evolutionnewsandviews--2020-08-01--A “Lush” World Defies Materialist Explanations, as Behe and Denton Confirm

It is well known , and accepted in scientific circles , that the conditions on our planet are extremely fine-tuned for life : the Earth is just the right size , it is just the right distance from its sun , our sun is the right type of star , our atmosphere has many rare and lucky features — the list goes on and on .
A few of these fine-tuned features are documented in Episode 4 of Science Uprising .
Of course materialists have an explanation for it all : there are many planets in the universe , only @ @ @ @ @ @ @ , but we are here because our Earth is one of these rare planets .
It is also well known , and documented in the same Science Uprising episode , that not only is our Earth an ideal planet for life to thrive , but our whole universe is finely tuned for life .
The smallest changes in most of the basic constants ( the gravitational constant , the charge and mass of the electron , etc . )
or in the initial conditions at the Big Bang , would have led to @ @ @ @ @ @ @ humans , could not have arisen .
Stephen Hawking wrote in A Brief History of Time ( 1988 ) : “ The remarkable fact is that the values of these numbers seem to have been very finely adjusted to make possible the development of life.
” According to materialists , there must be many universes , with many different laws and constants and initial conditions , and we are here because our universe is one of those rare universes where the conditions are just right for us to be here .
A.J .
@ @ @ @ @ @ @ of our universe in The Problems of Physics ( 1987 ) .
He concludes : If we believe there are countless other universes , either in space or time , or in superspace , there is no longer anything astounding about the enormous degree of cosmic organization that we observe .
We have selected it by our very existence… .
The many universes theory does provide an explanation for why many things around us are the way they are .
Just as we can explain why we are living on a planet near @ @ @ @ @ @ @ only in such locations can life form , so we can perhaps explain many of the more general features of the universe by this anthropic selection process .
If Their Assumptions Were True Well , there no doubt are many planets in our universe , so the materialists ’ explanation , that our planet is “ just right ” because otherwise we would not be here to wonder about it , seems plausible enough .
At least it would be plausible , if their assumptions were true that once you have a planet @ @ @ @ @ @ @ a universe where the laws are cleverly designed for life , then there is a reasonable chance that life would spontaneously arise , and intelligent beings would spontaneously evolve over time .
To see how flawed the first assumption is , you only have to realize that with all our advanced technology we are still not close to designing any type of self-replicating machine .
That is still pure science fiction .
So how could we believe that such a machine could arise by pure chance , even given ideal conditions and clever @ @ @ @ @ @ @ chemist James Tour , in Science Uprising Episode 5 , explains why we are nowhere close to explaining how life arose .
To see how flawed the second assumption is you only have to realize that what materialists believe is that the four fundamental , unintelligent , forces of physics alone could have rearranged the basic particles of physics into computers , encyclopedias , airplanes , and iPhones , as my new video , “ Why Evolution Is Different , ” brings out .
( The video also points out how similar the @ @ @ @ @ @ @ human technology , with large gaps where major new features appeared — for the same reasons . )
The laws of physics are very cleverly designed , and probably can explain everything that has happened on Jupiter , but I do not believe that they are clever enough to explain everything that has happened on Earth .
On the other hand , there is no evidence — there can be no evidence — that there are other universes out there , with the same laws of physics but random values for the basic @ @ @ @ @ @ @ physics also ? )
, so the explanation that our universe is just right because otherwise we would not be here to wonder about it is completely unscientific .
That this argument is just a desperate , last-ditch effort to avoid the obvious conclusion of design is evident from the fact that materialists do not use it to explain the evolution of life also .
If it is reasonable to explain astronomically improbable fine-tuning of the constants of physics by inventing enough other universes , why not invent a few more and claim @ @ @ @ @ @ @ intelligent beings arose by pure chance ?
In a section of The Edge of Evolution ( 2007 ) critiquing the multiverse explanation for fine-tuning , Michael Behe wrote , So Michael Denton ’ s current series at Evolution News is particularly interesting because he is confirming , in a more “ rigorous ” way , what Behe and many others of us have suspected : that the conditions on Earth , and the laws of physics , are not only fine-tuned for the survival of intelligent beings , they are also fine-tuned for @ @ @ @ @ @ @ not the only scientist who has noticed this more general fine-tuning .
Astronomer Guillermo Gonzales , for example , discusses in this video some of the lucky coincidences that make Earth an ideal place for discovery of the rest of the universe .
These fine-tunings for the development of technology , and for scientific discovery , are interesting because they can not be explained by “ The conditions were just right because otherwise we would not be here to wonder about it ” arguments .
We would still be here to wonder if @ @ @ @ @ @ @ properties of fire , water , and metals , were not so fine-tuned to make the development of advanced technology possible .
We would still be here to wonder , if our Earth were not so ideally situated for discovery of the universe .
Technology and scientific discovery are just “ extras , ” which result in a more “ lush ” world .
But not to worry , materialists will never run out of ways to avoid the obvious conclusion of design .
It is only a question of time until we @ @ @ @ @ @ @ our planet and universe are fine-tuned for the development of technology .
Otherwise you would not be reading Internet posts like this on your computer !
”

Photo credit: Matt Lamers, via Unsplash.
It is well known, and accepted in scientific circles, that the conditions on our planet are extremely fine-tuned for life: the Earth is just the right size, it is just the right distance from its sun, our sun is the right type of star, our atmosphere has many rare and lucky features — the list goes on and on. A few of these fine-tuned features are documented in Episode 4 of Science Uprising. Of course materialists have an explanation for it all: there are many planets in the universe, only a very few are suitable for life, but we are here because our Earth is one of these rare planets.
It is also well known, and documented in the same Science Uprising episode, that not only is our Earth an ideal planet for life to thrive, but our whole universe is finely tuned for life. The smallest changes in most of the basic constants (the gravitational constant, the charge and mass of the electron, etc.) or in the initial conditions at the Big Bang, would have led to a universe where life, and therefore humans, could not have arisen. Stephen Hawking wrote in A Brief History of Time (1988): “The remarkable fact is that the values of these numbers seem to have been very finely adjusted to make possible the development of life.”
Conditions — Just Right!
According to materialists, there must be many universes, with many different laws and constants and initial conditions, and we are here because our universe is one of those rare universes where the conditions are just right for us to be here. A.J. Leggett lists some of the fine-tuned properties of our universe in The Problems of Physics (1987). He concludes:
The list could be multiplied endlessly, and it is easy to draw the conclusion that for any kind of conscious beings to exist at all, the basic constants of Nature have to be exactly what they are, or at least extremely close to it. The anthropic principle then turns this statement around and says, in effect, that the reason the fundamental constants have the values that they do is because otherwise we would not be here to wonder about them.
Paul Davies, in Other Worlds (1980), wrote
If we believe there are countless other universes, either in space or time, or in superspace, there is no longer anything astounding about the enormous degree of cosmic organization that we observe. We have selected it by our very existence…. The many universes theory does provide an explanation for why many things around us are the way they are. Just as we can explain why we are living on a planet near a stable star by pointing out that only in such locations can life form, so we can perhaps explain many of the more general features of the universe by this anthropic selection process.
If Their Assumptions Were True
Well, there no doubt are many planets in our universe, so the materialists’ explanation, that our planet is “just right” because otherwise we would not be here to wonder about it, seems plausible enough. At least it would be plausible, if their assumptions were true that once you have a planet where conditions are just right, and a universe where the laws are cleverly designed for life, then there is a reasonable chance that life would spontaneously arise, and intelligent beings would spontaneously evolve over time.
To see how flawed the first assumption is, you only have to realize that with all our advanced technology we are still not close to designing any type of self-replicating machine. That is still pure science fiction. So how could we believe that such a machine could arise by pure chance, even given ideal conditions and clever laws of physics? World-renowned Rice University chemist James Tour, in Science Uprising Episode 5, explains why we are nowhere close to explaining how life arose. To see how flawed the second assumption is you only have to realize that what materialists believe is that the four fundamental, unintelligent, forces of physics alone could have rearranged the basic particles of physics into computers, encyclopedias, airplanes, and iPhones, as my new video, “Why Evolution Is Different,” brings out. (The video also points out how similar the fossil record is to the development of human technology, with large gaps where major new features appeared — for the same reasons.) The laws of physics are very cleverly designed, and probably can explain everything that has happened on Jupiter, but I do not believe that they are clever enough to explain everything that has happened on Earth.
A Desperate, Last-Ditch Effort
On the other hand, there is no evidence — there can be no evidence — that there are other universes out there, with the same laws of physics but random values for the basic constants (or perhaps random laws of physics also?), so the explanation that our universe is just right because otherwise we would not be here to wonder about it is completely unscientific. That this argument is just a desperate, last-ditch effort to avoid the obvious conclusion of design is evident from the fact that materialists do not use it to explain the evolution of life also. If it is reasonable to explain astronomically improbable fine-tuning of the constants of physics by inventing enough other universes, why not invent a few more and claim that in one of these many universes intelligent beings arose by pure chance?
In a section of The Edge of Evolution (2007) critiquing the multiverse explanation for fine-tuning, Michael Behe wrote,
On the finite random multiverse view, we should very likely live in a bare-bones world, with little or nothing in life beyond what’s absolutely required to produce intelligent observers. So if we find ourselves in a world lavished with extras — with much more than the minimum — we should bet heavily against our world being the result of a finite multiverse scenario…. It is difficult to make a rigorous argument on such a question. Yet it seems that our world is quite lush and contains much more than what’s absolutely needed for intelligence.
So Michael Denton’s current series at Evolution News is particularly interesting because he is confirming, in a more “rigorous” way, what Behe and many others of us have suspected: that the conditions on Earth, and the laws of physics, are not only fine-tuned for the survival of intelligent beings, they are also fine-tuned for the development of technology. Denton is not the only scientist who has noticed this more general fine-tuning. Astronomer Guillermo Gonzales, for example, discusses in this video some of the lucky coincidences that make Earth an ideal place for discovery of the rest of the universe.
A Lush Life
These fine-tunings for the development of technology, and for scientific discovery, are interesting because they cannot be explained by “The conditions were just right because otherwise we would not be here to wonder about it” arguments. We would still be here to wonder if the conditions on Earth, and the properties of fire, water, and metals, were not so fine-tuned to make the development of advanced technology possible. We would still be here to wonder, if our Earth were not so ideally situated for discovery of the universe. Technology and scientific discovery are just “extras,” which result in a more “lush” world.
But not to worry, materialists will never run out of ways to avoid the obvious conclusion of design. It is only a question of time until we hear, “Of course conditions on our planet and universe are fine-tuned for the development of technology. Otherwise you would not be reading Internet posts like this on your computer!”


evolutionnewsandviews--2020-07-31--Something Is Missing from Bronx Zoo’s Apology

Better late than never , the Bronx Zoo yesterday apologized for imprisoning an African Pygmy , Ota Benga , as a display in its Monkey House in 1906 .
They left something out , though .
But first , why did they choose this moment ?
From Fox News : Did the impact of the multiple awards-winning documentary Human Zoos , by Discovery Institute ’ s John West , now with 2.5 million views and powerfully documenting the horrific episode and others like it , play any role ?
They don ’ t say .
We ’ re supposed to @ @ @ @ @ @ @ 125th anniversary of the zoo ’ s opening combined with Black Lives Matter protests , that prompted them to start “ digging into ” the zoo ’ s history .
Well , fine .
Let them save a bit of face .
It ’ s commendable , too , that they admit the role of “ pseudoscientific racism ” and eugenics in the story of Ota Benga , his humiliation and dehumanization .
From the zoo ’ s statement : What ’ s missing , and it ’ s not fine , is @ @ @ @ @ @ @ came from .
What was the nature , the content , of the “ pseudoscientific racism ” that motivated Ota Benga ’ s treatment ?
To be accurate , the racism wasn ’ t “ eugenics-based ” it was “ evolution-based.
” That is left out .
Imprisoning and displaying an African man in a zoo was not an experiment in eugenics , although that phony “ science ” was in vogue at the time at the institutions of higher learning where today woke students and faculty lecture the country about its systemic @ @ @ @ @ @ @ the Alaska-Yukon-Pacific Exposition in Seattle , featured a display of supposedly primitive native people from the Philippines , the Igorot .
The 1909 Exposition grounds became the campus of the University of Washington , from which professor and “ white fragility ” expert Robin DiAngelo now holds forth .
Background like this never seems to make the cut .
The truth is that placing a man in the Monkey House was intended as an education for the public in Darwinian evolution .
As John West has said , Ota Benga was “ only @ @ @ @ @ @ @ were put on display in America in the name of Darwinian evolution.
” Though its article yesterday forgets to mention it ( “ Racist Incident from Bronx Zoo ’ s Past Draws Apology ” ) , the New York Times understood that clearly in 1906 .
Brushing aside protests from black clergymen that the African should be given an education not put in the cage , the newspaper explained : The suggestion that Benga should be placed in a school instead of a cage ignores the high probability that school would be a @ @ @ @ @ @ @ from which he could draw no advantage whatever .
The idea that men are all much alike except as they have had or lacked opportunities for getting an education out of books is now far out of date .
In other words , “ Listen to the science !
” In fact , racial hierarchy was hailed as solid science at the time .
The Times continued , The New York Times remains as haughty and scolding as it was 114 years ago .
But they were right that evolution was ( and @ @ @ @ @ @ @ of all the schools , ” as if it were as unquestionable as “ the multiplication table.
” The high school textbook at the center of the Scopes Trial in 1925 , Civic Biology , informed students about the ranking of the human races , with the “ Ethiopian or negro type ” at the bottom , as a straightforward conclusion of evolutionary science .
Facing up to history , not tearing it down or hiding from its lessons , is necessary and healthy .
The Bronx Zoo has gone a step in @ @ @ @ @ @ @ way .
They still shy from laying a hand on Darwinian theory .
That would be going too far .
The New York Times , in examining its own part in the same story , hasn ’ t even taken a step .

Photo: Bronx Zoo, Monkey House, by Antigng / CC BY-SA (https://creativecommons.org/licenses/by-sa/4.0).
Better late than never, the Bronx Zoo yesterday apologized for imprisoning an African Pygmy, Ota Benga, as a display in its Monkey House in 1906. They left something out, though. But first, why did they choose this moment? From Fox News:
The chief executive of the [Wildlife Conservation Society], Cristián Samper, told the [New York] Times that the group had started digging into its history because of its 125th anniversary this year. Samper said that process, combined with conversations about racial injustice sweeping the country after the police killing of George Floyd, prompted the apology.
Did the impact of the multiple awards-winning documentary Human Zoos, by Discovery Institute’s John West, now with 2.5 million views and powerfully documenting the horrific episode and others like it, play any role? They don’t say. We’re supposed to believe it was sheer coincidence, the 125th anniversary of the zoo’s opening combined with Black Lives Matter protests, that prompted them to start “digging into” the zoo’s history.
Saving Face
Well, fine. Let them save a bit of face. It’s commendable, too, that they admit the role of “pseudoscientific racism” and eugenics in the story of Ota Benga, his humiliation and dehumanization. From the zoo’s statement:
Specifically, we denounce the eugenics-based, pseudoscientific racism, writings, and philosophies advanced by many people during that era, including two of our founders, Madison Grant and Henry Fairfield Osborn, Sr. Excerpts from Grant’s book “The Passing of the Great Race” (with a preface by Osborn), were included in a defense exhibit for one of the defendants in the Nuremberg trials. Grant and Osborn were likewise among the founders of the American Eugenics Society in 1926.
What’s missing, and it’s not fine, is any mention of where these evil ideas came from. What was the nature, the content, of the “pseudoscientific racism” that motivated Ota Benga’s treatment? To be accurate, the racism wasn’t “eugenics-based” it was “evolution-based.” That is left out.
Candid and Shocking
For a candid and shocking treatment, I suggest watching Human Zoos.
Imprisoning and displaying an African man in a zoo was not an experiment in eugenics, although that phony “science” was in vogue at the time at the institutions of higher learning where today woke students and faculty lecture the country about its systemic racism. One human zoo, at the Alaska-Yukon-Pacific Exposition in Seattle, featured a display of supposedly primitive native people from the Philippines, the Igorot. The 1909 Exposition grounds became the campus of the University of Washington, from which professor and “white fragility” expert Robin DiAngelo now holds forth. Background like this never seems to make the cut.
The truth is that placing a man in the Monkey House was intended as an education for the public in Darwinian evolution. As John West has said, Ota Benga was “only one of thousands of indigenous peoples who were put on display in America in the name of Darwinian evolution.”
They Forgot to Mention
Though its article yesterday forgets to mention it (“Racist Incident from Bronx Zoo’s Past Draws Apology”), the New York Times understood that clearly in 1906. Brushing aside protests from black clergymen that the African should be given an education not put in the cage, the newspaper explained:
The suggestion that Benga should be placed in a school instead of a cage ignores the high probability that school would be a place of torture to him and one from which he could draw no advantage whatever. The idea that men are all much alike except as they have had or lacked opportunities for getting an education out of books is now far out of date.
In other words, “Listen to the science!” In fact, racial hierarchy was hailed as solid science at the time. The Times continued,
[T]he reverend colored brothers should be told that evolution, in one form or another, is now taught in the textbooks of all the schools, that it is no more debatable than the multiplication table.
Some Things Never Change
The New York Times remains as haughty and scolding as it was 114 years ago. But they were right that evolution was (and is) “taught in the textbooks of all the schools,” as if it were as unquestionable as “the multiplication table.” The high school textbook at the center of the Scopes Trial in 1925, Civic Biology, informed students about the ranking of the human races, with the “Ethiopian or negro type” at the bottom, as a straightforward conclusion of evolutionary science.
Facing up to history, not tearing it down or hiding from its lessons, is necessary and healthy. The Bronx Zoo has gone a step in that direction, but not the whole way. They still shy from laying a hand on Darwinian theory. That would be going too far. The New York Times, in examining its own part in the same story, hasn’t even taken a step.


evolutionnewsandviews--2020-07-31--Needed for Fire: All the Right Fuel

Needed for Fire: All the Right Fuel

Editor ’ s note : We are pleased to present a series adapted from biologist Michael Denton ’ s book , Fire-Maker : How Humans Were Designed to Harness Fire and Transform Our Planet , from Discovery Institute Press .
Find the whole series here .
Dr. Denton ’ s forthcoming book , The Miracle of the Cell , will be published in September .
Because of its atmosphere , its size , and its abundance of metals , the Earth is the right kind of planet to supply a home for a fire-making creature who can create new technologies @ @ @ @ @ @ @ the Earth ’ s environment that is absolutely crucial in allowing the utilization of fire for metal-based technologies .
To make a fire sufficiently hot to smelt metals requires the right fuel .
Thin twigs and dried grasses will burn , but such materials are unsuitable for making hot , sustainable fires that can reach high enough temperatures ( many hundreds of degrees ) to smelt metals from their ores .
Wood or wood products such as coal , charcoal , or coke are the only fuels that will do .
Without large @ @ @ @ @ @ @ , no charcoal , no coal ( essentially fossilized wood ) , and no sustainable fires for smelting metals .
Prometheus would be well and truly bound .
Again , it was not human inventiveness that provided either the wood for the manufacture of the charcoal that fired the primitive kilns in which the first metals were smelted nor provided the vital oxygen to burn the charcoal .
The existence of wood ( and nearly all the organic material on Earth ) and the oxygen in the atmosphere are the gifts of photosynthesis @ @ @ @ @ @ @ utilize the energy of sunlight to synthesize reduced carbon compounds which form the substance of wood and draw the hydrogen from water to release oxygen into the atmosphere .
As Stephen Pyne points out : Fire on Earth is a pervasive feature of the living world .
Life created the oxygen that combustion requires , and provides the hydrocarbon fuels that feed it… Fire takes apart what photosynthesis has put together ; its chemistry is a bio-chemistry .
Fire is not something extraneous to life to which organisms must adapt , it is @ @ @ @ @ @ @ nature of life on Earth.1 The fitness of nature for photosynthesis is a fascinating topic which I can not do full justice to here , but suffice to say that it depends on the atmosphere letting through the “ right ” visual light and absorbing the “ wrong ” dangerous radiation in UV , gamma , and X-rays regions of the electromagnetic spectrum .
The visual light energy raises the electrons in chlorophyll to higher energy levels , which allows them to escape and flow to the reaction centers in the chloroplast where @ @ @ @ @ @ @ same time , it creates a charge separation , drawing electrons from water , oxidizing it , and releasing oxygen.2 Altogether photosynthesis is a remarkable process which may even necessitate exploiting a process called quantum tunneling.3 • Tim Lenton , Revolutions That Made the Earth ( Oxford : Oxford University Press , 2011 ) , Chapter Eight .
• Johnjoe McFadden and Jim Al-Khalili , Life on the Edge : The Coming of Age of Quantum Biology ( New York : Crown Publishers , 2014 ) , Chapter Four .

Image: Prometheus Carrying Fire, by Jan Caussiers, via Wikimedia Commons.
It may form an interesting intellectual exercise to imagine ways in which life might arise, and having arisen might maintain itself, on a dark planet; but I doubt very much that this has ever happened, or that it can happen. George Wald, “Life and Light,” Scientific American 201, no. 4 (1959): 108.
Editor’s note: We are pleased to present a series adapted from biologist Michael Denton’s book, Fire-Maker: How Humans Were Designed to Harness Fire and Transform Our Planet, from Discovery Institute Press. Find the whole series here. Dr. Denton’s forthcoming book, The Miracle of the Cell, will be published in September.
Because of its atmosphere, its size, and its abundance of metals, the Earth is the right kind of planet to supply a home for a fire-making creature who can create new technologies. But there is another aspect of the Earth’s environment that is absolutely crucial in allowing the utilization of fire for metal-based technologies.
To make a fire sufficiently hot to smelt metals requires the right fuel.
Thin twigs and dried grasses will burn, but such materials are unsuitable for making hot, sustainable fires that can reach high enough temperatures (many hundreds of degrees) to smelt metals from their ores. Wood or wood products such as coal, charcoal, or coke are the only fuels that will do. Without large trees, there would be no wood, no charcoal, no coal (essentially fossilized wood), and no sustainable fires for smelting metals. Prometheus would be well and truly bound.
Thanks to Human Inventiveness? Nope
Again, it was not human inventiveness that provided either the wood for the manufacture of the charcoal that fired the primitive kilns in which the first metals were smelted nor provided the vital oxygen to burn the charcoal. The existence of wood (and nearly all the organic material on Earth) and the oxygen in the atmosphere are the gifts of photosynthesis, the process by which green plants utilize the energy of sunlight to synthesize reduced carbon compounds which form the substance of wood and draw the hydrogen from water to release oxygen into the atmosphere. As Stephen Pyne points out:
Fire on Earth is a pervasive feature of the living world. Life created the oxygen that combustion requires, and provides the hydrocarbon fuels that feed it… Fire takes apart what photosynthesis has put together; its chemistry is a bio-chemistry. Fire is not something extraneous to life to which organisms must adapt, it is something that has emerged out of the nature of life on Earth.1
The fitness of nature for photosynthesis is a fascinating topic which I cannot do full justice to here, but suffice to say that it depends on the atmosphere letting through the “right” visual light and absorbing the “wrong” dangerous radiation in UV, gamma, and X-rays regions of the electromagnetic spectrum. The visual light energy raises the electrons in chlorophyll to higher energy levels which escape from the chlorophyll and flow down electron transport chains providing energy for the synthesis of organic compounds in the chloroplast . At the same time, it creates a charge separation, drawing electrons from water, oxidizing it, and releasing oxygen.2 Altogether photosynthesis is a remarkable process which may even necessitate exploiting a process called quantum tunneling.3
Next, “The Role of Lignin for Fire, Explained.”
Notes


evolutionnewsandviews--2020-08-01--Intricately Designed Control Systems Sustain Your Life Right Now — A Doctor Explains

On a classic episode of ID the Future , biologist Ray Bohlin interviews physician Howard Glicksman about a common cause @ @ @ @ @ , using the subject as a doorway to explore some intricate , interdependent control systems @ @ @ @ @ of this would be possible in the absence of intelligent design .
Doctors , like @ @ @ @ @ grasp of why such things work , and why they don ’ t when they @ @ @ @ @ do many evolutionary biologists .
Download the podcast or listen to it here .
Dr. @ @ @ @ @ an extended series of posts at Evolution News , “ The Designed Body .
”

Photo credit: Alexandru Acea, via Unsplash.
On a classic episode of ID the Future, biologist Ray Bohlin interviews physician Howard Glicksman about a common cause of death, cardio-pulmonary arrest, using the subject as a doorway to explore some intricate, interdependent control systems that sustains life. None of this would be possible in the absence of intelligent design. Doctors, like engineers, have a better grasp of why such things work, and why they don’t when they don’t, than do many evolutionary biologists.
Download the podcast or listen to it here. Dr. Glicksman is the author of an extended series of posts at Evolution News, “The Designed Body.”


evolutionnewsandviews--2020-08-02--The Role of Lignin for Fire, Explained

The Role of Lignin for Fire, Explained

Editor ’ s note : We are pleased to present a series adapted from biologist Michael Denton ’ s book , Fire-Maker : How Humans Were Designed to Harness Fire and Transform Our Planet , from Discovery Institute Press .
Find the whole series here .
Dr. Denton ’ s forthcoming book , The Miracle of the Cell , will be published in September .
In addition to nature ’ s fitness for photosynthesis , the existence of large woody plants such as trees and the wood they provide for fire-making is only possible because of many other elements of @ @ @ @ @ @ @ properties of an unfamiliar but crucial component of plant cell walls : lignin .
Lignin is an essential component of all plant cell walls and provides the necessary element of strength for the construction of tall woody trees .
Because it is highly resistant to enzymatic catalysis , its breakdown in the soil is slow , allowing the formation of humus , which retains water and minerals in the soil.1 This in turn promoted the growth of large trees and allowed the build-up of vast volumes of undigested vegetation in the Carboniferous swamps @ @ @ @ @ @ @ steam engines of the early industrial age .
Without lignin , there would be no woody plants , no wood , no coal , no charcoal , no fire , no pottery , and certainly no iron and probably no other metals or metallurgy .
Many other conditions must be met for large woody trees to flourish .
First , their leaves must be able to lose heat in direct sunshine .
This is achieved by a “ Goldilocks ” combination of fundamental physical phenomena , including evaporative cooling , convection , conduction @ @ @ @ @ @ @ and branches must be made of a strong , durable material providing tensile strength ( resisting stretching ) and compressive strength ( resisting volume reduction ) to sustain bending and compressive pressures .
The combination of cellulose and lignin in plant cell walls provides the necessary strength and is in all probability uniquely fit for this role .
In addition to having strong trunks and being able to keep cool in the sun , trees must also have a method of absorbing water and drawing it to their leaves , which in the @ @ @ @ @ @ @ meters above the ground .
Water is the matrix of life on Earth and essential for cellular physiology and , in the case of plant cells , for photosynthesis .
Water is the source of both the hydrogen atoms for the synthesis of organic compounds , including wood , and of the oxygen atoms , which are released into the atmosphere .
Water is also utilized by plants for evaporative cooling , one of the factors that attenuates the temperature of leaves in hot sun .
• James C. Forbes , Plants in @ @ @ @ @ @ @ Cambridge University Press , 1992 ) , see figure 4.18 , page 100 , and section 4.9.1 , “ Thermal injury and its avoidance ” ; Hans Lambers , Plant Physiological Ecology , 2nd ed .
( New York : Springer , 2008 ) , 225–235 .

Photo credit: Patrick Selin, via Unsplash.
Editor’s note: We are pleased to present a series adapted from biologist Michael Denton’s book, Fire-Maker: How Humans Were Designed to Harness Fire and Transform Our Planet, from Discovery Institute Press. Find the whole series here. Dr. Denton’s forthcoming book, The Miracle of the Cell, will be published in September.
In addition to nature’s fitness for photosynthesis, the existence of large woody plants such as trees and the wood they provide for fire-making is only possible because of many other elements of fitness in nature, including the unique properties of an unfamiliar but crucial component of plant cell walls: lignin.
Lignin is an essential component of all plant cell walls and provides the necessary element of strength for the construction of tall woody trees. Because it is highly resistant to enzymatic catalysis, its breakdown in the soil is slow, allowing the formation of humus, which retains water and minerals in the soil.1 This in turn promoted the growth of large trees and allowed the build-up of vast volumes of undigested vegetation in the Carboniferous swamps, ultimately providing the coal for the steam engines of the early industrial age. Without lignin, there would be no woody plants, no wood, no coal, no charcoal, no fire, no pottery, and certainly no iron and probably no other metals or metallurgy.
Another “Goldilocks” Combination
Many other conditions must be met for large woody trees to flourish. First, their leaves must be able to lose heat in direct sunshine. This is achieved by a “Goldilocks” combination of fundamental physical phenomena, including evaporative cooling, convection, conduction, and radiation.2 Additionally, their trunks and branches must be made of a strong, durable material providing tensile strength (resisting stretching) and compressive strength (resisting volume reduction) to sustain bending and compressive pressures. The combination of cellulose and lignin in plant cell walls provides the necessary strength and is in all probability uniquely fit for this role.
In addition to having strong trunks and being able to keep cool in the sun, trees must also have a method of absorbing water and drawing it to their leaves, which in the case of large trees may be many meters above the ground. Water is the matrix of life on Earth and essential for cellular physiology and, in the case of plant cells, for photosynthesis. Water is the source of both the hydrogen atoms for the synthesis of organic compounds, including wood, and of the oxygen atoms, which are released into the atmosphere. Water is also utilized by plants for evaporative cooling, one of the factors that attenuates the temperature of leaves in hot sun.
Tomorrow, “The Amazing Circulation System of Trees.”
Notes
Matti Leisola, Ossi Pastinen, Douglas D. Axe, “Lignin—Designed Randomness,” BIO-Complexity 2012 (2012).


evolutionnewsandviews--2020-08-03--The Amazing Circulation System of Trees

The Amazing Circulation System of Trees

Editor ’ s note : We are pleased to present a series adapted from biologist Michael Denton ’ s book , Fire-Maker : How Humans Were Designed to Harness Fire and Transform Our Planet , from Discovery Institute Press .
Find the whole series here .
Dr. Denton ’ s forthcoming book , The Miracle of the Cell , will be published in September .
We come now in this series to a tale that Steven Vogel in his book The Life of a Leaf calls mirabile dictu ( wonderful to relate ) : the way water is raised to @ @ @ @ @ @ @ , unless water can be drawn several meters up the conduits in their tree trunks , large woody trees would be impossible .
Many trees are 30 meters tall and some are even 100 meters .
It turns out that this is only possible because of another ensemble of fitness in nature , which arises out of the so-called colligate properties of fluids , particularly water : primarily the remarkable and counterintuitive tensile strength of liquids working together with the fantastically great surface tension of a fluid confined in a narrow tube .
@ @ @ @ @ @ @ a generic property of all fluids ) can easily raise water up to 100 meters if the tube is small enough .
In tubes one hundredth of a micrometer ( 10 nanometers ) , the surface tension is so strong that it can support a column of water of 3 kilometers , or two miles high.2 But because of viscosity ( a measurement of internal friction ) , water ’ s resistance to flowing through such tiny conduits would be prohibitively high.3 In fact , the conduits in trees are between 0.03 and @ @ @ @ @ @ @ sufficiently wide to allow the sap to flow up through the tubes with minimal resistance .
But as Vogel comments : “ Thirty micrometers sends water only about 1.5 meters ( 5 feet ) upward , and 300 micrometers is ten times worse : 15 centimeters , or 6 inches.
” 4 So How Do Trees Do It ?
How do trees manage to exploit capillarity to hold a column of water 100 meters high ( which necessitates tiny tubes ) while at the same time overcoming the viscous drag that such tiny @ @ @ @ @ @ @ explain , plants solve the problem of the viscous or frictional cost of moving water through small tubes “ by connecting the small capillaries in leaves [ small enough to generate capillary forces powerful enough to hold a column 100 meters high ] to larger conduits that provide a much wider transport channel that runs from the veins in the leaf down through the stem and into the roots.
” 5 The key point is that the critical capillary forces are not generated in the major conduits .
As Holland and Zwienieki point @ @ @ @ @ @ @ not those of the large conduits that you would see if you cut down a tree and looked inside [ with diameters of 0.03-.3 mm ] … Rather , the appropriate dimensions are determined by the air-water interfaces in the cell walls of the leaves , where the matrix of cellulose microfibrils is highly wettable and the spacing between them results in effective pore diameters [ which function as tiny capillaries ] of something like 5 to 10 nm.6 This is the crucial point : The diameter of the pores is so small @ @ @ @ @ @ @ mentioned earlier ) is able to support a water column three kilometers high , much higher than the highest tree .
In other words , as the authors continue : “ Trees and other plants overcome [ the problem ] … by generating capillary forces in small-diameter pores [ at the interfaces in the leaves between the sap and the air ] but transporting water between soil and leaves through larger diameter conduits .
That strategy allows them to achieve greater heights than with a straight-walled microcapillary.
” 7 But while capillarity — @ @ @ @ @ @ @ at the interface — will suffice to hold up the 100-meter column , what pulls the sap upwards from the roots through the conduits to the stems and leaves at the top of the tree ?
How the Suck Is Caused The answer is that the evaporation or transpiration from the air-water interfaces in the leaf cell causes the suck by inducing a negative pressure in the fluid under the tiny menisci , which is transmitted to the whole system of conduits .
It is a basic law of hydraulics that pressure in @ @ @ @ @ @ @ is transmitted to all other parts .
As water molecules are lost from the leaves at the top of the tree , others must enter in the roots to take their place .
The continual loss of water molecules lowers what is termed the water potential in the regions below the interfaces .
This lowering of potential , transmitted to the whole hydraulic network , pulls the water up the conduits to the interfaces where it is lost by evaporation to the atmosphere .
Tomorrow , “ A Remarkable Mechanism for the Existence @ @ @ @ @ @ @ , The Life of a Leaf ( Chicago : Chicago University Press , 2010 ) , Chapter Six .
• N. Michele Holbrook , Maciej A. Zwieniecki , “ Transporting Water to the Tops of Trees , ” Physics Today 61 ( 2008 ) : 76–77 ; Vogel , Chapter Seven .

Photo: Coastal redwoods can grow up to 115.5 meters tall, by Goldblattster / CC BY-SA (https://creativecommons.org/licenses/by-sa/3.0).
Editor’s note: We are pleased to present a series adapted from biologist Michael Denton’s book, Fire-Maker: How Humans Were Designed to Harness Fire and Transform Our Planet, from Discovery Institute Press. Find the whole series here. Dr. Denton’s forthcoming book, The Miracle of the Cell, will be published in September.
We come now in this series to a tale that Steven Vogel in his book The Life of a Leaf calls mirabile dictu (wonderful to relate): the way water is raised to the top of a tall tree.1 Clearly, unless water can be drawn several meters up the conduits in their tree trunks, large woody trees would be impossible. Many trees are 30 meters tall and some are even 100 meters. It turns out that this is only possible because of another ensemble of fitness in nature, which arises out of the so-called colligate properties of fluids, particularly water: primarily the remarkable and counterintuitive tensile strength of liquids working together with the fantastically great surface tension of a fluid confined in a narrow tube.
Simple capillarity caused by surface tension (a generic property of all fluids) can easily raise water up to 100 meters if the tube is small enough. In tubes one hundredth of a micrometer (10 nanometers), the surface tension is so strong that it can support a column of water of 3 kilometers, or two miles high.2 But because of viscosity (a measurement of internal friction), water’s resistance to flowing through such tiny conduits would be prohibitively high.3 In fact, the conduits in trees are between 0.03 and 0.3 millimeters in diameter, which is sufficiently wide to allow the sap to flow up through the tubes with minimal resistance. But as Vogel comments: “Thirty micrometers sends water only about 1.5 meters (5 feet) upward, and 300 micrometers is ten times worse: 15 centimeters, or 6 inches.”4
So How Do Trees Do It?
How do trees manage to exploit capillarity to hold a column of water 100 meters high (which necessitates tiny tubes) while at the same time overcoming the viscous drag that such tiny tubes entail? As Holbrook and Zwienieki explain, plants solve the problem of the viscous or frictional cost of moving water through small tubes “by connecting the small capillaries in leaves [small enough to generate capillary forces powerful enough to hold a column 100 meters high] to larger conduits that provide a much wider transport channel that runs from the veins in the leaf down through the stem and into the roots.”5
The key point is that the critical capillary forces are not generated in the major conduits. As Holland and Zwienieki point out:
The relevant capillary dimensions are not those of the large conduits that you would see if you cut down a tree and looked inside [with diameters of 0.03-.3 mm]… Rather, the appropriate dimensions are determined by the air-water interfaces in the cell walls of the leaves, where the matrix of cellulose microfibrils is highly wettable and the spacing between them results in effective pore diameters [which function as tiny capillaries] of something like 5 to 10 nm.6
This is the crucial point: The diameter of the pores is so small that the surface tension generated (as mentioned earlier) is able to support a water column three kilometers high, much higher than the highest tree.
In other words, as the authors continue: “Trees and other plants overcome [the problem]… by generating capillary forces in small-diameter pores [at the interfaces in the leaves between the sap and the air] but transporting water between soil and leaves through larger diameter conduits. That strategy allows them to achieve greater heights than with a straight-walled microcapillary.”7
But while capillarity — given the tiny diameter of the tubes at the interface — will suffice to hold up the 100-meter column, what pulls the sap upwards from the roots through the conduits to the stems and leaves at the top of the tree?
How the Suck Is Caused
The answer is that the evaporation or transpiration from the air-water interfaces in the leaf cell causes the suck by inducing a negative pressure in the fluid under the tiny menisci, which is transmitted to the whole system of conduits. It is a basic law of hydraulics that pressure in one part of an enclosed hydraulic system is transmitted to all other parts. As water molecules are lost from the leaves at the top of the tree, others must enter in the roots to take their place. The continual loss of water molecules lowers what is termed the water potential in the regions below the interfaces. This lowering of potential, transmitted to the whole hydraulic network, pulls the water up the conduits to the interfaces where it is lost by evaporation to the atmosphere.
Tomorrow, “A Remarkable Mechanism for the Existence of Large Trees.”
Notes


evolutionnewsandviews--2020-08-04--To Avoid Debate, Darwinists at the AAAS Would Even Censor…Darwin

As you may remember from earlier coverage here , Herman Bouma is the attorney whose presentation on Darwin was canceled by the 2019 National Science Teaching Association ’ s National Conference .
The point of Bouma ’ s planned discussion was that Charles Darwin practiced open debate with his critics , an example from which teachers today could take a lesson .
This was too much , though , for the influential group to tolerate so they sent conference officials and security guards to escort him out .
Well , the story continues now as the American Association for the @ @ @ @ @ @ @ in giving Bouma the runaround .
This February , the AAAS held its annual meeting here in Seattle .
In addition to lectures and keynotes , the meeting is where different branches hold business meetings .
Bouma recently emailed us about what happened when he tried to submit a resolution to the Biological Sciences section for its consideration .
Bouma explained the situation this way : The resolution simply states that a teacher should feel free to teach how Darwin responded to his critics .
I was informed by the chair , Dr. @ @ @ @ @ @ @ of the AAAS would be handling the resolution because it dealt with the subject of evolution .
Last week I was informed by the current chair of the section , Dr. David Burgess , that the main office did not support the resolution .
When I asked why , he refused to give any reason .
It seems clear that the AAAS opposes the resolution because it does not want any discussion of scientific arguments against neo-Darwinian evolution , but is too embarrassed to state this publicly .
What Exactly Did the Resolution @ @ @ @ @ @ @ policy , or simply encouraging educators to treat Darwinian evolution like a science ?
Read the resolution for yourself : Resolution on Freedom to Teach Darwin ’ s Response to His Critics Whereas in his book The Origin of Species Darwin responded to eminent scientists of his day who had scientific arguments against his theory of natural selection , including Louis Agassiz , a world-renowned professor of geology and biology at Harvard University known as “ the father of the American scientific tradition ” ; Adam Sedgwick , a professor of geology and @ @ @ @ @ @ @ Britain ’ s most distinguished geologists ; and Karl Nageli , a Swiss professor of botany at the University of Munich who was famous for his work on plant cells ; Whereas Darwin took great care to reply thoughtfully to the scientific arguments against his theory and , by the time of the sixth edition of The Origin of Species in 1872 , approximately one-third of his book consisted of his response to his critics ; Whereas Darwin stated , “ I look with confidence to the future , —to young and rising @ @ @ @ @ @ @ view both sides of the question with impartiality ” ( The Origin of Species , p. 444 ) ; and Whereas the Statement on the Teaching of Evolution issued by the AAAS on February 16 , 2006 , might erroneously lead teachers and professors to think they should not teach Darwin ’ s response to his critics , RESOLVED : When teaching Darwin ’ s theory of natural selection , a teacher or professor should feel free to teach Darwin ’ s response to his critics , as set forth in his book @ @ @ @ @ @ @ ?
Disturbed ?
Actually , it ’ s a totally reasonable proposal — treat Darwin ’ s theory as Darwin himself treated it !
But it wasn ’ t received that way .
Bouma sent multiple courteous emails to the AAAS leadership , asking them to consider the resolution , but was stonewalled .
Here ’ s an example of one email Bouma sent on January 8 , 2020 : Happy New Year !
I hope you had an enjoyable time over the holidays .
My name is Herman Bouma and I have @ @ @ @ @ @ @ Biological Sciences Section over the last several years .
I have a resolution I would like to present to the Section for its approval at the business meeting next month in Seattle .
Would you be so kind as to tell me what procedure I should follow for doing this ?
Thank you very much for your assistance .
Chandler promised to “ review ” and “ respond ” to Bouma ’ s resolution .
Dr. Chandler later replied , declining even to consider it at the AAAS meeting .
Chandler gave Bouma @ @ @ @ @ @ @ emphasized instead how much the AAAS “ fight [ s ] the good fight ” to support teaching evolution : Bouma wrote back .
He asked , “ At some point will I be receiving a response from the AAAS main office ?
” He also wondered , “ Will the Biological Sciences Section and other sections be providing input to the AAAS main office about my resolution ?
” He pointed out that his resolution is fully consistent with Chandler ’ s stated position that the AAAS supports “ the teaching of @ @ @ @ @ @ @ the AAAS main office , a few weeks later , Bouma asked Chandler if they ’ d ever get back to him about the resolution .
Chandler replied , “ That is my expectation.
” This correspondence all took place before the AAAS annual meeting , which was February 13-16 .
An Evolution News correspondent reported on the Education business meeting at that same conference here .
It became clear that the AAAS main office was going to stonewall Bouma as well .
Nothing if Not Persistent On February 18 , Bouma contacted @ @ @ @ @ @ @ section of the AAAS , David Burgess , noting that he ’ d not heard back from the AAAS main office about the resolution : It ’ s good that Burgess gave Bouma something like a straight answer .
The disturbing news is that the answer indicated that the Biological Sciences section of the AAAS is so intolerant that they don ’ t support efforts to teach Darwin ’ s theory the way Darwin himself treated it — to acknowledge that criticisms exist and “ to teach Darwin ’ s response to his @ @ @ @ @ @ @ peculiar ” if mainstream science did not support Darwin ’ s approach to dealing with criticisms of his theory .
Instead , Darwin ’ s ideas are to be treated as sacred dogmas , beyond questioning .
But that was only the position of the AAAS Biological Sciences section .
Perhaps the AAAS central office would have a different perspective .
Months went by and Bouma received no reply from the AAAS central office .
So on July 6 Bouma sent an inquiry to Dr. Burgess , wondering why he ’ d heard @ @ @ @ @ @ @ following up with respect to my proposed resolution for AAAS .
As a reminder , the proposed resolution simply states that a teacher or professor should feel free to teach how Darwin responded to his critics .
After I submitted the proposed resolution to the Biological Sciences section , I was informed by Dr. Chandler that it would be handled by the AAAS main office , and in an email on February 21 you suggested I “ take it up with the main offices of AAAS.
” So far I have sent three @ @ @ @ @ @ @ 24 , April 24 , and May 18 ) to Dr. Parikh , the CEO of AAAS , but have received no response .
Do you have any information about the present status of my proposal ?
Dr. Burgess then explained what was really going on : This is most disconcerting .
Bouma ’ s modest proposal to teach evolution the way Darwin treated his own theory has “ no support ” from one of the world ’ s largest and most powerful scientific organizations , the AAAS .
Bouma then replied asking @ @ @ @ @ @ @ David ?
” but again no reply has been forthcoming .
Bouma explained to us what is really going on here : “ This is another instance of the scientific community ’ s zeal to prevent students from hearing any scientific arguments against neo-Darwinian evolution .
In furtherance of this objective , the AAAS , like the NSTA , is even willing to censor Darwin .
”

Photo: Statue of Charles Darwin, Shrewsbury Library, by Bs0u10e01 / CC BY-SA.
As you may remember from earlier coverage here, Herman Bouma is the attorney whose presentation on Darwin was canceled by the 2019 National Science Teaching Association’s National Conference. The point of Bouma’s planned discussion was that Charles Darwin practiced open debate with his critics, an example from which teachers today could take a lesson. This was too much, though, for the influential group to tolerate so they sent conference officials and security guards to escort him out.
Well, the story continues now as the American Association for the Advancement of Science has joined the NSTA in giving Bouma the runaround.
This February, the AAAS held its annual meeting here in Seattle. In addition to lectures and keynotes, the meeting is where different branches hold business meetings. Bouma recently emailed us about what happened when he tried to submit a resolution to the Biological Sciences section for its consideration.
Bouma explained the situation this way:
The resolution simply states that a teacher should feel free to teach how Darwin responded to his critics. I was informed by the chair, Dr. Vicki Chandler, that the main office of the AAAS would be handling the resolution because it dealt with the subject of evolution. Last week I was informed by the current chair of the section, Dr. David Burgess, that the main office did not support the resolution. When I asked why, he refused to give any reason. It seems clear that the AAAS opposes the resolution because it does not want any discussion of scientific arguments against neo-Darwinian evolution, but is too embarrassed to state this publicly.
What Exactly Did the Resolution Say?
Was Bouma proposing some distasteful policy, or simply encouraging educators to treat Darwinian evolution like a science? Read the resolution for yourself:
Resolution on Freedom to Teach Darwin’s Response to His Critics Whereas in his book The Origin of Species Darwin responded to eminent scientists of his day who had scientific arguments against his theory of natural selection, including Louis Agassiz, a world-renowned professor of geology and biology at Harvard University known as “the father of the American scientific tradition”; Adam Sedgwick, a professor of geology and paleontology at Cambridge University and one of Britain’s most distinguished geologists; and Karl Nageli, a Swiss professor of botany at the University of Munich who was famous for his work on plant cells; Whereas Darwin took great care to reply thoughtfully to the scientific arguments against his theory and, by the time of the sixth edition of The Origin of Species in 1872, approximately one-third of his book consisted of his response to his critics; Whereas Darwin stated, “I look with confidence to the future,—to young and rising naturalists, who will be able to view both sides of the question with impartiality” (The Origin of Species, p. 444); and Whereas the Statement on the Teaching of Evolution issued by the AAAS on February 16, 2006, might erroneously lead teachers and professors to think they should not teach Darwin’s response to his critics, RESOLVED: When teaching Darwin’s theory of natural selection, a teacher or professor should feel free to teach Darwin’s response to his critics, as set forth in his book The Origin of Species.
Are You Shocked?
Or dismayed? Disturbed? Actually, it’s a totally reasonable proposal — treat Darwin’s theory as Darwin himself treated it! But it wasn’t received that way. Bouma sent multiple courteous emails to the AAAS leadership, asking them to consider the resolution, but was stonewalled. Here’s an example of one email Bouma sent on January 8, 2020:
Dear Dr. Chandler, Happy New Year! I hope you had an enjoyable time over the holidays. My name is Herman Bouma and I have been attending the business meetings of the Biological Sciences Section over the last several years. I have a resolution I would like to present to the Section for its approval at the business meeting next month in Seattle. Would you be so kind as to tell me what procedure I should follow for doing this? Thank you very much for your assistance.
“The Good Fight”
Chandler promised to “review” and “respond” to Bouma’s resolution. Dr. Chandler later replied, declining even to consider it at the AAAS meeting. Chandler gave Bouma no official feedback on his resolution but emphasized instead how much the AAAS “fight[s] the good fight” to support teaching evolution:
We of course support the teaching of evolution. AAAS takes an active approach to informing the public about, and taking a stand for teaching evolution. Efforts to “fight the good fight” about teaching evolution are public on aaas.org, and have been ongoing for years. We believe working with the main office folks that handles the evolution effort and policies associated with teaching evolution is the best way forward, as teaching evolution is relevant to a large number of sections and AAAS membership. As such I have forwarded your request to AAAS main office.
Bouma wrote back. He asked, “At some point will I be receiving a response from the AAAS main office?” He also wondered, “Will the Biological Sciences Section and other sections be providing input to the AAAS main office about my resolution?” He pointed out that his resolution is fully consistent with Chandler’s stated position that the AAAS supports “the teaching of evolution”:
I wish to emphasize that the resolution is not in any way against the teaching of evolution. It takes the teaching of evolution as a given. The resolution simply seeks to make clear to teachers that they should feel free to teach Darwin’s response to critics of his theory of natural selection.
Having heard nothing from the AAAS main office, a few weeks later, Bouma asked Chandler if they’d ever get back to him about the resolution. Chandler replied, “That is my expectation.” This correspondence all took place before the AAAS annual meeting, which was February 13-16. An Evolution News correspondent reported on the Education business meeting at that same conference here. It became clear that the AAAS main office was going to stonewall Bouma as well.
Nothing if Not Persistent
On February 18, Bouma contacted the new chair of the Biological Sciences section of the AAAS, David Burgess, noting that he’d not heard back from the AAAS main office about the resolution:
As of this time I have not received any communication from the main office. If you hear anything about the status of the proposal and who is working on it, I would much appreciate your letting me know. I would also greatly appreciate your support of the proposal.
Burgess wrote back three days later:
Herman, thank you for your email. I know this has been moved up to the main offices of AAAS. There is no support among the officers of the Biological Sciences section to take this up at the section level. In viewing of your organization’s website, it is clear that you represent one whose views are in contrast to that of mainstream science on the issue of evolution and its teaching. I suggest you take it up with the main offices of AAAS.
It’s good that Burgess gave Bouma something like a straight answer. The disturbing news is that the answer indicated that the Biological Sciences section of the AAAS is so intolerant that they don’t support efforts to teach Darwin’s theory the way Darwin himself treated it — to acknowledge that criticisms exist and “to teach Darwin’s response to his critics.”
Bouma had a ready reply:
My organization is simply trying to promote an objective discussion of the scientific merits of the theory of natural selection. Even Darwin wanted that. It would be peculiar if mainstream science was at odds with the expressed wishes of Darwin.
It would indeed be “peculiar” if mainstream science did not support Darwin’s approach to dealing with criticisms of his theory. Instead, Darwin’s ideas are to be treated as sacred dogmas, beyond questioning.
Months Without a Reply
But that was only the position of the AAAS Biological Sciences section. Perhaps the AAAS central office would have a different perspective. Months went by and Bouma received no reply from the AAAS central office. So on July 6 Bouma sent an inquiry to Dr. Burgess, wondering why he’d heard nothing about his resolution:
I am following up with respect to my proposed resolution for AAAS. As a reminder, the proposed resolution simply states that a teacher or professor should feel free to teach how Darwin responded to his critics. After I submitted the proposed resolution to the Biological Sciences section, I was informed by Dr. Chandler that it would be handled by the AAAS main office, and in an email on February 21 you suggested I “take it up with the main offices of AAAS.” So far I have sent three emails about the resolution (on February 24, April 24, and May 18) to Dr. Parikh, the CEO of AAAS, but have received no response. Do you have any information about the present status of my proposal?
Dr. Burgess then explained what was really going on:
Herman, it is apparent that the lack of response is a direct message to you that there is no support.
This is most disconcerting. Bouma’s modest proposal to teach evolution the way Darwin treated his own theory has “no support” from one of the world’s largest and most powerful scientific organizations, the AAAS.
Bouma then replied asking “Why is there no support, David?” but again no reply has been forthcoming.
Bouma explained to us what is really going on here: “This is another instance of the scientific community’s zeal to prevent students from hearing any scientific arguments against neo-Darwinian evolution. In furtherance of this objective, the AAAS, like the NSTA, is even willing to censor Darwin.”


evolutionnewsandviews--2020-08-03--In Australia, Academic Freedom Case Will Have Far-Reaching Consequences

Until Covid came along , evolution and climate change were at the top of the heap as controversial issues at the intersection of science and culture .
Despite the newcomer , they remain as charged with potential for battle as ever .
That ’ s , of course , not only in the United States but internationally .
In Australia , as I ’ ve written here before , a prominent professor who critiqued climate change research has been in the spotlight for the past two years .
The case , however it turns out , will have profound consequences @ @ @ @ @ @ @ viewpoints on scientific topics , or not ?
Peter Ridd , head of the Marine Geophysical Laboratory at James Cook University , published a chapter in the book Climate Change : The Facts 2017 .
He doubted that the Great Barrier Reef was almost dead due to global warming , and argued as much .
Then , he talked about the chapter on TV and his university got wind of it .
He was hit with charges of academic misconduct .
After very tense interactions with the university and demands he was unwilling @ @ @ @ @ @ @ pursue the matter in court .
Ridd ended up winning $ 1.2 million ( Australian ) .
Judge Salvatore Vasta offered this endorsement of academic freedom : That is why intellectual freedom is so important .
It allows academics to express their opinions without fear of reprisals .
It allows a Charles Darwin to break free of the constraints of creationism .
It allows an Albert Einstein to break free of the constraints of Newtonian physics .
It allows the human race to question conventional wisdom in the never-ending search for knowledge and @ @ @ @ @ @ @ core , is what higher learning is about .
To suggest otherwise is to ignore why universities were created and why critically focused academics remain central to all that university teaching claims to offer .
Following that decision , the Federal Education Minister requested a model academic freedom and freedom of speech code , which ended up being drafted by a former member of the High Court .
But this July , the court ’ s decision was overturned by the Federal Court , 2-1 .
Ridd decided to appeal the case to @ @ @ @ @ @ @ highest judicial body .
I hope the High Court takes the case .
Gideon Rozner , director of policy at the Institute of Public Affairs , wrote for The Australian in July : The Ridd case is much more than a mere workplace relations dispute between an academic and his employer .
It is even bigger than a dispute about climate change .
It is about the free speech crisis at our universities , and goes to the heart of the ‘ cancel culture ’ epidemic engulfing the Western world .
A decision @ @ @ @ @ @ @ far-reaching implications for Australian universities , and in particular the scientific establishment .
It would echo in other countries , too , including ours .

Photo: Great Barrier Reef, by FarbenfroheWunderwelt via Flickr (cropped).
Until Covid came along, evolution and climate change were at the top of the heap as controversial issues at the intersection of science and culture. Despite the newcomer, they remain as charged with potential for battle as ever.
That’s, of course, not only in the United States but internationally. In Australia, as I’ve written here before, a prominent professor who critiqued climate change research has been in the spotlight for the past two years. The case, however it turns out, will have profound consequences.
Will Academic Freedom Win Out?
So, can academics voice controversial viewpoints on scientific topics, or not?
Peter Ridd, head of the Marine Geophysical Laboratory at James Cook University, published a chapter in the book Climate Change: The Facts 2017. He doubted that the Great Barrier Reef was almost dead due to global warming, and argued as much. Then, he talked about the chapter on TV and his university got wind of it. He was hit with charges of academic misconduct. After very tense interactions with the university and demands he was unwilling to meet, he raised funds to pursue the matter in court. Ridd ended up winning $1.2 million (Australian). Judge Salvatore Vasta offered this endorsement of academic freedom:
That is why intellectual freedom is so important. It allows academics to express their opinions without fear of reprisals. It allows a Charles Darwin to break free of the constraints of creationism. It allows an Albert Einstein to break free of the constraints of Newtonian physics. It allows the human race to question conventional wisdom in the never-ending search for knowledge and truth. And that, at its core, is what higher learning is about. To suggest otherwise is to ignore why universities were created and why critically focused academics remain central to all that university teaching claims to offer.
Following that decision, the Federal Education Minister requested a model academic freedom and freedom of speech code, which ended up being drafted by a former member of the High Court.
The Drama Keeps Unfolding
But this July, the court’s decision was overturned by the Federal Court, 2-1. Ridd decided to appeal the case to the High Court — Australia’s highest judicial body.
I hope the High Court takes the case. Gideon Rozner, director of policy at the Institute of Public Affairs, wrote for The Australian in July:
The Ridd case is much more than a mere workplace relations dispute between an academic and his employer. It is even bigger than a dispute about climate change. It is about the free speech crisis at our universities, and goes to the heart of the ‘cancel culture’ epidemic engulfing the Western world.
A decision in favor of academic freedom would have far-reaching implications for Australian universities, and in particular the scientific establishment. It would echo in other countries, too, including ours.


evolutionnewsandviews--2020-08-04--A Remarkable Mechanism for the Existence of Large Trees

Editor ’ s note : We are pleased to present a series adapted from biologist Michael Denton ’ s book , Fire-Maker : How Humans Were Designed to Harness Fire and Transform Our Planet , from Discovery Institute Press .
Find the whole series here .
Dr. Denton ’ s forthcoming book , The Miracle of the Cell , will be published in September .
In considering the circulation system of trees , as I did yesterday , an obvious question arises : Why does the column of water not break into pieces as it is tugged from above ?
@ @ @ @ @ @ @ — the tendency of the molecules in liquids to “ stick together ” — a tendency more pronounced in water than most other common fluids because of its colligate properties , which arise from the hydrogen bonding between neighboring water molecules .
And because of this tendency of water columns , although the notion is very counterintuitive , water has tensile strength.1 Tensile strength is the ability of a substance to resist being stretched .
You can pull a steel wire up 100 meters without it breaking because of the tensile strength of @ @ @ @ @ @ @ with a water column .
Remarkably , experiments show a rope of liquid water , a square centimeter in cross section in an enclosed tube , has sufficient tensile strength that one could hang from it a solid mass of nearly 300 kilograms .
Steel is stronger , but only ten times stronger !
2 It is this very counterintuitive tensile strength of a fluid — especially water , because its colligative properties are so pronounced — that allows the negative pressure caused by the evaporation in the leaves to pull sap from @ @ @ @ @ @ @ leaves without any break occurring in the column .
This remarkable mechanism , so vital to the existence of large trees , depends critically on two basic physical properties of water as a fluid : its tensile strength , which means the “ pull of evaporation ” will not break the water column , and the enormous surface tension generated by water in very narrow tubes or passages .
The mechanism represents a unique and stunningly brilliant solution to the problem of raising water to the top of large trees .
Significantly , @ @ @ @ @ @ @ in his The Life of a Leaf waxes lyrical in contemplating the way it ’ s done : And as Holbrook and Zwienieki comment in an article in Physics Today : Trees can be rightly called the masters of microfluidics .
In the stem of a large tree , the number of interconnected water transport conduits can exceed hundreds of millions , and their total length can be greater than several hundred kilometers .
Furthermore on a sunny day , a tree can transport hundreds of gallons of water from the soil to @ @ @ @ @ @ @ effortlessly , without making a sound and without using any moving parts… The physics that underlies water transport through plants is not exotic ; rather , the application of that physics in microfluidic wood matrix results in transport regimes operating far outside our day-to-day experience.4 • Melvin T. Tyree , “ The Tension Cohesion theory of sap ascent : current controversies , ” Journal of Experimental Botany 48 , no .
315 ( 1997 ) : 1753-1765 .

Photo: General Sherman tree, by Jim Bahn / CC BY (https://creativecommons.org/licenses/by/2.0).
Editor’s note: We are pleased to present a series adapted from biologist Michael Denton’s book, Fire-Maker: How Humans Were Designed to Harness Fire and Transform Our Planet, from Discovery Institute Press. Find the whole series here. Dr. Denton’s forthcoming book, The Miracle of the Cell, will be published in September.
In considering the circulation system of trees, as I did yesterday, an obvious question arises: Why does the column of water not break into pieces as it is tugged from above? The answer is the cohesiveness of liquids — the tendency of the molecules in liquids to “stick together” — a tendency more pronounced in water than most other common fluids because of its colligate properties, which arise from the hydrogen bonding between neighboring water molecules. And because of this tendency of water columns, although the notion is very counterintuitive, water has tensile strength.1
Tensile strength is the ability of a substance to resist being stretched. You can pull a steel wire up 100 meters without it breaking because of the tensile strength of steel, and it is the same with a water column. Remarkably, experiments show a rope of liquid water, a square centimeter in cross section in an enclosed tube, has sufficient tensile strength that one could hang from it a solid mass of nearly 300 kilograms. Steel is stronger, but only ten times stronger!2 It is this very counterintuitive tensile strength of a fluid — especially water, because its colligative properties are so pronounced — that allows the negative pressure caused by the evaporation in the leaves to pull sap from the roots up 100 meters to the leaves without any break occurring in the column.
The Physical Properties of Water
This remarkable mechanism, so vital to the existence of large trees, depends critically on two basic physical properties of water as a fluid: its tensile strength, which means the “pull of evaporation” will not break the water column, and the enormous surface tension generated by water in very narrow tubes or passages. The mechanism represents a unique and stunningly brilliant solution to the problem of raising water to the top of large trees. Significantly, no conceivable alternative will work.
Vogel in his The Life of a Leaf waxes lyrical in contemplating the way it’s done:
The pumping system has no moving parts, costs the plant no metabolic energy, moves more water than all the circulatory systems of animals combined, does so against far higher resistance, and depends on a mechanism with no close analogy in human technology.3
And as Holbrook and Zwienieki comment in an article in Physics Today:
Trees can be rightly called the masters of microfluidics. In the stem of a large tree, the number of interconnected water transport conduits can exceed hundreds of millions, and their total length can be greater than several hundred kilometers. Furthermore on a sunny day, a tree can transport hundreds of gallons of water from the soil to its leaves, and apparently do it effortlessly, without making a sound and without using any moving parts… The physics that underlies water transport through plants is not exotic; rather, the application of that physics in microfluidic wood matrix results in transport regimes operating far outside our day-to-day experience.4
Tomorrow, “Nature’s Magic and Its Breathtaking Parsimony.”
Notes


evolutionnewsandviews--2020-08-05--Fine-Tuning in a Nutshell: No Problem

Fine-Tuning in a Nutshell: No Problem

On a new episode of ID the Future , host Andrew McDiarmid interviews Dr. Robert Alston , an electrical engineer @ @ @ @ @ co-author of the new book Evolution and Intelligent Design in a Nutshell .
The two @ @ @ @ @ Nutshell book and the origin and fine-tuning of the universe .
Though cosmic fine-tuning is @ @ @ @ @ the fine-tuning problem , ” Alston says it ’ s really no problem at all @ @ @ @ @ re trying to shoehorn it into the box of philosophical materialism .
Download the podcast @ @ @ @ @ .

Photo: HBC 672 star, by NASA, ESA, and STScI.
On a new episode of ID the Future, host Andrew McDiarmid interviews Dr. Robert Alston, an electrical engineer working at Picatinny Arsenal and co-author of the new book Evolution and Intelligent Design in a Nutshell. The two discuss the origin of the Nutshell book and the origin and fine-tuning of the universe. Though cosmic fine-tuning is often referred to as “the fine-tuning problem,” Alston says it’s really no problem at all — not unless you’re trying to shoehorn it into the box of philosophical materialism. Download the podcast or listen to it here.


evolutionnewsandviews--2020-08-05--Next Phase of ENCODE Finds MORE Functional Information in Genome “Junk”

The first publications from the ENCODE project ( Encyclopedia of DNA Elements ) made a big splash at Evolution News in 2013 , and around the world , because it undermined the “ junk DNA ” myth and simultaneously fulfilled an ID prediction : that non-coding parts of the genome would prove functional .
Junk-DNA proponents like Dan Graur were upset at the time , admitting as Jonathan Wells reported , “ If ENCODE is right , evolution is wrong.
” Well , ModENCODE ( ENCODE for model organisms ) found “ unprecedented complexity ” in the fruit fly genome @ @ @ @ @ @ @ ” followed up with more discoveries of function .
Now , ENCODE 3 has just finished submitting its reports , with record numbers of DNA annotations listed , and ENCODE 4 is gearing up .
Nothing like a little overkill to drive the point home : “ … then evolution is wrong.
” Look at how much constructive science is being done with the assumption that DNA elements are there for a purpose .
Before introducing the latest results , Nature provides an overview , “ Perspectives on ENCODE , ” that recounts @ @ @ @ @ @ @ : The ENCODE Project was launched in 2003 , as the first nearly complete human genome sequence was reported .
At that time , our understanding of the human genome was limited .
For example , although 5 % of the genome was known to be under purifying selection in placental mammals , our knowledge of specific elements , particularly with regards to non-protein coding genes and regulatory regions , was restricted to a few well-studied loci .
ENCODE commenced as an ambitious effort to comprehensively annotate the elements in the human genome @ @ @ @ @ @ @ , and transcript isoforms , and was later expanded to annotate the genomes of several model organisms .
Mapping assays identified biochemical activities and thus candidate regulatory elements .
[ Emphasis added . ]
Annotations are like labels or comments on things .
For instance , if you have a stereo system with a lot of cables , you might affix tags on them to indicate where the TV plugs in , or where each speaker wire goes .
In computer programming , wise programmers add comments in English to explain what a @ @ @ @ @ @ @ not affect the function of the code , but help the next programmer follow the logic .
DNA is like a program , only it did not come with English comments !
That is why ENCODE is important ; the project is building a searchable database for researchers to find out what a string like ACCCTGTAAAGTG is doing .
Is it a gene ?
Is it a control region ?
Medical researchers will want to see if a SNP ( single nucleotide polymorphism ) in that string correlates with a disease .
The @ @ @ @ @ @ @ world on a treasure hunt for functions in the “ junk ” pile assumed to exist from evolutionary history .
The first results in 2013 indicated that over 80 percent of the genome was being transcribed .
That was a strong clue that most non-coding regions were functional , even if the functions were unknown , because a cell would be unlikely to spend the energy transcribing nonsense .
Indeed , many of those transcriptions turned out to be important regulatory regions .
The project began slowly but is accelerating .
The findings @ @ @ @ @ @ @ technologies .
The latest Phase III reports were published July 29 in Nature .
Some of the labs involved are telling what they found .
It begins with a striking moment where Ewan Birney , senior ENCODE researcher at CSHL , opens a huge tome containing a complete printout of the human genome .
He calls it “ a big achievement in 2000 , but it ’ s just a set of boring letters ” that ENCODE is bringing to life .
“ These letters actually do something , ” he says , @ @ @ @ @ @ @ is to find out what they mean — to learn their functions .
Magdalena Skipper , the next speaker , says that the ENCODE Consortium “ considers functional elements in very broad terms ” — beyond genes to the regulatory elements , switches and even to parts where “ we have no idea what they are doing , ” Birney adds .
This fits ID proponent Paul Nelson ’ s motto , “ If something works , it ’ s not happening by accident.
” So far ENCODE has produced a “ staggering @ @ @ @ @ @ @ in detailed form : Within the hundreds of cell types studied , ENCODE is helping scientists understand “ why your liver cell is different from your kidney cell , ” Birney says ; the secrets will be found in the switches that turn genes on and off .
“ It ’ s really a first view of that complexity that generates a human being.
” Skipper says it was “ striking ” to find that they were able to assign a “ biochemical function ” to 80 percent of the genome : striking @ @ @ @ @ @ @ time ago , we still considered that a vast proportion of the human genome was simply junk.
” Birney comments , “ It ’ s very hard to get over the density of information ” in the genome .
They found places that are “ much more complex ” than expected , and loci thought to be completely silent are actually “ teeming with life , teeming with things going on ; we still really don ’ t understand that.
” Another surprise is that portions corresponding with disease are being found in @ @ @ @ @ @ @ ’ s news release is titled , “ Bringing RNA into genomics.
” It describes the new technologies MIT used to identify candidate RNA transcripts and then determine their functions .
And “ function ” is the key word in their work : The National Institutes of Health ( NIH ) describes the search for genetic “ switches ” that turn genes on and off in different cell types and in various stages of development .
This is being determined for the mouse genome as well as the human genome .
“ A @ @ @ @ @ @ @ genes and functional regions are active in different cell types , ” said Elise Feingold , Ph.D. , scientific advisor for strategic implementation in the Division of Genome Sciences at NHGRI and a lead on ENCODE for the institute .
“ This means that we need to test a large and diverse number of biological samples to work towards a catalog of candidate functional elements in the genome.
” Significant progress has been made in characterizing protein-coding genes , which comprise less than 2 % of the human genome .
Researchers know much @ @ @ @ @ @ @ the genome , including how much and which parts of it perform other functions .
ENCODE is helping to fill in this significant knowledge gap .
The human body is composed of trillions of cells , with thousands of types of cells .
While all these cells share a common set of DNA instructions , the diverse cell types ( e.g.
, heart , lung and brain ) carry out distinct functions by using the information encoded in DNA differently .
The DNA regions that act as switches to turn genes on or @ @ @ @ @ @ @ of gene activity , help drive the formation of distinct cell types in the body and govern their functioning in health and disease .
Nature ’ s own “ News and Views ” story , “ Expanded ENCODE delivers invaluable genomic encyclopedia , ” boasts that Phase III has generated “ the most comprehensive catalogue yet ” of the functional elements that regulate our genes .
There are eight technical papers in the special issue of Nature , all open access .
Start with “ Expanded encyclopaedias of DNA elements in the human @ @ @ @ @ @ @ , scan through the other papers , and marvel at the exciting discoveries from Phase III .
Or you can read “ ENCODE explained ” for an overview with illustrations .
It ’ s all part of the ENCODE Collection going back to 2012 .
What is next for ENCODE ?
The “ Perspectives on ENCODE ” article cited earlier explains why much more research is still needed to understand the vast volume of functional information in our DNA : Further research may even find new functions for repetitive sequences , or for @ @ @ @ @ @ @ switched on under unique circumstances , or in particular cell types , or during certain stages of development .
In short : the search is on for function in the junk !

Image credit: Geralt, via Pixabay.
The first publications from the ENCODE project (Encyclopedia of DNA Elements) made a big splash at Evolution News in 2013, and around the world, because it undermined the “junk DNA” myth and simultaneously fulfilled an ID prediction: that non-coding parts of the genome would prove functional. Junk-DNA proponents like Dan Graur were upset at the time, admitting as Jonathan Wells reported, “If ENCODE is right, evolution is wrong.”
Well, ModENCODE (ENCODE for model organisms) found “unprecedented complexity” in the fruit fly genome in 2014, then “ENCODE 2” followed up with more discoveries of function. Now, ENCODE 3 has just finished submitting its reports, with record numbers of DNA annotations listed, and ENCODE 4 is gearing up. Nothing like a little overkill to drive the point home: “… then evolution is wrong.” Look at how much constructive science is being done with the assumption that DNA elements are there for a purpose.
History and Purposes
Before introducing the latest results, Nature provides an overview, “Perspectives on ENCODE,” that recounts the history and purposes of the project:
The ENCODE Project was launched in 2003, as the first nearly complete human genome sequence was reported. At that time, our understanding of the human genome was limited. For example, although 5% of the genome was known to be under purifying selection in placental mammals, our knowledge of specific elements, particularly with regards to non-protein coding genes and regulatory regions, was restricted to a few well-studied loci. ENCODE commenced as an ambitious effort to comprehensively annotate the elements in the human genome, such as genes, control elements, and transcript isoforms, and was later expanded to annotate the genomes of several model organisms. Mapping assays identified biochemical activities and thus candidate regulatory elements. [Emphasis added.]
Annotations are like labels or comments on things. For instance, if you have a stereo system with a lot of cables, you might affix tags on them to indicate where the TV plugs in, or where each speaker wire goes. In computer programming, wise programmers add comments in English to explain what a section of code does. Comments do not affect the function of the code, but help the next programmer follow the logic.
DNA is like a program, only it did not come with English comments! That is why ENCODE is important; the project is building a searchable database for researchers to find out what a string like ACCCTGTAAAGTG is doing. Is it a gene? Is it a control region? Medical researchers will want to see if a SNP (single nucleotide polymorphism) in that string correlates with a disease.
A Treasure Hunt
The project is sending scientists all over the world on a treasure hunt for functions in the “junk” pile assumed to exist from evolutionary history. The first results in 2013 indicated that over 80 percent of the genome was being transcribed. That was a strong clue that most non-coding regions were functional, even if the functions were unknown, because a cell would be unlikely to spend the energy transcribing nonsense. Indeed, many of those transcriptions turned out to be important regulatory regions.
The project began slowly but is accelerating.
Phase I (2003–2007) interrogated a specified 1% of the human genome in order to evaluate emerging technologies…. Phase II (2007–2012) introduced sequencing-based technologies (for example, chromatin immunoprecipitation with sequencing (ChIP–seq) and RNA sequencing (RNA-seq)) that interrogated the whole human genome and transcriptome. General assays such as transcript, open-chromatin and histone modification mapping were used on a wide variety of cell lines, while more specific assays, such as mapping transcription factor binding regions, were performed extensively on a smaller number of cell lines to provide detailed annotations on, and to investigate the relationships of, many regulatory proteins across the genome.
ENCODE Phase III
The findings of ENCODE are accelerating along with sequencing technologies. The latest Phase III reports were published July 29 in Nature. Some of the labs involved are telling what they found.
Cold Spring Harbor Laboratory includes a must-watch video:
It begins with a striking moment where Ewan Birney, senior ENCODE researcher at CSHL, opens a huge tome containing a complete printout of the human genome. He calls it “a big achievement in 2000, but it’s just a set of boring letters” that ENCODE is bringing to life. “These letters actually do something,” he says, “they mean something.” The goal is to find out what they mean — to learn their functions. Magdalena Skipper, the next speaker, says that the ENCODE Consortium “considers functional elements in very broad terms” — beyond genes to the regulatory elements, switches and even to parts where “we have no idea what they are doing,” Birney adds. This fits ID proponent Paul Nelson’s motto, “If something works, it’s not happening by accident.”
Not an Accident
So far ENCODE has produced a “staggering” hundreds of terabytes of raw data in detailed form:
In Phase 3, researchers took advantage of the latest genetic technologies to glean data from biological specimens and deeply investigate the regulatory regions outside of genes, where most of the genome’s person-to-person variation lies. Their data identifies some 900,000 candidate regulatory elements from the human genome and more than 300,000 from the mouse, which can be explored through ENCODE’s new online browser.
Within the hundreds of cell types studied, ENCODE is helping scientists understand “why your liver cell is different from your kidney cell,” Birney says; the secrets will be found in the switches that turn genes on and off. “It’s really a first view of that complexity that generates a human being.”
Skipper says it was “striking” to find that they were able to assign a “biochemical function” to 80 percent of the genome: striking, because “not such a long time ago, we still considered that a vast proportion of the human genome was simply junk.” Birney comments, “It’s very hard to get over the density of information” in the genome. They found places that are “much more complex” than expected, and loci thought to be completely silent are actually “teeming with life, teeming with things going on; we still really don’t understand that.” Another surprise is that portions corresponding with disease are being found in non-coding parts of the genome.
“This encyclopedia is a living resource. It has a beginning but really no end. It will continue to be improved, and grown, as time goes on.”
MIT’s news release is titled, “Bringing RNA into genomics.” It describes the new technologies MIT used to identify candidate RNA transcripts and then determine their functions. And “function” is the key word in their work:
These RNA sequences do not get translated into proteins, but act in a variety of ways to control how much protein is made from protein-coding genes. The research team, which includes scientists from MIT and several other institutions, made use of RNA-binding proteins to help them locate and assign possible functions to tens of thousands of sequences of the genome.
The National Institutes of Health (NIH) describes the search for genetic “switches” that turn genes on and off in different cell types and in various stages of development. This is being determined for the mouse genome as well as the human genome.
“A key challenge in ENCODE is that different genes and functional regions are active in different cell types,”said Elise Feingold, Ph.D., scientific advisor for strategic implementation in the Division of Genome Sciences at NHGRI and a lead on ENCODE for the institute. “This means that we need to test a large and diverse number of biological samples to work towards a catalog of candidate functional elements in the genome.” Significant progress has been made in characterizing protein-coding genes, which comprise less than 2% of the human genome. Researchers know much less about the remaining 98% of the genome, including how much and which parts of it perform other functions. ENCODE is helping to fill in this significant knowledge gap. The human body is composed of trillions of cells, with thousands of types of cells. While all these cells share a common set of DNA instructions, the diverse cell types (e.g., heart, lung and brain) carry out distinct functions by using the information encoded in DNA differently. The DNA regions that act as switches to turn genes on or off, or tune the exact levels of gene activity, help drive the formation of distinct cell types in the body and govern their functioning in health and disease.
Nature’s own “News and Views” story, “Expanded ENCODE delivers invaluable genomic encyclopedia,” boasts that Phase III has generated “the most comprehensive catalogue yet” of the functional elements that regulate our genes.
In the current third phase of the project, the consortium moved from cell lines to cells taken directly from human and mouse tissues, providing a more biologically relevant encyclopedia. They also introduced assays to investigate the broader aspects of functional elements — for example, to characterize the elements embedded in RNAs or to analyse chromatin looping, which brings separate CREs into close proximity to enable gene regulation.
There are eight technical papers in the special issue of Nature, all open access. Start with “Expanded encyclopaedias of DNA elements in the human and mouse genomes” for the details, scan through the other papers, and marvel at the exciting discoveries from Phase III. Or you can read “ENCODE explained” for an overview with illustrations. It’s all part of the ENCODE Collection going back to 2012.
ENCODE Phase IV
What is next for ENCODE? The “Perspectives on ENCODE” article cited earlier explains why much more research is still needed to understand the vast volume of functional information in our DNA:
It is now apparent that elements that govern transcription, chromatin organization, splicing, and other key aspects of genome control and function are densely encoded in the human genome; however, despite the discovery of many new elements, the annotation of elements that are highly selective for particular cell types or states is lagging behind…. Thus, as part of ENCODE 4, considerable effort is being devoted to expanding the cell types and tissuesanalysed … as well as mapping the binding regions for many more transcription factors and RNA-binding proteins.
Further research may even find new functions for repetitive sequences, or for “silent” sequences that only get switched on under unique circumstances, or in particular cell types, or during certain stages of development. In short: the search is on for function in the junk!