Reason and commonsense in retreat on the Russian front.

Russian Customs Officials Seize Shipments of Bibles and Bible Literature:

Over the past year, Russian authorities have taken another step in restricting religious freedom by refusing to allow Bibles published by Jehovah’s Witnesses to be imported. The Witnesses were astounded to learn that the Vyborg Customs Office claimed that the Bibles may contain signs of “extremism.” This has broad implications not only for the Witnesses but also for Russian citizens who consider the Bible to be a sacred text and integral to their faith.

Alarming Allegations Against the Bible

On July 13, 2015, Russian customs officials in the border city of Vyborg stopped a shipment of 2,013 Russian-language copies of the New World Translation of the Holy Scriptures. * The authorities confiscated three of the Bibles, sent them to an “expert” to determine whether they contained “extremist” language, and impounded the rest of the Bibles. Customs officials initiated an administrative case in August against the Finland branch office of Jehovah’s Witnesses (as the carrier of the literature into Russia).

Earlier, on May 5, 2015, customs authorities seized a shipment of religious literature that contained Ossetian-language Bibles published by Jehovah’s Witnesses. This has had a profound impact on Ossetian-speaking Christians in Russia because the New World Translation is currently the only complete Bible translation in the Ossetian language.

Although Russian officials have misapplied Russia’s Federal Law on Counteracting Extremist Activity to publications of Jehovah’s Witnesses before, this marks the first time authorities have alleged that a translation of the Bible could be linked to extremism. * If the courts declare these Bibles to be extremist, they will be banned from distribution in Russia.

Unlawful Blocking of Other Publications

Some of the literature denied import
In addition to blocking the importation of Bibles, customs officials have unlawfully blocked shipments of the Witnesses’ religious literature since March 2015. * Officials have followed the same procedure each time they seize a shipment. They first perform an unlawful search to obtain sample publications for an “expert study,” * and then the prosecutor’s office initiates proceedings to declare the publications extremist. Complicated legal battles are inevitable, since nearly every shipment will require litigation in administrative and arbitration courts.

In an attempt to release one of the shipments, Jehovah’s Witnesses presented the customs authorities with positive court decisions, expert studies, and other documentation showing that the government has already declared these publications to be nonextremist. Yet, customs officials ignored the evidence and seized the shipment.

The blocking of the Witnesses’ print publications comes amid fresh restrictions on access to their electronic publications. On July 21, 2015, Russia became the only nation in the world to ban jw.org—the official website of Jehovah’s Witnesses. Internet providers throughout Russia have blocked access to the site, and anyone in Russia who promotes the website faces administrative or criminal charges.

The ban severely impedes the Witnesses’ ability to obtain religious publications in electronic form, a loss particularly felt among Jehovah’s Witnesses who are deaf or blind. Since Bible education is fundamental to the Witnesses’ religious services, restricting access to their literature interferes with their worship.

Jehovah’s Witnesses Ask That Reason Prevail

Russian courts have dismissed or overturned previous attempts to ban other texts that are considered sacred. In 2011, a Russian court in Tomsk dismissed a claim to ban an edition of the Hindu Bhagavad Gita. In 2013, an appeal court overturned a decision that had declared a translation of the Koran to be extremist.

Jehovah’s Witnesses hope that Russian courts will reject the absurd claim made by the customs authorities that a translation of the Bible is extremist and order the release of the Bibles and other religious literature published by Jehovah’s Witnesses.

Time Line of Seized Shipments
March 1, 2015
Customs officials stop a shipment of literature and illegally confiscate copies of the publications.
May 4, 2015
Authorities stop a shipment intended for Russia. They later search the load and confiscate several items—including Ossetian-language Bibles—to investigate whether these contain signs of “extremism.”
May 28, 2015
Court assigns an institution in St. Petersburg to conduct an “expert study” of the items in the March 1, 2015, shipment.
June 2015
Customs officials stop two shipments at the border in Vyborg.
July 13, 2015
Customs officials stop a shipment containing only Russian-language Bibles.
August 13, 2015
Vyborg customs officials rule to seize all 2,013 Bibles in the July 13 shipment, claiming that they may contain signs of “extremism.” Officials initiate an administrative case against the Finland branch office of Jehovah’s Witnesses.
September 1, 2015
In a hearing regarding the May 4 shipment of Ossetian-language Bibles and other literature, the judge denies the Witnesses’ motions and prevents their attorneys from presenting concluding arguments.
October 30, 2015
The Vyborg City Court rules that customs officials unlawfully searched the May 4 shipment.
November 17, 2015

Court holds a hearing regarding the July 13 shipment of Bibles and adjourns.

The royal society declares the codes in living cells literal?

Is the Royal Society Finally Catching Up with Our Own Upright Biped?:
February 16, 2016 Posted by Barry Arrington under Intelligent Design

For some time now Upright Biped has been arguing that information cannot be reduced to chemistry, and last year he started his own website to further his key idea that when information is translated by cellular machinery, it organizes inanimate matter (carbon, hydrogen, nitrogen, etc) into all the living things on earth.  See biosemiosis.org  Essentially, UB says all of life is an artifact created by the manipulation of chemicals according to the information embedded in the cell.

Now comes the March 2016 issue of the Philosophical Transactions of the Royal Society with a special issue on DNA as Information.  The table of contents is here.

We would like to draw special attention to the article What is Information by Marcello Barbieri.  The abstract (but for the English spellings) could have been written by UB:

Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence of amino acids, a process that amounts to a transfer of information from genes to proteins. These discoveries have shown that theinformation of genes and proteins is the specific linear order of their sequences. This is a clear definition of information and there is no doubt that it reflects an experimental reality. What is not clear, however, is the ontological status of information, and the result is that today we have two conflicting paradigms in biology. One is the ‘chemical paradigm’, the idea that ‘life is chemistry’, or, more precisely, that ‘life is an extremely complex form of chemistry’. The other is the ‘information paradigm’, the view that chemistry is not enough, that ‘life is chemistry plus information’. This implies that there is an ontological difference between information and chemistry, a difference which is often expressed by saying that information-based processes like heredity and natural selection simply do not exist in the world of chemistry. Against this conclusion, the supporters of the chemical paradigm have argued that the concept of information is only a linguistic metaphor, a word that summarizes the result of countless underlying chemical reactions. The supporters of the information paradigm insist that information is a real and fundamental component of the living world, but have not been able toprove this point. As a result, the chemical view has not been abandoned and the two paradigms both coexist today. Here, it is shown that a solution to the ontological problem of information does exist. It comes from the idea that life is artefact-making, that genes and proteins are molecular artefacts manufactured by molecular machines and that artefacts necessarily require sequences and coding rules in addition to the quantities of physics and chemistry. More precisely, it is shown that the production of artefacts requires new observables that are referred to as nominable entities because they can be described only by naming their components in their natural order. From an ontological point of view, in conclusion, information is a nominable entity, a fundamental but not-computable observable.



And then there is The Meaning of Biological Information by Eugene Koonin.  Abstract:


Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with ‘meaning’, i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to ‘meaning’ of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.

Design debate:Coming soon to a theatre near you?

Disinherit the Wind: An Interview with Matt Chait About His Play
John G. West February 16, 2016 11:08 AM

I recently reviewed the intriguing new play Disinherit the Wind, which explodes many of the stereotypes about the current debate over Darwin and design. As a follow-up, I thought it would be interesting to talk with actor and playwright Matt Chait (pictured above right) about what inspired him to write and produce the play, which now can be watched on Vimeo and purchased as a book. Below is my interview with him.

Matt is interested in mounting the play again, so if you are interested in bringing it to your city, consider contacting him at complexhollywood@gmail.com.

John West: What is your background in the theater?

Matt Chait: I fell in love with acting during college and attended a wonderful acting conservatory right after graduation, the Neighborhood Playhouse. After the Playhouse I did acting work in New York and on tours, repertory companies, and summer stock. As much as I loved acting, the lifestyle of an actor was very difficult for me. I struggled with the insecurity of it, never knowing before hand if I would be working or where that work would take me. In an attempt to get more stability in my life, I got a masters degree in counseling psychology.

To support myself during this time I began working as an acting teacher at the American Academy of Dramatic Arts in their evening school. When I got my degree, the administrator of the evening school became the director of the entire Academy and offered me full time work teaching and directing. I did that for several years and then moved to Los Angeles where I taught acting at UCLA and began teaching private classes. My classes were successful and I bought the theater complex where I was renting space for my classes. I still own and operate that complex, called The Complex (catchy name), 25 years later. During all of this I have been acting, and producing and directing plays. Aside from a few sketches and adapting a British play for an American audience, however, I had never written a full-length play before Disinherit The Wind.

JW: What inspired you to write Disinherit the Wind? How did you get the idea?

MC: I was touring in a show in 1968 and was in the habit of calling my girlfriend back in New York about once a week (pay phones were much more expensive than cell phones, so daily calls were financially out of the question). During one of these calls she mentioned to me that she had begun doing exercises that "made you high." I couldn't imagine it. I was never fond of drugs -- acting being my drug of choice at the time -- but the notion that exercises could make you high really aroused my curiosity.

The exercises were called yoga (a word that I had never heard before) and I resolved to take some yoga classes as soon as I returned to New York. The classes that I found were taught by someone named Swami Satchidananda or by young people that had been studying with Swami, and they did make you high; at least for me they did. It was a kind of intoxication without toxins and I shortly found myself adapting a vegetarian diet, as Swami suggested, attending his lectures, and going on weekend yoga retreats that he ran from a place in upstate New York. This began a spiritual odyssey for me that lasted eight years and brought me in contact with a number of wonderful teachers.

At the end of this time I felt that I had a strong framework for understanding myself, my relationship to others, and to the universe and a strong sense of why we were here on this planet. I was very comfortable, within myself, with this framework, but not comfortable at all with sharing it with people that did not have a spiritual background.

When I met my wife and, especially, after we had children, we met a lot of people who had none of the spiritual background or experiences that I had had. Some of these people were scientists, as was my brother-in-law. They would say things casually in conversation regarding life and the body and the relationship between the two that made no sense to me at all. Sometimes when I interjected they would look at me as if I were delusional.

Evidently the things that I was saying were as nonsensical to them as their pronouncements were nonsensical to me. Not able to explain myself in a sound bite I held my peace, but as time went by it was not a very peaceful peace. I felt I was holding too much in and, although I was polite and friendly with these people, in a fairly shallow way, I wished that I could explain myself at a deeper level and have more open relationships with them.

I had a phone conversation once with a friend of mine who was a brain scientist. He was trying to explain to me the neo-Darwinian understanding of the beginning of life. It made no sense to me at all. I kept questioning him about it and he kept trying to put it to rest, since it was fairly late and well past his bedtime. I felt I just couldn't let him off the phone, however. I wanted my questions answered and everything that he said was just increasing my bewilderment.

Finally, as a last ditch effort to get me off the phone, he told me to read Richard Dawkins's The Selfish Gene, that Dawkins could explain it much better than he could, and before I had a chance to say anything else he said good night and quickly hung up the phone.

The Selfish Gene was the most infuriating piece of nonsense I had ever read. I could be silent no longer. I had heard about blogs and, although I had never read one, I thought that might be a good way to get my ideas out there in the open. One day I asked my assistant at work if he knew how I could go about starting a blog.

"Sure," he said, "you could start one right now."

"How long would it take?"

"About five minutes."

"You're kidding! How much would it cost?"

"It doesn't cost anything."

So, sure enough, within five minutes -- this was 2006, I believe -- I was the author of a blog. The title of the blog was, and still is, Beyond Evolution; Is There God After Dawkins? This is the origin of the following exchange in Disinherit the Wind, as Dr. Cates, acting as his own lawyer, questions the expert witness, Dr. Robert Hawkins:

CATES: It's a pleasure to meet you Robert. May I call you Robert?

HAWKINS: Not really.

CATES: Okay, Dr. Hawkins, then. It's still a pleasure. I'm familiar with many of your books, your lectures and interviews.

HAWKINS: And how did you find them?

CATES: Inspirational.

HAWKINS: Really? In what way?

CATES: Oh, much in the way that your King George inspired our Declaration of Independence or that Adolf Hitler inspired the United Nations Charter.

The more I wrote the blog, the more I discovered about the specific workings of science.

It really is remarkable how much you can learn, starting with almost no scientific background at all, just by using Google and Wikipedia. The first few years of writing this blog were a very fertile time for me. It wasn't just the excitement of learning all this new biological information but of finding ways to reframe it in a spiritual context.

It was a very natural step from this to Disinherit the Wind, which combined this new passion for writing about the relationship between spirituality and science with my old passion for theater.

JW: In the published script for your play, you thank "scientists Michael Denton, Michael Behe, Stephen C. Meyer, Jonathan Wells, and William Dembski both for their brilliance and for their indomitable courage to speak truth to power." I wondered if you could share with us how these scientists influenced you.

MC: As I said, in the beginning of writing my blog I was getting most of my scientific information from the Internet. I first heard of Discovery Institute when one reader commented that he was sure I was a member of it, with the same emotional intensity that one would accuse someone of being a member of the Nazi Party. I assured him, at that time, that not only was I not a member of DI, but that I had never heard of it until that moment. I don't think he believed me.

My readership was increasing and I was having a ball, fielding comments and expanding my knowledge of new areas of biology and physics. One reader introduced me to another blog with a wider readership called Michael Prescott's Blog: Occasional Thoughts on Matters of Life and Death. Michael became very enthused about my blog and published whole articles from it on his blog. I became an avid reader of Prescott's blog where I always found a lively discussion of important spiritual and scientific issues. Each week Michael had a feature article that first he discussed and then his readers continued to discuss. One week it was an excerpt from Michael Behe's book Darwin's Black Box.

I read Behe, then Denton, Stephen C. Meyer, etc. Each of these books was a revelation. Here was science explained in a way that made perfect sense to me. While Dawkins's writings undermined my spirituality, the writings of the scientists of Discovery Institute enhanced it. So I am greatly indebted to them for all the knowledge and insights that their wonderful, and wonderfully detailed and researched books have provided. They also exposed me to the role that politics plays in the world of science, particularly in the public face of science, and who gets to present that public face, especially in the area of evolution and the origin of life.

When I say that I honor the indomitable courage of the scientists of DI, I am not speaking hyperbolically. I have read enough to understand what happens. I can write whatever I want. I own theaters. No one is going to avoid any theater of mine because the owner does not believe in Darwinian evolution. Peer-reviewed journals will not publish my articles, but they wouldn't publish them anyway. Prestigious universities will not allow me to teach science or lecture there, but that was not part of the future that I envisioned for myself anyway. The scientists of Discovery Institute have put their careers, their financial futures, and their credibility at risk. I have no doubt that in twenty years' time their views will be the predominant ones and neo-Darwinian evolutionary biologists will be as rare as pay phones, but for the moment I believe that it is an act of enormous personal courage for a professional scientist to espouse any idea that challenges Darwinian orthodoxy.

JW: One of the intriguing things about your play is how it breaks stereotypes. For example, in our culture, people often think that there are no scientists who are skeptical of modern Darwinism. They also think that the only religious people are fundamentalist Christians. How does your play subvert those stereotypes?

MC: Before I ever started writing the play, my life experience itself had subverted all these stereotypes. The people that I have met whose words make the most sense to me and whose demeanor and bearing seem to reveal a deep understanding of life; all these wonderful people have deep concerns about neo-Darwinism and all reject materialist philosophy out of hand. I made sure to establish in my play that Dr. Cates and Howard Blair, both of whom present a scientific view in a spiritual context, were unquestionably brilliant scientists. Many religions are mentioned, but not Christian fundamentalism or any kind of fundamentalism.

There is one scene where Dr. Cates talks about some of his spiritual insights and experiences. In that scene I tried to turn the stereotype on its head. Here was the spiritual proponent making perfect sense and the "Darwinian" proponent incapable of hearing a word that the other one was saying. This inability to listen, to even consider another point of view is what we usually thing of as characteristic of fundamentalists. My point is that neo-Darwinism has become just as fundamentalist, just as resistant to change, just as fearful of new information, as the biblical orthodoxy that it replaced.

Discovery Institute is described on Wikipedia as " a non-profit public policy think tank ... best known for its advocacy of the pseudoscience intelligent design." Pseudoscience, indeed! People wonder how I can sustain an intensity of passion throughout the performance of this full-length and wordy play. It is precisely because of this kind of nonsense and all the acts of repression of anti-Darwinian information that I know of, and the demonizing of any one who questions Darwin, and the fraud committed by scientists in their attempts to prove Darwin's theories, and even the suppression before the public of the magnificent complexity of molecular biological life, for fear that it might engender wonder and awe, leading to a belief in design by a transcendent intelligence. All of this nonsense makes my blood boil. Just thinking about it before I perform keeps me razor-focused on unmasking the shallowness and inconsistencies of Hawkins (aka Dawkins) and the defense lawyer's neo-Darwinian thinking.

JW: You premiered the play in a six-week run in Los Angeles last year. What was the general reaction to the play?

MC: Amazing! There were a few fundamentalists, both religious and scientific, who literally could not hear the play. They were there to judge, not to listen. Even before the play began, someone refused to do technical work on it because it went against his neo-Darwinian views. On the other hand, an actor who auditioned for the play, and was effusive about the two pages that he had auditioned with, came back the next day to tell me that, now that he had read the whole thing, he realized that he couldn't do it because it went against his fundamentalist religious beliefs.

The argument of the play, however, is, I think, more compelling when you watch it than when you read it. So many people responded effusively, from atheists, who told me that the play had gotten them thinking and questioning in new ways, to religious people who told me that the play deepened their commitment and understanding of their own religious beliefs.

The biggest surprise was the number of people who told me that I was articulating and making more specific thoughts and feelings that they had entertained for years, but had never expressed. I think in our Darwinian/Freudian/Marxian environment, discussion of the deepest issues about the nature of ourselves and the universe rarely take place. We are under the false impression that omniscient "experts" have already answered these questions and our speculations might seem foolish or childish in a world in which we have been given the impression that these questions have already been answered and that we just don't know enough "scientific" or "psychological" or "economic" information to understand these answers. The "experts" are intentionally culpable, I believe, in giving this impression of omniscience. That is to the detriment of awe and wonder and the free discussion of these most profound issues, which, I think, are really part of our human birthright.

In the newest version of the play, Amanda, who is both the daughter of the chairman of the biology department and the love interest of Howard, the brilliant graduate student, is struck by the familiarity of Howard's ideas. She remembers that when she was a child she often thought about the connectivity of herself with others and the universe and about a sense of herself that was very distinct from her body. Rather than trusting in Howard's intelligence and background as an "expert," she accepts his ideas because they feel so right. They articulate thoughts and intimations that she had already had when she was a young girl, but never expressed in her "scientific" household, for fear that she would sound foolish.

JW: In watching the video of the play, I thought you were outstanding as Professor Bertram Cates. But I also loved the actor you had who played arch-Darwinist Robert Hawkins (above left), who was clearly a stand-in for Richard Dawkins. It's eerie just how much like Dawkins your actor was! Where did you find him?

MC: Two years earlier my friend and I were auditioning actors for a piece that he wrote based on hearings of the House Un-American Activities Committee. The two main roles were Whittaker Chambers, a staunch anti-Communist, who I was playing, and Alger Hiss, a statesman who worked with Roosevelt on the Yalta Agreements at the end of World War II and on the organization of the United Nations. Hiss was suspected of secretly being a Communist and of working to promote the interests of Joseph Stalin over our American interests. Like Dawkins, he was a real person and footage of him in interviews and hearings was available on the Internet. Although the project never got off the ground, there was one actor who made an indelible impression at his audition. He walked in as Alger Hiss; looked like him, talked like him, dressed like him, carried himself like him. It was really remarkable.

Two years later, when I was casting Disinherit the Wind, I contacted Circus-Szalewski, the actor who had impressed me two years earlier, and told him that I would like him to audition for Robert Hawkins who was modeled after Richard Dawkins and that footage existed on the Internet of Dawkins giving lectures and interviews. When he came in for his audition he arrived as Richard Dawkins. Just like he did with Hiss, he walked like him, dressed like him, talked like him. I confessed to him later that I had already cast him in the part before he started the actual audition.

Circus is a great guy and a total pleasure to work with and he is also wonderfully eccentric. He changed his name to Circus because he felt that he embodied a whole circus full of characters within him. He even refers to himself as a circus. For instance, if you ask him how things are going, he will say something like, "The circus has been very busy lately."

He also spoke with an English accent through the entire rehearsal and performance of the play. We kept asking him if he really was from England but he refused to tell us. I did find out his true origins from a friend of his who attended the play and said he had known Circus from childhood. I hope he will forgive me if I let you know that Circus is from Indiana. He is also about one hundred pounds lighter than Dawkins and looks nothing like him. His resemblance to Dawkins is not really eerie as much as it is a product of Circus's skill and hard work.

JW: Did you have any scientists who responded to the play? If so, how did they react?

MC: I can only tell you about the scientists that I spoke with after the play. That may not be a fair sampling, because if there were scientists who did not like the play they probably wouldn't have hung around afterward to talk. But the ones that I do know loved it! It seemed to me like the more they knew about science, the more they appreciated the play. We had several people from Caltech and from the Jet Propulsion Lab who gave us standing ovations. I just had dinner at Caltech two weeks ago with someone who had seen the play and who wants to have it performed there, where it would most likely be viewed by the head of the Jet Propulsion Lab and NASA. Now wouldn't that be exciting!

I find it quite remarkable that the world of theoretical physics is so rich and imaginative and exciting, while the world of theoretical biology does not even exist, because we have been given the impression that Darwin has moved us past the theoretical stage. It seems that physicists are having none of that nonsense.

I should mention two different women who told me, both in tears, almost the identical story after seeing the play. In both cases, their fathers were prominent scientists who, in later life, began to put their scientific understanding in a spiritual framework. Both of them were condemned by the scientific community that had embraced them. The pain inflicted on both these gentlemen was evident in the emotion that their daughters experienced as they told their stories. What they discovered from watching the play and what I discovered from doing the play, is that these ideas are not so "weird" or "isolating" as we once thought. I no longer have any hesitancy in letting people know, if asked, that neo-Darwinian materialist philosophy is myopic nonsense in my opinion and I am happy to explain why.

JW: What are your hopes for the play for the future?

MC: Well, I do hope that it has a future. As I said, I have already rewritten it. We received a couple of sensational reviews that I think will help promote it. I, personally, cannot afford to mount another production, so hopefully I can find another person or some institution that would be interested in producing it. You had suggested, John, that I might rework it into the format of a radio or television debate. That way we would have a cast of three or four as opposed to ten and it would be a much easier play to tour with. It would also open up the possibility of an audio version. If there is anyone reading this who might be interested in mounting a production, please contact me. You can reach me at complexhollywood@gmail.com.

Thank you, John, for giving me this opportunity and thank you, readers, for hearing me out.

The challenge of floral networking to Darwin

Secrets of the Plant "Intranet" Are Coming to Light
Evolution News & Views February 17, 2016 3:09 AM

Most companies are on the Internet these days, but many also keep an internal network called an "intranet" for passing messages within the organization. In both respects, flowering plants and conifers are similarly equipped. They send and receive messages through the air in the form of volatile organic compounds, and through the soil by networks of fungal hyphae. A tree under attack by beetles, for instance, can send out distress calls that other trees in the forest can pick up, giving them time to shore up their defenses.

The plant "intranet" is where things really get interesting. When you think about it, a plant has to keep in touch with itself. The roots underground need to know how things are going up top. The leaves and branches, in turn, need to know if there will be enough water and nutrients in the soil to proceed with costly enterprises like flowering and fruit bearing. Plants have a remarkable communications system that allows rapid signaling and response, comparable to an automated email system.

The messages come in the form of molecules that travel through the vascular bundles in the stems and roots. A paper in Current Biology by Chinese scientists explains part of what happens. In effect, they opened a plant's email and read it. The message was in the form of a transcription factor named HY5, a protein that binds to a gene and controls its transcription rate. Wikigenes says that HY5 "binds directly to the promoters of light-inducible genes, promoting their expression and photomorphogenic development." The email says, "Turn up the heat, guys -- the economy is booming!"

But HY5 should not turn up the heat if the roots aren't ready in the supply room down below. Here's where long-distance communication comes in (long distance, that is, in the context of a small plant). The Chinese researchers found that HY5 migrates from the shoot to the root with its message. They list these four highlights of their findings:

HY5 is essential for light-responsive coordination of the growth of shoots and roots.

Shoot-to-root translocated HY5 mediate light-activated root growth and N uptake.

Carbohydrate photosynthate-induced NRT2.1 expression and N uptake depend upon HY5.

HY5 contributes to maintain balance of C and N metabolism at varying light fluence. [Emphasis added.]

Did you catch that word "translocated"? That's the email system. HY5 travels down the plant's phloem vessels from "shoot to root" -- from top to bottom. Watch for the intranet analogy in the summary of the paper. (Gene names are italicized; protein names are not.)

Coordination of shoot photosynthetic carbon fixation with root inorganic nitrogen uptake optimizes plant performance in a fluctuating environment. However, the molecular basis of this long-distance shoot-root coordination is little understood. Here we show that Arabidopsis ELONGATED HYPOCOTYL5 (HY5), a bZIP transcription factor that regulates growth in response to light, is a shoot-to-root mobile signal that mediates light promotion of root growth and nitrate uptake. Shoot-derived HY5 auto-activates root HY5 and also promotes root nitrate uptake by activating NRT2.1, a gene encoding a high-affinity nitrate transporter. In the shoot, HY5 promotes carbon assimilation and translocation, whereas in the root, HY5 activation of NRT2.1 expression and nitrate uptake is potentiated by increased carbon photoassimilate (sucrose) levels. We further show that HY5 function is fluence-rate modulated and enables homeostatic maintenance of carbon-nitrogen balance in different light environments. Thus, mobile HY5 coordinates light-responsive carbon and nitrogen metabolism, and hence shoot and root growth, in a whole-organismal response to ambient light fluctuations.

The key to any intranet is movement of information-bearing signals. In human email systems, each message has a "header" of metadata signifying the sender and receiver and other information, so that the router on the communications channel knows what to do with it. Then there is the body of the message. The plant's messages, of course, are different from human email written in alphabetic text; they're more like signals indicating "on/off" or "speed up/slow down." They are encoded, though, by molecular text -- the language of DNA. Notice that there's nothing about HY5 that looks like or smells like the meaning of the message. The meaning involves a pre-ordained convention about what the presence of the signal indicates.

It's notable that the same signal can take on different meanings depending on context. The signal causes one reaction in the shoot, but a different reaction in the root. We also see a "To" and "CC" convention. HY5 lands on two genes: HY5 and NRT2.1. There's a unique aspect of this plant intranet in that it's "fluence-rate modulated," i.e., sensitive to message flow: the more signal, the more the response. Maybe that's like getting a flood of tweets.

Most importantly, the message is mobile and routable. HY5 has to carry its message over long distances and traverse numerous branching points to get to the intended recipient. As a result, just as with a corporate intranet, the plant benefits from "whole- organismal response" to what we might call the business environment. Just as a manufacturing plant needs to adjust its production to the availability of raw materials, a living plant must adjust its production to the availability of sunlight and soil nutrients.

The paper reads like a detective story. When they shined light of varying intensities on shoots, the roots grew. Intrigued by the rapid response of a distant part of the plant to the conditions at the top, they thought, Aha! -- "Shoot illumination promotes root growth, most likely via shoot-to-root signaling." It's no wonder that in the introduction to the paper, the scientists described it as "long-distance shoot-root communication." The hunt was on to find the emails.

Experiments honed in on the answer. Mutant plants that didn't grow stronger roots when illuminated were found to have a broken HY5 protein. Other tests confirmed that HY5 is the information-carrying molecule. But does it really travel long distance? To test that, they ran some experiments that first suggested "HY5 transcripts, HY5, or a HY5-dependent signal moves from shoot to root." Then they narrowed it down to HY5 itself. One clever test was fastening two other molecules onto HY5 in the shoots, and finding that none of them made it to the root. Why? "Most likely because its relatively large size prevents shoot-root mobility" -- i.e., the bigger emails clogged the communication channel.

But then, when they sent along a molecular scissors that cut off one of the hangers-on, the custom messages did arrive. Conclusion: "HY5 is a shoot-root phloem-mobile signal...." From there, they studied what the recipient of the "CC" email does (i.e., the gene NRT2.1). The second recipient, they found, promotes a gene that increases nitrate uptake.

In the conclusion, the authors recognized that what they were seeing was a case of real communications networking. The shoot is not just sending some sugar down the pipe for the roots to eat so they will work harder; sucrose is involved, but the HY5 protein transcription factor is a bearer of information. Here's how they express it in scientific jargon:

Although a previous study implicates phloem-mobile sucrose as a cotyledon-derived signal to control primary root elongation during early seedling development in Arabidopsis, the molecular mechanism of the shoot-root long-distance signaling regulating lateral root growth and N uptake remains unclear. Here, we show that HY5 is a shoot-root mobile signal that mediates light-regulated coupling of shoot growth and C assimilation with root growth and N uptake. This coupling is achieved via HY5 regulation of C fixation in the shoot and via sucrose-enhanced promotion of HY5-dependent N uptake in the root. In consequence, HY5 mediates homeostatic regulation of whole-plant C versus whole-plant N status. HY5 is already known to integrate multiple phytohormonal (e.g., abscisic acid) and environmental (e.g., low temperature) signaling inputs in the control of plant growth and development. Our discovery that HY5 is a mobile signal adds further dimension to this knowledge.


This is so cool; everyone should get a chill out of thinking that plants have email. They pass signals coded by a genetic language. They send them through communications channels to recipients. The recipients know what to do with that information. The resemblance to email is uncanny. When ID advocates see very similar concepts to email employed in living organisms like the humble rockcress, we have ample justification to celebrate. "You've got mail!"

Darwinism vs.the real world XXIX

Immune Defense: How Antibodies Work
Howard Glicksman February 16, 2016 4:08 PM

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News is delighted to offer this series, "The Designed Body." For the complete series,  see here. Dr. Glicksman practices palliative medicine for a hospice organization.

The body is constantly under attack from powerful microorganisms that, if given the chance, can cause serious infection and death. The body's first layer of defense is the skin and epithelium that lines the respiratory, gastrointestinal, and genitourinary tracts. If the microbes get past these barriers they come up against the body's immune system. The immune system can be divided into two parts.

The first is the innate immune system,which we have from birth and acts in the same way every time it encounters foreign matter. The second is the adaptive immune system, which develops over time and reacts in a specific way to the foreign matter it encounters. Without the first layer of defense or both components of the immune system, our earliest ancestors could not have lived long enough to reproduce.

In earlier articles I've shown how some of the immune cells and proteins of the innate system work together to defend the body from microbial attack. And in my immediately previous article I explored the immune cells of adaptive immunity: the lymphocytes, consisting of helper T-cells, which help other immune cells multiply and improve their killing ability; cytotoxic T-cells, which destroy infected host cells; and B-cells, each of whichproduces millions of identical antibodies. Now let's look at how antibodies -- the proteins of the adaptive immune system -- work to help the body's immune defense with extra intelligence, firepower, and precision accuracy.

Antibodies, also called immunoglobulins or gamma globulins,circulate in the blood as plasma proteins. When the first responders of innate immunity release chemicals to cause inflammation, this allows not only immune cells from the blood to come to the field of battle, but also proteins including immunoglobulins. Antibodies are good at helping other immune cells identify and kill bacteria, neutralizing toxins and limiting the effects of viruses before they can enter a cell. To understand how antibodies work, it is important to first look at their structure.

The antibody molecule consists of four chains of amino acids bonded to each other: two identical pairs of heavy and light chains joined together in the shape of a Y. The two connected heavy chains provide the basis of the Y-shaped structure while each light chain is connected to the outside of the branching portion of the heavy chain. The tips of the Y-shaped antibody molecule consist of the amino acids from the ends of each identical light and heavy chain. Together, they form a specific chemical pattern with a three-dimensional shape that is identical to the antigen receptors on the B-cell that produced them. These tips at the end of the antibody molecule act as antigen-binding sites and are known as the Fab portion (antigen binding fragment).

Human DNA is programmed to produce about one million different heavy chains and about ten thousand different light chains, each with their own unique amino acid pattern. Each B-cell produces only one specific antibody, made up of two pairs of identical heavy and light chains. That means that the body is able of make, as an estimate, over ten billion (one million times ten thousand) different antibodies, each with its distinct combination of binding sites. This gives the body a wide array of specific blood-borne sentries that can detect specific chemical patterns on different invading microbes. The amino acid structure that makes up the base of the Y-shaped antibody molecule remains constant and is called the Fc piece (constant fragment). It is the Fc piece that becomes activated after the Fab portions attach to the specific antigen and makes the antibodies ready for action.

There are a few ways that activated antibodies help the immune system defend the body from infection. As you may recall, the neutrophils and macrophages of the innate immune system have their own receptors that attach to large parts of foreign proteins on invading microorganisms. However, many pathogenic microbes have developed ways to evade detection and destruction by these phagocytic immune cells. They can often make themselves invisible, allowing them to multiply and spread throughout the body. When antibodies' Fab portions attach to the specific antigens on the cell surface of the pathogens, they activate, and the pathogens lose the ability to evade and resist the neutrophils and macrophages. These immune cells have receptors on their surface that attach to the Fc piece of the antibody once it activates, allowing them to see and capture the pathogen. This activity is called enhanced attachment, or opsonization (opsonein, Greek: to buy food); the antibodies help phagocytes attach to microbes and literally make microbial food available to them.

Complement activation is another very important mechanism by which antibodies help kill microbes and infected host cells. As we saw previously, there are three different pathways that activate the complement system. The most efficient one requires a specific antibody to activate its Fc piece by attaching its Fab to a specific antigen on the cell surface of the microbe. Complement attaching to the activated Fc piece triggers the various other complement proteins. These swing into action and sometimes form the Membrane Attack Complex, which drills a hole in the membrane surrounding the microbe and kills it. Some of the fragments of activated complement (e.g., C3b) can attach themselves to microorganisms as well. Neutrophils and macrophages have receptors for C3b that allow them to identify and attach to the pathogen and kill it through opsonization.

In addition to enhanced attachment and complement activation, attaching antibodies to specific antigens on infected host cells activates NK (natural killer) cells.These attach to the activated Fc piece and, in a process called antibody-dependent cellular cytotoxicity (ADCC), release chemicals into the infected cell, causing its death. Moreover, both viruses and bacteria have specific structures on their outer surfaces that allow them to grab human cells and cause infection.

When antibodies attach to the specific antigens on these outer structures, they block the virus or bacteria from attaching to human cells and prevent infection. Furthermore, some bacteria release toxins that must attach to receptors on the surface of host cells to cause damage. When antibodies attach to the specific molecular patterns on these toxins, they block them from attaching to the host cell. Finally, microbes have structures, like flagella and cilia for mobility, which allow them to spread throughout the body. When antibodies attach to antigens on these structures, they cause them to malfunction and inhibit their ability to spread and do damage.

In prior articles I explained that the body's immune system is irreducibly complex, because not only are the innate and adaptive immune systems each needed for survival, but each of their respective components is as well. It also demonstrates natural survival capacity, for our earliest ancestors could never have survived long enough to reproduce if they hadn't had enough properly working first responder immune cells in their tissues, or neutrophils and complement in their blood, or T-cells in their lymphatic systems to prevent infection. So what about antibodies?

Primary immunodeficiencies are genetic conditions a person is born with that result in a poor immune response to infection. One example involves defective B-cell function and an almost total absence of antibodies, called Agammaglobulinemia. Infants receive temporary immunity from their mothers by antibodies crossing through the placenta into their bloodstream. However, after six months, they start to have infections which, if it weren't for modern medicine, would quickly lead to death. This shows that even if our earliest ancestors had had all of the other parts of the immune system working properly, without antibodies, they would never have survived.

Finally, it's important to realize that just like the coagulation cascade and the complement system, this system must turn on only when needed and stay or turn off when not. When antibodies cause the body to overreact to itself or to relatively harmless antigens, this can lead to major debility and even death. Some allergies, such as hay fever and asthma, are caused by certain antibody responses to pollens. When applied to venom from a bee sting, such overreactions can cause anaphylactic shock. When antibodies react inappropriately to normal tissue and turn on the immune system in what is called autoimmune disease, this leads to inflammation, injury, and destruction of different tissues and organs. It's vital not only that all of the components of the immune system be present, but that they be properly controlled.

On December 14, 1799, George Washington was suffering from a severe case of tonsillitis. The theory of the day was that infections were caused by the presence of ill humors in the blood that must be treated by bloodletting. Over several hours, in the midst of an acute infection, his medical attendants removed about five pints of blood. Modern medical practitioners know that infections are caused by germs, not ill humors, and that bleeding someone who has an acute infection is not only likely to cause further weakness but possibly even death.

Even though microbes had been observed under the microscope for almost two hundred years, it was not until the late 19th century that medical science began to recognize that specific germs cause specific diseases. And it was not until Louis Pasteur disproved the theory of spontaneous generation (the belief that life could originate from inanimate matter) that medical science realized that many infectious diseases were indeed preventable.

Clearly, when it came to the understanding of infections, the medical profession of George Washington's day was in error. Moreover, their misguided notions of what caused disease led them to apply the standard treatment of the day (bloodletting), which likely contributed to his death.

This demonstrates how a strongly held, but erroneous, idea can lead to certain assumptions and actions that are detrimental to human development and prosperity. In other words, ideas have consequences. As presented by today's evolutionary biologists, the dominant theory of how life came into being would appear to involve a type of spontaneous generation called abiogenesis. The current thinking is that inanimate matter (chemical elements), under the influence of chance and the laws of nature alone, eventually became multi-system organisms with complex body plans, like us. For vertebrates such as fish, birds, reptiles, amphibians, and mammals, this means that the immune response needed for survival, as described in previous articles, arose solely by these processes.The consequences of this strongly held, but erroneous, idea are pervasive within our culture and affect almost every aspect of human endeavor.


Next time, we'll begin to look at the digestive system and how the body acquires what it needs to live, grow, and work properly.

Religious liberty remains under assault in Russia