Wednesday 31 August 2016
File under "well said" XXXIV
Success consists of going from failure to failure without loss of enthusiasm.
Winston Churchill
Winston Churchill
The talking ape continues to testify against Darwinism
In The Kingdom of Speech, Tom Wolfe Tells the Story of Evolution's Epic Tumble.
David Klinghoffer
Darwinian evolution explains biological trivia -- variable finch beaks and the like -- but stumbles when it comes to the major innovations in the long history of life. No innovation could be more revolutionary than how homo sapiens, as Discovery Institute biologist Michael Denton puts it, "slipped suddenly into being on the rich, game-laden African grasslands of the late Pleistocene."The most distinctive thing about man is of course his gift for language. On that, the great Tom Wolfe masterfully explains in a new book out today, Darwinism takes an epic tumble. Evolution cannot explain the very thing that preeminently makes us human. "To say that animals evolved into man," writes Wolfe on the last page of The Kingdom of Speech, "is like saying that Carrara marble evolved into Michelangelo's David."
The analogy is heavy with significance. An artist shapes his medium as an act of deliberate design. Wolfe, one of the most treasured writers alive today, hasn't come out for intelligent design, at least not directly. In previous statements he has shown sympathy for ID, comparing the persecution of ID scientists to the "Spanish Inquisition." Here too he refers to the "Neo-Darwinist Inquisition." But his focus is on the story of how evolution, from Darwin to Chomsky, came up short in explaining speech. He lets the implications of this speak for themselves.
The significance of speech goes beyond merely expressing our exceptional status as humans -- the "cardinal distinction between man and animal." As Wolfe points out, it grants us rule over the earth and its creatures, and even more than that.
In short, speech, and only speech, has enabled us human beasts to conquer every square inch of land in the world, subjugate every creature big enough to lay eyes on, and eat up half the population of the sea.
And this, the power to conquer the entire planet for our own species, is the minor achievement of speech's great might. The great achievement has been the creation of an internal self, an ego.
From that "internal self," endowed with curiosity and longing, flows the riches of civilization -- art, religion, philosophy, literature, science, and so much more. How impressive, really, is a theory of origins if it can shed no light on the origin of any of that?
Wolfe frames his story in terms of two pairs of rivals or doppelgängers -- Charles Darwin and Alfred Russel Wallace, on one hand, and linguists Noam Chomsky and Daniel Everett on the other. As in every other book of his that I've read, Wolfe is sharply attuned to matters of status, rank, class -- which explain so much not only in fashion or politics but in the history of ideas. In both of these pairs of scientists, one is the established figure, the man of rank and prestige (Darwin, Chomsky), while he was overtaken and nearly knocked from his pedestal by a field researcher of lesser cachet (Wallace, Everett), a "flycatcher" in Wolfe's phrase.
In 1858, Wallace panicked Darwin into going public with his theory, which Wallace had thought up independently while in a malarial swoon on the other side of the world. The co-discoverer of evolution by natural selection came later to reject the comprehensive explanatory power of his and Darwin's theory.
Wallace showed, writes Wolfe, that "natural selection can expand a creature's powers only to the point where it has an advantage over the competition in the struggle for existence." What's more, "natural selection can't produce any 'specially developed organ' that is useless to a creature...or of so little use that it is not until thousands and thousands of years down the line that the creature can take advantage of the organ's full power."
Speech is the most obvious example of a power inexplicable in terms of natural selection. Only a designer could look ahead that way, using foresight and working out a plan, which led Wallace to his proto-intelligent design view, arguing for "the agency of some other power," "a superior intelligence," a "controlling intelligence," at work in guiding evolution. Darwin, meanwhile, was left to speculate absurdly about speech being an extension of bird song.
And there the matter was left until Chomsky came on the scene in the 1950s with his own notion of an evolved language "organ," hidden somewhere, as yet undetected, in the brain. Known as much for this theory as for his "Radical Chic" (Wolfe's famous phrase) politics, Chomsky intimidated his field and looked askance at "flycatchers" who left the air-conditioned department building to investigate obscure languages in obscure, inconvenient, and unhygienic parts of the world.
Chomsky's theory reigned supreme until 2008 when a flycatcher, Daniel Everett, revealed a primitive language, that of the Pirahã, a people of the Amazon, that lacked a key linguistic feature (recursion) that Chomsky held to be universal. It must be universal if a shared, evolved "organ" was responsible for all human speech. The conclusion of Everett's research was that speech, not a product of evolution, was in truth an "artifact" of human devising.
The study of linguistics was thrown into chaos. Chomsky himself, even as he all but denied the existence of his rival, was compelled to admit that after decades of his labor, "The evolution of the faculty of language largely remains an enigma":
[I]n thirty years, Chomsky had advanced from "specific neural structures, though their nature is not well understood" to "some rather obscure system of thought that we know is there but we don't know much about it."
We hardly understand language today, what it is, any better today than Aristotle, who explained it as a system of "mnemonics," an aid to memory.
The Kingdom of Speech is a brief, wonderfully written book, often hilarious. The bits about Darwin's dog and Chomsky's "visiting Martian" (a fixture of his lectures), for example, are delicious. The role of social prestige, not science, in accounting for a failed idea's persistence is a theme that nobody is better suited to explore than Tom Wolfe. He tells how in Darwin's own day, "people began to judge one another socially according to their belief, or not, in Darwin's great discovery." How little has changed!
Wolfe, it's true, does not pull the obvious trigger. He fairly begs to be introduced to Michael Denton. If speech is an artifact, how did man acquire the capacity to devise and use it? As Dr. Denton writes in his recent book, Evolution: Still a Theory in Crisis, the exalted intellectual capacities shared by men and women of all races, and accessed only through language, probably were not much use in hunting mammoths. He writes:
One of the most curious features of human evolution, and one that poses at the outset an intriguing and still unanswered challenge to the Darwinian and functionalist narrative, is the fact that all modern humans share the same higher intellectual capabilities. This means, incredible though it may seem, a brain capable of the intellectual feats of an Einstein, a Newton, or a Mozart must have already emerged in our last common ancestors more than 200,000 years ago. Such intellectual abilities seem absurdly powerful, beyond any conceivable utility for hunter-gatherers on that ancient savanna, and hence beyond any functionalist explanation.
Language, Denton writes, the "Type-defining homolog," is "consistent with a saltational origin." In other words, it appears to have sprung into existence, "slipped suddenly into being," from no primitive or animal model before it.
Alfred Wallace, as ever, pointed the way. Such a power, coming into existence when it could not possibly serve an evolutionary purpose, can only be accounted for as the product of design. Wolfe prefers to let us pull that trigger for ourselves.
David Klinghoffer
Darwinian evolution explains biological trivia -- variable finch beaks and the like -- but stumbles when it comes to the major innovations in the long history of life. No innovation could be more revolutionary than how homo sapiens, as Discovery Institute biologist Michael Denton puts it, "slipped suddenly into being on the rich, game-laden African grasslands of the late Pleistocene."The most distinctive thing about man is of course his gift for language. On that, the great Tom Wolfe masterfully explains in a new book out today, Darwinism takes an epic tumble. Evolution cannot explain the very thing that preeminently makes us human. "To say that animals evolved into man," writes Wolfe on the last page of The Kingdom of Speech, "is like saying that Carrara marble evolved into Michelangelo's David."
The analogy is heavy with significance. An artist shapes his medium as an act of deliberate design. Wolfe, one of the most treasured writers alive today, hasn't come out for intelligent design, at least not directly. In previous statements he has shown sympathy for ID, comparing the persecution of ID scientists to the "Spanish Inquisition." Here too he refers to the "Neo-Darwinist Inquisition." But his focus is on the story of how evolution, from Darwin to Chomsky, came up short in explaining speech. He lets the implications of this speak for themselves.
The significance of speech goes beyond merely expressing our exceptional status as humans -- the "cardinal distinction between man and animal." As Wolfe points out, it grants us rule over the earth and its creatures, and even more than that.
In short, speech, and only speech, has enabled us human beasts to conquer every square inch of land in the world, subjugate every creature big enough to lay eyes on, and eat up half the population of the sea.
And this, the power to conquer the entire planet for our own species, is the minor achievement of speech's great might. The great achievement has been the creation of an internal self, an ego.
From that "internal self," endowed with curiosity and longing, flows the riches of civilization -- art, religion, philosophy, literature, science, and so much more. How impressive, really, is a theory of origins if it can shed no light on the origin of any of that?
Wolfe frames his story in terms of two pairs of rivals or doppelgängers -- Charles Darwin and Alfred Russel Wallace, on one hand, and linguists Noam Chomsky and Daniel Everett on the other. As in every other book of his that I've read, Wolfe is sharply attuned to matters of status, rank, class -- which explain so much not only in fashion or politics but in the history of ideas. In both of these pairs of scientists, one is the established figure, the man of rank and prestige (Darwin, Chomsky), while he was overtaken and nearly knocked from his pedestal by a field researcher of lesser cachet (Wallace, Everett), a "flycatcher" in Wolfe's phrase.
In 1858, Wallace panicked Darwin into going public with his theory, which Wallace had thought up independently while in a malarial swoon on the other side of the world. The co-discoverer of evolution by natural selection came later to reject the comprehensive explanatory power of his and Darwin's theory.
Wallace showed, writes Wolfe, that "natural selection can expand a creature's powers only to the point where it has an advantage over the competition in the struggle for existence." What's more, "natural selection can't produce any 'specially developed organ' that is useless to a creature...or of so little use that it is not until thousands and thousands of years down the line that the creature can take advantage of the organ's full power."
Speech is the most obvious example of a power inexplicable in terms of natural selection. Only a designer could look ahead that way, using foresight and working out a plan, which led Wallace to his proto-intelligent design view, arguing for "the agency of some other power," "a superior intelligence," a "controlling intelligence," at work in guiding evolution. Darwin, meanwhile, was left to speculate absurdly about speech being an extension of bird song.
And there the matter was left until Chomsky came on the scene in the 1950s with his own notion of an evolved language "organ," hidden somewhere, as yet undetected, in the brain. Known as much for this theory as for his "Radical Chic" (Wolfe's famous phrase) politics, Chomsky intimidated his field and looked askance at "flycatchers" who left the air-conditioned department building to investigate obscure languages in obscure, inconvenient, and unhygienic parts of the world.
Chomsky's theory reigned supreme until 2008 when a flycatcher, Daniel Everett, revealed a primitive language, that of the Pirahã, a people of the Amazon, that lacked a key linguistic feature (recursion) that Chomsky held to be universal. It must be universal if a shared, evolved "organ" was responsible for all human speech. The conclusion of Everett's research was that speech, not a product of evolution, was in truth an "artifact" of human devising.
The study of linguistics was thrown into chaos. Chomsky himself, even as he all but denied the existence of his rival, was compelled to admit that after decades of his labor, "The evolution of the faculty of language largely remains an enigma":
[I]n thirty years, Chomsky had advanced from "specific neural structures, though their nature is not well understood" to "some rather obscure system of thought that we know is there but we don't know much about it."
We hardly understand language today, what it is, any better today than Aristotle, who explained it as a system of "mnemonics," an aid to memory.
The Kingdom of Speech is a brief, wonderfully written book, often hilarious. The bits about Darwin's dog and Chomsky's "visiting Martian" (a fixture of his lectures), for example, are delicious. The role of social prestige, not science, in accounting for a failed idea's persistence is a theme that nobody is better suited to explore than Tom Wolfe. He tells how in Darwin's own day, "people began to judge one another socially according to their belief, or not, in Darwin's great discovery." How little has changed!
Wolfe, it's true, does not pull the obvious trigger. He fairly begs to be introduced to Michael Denton. If speech is an artifact, how did man acquire the capacity to devise and use it? As Dr. Denton writes in his recent book, Evolution: Still a Theory in Crisis, the exalted intellectual capacities shared by men and women of all races, and accessed only through language, probably were not much use in hunting mammoths. He writes:
One of the most curious features of human evolution, and one that poses at the outset an intriguing and still unanswered challenge to the Darwinian and functionalist narrative, is the fact that all modern humans share the same higher intellectual capabilities. This means, incredible though it may seem, a brain capable of the intellectual feats of an Einstein, a Newton, or a Mozart must have already emerged in our last common ancestors more than 200,000 years ago. Such intellectual abilities seem absurdly powerful, beyond any conceivable utility for hunter-gatherers on that ancient savanna, and hence beyond any functionalist explanation.
Language, Denton writes, the "Type-defining homolog," is "consistent with a saltational origin." In other words, it appears to have sprung into existence, "slipped suddenly into being," from no primitive or animal model before it.
Alfred Wallace, as ever, pointed the way. Such a power, coming into existence when it could not possibly serve an evolutionary purpose, can only be accounted for as the product of design. Wolfe prefers to let us pull that trigger for ourselves.
Speaking up in behalf of speaking out.
University of Chicago President Decries "Efforts to Suppress Discussion of Charles Darwin's Work"
Sarah Chaffee
Attempts to limit free speech on college campuses are many -- for example, at Yale, students berated professor Nicholas Christakis after he suggested that the school shouldn't regulate Halloween costumes that were not culturally sensitive.
Someone finally decided to stand up and defend freedom of speech as a defining principle of education. This summer, the University of Chicago's Dean of Students, John Ellison, sent a letter to all incoming freshman, stating:
Once here you will discover that one of the University of Chicago's defining characteristics is our commitment to freedom of inquiry and expression. This is captured in the University's faculty report on freedom of expression. Members of our community are encouraged to speak, write, listen, challenge, and learn, without fear of censorship. Civility and mutual respect are vital to all of us, and freedom of expression does not mean the freedom to harass or threaten others. You will find that we expect members of our community to be engaged in rigorous debate, discussion, and even disagreement. At times this may challenge you and even cause discomfort.
Our commitment to academic freedom means that we do not support so-called "trigger warnings," we do not cancel invited speakers because their topics might prove controversial, and we do not condone the creation of intellectual "safe spaces" where individuals can retreat from ideas and perspectives at odds with their own.
Fostering the free exchange of ideas reinforces a related University priority -- building a campus that welcomes people of all backgrounds. Diversity of opinion and background is a fundamental strength of our community. The members of our community must have the freedom to espouse and explore a wide range of ideas.
(Note that the University has clarified that this does not ban the use of trigger warnings or setting up safe spaces.) The letter has received national attention and generated controversy. Professors from the school and from different schools across the country, and the Foundation for Individual Rights in Education (FIRE), among others, rightly commend the university on its stance. FIRE notes that it "hopes that students, faculty, and administrators nationwide take a cue from UC and recommit to freedom of speech on their own campuses."
The letter follows a report generated by a specially-organized university group on freedom of expression.
Robert J. Zimmer, President of the University of Chicago, followed the letter with an op-ed in the Wall Street Journal, "Free Speech Is the Basis of a True Education." After discussing the intellectual skills students need for successful lives, including recognizing cultural differences, identifying complexity, and engaging in critical thinking about evidence, Zimmer states:
One word summarizes the process by which universities impart these skills: questioning. Productive and informed questioning involves challenging assumptions, arguments and conclusions. It calls for multiple and diverse perspectives and listening to the views of others. It requires understanding the power and limitations of arguments. More fundamentally, the process of questioning demands an ability to rethink one's own assumptions, often the most difficult task of all.
Essential to this process is an environment that promotes free expression and the open exchange of ideas, ensuring that difficult questions are asked and that diverse and challenging perspectives are considered. This underscores the importance of diversity among students, faculty and visitors--diversity of background, belief and experience. Without this, students' experience becomes a weak imitation of a true education, and the value of that education is seriously diminished.
One could not ask for a more thorough endorsement of free speech in universities. The concept of freedom of expression is crucial for many areas, not least in debate over Darwinism. Although he is almost certainly referencing it historically, note Zimmer's mention of evolution:
... Some assert that universities should be refuges from intellectual discomfort and that their own discomfort with conflicting and challenging views should override the value of free and open discourse.
We have seen efforts to suppress discussion of Charles Darwin's work, to insist upon particular political perspectives during the McCarthy era, to impose exclusionary acts of racial and religious discrimination, and to demand compliance with various forms of "moral" behavior.
The silencing being advocated today is equally problematic. Every attempt to legitimize silencing creates justification for others to restrain speech that they do not like in the future. [Emphasis added.]
Wow. Today the situation is reversed: those who question Darwin's work face discrimination. But the University of Chicago's position, at least in principle, would support free debate about neo-Darwinism and intelligent design, along with all other issues.
If only intelligent design proponents routinely faced this perspective. Perhaps Eric Hedin, physicist at Ball State University, would still be teaching his interdisciplinary honors course, "Boundaries of Science," which included some material on intelligent design. Perhaps the Michael Polanyi Center at Baylor University would still exist, with Dembski at its head.
Zimmer proclaims that violations of liberty pave the way for future restrictions. And professor Geoffrey Stone, chair of UC's Committee on Freedom of Expression, in an article quoted by FIRE, notes that academic freedom is key because first, "bitter experience has taught that even the ideas we hold to be most certain often turn out to be wrong," second, silencing some speech leads to more silencing, and third:
[A] central precept of free expression is the possibility of a chilling effect.... The potential costs of speaking courageously, of taking controversial positions, of taking risks, is greater than ever. Indeed, according to a recent survey, about half of American college students now say that it is unsafe for them to express unpopular views. Many faculty members clearly share that sentiment.
Stone's points hits home: intolerance of dissent from Darwinism has sparked all three of these issues.
Even though UC's position does not address intelligent design specifically, any step towards academic freedom on campus is beneficial. Freedom of speech staves off a downward spiral of viewpoint discrimination, allowing new (and sometimes more accurate) ideas to come forward.
After all, as Zimmer noted:
Universities cannot be viewed as a sanctuary for comfort but rather as a crucible for confronting ideas and thereby learning to make informed judgments in complex environments. Having one's assumptions challenged and experiencing the discomfort that sometimes accompanies this process are intrinsic parts of an excellent education. Only then will students develop the skills necessary to build their own futures and contribute to society.
It's high time for universities to extend protections to those who question neo-Darwinism. Perhaps Chicago's ringing endorsement of academic freedom will open more doors for evolution skeptics. We commend Robert Zimmer, John Ellison, and UC's Committee on Freedom of Expression for their courage.
Sarah Chaffee
Attempts to limit free speech on college campuses are many -- for example, at Yale, students berated professor Nicholas Christakis after he suggested that the school shouldn't regulate Halloween costumes that were not culturally sensitive.
Someone finally decided to stand up and defend freedom of speech as a defining principle of education. This summer, the University of Chicago's Dean of Students, John Ellison, sent a letter to all incoming freshman, stating:
Once here you will discover that one of the University of Chicago's defining characteristics is our commitment to freedom of inquiry and expression. This is captured in the University's faculty report on freedom of expression. Members of our community are encouraged to speak, write, listen, challenge, and learn, without fear of censorship. Civility and mutual respect are vital to all of us, and freedom of expression does not mean the freedom to harass or threaten others. You will find that we expect members of our community to be engaged in rigorous debate, discussion, and even disagreement. At times this may challenge you and even cause discomfort.
Our commitment to academic freedom means that we do not support so-called "trigger warnings," we do not cancel invited speakers because their topics might prove controversial, and we do not condone the creation of intellectual "safe spaces" where individuals can retreat from ideas and perspectives at odds with their own.
Fostering the free exchange of ideas reinforces a related University priority -- building a campus that welcomes people of all backgrounds. Diversity of opinion and background is a fundamental strength of our community. The members of our community must have the freedom to espouse and explore a wide range of ideas.
(Note that the University has clarified that this does not ban the use of trigger warnings or setting up safe spaces.) The letter has received national attention and generated controversy. Professors from the school and from different schools across the country, and the Foundation for Individual Rights in Education (FIRE), among others, rightly commend the university on its stance. FIRE notes that it "hopes that students, faculty, and administrators nationwide take a cue from UC and recommit to freedom of speech on their own campuses."
The letter follows a report generated by a specially-organized university group on freedom of expression.
Robert J. Zimmer, President of the University of Chicago, followed the letter with an op-ed in the Wall Street Journal, "Free Speech Is the Basis of a True Education." After discussing the intellectual skills students need for successful lives, including recognizing cultural differences, identifying complexity, and engaging in critical thinking about evidence, Zimmer states:
One word summarizes the process by which universities impart these skills: questioning. Productive and informed questioning involves challenging assumptions, arguments and conclusions. It calls for multiple and diverse perspectives and listening to the views of others. It requires understanding the power and limitations of arguments. More fundamentally, the process of questioning demands an ability to rethink one's own assumptions, often the most difficult task of all.
Essential to this process is an environment that promotes free expression and the open exchange of ideas, ensuring that difficult questions are asked and that diverse and challenging perspectives are considered. This underscores the importance of diversity among students, faculty and visitors--diversity of background, belief and experience. Without this, students' experience becomes a weak imitation of a true education, and the value of that education is seriously diminished.
One could not ask for a more thorough endorsement of free speech in universities. The concept of freedom of expression is crucial for many areas, not least in debate over Darwinism. Although he is almost certainly referencing it historically, note Zimmer's mention of evolution:
... Some assert that universities should be refuges from intellectual discomfort and that their own discomfort with conflicting and challenging views should override the value of free and open discourse.
We have seen efforts to suppress discussion of Charles Darwin's work, to insist upon particular political perspectives during the McCarthy era, to impose exclusionary acts of racial and religious discrimination, and to demand compliance with various forms of "moral" behavior.
The silencing being advocated today is equally problematic. Every attempt to legitimize silencing creates justification for others to restrain speech that they do not like in the future. [Emphasis added.]
Wow. Today the situation is reversed: those who question Darwin's work face discrimination. But the University of Chicago's position, at least in principle, would support free debate about neo-Darwinism and intelligent design, along with all other issues.
If only intelligent design proponents routinely faced this perspective. Perhaps Eric Hedin, physicist at Ball State University, would still be teaching his interdisciplinary honors course, "Boundaries of Science," which included some material on intelligent design. Perhaps the Michael Polanyi Center at Baylor University would still exist, with Dembski at its head.
Zimmer proclaims that violations of liberty pave the way for future restrictions. And professor Geoffrey Stone, chair of UC's Committee on Freedom of Expression, in an article quoted by FIRE, notes that academic freedom is key because first, "bitter experience has taught that even the ideas we hold to be most certain often turn out to be wrong," second, silencing some speech leads to more silencing, and third:
[A] central precept of free expression is the possibility of a chilling effect.... The potential costs of speaking courageously, of taking controversial positions, of taking risks, is greater than ever. Indeed, according to a recent survey, about half of American college students now say that it is unsafe for them to express unpopular views. Many faculty members clearly share that sentiment.
Stone's points hits home: intolerance of dissent from Darwinism has sparked all three of these issues.
Even though UC's position does not address intelligent design specifically, any step towards academic freedom on campus is beneficial. Freedom of speech staves off a downward spiral of viewpoint discrimination, allowing new (and sometimes more accurate) ideas to come forward.
After all, as Zimmer noted:
Universities cannot be viewed as a sanctuary for comfort but rather as a crucible for confronting ideas and thereby learning to make informed judgments in complex environments. Having one's assumptions challenged and experiencing the discomfort that sometimes accompanies this process are intrinsic parts of an excellent education. Only then will students develop the skills necessary to build their own futures and contribute to society.
It's high time for universities to extend protections to those who question neo-Darwinism. Perhaps Chicago's ringing endorsement of academic freedom will open more doors for evolution skeptics. We commend Robert Zimmer, John Ellison, and UC's Committee on Freedom of Expression for their courage.
Why Dawinism continues to go to seed.
How a Dry Seed Can Live a Thousand Years
Evolution News & Views
Maybe you have some in your garage: old seed packets that never made it into your gardening project years ago. Would they sprout if you planted them now? It's likely some would. Seeds can last for decades, sometimes centuries. In 2005, a date palm seed that survived dry conditions at Masada for 2,000 years germinated and remains on display in Israel, nicknamed Methuselah. The oldest carbon-dated seeds that have grown into viable plants are flowers that were buried under Siberian permafrost for 32,000 years, according to National Geographic.
What does it take to keep a seed viable for many years of slumber? At a basic level, we can envision some requirements. The seed must be able to shut down all non-critical operations. It must protect its vital parts, like its genetic information. And it must remain watchful for conditions that would allow it to wake up and carry out its growth program. The details, however, are truly astonishing. Some of them are described in an open-access paper in the Proceedings of the National Academy of Sciences, "Regulatory network analysis reveals novel regulators of seed desiccation tolerance in Arabidopsis thaliana." Seven geneticists in Mexico looked into this "remarkable" operation:
Desiccation tolerance (DT) is a remarkable process that allows seeds in the dry state to remain viable for long periods of time that in some instances exceed 1,000 y. It has been postulated that seed DT evolved by rewiring the regulatory and signaling networks that controlled vegetative DT, which itself emerged as a crucial adaptive trait of early land plants. Understanding the networks that regulate seed desiccation tolerance in model plant systems would provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants. In this work, we used an integrated approach that included genomics, bioinformatics, metabolomics, and molecular genetics to identify and validate molecular networks that control the acquisition of DT in Arabidopsis seeds. [Emphasis added.]
For now, we won't quibble about the evolution lingo, knowing that it's par for the course in journals these days (but maybe not for long, Doug Axe speculates in Chapter 12 of his new book Undeniable: How Biology Confirms Our Intuition That Life Is Designed). What's important to notice are the evidences of functional coherence that he shows are the hallmarks of invention, especially when arranged in a hierarchical manner for a high-level function. Here, the paper dazzles us with glimpses at astonishing complexity. "DT organisms orchestrate a complex number of responses to protect cellular structures and prevent damage to proteins and nucleic acids," they say in the introduction. Lest we overwhelm you with detail, let's get just a taste of what goes on in the plant preparing its seeds for long periods of dormancy:
As predicted, desiccation-intolerant (DI)-specific down-regulated genes were enriched (FDR < 0.05) in the following Gene Ontology (GO) categories: molecular function: oxidoreductase activity and nutrient reservoir; and biological process: lipid and carbohydrate biosynthesis, seed development, and ABA and stress responses such as water, oxidation, and temperature... A more detailed analysis of the same set of genes ... showed enrichment in processes such as abiotic stress, LEA protein synthesis, and metabolic pathways including raffinose, stachyose, and trehalose biosynthesis....
Enough said? We'll stick to layman terms from now on. Clearly, preparation for DT is no simple matter! To find out what genes and transcription factors are involved, they compared wild-type plants with mutants unable to prepare for desiccation. In their words, "The finding that genes that are not activated in desiccation-intolerant mutants during seed maturation belong to water stress and cell protection mechanisms confirmed that desiccation-intolerant mutants fail to activate mechanisms required to acquire DT in the seed."
The genes that prepare a seed for dryness cooperate in regulatory networks. Stephen Meyer shows in Chapter 13 of Darwin's Doubt that one does not just tweak developmental gene regulatory networks (dGRNs) willy-nilly and expect to get a new function (that was Charles Marshall's story for the Cambrian explosion, remember? See Debating Darwin's Doubt, Chapters 10-11). For one thing, GRNs "do not tolerate random perturbations to their basic control logic," all available evidence shows (p. 130). For another, it would require just as much information to rewire a GRN for a novel function as it would to evolve new genes, so that's no solution at all (p. 134). But enough about origins; let's get back to the mechanics of DT.
You can well imagine conditions in the soil that would attack a seed's genetic information. When the plant is growing, numerous processes survey and repair DNA. But what happens when the seed goes to sleep? Counter-intuitively, water can be one of the night stalkers.
One of the most intriguing questions about how seeds in the desiccated state can remain viable for periods of time that can exceed centuries is particularly how the integrity of DNA is preserved to prevent permanent damage making the seed unviable. Three types of DNA damage under physiological conditions have been reported: hydrolysis of the N-glycosyl bond, hydrolytic deamination of cytosine to form uracil, and DNA damage by oxidation. The first two types of DNA damage are catalyzed by water, and therefore the last layers of water that interact with DNA need to be removed or decreased to prevent damage, and the third is mediated mainly by reactive oxygen species (ROS).
The plant uses a clever trick to protect its DNA from attack by water. It replaces water molecules with sugars. Hydroxyl groups (OH) of certain sugars can provide the necessary bonds to stabilize proteins, DNA and membranes from these kinds of damage. The team found that biosynthesis of three particular sugars is up-regulated during the final stages of seed preparation, in agreement with this mechanism. They also found genes were increased for five kinds of enzymes involved in protection from reactive oxygen species (ROS).
Therefore, accumulation of antioxidant components during the late maturation stage contributes to controlling their storage potential, and helps to prevent damage from accumulated ROS during seed maturation. Accumulation of RFOs [the raffinose family of oligosaccharides, one of the types of protective sugars] and activation of mechanisms that prevent damage by ROS allow maximum metabolism reduction to decrease the production of toxic compounds and to prevent membrane, DNA, RNA, and protein damage.
All these genes are accompanied by transcription factors that switch them on and off. The authors speak about not only regulatory networks, but regulatory subnetworks. One, for instance, downregulates proteins involved in germination, to prevent early sprouting. Another is involved in stress tolerance. They identified at least four such subnetworks. Some of the subnetworks themselves involve hundreds of genes!
The researchers spoke mainly about preparation for desiccation. They didn't get into other equally fascinating questions: What activities continue during the decades or centuries of slumber? (We know from our own sleep that our hearts must still beat, we must continue breathing, and much more.) How are genes repaired by cosmic ray damage and other contingencies? And what re-activates growth processes when conditions are right for sprouting? How does a blind seed, buried in the dark soil, know when it's time to wake up? What are the first steps it takes to germinate?
This brief glimpse at desiccation tolerance in one model plant ensures is that the answers to those questions will likely be just as complicated -- and fascinating. Like so many things in the biosphere, the apparently simple process of a seed preparing for sleep is anything but simple. Evolution stories often trade in generalities. Intelligent design evidences are best seen in the details. Like Doug Axe says, biology with a design perspective becomes like a great geocaching game. "What makes finding a well-conceived geocache so delightful," he explains, "is not just the sense of having found something that was hard to find -- though that's part of it -- but the sense of having found something that was meant to be found and cleverly made hard to find" (Undeniable, p. 248). It appears we just found a good prize right under our feet.
Evolution News & Views
Maybe you have some in your garage: old seed packets that never made it into your gardening project years ago. Would they sprout if you planted them now? It's likely some would. Seeds can last for decades, sometimes centuries. In 2005, a date palm seed that survived dry conditions at Masada for 2,000 years germinated and remains on display in Israel, nicknamed Methuselah. The oldest carbon-dated seeds that have grown into viable plants are flowers that were buried under Siberian permafrost for 32,000 years, according to National Geographic.
What does it take to keep a seed viable for many years of slumber? At a basic level, we can envision some requirements. The seed must be able to shut down all non-critical operations. It must protect its vital parts, like its genetic information. And it must remain watchful for conditions that would allow it to wake up and carry out its growth program. The details, however, are truly astonishing. Some of them are described in an open-access paper in the Proceedings of the National Academy of Sciences, "Regulatory network analysis reveals novel regulators of seed desiccation tolerance in Arabidopsis thaliana." Seven geneticists in Mexico looked into this "remarkable" operation:
Desiccation tolerance (DT) is a remarkable process that allows seeds in the dry state to remain viable for long periods of time that in some instances exceed 1,000 y. It has been postulated that seed DT evolved by rewiring the regulatory and signaling networks that controlled vegetative DT, which itself emerged as a crucial adaptive trait of early land plants. Understanding the networks that regulate seed desiccation tolerance in model plant systems would provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants. In this work, we used an integrated approach that included genomics, bioinformatics, metabolomics, and molecular genetics to identify and validate molecular networks that control the acquisition of DT in Arabidopsis seeds. [Emphasis added.]
For now, we won't quibble about the evolution lingo, knowing that it's par for the course in journals these days (but maybe not for long, Doug Axe speculates in Chapter 12 of his new book Undeniable: How Biology Confirms Our Intuition That Life Is Designed). What's important to notice are the evidences of functional coherence that he shows are the hallmarks of invention, especially when arranged in a hierarchical manner for a high-level function. Here, the paper dazzles us with glimpses at astonishing complexity. "DT organisms orchestrate a complex number of responses to protect cellular structures and prevent damage to proteins and nucleic acids," they say in the introduction. Lest we overwhelm you with detail, let's get just a taste of what goes on in the plant preparing its seeds for long periods of dormancy:
As predicted, desiccation-intolerant (DI)-specific down-regulated genes were enriched (FDR < 0.05) in the following Gene Ontology (GO) categories: molecular function: oxidoreductase activity and nutrient reservoir; and biological process: lipid and carbohydrate biosynthesis, seed development, and ABA and stress responses such as water, oxidation, and temperature... A more detailed analysis of the same set of genes ... showed enrichment in processes such as abiotic stress, LEA protein synthesis, and metabolic pathways including raffinose, stachyose, and trehalose biosynthesis....
Enough said? We'll stick to layman terms from now on. Clearly, preparation for DT is no simple matter! To find out what genes and transcription factors are involved, they compared wild-type plants with mutants unable to prepare for desiccation. In their words, "The finding that genes that are not activated in desiccation-intolerant mutants during seed maturation belong to water stress and cell protection mechanisms confirmed that desiccation-intolerant mutants fail to activate mechanisms required to acquire DT in the seed."
The genes that prepare a seed for dryness cooperate in regulatory networks. Stephen Meyer shows in Chapter 13 of Darwin's Doubt that one does not just tweak developmental gene regulatory networks (dGRNs) willy-nilly and expect to get a new function (that was Charles Marshall's story for the Cambrian explosion, remember? See Debating Darwin's Doubt, Chapters 10-11). For one thing, GRNs "do not tolerate random perturbations to their basic control logic," all available evidence shows (p. 130). For another, it would require just as much information to rewire a GRN for a novel function as it would to evolve new genes, so that's no solution at all (p. 134). But enough about origins; let's get back to the mechanics of DT.
You can well imagine conditions in the soil that would attack a seed's genetic information. When the plant is growing, numerous processes survey and repair DNA. But what happens when the seed goes to sleep? Counter-intuitively, water can be one of the night stalkers.
One of the most intriguing questions about how seeds in the desiccated state can remain viable for periods of time that can exceed centuries is particularly how the integrity of DNA is preserved to prevent permanent damage making the seed unviable. Three types of DNA damage under physiological conditions have been reported: hydrolysis of the N-glycosyl bond, hydrolytic deamination of cytosine to form uracil, and DNA damage by oxidation. The first two types of DNA damage are catalyzed by water, and therefore the last layers of water that interact with DNA need to be removed or decreased to prevent damage, and the third is mediated mainly by reactive oxygen species (ROS).
The plant uses a clever trick to protect its DNA from attack by water. It replaces water molecules with sugars. Hydroxyl groups (OH) of certain sugars can provide the necessary bonds to stabilize proteins, DNA and membranes from these kinds of damage. The team found that biosynthesis of three particular sugars is up-regulated during the final stages of seed preparation, in agreement with this mechanism. They also found genes were increased for five kinds of enzymes involved in protection from reactive oxygen species (ROS).
Therefore, accumulation of antioxidant components during the late maturation stage contributes to controlling their storage potential, and helps to prevent damage from accumulated ROS during seed maturation. Accumulation of RFOs [the raffinose family of oligosaccharides, one of the types of protective sugars] and activation of mechanisms that prevent damage by ROS allow maximum metabolism reduction to decrease the production of toxic compounds and to prevent membrane, DNA, RNA, and protein damage.
All these genes are accompanied by transcription factors that switch them on and off. The authors speak about not only regulatory networks, but regulatory subnetworks. One, for instance, downregulates proteins involved in germination, to prevent early sprouting. Another is involved in stress tolerance. They identified at least four such subnetworks. Some of the subnetworks themselves involve hundreds of genes!
The researchers spoke mainly about preparation for desiccation. They didn't get into other equally fascinating questions: What activities continue during the decades or centuries of slumber? (We know from our own sleep that our hearts must still beat, we must continue breathing, and much more.) How are genes repaired by cosmic ray damage and other contingencies? And what re-activates growth processes when conditions are right for sprouting? How does a blind seed, buried in the dark soil, know when it's time to wake up? What are the first steps it takes to germinate?
This brief glimpse at desiccation tolerance in one model plant ensures is that the answers to those questions will likely be just as complicated -- and fascinating. Like so many things in the biosphere, the apparently simple process of a seed preparing for sleep is anything but simple. Evolution stories often trade in generalities. Intelligent design evidences are best seen in the details. Like Doug Axe says, biology with a design perspective becomes like a great geocaching game. "What makes finding a well-conceived geocache so delightful," he explains, "is not just the sense of having found something that was hard to find -- though that's part of it -- but the sense of having found something that was meant to be found and cleverly made hard to find" (Undeniable, p. 248). It appears we just found a good prize right under our feet.
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