

Nov 21, 2014
Another article with a headline intended to titillate, this time the anti-evolution crowd. I imagine old JVK is barking his usual inane ranting about the "minions" of someone or other. It's hilarious that he insists that evolution is not happening, while chanting about his own theory that is -- get ready for it---a description of evolution! Seriously, the guy has to be a comic or something!

For any that don't know, JVK is the peddler some pheromone based snakeoil he convinces young, naive men can make women fall at your feet if you buy it and wear it in public. He gets right ticked when people point that out, so I love pointing it out!.

To the article: I'm not sure too many scientists thought that mountain building or continental drift we the culprits responsible for speciation. Such slow acting geological phenomena would not seem, to me, to be able to push speciation. Isolation is the key.

Nov 21, 2014
Diversity in the living world is due to the built in mechanisms in DNA for recombination of genes from the gene pool of the species and expression or supression of different genes


Recombination and epigenetics (control of expression) don't make new genes.

All idiots who don't understand enough about the laws of physics; the chemistry of protein folding...


Remember that time I provided you with links concerning biophysical studies and models of mutations? It was only 18 hours ago. Since your short term memory seems to be declining, I'll link them again:

http://www.nature...672.html
http://www.cell.c...901268-8
http://rsif.royal...19?rss=1
http://faculty.ch...ications

Nov 22, 2014
The immune system doesn't operate on the DNA of the host. At least not normal cells in the host; one of its functions is to kill cancerous cells, and another is to remove dead cells. It's not perfect so sometimes we get cancer. But its main function is to detect pathogens and generate antibodies to inactivate them; it then uses its removal mechanism to take out the garbage.

Maybe you'd care to be a little more specific about those "complex cellular mechanisms." Are you referring to the consistency checks and repair functions for DNA? These also are not perfect, and as a result some types of mutations don't get caught or corrected. Furthermore, since much of our DNA is not actually expressed, and some of it isn't involved in any regulation either, mutations in these areas that evade the check and repair functions are inoperative in the organism, but are passed along to its descendents. Later, through recombination or error, these genes are expressed.

Nov 22, 2014
I have not mentioned in my posts that the immune system operates on the cell'sDNA.
You said:
the immune system and the complex cellular mechanisms are fighting with the random mutations
The immune system has nothing to do with it. It doesn't fight mutations. Mutations are undesired modification of the DNA of the host. The immune system doesn't operate on the DNA of the host.

And you didn't specify any of those "complex cellular mechanisms" either.

Nov 22, 2014
Bah. You're quoting Wikipedia without attributing it. Plagiarizing. See ya.

Nov 22, 2014
The immune system attacks the mutated cells
Ummm, we're talking about mutations in the sex cells here; otherwise they're not inherited. Not only that, but mutations that leave the sex cells functional, because otherwise there won't be a successful fertilization. And of course, if they get attacked by the immune system, then they won't be functional, will they?

Fail.

Nov 22, 2014
A single ejaculation contains millions of spermatozoa for mammals around our size. How many of those spermatozoa do you think are imperfect? It's extremely unlikely they all are perfect; otherwise we wouldn't waste so many. Only one of them will fertilize the egg, if there's an egg and it's not defective itself. The contents of the particular spermatozoon that succeeds are not important to the success in fertilizing, as long as they don't hinder it; thus, mutations are not selected against. And the same is true of the egg; if the outside is functional, and a mutation on the inside doesn't interfere with fertilization, then it will be successful and the mutation will be passed down to the eventual offspring (assuming the mutation doesn't interfere with its development). And, of course, if the mutation is in nonfunctional DNA, then there will be no barrier to passing it along at all.

In case it's not clear to you yet, mutations are pretty common, and mostly benign.

Nov 22, 2014
This is due to the fact that you are bombarded with many cosmic rays and with radiation from the environment (called "background radiation;" it's around 5-10mSv/yr for most of us here on Earth, which is equivalent to being struck by one particle of radiation every second). They hit you everywhere randomly, so the size of your testicles or ovaries compared to your body determines how often they are irradiated; you can see that it will be many times a day. Sperm take about 72 days to produce in humans, so obviously there are hundreds of opportunities for them to be damaged.

Worse yet, alcohol, smoking, air pollution, and other environmental and dietary factors can also cause mutations.

The case for eggs is even worse, because a woman is born with all she will have for her whole life. They're dispensed one at a time (usually) once a month; there are many more than she will ever need.

You can see that mutations must be very common indeed.

Nov 22, 2014
When we talk about sex cells, they have the same mechanisms for correction of genetic errors.
Actually, those mechanisms work during fertilization. And remember, they're not perfect. They probably also operate during meiosis, when the genetic material is produced, but then it sits there either for 72 days or for a lifetime, depending on whether you're male or female, and can be damaged.

My question is what should be the percentage of mutated germ cells, which have not been corrected by cell's protective mechanisms, to have sufficient probability that such cells can be mergeed in a zygote and pass these mutations to the next generation?
Good question. On average, every human has about 60 mutations compared to the original DNA from their mother and father. That's actually pretty good considering there are three billion base pairs in human DNA; you can see that the protections against mutations are quite good.

contd

Nov 22, 2014
Source: http://www.livesc...ons.html

I have another estimate from another source that is three times higher; it's Panda's Thumb, a very well-known evolution information site. But we'll go with the low estimate.

And to ensure sufficient frequency of mutations for the proccess of evolution, if we accept the compromise that they move hypothetical evolution.
I'd say 60 mutations per individual is plenty to be going on with, especially over a hundred thousand years or so; that's two million generations of humans (at 20 years per generation). We evolved to our current genetics around 75,000 years ago. Neanderthals evolved more than twice as long ago. Sounds about right.

contd

Nov 22, 2014
Do you have any idea why the female individuals have duplicated sex chromosome?
I'm not quite sure what you want to know when you ask "why." It's a feature that was developed sometime before mammals split off from the ancestral line; birds don't have X and Y chromosomes, they have W and Z chromosomes, and it's males that have the ZZ and females that have the WZ. At meiosis the female ovum gets either a W or a Z; all male spermatozoa are Z. "Why," then, would be the precise environmental pressure that caused that split, and we don't know that.

Perhaps you had another "why" in mind?

So уоu realize how important аre defense mechanisms in organisms against mutations and how effective are built in mechanisms which ensure diversity within species.
Well, considering they only allow 60 errors out of 3,000,000,000 sites, like I said, they work pretty well.

But there's something you haven't considered:

contd

Nov 22, 2014
At each fertilization, only half of the original mutations from each parent make it to the offspring. Remember, the genes from each parent are split in half during meiosis; only the mutations on the half that made it to fertilization count. And on average, that's 30. Thus, mutations do not build up as fast in sexually reproducing organisms as they do in asexually reproducing ones. This is the advantage of sexual reproduction; on average, if each couple produces two offspring, each will contain only half of the mutations from each parent. Natural selection will also remove any severely deleterious mutations. So they don't build up in the genome, as a result of this.

if mutations are so frequent as needed for evolution theory, organisms would be disappear due to loss of functionality long ago.
No, sex and natural selection weed them out.

JVK
Nov 22, 2014
A new book links quantum physics, quantum smell, quantum biology, and quantum consciousness via experience-induced, light-induced, nutrient-induced amino acid substitutions that differentiate all cell types via a direct link from the epigenetic landscape to the physical landscape of DNA in organized genomes.

"Nature" is portrayed as the physicist that makes evolution happen

http://www.econom...e-nature

"Subatomic particles tunnelling across gaps in the nose when aroma molecules are around may be the first step in how animals sense scent. This same tunnelling is presumed to be at work in the action of enzymes, those proteins that shuffle chemical reactions along in living things (among them, the breakdown of tadpoles' tails as they become frogs)."

The "Nature" of everything quanta does not support claims that mutations are beneficial.

JVK
Nov 22, 2014
The "Nature" of everything quanta supports all claims that mutations are neutral or deleterious, which means they can be linked to diseases and disorders but not to increasing organismal complexity via

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

and/or

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

That means evolutionary theorists are pseudoscientists who are training others to be or to become pseudoscientists, anonymous fools, or their idiot minions. That explains why most of you are here denigrating the works or the comments of serious scientists.

For contrast, those who understand the role of the microRNA/messenger RNA balance and ternary switches have linked via odors to de novo gene creation -- as recently reported with links from amino acid substitutions in the creation of new cell types. They will continue to find the displays of ignorance here to be laughable, but deadly to scientific progress.

JVK
Nov 22, 2014
While most of you revel in your ignorance, serious scientists have raised the practice standard with links from epigenetics to pharmacogenomics and to personalized medicine based on levels of evidence established by the pairing of patient outcomes with DNA testing.

The results of a 10,000 (now 14,000) patient cohort were reported as "Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing" http://www.nature...29a.html

The ignorance of theorists is not specifically addressed because theorists are not capable of recognizing their own ignorance. Besides, their ignorance will be naturally selected against when they fail to seek testing that epigenetically links nutrient-uptake and drug metabolism via RNA-mediated events to the genetic networks (and metabolic networks) that are manifested in the physical landscape of DNA in the organized genomes of species from microbes to man.

JVK
Nov 22, 2014
https://plus.goog...tjHwY3aC

The gene, cell, tissue, organ, organ-system pathway is a neuroscientifically established link between sensory input and behavior. Marts and Resnick (2007) stress the importance of this pathway in the context of a systems biology approach to pharmacogenomics.


Excerpted from: "Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors" http://www.ncbi.n...24693349 Socioaffect Neurosci Psychol. 2012; 2: 17338.
Published online Mar 15, 2012.

CAVEAT: It is obvious to intelligent researchers that behaviors don't evolve. However, even intelligent researchers must often use the terms used by theorists -- if only to get past the theorists who review their published works and reject them if they refute evolutionary theory with claims of ecological speciation, which is obviously what epigenetically occurs.

Nov 22, 2014
The "Nature" of everything quanta does not support claims that mutations are beneficial
Lenski and Extavour do
http://myxo.css.m...dex.html
http://www.oeb.ha...oeb.html
Plus, they specifically state that your "interpretations" of their work are WRONG
So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
so much for your ability to read
evolutionary theorists are pseudoscientists
a PSEUDOSCIENTIST redefines words at will and molds data to fit the belief, not accepts the data as is
so that means kohl is a pseudoscientist (and a creationist as well), not a real scientist
especially since he fails to comprehend that his own model CAUSES mutations, which then support the Theory of Evolution

jk=pseudoscience crackpot troll
right there with Ren

JVK
Nov 22, 2014
demonstrate to opponents of the theory of evolution


Your accurate information was immediately followed by another post from the idiot "Captain Stumpy."

He twists this:
So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution


I have never claimed that their works provide evidence AGAINST anything.

Their works do not provide evidence FOR a role of mutations in the increasing organismal complexity of biodiversity manifested only in the context of nutrient-uptake and pheromone-controlled reproduction.

As we continue to see, even though no experimental evidence of biologically-based cause and effect links mutations to increasing organismal complexity, theorists and their idiot minions claim there is no evidence AGAINST the role of mutations.

Pseudoscientists say "prove me wrong." Scientists provide data to correctly represent what is right.

JVK
Nov 22, 2014
Extravour: "Given the commonality of BMP signaling in mouse and cricket germ cell induction, we suggest that BMP-based germ cell formation may be a shared ancestral mechanism in animals."

She links mouse and cricket germ cell induction via the de novo creation of olfactory receptor genes in the cricket, because the creation of receptors is needed for organisms to find food in the context of ecological speciation.

See: Ecological selection as the cause and sexual differentiation as the consequence of species divergence? http://rspb.royal...abstract

See also: http://phys.org/n...tml#nRlv

It shows how theorists will misrepresent all evidence of biologically-based cause and effect as if it linked mutations to biodiversity. They seem to believe the crickets mutated and evolved via natural selection into mice, rats, and humans. Is it too polite to call them idiots?

JVK
Nov 22, 2014
Lenski is worse. He seems to think that bacteria evolved via mutations and became insects, mice, rats and humans based on his experiments with nutrient-dependent ecological adaptation in E. coli.

The Man Who Bottled Evolution http://www.scienc...90.short
Excerpt: "...evolution is roughly reproducible but also endless, even in a stable environment."

Nutrient uptake linked to pheromone-controlled reproduction ensures the environment is not stable. Unless their natural genetic engineering enabled some strains to use a different nutrient source, their populations would starve to death. They would not find something else to eat that stabilized the DNA in their organized genomes, which is what Eshel Ben-Jacob and his group have continued to show in the context of the bio-physically constrained chemistry of protein folding linked to amino acid substitutions in species from microbes to man.

Nov 22, 2014
And of course we know from 19th century thermodynamics and on, that magic is wrong. There isn't any, and we know this.
So? Religion, when not practiced by crazy fundies, is not incompatible with evolution
Sure it is. Theism as opposed to deism, presupposes that the gods described in the books created everything despite having no evidence for it. This enables unwarranted speculation and the arbitrary rejection of science they don't like. God allows them to pick and choose; science doesn't.

Fundies and moderates all read the same books. They might emphasize different parts but given the situation, moderates can quickly radicalize by simply deciding to adhere more strictly to gods word.

Religionists who accept evolution do this. They arbitrarily acknowledge some evidence but reject that which disproves their bookgod.

Nov 22, 2014
Either you believe in evidence or you don't. Evidence says evolution is real and bookgods are not. You can't have both.

Nov 22, 2014
I have never claimed that their works provide evidence AGAINST anything
your specific claims were in reference to Dr. Extavour's site ( http://www.oeb.ha...oeb.html ) and you claim this supported your (anti-mutation) conjecture, which was followed by anti-mutation discourse where you specifically stated
This is the kind of question not asked by idiot minions of biology teachers, like PZ Myers, who teach others to believe in mutation-driven evolution and never question why there is no model for that
which, by definition and by use in the thread ( http://phys.org/n...firstCmt ) states that you are supplying the link in reference to your anti-mutation diatribe (as interpreted by all readers queried) as well as support for your model which, by the way, causes mutations

cont'd


Nov 22, 2014
Their works do not provide evidence FOR a role of mutations in the increasing organismal complexity of biodiversity
so when we directly queried Dr. Extavour, we get the following reply
I can clarify that although our work does, we hope, provide an example of how nutrition/ecology could affect the evolution of potentially adaptive traits, you are right that we in no way claim that mutations in the heritable genome play no role in evolution. Indeed, as you correctly state, just because we provide evidence that nutritional conditions play a role, this does not negate a role for mutations. Indeed, in that very same paper, we provide evidence that heritable differences in the genome sequences between Drosophila species, in other words, mutations, ALSO play a role in the evolution of the trait we are studying.

So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution.
cont'd

Nov 22, 2014
so what does jk respond with now?
It shows how theorists will misrepresent all evidence of biologically-based cause and effect as if it linked mutations to biodiversity
1- Lenski and Dr. Extavour are experimentalists, not theorists
2- they are far more credible than you as they actually are educated and utilize the correct nomenclature/lexicon of the field, which facilitates communication and education
3- you are pissed off that they undermined your diatribe directly so now you call them idiots?
WTF? (I hope you don't mind me sending them this direct libelous attack... i am sure they will have much to say about it )

last thing: PSEUDOSCIENCE never gives evidence for their "proof"
or, when they do, they try to "interpret it" in the light of their religion/delusion

we can see jk blatantly doing this and lying when caught
or trying to wiggle out with double talk and kohl-slaw word salads

jk=liar=pseudoscience

Nov 22, 2014
post script to kohl

i noticed that you also provide a blatant example of "reinterpretation of evidence" above as well as the willingness to dismiss evidence for the sake of your religion

Specifically, i am referring to your libelous diatribe against Dr. Extavour and Lenski

whereas you used them in the past to "support" your anti-mutation position, now that you've been directly refuted by the source and have been proven wrong, you will ignore their evidence and call them idiots

the mark of a true PSEUDOSCIENTIST who is blinded by their religion/faith/delusion


JVK
Nov 22, 2014
What
libelous diatribe against Dr. Extavour and Lenski
?

You seem to think that any factual representations of biologically based cause and effect are libelous because you believe in pseudoscientific nonsense.

Try reading about Science -- in "Science Magazine" for example: Combating Evolution to Fight Disease http://www.scienc...88.short

Excerpt: ..."nothing in evolution makes sense except in the light of biology." Although the latter might be an exaggeration, an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve."

Ecological variation confers the ability to ecologically adapt via conserved molecular mechanisms that limit the ability of any species to mutate and become another species.

If serious scientists believed in the pseudoscientific nonsense touted by theorists, there would be no reason for them to fight against it.

Nov 22, 2014
What

libelous diatribe against Dr. Extavour and Lenski

?
You seem to think that any factual representations of biologically based cause and effect are libelous because you believe in pseudoscientific nonsense
you called them idiots above, you moron
They seem to believe the crickets mutated and evolved via natural selection into mice, rats, and humans. Is it too polite to call them idiots?

Lenski is worse. He seems to think that bacteria evolved via mutations...
YOUR WORDS, not mine
and as for FACTS:
1- a mutation is any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
2- your model CAUSES MUTATIONS
3- this is supported by Prof. Lenski and Dr. Extavour (both educated and FAR more experienced than you)
4- this is PROVEN by both mentioned scientists
5- this is DENIED by you (and only you and the creationists do this)

therefore it is YOU ignoring FACTS

liar=jk=PSEUDOSCIENCE

Nov 22, 2014
All the necessary genes for a certain species are contained in the gene pool of the species and are prebuilt. Organisms do not need the emergence of new genes


They don't need new genes? Well, that's too bad, because new genes emerge anyway. We've seen this happen in real time.

http://en.wikiped...periment

As we continue to see, even though no experimental evidence of biologically-based cause and effect links mutations to increasing organismal complexity, theorists and their idiot minions claim there is no evidence AGAINST the role of mutations.


I've provided you with more than enough experimental evidence. For the 3rd time now:

http://www.nature...672.html
http://www.cell.c...901268-8
http://rsif.royal...19?rss=1
http://faculty.ch...ications

JVK
Nov 22, 2014
Experience-dependent de novo gene creation occurs with of food odor exposure linked to receptor-mediated behavior via metabolism of food to species-specific pheromones.

The link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species is RNA-mediated amino acid substitutions fixed in DNA by species-specific reproduction.

Vosshall's group showed this again in "Evolution of mosquito preference for humans linked to an odorant receptor" http://www.nature...964.html

This was after her group showed mutations perturb the protein folding required for the de novo creation of olfactory receptor genes in "orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET" http://www.ncbi.n...3696029/

It's more important to note, however, that her group has repeatedly shown evidence of overwhelming ignorance among evolutionary theorists.

JVK
Nov 22, 2014
The anonymous fool continues to make claims based on pseudoscientific nonsense about proteins that somehow evolve.

1) Missense meanderings in sequence space: a biophysical view of protein evolution
2) A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
3) Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

Only an anonymous fool would provide citations that appear to claim that new genes somehow evolve via the evolution of proteins. It's as if their anonymity invites fools to claim that proteins evolve outside the biophysical constraints of amino acid substitutions that stabilize protein folding.

Only a bigger anonymous fool or idiot, like Captain Stumpy, would claim that Lenski and Extavour have show that species evolve via mutations in the context of population genetics.

Nov 22, 2014
I think this line says it best:

So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution.


In other words, the charlatan has no clue what he is talking about. Not surprising of course, to anyone who has tried to follow his meandering, stunted, illogical diatribes, but it is nice to have the author of the study confirm it directly.

Oh wait, maybe THIS line says it best!

jk=liar=pseudoscience

Nov 22, 2014
Only an anonymous fool would provide citations that appear to claim that new genes somehow evolve via the evolution of proteins.


That "appear"? You're preemptively dismissing the evidence you're asking for. How are we expected to provide you with evidence for mutation and selection if you dismiss what we provide BECAUSE it's evidence for mutation and selection? Do you see the logical disconnect in what you're doing? It's circular reasoning.

You've asked for models and claimed that mutation doesn't jive with biophysics. I've provided both of those in those links. Plain as day.

JVK
Nov 22, 2014
What's plain as day is this:

"We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms."

http://www.nature...306.html

You took what has been plain as day for more than 40 years and cited works that claim proteins evolve, which suggests they evolved before the last universal common ancestor of all extant organisms. Then, after the proteins evolved, organisms evolved.

What kind of idiot provides citations to works that attest to utter nonsense, just because they seem to support a ridiculous theory? That was a rhetorical question.

JVK
Nov 22, 2014
A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
is open access at http://www.cell.c...901268-8

When the first cited work was reported here, I commented on it. http://phys.org/n...ion.html

Since then, we've seen reports that link single amino acid substitutions from RNA-mediated events to cell type differences in all cells of all individuals of all species. For example, see: Using stable isotope biogeochemistry to study marine mammal ecology http://onlinelibr...4.x/full

It links ecological variation to ecological speciation via amino acid substitutions in all marine mammals.

See also: Kondrashov (2012) "One of the main duplicated gene families are the olfactory receptor proteins..."

What kind of idiot tells other idiots that de novo gene creation occurs via concurrent mutations?

JVK
Nov 22, 2014
Kondrashov (2012) Gene duplication as a mechanism of genomic adaptation to a changing environment http://rspb.royal...abstract "A clear example of a gene duplication conferring an adaptive response to nutrient limitation is that of the yeast hexose transporter."

We linked nutrient-dependent cell type differentiation in yeasts to mammals via the pheromone-controlled physiology of reproduction in the context of molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

The model has since been extended via what's known about RNA-mediated amino acid substitutions and cell type differentiation in species from microbes to man.

Ignorant pseudoscientists still think that mutations somehow lead to increasing organismal complexity manifested in biodiversity. How can anyone be that ignorant?

JVK
Nov 22, 2014
In other words, the charlatan has no clue what he is talking about.


I'm talking about nutrient-dependent RNA-mediated cell type differentiation in species from microbes to man, which is controlled by the physiology of reproduction.

See: Search Results for: RNA-mediated Number of Results: 149
http://perfumingt...mit.y=22

What are you talking about?

JVK
Nov 22, 2014
See also: Alternative RNA Splicing in Evolution http://jonlieffmd...volution

Networks of Genes Respond to Social Experiences http://jonlieffmd...eriences

and virtually anything else posted Jon Lieff's site

There is simply no reason for anyone to remain as ignorant as the anonymous fools and idiot minions of biology teachers like PZ Myers have remained.

Clearly, "If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based. (p 1014)" http://jp.physoc....abstract

Nov 22, 2014
What's plain as day is this:


I'm still not sure what you interpret that to mean or how you think it supports you. What they're saying is that the trend they note in all the groups they studied was more likely to have evolved in their shared ancestor instead of separately in all groups.

What kind of idiot provides citations to works that attest to utter nonsense...


It's not nonsense if I can provide citations containing solid evidence to support it. You asked for models and I have provided them. You can't dismiss evidence just because you don't like the conclusion it leads to. If you have a problem with the evidence itself, you can contest how it was gathered. If you have a problem with the conclusions it leads to, you can reason as to why the evidence doesn't lead to those conclusions. You have done neither of these things.


Nov 22, 2014
we've seen reports that link single amino acid substitutions from RNA-mediated events


If you're talking about those that occur as part of RNA editing, then sure, but base substitutions in DNA are due to mutations. We know they're do to copying errors during replication. We know the error rates of the various polymerases. We know how many of those errors end up not being corrected and are passed down to the subsequent generation. This is well studied.

Example: http://www.jbc.or...full.pdf

Reactive oxygen species cause some G's to become 8-oxoguanine. This causes G to T and C to A substitutions. This occurs at random. Translocations and rearrangements can also be random. As Noble implies, these processes can also be non-random and induced.

Mutations can cause both positive and negative changes. Here's an example of a mutation leading to an increase in enzyme activity, not a detriment:

http://europepmc....24818485

Nov 22, 2014
What kind of idiot tells other idiots that de novo gene creation occurs via concurrent mutations?


Gene duplication is a type of mutation. Like others, duplication can have negative and positive effects, as seen here:

http://users.rcn....ons.html


Nov 22, 2014
Natural selection is very overvalued by evolutionists. Many of them believe in its magcal capabilities, without bothering to rationalize its mechanism in detail.
Rationalization is a tactic for making a lie look like the truth so it will be accepted. You're correct, biologists do not rationalize.

What detail? Those more fit are more likely to reproduce more often. The buck of every herd understands this, and has nearly exclusive reproduction rights. And will fight and kill to preserve those rights. That's natural selection.

They have a very vague idea about how this process works.
Looks more like you have a very vague idea of what they mean when they talk about it, and have trouble understanding how it applies in different contexts.

contd

Nov 22, 2014
Whether an individual would have successors or not depends much more of random environmental factors, rather than its inherited characteristics.
Yes, but the evolutionary response to environmental factors is orderly, and those that live carry on living.

Man has evolved-- i.e. bred-- wolves into chihuahuas. If we can do that simply by culling all the larger dogs from the genetic line and breeding the smallest ones, then evolution is a fact.

That's human selection, as opposed to natural selection, but it works just the same.

contd

Nov 22, 2014
Natural selection do not allow only the individuals in the local group which have severe mutations, that lead to some degree of disability, to have offspring, and thus preserve the original gene pool as long as possible.
But bad genes will be passed to their descendents, and if bad times come they'll be less likely to live. And using my buck example, only the most fit buck for each herd breeds (other than the occasional rape or illicit liason). As I said, natural selection weeds them out; remember again that the successful buck got the least number of harmful as well as the greatest number of helpful alleles.

But it does not affect a minor mutations that do not affect the ability of individuals to survive and to have offspring.
But natural selection does. And when combined with the reduction during meiosis this eliminates those bad genes from the gene pool; their carriers die without reproducing (or without reproducing much) and eventually they die out.

contd

Nov 22, 2014
If a point mutation can causing any serious genetic disease, what is the chance to have for a species to survived, relying only on random mutations?
Ummm, how often does a point defect cause such a disease? I point to the human population the vast majority of which do not suffer from such diseases, even though they each contain 60 "point defects" (i.e. mutations).

And yet again, I remind you that the bad genes are eliminated by reduction in meiosis and natural selection, as I originally said.

Nov 22, 2014
How do random mutations create such precise mechanisms to combat them and such a complex organization in cells?
They evolve them. The ones that don't have that mutation die out.

It's hard to believe that rundom events can create miracles,
What random events? Evolution by natural selection is an orderly response. In fact, we have evolved to evolve, and not only that, at the right rate for conditions. And when I say "we" I don't just mean humans; I mean every living organism on Earth. We evolved to evolve, and evolve right, or we wouldn't be here.

that educated scienties with their intelligence, smart approach and sophisticated laboratory equipment can not achieve and demonstrate to opponents of the theory of evolution.
I will point to the Miller-Urey experiment and the many recapitulations of it in the lab.

I will point to Stuart Kauffman's demonstration of the inevitability of life in At Home In The Universe.

contd

Nov 22, 2014
One of the places you are making a logical error, Ren, is in trying to link environmental changes to evolution as if they were on the same level. Evolution is a *response* to environmental changes; and those might include the evolution of other species. But it is only a *response.* Just because the stimulus is random doesn't make the response random. Natural selection is not random; it favors those that breed. That's the main justification for the theory of evolution by natural selection. Furthermore, it's obvious from the fact we can evolve wheat from grass, chihuahuas from wolves, and domestic cats from wild North African cats that will not approach humans. Unnatural selection seems to work fine. Why shouldn't natural selection?

Nov 23, 2014
what types of mutations occur in the cell


There are a bunch of classes of mutations. Point mutations, deletions and insertions (indel), inversions, rearrangements, transposons, polyploidy, duplications, etc.

their mechanisms of occurrence


Point mutations can occur due to DNA damage in interphase and failure during repair, indels can occur in a number of ways, including slippage of strands during replication, inversions and rearrangements can occur during double strand breakage where the parts aren't joined back up in the same sequence or direction that they started in, polyploidy is the result of interrupted mitosis, and duplications are the result of uneven crossing over of homologous chromosomes.

how change in their chemical composition reflects their 3D structure, stability and functions?


That's entirely dependent on the protein structure and the type of mutation. Although there are 21 amino acids, there are classes that act similarly.

Nov 23, 2014
Some substitutions have little to no effect because the new amino acid acts similarly to the old one.

Let's give specific examples of errors in DNA that have led to improvements in the functions in humans.


http://bigthink.c...n-humans
http://evolution....altitude

Also, lactase persistence.

To operate evolution what should be the percentage of conditional beneficial mutations in the total number of mutations in the group?


There has been a lot of work done on optimizing mutation rate. Here's one:

http://www.pnas.o...154.full

Lenski also covered this. They noted mutations that resulted in higher mutation rates came to dominate.

What is the mechanism by which a mutation becomes useful


Entirely dependent on what the mutation is and how it affects phenotype.

http://europepmc....24818485

Nov 23, 2014
By Itself a change would not improve if there are no simultaneous changes in many other places in the system


Example: One of Lenski's E. coli populations had a translocation mutation that put an oxic promoter in front of the citrate transporter gene. It began expressing the transporter and therefore had an extra energy source that gave it an advantage over those that didn't mutate that way. No simultaneous change needed.

Explain how our natural selection works in small unnoticeable mutations that each person has


It doesn't necessarily. Beneficial mutations of small effect are lost to genetic drift all the time and even maladaptive mutations of small effect can remain if selective pressure against them isn't high enough. Genetic drift is involved.

Nov 23, 2014
Evolution is a *response* to environmental changes;

Careful. This is often misunderstood (I know you mean the right thing but I'm sure Ren doesn't have the grasp of it that you do)

To quote my favorite quote from bash.org
Some people...have the idea that evolution is a fucking system of...
"oh i need flippers, i'd better grow some" type bullshit. :P
It's more like "Oh shit look at that freak over there with the flippers hahaha OH SHIT I AM DROWNING OH GOD SAVE ME FLIPPER BOY".

Environment selects among the mutations. Mutations are not directed at fitting to a change in environment. Mutation is a scattershot approach where one can hope that some mutation will be viable.

That is why climate change is so dangerous. The number of pellets (mutations per generation) is limited. The more rapid the environmental change the farther the target has moved between shots (generations). If you miss with all pellets during one shot it's "game over" for a species.

Nov 23, 2014
how different bacterial samples are kept of contamination by other bacterial species


This is not hard to test for and not hard to notice. As you can see here:

http://myxo.css.m...iew.html

They take samples from the liquid culture and plate them. Different bacteria have different colony morphologies and are easily distinguishable.

What were the mutagenic factors during the experiment?


In Lenski's? Nothing. No treatments were applied as far as I've read. They're subject to normal background radiation and replicative/other molecular errors.

By what percentage has changed the DNA of the last against DNA of the first generations?


You can read here what genotypic changes occured:

http://books.goog...;f=false

Discussion of mutation rate begins on page 246. You can do the math yourself considering they've gone through 60,000 generations.

Nov 23, 2014
Under normal conditions in their natural environment first or the last generations are more tailored and have more vitality and capability for replication?


Impossible to say since they're not in their natural environment. One could introduce them into an animal's GI tract to see how they fare over time while competing with wild type E. coli and other gut flora.

Out of the 20 essential amino acids, none of these have no similar chemical characteristics


Not quite. Certain amino acids can be functionally equivalent to others due to similarities in structure and depending on where they are in a protein once it's folded. Folding is largely driven by hydrophobicity and hydrophilicity, which are the two categories amino acids are put into. Last few sentences of the first paragraph:

http://www.protei...ent.html

JVK
Nov 23, 2014
Gene duplication is a type of mutation.


Gene creation is not a type of mutation. Odor exposure causes de novo creation of beneficial olfactory odor receptors.
See: Evolution of mosquito preference for humans linked to an odorant receptor http://dx.doi.org...ure13964 http://www.nature...964.html "More generally, such host shifts not only impact the efficiency of mosquitoes as vectors of infectious disease, but contribute to the economic damage caused by agriculturalpests49 and play a key role in the formation of new species50."

Mutations perturb that ability. See: orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET http://www.ncbi.n...3696029/ "We conclude that the odorant receptor pathway is crucial for an anthropophilic vector mosquito to discriminate human from non-human hosts..."

How do mutations cause gene duplication that is beneficial?

JVK
Nov 23, 2014
anonymous fool:
Gene duplication is a type of mutation.


"...as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection... To some extent, it just happens." http://www.scient...plexity/

"...alternative splicing may be the critical source of evolutionary changes differentiating primates and humans from other creatures such as worms and flies with a similar number of genes." http://jonlieffmd...volution

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation -- http://www.hawaii...ion.html

How do mutations cause gene duplication that is beneficial?

Nov 23, 2014
How do mutations cause gene duplication that is beneficial?


Duplication is the result of uneven crossing over during meiosis. It's not like the cell intentionally messes up crossing over. Like I said before, duplications can also be detrimental. Like trisomy, too many copies of a gene can be bad. There's a form of hereditary hypertension that's the result of aldosterone synthase duplication.

As for being beneficial, redundant copies aren't under selective pressure, so they're free to accumulate all other types of mutations to produce a novel protein.

JVK
Nov 23, 2014
Duplication is the result of uneven crossing over during meiosis.


Duplication is nutrient dependent.
Gene duplication as a mechanism of genomic adaptation to a changing environment (link opens pdf) rspb.royalsocietypublishing.org/content/early/2012/09/05/rspb.2012.1108.full.pdf+html "One of the main duplicated gene families are the olfactory receptor proteins..."

...redundant copies aren't under selective pressure, so they're free to accumulate all other types of mutations to produce a novel protein.


Genes and circuits of courtship behaviour in Drosophila males http://dx.doi.org.../nrn3567 "The Fru proteins encoded by the P1 promoter transcripts have a 101‑amino-acid amino‑terminal stretch called the M‑sequence (M for male-specific), which is absent from
non-sex-specific Fru proteins (called FruCOM; COM for common)12,16."

What mutated gene(s) are you claiming leads to sexual differentiation in all cell types of all males of all species?

JVK
Nov 23, 2014
Thanks, Ren82

As you know, all of the pseudoscientific nonsense that has been introduced into this discussion by theorists has been repeatedly addressed with refutations in the current extant literature.

As always, the problem remains, pseudoscientists will not read the extant literature or they simply cannot understand it. Intelligent serious scientists are faced with an insurmountable problem: IGNORANCE.

See for comparison: THE ROLE OF ECOLOGICAL EPIGENETICS IN INTEGRATIVE BIOLOGY 109 http://books.goog...;f=false
Aaron W. Schrey, Joshua Banta, Holly J. Kilvitis, and Christina L. Richards


Nov 23, 2014
hypothetical positive mutations
@dumb&dumber-REN
this is bias based upon religion and is not science
there is ample evidence of positive mutations: http://myxo.css.m...dex.html
even jk's idiotic rantings show that his model causes beneficial mutation in his own words, even, so ignoring it is simply ignoring reality

you are a TROLL

all of the pseudoscientific nonsense that has been introduced into this discussion
the only pseudoscience being promoted by anyone is:
your continual kohl-slaw-word-salad obfuscation and ignorance and your intentional misinterpretations (these are called blatant lies and are considered wrong per your own religion), as well as your anti-evolution stance
has been repeatedly addressed with refutations
you've not refuted anything
you've supported evolution the whole time
you just can't see that
Try re-reading Anon's posts, mensa boy

jk=TROLL

Nov 23, 2014
Intelligent serious scientists are faced with an insurmountable problem: IGNORANCE.
this is the only thing jk has said that is 100% true
and here is why
pseudoscientists will not read the extant literature or they simply cannot understand it.
this is jk in a nutshell
and this is PROVEN by his own comments, especially when initially referring to Dr. Extavour's work as supporting his position that mutations are never beneficial and that mutations don't help with biodiversity... and when the good Dr. refuted jk's BS with
So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
suddenly everyone else is an idiot (and he even posted that above!)

http://math.ucr.e...pot.html
http://sci-ence.o...-flags2/

the ONLY idiot or pseudoscience here is jk, ren and the other TROLLS


Nov 23, 2014
Duplication is nutrient dependent.


I'm still not sure what you mean by this. Are you saying certain nutrients induce duplications? We know the molecular mechanisms that result in duplications quite well:

http://adi-38.bio...oXIa.pdf

Let leave hypothetical positive mutations aside for a moment.


Hypothetical? I gave you direct examples.

What happens with the bad mutations accumulated over generations, that do not lead to direct disability?


If they're not detrimental to be purged by selection, what's the problem?

What is the ratio between conditionally positive and harmful mutations in normal environmental conditions?


http://www.geneti...17.short

We found that 5.75% of the fitness-altering mutations accumulated were beneficial.


http://onlinelibr...abstract
http://mic.sgmjou...47.short

JVK
Nov 23, 2014
Conclusion: "the physical nature of hydrophobic and electrostatic interactions... plays a key role in maintaining the network topology while allowing the protein amino acid sequence to evolve." http://www.cell.c...)00841-8

That fact suggests proteins do not evolve outside the biophysical constraints of nutrient-dependent amino acid substitutions, which means proteins do not evolve. Instead, new proteins are created in the context of epigenetically effected nutrient-dependent RNA-mediated amino acid substitutions.

The bio-physically constrained context (above) is the basis for the chemistry of epigenetic pharmacology, which eliminates any consideration of mutations and/or natural selection in the context of evolved biodiversity.

Obviously, biodiversity did not evolve via mutations if epigenetically effected RNA-mediated events lead to pheromone-controlled reproduction via amino acid substitutions that stabilize DNA in organized genomes.

JVK
Nov 23, 2014
Are you saying certain nutrients induce duplications?


No. Everyone with any common sense already knows that. What I did was supply a reference to support that fact, so that others can compare your ridiculous claims to facts that would be common sense even among theorists -- if only the theorists had not been taught to believe in pseudoscientific nonsense.

Did the link to Kondrashov (2012) not work for you? Gene duplication as a mechanism of genomic adaptation to a changing environment http://rspb.royal...abstract

Is it not clear that gene duplication is nutrient-dependent? If not, are you even more ignorant than anyone could possibly imagine?

Nov 23, 2014
Why in areas with increased mutagenic factors do not appear super people but only mass morbidity in the population?


My second to last link covers that.

As always, the problem remains, pseudoscientists will not read the extant literature or they simply cannot understand it.


Speaking of, let's all take another look at this laughable mistake of yours:

http://www.educat...nicorns/

JVK
Nov 23, 2014
Bershtein S, Mu W, Serohijos AW, Zhou J, Shakhnovich EI: Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness. Mol Cell 2013, 49:133-144.
Cited in Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics (in the context below)

"In this work the authors use genome editing approach to introduce rational variation into E. coli gene encoding DHFR proteins and dissect relative contributions of molecular effect of mutaions and homeostatic response to fitness effect of mutations. The authors provide a model that accounts for observed effects."

Captain Stumpy should discuss this with his colleagues: Lenski and Extavour who will no doubt provide a model for comparison that explains what is known about nutrient-dependent pheromone-controlled ecological adaptations in every other species on the planet.

Nov 23, 2014
No. Everyone with any common sense already knows that.


Let's say I have a population of bacteria. What nutrient should I add to the media in order to induce duplications?

Duplications are mutations like any other. They occur randomly and are implicated in disorders as well as beneficial situations.

Did the link to Kondrashov (2012) not work for you? Gene duplication as a mechanism of genomic adaptation to a changing environment http://rspb.royal...abstract


Somehow, I doubt you even read that. As always, you mix up cause and effect. Kondrashov isn't saying that the environment causes duplications to occur. He's saying that duplications occur and they may result in beneficial phenotypes and end up conferring an advantage.

JVK
Nov 23, 2014
See:
Criticisms of the nutrient-dependent pheromone-controlled evolutionary model http://www.ncbi.n...4049134/

Andrew Jones (aka anonymous_9001) uses his extensive knowledge of biologically-based effect to claim:

Duplications are mutations like any other. They occur randomly and are implicated in disorders as well as beneficial situations.


Anyone who does not agree that a statement like that could only come from a fool should see his criticisms of: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...3960065/

My model has been viewed nearly 12,000 times since tracking began in January 2014. Every aspect of the model has since been extended across species to what is known about RNA-mediated events and amino acid substitutions that differentiate all cell types.

Fools still claim random mutations are beneficial and that they lead to evolved biodiversity. I give up!

Nov 23, 2014
You disagree that duplications are random or you disagree that they're implicated in both positive and negative changes?

Nov 24, 2014
Duplication is nutrient dependent.

Well, duh.
No eat, no energy to duplicate.
And no amount of pheromones are gonna make a woman want to have sex with a scarecrow looking guy.
Money, on the other hand...

Nov 24, 2014
What happened to mutations, natural selection, and the evolution of biodiversity?
Nothing much.

It's just that everybody else in biology isn't a nutjob and *expects* mutations, natural selection, and the evolution of biodiversity. It's kind of like how pilots expect gravity, or sailors expect water.

And how artists expect rejection...

Nov 24, 2014
I read some of the sites and assured how wishful thinking can lead to reckless conclusions.


If they're reckless conclusions not supported by the data, you should be able to point out exactly what's wrong with them.

The strange thing is that in most materials there are no solid criteria by which to judge whether a mutation is possitive or not


That's because the effect of a mutation is often times dependent on the environment and needs to be judged after examining the resulting survivability, fecundity, etc. You can't just look at a gene sequence and say whether a change will be good or bad. You need to wait and see how it affects the phenotype and the organism overall.

how many generations you give to this species to survive? How fast will acumulate damage to the DNA of the species?


Genetic entropy is a flawed concept. If it held any water, every species would have been extinct eons ago.

Nov 24, 2014
If you want detailed refutation of genetic entropy, it's covered extensively here:

http://newtonsbin...e-i.html
http://newtonsbin...nts.html
http://newtonsbin...-ii.html
http://newtonsbin...-ii.html
http://newtonsbin...dum.html

Tell me what causes the difference between you and your parents? Mutations or there is another reason?


Mutation and meiosis including independent assortment.

cjn
Nov 24, 2014
Just a note: Genomic mutations aren't random in the sense that anything can happen anywhere in the genome. Its a mistake to phrase it that way, and it only leads to further confusion among those that aren't familiar with the process. DNA mutations occur at different rates within the genome, with "conserved" regions more likely to be copied and proofread correctly, and other regions whose propensity for mutations enables genetic diversity within the species. Beyond that, there are specific traits of the sequence and structure which favor specific types of mutations.

Over billions of years of selection, the fact that mutations occur at all in the most fundamental element of biology indicates that it is a desired behavior. If it was not desired, copying and proofreading would have been optimized to the point of perfection.

Nov 24, 2014

Tell me what causes the difference between you and your parents? Mutations or there is another reason?

addition.

Nov 24, 2014
Obviously, biodiversity did not evolve via mutations
well, jk... there goes your own model out the window
remember when 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 given that your model causes mutations, your model cannot, by your own words, help with the biodiversity issue
if only the theorists had not been taught to believe in pseudoscientific nonsense
yes, yes, we get it
no one in the world but you and your trained monkey's can comprehend the issues correctly... you are the only one who understands the science
perhaps you should read the following links
http://math.ucr.e...pot.html
http://sci-ence.o...-flags2/

look at this laughable mistake
@anonymous_9001
jk can't even get it right with his PALS!
ROTFLMFAO

Nov 24, 2014
Speaking of, let's all take another look at this laughable mistake of yours:
http://www.educat...nicorns/
@Anonymous9001
I am laughing so hard reading this that i almost spit coffee all over my new laptop!
THANKS for posting this link!
not only does jk like to misinterpret it, but he can't even get it right when talking to one of his creationist pals who should be supporting him!
maybe it is because he (self admitted) failed out of college?

And this, ladies and gentlemen, is the reason you should STAY IN SCHOOL and get an education!
and more proof that jk promotes PSEUDOSCIENCE
My model has been viewed nearly 12,000 times since tracking began in January 2014
And most of those links came from your atempts to spam PO here!
Fools still claim random mutations are beneficial and that they lead to evolved biodiversity. I give up!
no, a FOOL ignores the literature and makes stuff up as he goes
like definitions (JK)

cjn
Nov 24, 2014
Ren82:
How will you prove that mutations are not random events? Ionizing radiation is there a preference for certain areas of DNA or can affect any part of it without selectivity. In DNA is there areas less protected from errors than other areas in the DNA molecule during the replication process? Aggressive chemical agents may show some selectivity towards certain areas of DNA but they are very different and their combined effect leads to the same lack of selectivity.


You're too narrowly focused on extra-cellular actors (which just a red herring). Read up on DNA packaging and physical structures -specifically histones, nucleosomes, and chromatin. These, along with modifications like DNA phosphorylation support control of replication.

You failed to respond to my key point though, which is: If DNA mutation was not desired, why does it occur after billions of generations?

cjn
Nov 24, 2014
Why you think that there were billions of generations? Who told you that? At this rate of mutations despite defense mechanisms against them, which genome will survive so many generations?


You're kidding, right? We've found evidence of life on Earth as old as 3.5Bn years old. Considering that microbial generations are measured in days or hours, yes Billions of generations.

cjn
Nov 24, 2014
Mutations are causing by mutagenic environmental factors and are not desirable and necessary. Therefore the cells have the protective mechanisms that restore DNA. When these mechanisms fail to restore the correct structure and sequence of DNA, the immune system attacks the cells that do not function properly.


Mutations are not solely caused by environmental factors; they occur as a result of mistakes made in DNA replication. The vast majority of mistakes that are made get caught by proofreading proteins, but some do not. Its like you didn't even try to study any actual biology:
http://www.nature...tion-409


Nov 24, 2014
"It doesn't bother me. If people need an imaginary super magic sky daddy, they can have one, as long as they don't start denying reality."
the damage caused by belief in a "sky daddy" is far more reaching and crippling to the advancement of the human condition than any tyrant or disease has every dreamed of inflicting.
Actually, religion is just another mind virus, just like language or good music or good books. Or for that matter science.

Such mind viruses are called "memeplexes," and they form pretty much everything we call "culture." I'm not in favor of removing culture from humans; it's what keeps us from being little bands with a boss who gets all the best food and sex.

Blaming religion for the natural aggression of humans is like blaming wind for rain. Obviously, most humans have an emotional need for it; look how many have a religion, and how many don't.

contd

Nov 24, 2014
Science is a mind virus with a special characteristic: it leads us to deeper understanding of the world around us, which enables us to make better survival decisions, and better ethical decisions, than are suggested by our reactive (i.e. emotional) natures. It's a benign mind virus that helps us survive, in other words.

In the long term, all religions will have to accommodate science; it's inevitable. I have called before now for religion that doesn't contradict science. I think it's clear the majority of humans require a religion, and we should have one that gives them what they need without denying science. It should be flexible enough that when scientific theories are disproved, it doesn't hiccup. It should give the emotional satisfaction and tribal experience people need without leading them into denying reality.

contd

Nov 24, 2014
Pretending people will give up religion is silly.

Having experienced its emotional pull personally, I will tell you that if you try to force people to become non-religious, you are fomenting the revolution against you. Religions are built to repel challenges to their beliefs. You are attacking their strength. It's better to attack weaknesses, and so change this apparently necessary emotional phenomenon into something that helps us.

if one strictly isolates to a 600 year period and strictly to one religion (beginning at 900AD/christianity), one would be severely challenged to disprove the previous statement.
Your definition of a religion is very narrow. You seem to be speaking fairly exclusively of Christianity and Islam. They aren't the only two out there, you know.

contd

Nov 24, 2014
I can't see a way of responding to your last two statements without becoming judgmental. Since I don't want to talk that way, I won't respond.

OTOH, the other points were worth responding to. I wish you'd stick to reasoning and avoid emotional content.

Nov 24, 2014
How will you prove that mutations are not random events?


Not all parts of a genome acquire mutations at the same rate. This can be due to how tightly packed the genome is at particular points and other factors. There's been a lot of research showing that some points are more prone to mutations than others.

Recombination of the genetic information is built in mechanism.


What's your point? All recombination does is shuffle existing genes. It doesn't make new genes.

What is the logic ... these cellular mechanisms are preserved and continue to work effectively?


Selection maintains functional phenotypes.

Without them and the immune system no one species would survive for more than a few generations because of mutations.


You say that very matter-of-factly when it is not true. Mutations do not accumulate that fast. Schneib already pointed out to you that you only differ from your parents by 60 mutations.

Nov 24, 2014
Mutations are causing by mutagenic environmental factors and are not desirable and necessary.


Can you please read what's presented to you? I already gave you a link showing optimization of mutation rate. There's a sweet spot between too little and too much that offers enough variation without outpacing repair and resulting in extinction.

www.pnas.org/cont...154.full

Why you think that there were billions of generations? Who told you that?


Common sense and science tells us that. Lenski's E. coli went through 60,000 generations in ~9100 days. Scale that up to billions of years and get back to us after you do the math.

JVK
Nov 24, 2014
Ren82

As you can see, there is nothing you can do to educate anonymous fools and idiot minions of biology teachers linke PZ Myers who have taught them to believe in a ridiculous theory.

All any serious scientist needs to do is look at a few of these articles: http://www.ncbi.n...25413365

If they cannot grasp the fact that cell type differentiation is nutrient-dependent and RNA-mediated via the conserved molecular mechanisms of species-specific reproduction controlled by pheromones, they are not serious scientists and may never be.

We see that here, and it only becomes more ridiculous the longer you watch.

Nov 25, 2014
@jvk

Why don't you just admit you hate P.Z. Myers because he so effortlessly demolishes the arguments of creationists such as yourself.

Nov 25, 2014
Ren82

As you can see, there is nothing you can do to educate anonymous fools and idiot minions of biology teachers linke PZ Myers who have taught them to believe in a ridiculous theory.

All any serious scientist needs to do is look at a few of these articles: http://www.ncbi.n...25413365
If they cannot grasp the fact that ....
We see that here, and it only becomes more ridiculous the longer you watch.
@jk
WAIT...
so you are telling me that if i take the time to POLL all the authors of all 101 studies linked on that page you linked, they will all categorically deny mutations, their existence and the fact that mutations can be beneficial?
You are saying that all 101 studies authors will ALL validate your belief that mutations are always harmful?
(using the accepted definition, of course)

OK
challenge accepted

would you like the results posted here or to your home page, mensa boy?
maybe forward it to Myers?
Hmm?

Nov 25, 2014
@Ren I can not understand how some people can believe that random processes can create such high ordered cosmic structures and so coplex biological lifeforms?
You are too dim to understand how order emerges from chaos, yet you believe in an invisible. omnipotent skyfairy. Hilarious!

Nov 25, 2014
>kochevnik

Explain how random events can create highly organized systems from chaos. Which physical laws allow it? Give examples. What causes a reverse process of increase in the entropy of the system? What dominates in the universe? Self organization or an increase of entropy over time? Give an example. For what is the human intelligence after the most simple organisms cope wonderful on planet Earth. Bacteria will outlive all other organisms in the deterioration of the living environment. What advantage then have highly organized forms of life from the perspective of evolution compared to bacteria?
You need to go to school, Ren. Teachers get paid so if you want it for free visit your library or use the Internet as it was intended. Wikipedia would be a starting place. I have seen much, much more than you so I invite you to indulge your curiosity I am confident you will the find the investment worthwhile

I will mention that overspecialization is usually extinction

cjn
Nov 25, 2014
Ren82:
I think I have a good education and continue constantly to self educate in the areas that interest me.... Jast give explatnation with your words.


I'm sure that you have sufficient knowledge of a number of things, I just wouldn't consider Biology among them. Your fundamental misunderstanding with everything discussed so far is that things are not "random". There are controls on each process which are dictated by chemistry, physics, mathematics, and statistics. These controls drive the affinities of molecular interactions, the selection of traits, and a thousand other phenomena which have resulted in life as it exists today.

Again, evolution isn't a random sequence of events, it is a series of unplanned events occurring with in a framework of quantifiable controls.

Nov 25, 2014
Incidentally Wikipedia is not the best place from which someone can draw reliable information. I prefer more reliable sources of scientific information.
@dumb&dumberREN
1- wiki is a good place to START
2- wiki has references and links to source material, which is why it is a good place to START because it gives you the ability to validate a claim or verify that the data exists
if it doesn't have links/references, it can then be said to not be a good source of info.
3- no place is a good place for information when you have religious goggles on that will not let you assimilate information or think rationally and logically

when you can overcome your religion, then perhaps you will see the reality of the universe around you, which is far more grandiose than you've portrayed it with your skewed perspective


JVK
Nov 25, 2014
Why don't you just admit you hate P.Z. Myers because he so effortlessly demolishes the arguments of creationists such as yourself.


Thanks for asking. I like to use him as an example of how even the most ignorant biology teacher I have ever encountered can develop a following of anonymous fools and idiot minions.

For contrast, anyone who has followed the recent literature knows that chromosomal rearrangements, which are linked directly from nutrient-uptake to RNA-mediated events and pheromone-controlled reproduction, result in morphological and behavioral diversity.

When PZ Myers attacked me for stating the facts and let his idiot minions take it from there -- he did precisely as he has always done to display his ignorance and that of many other theorists -- all on one atheistic blog site.

See: One crank dies, another rises to take his place http://freethough...s-place/

cjn
Nov 25, 2014
When PZ Myers attacked me for stating the facts and let his idiot minions take it from there -- he did precisely as he has always done to display his ignorance and that of many other theorists -- all on one atheistic blog site.


Serious question: Who is PZ Myers? I honestly have no idea, and have only ever heard of him through your relentless assaults on his name.

JVK
Nov 25, 2014
Ren82 will like this from the link above:
I wrote: "Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.
These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don't we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete..."

JVK
Nov 25, 2014
Who is PZ Myers?


I just told you who he is "... the most ignorant biology teacher I have ever encountered..." and I linked to his blog site.

He made an excuse to ban me from participation after I provided links on January 16 to works by Denis Noble and by Bruce Horton that made two things clear:

1) Neo-Darwinism is the ridiculous invention of population geneticists. http://gbe.oxford...abstract
"…population geneticists such as Wright (1941) showed that the probability of fixation of these chromosomal rearrangements is so low that they would not be easily established..."
2) Chromosomal rearrangements differentiate morphological and behavioral phenotypes of white-throated sparrows via conserved molecular mechanisms in species from microbes to man. http://www.pnas.o...abstract

Details about the underlying RNA-mediated events were in our 1996 review http://www.ncbi.n.../9047261

Nov 25, 2014
P.Z. Myers is an atheist and biologist, a ridiculer of creation/intelligent design.

http://en.wikiped...PZ_Myers

JVK
Nov 25, 2014
1- wiki is a good place to START


Only if you are not an idiot minion of a biology teacher who taught you to believe in pseudoscientific nonsense. If you are not, see:

http://en.wikiped...R._Ellis

for comparison to

http://en.wikiped...PZ_Myers

Note: George Ellis is portrayed in the movie: "The Theory of Everything" http://www.focusf...erything because he co-authored with Stephen Hawking.

PZ Myers is not featured, because he never contributed to any accurate representations of biologically-based cause and effect. George Ellis has also co-authored with Denis Noble.

Top-down causation: an integrating theme within and across the sciences? This is one article from the Top-down causation Organized by George F. R. Ellis, Denis Noble and Timothy O'Connor http://rsfs.royal.../2/1.toc

I hope to hear from George Ellis soon about whether the movie portrayal is accurate.

Nov 25, 2014
Serious question: Who is PZ Myers? I honestly have no idea, and have only ever heard of him through your relentless assaults on his name
@cjn
Myers is a Biologist and professor who pointed out the pseudoscience behind jk and his idiot no mutation pheron=mone stuff... read his article i am linking and you will see why jk hates him
Go here: http://freethough...s-place/

(P.S. What Vietvet Says)

When PZ Myers attacked me for stating the facts
he didn't attack you for stating the facts, he did it because you were obfuscationg science as well as denying FACTS and REALITY, like mutations (which, by your own admission, your own model creates)

JVK
Nov 25, 2014
P.Z. Myers is an atheist and biologist, a ridiculer of creation/intelligent design.


Thanks. This shows that many people know that he is an idiot. Like Masatoshi Nei in "Mutation-Driven Evolution" http://www.amazon...9661731, Myers has been touting the same pseudoscientific nonsense for decades, while ignoring what is known about the laws of physics and the chemistry of protein folding.

Nei concludes: "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements."

I don't think that "The Theory of Everything" movie will support that pseudoscientific nonsense, which makes me wonder what PZ Myers and his idiot minions will claim after they see the movie.

JVK
Nov 25, 2014
he didn't attack you for stating the facts, he did it because you were obfuscationg science..."


Everything published by serious scientists during the past 5 decades links nutritional epigenetics to pharmocogenomics via the conserved molecular mechanisms we detailed in our 1996 Hormones and Behavior review.

See also: Evaluation of reference genes for quantitative real-time PCR in the brain, pituitary, and gonads of songbirds, which was published earlier this year in Hormones and Behavior:
http://www.scienc...14000786

"Overall, qPCR has been used in songbirds to quantify expression of mRNA in relation to stress responses, maternal care, photoperiod, circadian rhythm, migration, aggression, sexual differentiation, and singing behavior. Thus, this technique is already advancing the study of gene expression in songbirds as it has in rodents."

Nov 25, 2014
P.Z. Myers is an atheist and biologist, a ridiculer of creation/intelligent design.


Thanks. This shows that many people know that he is an idiot. Like Masatoshi Nei in "Mutation-Driven Evolution" http://www.amazon...9661731, Myers has been touting the same pseudoscientific nonsense for decades, while ignoring what is known about the laws of physics and the chemistry of protein folding
you do realise that you have just PROVEN that you are a pseudoscience crackpot creationist, right?
there is NO science in the creationist movement... and even the judges can see that for themselves: https://en.wikipe...Arkansas

your anger is misplaced... you should be angry at the idiots who programmed you to believe in religion OVER science

JVK
Nov 25, 2014
be angry at the idiots who programmed you to believe in religion OVER science


I wasn't programmed. Like many who have worked in the medical profession, I observed cause and effect at the molecular level, which is where it is simply not possible for intelligent humans to attribute it to "constraint-breaking mutations."

Only the idiot minions of teachers like PZ Myers still do that. Everyone else has learned enough about RNA-mediated amino acid substitutions to either quit touting pseudoscientific nonsense, or to not start.

There will always be idiots like you who challenge the beliefs of intelligent people, but there will always be intelligent scientists who link nutritional epigenetics to pharmacogenomics in studies of 10,000 human patients like this one.

Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing http://dx.doi.org...2013.229

In the end, the idiots are exposed, as always. Thanks for helping!

JVK
Nov 25, 2014
http://www.biomed...abstract

"...our findings underscore the complexity of the interactions between environment and physiology in shaping the development of different body parts."

What's amazing is that anyone is still foolish enough to attribute this complexity to mutations and natural selection. Their claims are so ridiculous that anyone who accepts them assures others that they are among the idiot minions of biology teachers who taught them to believe in the pseudoscientific nonsense they were taught to believe in. Only after several generations are intelligent people beginning to get others to think about their own ignorance.

Yet, as we've seen here, the ignorant remain vocal advocates of pseudoscience long after it is known to be pseudoscience, and long after a history of accurate representations should have removed mutations from any further consideration whatsoever in the context of increasing organismal complexity.

JVK
Nov 25, 2014
Ren82 tried unsuccessfully to convey the message that follows to the idiot minions of biology teachers like PZ Myers and the anonymous fool (aka Andrew Jones, whose review of my model is linked here: http://www.ncbi.n...24959329

Now see: http://www.bsd-jo...t/5/1/10

Transcripts (2,527), many of which were linked to proteolysis, the proteasome, metabolism, catabolic, and biosynthetic processes, ion transport, cell growth, and proliferation, were found to be differentially expressed in A. aegypti female vs. male pupal heads.


Leslie Vosshall's group published one paper last year that showed mutations were detrimental to all required changes mentioned above, and one paper this year that linked nutrient-dependent amino acid substitutions to the differences in cell types.

Watch what happens when even the idiot minions and anonymous fools are overwhelmed by experimental evidence of biologically-based cause and effect.


Nov 25, 2014
Like many who have worked in the medical profession, I observed cause and effect at the molecular level, which is where it is simply not possible for intelligent humans to attribute it to "constraint-breaking mutations."
funny... i've been in in the medical profession far longer than you, and yet i believe in reality
but maybe it is because i dealt with reality on a daily basis!
so, if your model CAUSES mutations, how do you deal with it???
In the end, the idiots are exposed, as always
this is absolutely right!
and you have shown everyone that you are a religious idiot who ignores empirical evidence for the sake of a RELIGION
you've shown that you are willing to do WHATEVER it takes, even re-defining words to suit your own delusion (like your own mutation causing model)... so that your faith is not challenged by your findings
and THAT is what makes you a PSEUDOSCIENTIST

Nov 25, 2014
long after a history of accurate representations should have removed mutations from any further consideration whatsoever in the context of increasing organismal complexity.
Well. now... mutations are pseudoscience, are they?

i only have one thing to remind you of....
remember when 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
how do you live with yourself when you say that mutations are all pseudoscience and yet you promote mutations in your own model

after all, this means, by your own admission, you are promoting pseudoscience!

just because you have a religion doesn't mean it is the correct one
just another one

and now you see why you should have stayed in college and learned a thing or two... perhaps you would not be considered a pseudoscience TROLL

Nov 26, 2014
> JVK

"Watch what happens when even the idiot minions and anonymous fools are overwhelmed by experimental evidence of biologically-based cause and effect."

I can imagine how these people will react. Of the most ardent and noisy defenders of evolution, will become the most ardent defenders of creation..


You two idiots are a laugh riot.

Nov 26, 2014
while ignoring what is known about the laws of physics and the chemistry of protein folding.


And you still have yet to point out how mutation is at odds with biophysics and biochemistry. Citing Nei's biophysical constraints is not an argument against them. You take that quote out of context, as you do with most of what you cite. A constraint is a limitation, not a complete prevention. It's a measure of how much a protein can mutate without adversely affecting function. You can read more about them here:

http://mbe.oxford...179.full

Also discussed in great detail here:

http://www.plosco...674-g006


Nov 26, 2014
"...our findings underscore the complexity of the interactions between environment and physiology in shaping the development of different body parts."


Developmental phenotype plasticity is not news to anyone and it certainly isn't at odds with mutation and selection, the latter of which they discuss quite a bit in that paper. Plasticity is an epigenetic process. It doesn't affect the genes themselves. That's where mutation comes in.

Leslie Vosshall's group published one paper last year that showed mutations were detrimental to all required changes mentioned above, and one paper this year that linked nutrient-dependent amino acid substitutions to the differences in cell types.


Big surprise. More misinterpretations. Should I or Stumpy contact Vosshall to find out what she really thinks of your interpretation?

Nov 26, 2014
Explain what is the difference between random events and unplanned events?


What he means is that mutations are (quasi-)random and selection isn't.

What are these unplanned events that do miracles?


Modifying proteins through trial and error is not a miracle.

How they work at the molecular level?


I've already pointed out what causes mutations. Polymerase errors, uneven crossing over, mutagens, etc.

These events work in more intelligent way than scientists?


No, it's just the sheer number of the occurring. It's how we do directed evolution in vitro.

Why none of supporters of evolution does not answer the specific questions I asked above...


What questions? If you don't understand a link, ask.

if one amino acid in the chemical composition of one protein is changed with another amino acid, what is the probability for improvement...


This is exactly what you're looking for:

http://www.pnas.o...13.short

JVK
Nov 26, 2014
What misinterpretation? I quoted http://www.bsd-jo...t/5/1/10 :

"Transcripts (2,527), many of which were linked to proteolysis, the proteasome, metabolism, catabolic, and biosynthetic processes, ion transport, cell growth, and proliferation, were found to be differentially expressed in A. aegypti female vs. male pupal heads."

What kind of idiot takes a one-sentence summary of how sex differences arise during development and claims it is a misrepresentation because he wants mutations, which perturb protein folding, to be involved?

Tell us how sex differences and sexual orientation arise via mutations in yeasts.

"The beauty of the yeast system is that it provides one with a practically unlimited arsenal of tools to study the mechanisms of genome functioning," says Mirkin.
http://medicalxpr...ons.html

You two idiots are a laugh riot./q]

Tell us what you know about transcription.

Nov 26, 2014
If оне couple in a local group has conditionally positive mutations, how these mutations will spread across much of the group when other couples also have a offspring?


Beneficial mutations increase their representation over time by allowing those individuals to breed more/faster or survive better. In Lenski's experiment, the media that his E. coli grew on had citrate in addition to glucose. Normally, E. coli can't use citrate when they're exposed to oxygen, but a mutation occurred in one bacteria that allowed it to use citrate. Since it had more food available, it outcompeted the others and had more offspring.

Explain how it works the mechanism of natural selection in the case of small mutations?


This seems to be a good resource concerning weak selection:

http://www.ncbi.n...22964835

JVK
Nov 26, 2014
you still have yet to point out how mutation is at odds with biophysics and biochemistry.


I've cited Eshel Ben-Jacob's group
1) The three-way switch operation of Rac1/RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition
2) MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination

and

3) Baverstock "Life as physics and chemistry: A system view of biology"
with
4) Annila "Genes without prominence: a reappraisal of the foundations of biology"

You're treachery/idiocy is showing. You just cited a 2001 article: Fitness effects of advantageous mutations in evolving Escherichia coli populations

See: "If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based." (p 1014)

http://jp.physoc....abstract

JVK
Nov 26, 2014
http://medicalxpr...ons.html
"The beauty of the yeast system is that it provides one with a practically unlimited arsenal of tools to study the mechanisms of genome functioning," says Mirkin.

Like the system of all other organisms, the yeast system is nutrient-dependent and pheromone-controlled. " ...the fitness effect of a gene duplication, when present, lies primarily in that the increased copy number causes an increase in protein dosage. A clear example of a gene duplication conferring an adaptive response to nutrient limitation is that of the yeast hexose transporter." Kondrashov (2012)

Andrew Jones:
Beneficial mutations increase their representation over time by allowing those individuals to breed more/faster or survive better. In Lenski's experiment, the media that his E. coli grew on had citrate in addition to glucose.


What caused the beneficial mutations and how are they controlled?

JVK
Nov 26, 2014
This seems to be a good resource concerning weak selection: http://www.ncbi.n...22964835 "Weak selection and protein evolution."


Assuming that protein evolution occurs via selection without knowing that nutrient-dependent amino acid substitutions stabilize protein folding is one of the most ridiculous assumptions that has ever been made. Yet, it is an assumption typically made by evolutionary theorists and anonymous fools.

They know nothing about physics, chemistry, or conserved molecular mechanisms and must assume everything. Their assumptions are incorporated into their ridiculous theories as definitions.

Behold: Neo-Darwinism
"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted..."
http://www.huffin...211.html

cjn
Nov 26, 2014
anonymous 9001: Thanks for fielding that one for me.

Ren82: If you don't understand that there is a difference between probability-driven events -like reactions based upon a concentration gradient and chemical affinity, and "random events", then I'm not sure where this conversation can go.

My last exercise would be for you to consider the evolution of the automobile. Some engineer didn't just dump random pieces of metal, polymer, and glass together and end up with Tesla Model D. It has been almost 250 years from the invention of the wood, brass, and iron steam trolley, with very distinct controls guiding the progression. These controls include the materials available, enabling technologies, laws and regulations, human factors, utility and purpose, and consumer need and interest.

Nov 26, 2014
Do you have any idea how a bacterium can change diet by random change in DNA? How should change its DNA in targeted way to change its metabolism? Improvement based on innate potentials or based on random factors is the question?
Einstein didn't believe in chance, Ren. I don't know why you are so obsessed with randomness. Must be all that Garbage-In-Garbage-Out in your bible, like text translated twenty times in twenty languages through google translate. That is a good simulation of the dynamic-stochastic processes which made your bible

"While genetic errors that occur during DNA replication may have different frequencies in different areas of DNA, this trend would vary with the DNA over time. Other causes of mutations have no preference for certain areas in the DNA, but they are more common causes of mutations. Therefore we can conclude that mutations have no selectivity."

That conclusion doesn't follow at all. Fail

cjn
Nov 26, 2014
^Cont
Carbon, Hydrogen, Nitrogen, Phosphorous, and Oxygen molecules didn't spontaneously bond into a functional cell, it formed over time within the environmental pressures, chemical constraints, and selective pressures. Life favors order, order is enabled by chemical/physical affinities and concentrations. This is why you can observe the spontaneous formation of lipid bi-layers in a mixed solution.

cjn
Nov 26, 2014
Ren82:
This is what I constantly explain in this forum. Everything around us is a product of the will and intellect, and has a purpose and direction. And exists thanks to the brilliant ideas and engineering thought of the Creator, but not by pure chance.


I figured you would misconstrue my point as I was submitting, but I always hope for the best in people. Sigh.

Just because you don't understand something doesn't mean that it is "magic". If it was magic, things would be in a perfect state of equilibrium, there would be no vestigial organs, and the shear biodiversity of life would be unnecessary.

Nov 26, 2014
Wow I got a downvote from JVK. For that to happen I must be making 5 star arguments!

Ren your word soup still stinks of bullshiyte and ADHD + meth-addled incoherence reminiscent of JVK

Nov 26, 2014
What percentage should be hypothetically positive mutations against the total number of mutations to be passible the evolution of certain species. And by what criteria we can judge whether one mutation is positive or negative.


Instead of positive or negative I'd substitute successful or not successful and you answer your own questions.

JVK
Nov 26, 2014
I asked that Ellis be compared to PZ Myers because George co-authored with Stephen Hawking, but George's expertise is not limited to physics. No one seems interested in comparing the creationist views of Ellis, which can be placed into the context of what is known about physics, chemistry and molecular biology, to the atheistic nonsense touted by theorists like PZ Myers.

The same comparisons could be made between any serious scientist and any other pseudoscientist, beginning from what Dobzhansky (a creationist) wrote in 1964 "...the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting." http://icb.oxford...citation

and in 1973 "...the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla." http://www.jstor..../4444260

JVK
Nov 26, 2014
Why hasn't anyone besides Ren82 and me compared the ridiculous opinions of people like PZ Myers to the facts about creation touted by Dobzhansky and Ellis? All we continue to see is claims based on ridiculous theories with no comparison to what is known about biologically-based cause and effect.

For example, if you don't agree that amino acid substitutions differentiate all cell types in all individuals of all genera, provide an alternative explanation of cell type differentiation that has been shown to occur via conserved molecular mechanisms that are bio-physically constrained by the chemistry of protein folding.

Alternatively, admit that you have no clue as to how species diverge via mutations that perturb protein folding and cause diseases and disorders -- or tell us how that might be possible via a series of evolutionary events.

Nov 26, 2014
Schneib, i was right, unfortunately;

"Such mind viruses are called "memeplexes," and they form pretty much everything we call "culture." I'm not in favor of removing culture from humans; it's what keeps us from being little bands with a boss who gets all the best food and sex."

perhaps you will one day see enough of this world to accept evolution as the reality of existence.
Ummmm, I'm an atheist and I accept both evolution and natural selection.

Jump to conclusions much?

Just askin'.

Nov 26, 2014
you are disappointingly judgmental, ironic, and ignorant bud. but thanks for sharing your perception on dogma. goes to show just how much work is left to be done to correct humanitys path
You could, you know, have avoided looking like an idiot by noticing that I'm not denying evolution but supporting it. Do try to keep up.

JVK
Nov 26, 2014
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..."

http://jonlieffmd...volution "...alternative splicing is, perhaps, the most critical evolutionary factor determining the differences between human beings and other creatures."

http://genomebiol...15/1/401 "...the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6]."

http://www.cell.c...)00166-4 "This article represents a first step in developing the concepts of the morphome..."

The 2014 claims represent the ignorance displayed here of what we detailed in 1996.

JVK
Nov 26, 2014
http://journal.fr...127/full

In the comments, I wrote:

"Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing."


See the rest of the comments with the replies from George F.R. Ellis, which include:

This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics.


Anyone who cannot grasp the fact that physics, chemistry, and conserved molecular mechanisms MUST be integrated into models of biologically-based ecological speciation should join PZ Myers' idiot minions and anonymous fools in their discussions.

If you're not a serious scientist, stay out of discussions that require more intelligence than theorists have ever displayed.


Nov 26, 2014
I've cited Eshel Ben-Jacob's group


Summaries of your links:

1. This concerns mutual and self regulation of Rac1 and RhoA.

2. Characterization of miRNAl-regulated gene expression.

3. Survival is a function of how well an organism utilizes energy.

4. This paper explicitly talks about natural selection. You're just trying to twist because the point of the paper is that there isn't a 1:1 link between genotype and phenotype, which everybody already knows due to the advent of epigenetics.

All in all, none of these papers either explicitly or implicitly deny mutation and selection. The first two don't mention it because that's not what they're studying.

What caused the beneficial mutations and how are they controlled?


Duplications are due to errors during meiosis. In the hexose example you give, the individuals that acquired the mutation were granted better access to nutrients around them. The mutation was maintained by differential survival.

Nov 26, 2014
Therefore we can conclude that mutations have no selectivity.


Simple math says you're wrong. Let's say, due to inherent stability, gene 1 has a mutation rate of 10^-5 and gene 2 has a rate of 10^-6. If the overall rate due to outside factors is another 10^-6 across the whole genome, that doesn't mean the per gene rates are suddenly nullified and everything's equal. It's additive.

conclusions without preconditions ready for them


Such as? Don't be vague.

There is no set criteria for determining whether the hypothetical improvements are based on random mutations or built-in mechanisms.


There's no built-in mechanism that makes deterministic changes to DNA sequence.

what is the probability for improvement in some functions in the cell to the probability of their deterioration.


Did you even read the link I posted?

http://www.pnas.o...13.short

Third sentence from the end of the abstract.

Nov 26, 2014
Do you have any idea how a bacterium can change diet by random change in DNA?


That's literally what I told you in that quote.

How should change its DNA in targeted way to change its metabolism? Improvement based on innate potentials or based on random factors is the question?


There's no mechanism or pathway by which the E. coli could recognize the presence of citrate and cause a specific translocation.

If mutations are quasi random, all individuals in the population will have the same or almost the same mutation


By what logic? Just because some parts are more prone to mutate doesn't guarantee that they will in all individuals. We can't predict when a mutation will happen. All we can know is that some will happen more or less frequently than others.


Nov 26, 2014
Then how will emerge dominant individuals with more positive mutations to spread to the local group when no individual in it will have a significant advantage over the other in every respect?


Not all positive mutations are of small effect. The benefit the Cit+ E. coli got was quite significant.

Why do you think that such (small effect) mutations will allow him to leave more offspring by other group members?


I've already covered this. Small effect mutations are often times eliminated by drift.

What prevents parallel with the most positive mutations have more negative mutations, as might be expected from an individual more prone to mutations.


Selection. Just consider the probabilities. If the probability of a positive mutation is 10^-8 and that of a negative one is 10^-7, then the probability of both occurring in the same organism is 10^-15.

Nov 26, 2014

Should I accept any idea as reliable? Does that mean that I do not understand such idea or mean that I understand it, but do not accept it as logical?


The issue here isn't are you or are you not going to accept an idea, but are you going to allow facts to penetrate your worldview...

You are under the impression that your faith based arguments are equivalent to logical arguments and solid facts...they simply aren't.

Your only two choices are to accept that a supernatural force created all life on this planet whole cloth, OR that life emerged, mutated, and created the stupendously staggering amount of biodiversity we see today. If there is a third option, state it and give observations, facts, or logic to support it. Otherwise you're just STATING wrote belief in a text written by people who are incredibly ignorant (not stupid) by modern standards....that isn't a debate. It's the equivalent of a three year old stamping his feet and saying "IS SO!".

Nov 26, 2014
Dobzhansky (a creationist) wrote in 1964 "...the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting."


After all this time and having this particular part pointed out to you in full, you still don't know what proper context is?

In addition, I've emailed Ellis to see what his thoughts on mutation and selection TRULY are, since we know your track record of claiming support for you on other peoples' behalf.

JVK
Nov 26, 2014
individuals that acquired the mutation were granted better access to nutrients around them. The mutation was maintained by differential survival.


The anonymous fool thinks that happens in the context of thermodynamic cycles of protein biosynthesis and degradation, which enable organism level thermoregulation via RNA-mediated events that link networks of genes to metabolic networks in species from microbes to man.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
http://www.ncbi.n...24693353 It includes cross-species examples of biologically-based cause and effect in the context of everything currently known about physics, chemistry, and molecular biology.

See also: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing http://dx.doi.org...2013.229

Preemptive testing does no good when patients acquire mutations and differential survival leads to speciation.

Nov 26, 2014
...The world we live in is too ordered and well designed. If randomness and luck of idea can create such highly orfered world according to evolutionists, what can do the intellect of man? But is funny and paradoxical that intelligence fails where randomness according to evolutionary theory has made miracles. Evolutionists turn things to 180 degrees, following their strange mirror logic.


I'm waiting for an argument based on logic. We see no evidence if intervention, or impossibility (in fact by definition the opposite). That YOU apply man made concepts of "order" and "complexity" to a system that we consistently see simply cycle and obey completely mechanistic laws with zero evidence of supernatural intervention is not an "argument"...it's a cultural bias and an opinion. It's not a bad one, I used to share it, but it's simply an issue of credulity. The limits of human credulity have absolutely nothing to do with the universe or science.

Nov 26, 2014
Can complex organic molecules necessary for the simplest bacteria can be synthesized in the external environment due to random chemical reactions in one place within a very short period of time? Do you have any idea how different organic molecules are required for this purpose and how will self assemble in single cell organism? .....


I'm still waiting for an argument other than probability. Show me evidence of intervention, an ACTUAL OBSERVATION...otherwise you're not talking science. If the "creator" designs then he does it naturally...in which case why do we need him? It seems simpler without someone who moralizes with illiterate goat herders, and gives erroneous creation myths to the same.

If you want to talk about logic and philosophy WITHOUT science we can take it to PMs.

I could ask you why, if it's so important that everyone is saved, he doesn't simply come down and explain it to us all, but that isn't science.

JVK
Nov 26, 2014
I've emailed Ellis to see what his thoughts on mutation and selection TRULY are


You could have asked him to read your "Criticisms of the nutrient-dependent pheromone-controlled evolutionary model" http://www.ncbi.n...4049134/

You could also have told him
individuals that acquired the mutation were granted better access to nutrients around them. The mutation was maintained by differential survival.


That way, he would know what your thoughts on mutation and selection TRULY are, and he would know you are a science idiot.

"Interview – Prof Brian Cox and Robin Ince
Robin Ince "Am I wrong to sometimes be scared of science idiots?"
Brian Cox "…my favoured response would be: 'you bunch of utter nob ends'." -- http://perfumingt...mit.y=19

Nov 26, 2014
@Ren The world we live in is too ordered and well designed. If randomness and luck of idea can create such highly orfered world according to evolutionists, what can do the intellect of man?
This "randomness" exists mostly in your head, and prevents you from seeing obvious cause and effect. If the world is ordered where is the randomness? If the world is randomness (=your brain) then why did you say it is too ordered? You are stuck in a logical Möbius loop

How do you know the world is "designed?" Did you encounter the blueprints? Did your imaginary friend file a patent? Did your god obtain a doctorate in universal design?

Nov 26, 2014
Here's a starting point, Ren:

http://www.d.umn....orld.pdf

Nov 26, 2014
Should I or Stumpy contact Vosshall to find out what she really thinks of your interpretation?
&
In addition, I've emailed Ellis to see what his thoughts on mutation and selection TRULY are, since we know your track record of claiming support for you on other peoples' behalf.
@anonymous_9001
I also have direct inquiries to them asking for the same information

like you pointed out... his track record is horrible
isn't it strange that someone would violate the basic laws/tenets of their own religion (in this case, lying) in order to support their religion????
considering his historical blatant lies, i have also taken to task of contacting everyone in his other link (shown above but linked here: http://www.ncbi.n...25413365 ) and having them respond to his claims regarding their work

lets see what happens, right?

JVK
Nov 26, 2014
Emergence of single-molecular chirality from achiral reactants http://www.nature...543.html

This is the most recent published work to address biophysical constraints on protein folding at the level of RNA-mediated events, which I incorporated into my model of cell type differentiation in species from microbes to man. However, in everything I've read about the origins of life, amino acids are represented as always being homochiral (all left-handed).

The problem that arises is when an achiral amino acid substitution appears to stabilize the entirety of the vertebrate lineage and link it to cell type differentiation in yeasts, which is obviously nutrient-dependent and pheromone-controlled.

What happens next is that someone will need to tell intelligent researchers how homochirality at the origin of life led to an achiral amino acid substitution that links nutrient uptake to pheromone-controlled reproduction in all vertebrates.

Nov 26, 2014
That article has nothing to do with biophysical constraints on protein folding. It's about achiral reactants making chiral products.

However, in everything I've read about the origins of life, amino acids are represented as always being homochiral (all left-handed).


What's meant by that is that all the chiral amino acids are L as opposed to D. Everybody knows that glycine is achiral.

What happens next is that someone will need to tell intelligent researchers how homochirality at the origin of life led to an achiral amino acid substitution


How is that in conflict with anything? Just because those that are chiral are all homochiral doesn't necessarily exclude an achiral one.

JVK
Nov 26, 2014
Everybody knows that glycine is achiral.


What kind of fool makes such claims, while failing to recognize the importance of achiral glycine to the vertebrate lineage in the context of cell type differentiation in yeasts?

http://www.scienc...4822.htm "...only the left-oriented amino acids and the right-oriented sugars ever make into life as we know it.
http://link.aps.o...3.118103

All molecular forms of life possess a chiral asymmetry, with amino acids and sugars found, respectively, in L- and D-enantiomers only [1].

"amino acids... found... in L- enantiomers only" with a citation to:

Chirality, photochemistry and the detection of amino acids in interstellar ice analogues and comets http://pubs.rsc.o...Abstract

-- as if the origins of life came from outer space instead of from light-induced amino acid substitutions in plants and animals.

JVK
Nov 26, 2014
The molecular building blocks of life, for example, amino acids and sugars, as well as many pharmaceutical drugs are intrinsically chiral.
http://www.nature...543.html

""The chirality accumulates," Kotov said." http://www.scienc...4822.htm

Except when it doesn't -- Kohl says. But, when it doesn't accumulate and instead the achiral glycine is substituted in the GnRH decapeptide of all vertebrates, that fact can be ignored as if it "...has nothing to do with biophysical constraints on protein folding."

The fact that an anonymous fool tells us it can be ignored in the context of a link between sugars and fats is proof that there is more ignorance among fools than anyone can imagine could be found on this planet or anywhere in outer space.

Nov 26, 2014
"amino acids... found... in L- enantiomers only"


Meaning they aren't found in D. Glycine is neither, so that statement still stands.

JVK
Nov 26, 2014
Where is D. Glycine found? What statement still stands? You seem to know nothing about this.

Attempting to move forward: "We acknowledge that small changes in amino acid sequence can have profound effects on protein function, so we have removed the statement that suggests changes in gene expression pattern is more likely than changes in protein function to contribute to the differences in ZTDO sensitivity between C. elegans and P. pacificus."
http://elifescien...3/e03229

http://phys.org/n...ing.html "The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans"

The link from feeding patterns to pheromone-controlled fixation of amino acid substitutions is clear in my model. Please tell us everything you know about how mutations led to the divergence of grazing and predatory nematodes via natural selection and/or evolution.

Nov 26, 2014
Where is D. Glycine found? What statement still stands? You seem to know nothing about this.


Hahaha. I know nothing about this? Stereochemistry is organic 101, Kohl. There is no such thing as D-glycine.

There's nothing wrong with the statement "amino acids are found in L-enantiomers only", because it's implicit that it refers to those can have have stereochemistry in the first place.

JVK
Nov 26, 2014
In vertebrates and yeasts, "glucosensing functions" ensure that the pheromone-controlled physiology of reproduction occurs only in the presence of an adequate nutrient supply.

Nutrient-dependent RNA-mediated events link the epigenetic landscape to the physical landscape of DNA in organisms from microbes to man via conserved molecular mechanisms.

The mechanisms link the alpha mating pheromone of yeasts to sex differences in an LH response in cultured rat pituitary cells that also are epigenetically-effected by nutrient-uptake and species-specific pheromones.

I asked you to
Please tell us everything you know about how mutations led to the divergence of grazing and predatory nematodes via natural selection and/or evolution.


You selectively avoid responding to anything that might clarify your ridiculous thoughts about cause and effect.


Nov 27, 2014
Man supporting such an idea shows ignorance or desperation and denial of reality in his desire to deny the supreme authority before who is responsible for his faith and actions. Whether you like this reality or not does not matter. You can not change the world created by the Creator, but this world will change you. Human have no potential to take the place of God, which is the desire of some scientists and its funny when they trying to do this. The result is antiscience


This is a science site, not a religious one. Reported.

Nov 27, 2014
If gene 1 is likely to mutate more frequently, once mutated, this will change its probability for mutation compared to gene 2


You're correct. Certain regions are more prone to mutation due to their particular sequence. Will this homogenize mutation rate over the entire genome over time? I can't say for sure, but it obviously hasn't happened yet.

Because if there were, as descended of a common ancestor, there would be no such bio diversity


Where are you getting this idea that mutation rate heterogeneity negates biodiversity? Are you implying that an equal mutation rate will eventually produce the same genotype in all lineages? That's not correct because although we know some regions are more prone to mutation, there's no way to predict when a mutation will occur, what type of mutation will occur, or precisely where it will occur.


Nov 27, 2014
What are the benefits of small hipoteticaly possitive mutations for one individual in the group


Random sampling is one. Linkage with a more strongly selected region is another. As I've said multiple times before though, weak beneficial mutations are oftentimes lost through drift, especially in small populations.

why evolutionists constantly forget negative mutations and random environmental factors that strongly influenced the fate of all individuals in the group?


They don't. Why are you under the impression they do?

But the tendency of order to chaos, and not vice versa


Entropy is not an argument against evolution because the Earth receives a constant input of energy from the Sun. Order is a consequence of the physical laws. RNA bases and amino acids readily form spontaneously from simple organic molecules under a reducing atmosphere. Lipid bubbles form spontaneously in solution under a number of different conditions. Order from nothing.

Nov 27, 2014
>Vietvet
I see that you are awake participant in the forum, but you failed to notice that with the other participants in the forum we comment scientific issues related to the topic. Do not go into the role of censor when you are so selective when you decide to report, failing to notice the regular insults without reason from certain participant in forum. This fair or personal attitude is?


Without realizing it every time you post you are making a fool of yourself.

Nov 27, 2014
The link from feeding patterns to pheromone-controlled fixation of amino acid substitutions is clear in my model. Please tell us everything you know about how mutations led to the divergence of grazing and predatory nematodes via natural selection and/or evolution.


Are you referring to differences between C. elegans and P. pacificus or the stoma dimorphism in pacificus?

Nov 27, 2014
say that quasi random mutations would reduce biodiversity


How so? Mutation is how genomes change. If mutation didn't occur, all organisms would have the same genotype.

Natural selection as evolutionists are understood and expect to work would destroy biodiversity in species.


Natural selection DOES reduce biodiversity. It's the process by which unfit phenotypes are eliminated. What's your point? Mutation balances it so populations don't become completely homogenous.

Luckily it does not work in the way as they expected and the main effect of this process is to preserve the original gene pool of species as long as possible.


Selection doesn't have the ability to know what the original gene pool was. All it does is preserves what works.

At the same time there is built in mechanism in the DNA to provide biodiversity and rapid adaptation


Phenotypic plasticity does indeed exist. What's your point?

Nov 27, 2014
I say that quasi random mutations would reduce biodiversity

Whatever makes you think that?
Simplest counterexample: Take a completely homogeneous population (DNA of every individual exactly identical). Now add mutation. Does that increase or decrease biodiversity?

You also have to understand that selection happens only up to the point where offspring is created. Any (positive or negative) mutation that is expressed after an individual has left the age when it can bear offspring is not selected for (or against) by natural selection.

Nov 27, 2014
Which RNA bases and amino acids are randomly synthesized in reduced atmosphere?


All bases have plausible prebiotic synthesis routes. I'm not too keen on the amino acids, but here are a couple links to start off with:

http://link.sprin...9#page-1
http://www.nature...769.html

As for your other questions, I'll point you to my undergrad thesis:

http://www.scribd...ibozymes

Here it is a tremendously small probabilities that are actually zero.


Actually zero? You base this off of what?

Nov 27, 2014
but always within species. Limit that can not be crossed.


Consider the following:

1. The species barrier isn't quite as cut and dried as you think. DNA exchange can occur between many different species of bacteria.

2. We've observed the appearance of reproductive isolation:

http://www.jstor....71081551

Nov 27, 2014
Stumpy, you'll be glad to hear that I got a response from Dr. Ellis. The part in quotes is what I wrote to him.

"He has also claimed that your recent work with the emergence of complexity and top down causation is evidence that you deny the contribution of mutation and selection to evolution."

Certainly not. Natural selection as usually envisaged is a form of top down causation (because the environment is a major causal factor in the outcomes). Selection is a key process in the rise of complexity. That is quite clear in what I have written. Indeed I claim that multilevel selection is a key to complexity

Nov 27, 2014
@Ren
>kochevnik In the world we live in is very complex hierarchical organization of matter that is supported temporarily by physical laws we know.
Permanently, not temperately
But the tendency of order to chaos, and not vice versa.
Chaos orders energy, which can spontaneously localize and product useful work. You don't know what chaos is
And this complex organization did not appear by accident of chaos before it
Sometimes yes and sometimes no
and there was a purposeful impact on our universe as a closed system.
You presuppose intent but without any being acting. The universe is open system, not closed
If you heard of entropy and chaotic movement of elementary particles will not make such conclusions.
If you studied chaos you would not be making incorrect statements, or you would be able to lie instead of simply speaking from a position of gross ignorance

Nov 27, 2014
Stumpy, you'll be glad to hear that I got a response from Dr. Ellis. The part in quotes is what I wrote to him.
@Anon
I notice this happens a LOT when i ask authors about the studies with regard to jk comments... they always (inevitably) return with something along the lines of what you posted.

THANK YOU for keeping up the great posts, and Happy Thanksgiving

Maybe if I put it into an analogy, it will register.
@Mayor__Dooley
WOW
what a cogent and insightful post!

Very well written and right on the mark... i am thinking the same thing may well apply to jk and his intentional stupidity as well... especially when he "interprets" another author

Happy Thanksgiving to you as well

and everyone else who loves science too, whether you participate in the event or not
as for myself, i am really looking forward to being stuffed!

PEACE yall

cjn
Nov 27, 2014
There is a fly in your house, it constantly butts its head against a window. It's brain seems not to comprehend what is before it, nor does it take note of the result of its failures, it is fixed in its behaviour, immutable belief.
You kindly open the window for this creature, but this is no normal fly, it is a Ren-Fly! So instead of flying free, thinking that it's belief won over reality, and moving on to a more suuitable forum, the Ren-Fly flies back into your home and deliberatley finds another closed window to batter its head against.
You open window after window, but the Ren-Fly just finds another. It is not seeking freedom, your help is not wanted. It seeks attention and sympathy, it wants to harm itself in public, it wants you to swat it.


Thank you Dooley, this is brilliant.

JVK