Should Evolutionary Theory Evolve?

By Bob Grant Should Evolutionary Theory Evolve? Some biologists are calling for a rethink of the rules of evolution. Evolution, by its very nature, is a dynamic process. But just as fluid are humankind’s efforts to understand, describe, and conceptualize that process. Out went Lamarck, in came Darwin. Mendel’s insights set the rules for genetic inheritance, then certain exceptions to Mendel’s rules materialized. So forth

By | January 1, 2010

Should Evolutionary Theory Evolve?

Some biologists are calling for a rethink of the rules of evolution.

Evolution, by its very nature, is a dynamic process. But just as fluid are humankind’s efforts to understand, describe, and conceptualize that process. Out went Lamarck, in came Darwin. Mendel’s insights set the rules for genetic inheritance, then certain exceptions to Mendel’s rules materialized. So forth and so on.

The most recent, broadly recognized codification of evolutionary theory is known as the Modern Synthesis. After nearly 3 decades of theorizing, experimentation, and writing by paragons of evolutionary thought—Ronald Fisher, J.B.S. Haldane, and Sewall Wright, to name but a few—British biologist Julian Huxley cemented the term in 1942 with the publication of his book Evolution: The Modern Synthesis. The theoretical framework brought Darwin’s ideas into the 20th century and married them to the gene’s-eye-view of biology that was emerging at the start of the century, with the rediscovery of Gregor Mendel’s inheritance research.

According to the Modern Synthesis, populations containing some level of genetic variation evolve via changes in gene frequency induced mostly by natural selection. Phenotypic changes are gradual, and speciation and diversification into higher taxonomic levels come about over long periods of change. These ideas have remained largely unchallenged for more than a half-century.

But since the 1940s, science’s concept of evolutionary dynamics has, well, evolved. Indeed, these days, calling the Modern Synthesis “modern” might be a stretch.

Some evolutionary biologists say that the body of knowledge concerning evolutionary processes has simply outgrown the confines of the Modern Synthesis, which was crafted before science had a strong grasp of genomics, molecular biology, developmental biology, and other, more recently derived disciplines, such as systems biology.

City University of New York evolutionary biologist and philosopher Massimo Pigliucci insists that expanding evolutionary theory so that it captures recent insights doesn’t mean throwing out 150 years of sound thinking. “We’re not talking a revolution,” he says. “Nobody’s going to deny Darwin and all that stuff. But it has been several decades since the last time evolutionary biologists actually sat around the table, so to speak, and came up with the basic principles of their field.”

In the summer of 2008, Pigliucci and his colleague, University of Zurich researcher Gerd Müller, invited 14 other researchers to the Konrad Lorenz Institute in Altenberg, Austria, near Vienna, to discuss how to rethink the Modern Synthesis. This spring, Müller and Pigliucci plan to publish a tome that arose from the Altenberg meeting, with chapters written by its attendees. It will be titled, Evolution: The Extended Synthesis. “The word ‘extended’ is important because it implies quite clearly that there is no rejection of the previous synthesis,” Pigliucci says. “There is no rejection of the Modern Synthesis. There is no rejection of Darwinism. It’s an extension of it—we think a significant extension in a lot of different directions which neither Darwin nor the Modern Synthesis could have possibly thought of.”

Of course, not all biologists agree. Critics argue, for instance, that the field has been adapting for years, and a handful of new data doesn’t warrant formally expanding a theory that forms the field’s fundamental framework.

To judge for yourself, here are just a few of the concepts that Pigliucci, Müller, and other Altenberg meeting attendees believe evolutionary theory should adapt to include.

Evolvability

Yeast colonies carrying the [PSI+] prion assume a puckered phenotype
Courtesy of Susan Lindquist

What is it?

Evolvability, taken simply, means the ability to evolve or to produce heritable, phenotypic variation. Some lineages are suspected to be more evolvable than others, meaning that dramatically different phenotypes—what University of Vienna evolutionary biologist Andreas Wagner calls “game changers”—may arise quicker in these lineages, independent of how much baseline genetic variation is present. In this way, researchers who study evolvability consider it a metaproperty that, itself, can evolve.

Why is the Modern Synthesis lacking?

The Modern Synthesis addresses evolvability in a population genetics sense—some populations have more genetic variation than others and would therefore be expected to generate phenotypic variation at a faster rate. But it does not treat evolvability as a distinct trait of those populations, independent of the underlying genetic variation.

According to Wagner, the Modern Synthesis also fails to adequately conceptualize the major evolutionary milestones (i.e., photosynthesis, flight, multicellularity) that stand out against a backdrop of slow and steady evolution. “You can look at the history of life as the evolution of game-changing innovations,” he says. “If you’re interested in evolutionary innovation, you can’t get away anymore with a very simple, one-dimensional notion of a phenotype. Now we can recognize that there is a deficiency in the Modern Synthesis.”

[PSI+] could act as a “capacitor and potentiator” of evolvability. — Susan Lindquist

Where is the evidence?

“There has been a surge in theoretical studies of evolvability, and now we’re beginning to look at some of the first empirical results coming out,” Pigliucci says.

Validating the concept of evolvability hinges on deciphering the mechanism for evolvability’s inheritance. What property might bestow on its holders the ability to evolve at a different speed than other species? One researcher claims to have found an answer. Susan Lindquist, a molecular biologist at the Massachusetts Institute of Technology who specializes in protein folding, says that [PSI+]—a prion that results from the misfolding of the Sup35 protein in the yeast Saccharomyces cerevisiae—may serve as a conduit for the evolution of novel traits and a molecular vehicle for evolvability.

Sup35, the functional domain of which is highly conserved in a variety of organismal groups, normally serves as a translation termination factor. That is, it helps ribosomes recognize stop codons on mRNA and therefore mediates the normal translation of proteins. The misfolded [PSI+] cannot perform this function correctly, and yeast cells containing aggregations of the prion read through about 5 to 10 percent of stop codons in a given cell. This means that cells with [PSI+] could express normally silent sequences beyond the c termini of genes or express different levels of normal proteins, because without a stop codon, mRNA may stick around longer in cells, enabling the cells to express more protein. These cells end up expressing a wide variety of phenotypes that essentially can’t arise in normal cells.

When Lindquist coaxed several genetic strains of S. cerevisiae into carrying [PSI+], then subjected them and genetically identical cells with normal Sup35 to a variety of growth conditions, she saw phenotypic variation in the [PSI+] cells come out of the woodwork.1 In nearly half of the conditions Linquist tested, having [PSI+] led to significant phenotypic effects in some of the strains. [PSI+] was essentially uncovering previously hidden phenotypic variation in the yeast cells, and in some of the conditions to which they were subjected this variation was advantageous.

This means that [PSI+] could act as what Lindquist calls a “capacitor and potentiator” of evolvability, because switching into the [PSI+] state makes a yeast population more likely to produce phenotypic diversity when environmental conditions change.

What’s more, Lindquist showed that the [PSI+] prion can be passed from mother to daughter yeast cells when they divide either mitotically or meiotically. Even if a lineage were to revert back to the non-prion state (which occurs naturally once every 100,000–1,000,000 cell divisions or so, depending on the strain), selection may have fixed the advantageous adaptations that resulted from the [PSI+] read-throughs. Linquist says she’s looking at differences in [PSI+] states among wild fungal populations now.

These results are interesting, but might create few waves in the flow of evolutionary history, says Indiana University evolutionary biologist and population geneticist Michael Lynch. “It’s an observation that if you stress the hell out of an organism, it does weird things,” he said. “There’s no question you get more extreme phenotypes than you would in a benign environment. But there’s no evidence whatsoever that the tendency for organisms to do this kind of thing when they’re stressed is there because natural selection favored it.”

Facilitated Variation
A developing finch embryo is shaped by chemical and physical forces before it is subjected to selection
© Alex Badyaev

What is it?

Facilitated variation is a simple way to refer to a complex set of physical and chemical forces, usually coming into play during development, that can affect structures and functions in a way that goes beyond simple, one-to-one (genome-to-phenotype) translation.

Researchers have proposed several mechanisms for facilitated variation, from the oscillation of certain regulatory elements that can affect segmentation in embryos to chemicals acting during development that can give organisms patterns of stripes or spots.

Facilitated variation may also spark quicker evolutionary change than would result from random mutations, because developmental changes can create additional phenotypes upon which selection can act.

Why is the Modern Synthesis lacking?

The intricacies of developmental biology did not feature prominently in the formulation of the Modern Synthesis. Genotypes were assumed to translate more or less directly into phenotypes, and evolutionary change stemmed from the slow, gradual accumulation of random genetic mutations. But with the rise of the EvoDevo field—which incorporates the vagaries of embryonic development into a broader view of evolution—this simplified picture is becoming more complex. Stuart Newman, developmental biologist at New York Medical College, says that complex gene interactions and sudden morphological reorganizations during development, to which the EvoDevo perspective has opened a window, are not dealt with sufficiently by the Modern Synthesis. “It turns out that in many experimental and natural setups, you find discordance between genotype and phenotype,” he says.

Where is the evidence?

Like many of the concepts considered part of an Extended Synthesis, facilitated variation is largely a theoretical concept. Pigliucci himself admits that facilitated variation is a concept in waiting for illustration in natural systems. However, a recent example of the phenomenon at work in natural populations comes from a bird species that is invading new North American territories and habitats, while displaying remarkably rapid adaptive change.

Alexander Badyaev, an evolutionary biologist at the University of Arizona, has been studying little songbirds called house finches, which were native to deserts in the American Southwest and Mexico before they began spreading throughout the United States in the 1940s through the pet trade and natural dispersal.

Badyaev tracked the birds through 19 generations over a span of 15 years at a study site in Montana, and found that the population was developing unique beak morphologies as adaptations to the new environment at a surprisingly rapid rate. According to the Modern Synthesis, beak shape should change as random mutations create a pool of phenotypes, which eventually get whittled down to those that are most advantageous. But the new habitats were so different from their original habitats, the only way for finches to survive would be if their beak shape had changed rapidly—too rapidly to have resulted from just random mutations. If that were the only way for them to evolve, the original desert-dwelling house finch populations would have been wiped out by the pressures present in their new habitats, Badyaev reasons. Instead, they’re thriving.

“You’re not only what you eat, but what your parents ate, and potentially what your grandparents ate.” — Randy Jirtle

How was this possible? To answer the question, Badyaev looked into the developmental patterns that give rise to the beak’s structure in house finches. He found a complex interplay of processes, such as the migration of five islands of neural crest cells that constitute skeletal beak components in the embryo. Interacting embryonic processes result in an initial level of phenotypic variation greater than what would be predicted from underlying genotypic variation alone.2

Because the drivers of this baseline phenotypic variation acted during development in the egg, Badyaev says, selection was essentially blind to the creation of this initial pool of phenotypic variation. It was only later, when young birds began feeding on the foods available in their new habitat, that selection could determine which beaks were more or less suited to the environment. “Selection does not see the developmental process by which this beak was produced,” he notes. “But it’s exactly there that resides the opportunity for diversification.”

Multilevel Inheritance

Epigenetic changes make mice that are larger and yellower than their genetically identical counterparts
Courtesy of Jirtle Lab

What is it?

Multilevel inheritance describes passing on phenotypic changes to subsequent generations in ways that lie outside the genetic code of DNA. Chief among these modes is epigenetic inheritance, where elements such as chromatin structure, remodeled histone proteins, or methylated DNA—often mediated by environmental conditions—can be passed from parent to offspring without changing the actual sequence of the inherited genome.

Why is the Modern Synthesis lacking?

Though science did not have a clear concept of the molecular mechanics involved in genetic inheritance at the time its architects were constructing the Modern Synthesis, they believed genes were the primary units of inheritance. Evolution was defined as a change in the genetic composition of populations.

Where is the evidence?

For epigenetic inheritance to play a profound role in evolutionary change, scientists must demonstrate that the changes last, are stable, and cause heritable effects through several generations.

Last year, Eva Jablonka, an epigeneticist at Tel Aviv University in Israel, published a review article in the Quarterly Review of Biology that details more than 100 published cases of transgenerational epigenetic inheritance, documented in groups from bacteria and protists to plants and animals.3

In one recent experiment, two groups of genetically identical Arabidopsis plants were exposed to either hot or cold conditions for two (P and F1) generations. The next generation (F2) from both experimental groups was grown at normal temperatures, but the offspring (F3) from both groups were grown in either hot or cold conditions. The F3 plants that were grown in hot conditions and descended from P and F1 plants also grown in hot conditions produced five times more seeds than did the F3 plants grown in hot conditions but descended from cold-treated ancestors.4 Because the chance of accumulating mutations within just two generations that led the heat-conditioned plants to thrive in hotter conditions was essentially nil, the authors conclude that inherited epigenetic factors affecting flower production and early-stage seed survival in those plants had to be at play.

“The Modern Synthesis was never monolithic. I don’t think that we need to talk about it as a major movement that’s happening now. It’s happening all the time.” — Richard Dawkins

The poster child for tractable epigenetic changes in mammals is the yellow agouti mouse that Randy Jirtle studies at Duke University. These fat, yellow mice owe their appearance to epigenetics, specifically, an epigenetic modification that removes methyl groups from the normally methylated agouti gene. When this modification occurs shortly after fertilization in a developing mouse fetus, the mouse will exhibit the yellow fur and high-weight phenotype, as well as an increased risk of developing cancer and diabetes. Its genetic code, however, remains unchanged from normal mice.

Jirtle and his colleagues have successfully jiggered the methylation or demethylation of the agouti gene simply by altering the nutritional intake of nutrients that serve as methyl group donors in mouse mothers.5 They’ve shown that upping the amount of choline, betaine, folic acid, and vitamin B12 in the diet of pregnant yellow agouti mice can reduce the incidence of the deleterious phenotype in offspring by allowing for the remethylation of the agouti gene. But should those mice be born with the agouti phenotype, they can pass that deleterious epigenetic trait onto their offspring, regardless of their diet during pregnancy. This means that environmental conditions (in this case, diet) can cause phenotypic changes that can be passed on through cell division and mating. “You’re not only what you eat, but what your parents ate, and potentially what your grandparents ate,” Jirtle says.

But this mode of inheritance needs to penetrate more than a few generations before it earns a spot in evolutionary theory, says Vincent Colot, a molecular geneticist who studies chromatin-based epigenetic inheritance in Arabidopsis at Ecole Normale Supérieure in France. Epigenetic inheritance is widespread, he says, but that doesn’t mean it lasts and causes evolutionarily meaningful effects. “If [epigenetic changes are] not stable for 20 to 30 generations, is it relevant to evolution and adaptation?” asks Colot. “That’s not clear yet.”

What the critics say:

Massimo Pigliucci and his colleagues emphasize the fact that they suggest expanding—not revising or reimagining—the Modern Synthesis, but several evolutionary biologists bristle at the suggestion that (even subtle) official modifications are needed.

There’s no need to formally revisit the Modern Synthesis, argues Douglas Futuyma, an evolutionary biologist at the State University of New York at Stony Brook, because evolutionary theory is flexible enough to incorporate well-substantiated new ideas as they arise. “I think the evolutionary synthesis has already been extending itself almost continually for the last few decades,” he says. “I’m not saying that there’s nothing interesting [in the Extended Synthesis]. I just think the self-conscious labeling of it as a new point of view or a challenge to the old, most people don’t buy.”

For example, Futuyma points to the groundbreaking, mid-century discovery and description of transposable elements by famed geneticist Barbara McClintock. When she found that parts of the genome could jump around and cause mutations or change gene expression, skewing Mendelian ratios and inheritance patterns, this disrupted the predictable Mendelian system that went into building the Modern Synthesis. Here, evolutionary biology absorbed and incorporated this principle without the need for a formal reconsideration of evolutionary theory. “Basically, population geneticists took the standard models of mutation and selection, and adapted them to this new phenomenon,” Futuyma says. “This kind of addition has gone on constantly throughout my entire career.”

Richard Dawkins, renowned evolution popularizer, agrees that science’s fundamental understanding of evolutionary theory is not in need of official expansion. “I think that we have already expanded the Modern Synthesis,” he says. “The Modern Synthesis was never monolithic. I don’t think that we need to talk about it as a major movement that’s happening now. It’s happening all the time.”

Other skeptics cite the dearth of concrete evidence for some of the concepts that Pigliucci and his colleagues suggest using to expand the Modern Synthesis, such as the lack of sufficient examples of transgenerational epigenetic effects. “Usually epigenetic characters aren’t inherited past one or two generations,” says Jerry Coyne, a University of Chicago evolutionary geneticist who studies speciation using Drosophila as a model organism. “Given the billions of characters that have evolved over evolutionary time, that’s not going to change our concept of evolution.”

“One has to have a certain degree of reservation about claims that are made on the basis of one or two examples that are going to be a major challenge or a new expansion,” Futuyma adds. “Otherwise you’re talking about jumping on one bandwagon after another.”

The push for a radical re-think of evolutionary theory is far from reaching a critical mass, agrees Michael Lynch from Indiana University. “There’s no general clamoring in the community for a new synthesis,” he says. “There are more things to explain, but I think a lot of us are happy with the fundamental framework to do that explaining in.”

Have a comment? E-mail us a mail@the-scientist.com

1. H. L. True and S. L. Lindquist, “A yeast prion provides a mechanism for genetic variation and phenotypic diversity,” Nature, 407:477–83, 2000.
2. A. Badyaev, “The beak of the other finch: Coevolution of genetic covariance structure and developmental modularity during adaptive evolution,” Phil. Trans. of the Royal Soc. 365: in press.
3. E. Jablonka and G. Raz, “Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution,” Q Rev Biol, 84:131–76, 2009.
4. C.A. Whittle et al., “Adaptive epigenetic memory of ancestral temperature regime in Arabidopsis thaliana,” Botany, 87:650–57, 2009.
5. R.A. Waterland and R.L. Jirtle, “Transposable elements: targets for early nutritional effects on epigenetic gene regulation,” Mol Cell Biol, 23:5293-300, 2003.
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Comments

Avatar of: Andrew Brower

Andrew Brower

Posts: 12

January 12, 2010

If we take the British population geneticists mentioned, plus Mayr, Dobzhansky and Simpson as the archetypal "architects" of the New Synthesis and say that the synthesizing was finished by the end of World War II, then it is obvious that evolutionary theory has undergone immense change over the past 65 years. Some notable instances include the development of ideas about inclusive fitness, the neutral theory of molecular evolution, and punctuated equilibrium in paleontology. And that's just stuff from the 1960's!\nWe could also incorporate into a broad concept of "evolution" all the advances from systematics that provide more detailed and/or objective hypotheses of the patterns of relationship among living things, including numerical taxonomy, cladistics and molecular phylogenetics.\n\n\n
Avatar of: anonymous poster

anonymous poster

Posts: 4

January 12, 2010

Neutralism, historical constraint and epigenesis about cover it from my perspective. I think Massimo et al. are exaggerating the need for a revolution.\n\n(Hi Andy.)\n\n
Avatar of: Matthew Grossman

Matthew Grossman

Posts: 27

January 12, 2010

The realities of evolution is we have to evolve out theory as new data is generated.\n\nDarwin was not working with our knowledge of molecular biology, yet he was able to produce a general theory of evolution not unlike Einstein?s general theory of relativity. Einstein was never able to reconcile his theory with quantum mechanics, now a mainstream theory in physics. So I think it is obvious that as new data emerges, which shows that evolution may work in different ways than Darwin understood, we need to add to and revise our theory. So we need to understand these things and adjust, not unlike the Constitution of the United States of America, our theory of evolution must accommodate new data.\n\nSo we have to evolve our theory of evolution to be consistent with the data.
Avatar of: anonymous poster

anonymous poster

Posts: 107

January 12, 2010

Very informative well-written article about what is, after all, basically a semantic argument.

January 12, 2010

I was surprised to no mention of horizontal gene transfer. This is the basis of serial endosymbiosis and from what I have read a significant force in microbial evolution.\n\nOr am I missing something?
Avatar of: Sarvesh Kumar

Sarvesh Kumar

Posts: 5

January 12, 2010

I read with great interest this thought provocating article n feel there is hardly any need to go for a change from Modern Synthesis to Extended Synthesis as Evolution is an ongoing process so also the researches n whatever newer ideas develope due to accumulation of data after new findings can be incrporated for better explanation of THEORY OF EVOLUTION without making further changes in nomenclature.If at all this is inevitable I would suggest it to be Advanced Synthesis in place of Extended Synthesis.
Avatar of: Diogenes Infante

Diogenes Infante

Posts: 1

January 13, 2010

Stephen Hawkin in his book "A brief history of time" states:\n?Any physical theory is always provisional, in the sense that it is only a hypothesis: you can never prove it. No matter how many times the results of experiments agree with some theory, you can never be sure that the next time the result will not contradict the theory?\n\nPhysicists know after centuries that paradigms go up and down, biologists think theories are forever. In the light of new knowledge from genomic, metagenomic and metabolomic, or just by studying asexual reproduction in plants, the concept of species must be revised, so evolution which is based on the origin of species will not hold any more in the sense that many evolutionary biologists think about it. I repeat Hawkin statement: ?you can never be sure that the next time the result will not contradict the theory?. Evolution is a theory.\n
Avatar of: Rivkah Rubinstein

Rivkah Rubinstein

Posts: 11

January 13, 2010

When a theory makes no sense, when no driver for increasing complexity can be found, and when it's only reason for being is as a rationale for secularism, then by all means updating the wording makes sense.
Avatar of: JOHN COLLINS

JOHN COLLINS

Posts: 37

January 13, 2010

Thanks a lot for this most informative article. \n\nPerhaps the semantic problem had its origin in giving names to random episodes during the development of evolutionary theory, starting with neo-darwinism and 'the modern synthesis'.\n\nI find the main interest in the common quality of the new insights which I would summarize as follows: rapid adaptation to environmental change can be better explained by considering that in the past many long-range environmental changes gave selective advantage to mechanisms that allow high phenotypic variation under the stress of changing environments. \n\nThis variation is larger than expected from looking at stable populations in stable environments, and allows more rapid adaptation than had previously been predicted.\n\nThis is independent of what the mechanisms are; we should still expect lots of new surprises!
Avatar of: boris kotchoubey

boris kotchoubey

Posts: 1

January 13, 2010

Evolution theory IS evolving. It is enough to read Jablonka's "Evolution in 4 dimensions" in order to see how far we already are from the Modern Synthesis. It is rather, not the leading evolutionary biologists but the broad mass of general biologists, physicians, neuroscientists and (the worst!) philosophers, who make from the classical theory a dogma. People like E.O.Wilson, Dawkins and Dennett contributed a lot to replace Christianity with Darwinism (which means, to make Darwinism a new religion without God). Not surprising, this attempts of canonisation of one particular state of a theory provoked a furious response on the other side in form of "ID" etcetera. But all this, both Evangelican dismission of evolution and Dawkins dogmatization of its, belong to the domain of ideology. The science develops its way.
Avatar of: jane hay

jane hay

Posts: 1

January 13, 2010

I'm afraid I agree with Doug Futuyma - the Modern Synthesis has been accommodating genetic advances for 60 years, with no problem. As for the examples listed in the article, in the case of the house finch beaks, I fail to see how the findings are so outside the mainstream that they constitute a paradigm shift that would require "rethinking" the Synthesis. The principles of evodevo account quite nicely for the changes - i.e. underlying genetic variation in switch genes, which, when manifested in phenotype variation are acted on by selection in new environments. Except for the hypothesis of prion evolution, which is very interesting, I see nothing that cannot be accommodated within the existing framework. With the discovery of post-transcriptional and post-translational modification, and the proposal of "RNA world", no one recommended abandoning the Central Dogma and starting over.
Avatar of: Dov Henis

Dov Henis

Posts: 97

January 13, 2010

Life's Is A Fractal Of The Cosmos Evolution\nThe Origin, Nature And Mechanism of Life's Evolution\n\n\nA. "Should Evolutionary Theory Evolve?"\nhttp://www.the-scientist.com/article/display/56251/\nSome biologists are calling for a rethink of the rules of evolution.\n\n\nB. Life's evolution is a fractal of the cosmos evolution\n\nDear Bob Grant, you can extend the list of evolution theorists and the descriptions of their theories, but IMO none of them will survive into the 22nd century. Just wait and see.\n\nLife is just one of many forms of mass in the universe, All of which are forms of energy. Life's evolution is a fractal of the cosmos evolution. It is so plain and simple, therefore unbelievable in view of the immense mountains of verbiage about it. The origin, nature and mechanism of life's evolution is the origin, nature and mechanism of the evolution of mass formats in the cosmos. So plain and simple that it hurts, it's embarassingly clear. \n\n\nC. Take a peek at the Evolution Theory of the future. Brace yourself at the realization of its obviousness and simplicity. Start the search at the three brief basic English notes listed below.\n\n\nDov Henis\n(Comments From The 22nd Century)\nUpdated Life's Manifest May 2009 \nhttp://www.the-scientist.com/community/posts/list/140/122.page#2321\n28Dec09 Implications Of E=Total[m(1 + D)] \nhttp://www.the-scientist.com/community/posts/list/184.page#4587\nCosmic Evolution Simplified\nhttp://www.the-scientist.com/community/posts/list/240/122.page#4427
Avatar of: Lawrence Lerner

Lawrence Lerner

Posts: 2

January 13, 2010

The wonderful thing about a grand theory is its ability to expand and embrace and explain things that were far beyond the imagination and experience of its original proponents. Newton knew nothing about electromagnetic radiation, but in a real sense Newtonian mechanics expanded to embrace this and many other things with the later discovery of new phenomena (e.g., Ampere's and Faraday's laws.)\nIn the same way, Darwin's original ideas have expanded hugely and have served as the basis for understanding and explaining many things far beyond Darwin's experience. That's why we don't call evolution Darwinism, any more than we call modern physics Newtonism (unless we're creationists!)\nNow, we do speak of "modern physics" to describe in a general and rather vague way the things that have been discovered and explained over the past century or so. And the term "modern synthesis" does pretty much the same thing for evolutionary theory. But whether one chooses to do so or not makes little difference to the meat and bones of the subject matter and its study. \nSo let everyone please him/herself on this point. I am not surprised that philosophers will prefer a new name, and Pigliucci's suggestion seems a good enough one. But I am not going to get excited about the issue.
Avatar of: HENRY HENG

HENRY HENG

Posts: 3

January 13, 2010

\nDear Bob,\n\nYes, evolutionary theory must evolve! Otherwise it would be against the evolutionary principle. The major challenges for the modern synthesis are hard to ignore, and the key step to address these challenges is to depart from gene-centric concept by re-synthesizing evolutionary concept using the genome theory.\n\nI have published a piece to do just that.\n\nThe genome-centric concept: resynthesis of evolutionary theory\nBioEssays 31: 512-525 (2009)\n\nYour comments are welcomed.\n
Avatar of: DENNIS HOLLENBERG

DENNIS HOLLENBERG

Posts: 26

January 13, 2010

We can all be impressed as to how the established apologists for the 'modern synthesis' have answers to all the subject's conventional and little questions. Yet, we notice that they, necessarily politically correct to have gotten where they are in the pecking order, don't attempt answering questions that have importance beyond academic soirees and entertaining clueless audiences.\n\nExamples:\na. Why is there no useful, boilerplate definition of the "gene"? Answer: Genes don't exist in nature except as obfuscatory concepts in the minds of gene centrists.\n\nb. Since genes don't exist how could that clever 'selfish gene and snake-oil guy' have fooled us nitwits for so long? Answer: Because we're tribal and we want to fit in (and get grants from the intellectually neutered nitwits that apportion them)(stupid question -- we gotta eat!).\n\nc. Why is there no concise theory of life that encompasses all length scales? Answer: Because developing one necessitates interdisciplinary work, and such an effort would diminish the importance of our sub-sub-disciplines and, thereby, our personal stature for getting grants, book deals, and free lecture junkets on public money. For those reasons, we're telling everyone that the 'modern synthesis' is the big theory, so don't rock the boat!\n\nd. Why, after all these centuries, have we no concise and encompassing definition of life? Answer: If this pertains to my grant, we have such a definition; it's in my wallet, but I left it at home and can't remember it. One of my colleagues will tell you.\n\ne. Similarly, why don't we know how life organizes itself, such that we know how it works (the mechanics)? Answer: We do know how it works; you can get the answer just by looking through the library stacks starting with the A section (you lazy non-combatant!).\n\nf. More specifically, why don't we know how the GLOBAL development of an animal, from the zygote stage to maturity, is controlled and the identity of the globally controlling architecture and mechanism? Answer: genes (and their products).\n\ng. Exactly how do genes GLOBALLY control the animal's development? Answer: Other genes (and their products) control them.\n\nh. What controls the controlling genes? Answer: OTHER other genes (and their products) control them.\n\ni. And what controls those OTHER other genes? Answer: It's genes, GENES all the way down (stupid question)!\n\nj. Doesn't that infinite regress strike you as being an absurd and undefendable position for an adult academician and researcher? Answer: No, the answer gets me grants, so I don't care.\n\nk. People by the tens of thousands die each year of various cancers. How can we pretend to search for restorative cures when we don't know how the organism is controlled? Answer: That's why I can get grants; care to donate?\n\nAnyone who suggests that the modern synthesis is somehow complete or sufficient or does not need throwing out is either limited by their dogmatic rut or out of touch with the issues.
Avatar of: Edward Mikol

Edward Mikol

Posts: 8

January 13, 2010

As Scientific insights spread into unsupected realms, the way Chaos Theory and fractal developments have unveiled deeper patterns in Nature, and which then wash over the world, Evolutionary Theory will need to be rethought in their wake.\n\nAnd as we become aware of "field forces" that appear to predeterminine morphological possibilities ~the way gravity tends to the spherical shape, which became the ur-form of the Universe (showing up in creatures from the Volvox to the fugu fish), Darwin's acute insight will either adapt to the new environment of knowledge, or be superceded.\n\nThe DNA of the Natural Selection Theory seems flexible enough to adjust to this need to shed dead concepts and grow into fresh regions.\n\nWhich is the charm of a truly profound proposition.
Avatar of: C. David Rollo

C. David Rollo

Posts: 1

January 14, 2010

\nThe classical view of evolution envisioned the mapping of genes onto functional proteins, suggesting that radical divergence of morphologies among phylogenies must reflect similar divergence in coding and proteins. The progressive addition of aspects such as strongly conserved genes, duplications, alternative splicing, promoter binding by diverse regulatory molecules, regulated and heritable histone chromatin structure and most recently, regulatory non-coding RNA does not represent gradual expansion of theory but conceptual punctuation. Growing appreciation of regulatory evolution rests on a firm neo-Darwinian foundation, but the flower differs radically from its roots. Consider the quandary and rejection of sexual reproduction as an adaptation for evolvability by genic theorists beginning in the 1960?s. What was not considered was that organisms express relevant genetic variation in response to stressors (e.g. cold versus heat), that numerous regulatory variants contribute to resisting selection among individuals, and that sexual reproduction among survivors will combine diverse regulatory variants all working in the same direction. Thus, the evolvability value of sex could provide additive and synergistic regulatory benefits even in the immediate generation of offspring. Even the whisper of regulated expression of favourable genetic variation (largely of a regulatory nature) is not only missing from the classical synthesis, it is somewhat heretical. \n

January 14, 2010

Merely because the theory carries the word evolution, it is not binding that it must evolve. One can then ask "If a book entitled 'How to fail' does not sell is it a success"? History of Science in general clearly shows that all sciences do evolve. Is it not the very purpose of "Re-search"? The debate here seems to be spurious ab initio. There is no doubt that there have been substantial gains and insights in evolutionary biology over last 6 decades. While there is need for updation of evolutionary theory and for opening the areas - where existing premies fall short in explaining observed phenomena - there does not seem to be a substantial challange to the foundations of evolutionary theory. There of course is a need for precise definition for 'gene' and consensus on meaning of 'Evolution'. At best there is need for an international study group/s to update/amend/augment Evolutionary Theory. But there is no reason to believe that there is any intellectual storm/tornado/tsunami brought about by any glaring contemporary discovery.
Avatar of: anonymous poster

anonymous poster

Posts: 2

January 15, 2010

More important than details of the 'how' is the disturbing fact that over half of our population does not accept evolution, in any form science can describe. If you want to do something good for science, and just as directly for humanity, work to change that.\n This is a discussion about what color to make the curtains when we don't have a roof. \n
Avatar of: anonymous poster

anonymous poster

Posts: 85

January 15, 2010

I have no opinion about whether or not the new information requires a "revolution" in evolutionary theory -- it really depends on how specific (or how vague) you want a "theory" to be. That part of the controversy, I agree, is "semantic." However, I do have some specific comments re SUP35, and also a point of "violent agreement" with one of the previous commentators.\n\nRe SUP35: The article tells us that ?These results are interesting, but might create few waves in the flow of evolutionary history, says Indiana University evolutionary biologist and population geneticist Michael Lynch. ?It?s an observation that if you stress the hell out of an organism, it does weird things,? he said. ?There?s no question you get more extreme phenotypes than you would in a benign environment. But there?s no evidence whatsoever that the tendency for organisms to do this kind of thing when they?re stressed is there because natural selection favored it.? I respectfully disagree with Dr. Lynch, for two reasons:\n1. In terms of ?weird? responses to stress: it seems reasonable and logical that natural selection would indeed favor situations in which an organism exhibits ?weird [phenotypic] responses? when ?you stress the hell out of an organism? ? i.e., natural selection would be expected to favor the ability of an organism to adapt to its environment. Think of the alternative!\n2. It seems clear to me that natural selection DID favor prions. After all, most of the time, prions are quite deleterious to the organism (e.g., mad cow disease, scrapie, Jakob-Creutzfeld disease, etc.). If there hadn?t been a fairly strong natural selection FOR prions, such proteins (i.e., proteins that are susceptible to persistence after misfolding and susceptible to post-folding refolding to a misfolded state through the physical influence of misfolded neighbors) would have disappeared by now. But in fact, prions have persisted extensively throughout time and widely across phyla. It seems to me that Dr. Lindquist is on to something extremely important here, and her work (and tentative interpretations) should not be so cavalierly dismissed out of hand. \n\nNext: I wholeheartedly agree with Christophe Harendza?s disappointment about the failure to mention horizontal gene transfer in this article. It?s not only a force in microbial evolution (where uptake of exogenous DNA from the environment is often a normal activity ? e.g., pneumococcal ?transformation,? a normal microbial physiological process that led to the discovery of DNA as the genetic material), it?s also a factor in eukaryotic evolution as well (e.g., viruses that integrate into the genome and then emerge to create infectious particles can sometimes leave pieces of themselves behind in the host genome and/or take neighboring pieces of the host DNA with them which then can be integrated into the genome of a new host organism). \n\nAs an overall comment, I must say that I am continually disappointed when people who call themselves ?scientist? are adamantly reluctant to re-evaluate their own perceptions and paradigms when presented with new information.\n
Avatar of: eve barak

eve barak

Posts: 85

January 15, 2010

\n\n \nThe anonymous poster who wrote A bigger issue is right on target. \n\nUnfortunately, I don't have a solution to the problem. If some scientists can't even re-evaluate their own perceptions and paradigms when presented with new information, how can we convince scientifically illiterate laymen that what they were taught as small children might not be literally true?
Avatar of: Bob Grant

Bob Grant

Posts: 22

January 15, 2010

A couple of comments have mentioned horizontal gene transfer as a phenomenon that might strain at some of the Modern Synthesis' confines and have questioned my omission of the concept in this story. \n\nFirst, it was necessary for me to whittle down the many ideas that Pigliucci and his colleagues propose as elements of an expanded evolutionary synthesis simply due to space constraints.\n\nThat being said, some of the Altenberg meeting attendees do indeed focus on the role of horizontal gene transfer in bringing about major evolutionary transitions, such advent of the eukaryotic cell, that are more difficult to explain using the gradual evolutionary pace at the core of the Modern Synthesis.\n\nMany other concepts explored by these researchers did not make it into my story, but the book should be coming out soon, and it will explain in much more detail all of the ideas that Pigliucci et al. feel should expand our understanding of evolutionary dynamics.\n\nThanks very much for reading,\n\nBob Grant
Avatar of: anonymous poster

anonymous poster

Posts: 23

January 16, 2010

Evolutinary Theory must evolve! Also the Theory of Relativity must find relatives to support it. And yes, "Game Theory" must play games.
Avatar of: Roy Niles

Roy Niles

Posts: 32

January 18, 2010

?There?s no question you get more extreme phenotypes than you would in a benign environment. But there?s no evidence whatsoever that the tendency for organisms to do this kind of thing when they?re stressed is there because natural selection favored it.?\n\nAye, that's the rub, evidence that selection is not all that natural, or mystical, is of course not evidence that nothing about the original concept should change.\n\nAnd what no-one here seems to want to say out loud is that life seems to have had much of the selective process under its own control from the get-go.
Avatar of: Mike Serfas

Mike Serfas

Posts: 35

January 19, 2010

There is a poignant irony in the Arabidopsis temperature experiment, because it is so reminiscent of the ideas of Trofim Lysenko. If his country had upheld the freedom of scientific inquiry, it is now at least conceivable that some of his ideas might have borne fruit, literally and figuratively. Some of the "new ideas" being considered now might have emerged from the Soviet Union of the 1940s. But the attempt to force the success of Lysenko's doctrines doomed them instead to failure and infamy.\n\nOf course, the modern theory of largely temporary epigenetic changes is not the same as Lamarckism or Lysenkoism. Some epigenetic responses could be the adaptive result of a long history of natural selection over previous slow cycles of environmental change, but there is no sure warranty that epigenetically conditioned changes will actually be an improvement, even in the environment that triggered them. For example, it is possible that seemingly benign factors in our pampered modern environment could cause one generation after the next to become less fertile, more prone to become overweight, or more vulnerable to diabetes. Even so, an old hopeless dream of the Soviets is also free to wander once again: that if the living conditions are improved for the poor and disenfranchised, their progeny might enjoy a lasting epigenetic benefit. This should be food for thought for many outside the field of biology.\n
Avatar of: Bill Sardi

Bill Sardi

Posts: 7

October 22, 2010

This report beats around the evolutionary bush. What Darwin saw over a period of two months on the Islands of Galapagos were obvious epigenetic changes -- alterations in the shape of bird beaks. These changes represented adaptation and variation, not new species. Generational change -- true gene mutations, appear to take time and largely appear to be negative. Mutations represent maybe 2% of disease and do not explain biological aging or any purely directional Darwinism. Is biology afraid to say this in plain language? Out with the old, in with the new. Biology has so encamped itself into defending the Darwinian model that it can't move into the current century.

November 5, 2010

a long time ago many so-called scientists and their cousins appeared to believe the Ptolomeic geocentric concept. It was even accepted by the distorted Roman church founded by the emperor Costantino in the 4th century of this age. \nThen a bright Polish astronomer postulated the heliocentric concept and many people went nuts. \nIn the 1970s of last century, the strongly materialistic soviet science affirmed that this universe had no beginning. Perhaps that was accepted as a scientific fact in many places outside the Soviet Union too. However, later many scientists talked about the beginning of this universe happening around 15 billion years ago. The difference between infinite (no beginning) and 15 billion is -in serious mathematical terms- simply infinite. That's quite a gross error for respectful science to make. \nDefinitely enough to erode its authority. \nBut that's not all. The pseudo-scientific obsession with the macro-evolutionary ideas practically persuaded many brilliant scientists to ignore the non-coding DNA when researching the complex mechanisms behind genetic regulatory networks, gene expression pathways, spliceosomes, bio clocks, etc. Then lately scientists are talking about the functionality associated with at least some parts of that so-called "junk" DNA. \nAnother huge scientific hickup -Oops! Shame on that kind of pseudo-science. \nSo much for the benefits of macro-evolutionary concepts taken at face value as a dogma. \nTrue science should not convert speculation into dogma or doctrine. \nThat degrades the beautiful value of science. \n\n
Avatar of: Keith Oliver

Keith Oliver

Posts: 1

April 21, 2011

In addition to the notable omission of horizontal gene transfer, and of punctuated equilibrium, the omission of the major part played in evolution by Transposable Elements (TEs) is inexcusable. See Oliver K R & Greene W K 2009 Transpoable elements: powerful facilitators of evolution. BioEssays 31:703-714. There is also Zeh D W, Zeh J A & Ishida 2009 Transposable elements and an epigenetic basis for punctuated equlibria. BioEssays 31:715-726. There are also many other papers along similar lines that have been published in the last decade or so. A major revision of the 'Modern Synthesis' is definitely needed.\nKeith Oliver

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