Showing posts with label evolution. Show all posts
Showing posts with label evolution. Show all posts

Monday, January 6, 2014

Scientists discover double meaning in genetic code




A team of researchers have made the discovery that the genetic code used by DNA to store information actually contains a double meaning, with the second set of coded information having major implications for how scientists read and interpret the instructions within it.  According to the authors of this study, this fascinating find could help them to better understand both disease and health.
DNA, or deoxyribonucleic acid, is present in the cells of all humans, as well as almost every other living organism.  It contains the information for building and maintaining an organism in the form of a chemical code.  Four basic chemical bases – adenine, guanine, cytosine and thymine – are strung together in various sequences; and, the sequencing of these bases is what determines what information is coded within them, much like letters of the alphabet can be put together to create many different words and sentences.
The overall structure of DNA is what is known as a double helix.  The bases of DNA pair up with each other, with adenine pairing with thymine and cytosine pairing with guanine.  Each base pair then attaches to a sugar molecule as well as a phosphate molecule and this complete package is called a nucleotide.  Sequences of nucleotides arrange themselves in two long strands, somewhat like a ladder joined by base pair rungs, and the DNA molecule takes on a spiraling, helical shape.
DNA is able to make copies of itself by “unzipping” its two strands, allowing each strand to serve as a template for new DNA to be formed.  This process is how new DNA is created whenever cells divide and multiply.
Since 1962, when James Watson and Francis Crick received the Nobel Prize in Physiology or Medicine for discovering DNA, it has been thought that this was all there was to know about how DNA worked.  However, a research team lead by Dr. John Stamatoyannopoulos of the University of Washington, has made a startling new discovery.  DNA is actually used to write in two different languages, giving a double meaning to the genetic code.
One of these languages, the one that was discovered by Watson and Crick, is used to code information about proteins.   The second one, which was just discovered, codes information which tells the cell how to control genes.  Genes are sections of DNA molecules which, when taken by themselves, code for specific proteins.  Humans have thousands of genes, all of them controlling different traits, such as eye color or height.
It took scientists a long time to locate this second language because one language is superimposed over the other one.
Speaking about this new find,  Stamatoyannopoulos note that “[t]hese new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”
According to the UW team, the genetic code uses a 64-letter “alphabet” called codons.  What they discovered in their work was that some of these codons actually had two different meanings, one which affected protein sequencing and one which affected gene control.  These codons, which they call duons, seem to have evolved these double meanings in order to help stabilize certain beneficial features of proteins and their manufacture.
Their findings have important implications for how scientists interpret a person’s genome, they say, opening up new ways to diagnose and treat disease.  Because the genetic code is communicating two different types of information at the same time, diseases which appear to be the result of alterations in protein sequencing might actually be caused by changes in gene control programs, or even both factors.
The findings from the study were published in the December 13, 2013 issue of Science.
By Nancy Schimelpfening
Sources:


If Chemistry Can Be Wrong, How Much More Evolutionary Theory?


salt-320-use-this-one.jpgAlong with astronomy, chemistry is one of the ancient sciences. Progressing from alchemy to rational chemistry, physical chemistry and quantum mechanics of our day, its status as "hard science" seems secure. Its theories have been refined for centuries. Moreover, its experiments (unlike macroevolution) are observable and repeatable. How, then, could researchers at Stony Brook University (academic home, by the way, of ENV contributor Dr. Michael Egnor, Vice-Chairman, Department of Neurological Surgery) say that a discovery has challenged the foundation of chemistry?
Experiments at the lab are causing a stir -- if not a revolution -- in this hallowed science:
All good research breaks new ground, but rarely does the research unearth truths that challenge the foundation of a science. That's what Artem R. Oganov has done, and the professor of theoretical crystallography in the Department of Geosciences will have his work published in the Dec. 20 issue of the journal Science....
"I think this work is the beginning of a revolution in chemistry," Oganov says. "We found, at low pressures achievable in the lab, perfectly stable compounds that contradict the classical rules of chemistry. If you apply the rather modest pressure of 200,000 atmospheres -- for comparison purposes, the pressure at the center of the earth is 3.6 million atmospheres -- everything we know from chemistry textbooks falls apart." [Emphasis added.]
We all know NaCl, table salt. Ever heard of NaCl3? How about Na3Cl? Those are some of the novel compounds Oganov's lab has produced. They were stunned to find them to be stable, real compounds.
"We found crazy compounds that violate textbook rules -- NaCl3, NaCl7, Na3Cl2, Na2Cl, and Na3Cl," says Weiwei Zhang, the lead author and visiting scholar at the Oganov lab and Stony Brook's Center for Materials by Design, directed by Oganov. "These compounds are thermodynamically stable and, once made, remain indefinitely; nothing will make them fall apart. Classical chemistry forbids their very existence. Classical chemistry also says atoms try to fulfill the octet rule -- elements gain or lose electrons to attain an electron configuration of the nearest noble gas, with complete outer electron shells that make them very stable. Well, here that rule is not satisfied."
The discoveries open up new possibilities for the supposedly mature science. "When you change the theoretical underpinnings of chemistry, that's a big deal," one team member says. "But what it also means is that we can make new materials with exotic properties."
How could this happen in a "hard" science? For one, Oganov, described as curious and obstinate, was driven by the word "impossible" to explore its limits.
To Oganov, impossible didn't mean something absolute. "The rules of chemistry are not like mathematical theorems, which cannot be broken," he says. "The rules of chemistry can be broken, because impossible only means 'softly' impossible! You just need to find conditions where these rules no longer hold."
Oganov compares the team's findings to discovering a new continent. Understanding and predicting high-pressure compounds can lead to new theories. And he envisions applications for astrophysics and planetary sciences, where high pressures abound.
If an unexpected foundation-shaking paradigm shift can occur in a "hard" science like chemistry, where findings can be checked by observation and experiment, how confident can evolutionists be that their theories about the unobservable past?
In recent years, major problems have surfaced in evolutionary theory: the overthrow of "junk DNA," the discovery of codes within codes, the intransigence of the Cambrian enigma to name a few. Yet its advocates continue to bully anyone who doesn't toe the line. Darwinism acts like a religion, not science. If Darwinists were proper scientists, they would embrace the new discoveries that break their rules. They would gladly follow the mounting evidence that points in a new direction for the biology of the 21st century -- intelligent design.
Image credit: Electron localization function in the cubic NaCl3 structure/Stony Brook University.
- See more at: http://www.evolutionnews.org/2014/01/if_chemistry_ca080711.html#sthash.fPEpn8OB.dpuf

Sunday, October 6, 2013





Evolution, Speeded by Computation

‘Probably Approximately Correct’ Explores Nature’s Algorithms

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Our daily lives are growing ever more dependent on algorithms, those omnipresent computational procedures that run programs on our laptops, our smartphones, our GPS devices and much else. Algorithms influence our decisions, too: when we choose a movie on Netflix or a book on Amazon, we are presented with recommendations churned out by sophisticated algorithms that take into account our past choices and those of other users determined (by still other algorithms) to be similar to us.

The importance of these algorithms in the modern world is common knowledge, of course. But in his insightful new book “Probably Approximately Correct,” the Harvard computer scientist Leslie Valiant goes much further: computation, he says, is and has always been “the dominating force on earth within all its life forms.” Nature speaks in algorithms.
Dr. Valiant believes that phenomena like evolution, adaptation and learning are best understood in terms of “ecorithms,” a term he has coined for algorithms that interact with and benefit from their environment. Ecorithms are at play when children learn how to distinguish cats from dogs, when we navigate our way in a new city — but more than that, Dr. Valiant writes, when organisms evolve and when brain circuits are created and maintained.
Here is one way he illustrates this complex idea. Suppose we want to distinguish between two types of flowers by measuring their petals. For each petal we have two numbers, x for length and y for width. The task is to find a way to tell which type of flower a petal with given measurements x and y belongs to.
To achieve this, the algorithm is fed a set of examples meant to “train” it to come up with a good criterion for distinguishing the two flowers. The algorithm does not know the criterion in advance; it must “learn” it using the data that are fed to it.
So it starts with a hypothesis and tests it on the first example. (Say flower No. 1’s petals can be described by the formula 2x—3y>2, while for Flower No. 2 it’s 2x—3y<2 .="" a="" algorithm="" along.="" an="" and="" applied="" as="" by="" certain="" example.="" example="" goes="" hypothesis="" if="" is="" it="" learning="" literally="" misclassifies="" new="" next="" p="" precise="" proceed="" rule="" that="" the="" to="" updated="" we="" works="">
A striking mathematical theorem is that if a rule separating the two flowers exists (within the class of criteria we are considering, such as linear inequalities), then our algorithm will find it after a finite number of steps, no matter what the starting hypothesis was.
And Dr. Valiant argues that similar mechanisms are at work in nature. An organism can adapt to a new environment by starting with a hypothesis about the environment, then testing it against new data and, based on the feedback, gradually improving the hypothesis by using an ecorithm, to behave more effectively.
“Probably Approximately Correct,” Dr. Valiant’s winsome title, is his quantitative framework for understanding how these ecorithms work. In nature, there is nothing so neat as our idealized flower algorithm; we cannot really hope to get a precise rule distinguishing between two types of flowers, but can hope only to have one that gives an approximate result with high probability.
The evolution of species, as Darwin taught us, relies on natural selection. But Dr. Valiant argues that if all the mutations that drive evolution were simply random and equally distributed, it would proceed at an impossibly slow and inefficient pace.
Darwin’s theory “has the gaping gap that it can make no quantitative predictions as far as the number of generations needed for the evolution of a behavior of a certain complexity,” he writes. “We need to explain how evolution is possible at all, how we got from no life, or from very simple life, to life as complex as we find it on earth today. This is the BIG question.”
[[Shades of Thomas Nagel!! - D.G.]]
Dr. Valiant proposes that natural selection is supplemented by ecorithms, which enable organisms to learn and adapt more efficiently. Not all mutations are realized with equal probability; those that are more beneficial are more likely to occur. In other words, evolution is accelerated by computation.
This is an ambitious proposal, sure to ignite controversy. But what I find so appealing about this discussion, and the book in general, is that Dr. Valiant fearlessly goes to the heart of the “BIG” questions. (I don’t know him, though we share an editor at Basic Books.) He passionately argues his case, but is also first to point out the parts of his theory that are incomplete, eager to anticipate and confront possible counterarguments. This is science at its best, driven not by dogma and blind belief, but by the desire to understand, intellectual integrity and reliance on facts.
Many other topics are discussed, from computational complexity to intelligence (artificial and not), and even an algorithmic perspective on teaching. The
book is written in a lively, accessible style and is surprisingly entertaining. It’s funny how your perception of even mundane tasks can change after reading it — you start thinking algorithmically, confirming Dr. Valiant’s maxim that computer science is “more about humans than about computers.”
Edward Frenkel, a professor of mathematics at the University of California, Berkeley, is the author of the new book “Love and Math.”

Monday, July 8, 2013

Plant communications:Beans’ talk| TheEconomist
www.economist.com/news/science-and-technology/21580443-vegetables-employ-fungi-carry-messages-between-them-beans-talk/print 1/3
[[The kind of immense sophistication that is being discovered in the plant realm, which evolution - were it viable - would have to explain. D.G.]]
Plant communications
Beans’ talk
Vegetables employ fungi to carry messages between them
Jul 6th 2013 | From the print edition
THE idea that plants have developed a subterranean internet, which they use to raise the alarm
when danger threatens, sounds more like the science-fiction of James Cameron’s film “Avatar”
than any sort of science fact. But fact it seems to be, if work by David Johnson of the University
of Aberdeen is anything to go by. For Dr Johnson believes he has shown that just such an
internet, with fungal hyphae standing in for local Wi-Fi, alerts beanstalks to danger if one of
their neighbours is attacked by aphids.
The experiment which suggests this was following up the discovery, made in 2010 by a Chinese
team, that when a tomato plant gets infected with leaf blight, nearby plants start activating
genes that help ward the infection off—even if all airflow between the plants in question has
been eliminated. The researchers who conducted this study knew that soil fungi whose hyphae
are symbiotic with tomatoes (providing them with minerals in exchange for food) also form a7/8/13 Plant communications:Beans’ talk| TheEconomist
www.economist.com/news/science-and-technology/21580443-vegetables-employ-fungi-carry-messages-between-them-beans-talk/print 2/3
network connecting one plant to another. They speculated, though they could not prove, that
molecules signalling danger were passing through this fungal network.
Dr Johnson knew from his own past work that when broad-bean plants are attacked by aphids
they respond with volatile chemicals that both irritate the parasites and attract aphid-hunting
wasps. He did not know, though, whether the message could spread, tomato-like, from plant to
plant. So he set out to find out—and to do so in a way which would show if fungi were the
messengers.
As they report in Ecology Letters, he and his colleagues set up eight “mesocosms”, each
containing five beanstalks. The plants were allowed to grow for four months, and during this
time every plant could interact with symbiotic fungi in the soil.
Not all of the beanstalks, though, had the same relationship with the fungi. In each mesocosm,
one plant was surrounded by a mesh penetrated by holes half a micron across. Gaps that size
are too small for either roots or hyphae to penetrate, but they do permit the passage of water
and dissolved chemicals. Two plants were surrounded with a 40-micron mesh. This can be
penetrated by hyphae but not by roots. The two remaining plants, one of which was at the
centre of the array, were left to grow unimpeded.
Five weeks after the experiment began, all the plants were covered by bags that allowed carbon
dioxide, oxygen and water vapour in and out, but stopped the passage of larger molecules, of
the sort a beanstalk might use for signalling. Then, four days from the end, one of the 40-
micron meshes in each mesocosm was rotated to sever any hyphae that had penetrated it, and
the central plant was then infested with aphids.
At the end of the experiment Dr Johnson and his team collected the air inside the bags,
extracted any volatile chemicals in it by absorbing them into a special porous polymer, and
tested those chemicals on both aphids (using the winged, rather than the wingless morphs) and
wasps. Each insect was placed for five minutes in an apparatus that had two chambers, one of
which contained a sample of the volatiles and the other an odourless control.
The researchers found, as they expected from their previous work, that when the volatiles came7/8/13 Plant communications:Beans’ talk| TheEconomist
www.economist.com/news/science-and-technology/21580443-vegetables-employ-fungi-carry-messages-between-them-beans-talk/print 3/3
from an infested plant, wasps spent an average of 3½ minutes in the chamber containing them
and 1½ in the other chamber. Aphids, conversely, spent 1¾ minutes in the volatiles’ chamber
and 3¼ in the control. In other words, the volatiles from an infested plant attract wasps and
repel aphids.
Crucially, the team got the same result in the case of uninfested plants that had been in
uninterrupted hyphal contact with the infested one, but had had root contact blocked. If both
hyphae and roots had been blocked throughout the experiment, though, the volatiles from
uninfested plants actually attracted aphids (they spent 3½ minutes in the volatiles’ chamber),
while the wasps were indifferent. The same pertained for the odour of uninfested plants whose
hyphal connections had been allowed to develop, and then severed by the rotation of the mesh.
Broad beans, then, really do seem to be using their fungal symbionts as a communications
network, warning their neighbours to take evasive action. Such a general response no doubt
helps the plant first attacked by attracting yet more wasps to the area, and it helps the fungal
messengers by preserving their leguminous hosts.
Plant-fungus symbiosis is a surprisingly underexplored area of biology. The limited data
available suggest most plants go in for it in one form or another, but its role is only slowly being
illuminated. Work like Dr Johnson’s suggests this is a serious omission, not least for the
understanding of how crops like beans actually grow. The underground world, though invisible
to the human eye, should not for that reason be ignored or underestimated.
From the print edition: Science and technology

Sunday, June 30, 2013

Origin of Life and Philosophical Outlook

[Article by Rabbi Yoram Bogacz, author of Genesis and Genes; see his website TorahExplorer]
June 28, 2013
In Signature in the Cell, Dr. Stephen Meyer presented a comprehensive and accessible history of research into the origin of life. In this post, we take a bird’s eye view of research into this area over the past three-quarters of a century. We shall also digress in order to get a snapshot of how ideological commitments shape the views of many scientists.
***
Let’s begin with Dr. Ernst Chain. Chain won a Nobel Prize for his contribution to the development of penicillin. I mentioned him inGenesis and Genes, in the context of the discussion about whether evolutionary theory is relevant to nuts-and-bolts research in biology. I cited an article by Philip Skell (1918-2010), who was a distinguished professor of chemistry and a member of the National Academy of Sciences in the USA and a prominent Darwin sceptic. In a 2009 article in Forbes.com entitled The Dangers of Overselling Evolution, he made the point that evolutionary theory makes no contribution to actual research:
In 1942, Nobel Laureate Ernst Chain wrote that his discovery of penicillin (with Howard Florey and Alexander Fleming) and the development of bacterial resistance to that antibiotic owed nothing to Darwin’s and Alfred Russel Wallace’s evolutionary theories.[1]
Chain understood the immensity of the task of trying to explain life in naturalistic terms. In The Life of Ernst Chain: Penicillin and Beyond, we read that:
I have said for years that speculations about the origin of life lead to no useful purpose as even the simplest living system is far too complex to be understood in terms of the extremely primitive chemistry scientists have used in their attempts to explain the unexplainable that happened billions of years ago.[2]
In August 1954, Dr. George Wald, another Nobel Laureate, wrote inScientific American:
There are only two possibilities as to how life arose. One is spontaneous generation arising to evolution; the other is a supernatural creative act of God. There is no third possibility… a supernatural creative act of God. I will not accept that philosophically because I do not want to believe in God, therefore I choose to believe that which I know is scientifically impossible; spontaneous generation arising to Evolution.
 This statement may seem astonishingly frank to many members of the public. Informed consumers of science, in contrast, are aware that much of the debate around the origin of life and biological evolution has precious little to do with drawing inevitable conclusions from straightforward evidence. It is far more about worldviews and ideologies, and only extremely naive observers assume that this does not apply to scientists who participate in the debate. Wald makes it perfectly clear that his direction was dictated by his philosophical leanings, and that is true of many scientists and Western intellectuals. Consider the views of Thomas Nagel. Nagel is a courageous thinker whose latest book, Mind and Cosmos, is a fierce demolition of Darwinian evolution.[3] But Nagel will only go so far. In The Last Word, which appeared in 1997, he offered a candid account of his philosophical inclinations:
I am talking about something much deeper—namely, the fear of religion itself. I speak from experience, being strongly subject to this fear myself: I want atheism to be true and am made uneasy by the fact that some of the most intelligent and well-informed people I know are religious believers… It isn’t just that I don’t believe in God and, naturally, hope that I’m right in my belief. It’s that I hope there is no God! I don’t want there to be a God; I don’t want the universe to be like that.[4]
 The fact that faith – the faith of many scientists in the ability of unguided matter and energy to create life – drives much of the discussion about evolution, was underscored by Dr. Gerald Kerkut, Professor  Emeritus of Neuroscience at the University of Southampton, who wrote in 1960 that: 
The first assumption was that non-living things gave rise to living material. This is still just an assumption… There is, however, little evidence in favor of abiogenesis and as yet we have no indication that it can be performed… it is therefore a matter of faith on the part of the biologist that abiogenesis did occur and he can choose whatever method… happens to suit him personally; the evidence for what did happen is not available.
 Harold Urey won a Nobel Prize for chemistry, but is probably more famous for participating, with his graduate student Stanley Miller, in what became known as the Miller-Urey experiment. Writing in The Christian Science Monitor on 4th January 1962, Urey wrote: 
All of us who study the origin of life find that the more we look into it, the more we feel it is too complex to have evolved anywhere. We all believe as an article of faith that life evolved from dead matter on this planet. It is just that its complexity is so great, it is hard for us to imagine that it did.
 Hubert Yockey, the renowned information theorist, wrote in theJournal of Theoretical Biology in 1977 that:
One must conclude that… a scenario describing the genesis of life on earth by chance and natural causes which can be accepted on the basis of fact and not faith has not yet been written.
Richard Dickerson, a molecular biologist at UCLA, wrote in 1978 inScientific American that: 
The evolution of the genetic machinery is the step for which there are no laboratory models; hence one can speculate endlessly, unfettered by inconvenient facts. The complex genetic apparatus in present-day organisms is so universal that one has few clues as to what the apparatus may have looked like in its most primitive form.[5]
 Francis Crick needs no introduction. In Life Itself, published in 1981, he wrote that: 
Every time I write a paper on the origin of life, I determine I will never write another one, because there is too much speculation running after too few facts.
 Crick’s conclusion is that:
The origin of life seems almost to be a miracle, so many are the conditions which would have had to have been satisfied to get it going.[6]
 Prominent origin-of-life researcher Leslie Orgel wrote in New Scientistin 1982 that:
Prebiotic soup is easy to obtain. We must next explain how a prebiotic soup of organic molecules, including amino acids and the organic constituents of nucleotides evolved into a self-replicating organism. While some suggestive evidence has been obtained, I must admit that attempts to reconstruct the evolutionary process are extremely tentative.[7]
 The views of Nobel Prize winner Fred Hoyle are particularly interesting. He struggled with the conflict between his ardent atheism and his knowledge of the excruciating difficulty of positing a naturalistic start to life. Writing in 1984, Hoyle stated that: 
From my earliest training as a scientist I was very strongly brain-washed to believe that science cannot be consistent with any kind of deliberate creation. That notion has had to be very painfully shed. I am quite uncomfortable in the situation, the state of mind I now find myself in. But there is no logical way out of it; it is just not possible that life could have originated from a chemical accident.[8]
 The writer Andrew Scott hit the nail on the head when he wrote, in 1986, that most scientists’ adherence to naturalistic accounts of the origin of life owed little to the evidence and much to ideological commitments:
But what if the vast majority of scientists all have faith in the one unverified idea? The modern ‘standard’ scientific version of the origin of life on earth is one such idea, and we would be wise to check its real merit with great care. Has the cold blade of reason been applied with sufficient vigor in this case? Most scientists want to believe that life could have emerged spontaneously from the primeval waters, because it would confirm their belief in the explicability of Nature – the belief that all could be explained in terms of particles and energy and forces if only we had the time and the necessary intellect.[9]
 This conclusion is mirrored in the words of Paul Davies, a theoretical physicist and authority on origin-of-life studies. Writing in 2002, Davies affirms that it is scientists’ adherence to methodological naturalism that drives their agenda and conclusions:
First, I should like to say that the scientific attempt to explain the origin of life proceeds from the assumption that whatever it was that happened was a natural process: no miracles, no supernatural intervention. It was by ordinary atoms doing extraordinary things that life was brought into existence. Scientists have to start with that assumption.[10]
 In 1988, Klaus Dose, another prominent origin-of-life theorist, summed up the situation nicely when he wrote that: 
More than 30 years of experimentation on the origin of life in the fields of chemical and molecular evolution have led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution. At present all discussions on principal theories and experiments in the field either end in stalemate or in a confession of ignorance.[11]
 Carl Woese was a pioneer in taxonomy, and one of the major figures in 20th century microbiology. His view of the origin of life: 
In one sense the origin of life remains what it was in the time of Darwin – one of the great unsolved riddles of science. Yet we have made progress…many of the early naïve assumptions have fallen or have fallen aside…while we do not have a solution, we now have an inkling of the magnitude of the problem.[12]
 Paul Davies, too, writes that no substantive progress has been made in this area since Darwin’s time. In a recent short paper suggesting that life be viewed as a software package, Davies writes:
Darwin pointedly left out an account of how life first emerged, “One might as well speculate about the origin of matter,” he quipped. A century and a half later, scientists still remain largely in the dark about life’s origins. It would not be an exaggeration to say that the origin of life is one of the greatest unanswered questions in science.[13]
 Readers of Genesis and Genes will recall Richard Lewontin’s admission that his mathematical models of evolutionary mechanisms are a sham – they do not correspond to reality. The biologist Lynn Margulis reminisced:
 Lewontin, who is one of the most prominent geneticists in the world and a protégé of one of the founders of neo-Darwinism, Theodosius Dobzhansky, was equally forthright about the role that faith plays in moulding scientists’ approach to important issues. In his review of a book by Carl Sagan, Lewontin wrote in 1997 that:
We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.[14]
 Stuart Kauffman of the Santa Fe Institute is one of the world’s leading origin-of-life researchers and a leading expert on self-organisational systems. He writes:
Anyone who tells you that he or she knows how life started on the earth some 3.45 billion years ago is a fool or a knave. Nobody knows.[15]
 In Genesis and Genes, I also quoted the biochemist Franklin Harold. In his book The Way of the Cell, Harold frankly acknowledged that “We must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”[16] Regarding the origin of life, Harold writes that:
It would be agreeable to conclude this book with a cheery fanfare about science closing in, slowly but surely, on the ultimate mystery; but the time for rosy rhetoric is not yet at hand. The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication.[17]
 Massimo Pigliucci was formerly a professor of evolutionary biology and philosophy at the State University of New York at Stony Brook, and holds doctorates in genetics, botany, and the philosophy of science. He is currently the chairman of the department of philosophy at City University of New York. He is a prominent international proponent of evolution and the author of several books. Writing in 2003, Pigliucci writes that “[I]t has to be true that we really don’t have a clue how life originated on Earth by natural means.”[18]
In 2007, we find science writer Gregg Easterbrook writing in Wired: “What creates life out of the inanimate compounds that make up living things? No one knows. How were the first organisms assembled? Nature hasn’t given us the slightest hint. If anything, the mystery has deepened over time.”[19]
 Also in 2007, Harvard chemist George M. Whitesides, in accepting the highest award of the American Chemical Society, wrote: “The Origin of Life. This problem is one of the big ones in science. It begins to place life, and us, in the universe. Most chemists believe, as do I, that life emerged spontaneously from mixtures of molecules in the prebiotic Earth. How? I have no idea… On the basis of all the chemistry that I know, it seems to me astonishingly improbable.”[20] 
As recently as 2011, Scientific American acknowledged that origin-of-life research has gotten nowhere in the last century. In an article by John Horgan, we read that:
Dennis Overbye just wrote a status report for the New York Timeson research into life’s origin, based on a conference on the topic at Arizona State University. Geologists, chemists, astronomers, and biologists are as stumped as ever by the riddle of life.[21]
 Also writing in 2011, Dr. Eugene Koonin provided a neat summary of the utter failure of this endeavour: 
The origin of life is one of the hardest problems in all of science… Origin of Life research has evolved into a lively, interdisciplinary field, but other scientists often view it with skepticism and even derision. This attitude is understandable and, in a sense, perhaps justified, given the “dirty” rarely mentioned secret: Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure – we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. Certainly, this is due not to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life… these make the final outcome seem almost like a miracle.[22]
***
The area of origin-of-life research is fascinating not only for its own sake, but also in the way that it exposes what many uninformed members of the public take for granted, namely, that scientists are driven by data, and data alone. I elaborated on this misconception inGenesis and Genes, demonstrating that the commitment of many scientists to methodological naturalism is a far more important factor than the scientific evidence in reaching conclusions about life on Earth.
***
 See Also:
The post Certitude and Bluff:
http://torahexplorer.com/2013/01/15/certitude-and-bluff/
References:
Some of the quotations in this post come from an article by Rabbi Moshe Averick, published in The Algemeiner. The article can be read here:
http://www.algemeiner.com/2012/09/27/speculation-faith-and-unproven-assumptions-the-history-of-origin-of-life-research-in-scientists-own-words/
Retrieved 26th June 2013.

[1] The article can be read here:
.
Retrieved 2nd November 2010.
[2] R.W. Clark, Weidenfeld and Nicolson, London (1985), page 148.
[3] To read more about Nagel and his latest book, see these reviews:
http://www.newrepublic.com/article/112481/darwinist-mob-goes-after-serious-philosopher
http://www.weeklystandard.com/articles/heretic_707692.html
[4] See http://www.jidaily.com/914e2?utm_source=Jewish+Ideas+Daily+Insider
Retrieved 27th June 2013.
[5] Richard E. Dickerson, “Chemical Evolution and the Origin of Life”, Scientific American, Vol. 239, No. 3, September 1978, page77.
[6] Life Itself, New York, Simon and Schuster, 1981, page 88.
[7] Leslie E. Orgel, “Darwinism at the very beginning of life”, New Scientist, Vol. 94, 15 April 1982, page 150.
[8] Fred Hoyle, Evolution from Space, New York, Simon and Shuster, 1984, page 53.
[9] Andrew Scott, “The Creation of Life: Past, Future, Alien”, Basil Blackwell, 1986, page 111.
[10] Paul Davies, “In Search of Eden, Conversations with Paul Davies and Phillip Adams”.
[11] Klaus Dose, “The Origin of Life: More Questions Than Answers”,Interdisciplinary Science Reviews, Vol. 13, No. 4, 1988, page 348.
[12] Carl Woese, Gunter Wachtershauser, “Origin of Life” in Paleobiology: A Synthesis, Briggs and Crowther – Editors (Oxford: Blackwell Scientific Publications, 1989.
[13] Seehttp://arxiv.org/abs/1207.4803.
Retrieved 27th June 2013.
[14] “Billions and Billions of Demons”, Richard Lewontin, 9th January 1997, New York Times Book Review.
[15] At Home in the Universe, London, Viking, 1995, page 31.
[16] Franklin Harold, The Way of the Cell: Molecules, Organisms and the Order of Life, Oxford University Press, 2001, page 205.
[17] Ibid. page 251.
[18] Massimo Pigliucci, “Where Do We Come From? A Humbling Look at the Biology of Life’s Origin,” in Darwin, Design and Public Education, eds. John Angus Campbell and Stephen C. Meyer (East Lansing, MI: Michigan State University Press, 2003), page 196.
[19] Gregg Easterbrook, “Where did life come from?” Wired, page 108, February, 2007.
[20] George M. Whitesides, “Revolutions in Chemistry: Priestly Medalist George M. Whitesides’ address”, Chemical and Engineering News, 85 (March 26, 2007): p. 12-17. Seehttp://ismagilovlab.uchicago.edu/GMW_address_priestley_medal.pdf.
Retrieved 22nd April 2012.
[21] John Horgan, Scientific American, 28th February 2011.
[22] Eugene Koonin, The Logic of Chance: The Nature and origin of Biological Evolution (Upper Saddle River, NJ, FT Press, 2011, page 391.

Sunday, March 17, 2013



http://ricochet.com/main-feed/The-Perils-of-Intellectual-Apostasy

Paul A. Rahe · March 14, 2013 at 1:43am
When I was an undergraduate at Cornell , then Yale and a graduate student at Oxford, then Yale once again, the American university was an exceedingly lively place in which students were encouraged to explore a diversity of perspectives. The people in charge were, by and large, New Deal liberals -- moderate in manner, open to argument, and distinguished first and foremost by their curiosity. They welcomed into the ranks of their colleagues both those to their left and those to their right -- for they did not regard the university as an instrument for transforming the world. They supposed, instead, that it was a space within which one could spend one's time trying to understand that world. Intellectual sparring partners were, in their opinion, a great boon.
Most of the New Deal liberals that I once knew have passed on. They have been replaced in positions of authority by a generation for whom everything is political. Its motto is "the personal is political and the political is personal." What this means in practice is that the members of this generation tend to regard those at odds with them not as merely wrong and perhaps intriguingly, interestingly wrong but as simply immoral. In the face of an argument or observation that does not sit comfortably with what they believe, they resort to denunciation. The dissenter is labeled a racist or a fascist or something worse, and he is read out of the human race. In this environment, conservatives are no longer welcome. No advertisement states that they need not apply for jobs at certain institutions, but that is nearly always the case.
The key to understanding what has happened is that the new generation has made of the university a political instrument. Its purpose, as they see it, is to help them transform the larger world. Those not on board with the program are interlopers to be demonized and driven out, and the quality of the scholarly work and the teaching they do has no weight. One can write and be widely read. One can be invited to conferences and to give lectures. But, if a job comes open at a major university, one will not even be interviewed. Trust me. I know from long experience.

Every once in a while, however, something happens that shakes things up, and then one sees that things are, in fact, far worse than one ever imagined. Take, for example, the recent furor regarding Thomas Nagel's book Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False.
Nagel is a distinguished professor of philosophy with an impeccable pedigree. He was born in 1937; did his BA at Cornell, did a B.Phil. at Corpus Christi College, Oxford; and completed his Ph.D. at Harvard in 1963 under the direction of John Rawls before going on to teach at Berkeley, Princeton, and New York University. He has in the intervening years published a host of books, all of them well-received, and he has won just about every honor reserved for members of his profession. On the 4th of July 2012, when he reached the ripe old age of 75, he was at the very top of the heap. But, thanks to his new book, he is rapidly becoming a pariah. The title is sufficient to explain why.
When Steven Pinker of Harvard turned to Twitter and denounced the book as “the shoddy reasoning of a once-great thinker,” Leon Wieseltier, a throwback to the old days of New Deal liberalism who has been the literary editor of The New Republic for decades, responded:
Here was a signal to the Darwinist dittoheads that a mob needed to be formed. In an earlier book Nagel had dared to complain of “Darwinist imperialism,” though in his scrupulous way he added that “there is really no reason to assume that the only  alternative to an evolutionary explanation of everything is a religious one.” He is not, God forbid, a theist. But he went on to warn that “this may not be comforting enough” for the materialist establishment, which may find it impossible to tolerate also “any cosmic order of which mind is an irreducible and non-accidental part.” For the bargain-basement atheism of our day, it is not enough that there be no God: there must be only matter. Now Nagel’s new book fulfills his old warning. A mob is indeed forming, a mob of materialists, of free-thinking inquisitors. “In the present climate of a dominant scientific naturalism, heavily dependent on speculative Darwinian explanations of practically everything, and armed to the teeth against religion,” Nagel calmly writes, “... I would like to extend the boundaries of what is not regarded as unthinkable, in light of how little we really understand about the world.” This cannot be allowed! And so the Sacred Congregation for the Doctrine of the Secular Faith sprang into action. “If there were a philosophical Vatican,” Simon Blackburndeclared in the New Statesman, “the book would be a good candidate for going on to the Index.” . . .
I understand that nobody is going to burn Nagel’s book or ban it. These inquisitors are just more professors. But he is being denounced not merely for being wrong. He is being denounced also for being heretical. I thought heresy was heroic. I guess it is heroic only when it dissents from a doctrine with which I disagree. Actually, the defense of heresy has nothing to do with its content and everything to do with its right. Tolerance is not a refutation of heresy, but a retirement of the concept. I am not suggesting that there is anything outrageous about the criticism of Nagel’s theory of the explanatory limitations of Darwinism. He aimed to provoke and he provoked. His troublemaking book has sparked the most exciting disputation in many years, because no question is more primary than the question of whether materialism (which Nagel defines as “the view that only the physical world is irreducibly real”) is true or false.
In fact, the question raised by Nagel is a very old question. It accounts for the so-called Socratic turn. The Athenian Socrates began his philosophical career as a would-be scientist. But somewhere along the way he realized that the process physics of Thales, Anaximander, Anaximenes, and their successors could not make sense of the greatest mystery of all: the existence of the scientist. Put in simple terms, the reductionist science of the materialists is self-refuting -- for it eventuates in the reduction of the scientist himself to mere matter in motion. It eventuates in a theory that explains in materialist terms why the theory itself is being proposed and thereby subverts any claim it has to be true. Reduce the scientist to a biochemical reaction and you destroy the science.
Nagel has returned to this conundrum with a vengeance. In doing so, he has broken ranks, and he has been relegated to the class of apostates. It is a good thing that he is 75 and not 25. If he were just starting his career, this book would have ended it.
The most vigorous denunciations have come from the ranks of the scientists. Wieseltier reminds us, however, that Nagel's book is not a work of science. It is a work of philosophy. It is, he observes,
entirely typical of the scientistic tyranny in American intellectual life that scientists have been invited to do the work of philosophers. The problem of the limits of science is not a scientific problem. It is also pertinent to note that the history of science is a history of mistakes, and so the dogmatism of scientists is especially rich. A few of Nagel’s scientific critics have been respectful: inThe New York Review of Books, H. Allen Orr has the decency to concede that it is not at all obvious how consciousness could have originated out of matter. But he then proceeds to an almost comic evasion. Finally, he says, we must suffice with “the mysteriousness of consciousness.” A Darwinii mysterium tremendum! He then cites Colin McGinn’s entirely unironic suggestion that our “cognitive limitations” may prevent us from grasping the evolution of mind from matter: “even if matter does give rise to mind, we might not be able to understand how.” Students of religion will recognize the dodge—it used to be called fideism, and atheists gleefully ridiculed it; and the expedient suspension of rational argument; and the double standard. What once vitiated godfulness now vindicates godlessness.
The thing that bothers Wieseltier the most, however, is another dimensiont of the attack on Nagel:
The most shabby aspect of the attack on Nagel’s heterodoxy has been its political motive. His book will be “an instrument of mischief,” it will “lend comfort (and sell a lot of copies) to the religious enemies of Darwinism,” and so on. It is bad for the left’s own culture war. Whose side is he on, anyway? Almost taunting the materialist left, which teaches skepticism but not self-skepticism, Nagel, who does not subscribe to intelligent design, describes some of its proponents as “iconoclasts” who “do not deserve the scorn with which they are commonly met.” I find this delicious, because it defies the prevailing regimentation of opinion and exemplifies a rebellious willingness to go wherever the reasoning mind leads. Cui bono? is not the first question that an intellectual should ask. The provenance of an idea reveals nothing about its veracity. “Accept the truth from whoever utters it,” said the rabbis, those poor benighted souls who had the misfortune to have lived so many centuries before Dennett and Dawkins.
I would like to think that Nagel's debunking of the scientistic orthodoxy now dominant in the academy would usher in a new age of sharp intellectual debate. But nothing that I see in the contemporary university suggests that such a dream is at all plausible. As long as the university is seen as a political instrument, there really are no grounds for hope.
After I posted my piece last night on The Perils of Intellectual Apostasy, a colleague drew my attention to the comments attracted by Leon Wieseltier's defense of Thomas Nagel's controversial recent book Mind and Cosmos.
These, too, deserve attention -- and none more so than the reply composed by Steven Pinker of Harvard University, which captures brilliantly the closed-mindedness that typifies the modern academy. Here is a juicy snippet:
The fact that Nagel’s wildly intemperate subtitle (that Darwinism is “almost certainly false”) will give ammunition to disturbing anti-science, anti-reason forces in the contemporary political power structure is, of course, not in itself a refutation of his argument. But surely it is not inappropriate of reviewers to bring this issue up. Nagel—and Wieseltier—have to know that there is a powerful and well-funded lobby in this country that is trying to discredit the entire institution of science as a close-minded, ideological propaganda front which is determined to promote a secular, materialistic, anti-Judaeo-Christian liberalism. This is emboldens them to blow off the scientific consensus about man-made climate change, corrupt science education, suppress research on gun violence, and criminalize lifesaving medical research. For several years Nagel has been expressing casual opinions and overstating claims in ways that are guaranteed to credit and energize this lobby. While the substance of his claims have to be evaluated on their merits, it is completely legitimate to criticize the way he has expressed them. This is not about the culture war. This is about the future of the planet.
If Wieseltier had wanted to gather further evidence for the strength of political correctness in the academy and the politicization of science, he could not have found anything elsewhere quite as compelling as this. When a distinguished scholar, such as Pinker, writes of "the scientific consensus about man-made climate change," you know he lives in a bubble where he talks only with those who agree with him. There never was such a consensus among scientists on this matter, and with every passing day there is less of one.