Friday, September 27, 2013

The Uncertain Gene - 2

The Red-Rectangle Nebula
It is Friday so we are going to talk some science, even though the title does not contain the phrase "Weekend Rebel Science" as it often does.

In this series we are focusing on one area of the general history of the theory of evolution in its current dogmatic format, following "the synthesis" (Modern Evolutionary Synthesis).

That "one area" is the area where one of our most celebrated "hard sciences", Physics, intersects and impacts upon the theories of the evolutionary biological sciences.

The specific area of inquiry and intersection we focus on in this series is quantum mechanics.

The specific phenomenon within quantum mechanics which we are looking at is quantum tunneling.

The first post demonstrated an undisputed phenomenon, the dynamics of proton tunneling, together with its impact on DNA replication and/or mutation.

Yes, DNA replication in the context of proton tunneling's very real potential for initiating genetic mutation (The Uncertain Gene).

Around the Dredd Blog System, over the years, we have generally considered this subject matter area primarily to come under the heading of abiotic evolution:
The Earth is said to have formed "around 4.54 billion ... years ago" (History of Earth).

Therefore The Big Bang happened about 9.21 billion years before the Earth formed (13.75 - 4.54 = 9.21).

Biological organisms formed on the Earth about a billion years later, which would be ~10.21 billion years after The Big Bang.

Humans, e.g. homo sapiens,  are said to have evolved about 200,000 years ago, which would be ~13.7498 billion years after The Big Bang (13.7498 + 00.0002 = 13.75 billion years). Homo sapien evolution is a very tiny 0.0002 billion years of the 13.75 billion year story.

The abiotic epoch which preceded the biotic epoch involved a vast amount of "time" as we know it, populating vast areas of space with the atoms that make up chemicals, the subject of the scientific discipline Chemistry ...
(Putting A Face On Machine Mutation - 3, cf. Did Abiotic Intelligence Precede Biotic Intelligence?). In terms of time, the major portion of evolution, then, is abiotic evolution.

The modern human evolution portion of that time-line is: .2m / 13.75bn = 0.000014545, or  0.0015% (i.e. way, way less than 1%) of the time involved in the complete evolutionary time-line since the Big Bang.

Total biotic evolution is: 3.54 / 13.75 = .257, or ~26% of the total evolutionary time-line since the Big Bang.

Microbial evolution takes up about 3 billion years (~85%) of that total 3.54 billion year time-line of biotic evolution on Earth.

Thus, the minor portion of the evolutionary time-line is biotic evolution, (i.e. the events following the advent of carbon atoms, as well as the subsequent advent of carbon based life forms) while by far the major portion of the evolutionary time-line is abiotic evolution.

With that in mind, in the first post I indicated that:
In the next episode of this series, then, we will zoom in on the book "Quantum Aspects of Life", a scientific textbook, to further explore the impact of The Uncertain Gene on the evolution of carbon based life ("us").
(The Uncertain Gene). That book, Quantum Aspects of Life, offers several monumental efforts to bridge the great mysterious gap (where the things we do not know about "life" or how it first formed) stand out:
When the remarkable book What is Life? was published in 1944, written by the great quantum physicist Erwin Schrödinger and based on lectures that he had given at Trinity College Dublin in February 1943, it had a very considerable influence on several key figures in the development of molecular biology.
...
One of the basic questions that Schrödinger raised was whether the ideas of classical physics, as normally employed by biologists in their understanding of the behaviour of the physical world, can be sufficient for explaining the basic features of life.
...
[Schrödinger] pointed out that a key feature of the Darwinian/Mendelian nature of inheritance is its basis in discreteness, which could only be explained through a quantum discreteness and stability, in the basic carriers of genetic information. He argued that these carriers had to be molecules of some nature—the molecules that we now know as DNA.
...
Schrödinger argues [that] it is certainly possible that new physical ingredients, going beyond those of 20th century physics, might be needed for a full understanding of the physical underpinnings of life. There are probably not many biologists today who would argue for the necessity of such new physical ingredients in order to explain life.
...
The possible physical need for going beyond this framework had already been raised by Schrödinger himself some eight years before his Dublin lectures, when he introduced his famous “cat paradox”. Although he did not refer to this paradox explicitly in What is Life? (presumably because he had no desire to confuse his lay audience by introducing such unsettling issues into his descriptions of quantum mechanics), this unsatisfactory state of affairs in the foundations of quantum theory no doubt led him to be sceptical of the current dogma that the rules of quantum mechanics must hold true at all levels of physical description. (It may be pointed out that three others of the key figures in the development of quantum mechanics, namely Einstein, de Broglie, and Dirac, have also expressed the opinion that existing quantum mechanics must be a provisional theory.) There is, indeed, a distinct possibility that the broadening of our picture of physical reality that may well be demanded by these considerations is something that will play a central role in any successful theory of the physics underlying the phenomenon of consciousness.
...
These deep matters are still subject to much controversy, and the present volume provides a multitude of closely argued opinions on the issues that Schrödinger raised concerning the relation of biology to quantum physics.
...
Does life in some way make use of the potentiality for vast quantum superpositions, as would be required for serious quantum computation? How important are the quantum aspects of DNA molecules?
...
It would be too optimistic to expect to find definitive answers to all these questions, at our present state of knowledge ...
(Quantum Aspects of Life, "Foreward by Roger Penrose", p. vii-ix, emphasis added). I am reminded of the recent Dredd Blog post quote where a noted physicist became as candid as Dr. Penrose can be:
This is said to be the golden age of cosmology and it is from an observational point of view, but from a theoretical point of view it's almost a disaster. It's crazy the kind of ideas that we find ourselves thinking about.
(If Cosmology Is "Off," How Can Biology Be "On?"). Let's take a look, then, at how important Dr. Penrose's statement was when he wrote that there "are probably not many biologists today who would argue for the necessity of such new physical ingredients in order to explain life."

My interpretation of that statement is that Dr. Penrose thinks that evolutionary biologists utilize too much teleological language, and other observers agree with Penrose:
Since at least the 17th century (and mostly because of Newton), natural scientists have stopped using formal or final causes to explain natural phenomena ... except in biology. This was first pointed out by Colin Pittendrigh (Pittendrigh, C. S. Behavior and Evolution) (ed. by A. Rose and G. G. Simpson), Yale University Press, 1958), who coined the term "teleonomy" to refer to the kind of teleological phenomena observed in biological processes.
(Teleological Explanations in Biology, emphasis added). The piece "Teleological Notions in Biology" adds further insight.

This teleological factor lingers in the literature even after many years have passed since "the modern synthesis":
The modern evolutionary synthesis is a 20th-century union of ideas from several biological specialties which provides a widely accepted account of evolution. It is also referred to as the new synthesis, the modern synthesis, the evolutionary synthesis, millennium synthesis and the neo-Darwinian synthesis.

The synthesis, produced between 1936 and 1947, reflects the consensus about how evolution proceeds. The previous development of population genetics, between 1918 and 1932, was a stimulus, as it showed that Mendelian genetics was consistent with natural selection and gradual evolution. The synthesis is still, to a large extent, the current paradigm in evolutionary biology.

The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century.
(Wikipedia, emphasis added). That has led me to zero in on 1) teleology, 2) the modern synthesis, and 3) the issue of the impact of quantum mechanical concepts on evolutionary biology.

Let me do so by first referring to a section contained in the first post of this series:
Today, then, we offer you a much more recent paper (6/7/13) which focuses on, and details, that same phenomenon a bit more:
By treating the proton as a quantum ”wave packet” it becomes possible to model the hydrogen bond as a quantum body problem. Due to quantum tunneling, however, there is a small but finite probability that the protons will change place within the hydrogen bond, altering the genetic code, and giving rise to mutations.
(Quantum Tunneling in DNA, by Megan Wolfe). That "small but finite probability" gets much more probable by happening millions of repetitions per short amount of time (like a second or a minute) in the trillions of cells inside us.
(The Uncertain Gene). The author Megan Wolfe goes on to then write:
Mutations of this type have been called transitions and they are characterized by the fact that they are reversible, meaning the mutant DNA strands may continue replicating and if a transition happens again, they will revert back to their original ordering. Most often though in this type of mutation the once functioning DNA strand turns into junk DNA and so fails to pass on its
Proton tunneling into Life?
encoded information and directions, or even worse, turns into malfunctioning DNA which gives destructive information.

In the case of bases with unequal charge, one of the bases in a nucleotide pair has obtained an extra charge, changing the shape of the double well potential. The tunneling of a proton occurs only in one direction in this case. This results in transitions of the type A-T to A+ -T− or A− -T+ which does not appear in the Watson-Crick model. There is no nucleotide which can or will combine with the transitioned A+ and G+ so the genetic code is lost, deleted from the larger DNA strand. This means that this type of mutation is irreversible–once lost, the genetic information can never be recovered.
(ibid, Quantum Tunneling in DNA, pp. 7-8, emphasis added). The use of the term "junk DNA" is one of the types of things that The Modern Synthesis sought to eradicate.

Interdisciplinary as well as intra-disciplinary misunderstandings and loose language were targets, because they generate confusion rather than clarity and consistency.

The physicist Megan Wolfe, in her paper (quoted from above) shows that she has a very good handle on her specialty, Physics, yet does not adequately grasp current genetics:
In genomics and related disciplines, noncoding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some noncoding DNA is transcribed into functional noncoding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAs), while others are not transcribed or give rise to RNA transcripts of unknown function. The amount of noncoding DNA varies greatly among species. For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.

Initially, a large proportion of noncoding DNA had no known biological function and was therefore sometimes referred to as "junk DNA", particularly in the lay press. Some sequences may have no biological function for the organism, such as endogenous retroviruses. However, many types of noncoding DNA sequences do have important biological functions, including the transcriptional and translational regulation of protein-coding sequences. Other noncoding sequences have likely, but as-yet undetermined, functions. (This is inferred from high levels of homology and conservation seen in sequences that do not encode proteins but, nonetheless, appear to be under heavy selective pressure.)
(Wikipedia, emphasis added). Thus, even if she is correct that proton tunneling induced mutant DNA is placed in the non-coding section, along with the other 98% of the human genome, that does not mean that RNA of various sorts will not later utilize it or that it will not be passed on to future iterations of that DNA molecule (to be covered exhaustively in next post of this series).

The mistake, in the sense that it reads like she presumes that "natural selection" would cause the mutation to somehow become extinct, gets a bit into teleology:
A teleology is any philosophical account that holds that final causes exist in nature, meaning that, analogous to purposes found in human actions, nature inherently tends toward definite ends.
...
Some disciplines, in particular within evolutionary biology, are still prone to use language that appears teleological when they describe natural tendencies towards certain end conditions ...
(Teleology). Now, let's reverse the scenario to show that physicists also labor under some fundamental teleological pulls at times:
But that's a really weird idea [for scientists] if you think about it because it involves the kind of mystical and metaphysical notion of something that is not physical, something that is not part of the state of the world, something that is not changeable, acting from outside the system to cause things to happen. And, when I think about it, that is kind of a remnant of religion. It is a remnant of the idea that God is outside the system acting on it.
(If Cosmology Is "Off," How Can Biology Be "On?", emphasis in original). So, let's get back to the book (Quantum Aspects of Life) to further emphasize that physicists also can get loose with their discipline, i.e. can get off into the weeds of teleology, unless they are careful:
Expressed differently, how does a quantum superposition recognize that it has “discovered” life and initiate the said collapse? There seems to be an unavoidable teleological component involved: the system somehow “selects” life from the vastly greater number of states that are nonliving ... But this implies the environment somehow favours life—that life is “built into” nature in a preordained manner. So an element of teleology remains. (p. 11) ... an element of teleology is required; namely that the molecule must somehow know before hand what it is aiming for. (p. 42) There is no teleology needed here since we describe the measurement as a two-step process ... (p. 45) ... there’s the teleological point that, hey, we search for something ... (p. 357) ... As far as the teleological aspects are concerned (p. 360) ... Teleological aspects and the fast-track to life ... there is a teleological issue here ... (p. 392)
(ibid, Quantum Aspects of Life, emphasis added). The point being made is that "natural selection" discussions by either evolutionary biologists or physicists can become fundamentally teleological unless great care and focused technical language skills are employed:
"The concept of natural selection was originally developed in the absence of a valid theory of heredity; at the time of Darwin's writing, nothing was known of modern genetics. The union of traditional Darwinian evolution with subsequent discoveries in classical and molecular genetics is termed the modern evolutionary synthesis. Natural selection remains the primary explanation for adaptive evolution."
(Natural Selection, emphasis added). What we are attempting to grasp in this series is that various scientists realize that teleological factors are at the very foundation of our current scientific understanding, because, so far the modern synthesis has not filtered it all out.

Heretofore in this series, the only "pure" dynamic we have discussed, in the sense of trying to be free from teleological influences, is genetic molecular mutation through proton tunneling.

This real impact that teleological impurity has in natural selection discussions will continue to be pointed out in future posts of the series.

The next post in this series is here, the previous post in this series is here.

Country sex genes explained in Teleological terms:


Thursday, September 26, 2013

ObamaCare: Good Foreign Policy

Yes, I know, what does The Affordable Care Act possibly have to do with foreign policy?

In the sense that a substantial amount of foreign policy is involved with projecting a good image to the rest of the people of the world, it has a lot to do with it.

Remember that our reputation has in general been severely stained and strained over the past decade or so (see e.g. Decline of U.S. Reputation - Why?, U.S. Scholars & Statesmen Reap Scorn, and Ye Olde Gunboat Diplomacy Rides Again).

Think about the reality that the U.S.A. was the only major nation to not have some form of public health care:
Germany has the world's oldest national social health insurance system, with origins dating back to Otto von Bismarck's social legislation, which included the Health Insurance Bill of 1883, Accident Insurance Bill of 1884, and Old Age and Disability Insurance Bill of 1889. In Britain, the National Insurance Act 1911 included national social health insurance for primary care (not specialist or hospital care), initially for about one third of the population—employed working class wage earners, but not their dependents. This system of health insurance continued in force until the creation of the National Health Service in 1948 which created a universal service, funded out of general taxation rather than on an insurance basis, and providing health services to all legal residents. Most other countries' national health insurance systems were implemented in the period following the Second World War as a process of deliberate healthcare reform, intended to make health care affordable to all, in the spirit of Article 25 of the Universal Declaration of Human Rights of 1948 by nations which had adopted the declaration as signatories. The US did not ratify the social and economic rights sections, including Article 25's right to health.
(Wikipedia, emphasis added). Think about the raised eyebrows that policy causes when we pontificate at The United Nations ("I believe America is exceptional") that our form of government is exceptional because it is "of the people, by the people, and for the people" (i.e. for the public good).

Think about very recent events where Britain, our number one pal and partner in our war-infested misadventures of recent history, could not resist the public outcry over there against our planned bombing of Syria.

They publicly and loudly declined to join us in our senseless gunboat diplomacy (Syria War “Coalition” Dissolves).

Think about the snubbing and worldwide disgust exhibited towards us when it was revealed that our military NSA was snooping on the privacy of the rest of the world, and on our own citizens too:
It's worth remembering that as the US and UK run around the world protesting the hacking activities of others and warning of the dangers of cyber-attacks, that duo is one of the most aggressive and malicious, if not the most aggressive and malicious, perpetrators of those attacks of anyone on the planet. As Slate's Ryan Gallagher put it in a typically excellent analysis of this report:
"The disclosures are yet another illustration of the extremely aggressive scope of the clandestine spy operations that have been conducted by ... the United States. Infiltration of computer networks is usually more commonly associated with Russian and Chinese government hackers, but the ... Americans are at it, too, even targeting their own allies' communications. The surveillance tactics appear to have few limits, and while government officials have played up the necessity of the spying for counter-terrorism, it is evident that the snooping is often highly political in nature."
Nobody hacks as prolifically and aggressively as the two countries who most vocally warn of the dangers of hacking.
(Greenwald @Guardian; see also ACLU vs. Clapper). And don't forget that the president of a nation of over 201 million people, Brazil, canceled a state visit to the U.S. because of that illegal spying.

Later, during a recent speech at the United Nations, the Brazilian president even condemned U.S. spying on other democracies (Brazilian President Calls U.S. Spying 'Meddling').

So, in that context ObamaCare is positive for our national image in the world today, as is our new-found participation in diplomacy and United Nations activities.

We should continue such policies for our reputation's sake if nothing else.

The next post in this series is here.

Wednesday, September 25, 2013

The Uncertain Gene

Proton induced evolution
Most everyone has heard of "The Selfish Gene" concept.

If you haven't, then perhaps you have heard about the book of that name written by Dr. Richard Dawkins.

We mentioned it in a recent post (If Cosmology Is "Off," How Can Biology Be "On?").

Today, we are going to introduce The Uncertain Gene and associate it once again with Quantum Mechanics.

This will not be the first time "The Uncertain Gene" has been a subject that has been a factor in various Dredd Blog System posts, but those previous times did not consider the dynamics that will be discussed today.

For example, in past posts we noted some rather unnoticed, some rather odd, but never-the-less certain to become genetic-world-shaking news:
"The analysis of the original proton wave packet involves an interesting phase problem, and, since the energy distribution is temperature dependent, the whole phenomenon is also temperature dependent."
...
"The tunneling times will depend essentially on the height and the form of the barrier. In DNA, the form of the double-well potentials regulating the hydrogen bonds depend not only on the base pair involved but also on neighboring pairs, their net charges, and the entire electric environment. The tunneling time is hence not only characteristic for a certain biological specimen but is also a function of the position in the DNA molecule involved. The tunneling time is very likely also temperature dependent, even if the protons are well shielded in the double helix. The main problem is whether the tunneling time is very short in comparison to the replication time, or whether there exist organisms where the penetration of the barrier is slow in comparison to the replication." 
...
"It should always be remembered that, in Born's interpretation of quantum mechanics, the quantity |¥|² represents the probability density for finding the proton in a specific position. The tunneling of the wave packet is hence a time-dependent process which is going to influence the properties of the genetic code."
...
"In this connection, it should be observed that the tunneling probabilities depend not only on the base pair involved but also on the electrostatic environment, the neighboring base pairs, etc., which may explain the occurrence of "hot spots."
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At a DNA replication, the protons have to "choose sides," and the proton code immediately after a DNA replication represents actually a nonstationary state from the quantum-mechanical point of view. The time evolution of the system and particularly the penetration of the potential barrier in the double-well potential represents a loss of the genetic code which should perhaps be considered as the primary cause of aging. The
Proton Tunnelling induced mutation
aging is thus a process which goes on continuously in the DNA molecule but gets "manifested" at the replications.
...
Proton tunneling may finally be of importance in connection with the occurrence of spontaneous tumors. The growth of an individual is a highly refined balance between factors which enhance the cell duplication and other factors which limit this duplication so that the organism takes a specific shape. The entire process is stimulated and controlled by various enzymes, and there is a feedback from the environment about which we know, at present, very little. If there is a somatic mutation, i.e., a change of the genetic code in a DNA molecule in the body of an organism, the change may influence the protein synthesis and the balance between the enhancing and controlling enzyme actions in the growth cycle. Actually, the new genetic code may lead to the development of a "new individual" within the individual, i.e., a tumor."
...
"In this paper we have pointed out that, since the protons are not classical particles but "wave packets" obeying the laws of modern quantum theory, the genetic code cannot --in spite of all precautions-- be 100% stable. Due to the quantum-mechanical "tunnel effect," there is always a small but finite probability that the protons will change place, alter the genetic code, and give rise to mutations. This implies also that this transfer of protons over a distance of about 10-8 cm may be one of the driving forces in the evolution of living organisms on the earth."
(Stem Cell Malfunction A Quantum Toxin Source?, quoting Löwdin). That quote is from a 1963 paper in a scientific journal, which evidently did not garner as much interest as it could or should have.

Today, then, we offer you a much more recent paper (6/7/13) which focuses on, and details, that same phenomenon a bit more:
By treating the proton as a quantum ”wave packet” it becomes possible to model the hydrogen bond as a quantum body problem. Due to quantum tunneling, however, there is a small but finite probability that the protons will change place within the hydrogen bond, altering the genetic code, and giving rise to mutations.
(Quantum Tunneling in DNA, by Megan Wolfe). That "small but finite probability" gets much more probable by happening millions of repetitions per short amount of time (like a second or a minute) in the trillions of cells inside us.

In the next episode of this series, then, we will zoom in on the book "Quantum Aspects of Life", a scientific textbook, to further explore the impact of The Uncertain Gene on the evolution of carbon based life ("us").

Stay tuned if you like.

The next post in this series is here.

Tuesday, September 24, 2013

If Cosmology Is "Off," How Can Biology Be "On?"

"Survival of the fittest"
Two physicists gave me the idea for today's post.

I thought of a couple of things the two scientists have said, and just had to write some more about that.

To give some context, my recollection of their statements happened while I was thinking once again about cosmology in terms of abiotic evolution (see e.g. Putting A Face On Machine Mutation - 3).

These two physicists I am writing about are two prominent scientists.

At least in the sense of having wide ranging impact on modern scientific theory, if what they say is true, with some of that impact causing worldwide controversy as well as lots of conversation back and forth.

The first one is Roger Penrose who we have quoted before on this blog:
Quantum mechanics is an incredible theory that explains all sorts of things that couldn’t be explained before, starting with the stability of atoms. But when you accept the weirdness of quantum mechanics [in the macro world], you have to give up the idea of space-time as we know it from Einstein. The greatest weirdness here is that it [quantum mechanics] doesn’t make sense. If you follow the rules, you come up with something that just isn’t right.
(The Memes of Penrose). The second one is Dr. Lee Smolin, who mentions some basic science in the same vein as the quote of Dr. Penrose:
This is said to be the golden age of cosmology and it is from an observational point of view, but from a theoretical point of view it's almost a disaster. It's crazy the kind of ideas that we find ourselves thinking about.
...
And the metaphor here—which comes from atomism that comes from Democritus [c. 460 – c. 370 BC] and Lucretius [c.99—c.55 BC] —is that physics is nothing but atoms moving in a void and the atoms never change. The atoms have properties like mass and charge that never change in time. The void—which is space in the old days never changed in time—was fixed and they moved according to laws ...
...
Why are we confident of that? We're confident of that because we have a kind of metaphysical belief that there are laws of nature that are outside time and those laws of nature are causing the outcome of the experiment to be what it is. And laws of nature don't change in time. They're outside of time. They act on the system now, they acted on the system in the same way in the past, they will act the same way in a year or a million or a billion years, and so they'll give the same outcome. So nature will repeat itself and experiments will be repeatable because there are timeless laws of nature.

But that's a really weird idea [for scientists] if you think about it because it involves the kind of mystical and metaphysical notion of something that is not physical, something that is not part of the state of the world, something that is not changeable, acting from outside the system to cause things to happen. And, when I think about it, that is kind of a remnant of religion. It is a remnant of the idea that God is outside the system acting on it.
(Weekend Rebel Science Excursion - 20). Ok, that brings in some of the controversy on the physics side, so now let's tie in with the title of today's post by fitting biological evolution into today's thought storm:
There have been five mass extinctions, and we are well into the sixth mass extinction, the Anthropogenic Mass Extinction.

One interesting aspect of the recent asteroid impact science is that Darwin was unaware of it.

He did not know that most of the life forms existing 65 million years ago did not become extinct by failing to adapt via natural selection.

An abiotic cosmic catastrophe of non-biological proportions rendered those millions of species extinct, even though they were dominating and successful in their environment.

Something just as interesting, with just as much surprise, is that Darwin was not aware of genes either.
(The Evolution of Anthropogenic Extinction by Catastrophe). Darwin did not know about natural selection asteroid-selected extinction or genes, human or otherwise.

Currently, some geneticists have been rocked back on their heels by challenges to what was once thought to be knowledge.

The cult hero Dr. Dawkins is even being called an asshole after having theorized as if we knew it all about genes.

But Dawkins pontificated what we "know" about genes in vain, because we now know that we knew lots less than we thought we knew:
... some 90 percent of the protein-encoding cells in our body are microbes ... 99 percent of the functional genes in the body are microbial ... exchanging messages with genes inside human cells ... microbes cohabitating our body outnumber human cells by a factor of 10, making us actually “superorganisms” that use our own genetic repertoire as well as those of our microbial symbionts ... We just happen to look human because our human cells are much larger than bacterial cells ... no matter how you look at it, it’s high time we acknowledge that part of being human is being microbial ...
...
Microbes may indeed be subtly changing our brain early on — and for what purposes we cannot yet say ... the mere fact that microorganisms can shape our minds brings up many more questions about how humans develop their identity ... these findings call for a complete re-examination of human physiology and immunology. Attributes that were assumed to be human traits have been shown to result from human–microbe interactions.
...
Some would say that genomics has been able to distil some humility into humankind. The finalised version of the human genome deprived us of the illusion that we are one of the most complex creatures on Earth — an illusion that was at the basis of some guesses that Homo sapiens was expected to have at least 100,000 genes. When we look at a table of genomes by species, and specifically at the number of genes that have been counted or estimated for each species, we notice that humans are surpassed by several plants and invertebrates.
(The Human Microbiome Congress). This is more serious than a simple or even a complicated academic exercise, because human lives and systems are now implicated in potentially troubling ways:
From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity. Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information — or, as 23andme, a prominent genetic testing company, says on its Web site, “The more you know about your DNA, the more you know about yourself.”

But scientists are discovering that — to a surprising degree — we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people.
...
Medical researchers aren’t the only scientists interested in our multitudes of personal genomes. So are forensic scientists. When they attempt to identify criminals or murder victims by matching DNA, they want to avoid being misled by the variety of genomes inside a single person.

Last year, for example, forensic scientists at the Washington State Patrol Crime Laboratory Division described how a saliva sample and a sperm sample from the same suspect in a sexual assault case didn’t match.
(The "It's In Your Genes" Myth - 2). Can you imagine the furor within the criminal justice system in both state and federal courts, if it turns out that the human DNA science which has been used to put people to death in gas chambers, or to free others from that fate, is found to be not so trustworthy?

That human genetics has been revolutionized since The Selfish Gene, and still is being revolutionized, leaves us wondering why even The Primal Soup has fallen by the scientific wayside (Soupy Sales & Evolutionary Tales).

Anyway, at the heart of cosmology is the physics of Dr. Penrose and Dr. Smolin who are intellectually honest enough to say that our sciences are off track in some places.

That would seem to implicate our science about intelligence as well (see e.g. What Kind of Intelligence Is A Lethal Mutation? and Did Abiotic Intelligence Precede Biotic Intelligence?).

Monday, September 23, 2013

Terrorism We Can Believe In? - 3

Warmonger Holy Fear Machine
On June 11, 2009 Dredd Blog began this series (Terrorism We Can Believe In?).

It is a venture into available information which shows that rogue elements in the American government, through propaganda, have made an industry of convincing the American people to embrace "Worst Case Thinking" so fear will spread in the populace.

We followed up with another post in this series, Terrorism We Can Believe In? - 2, on May 23, 2013.

Today we review what that vast and well funded fear industry is doing to instill fear in order to make it advantageous to their goal of peddling war and destruction even as it causes the impoverishment of the middle class and the poor of the entire nation.

The intellectual dishonesty which the rogue government propagandists used was, and still is, to make the public afraid of terrorists and terrorism.

Their intellectual dishonesty has gotten worse but the public is not buying it, and the propagandists now look silly:
U.S. Representative Peter King, a Republican member of the House intelligence committee, said he’s worried that the terrorist group that killed at least 59 people in a Nairobi shopping mall will attack in the U.S.

The Somalia-based al-Shabaab Islamist militant group is one of the only al-Qaeda affiliates that has actively recruited in the U.S., King said today on ABC’s “This Week.” The group has trained at least 40 or 50 Somali-Americans, he said.
(Bloomberg). In today's post we will show that warmongering fear-mongers like Peter King on the "intelligence" committee still use the see-through, plastic-propaganda tactics of terrorists.

In today's post we will see that Americans are more likely to be killed or harmed by multitudes of dangers far greater than any danger posed by terrorists.

First off, let's take a look at a scientific study of neoCon right-wing fear mongering, conducted by John Mueller and Mark G. Stewart, which looked into the cost-benefit ratios of that fear mongering on the economy:
The cumulative increase in expenditures on US domestic homeland security over the decade since 9/11 exceeds one trillion dollars. It is clearly time to examine these massive expenditures applying risk assessment and cost-benefit approaches that have been standard for decades. Thus far, officials do not seem to have done so and have engaged in various forms of probability neglect by focusing on worst case scenarios; adding, rather than multiplying, the probabilities; assessing relative, rather than absolute, risk; and inflating terrorist capacities and the importance of potential terrorist targets. We find that enhanced expenditures have been excessive: to be deemed cost-effective in analyses that substantially bias the consideration toward the opposite conclusion, they would have to deter, prevent, foil, or protect against 1,667 otherwise successful Times-Square type attacks per year, or more than four per day. Although there are emotional and political pressures on the terrorism issue, this does not relieve politicians and bureaucrats of the fundamental responsibility of informing the public of the limited risk that terrorism presents and of seeking to expend funds wisely. Moreover, political concerns may be over-wrought: restrained reaction has often proved to be entirely acceptable politically.
(Terror, Security, and Money, PDF, emphasis added). The neglectful thinking which the perverted propagandists use is based in paranoia:
There's a certain blindness that comes from worst-case thinking. An extension of the precautionary principle, it involves imagining the worst possible outcome and then acting as if it were a certainty. It substitutes imagination for thinking, speculation for risk analysis and fear for reason. It fosters powerlessness and vulnerability and magnifies social paralysis. And it makes us more vulnerable to the effects of terrorism.
(Worst-Case Thinking Makes Us Nuts, Not Safe). Clearly, officials seek to institutionalize a type of social paranoia, which actually is a mental disorder:
It is common to have suspicious thoughts or worries about other people from time to time. These fears are described as paranoid when they are exaggerated and not based in fact. There are three key features of paranoid thoughts:
  • you fear that something bad will happen
  • you think that others are responsible
  • your belief is exaggerated or unfounded.
(Understanding Paranoia, emphasis added). Again, worst-case thinking is a sign of paranoid thinking, which is made plain by the fact that we are more likely to die from being struck by lightning than by a terrorist:
  • You are 35,079 times more likely to die from heart disease than from a terrorist
  • You are 33,842 times more likely to die from cancer than from a terrorist
  • obesity is 5,882 to 23,528 times more likely to kill you than a terrorist
  • you are 5,882 times more likely to die from medical error than terrorism
  • you’re 4,706 times more likely to drink yourself to death than die from terrorism
  • you are 1,904 times more likely to die from a car accident than from a terrorist
  • your meds are thousands of times more likely to kill you than Al Qaeda
  • you’re 2,059 times more likely to kill yourself than die at the hand of a terrorist
  • you’re 452 times more likely to die from risky sexual behavior than terrorism
  • you’re 353 times more likely to fall to your death ... than die in a terrorist attack
  • you are 271 times more likely to die from a workplace accident than terrorism
  • you are 187 times more likely to starve to death in America than be killed by terrorism
  • you’re about 22 times more likely to die from a brain-eating zombie parasite than a terrorist
  • you were more than 9 times more likely to be killed by a law enforcement officer than by a terrorist
  • [being] “crushed to death by ... [TV] or furniture” [as likely as] being killed by terrorist
  • Americans are 110 times more likely to die from contaminated food than terrorism
  • you are more likely to be killed by a toddler than a terrorist
  • you [are] four times more likely to be struck by lightning than killed by a terrorist
(More Likely To Be Killed By Lightning Than Terrorists). To show how naked the emperor is without the propaganda clothing, note that we are far, far more likely to die from Oil-Qaeda than al-Qaeda:
More than 100 million people will die ... by 2030 if the world fails to tackle climate change, a report commissioned by 20 governments said on Wednesday.
...
It calculated that five million deaths occur each year from air pollution, hunger and disease as a result of climate change and carbon-intensive economies, and that toll would likely rise to six million a year by 2030 if current patterns of fossil fuel use continue.
...
"A combined climate-carbon crisis is estimated to claim 100 million lives between now and the end of the next decade," the report said.
(Oil-Qaeda - The Indictment, see also IPCC Report #5). Regular readers will remember the Dredd Blog series Etiology of Social Dementia, 9/18/09, through Etiology of Social Dementia - 10, 9/5/13, wherein we isolate significant social dementia to government and business propaganda sources.

Let's shake the paranoia disease by requiring all government officials to tell the truth (The Dredd Philosophy Is The Dread Truth).

Fifty Ways To Leave Your Lover, by Paul Simon: