How repeatable is evolutionary history?

Jun 23, 2014
How repeatable is evolutionary history?
Evolutionary biologist Ken Olsen and Cynthia Vigueira, then a postdoctoral associate in the Olsen lab, examine white clover in the Washington University greenhouse. One morph of this species of clover releases cyanide gas to discourage nibbling.

Writing about the weird soft-bodied fossils found in the Burgess Shale in the Canadian Rockies, paleontologist Stephen Jay Gould noted that of 25 initial body plans exhibited by the fossils, all but four were quickly eliminated. If we rewound the tape, he asked, and cast the dice once more, would the same four body plans be selected? He thought it unlikely.

We can't repeat the Burgess Shale experiment, but Washington University in St. Louis biologist Ken Olsen, PhD, says there are other ways to ask whether evolution is repeatable. One is to look at related species that have independently evolved the same traits and ask if the same genes are responsible and, if so, whether the same mutations led to the trait.

Looking at 27 species in the genus Trifolium (clovers), Olsen, an associate professor of biology, showed that six of them displayed what is called a balanced polymorphism. In some environments, natural selection favors plants that release hydrogen to discourage nibbling, while in others, plants that do not release cyanide are favored. The polymorphism evolved independently in each of the six species.

Often, we think of evolution as driven by chance mistakes in DNA replication, some of which produce novel traits. But in this case, chance played little part. The clover species are in a sense predisposed to develop this trait.

"We see exactly the same genetic mechanism—and it's kind of a weird mechanism—underlying the repeated evolution of the acyanogenic (cyanide-less) trait in different clover species," Olsen said.

The plants that don't make cyanide have deletions in their genomes in the spots where the required genes would normally be found. It's not that the gene is mutated; it's missing entirely.

"This is interesting," he said, "because it gets at the question of how constrained evolution is. The more it is constrained, the more predictable it is, but also the less adaptive flexibility there is."

"If you look at life on the planet, there's such an incredible diversity of life forms and traits that we tend to think anything goes," Olsen said. "But when we look more carefully, we see there are constraints. There aren't any living species of limbed vertebrates with six toes, for example; it's five toes or fewer."

The work appears in a special issue of Philosophical Transactions of the Royal Society B published online June 23. The issue honors the scientific contributions of Leslie D. Gottlieb, an early advocate of the use of biochemical and molecular data to study plant evolution.

The clover genus Trifolium is surprisingly varied. Of the clover species shown here, T. repens (bottom right), commonly known as white clover, and T. isthmocarpum (middle left), a salt-tolerant species known as Moroccan clover, include both cyanide-producing and cyanide-less plants, although some of the other species have one of the two genes needed to synthesize cyanide.

The cyanide bomb

Scientists have known that some forms of white clover release hydrogen cyanide for more than a century. They also quickly realized that white clover is polymorphic for the trait, meaning the species includes both cyanogenic and acyanogenic morphs.

This polymorphism has been the subject of a large number of studies to determine both the distribution of the two morphs and the nature of the selective forces responsible for maintaining the polymorphism.

Plants that release cyanide have a two-chemical "cyanide bomb" that is activated only when plant cells are crushed and the chemicals come in contact. Stored in the central vacuole of the plant cells are cyanogenic glucosides: sugar molecules with an attached cyanide group. In the 's wall, an enzyme called linamarase can cleave the bond attaching the cyanide to the sugar.

When a slug, snail or chewing insect—the major predators on clover in the seedling lifestage—crushes the tender cells, the enzyme cleaves the cyanide, which combines with hydrogen to form gaseous .

Many plants have this ability. It's what makes peach pits and apple seeds poisonous, for example. "In the case of clover, cyanide release probably doesn't kill herbivores outright," Olsen said. " It's more likely to just taste terrible—so it serves as a feeding deterrent. The level of cynanide released is much higher in other species, such as birdsfoot trefoil (the yellow-flowered plant that blooms along highways in June). In that case, it probably could kill them."

But white clover plants that make cyanide don't grow everywhere. You're much more likely to find them in warmer climates than in cold ones. In New Orleans, for example, 85 percent of the white clover plants growing in lawns might be cyanogenic, while in Wisconsin, only 10 percent might be.

A working hypothesis, Olsen said, is that in cooler climates, there are fewer herbivores around. "Since making these compounds is energetically expensive, plants that don't spend their resources making them have a competitive advantage in the cooler climates."

Just press DELETE

Making the bomb requires two genes that are located in different parts of the clover genome. One of these genes controls the synthesis of the cyanogenic glucosides, and the other encodes the linamarase protein.

What happens when a cyanide-less morph pops up, Olsen said, is that one of these genes is deleted. "We see independent gene deletions occurring repeatedly in multiple species. So lots and lots of gene deletion."

This is not the "normal" way we think of adaptive variation occurring, Olsen said. Most of the time, random mutational changes affect one or a few nucleotides within one gene, which might convert one amino acid to another, which might alter a protein's function. So the changes are random and incremental. Instead, in this case, the entire gene disappears.

In the clover genus, something is making it easier for adaptive variation to arise through gene deletions than through simple mutations, Olsen said.

He thinks that "something" might be repetitive nucleotide sequences (repeats) near the cyanide bomb genes. In that case, chromosomes align to the "wrong" repeat when they pair during meiosis and swap genetic material. Unequal swaps caused by the misalignment can delete or add on extra chunks of DNA within the chromosome.

"Normally, a deletion like this would be detrimental," Olsen said. "But when these genes are deleted, the plant is favored in certain environments, and so this morph is maintained. That's why we see this polymorphism so often in natural populations."

It's not that evolution, restarted, would repeat itself exactly, Olsen said. But the closer the evolutionary relationship between species, the more likely there will be underlying predispositions that make the same traits pop up repeatedly in the same way.

In some ways, these predispositions are analogous to the crease patterns in origami paper that make it easier to fold the paper into some shapes than others. Evolution can fold across a crease—but it is much easier to fold along one.

Explore further: Sorghum wards off pests by releasing hydrogen cyanide

add to favorites email to friend print save as pdf

Related Stories

Genetic differences in clover make one type toxic

Oct 01, 2007

That clover necklace you make for your child could well be a ring of poison. That’s because some clovers have evolved genes that help the plant produce cyanide – to protect itself against little herbivores, such as snails, ...

Plants and caterpillars make the same cyanide

Apr 13, 2011

(PhysOrg.com) -- With an amazing example of convergent evolution, Niels Bjerg Jensen of the University of Copenhagen published a report in Nature Communications discussing the bird's-foot trefoil plant and th ...

Probing hydrogen catalyst assembly

Jan 23, 2014

Biochemical reactions sometimes have to handle dangerous things in a safe way. New work from researchers at UC Davis and Stanford University shows how cyanide and carbon monoxide are safely bound to an iron atom to construct ...

Recommended for you

Getting a jump on plant-fungal interactions

15 hours ago

Fungal plant pathogens may need more flexible genomes in order to fully benefit from associating with their hosts. Transposable elements are commonly found with genes involved in symbioses.

The microbes make the sake brewery

Jul 24, 2014

A sake brewery has its own microbial terroir, meaning the microbial populations found on surfaces in the facility resemble those found in the product, creating the final flavor according to research published ahead of print ...

User comments : 71

Adjust slider to filter visible comments by rank

Display comments: newest first

verkle
1.2 / 5 (21) Jun 23, 2014
How repeatable is evolutionary history?


What a loaded title. It implies that evolution is historical. But it has never been observed, and is completely non-scientific. So it can't be repeatable because it never took place.

Articles focused on evolution are mostly junk articles. Very little science, and much postulation.

Seareut
4.5 / 5 (18) Jun 23, 2014
Verkle, shouldn't you be posting things like that on a creationist forum instead of a scientific news site? I'm curious to know what your qualifications are for stating that evolution hasn't been observed because by nearly all reasonable accounts, you are wrong. Would you like me to cite several scientific studies where evolution has been observed, by humans, on a relatively small time scale? I will gladly post them here but I want to know if you will actually read them, and analyze the data yourself if necessary. Rationally, the burden of proof is on you to disprove evolution since your statements fly in the face of evidence stemming from nearly all branches of modern science, but I am happy to offer you some observations of evolution if you would actually take the time to read them.
cl3186
4.5 / 5 (15) Jun 23, 2014
verkle, evolution has been observed and experimented constantly since Darwin first proposed it almost 200 years ago. I suggest you go to any reputable and peer reviewed journal website ,such as Cell or Nature, and you will see that 9 out of 10 research papers that get submitted from all over the world are based on evolution.

If you want any attention from those of us who are in academia, please cite a research paper that supports your claim. No matter what subject you pick (geology, zoology, embryology, paleontology, chemistry, etc), just provide a legitimate research paper. Whenever you religious nutjobs say anything about evolution, it further shows that you really have no idea what evolution is and what we currently know about it.
verkle
1.3 / 5 (14) Jun 24, 2014
Hi Seareut and cl3186,

Thanks for your feedback.
I'm very interested in your claims that evolution has been observed for the last 200 years. Can you please expound further?

Let me clarify---when I say evolution I mean macroevolution, which is really what these articles are referring to. I don't mean variation within a species, which is not real evolution.

Seareut---I do think you are dead wrong in saying the burden of proof for or against evolution is on me. That is not scientific thinking. The burden of proof lies with those who continue to choose to follow the theory of evolution.

I hope this clears up your concerns.

animah
4.7 / 5 (12) Jun 24, 2014
Verkle come on! You can google this stuff by the thousand. Small sample:

- Bacteria evolving genes that didn't exist before to consume nylon and other products that are completely new to nature.

- Similar in the lab: http://www.ncbi.n...Abstract

- Mammalian hybrids e.g. Procyon lotor × Vulpes vulpes

- List of Transitional fossils: http://en.wikiped..._fossils

Now here's what you would have to prove:

It's obvious that small positive change accumulates (e.g. pesticide and other toxicity resistance in plants and insects, new medication-resistant diseases and parasite strains and descendents etc etc).

Now show that there is some kind of mechanism, a barrier or threshold stopping this resulting in large change over time.

That would be a first!
cl3186
4.6 / 5 (10) Jun 24, 2014


I'm very interested in your claims that evolution has been observed for the last 200 years. Can you please expound further?

Let me clarify---when I say evolution I mean macroevolution, which is really what these articles are referring to. I don't mean variation within a species, which is not real evolution.



Your question is not very clear. Because "macroevolution" and "microevolution" are not viewed separately in evolutionary biology. Because they are essentially the same on different time scales. You didn't expect speciation to happen in overnight did you?

If you are using the two terms differently than in the academia, please state what you mean by them clearly.

Again, if you are looking for well written research papers on this matter, all you have to do is search. There are so many researches on this that if I were to list only their titles, it would probably be over 100 pages. My suggestion is to look at palentology or genomics journals.
mooster75
3.9 / 5 (7) Jun 24, 2014
Creationist drivel aside, the article was quite interesting.
nowhere
2.3 / 5 (6) Jun 24, 2014
But it has never been observed, and is completely non-scientific.

Verkle has raised a good point. If something hasn't been observed it cannot be true. For this reason we should scrub all forensic "pseudo"science, a crime must have a witness or there simply is no crime. Geology is also bs. Has anyone ever seen a mountain form? Im talking about macro-mountain formation, not micro-hill formation. Have you seen the centre of the earth? Of course not. Mountain's simply exist, they cannot be formed and the earth has equal chance to have no centre at all. Also electrons and the wind are bs. Never seen either.
alfie_null
4.3 / 5 (6) Jun 24, 2014
How repeatable is evolutionary history?


What a loaded title. It implies that evolution is historical. But it has never been observed, and is completely non-scientific. So it can't be repeatable because it never took place.

Articles focused on evolution are mostly junk articles. Very little science, and much postulation.


Keeping in mind that what Verkle would replace evolution with has absolutely no science. Guess I'd stick with what even Verkle admits has some science.
verkle
1 / 5 (8) Jun 24, 2014
"macroevolution" and "microevolution" are not viewed separately in evolutionary biology. Because they are essentially the same on different time scales. You didn't expect speciation to happen in overnight did you?


Don't mix up these terms, as they are very different. Just show me 1 example where a new gene has evolved, providing some benefit to the host. Just 1 example. Please.

verkle
1 / 5 (10) Jun 24, 2014
Unforunately, you can't, because none exist! There has been no proof of any of kind of real evolution. Zero. You say it exists in the literature, but I have yet to see it.

It is all posture.

Go ahead, vote me down, call me a pseudo scientist, other unmentionable names. Doing so will just hurt your cause.

animah
5 / 5 (6) Jun 24, 2014
just show me 1 example


Okay:

http://www.pnas.o...195.long

2 sides of a narrow but deep valley, one lush and wet -always in the shade- and the other arid and inhospitable -always in the sun. Because the distance between the 2 is so small, there is no reason for the observed genetic differences at all -except for the extreme environment barrier to force opposite mutations to be favored. The case is so clear that place has been nicknamed "evolution canyon".

How about 20 more: section 5 in: http://www.talkor...ion.html

How about 1000 more: google "examples of recent speciation".
Seareut
5 / 5 (7) Jun 24, 2014
Verkle, I'm at work currently but I will cite several examples this evening that give direct evidence that all mammalian species can be traced back to a common ancestor. Evolutionary history is written all over us and the rest of our mammalian cousins. Looking at basic anatomy for one is a great example, showing that at no point in any species, or "kind" as creationists like to put it, has an intelligent designer ever gone back to the drawing board, or life would look very different.
cl3186
5 / 5 (6) Jun 24, 2014
"macroevolution" and "microevolution" are not viewed separately in evolutionary biology. Because they are essentially the same on different time scales. You didn't expect speciation to happen in overnight did you?


Don't mix up these terms, as they are very different. Just show me 1 example where a new gene has evolved, providing some benefit to the host. Just 1 example. Please.



No... They are the very same processes on DIFFERENT TIME SCALE. I mean the more I talk to you about evolution, the more I realize that you have no idea about it. Please go and look at the terms in a biology textbook and learn about them. I exactly know how you use those terms as a creationist, but I refuse to use them that way because that's not how we use them among researchers.

There are so many researches done on genomic evolution. This is what genecists have been doing for decades! What you are saying is just as ridiculous as creationists saying the earth is 6000 years old.
Doiea
Jun 24, 2014
This comment has been removed by a moderator.
TheGhostofOtto1923
4.4 / 5 (8) Jun 24, 2014
Verkle, shouldn't you be posting things like that on a creationist forum instead of a scientific news site?
Verkle truly believes this is indeed a creationist site and further feels that its his duty to inform everyone here of this. Because in his mind the only viable explanation for everything is god.

Of course to maintain this bellef of his he has to consciously ignore an enormous amount of evidence which is thrown at him in each thread. But faith in the face of tribulation is a hallmark of religionists. They feel that the ability to ignore the obvious is a strength, not a weakness.

"Psalm 18:2
The LORD is my rock, my fortress and my deliverer; my God is my rock, in whom I take refuge, my shield and the horn of my salvation, my stronghold."

God protects believers from the discomforts of reality like the doghouse a dog.
TheGhostofOtto1923
4.5 / 5 (8) Jun 24, 2014
An example of religionist deception:

"James Madison said this: We have staked the future of all of our political institutions upon the capacity of mankind of self-government... according to the Ten Commandments of God."
http://www.nowthe...?p=13830

-Sounds nice but its a lie. Madison never said this.
http://candst.tri...isq1.htm

-The denial of evidence is self-deception. The expression of this denial is called lying. Religionists feel justified in lying because they believe the original truth ie god is responsible for everything, negates all evidence.

Contrary evidence is the devils work. Humans cannot properly interpret gods evidence because they are hopelessly corrupt. Etc. And so religionists will lie and ignore and obfuscate because they feel it is their sacred duty to do so.

Verkles universal argument is also ken hamms. 'Nobody saw it happen so who knows?' Well nobody saw creation including the bible authors. Evidence says they lied.
Seareut
5 / 5 (6) Jun 24, 2014
Verkle,

Firstly, the burden of proof IS on you to show an alternative to the theory of evolution that has the same predictive and explanatory power as our current theory. You act like evolution is not the only game in town, when in fact, it IS the only game in town. To say it's not scientific is a fine example of your own incredulity, but by all means, if you have a better theory that explains the biodiversity of life on Earth, we would all love to hear it, but to figuratively stick your fingers in your ears in the face of copious amounts of evidence, and blatantly disregard that evidence is so silly that I find it hard not to insult you. Your mindset that evolution has never been witnessed should therefore carry over to your religious convictions-- nobody has ever directly witnessed Jesus either-- and yet there is far more evidence for evolution than Jesus ever existing.

http://myxo.css.msu.edu/ecoli/ -example where a new gene has evolved. I have more if you are still not sold
Maggnus
4.2 / 5 (5) Jun 24, 2014
-The denial of evidence is self-deception. The expression of this denial is called lying. Religionists feel justified in lying because they believe the original truth ie god is responsible for everything, negates all evidence.
Sounds exactly like a person who denies that humans loading of the atmosphere with CO2 causes warming. Denialists feel justified because they wish to blame it all on a single political figure(or political group), and any evidence contrary to that chosen position is negated by their belief that it "must" be politically motivated.
TheGhostofOtto1923
2.2 / 5 (5) Jun 24, 2014
-The denial of evidence is self-deception. The expression of this denial is called lying. Religionists feel justified in lying because they believe the original truth ie god is responsible for everything, negates all evidence.
Sounds exactly like a person who denies that humans loading of the atmosphere with CO2 causes warming. Denialists feel justified because they wish to blame it all on a single political figure(or political group), and any evidence contrary to that chosen position is negated by their belief that it "must" be politically motivated.
Sorry youre way off topic. Or are you like the religionist who thinks everything is about his pet ideology?
Maggnus
5 / 5 (6) Jun 24, 2014
Sorry youre way off topic. Or are you like the religionist who thinks everything is about his pet ideology?


Says the guy posting anti-religious barbs in a comment thread on an article discussing the repeatability of historic evolution. Not that I disagree with them, but one throwing stones should be aware of the glass house he lives in.

Is this a bitch slap fight again?
Maggnus
5 / 5 (5) Jun 24, 2014
Both fossil both genetic records indicate, that the various features of living organisms (eye, wings) evolved at multiple instances independently at the moment, when selection pressure required it. It can serve as an evidence of high reproducibility of the evolutionary process. Of course, when the selection pressure didn't replicate its conditions exactly, then even its result couldn't be quite the same.


Oops wrong button, I agree with this.
cjn
4.5 / 5 (8) Jun 25, 2014
Let me clarify---when I say evolution I mean macroevolution, which is really what these articles are referring to. I don't mean variation within a species, which is not real evolution.


verkle, the "macroevolution" to which you are referring is called "speciation" in the proper evolutionary biology terminology. In sexually reproducing species, it is the point in which one population of the species cannot mate with other populations. This is often the result of geography, behavior, and mechanical differences, or a genetic incompatibility.

Broadly, "microevolution" is the natural selective pressures which influence the values of allelic diversity within a species population. These values will impact their persistence.

"Genetic diversity" or "population diversity" is the composite of the allelic variation which naturally occurs within a species population. It is a product of the very specific and quantified rate of DNA mutation.

This should help frame this discussion.
JVK
1 / 5 (5) Jun 25, 2014
The discussion must be framed in the context of ecological variation that leads to ecological adaptations -- not in the context of mutations. Nutrient-dependent allelic variation is controlled by the metabolism of nutrients to species-specific pheromones that control reproduction.
http://www.scienc...5009.htm
"This is not the "normal" way we think of adaptive variation occurring, Olsen said. Most of the time, random mutational changes affect one or a few nucleotides within one gene, which might convert one amino acid to another, which might alter a protein's function. So the changes are random and incremental. Instead, in this case, the entire gene disappears."

De novo gene creation of genes and the dissapearance of entire genes occur in the same context. If an olfactory receptor gene is required for nutrient uptake, it is created. When it is no longer required it disappears. Mutations don't create via evolution; they make genes and species disappear.
TheGhostofOtto1923
3.7 / 5 (3) Jun 25, 2014
Says the guy posting anti-religious barbs in a comment thread on an article discussing the repeatability of historic evolution. Not that I disagree with them, but one throwing stones should be aware of the glass house he lives in.
Like I say creationists who try to explain phenomena with superstition need to be countered. It's a civic duty. As usual the godder struck first.
Is this a bitch slap fight again?
No this is a bitch slap fight.
http://youtu.be/hf_XpLOYfog
cjn
4.2 / 5 (5) Jun 25, 2014
De novo gene creation of genes and the dissapearance of entire genes occur in the same context. If an olfactory receptor gene is required for nutrient uptake, it is created. When it is no longer required it disappears. Mutations don't create via evolution; they make genes and species disappear

JVK, if you took a second to read the article you would have noticed that the polymorphism discussed in White Clover is within the same species and in the same geographic area. Each member of the species is exposed to the same "nutrients" or whatever other stimuli you think to which these [phantom] olfactory genes respond. And yet, even in the same environment, with the same stimuli, the White Clover express both HCN and no-HCN forms.
"But white clover plants that make cyanide don't grow everywhere.... In New Orleans, for example, 85 percent of the white clover plants growing in lawns might be cyanogenic, while in Wisconsin, only 10 percent might be."
Modernmystic
4.2 / 5 (5) Jun 25, 2014
Verkle, if evolution can't account for all the various species then what can?

Follow up: Has that phenomena ever been observed?
JVK
1 / 5 (5) Jun 25, 2014
Polymorphisms that differentiate the cell types of morphological and behavioral variants in white-throated sparrows arise in the context of genetically predisposed differences in feeding behavior. http://www.pnas.o...abstract

That means they arise as all polymorphisms in all vertebrate species arise in my model. They are nutrient-dependent pheromone-controlled ecological adaptations. http://www.ncbi.n...24693353

I'm not sure what point cjn tried to make, and hope I have made mine. But, here it is again.

Ecological variation leads to biophysically constrained ecological adaptations. Mutations may lead to gene loss, but they do not lead from the epigenetic landscape to the physical landscape of DNA in organized genomes, which is required.

Experimental evidence of de novo gene creation is required if evolutionary theorists want to continue to tout their theories that without experimental evidence are pseudoscientific nonsense,
animah
5 / 5 (3) Jun 25, 2014
evidence of de novo gene creation


Look, 20 years ago you had a point, but this research area is really taking off right now and the latest is pushing the envelope very fast.

That's because de novo gene creation is science fiction medicine we think we can achieve in 20 years, so it's attracting billions of dollars from industry.

I'm not saying it's not early days, but in 5 years you're going to look like a 19th century flat-Earther. Check this out and think of the implications:

http://www.ploson....0099480
JVK
1 / 5 (5) Jun 25, 2014
The link is to: Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions ( a striking change to amino acid substitutions from mutation-initiated natural selection and the evolution of biodiversity reported two years ago by Lovell's group) http://www.biomed...8/12/238

However, nothing about cell type differentiation has changed since we published our 1996 review in Hormones and Behavior and used yeast as the example of nutrient-dependent pheromone-controlled sex differences in cell types.

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

What has changed is the fact that serious scientists know how de novo Creation of olfactory receptor genes occurs and that it is the basis for experience-dependent cell type differentiation in other cell types. Only social scientists are confused about the science fiction of evolutionary theory.
animah
4.2 / 5 (5) Jun 25, 2014
Okay JVK this is a bit awkward. Are you aware that pheromones (and indeed sexual reproduction) did not always exist, and therefore the evolutionary mechanism predates it by necessity?
JVK
1.2 / 5 (5) Jun 25, 2014
Yes, thanks for asking. I've included the fact that light induced amino acid substitutions link cell type differentiation in plants and the glucose-dependent amino acid substitutions are responsible for virulence in viruses (that get their glucose from the cells the attack). However, at the advent of sexual reproduction in yeast, there is clear evidence that amino acid substitutions link the epigenetic landscape to the physical landscape of DNA in all organisms via conserved molecular mechanisms,

Are you aware that no experimental evidence supports ideas about mutation-initiated natural selection and the evolution of biodiversity? Even in Lenski's experiments the changes are nutrient-dependent and pheromone-controlled. What is the evolutionary mechanism that you think precedes nutrient-dependent amino acid substitutions in the context of cell type differentiation?
Vietvet
4 / 5 (5) Jun 26, 2014
Okay JVK this is a bit awkward. Are you aware that pheromones (and indeed sexual reproduction) did not always exist, and therefore the evolutionary mechanism predates it by necessity?

Sorry, meant to give you 5 stars.
animah
5 / 5 (4) Jun 26, 2014
What is the evolutionary mechanism?


Problem: I think (sincerely - I have no beef with you) that you are splitting hairs. I think what you are describing makes a lot of sense, but that it fits quite nicely in evolution and you are ruining your research by insisting it's not and you are the only biology in town.

In particular, I note Doty and Gilbert for example dispute your findings a lot less than your belief it disproves every other evolutionary mechanism known to man. Nature's a lot more complicated than that and I believe a man of your intelligence should know better.

Now what does annoy me is that it just dawned on me your constant copy/paste of the same blurb is an obvious SEO ploy for google rankings on glorified sex paraphernelia.

So now I'm no longer sure if you really believe your ego, or if you're just preying on human weakness, or worse: Both.
JVK
1 / 5 (5) Jun 26, 2014
Thanks again.

Re: "...the only biology in town."

See: Biology, molecular and organismic (Dobzhansky, 1964) http://icb.oxford...citation
"The notion has gained some currency that the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting." Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!"

Dobzhansky, and others, knew more than 50 years ago that amino acid substitutions differentiated cell types. What's surprising is that others seem not to recognize that fact, when it has been repeatedly asserted by others in the context of refutations of neo-Darwinism.

The bird watchers and butterfly collectors never learned about the nutrient-dependent physiology of reproduction which controls mutations that cannot contribute to the creation of new fixed alleles because perturbed protein folding typically leads to their elimination not to the creation of a mutant species.
Whydening Gyre
5 / 5 (6) Jun 26, 2014
Now what does annoy me is that it just dawned on me your constant copy/paste of the same blurb is an obvious SEO ploy for google rankings on glorified sex paraphernelia.

So now I'm no longer sure if you really believe your ego, or if you're just preying on human weakness, or worse: Both.

An excellent observation. Good catch.
JVK - wouldn't evolution just be considered as a "bigger picture" of all those nutrient adaptations?
Modernmystic
4.3 / 5 (6) Jun 26, 2014
JVK,

Not that I expect to change your mind or get actual answers, but I do have a few questions.

Why is it do you think that every life form on Earth uses DNA if we have no biological relationship?

If we do have a relationship what is the nature of it?

Why do we have vestigial organs?

Why does ontogeny recapitulate phylogeny?

Why many species of animals have hair, many others feathers, and many others scales? IOW why doesn't every species have different adaptations of this kind?

Just a few, there are more complex ones, but these will do to start...
Maggnus
5 / 5 (3) Jun 26, 2014
Is this a bitch slap fight again?
No this is a bitch slap fight.
http://youtu.be/hf_XpLOYfog
Bahahaha! That it is!
Maggnus
5 / 5 (5) Jun 26, 2014
Polymorphisms that differentiate the cell types of morphological and behavioral variants in white-throated sparrows arise in the context of genetically predisposed differences in feeding behavior. http://www.pnas.o...abstract

I'm not sure what point cjn tried to make, and hope I have made mine. But, here it is again.
,

The point cjn tried to make is that your pretended "model" is psuedoscience, and he succeeded quite well.

You have made no point except to further enhance your reputation as a persistent snake-oil peddler whose modus operandi is to crash into a thread of laymen throwing around scientific jargon and sciency-sounding babble in support of the model that has already been debunked many times. Quack quack quack quack quack....
Whydening Gyre
5 / 5 (2) Jun 27, 2014
Is this a bitch slap fight again?
No this is a bitch slap fight.
http://youtu.be/hf_XpLOYfog
Bahahaha! That it is!

Otto, you can be mildly irritating at times, but THAT was funny and makes up for it...:-)
Eikka
3.7 / 5 (3) Jun 28, 2014
"But when we look more carefully, we see there are constraints. There aren't any living species of limbed vertebrates with six toes, for example; it's five toes or fewer."


Wrong. Giant Pandas have. There is a vestigal pisiform bone in humans as well in the same place. It's not classified as a proper finger though because of... reasons.

The number of toes really comes from the general layout of the body, because it is built like a fractal. The embryo divides into parts: head and four legs. The same genes that are responsible for that splitting also split the ends of each leg into toes and fingers, so aside for abnormalities, in order to have more toes you'd also need to have a second head or an extra arm etc.

Returners
1 / 5 (2) Jun 28, 2014
One is to look at related species that have independently evolved the same traits and ask if the same genes are responsible and, if so, whether the same mutations led to the trait.


Aquatic organisms and most reptiles have morphology similar to the simple Sperm from which they all came. This includes: worms, fish, whales (including the Sperm Whale,) sharks (redundant but notable,) snakes, and crocodillians.

The modifications from the initial microscopic morpholoy in the gamete phase is typically the growth of more organs and limbs to adapt to the environment, but it's non-the-less the same morphology scaled up. The advantages are more stable, adaptable life, as a microbe is much easier to kill (individually,) and has less ability to navigate itself around an environment.

It makes sense for a microbe to produce a macroscopic carrier/producer, just as it makes sense for a macroscopic organism to produce a microscopic "seed" from which to reproduce.

If it isn't broke don't fixit
Returners
not rated yet Jun 28, 2014
"Normally, a deletion like this would be detrimental," Olsen said. "But when these genes are deleted, the plant is favored in certain environments, and so this morph is maintained. That's why we see this polymorphism so often in natural populations."


I saw a video on science channel, probably from "Through the Wormhole," which showed a similar deletion shows huge correlation to humans who live greatly past the average expectancy when compared to normal life span humans who have the gene.

It appears that most humans have a "kill switch" gene in their DNA, but some ridiculously healthy elderly people do not have this Gene, and remain healthy regardless of lifestyle.

One (90-something) ate "healthy" and worked out every day, and never drank or smoked.

The other (mid-eighties) ate hamburgers almost daily, drank soda, smoked daily for a long time, and drank alcohol, and didn't get cancer, and was only mildly over-weight, and looked better than most 60 year olds.
JVK
1 / 5 (4) Jun 28, 2014
"The concept of biological evolution is an illogic and insensible hypothesis since it stands in direct contradiction with our current knowledge regarding the behavior as well as the structural and functional characteristics of the human genome and human proteome."

http://www.ajol.i...w/100836
JVK
1 / 5 (4) Jun 28, 2014
Historical contingency and its biophysical basis in glucocorticoid receptor evolution
http://dx.doi.org...ure13410

Reported as: http://www.scienc...0554.htm

"Tracing these alternative evolutionary paths, the researchers discovered that the protein - the cellular receptor for the stress hormone cortisol - could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first."
anonymous_9001
5 / 5 (5) Jun 29, 2014
"The concept of biological evolution is an illogic and insensible hypothesis since it stands in direct contradiction with our current knowledge regarding the behavior as well as the structural and functional characteristics of the human genome and human proteome."

http://www.ajol.i...w/100836


That "paper" is a lot of hand-wavey nonsense packaged as a legitimate scientific criticism of evolution. It basically boils down to "we haven't figured out abiogenesis, therefore evolution is bunk" and "we've eliminated natural selection in humans by treating diseases, therefore evolution is bunk". It's completely illogical and only has 10 citations, which aren't used to reliably support the thesis at all.
JVK
1.3 / 5 (4) Jun 29, 2014
http://www.scienc...88.short

"Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations. However, these domains are beginning to converge in laboratories addressing molecular mechanisms that explain how evolutionary processes work, and bring these processes to bear on medical problems such as cancer and infectious disease. Each discipline can be viewed as a missing link in the other's description of biology, and in medicine."

I'll keep citing the published reports containing evidence so that you can continue ignoring them, just to show how pervasive your ignorance is. No one else even attempts to challenge it by providing evidence. And you never provide any experimental evidence of biologically based cause and effect to support your ridiculous claims.
anonymous_9001
5 / 5 (5) Jun 29, 2014
How many times have I linked you to Google Scholar's thousands/hundreds of thousands of papers concerning mutation and natural selection?

This year alone:

http://scholar.go...sdt=1,50

http://mbe.oxford...23.short

http://arxiv.org/abs/1405.0518

http://www.nature...709.html

http://www.nature...734.html
JVK
1 / 5 (4) Jun 29, 2014
Physical attractiveness as a phenotypic marker of health: an assessment using a nationally representative sample of American adults http://www.ehbonl...abstract

Tell us all how mutations are manifested in morphological or in behavioral phenotypes that somehow indicate fittess.
anonymous_9001
5 / 5 (5) Jun 29, 2014
Phenotyoe doesn't *indicate* fitness. Phenotype directly determines fitness. Mutations alter DNA sequence, which alters AA sequence, which alters how proteins fold, which ultimately alters phenotype. Mutation results in phenotypic variety. This can be observed through any number of induced mutagenesis studies, which I have cited for you previously.
JVK
1 / 5 (4) Jun 29, 2014
How does anything about induced mutagenesis lead to claims that involve mutations and natural selection, which somehow lead to the evolution of biodiversity?
anonymous_9001
5 / 5 (4) Jun 30, 2014
Induced mutagenesis is merely a way of triggering and accelerating the natural mutation process that alters genes as is.
JVK
1 / 5 (4) Jun 30, 2014
Induced mutagenesis is merely a way of triggering and accelerating the natural mutation process that alters genes as is.


I asked "How does anything about induced mutagenesis lead to claims that involve mutations and natural selection, which somehow lead to the evolution of biodiversity?"

Note to everyone else: The anonymous fool cannot answer any question with information based on the theory of evolution. I have published a series of articles since 1996 that detail all aspects of cell type differentiation, which is obviously nutrient-dependent and pheromone-controlled. It is time to discuss amino acid substitutions because in my model they differentiate all cell types in all individuals of all species via conserved molecular mechanisms.

All other discussion of the pseudoscientific nonsense of neo-Darwinism is pointless.
see: http://www.ncbi.n...24693353
Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

JVK
1 / 5 (4) Jun 30, 2014
http://www.biolog...abstract
Excerpt: "Biochemical and bioinformatic results substantially enhance the posterior probability that ancestors of the two synthetase classes arose from opposite strands of the same ancestral gene. The remarkable acceleration by short peptides of the rate-limiting step in uncatalyzed protein synthesis, together with the synergy of synthetase Urzymes and their cognate tRNAs, introduce a new paradigm for the origin of protein catalysts, emphasize the potential relevance of an operational RNA code embedded in the tRNA acceptor stems, and challenge the RNA-World hypothesis."

Most evolutionary theorists are probably unable to understand anything about the above excerpt and they remain stuck with a ridiculous theory that has no explanatory power because they refuse to look at any current experimental evidence.
Modernmystic
5 / 5 (2) Jun 30, 2014
So if we're (humans and every other life form on Earth) biologically unrelated why do we all share common DNA?
JVK
1 / 5 (4) Jun 30, 2014
Who told you we're biologically unrelated?

"Efforts in the field of molecular evolution have recently focused on the role of epistasis among fixed substitutions (see [1 and 2]). Epistasis, a phenomenon when fitness is influenced by the interaction of amino acid residues at different sites, has been suggested to be prevalent and playing a role in determining the fate of which substitutions occur in evolution. Such interdependence of amino acids bears strong resemblance to the nature of protein structures. In principle, the amino acid sequence of a protein is sufficient to determine the tertiary structure [3] by specific amino acid interactions."

http://www.scienc...1400058X

Fixed amino acid substitutions are the central feature of my model:
http://www.ncbi.n...24693353
cjn
5 / 5 (5) Jun 30, 2014
I asked "How does anything about induced mutagenesis lead to claims that involve mutations and natural selection, which somehow lead to the evolution of biodiversity?"


The fact that errors in DNA replication (insertions, deletions, point mutations, translocations, etc...) happen at all after 1,000,000,000+ years of DNA based life indicates that it is a desired property of DNA-based genetics. These errors in replication are what create the genetic diversity within the species, resulting in different observed phenotypes. Those phenotypes determine the fitness of the organism within its environment.

To say that mutations do not occur when there is a regular, quantifiable rate of replication error is simply being ignorant of biology. To say that mutations don't persist in a population and influence fitness and selection, and thus speciation, is to be ignorant of science.
JVK
1 / 5 (4) Jun 30, 2014
Attempts to make others believe I am saying that mutations do not occur when I am saying that they don't contribute to the genomic stability required for biodiversity are the most ignorant of all attempts to reintroduce the pseudoscientific nonsense of neo-Darwinism into accurate representations of biologically based cause and effect.

I asked "How does anything about induced mutagenesis lead to claims that involve mutations and natural selection, which somehow lead to the evolution of biodiversity?"

If you're answer is "automagically" you have summed up what most evolutionary theorists seem to believe.

animah
5 / 5 (5) Jun 30, 2014
How does anything about

Because of statistics: To put it simply, given enough time everything that can happen does happen. If the environment was radom, this time would be very long indeed. But it's not. So when you say:
genomic stability

I think you are misleading yourself. Genomic stability only exists when the environment is benign and unchanging, and over long timescales that's rare.

The norm for probability distributions across non-random environments is for patterns to emerge, in this case for example:

- Stabilising Selection
- Balancing Selection
- Disruptive Selection
- Directional Selection

http://en.wikiped...election

It's (literally :-) the most natural thing in the world. And it makes perfect mathematical sense.
cjn
5 / 5 (5) Jul 01, 2014
If you're answer is "automagically" you have summed up what most evolutionary theorists seem to believe.


There is nothing "automagical" about DNA replication error rates. They are quantified and consistent within a species (barring environmental factors, like radiation), and with even individual genes having a unique, consistent rate of replication errors. Given that "bad" replication errors (e.g. "mutations") can significantly reduce the fitness of individuals in their environment, one would think that more effective polymerase proof reading would exist. Alas, it does not.

Thus, we are left with the question of why DNA mutations exist at all. After a billion years and nearly as many generations, one would believe that if mutations were undesirable, they would have been selected against, and that perfect replication would exist by now, no?
Captain Stumpy
5 / 5 (4) Jul 03, 2014
I am saying that they [mutations] don't contribute to the genomic stability required for biodiversity
@jk
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
therefore, PER YOUR OWN WORDS, POSTS and LOGIC, YOUIR OWN MODEL CANNOT CONTRIBUTE TO GENOMIC STABILITY AND BIODIVERSITY
so then, ALSO per your own words
I am saying that they don't contribute to the genomic stability required for biodiversity are the most ignorant of all attempts to reintroduce the pseudoscientific nonsense
YOU ARE SAYING YOUR OWN MODEL IS PSEUDOSCIENCE and therefore we should just ignore whatever you post as KNOWN PSEUDOSCIENCE CRACKPOT IDEAS

YOUR WORDS
YOUR PRONOUNCEMENTS
YOUR STUPIDITY

thanks for continuing to show us what pseudoscience looks like
JVK
1 / 5 (3) Jul 03, 2014
Duplication of genes is nutrient-dependent and controlled by the physiology of reproduction. Cell type differentiation is not a function of mutations and natural selection, but it does result in biodiversity via conserved molecular mechanisms. Mutations are pathological; they do not create new species.
cjn
5 / 5 (5) Jul 03, 2014
JVK: .... Mutations are pathological; they do not create new species.


Mutations alone don't create new species, its insane to suggest otherwise since you need a population to have a "species". Selection and Speciation are the mechanisms which create new species.
JVK
1 / 5 (3) Jul 03, 2014
Selection and Speciation are the mechanisms which create new species.


What is selected that enables speciation via creation? In my model, selection of nutrients and their metabolism to species-specific pheromones enables speciation.

No one has provided an alternative model of biologically based cause and effect. Aren't you simply another idiot minion or anonyjmous fool who continues to assert the pseudoscientific nonsense of population genetics?
cjn
5 / 5 (4) Jul 03, 2014
In my model, selection of nutrients and their metabolism to species-specific pheromones enables speciation.


This is an honest question on your model (i.e.: not a loaded question): How "species-specific" do you propose these pheromones to be? How similar are they in related species? Also, do you have a list of nutrients and their influence?
Captain Stumpy
5 / 5 (3) Jul 03, 2014
Mutations are pathological; they do not create new species
@jk
well according to you
In my model, selection of nutrients and their metabolism to species-specific pheromones enables speciation
as well as 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
thus, according to the above, your model CANNOT ENABLE SPECIATION NOR CREATE NEW SPECIES because, by your own admission, your model creates mutations, and therefore cannot do what you say it can do

Either that, or you are being STUPID again, and you cannot (like always) comprehend the lexicon of your own field and are making blanket statements with NO MERIT to them, basically being an IDIOT MINION

try answering cjn's questions... and try NOT to dig yourself into yet another hole of stupidity, please
JVK
1 / 5 (3) Jul 03, 2014
A series of published works on cell type differentiation began with From Fertilization to Adult Sexual Behavior in 1996.

Excerpt: "Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes." (p. 337)

Sex differences in cell types that are responsible for sex differences in morphology and behavior arise in the context of ecological variation and the conserved molecular mechanisms that have since been detailed in my other published works on adaptive evolution sans mutations.
anonymous_9001
5 / 5 (4) Jul 04, 2014
James:

Can you expand upon the role of splicing in the adaptation of Lenski's E. coli in relation to citrate?
JVK
1 / 5 (3) Jul 04, 2014
Lenski himself did that with co-authors. Anonymous fools like you and idiot minions of biology teachers like PZ Myers have ignored the experimental evidence of biologically-based cause and effect.

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss
http://mbio.asm.o...abstract
anonymous_9001
5 / 5 (4) Jul 04, 2014
I asked you a very simple question. In your own words, can you explain the involvement/contribution of splicing in the adaptation of Lenski's E. coli in response to citrate. How did the citrate affect splicing?
JVK
1 / 5 (3) Jul 04, 2014
I have explained this to the anonymous fool before, and he has "interpreted" my explanation and regurgitated it in an incomprehensible manner. It is not possible to explain the role of food odors in the context of the thermodynamics and organism-level thermoregulation via pheromone-controlled reproduction to anyone who does not understand anything about biologically based cause and effect that begins with amino acid substitutions and cell type differentiation. No matter what you tell anonymous fools and idiot minions, they will insist that mutations are beneficial because they've been taught to believe in evolutionary theory, not biological facts.
anonymous_9001
5 / 5 (4) Jul 04, 2014
I have asked you this particular question once before and you did not answer me:

http://medicalxpr...ent.html

I asked "So the presence of citrate affected alternative splicings in Lenski's E. coli which lead to the expression of citrate metabolism genes?" and got no response. It's a simple question.