Evolutionary mechanisms more important than natural selection?

[Zoe Doidge]

If all or most of the above evolutionary mechanisms / processes exist then why do some scientists still claim natural selection is the prime mechanism in evolution?

Evolution is the change in living organisms over generations, and the actual change is driven by the various processes listed in the OP.

Natural selection acts as a filter on existing changes, creating a tendency towards increased fitness. So you could rightly say that if anything, natural selection actually reduces variety (albeit in a positive way).

Because natural selection is the inevitable result of any such changes, it is a key part of evolution even though it doesn’t directly cause changes itself.

 

[Agnostic75]

I have not moved goal posts. Natural selection is not creative, we have many scientific publications pointing this out.

Charles Darwin wrote in The Origin of Species that “… unless profitable variations do occur, natural selection can do nothing.”

Natural selection, far from increasing variation in species, reduces variation constantly in favour of an optimum type. Natural selection is not evolutionary.

The central story of evolution is all about increasing variation and complexity but natural selection can not do that, that is why I say it does nothing for evolution.

What then is the true source of variation in evolutionary systems? Hint it is not natural selection, so choose which mechanisms from the OP.

Do you accept naturalism, theistic evolution, or creationism?

 

[Agnostic75]

Edit: Deletion of duplicate post.

 

[Agnostic75]

PLOS Biology: Natural Selection Molds Genomic Insulator Elements

Natural Selection Molds Genomic Insulator Elements

Citation: Robinson R (2012) Natural Selection Molds Genomic Insulator Elements. PLoS Biol 10(11): e1001421. doi:10.1371/journal.pbio.1001421

Published: November 6, 2012

The “modern synthesis” of evolutionary biology, first formulated in the early 20th century, combined the ideas of Mendelian genetics and Darwinian evolution to create an outline for evolutionary theory that stressed the central role of genes in evolutionary processes. Of the genetic changes that drive evolution, the earliest to be studied were in proteins with familiar and prominent roles in the cell, such as enzymes or structural proteins.

But since then, the astonishing complexity of genomic regulation has come to be better understood. With that understanding has come the recognition that evolutionary change is often driven by changes in regulatory systems acting behind the scenes, changes that affect when, where, and how much those more familiar genes are expressed. Much of the morphologic diversity within and between species is due these kinds of changes.

Despite their importance, it has been challenging to investigate the exact nature of the processes driving the evolution of specific regulatory elements; for instance, whether observed changes are due to positive evolutionary selection or to neutral drift. In this issue of PLOS Biology, Xiaochun Ni, Kevin White, and colleagues tackle this question by examining genome-wide changes in the binding sites for a key gene regulatory protein in multiple species of fruit fly.

CCCTC binding factor (CTCF) is a so-called insulator protein. It binds to DNA to mark the boundaries of large-scale chromosomal regulatory units (such as chromatin domains), preventing unwanted spreading of transcription regulatory signals to adjacent genes. Previous work has shown that the number of CTCF binding sites, and the sequences of those individual sites, has changed over time.

To investigate that nature of that evolutionary change in CTCF binding sites, the authors began by mapping all the binding sites in four species of fly: Drosophila melanogaster, the standard laboratory fruit fly; D. simulans, which diverged from D. melanogaster 2.5 million years ago; D. yakuba, which diverged 6 million years ago; and D. pseudoobscura, which diverged 25 million years ago. They isolated the binding sites by chromatin immunoprecipitation, in which an antibody to CTCF is used to purify the protein along with its DNA binding sites. They then sequenced these sites and pinpointed their positions in the genomes; this allowed them to determine what sequence changes occurred at equivalent sites among the four species.

They first noticed that, not unexpectedly, the more evolutionary time separating each species from D. melanogaster, the further diverged was the set of CTCF binding sites, in both sequence and number. Evolutionary processes were clearly acting on these sites within each species, causing them to change over time. But were these changes an adaptive response to selective pressure, or simply due to random drift in the genetic code?

One piece of evidence favoring selection, the authors found, was that the creation of new sites occurred in each species at a rate far higher than the loss of old sites. In each pair of species where site gain and loss could be inferred, the authors observed that more new sites were created over time than were lost. The authors surmised that this pattern hinted at the work of positive selection for CTCF binding sites.

More rigorous support for the effects of selection came from applying a series of statistical tests to comparisons among older versus newer CTCF sequences. They found that older CTCF sites tended to become stabilized over time, by a process called purifying selection, in which variations away from a given sequence reduce fitness. By contrast, comparing younger CTCF sequences to sequences presumed to evolve neutrally, they found reduced variation within species (polymorphism) in the CTCF sites, evidence of positive selection for the evolution of the binding sites.
Finally, the evolution of new binding sites also correlated with changes in gene expression, in keeping with their gene regulatory role. Moreover, the authors found that among 42 “young” genes essential for fly survival, eight had new CTCF sites nearby that had arisen at about the same time as the gene itself, further supporting a central role for CTCF site creation in fly evolution.

Taken together, these results show that natural selection can and does act on gene regulatory elements, shaping their evolution along with the genes they control. A full understanding of the evolution of the fly will need to take such events into consideration. Similar forces have no doubt been at work in our own lineage, and will be just as important to unravel.

Ni X, Zhang YE, Nègre N, Chen S, Long M, et al. (2012) Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome. doi:10.1371/journal.pbio.1001420

 

[Agnostic75]

According to an article at James Shapiro goes after natural selection again (twice) on HuffPo « Why Evolution Is True, natural selection is an important part of evolution. Consider the following excerpts:

I hate to give attention to my Chicago colleague James Shapiro’s bizarre ideas about evolution, which he publishes weekly on HuffPo rather than in peer-reviewed journals. His Big Idea is that natural selection has not only been overemphasized in evolution, but appears to play very little role at all. Even though he’s spreading nonsense in a widely-read place, I don’t go after him very often, for he just uses my criticisms as the basis of yet another abstruse and incoherent post. Like the creationists whose ideas he appropriates, he resembles those toy rubber clowns that are impossible to knock down.

In his post of August 12, “Does natural selection really explain what makes evolution succeed?” (his answer, of course, is “no&#8221, Shapiro simply recycles some discredited arguments used by creationists against evolution.

This is the old canard that artificial selection doesn’t create “new features.” His definition of a “new organismal feature” is, of course, one that hasn’t been generated by artificial selection, so it’s all tautological. Of course we haven’t seen whole new organs or limbs arise in the short term, for people have been doing serious selection for only a few thousand years, and have not even tried to create new organs or limbs. But we can create a strain of flies with four wings, breeds of dogs that would be regarded as new genera if they were found in the fossil record, and whole new biochemical systems in bacteria. Both Barry Hall and Rich Lenski, for example, have demonstrated the evolution of brand new biochemical pathways that have evolved to deal with new metabolic challenges. Now that is a “new organismal feature”!

Often new species are created by hybridization, but Shapiro forgets that that hybridization is often followed by either natural or artificial selection for increased interfertility of the new hybrid form, so it truly becomes an interbreeding population that characterizes a species. And that, of course, gives a crucial role to selection, as it did in the experiments of Loren Rieseberg and his colleagues on hybrid sunflowers.

Finally, we have selected for increased reproductive isolation in the laboratory, showing that full speciation is possible via artificial selection. My own student Daniel did this, as did Bill Rice and William Salt in lab experiments on Drosophila, which in effect created—by artificial selection—new species from a single original species.

What Shapiro fails to offer is an alternative mechanism for the origin of those features of organism that appear “designed”? Was it God? What turned an artiodactyl like Indohyus into a whale—a transition that is fully documented in the fossil record? Was it simply the “self-organization of the genome” that somehow fortuitously moved the nostrils atop the head, turned the front limbs into flippers, got rid of the hair and external ears, and wrought many other morphological and internal changes? How exactly did this happen, Dr. Shapiro? Might natural selection have played a role? Or was it “spontaneous genome organization,” whatever that means?

 

[Agnostic75]

Sandwalk: What Does James Shapiro Think?

James Shapiro is one of those scientists who think that evolutionary theory is due for a "paradigm shift." His schtick is that mutations often involve genome rearrangements and that reorganization of the genome may be a sort of "natural genetic engineering" that cells use to direct evolution. It's hard to figure out what Shapiro actually means and even harder to figure out his motives. I posted an earlier comment from him that suggests he is looking for a middle ground between science and Intelligent Design Creationism.

I wrote the review that will soon appear on the NCSE [National Center for Science Education] site. I can assure him that I'm well aware of many exciting developments in evolutionary theory. The ones that are important (population genetics, random genetic drift, Neutral Theory, punctuated equilibria, speciation) are ones that Shapiro doesn't understand or mention in his book. (Gould isn't even in the index!) The ones that are trivial and were dismissed as minor embellishments decades ago are the ones that, in his mind, are going to cause a paradigm shift.

 

[Agnostic75]

Here is evolutionary biologist Adam Wikins on natural selection in 2011:

"My impression is that evolutionary biology is increasingly separating into two camps, divided over just this question. On the one hand are the population geneticists and evolutionary biologists who continue to believe that selection has a “creative” and crucial role in evolution, and on the other, there is a growing body of scientists (largely those who have come into evolution from molecular biology, developmental biology or developmental genetics, and microbiology) who reject it. In contrast to Victorian scientists who regarded Darwinian natural selection as “incapable” of creating high degrees of biological complexity, the modern sceptics tend to regard it as of “trivial” importance: the “right” variant for the right place and time arises and, presto, the population changes! The two contemporary groups, divided over this point, are not so much talking past each another as ignoring one another"

So yes selection does exist, but theres no evidence it is a major mechanism, and like many scientists in evo-devo claim it is of trivial importance.

In the next paragraph, Wilkins says:

"The arguments from paleontological evidence for the importance of natural selection largely concern the observed long-term trends of morphological change, which are visible in many lineages. It is hard to imagine what else but natural selection could be responsible for such trends, unless one invokes supernatural or mystical forces such as the long-popular but ultimately discredited force of “orthogenesis.”

Doubt and dogmatism in science -- questioning natural selection | Science and Technology

 

[ecologist88]

Do you accept naturalism, theistic evolution, or creationism?

I accept evolution.

James Shapiro is one of those scientists who think that evolutionary theory is due for a "paradigm shift." His schtick is that mutations often involve genome rearrangements and that reorganization of the genome may be a sort of "natural genetic engineering" that cells use to direct evolution. It's hard to figure out what Shapiro actually means and even harder to figure out his motives. I posted an earlier comment from him that suggests he is looking for a middle ground between science and Intelligent Design Creationism.

Totally false information. If you want to learn about Shapiro then read his book or his online essays not the opinions of loons on random blogspots. He is not looking for a middle ground between science and intelligent design. He has rejected intelligent design openly.

I hate to give attention to my Chicago colleague James Shapiro’s bizarre ideas about evolution, which he publishes weekly on HuffPo rather than in peer-reviewed journals. His Big Idea is that natural selection has not only been overemphasized in evolution, but appears to play very little role at all. Even though he’s spreading nonsense in a widely-read place, I don’t go after him very often, for he just uses my criticisms as the basis of yet another abstruse and incoherent post. Like the creationists whose ideas he appropriates, he resembles those toy rubber clowns that are impossible to knock down.

Shapiro has responded to the criticism of Coyne elsewhere. You can read his post here which Coyne is talking about James A. Shapiro: Does Natural Selection Really Explain What Makes Evolution Succeed?

I am not sure why all this is being spammed into this thread.

In the next paragraph, Wilkins says:

"The arguments from paleontological evidence for the importance of natural selection largely concern the observed long-term trends of morphological change, which are visible in many lineages. It is hard to imagine what else but natural selection could be responsible for such trends, unless one invokes supernatural or mystical forces such as the long-popular but ultimately discredited force of “orthogenesis.”

Firstly orthogenesis is not about mystical forces and it is not totally discredited, it is a view that some internal mechanism can direct evolution, it does not have to be mystical and can be perfectly natural like some scientists have suggested. The long-term trends could easily be explained by other mechanisms which are listed in the OP.

 

[ecologist88]

Natural selection acts as a filter on existing changes, creating a tendency towards increased fitness

Is that your definition of natural selection? Here are some others?

According to the following sources natural selection is:

The process whereby organisms better adapted to their environment tend to survive and produce more offspring. The theory of its action was first fully expounded by Charles Darwin and is now believed to be the main process that brings about evolution.

Google Dictionary

survival of the fittest,” the principle that in nature those individuals best able to adapt to their environment will survive and reproduce, whereas those less able will die.

Medical Dictionary

According to which organisms tend to produce progeny far above the means of subsistence; in the struggle for existence that ensues, only those progeny with favorable variations survive; the favorable variations accumulate through subsequent generations, and descendants diverge from their ancestor.

Parker, S. P. (Ed.). (1997). McGraw-Hill Dictionary of Bioscience. New York: McGraw-Hill.

survival: a natural process resulting in the evolution of organisms best adapted to the environment

http://wordnetweb.princeton.edu/perl/webwn?s=natural%20selection

Natural selection is the process by which traits become more or less common in a population due to consistent effects upon the survival or reproduction of their bearers. It is a key mechanism of evolution.

Wikipedia (old version)

Natural selection is the gradual, non-random, process by which biological traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution.

http://en.wikipedia.org/wiki/Natural_selection (new version)

Natural Selection: The main mechanism of evolutionary change. In a given population of organisms, there are heritable traits that enable some members to contribute a larger number of offspring than others. If these offspring also have a greater reproductive success, then the genetic composition of the population is altered, thus evolution.

http://www.oceanlink.info/glossary.html

The mechanism for evolutionary change in which environmental pressures cause certain genetic combinations in a population to become more abundant; genetic combinations best adapted for present environmental conditions tend to become predominant.

http://www.mhhe.com/biosci/pae/glossaryn.html

An evolutionary process where heritable traits that arise through mutation give an organism a higher chance of survival in their environment and become more common in a population as these organisms have a higher likelihood of reproducing.

http://www.sciencelearn.org.nz/About-this-site/Glossary/(namefilter)/n

The preservation of favorable alleles and the rejection of injurious ones.

http://www.ncbi.nlm.nih.gov/books/NBK21126/

The process described by Darwin's theory of evolution that favors certain genotypes and disfavors others. This process is entirely guided by the interaction of an organism with its environment.

www.whatislife.com/glossary.htm

Natural selection is the process in which some organisms live and reproduce and others die before reproducing.

http://www.enchantedlearning.com/subjects/dinosaurs/glossary/indexn.shtml

A principle of Darwins theory of evolution that animals that have adapted better to their environment allows some members of a species to produce more offspring that others, as a result of possessing advantageous traits that improve survival chances and increase reproductive success.

Lost the link to this one.

The natural filtering process by which individuals with higher fitness are more likely to reproduce than individuals with lower fitness.

mitpress.mit.edu/books/FLAOH/cbnhtml/glossary.html

The directional process of evolutionary change. Some genes or allelles become more common over time because of beneficial effects that they have on survival and reproduction.

web.missouri.edu/~flinnm/courses/mah/glossary.htm

Differential survival and reproduction among members of a population or species in nature; due to variation in the possession of adaptive genetic traits.

www.streamnet.org/glossary.html

The concept developed by Charles Darwin that genes which produce characteristics that are more favorable in a particular environment will be more abundant in the next generation.

http://www.csrees.usda.gov/nea/biotech/res/biotechnology_res_glossary.html

The process in nature by which, according to Darwin's theory of evolution, only the organisms best adapted to their environment tend to survive and transmit their genetic characteristics in increasing numbers to succeeding generations while those less adapted tend to be eliminated.

American Heritage Dictionary

The process by which organisms that are better suited to their environment than others produce more offspring.

http://science.yourdictionary.com/natural-selection

a natural process resulting in the evolution of organisms best adapted to the environment

http://dictionary.kids.net.au/word/natural_selection

Natural selection is the theory that only the strong survive.

http://www.vocabulary.com/dictionary/natural%20selection

a process resulting in the survival of those individuals from a population of animals or plants that are best adapted to the prevailing environmental conditions. The survivors tend to produce more offspring than those less well adapted, so that the characteristics of the population change over time, thus accounting for the process of evolution

http://www.collinsdictionary.com/dictionary/english/natural-selection

The process by which genetic traits are passed on to each successive generation. Over time, natural selection helps species become better adapted to their environment. Also known as “survival of the fittest,” natural selection is the driving force behind the process of evolution.

National Geographic Glossary

Evolutionary change based on the differential reproductive success of individuals within a species

Michael A.Park, Introducing Anthropology: An Integrated Approach, 2nd Ed., glossary


.

 

[ecologist88]

The list goes on and on, indeed pretty much every website or dictionary or scientist defines natural selection in different terms.



Note the following from some of the above definitions:

The main mechanism of evolutionary change
It is a key mechanism of evolution
An evolutionary process
The natural filtering process
The directional process of evolutionary change
The concept
The process in nature
Natural selection is the theory
The driving force


Which is it? A main mechanism, a key mechanism, an evolutionary process, "the natural filtering process", "the directional process", "the concept", "the process", the "theory" or "the driving force"?


So I ask is natural selection a "process", a "force" or a "mechanism"? Does natural selection only work in individuals or in populations? Scientists are saying many different things about it.


"The general principle of natural selection, in fact, merely amounts to the statement that the individuals which leave the most offspring are those which leave the most offspring. It is a tautology." C.H. Waddington in The Strategy of the Genes


"Selection cannot be measured in well-defined units such as millimetres, it cannot be poured into a vial and cannot be weighed on a balance"

"Natural selection... is an abstract concept and not material" Lima-de-Faria in Evolution without Selection. Form and Function by Autoevolution.

If natural selection is nothing more than a concept of species surviving and leaving offspring and some not then is there really any need to call this an evolutionary "mechanism "or "force". It seems natural selection is nothing more than a tautology.

 

[Zoe Doidge]

If natural selection is nothing more than a concept of species surviving and leaving offspring and some not then is there really any need to call this an evolutionary "mechanism "or "force". It seems natural selection is nothing more than a tautology.

Different people define it in slightly different ways, because it is an abstract concept. That doesn’t make it any less vital though. Understanding how natural selection works is critical to understanding why all those processes in the OP create a trend towards greater fitness and hence, critical for understanding our own evolution. Because of that, it needs a name and a definition, even if not everyone agrees on the specifics of the latter.

Any or all of the terms you’ve listed could reasonably be said to apply given standard dictionary definitions of them.

 

[Agnostic75]

Gene flow
Genetic draft,
Genetifc drift
Genetic hitchhiking
Horizontal gene transfer
Co-operation
Endosymbiosis
Symbiogenesis
Symbiosis
Paleopolyploidy (genome dupiclations)
Gene duplication
Group selection
Kin selection
Social selection
Somatic selection
Autoevolution
Molecular drive
Mutation
Niche construction
Saltationism
Self-organization
Epigenetics
Semiotics
Hybridization
Isolating mechanisms (Prezygotic and Postzygotic)
Natural genetic engineering
Orthogenesis
Nomogenesis
Hopeful Monsters
Directed Mutagenesis (directed mutation)
Adaptive mutation
Morphogenetic fields
Transposable element (jumping genes)
Hox genes
Controlling elements (Mcclintock)
Phenotypic plasticity
Genetic assimilation
Quantum Evolution
Process structuralism
Neo-Lamarckism
Panbiogeography

If all or most of the above evolutionary mechanisms / processes exist then why do some scientists still claim natural selection is the prime mechanism in evolution?

Why don't you ask some college biology professors your question and post your findings at this forum? You could easily find many of them who believe that natural selection is an important part of evolution. Or, do you really want that kind of competition?

Do you have any comments to make about my post #24? The last paragraph of that peer-reviewed article says "taken together, these results show that natural selection can and does act on gene regulatory elements, shaping their evolution along with the genes they control. A full understanding of the evolution of the fly will need to take such events into consideration. Similar forces have no doubt been at work in our own lineage, and will be just as important to unravel."

True scientists are not bothered by having to revise scientific theories. They welcome advances in science. As you know, much of Darwin's work has been revised. For that matter, so has much of Newton's work, and Einstein's work. If it turns out that the importance of natural selection has been overstated, the necessary revisions will happen, and science will continue to move on.

Do you believe that humans and chimps share a common ancestor? If Charles Darwin was right about that, but wrong about explaining some of the mechanisms of evolution, he was merely in the same boat as today's biologists since 100 years from now, biologists will be talking about mistakes that today's biologists made, and Charles Darwin will still be admired for his major scientific contributions. If the importance of natural selection has been overstated, that is ok since scientists can only do the best that they can do, and everyone makes mistakes.

 

[ecologist88]

Why don't you ask some college biology professors your question and post your findings at this forum? You could easily find many of them who believe that natural selection is an important part of evolution. Or, do you really want that kind of competition?

I have asked them for a period of over two years and still continue to do so, including the ones at my own university. I speak to biology professors all the time. I have discovered half of them dismiss natural selection like myself and the others dogmatically defend it.

Richard Lewontin is contactable and he still stands to these words which he wrote over 30 years ago.

Harvard Professor Richard Lewontin on natural selection:

"Darwin's theory of evolution by natural selection in particular is
hopelessly metaphysical, according to the rules of etiquette laid down
in the Logic of Scientific Inquiry and widely believed in by practicing
scientists who bother to think about the problem. The first rule for
any scientific hypothesis ought to be that it is at least possible to
conceive of an observation that would contradict the theory. For what
good is a theory that is guaranteed by its internal logical structure
to agree with all conceivable observations, irrespective of the real
structure of the world? If scientists are going to use logically
unbeatable theories about the world, they might as well give up natural
science and take up religion. Yet is that not exactly the situation
with regard to Darwinism? The theory of evolution by natural selection
states that changes in the inherited characters of species occur,
giving rise to differentiation in space and time, because different
genetical types leave different numbers of offspring in different
environments... Such a theory can never be falsified, for it asserts
that some environmental difference created the conditions for natural
selection of a new character. It is existentially quantified so that
the failure to find the environmental factor proves nothing, except
that one has not looked hard enough. Can one really imagine
observations about nature that would disprove natural selection as a
cause of the difference in bill size? The theory of natural selection
is then revealed as metaphysical rather than scientific. Natural
selection explains nothing because it explains everything."
"Testing the Theory of Natural Selection" Nature March 24, 1972
p.181

Of course evolution is true, but there is no evidence natural selection is an evolutionary mechanism. Natural selection is a metaphysical concept, not a testable physical evolutionary mechanism or process.

 

[McBell]

I have asked them for a period of over two years and still continue to do so, including the ones at my own university. I speak to biology professors all the time. I have discovered half of them dismiss natural selection like myself and the others dogmatically defend it.

Richard Lewontin is contactable and he still stands to these words which he wrote over 30 years ago.

Harvard Professor Richard Lewontin on natural selection:



Of course evolution is true, but there is no evidence natural selection is an evolutionary mechanism. Natural selection is a metaphysical concept, not a testable physical evolutionary mechanism or process.

Define "Evolutionary Mechanism"
I ask because it seems to me that you are merely making a mountain out of a mole hill with semantics.

 

[painted wolf]

I have asked them for a period of over two years and still continue to do so, including the ones at my own university. I speak to biology professors all the time. I have discovered half of them dismiss natural selection like myself and the others dogmatically defend it.

I find the terms "dismiss" and "dogmatically defend" to be problematic here. From what I've read from every one of your sources they have a much more nuanced view than you present.

Of course evolution is true, but there is no evidence natural selection is an evolutionary mechanism. Natural selection is a metaphysical concept, not a testable physical evolutionary mechanism or process.

Except that selective pressures have been demonstrated time and again both in the lab and in the field.

wa:do

 

[Gjallarhorn]

I'm wondering something: if selection is not natural, are we talking random or supernatural selection?

 

[Skwim]

I'm wondering something: if selection is not natural, are we talking random or supernatural selection?

The "natural" kinda separates the selection from artificial selection, such as our dog breeding ventures.

 

[painted wolf]

Selection can be random.

It's still debated how much of a role random selective events play in evolution, but it's not insignificant.

wa:do

 

[ecologist88]

Selection is not the mechanism of evolution for the simple reason that it cannot be weighed on a balance, poured into a vial, or measured in specific units. Only a material component can be the mechanism of evolution and a metaphysical concept such as natural selection does not qualify.

 

[LuisDantas]

Selection is not the mechanism of evolution for the simple reason that it cannot be weighed on a balance, poured into a vial, or measured in specific units.

I'm afraid that this is quite the non sequitur.

Only a material component can be the mechanism of evolution and a metaphysical concept such as natural selection does not qualify.

Natural selection is not at all a metaphysical concept.