Seeing X Chromosomes in a New Light

By CARL ZIMMERJAN. 20, 2014 New York Times

 

In a female mouse’s brain, a left-to-right pattern in the silencing of the X chromosome. These patterns may influence how individual brains function. Hao Wu and Jeremy Nathans/Cell Press

 

The term “X chromosome” has an air of mystery to it, and rightly so. It got its name in 1891 from a baffled biologist named Hermann Henking. To investigate the nature of chromosomes, Henking examined cells under a simple microscope. All the chromosomes in the cells came in pairs.

 

All except one.

 

Henking labeled this outlier chromosome the “X element.” No one knows for sure what he meant by the letter. Maybe he saw it as an extra chromosome. Or perhaps he thought it was an ex-chromosome. Maybe he used X the way mathematicians do, to refer to something unknown.

 

Today, scientists know the X chromosome much better. It’s part of the system that determines whether we become male or female. If an egg inherits an X chromosome from both parents, it becomes female. If it gets an X from its mother and a Y from its father, it becomes male.

 

But the X chromosome remains mysterious. For one thing, females shut down an X chromosome in every cell, leaving only one active. That’s a drastic step to take, given that the X chromosome has more than 1,000 genes.

Cells silence X chromosomes in different patterns, sometimes skewing entire organs toward one parent. Clockwise from top left, a mouse’s cornea, skin, cartilage and inner ear. Dr. Jeremy Nathans hopes his colored maps serve as an atlas for the effects of X-chromosome inactivation on women. Hao Wu and Jeremy Nathans/Cell Press

 

In some cells, the father’s goes dormant, and in others, the mother’s does. While scientists have known about this so-called X-chromosome inactivation for more than five decades, they still know little about the rules it follows, or even how it evolved.

 

In the journal Neuron, a team of scientists has unveiled an unprecedented view of X-chromosome inactivation in the body. They found a remarkable complexity to the pattern in which the chromosomes were switched on and off.

 

At the same time, each copy of the X chromosome contains versions of genes not found on its partner. So having two X chromosomes gives females more genetic diversity than males, with their single X chromosome. Because of that, females have a genetic complexity that scientists are only starting to understand.

 

“Females simply have access to realms of biology that males do not have,” said Huntington F. Willard, the director of Duke University’s Institute for Genome Sciences & Policy, who was not involved in the research.

But while the additional genes provided by their second X chromosome may in some cases provide females with a genetic advantage, X chromosomes also have a dark side. Their peculiar biology can lead to genetic disorders in males and, new research suggests, create a special risk of cancer in females. Understanding X-chromosome inactivation can also shed light on the use of stem cells in therapies.

 

A Japanese biologist, Susumu Ohno, first recognized X-chromosome inactivation in the late 1950s. In every female cell that he and his colleagues studied, they found that one of the two X chromosomes had shriveled into a dormant clump. Scientists would later find that almost no proteins were being produced from the clump, indicating that it had been shut down.

The British geneticist Mary F. Lyon realized that she could learn more about X-chromosome inactivation by breeding mice, because some color genes sit on the X. In 1961 she reported that female mice sported patches of hair with their mother’s color and others with their father’s.

 

Getting a deeper look at how females shut down their X chromosomes has remained a challenge in the decades since Dr. Lyon’s discovery. In recent years, Dr. Jeremy Nathans, a Howard Hughes Medical Institute investigator at Johns Hopkins University, and colleagues have developed a way to make X chromosomes from different parents light up. They inserted a set of genes into the X chromosomes of mice. The genes produced a green fluorescent protein, but only if their X chromosome was active and they were exposed to a particular chemical trigger.

 

Dr. Nathans and his colleagues engineered other mice to produce a red protein from active X chromosomes in response to a different chemical. The researchers bred the altered mice to produce female pups. The pups inherited a green X from one parent and a red one from the other.The scientists then added both of their color-triggering chemicals to the mouse cells. The cells lit up in a dazzling mosaic of reds and greens. One cell might shut down the mother’s X, while its neighbor shut down the father’s.

 

In recent years, scientists have increasingly appreciated that our cells can vary genetically — a phenomenon called mosaicism. And X-chromosome inactivation, Dr. Nathans’s pictures show, creates a genetic diversity that’s particularly dramatic. Two cells side by side may be using different versions of many different genes. “But there is also much larger-scale diversity,” Dr. Nathans said.

In some brains, for example, a mother’s X chromosome was seen dominating the left side, while the father’s dominated the right. Entire organs can be skewed toward one parent. Dr. Nathans and his colleagues found that in some mice, one eye was dominated by the father and the other by the mother. The diversity even extended to the entire mouse. In some animals, almost all the X chromosomes from one parent were shut; in others, the opposite was true.

To learn more about how females shut down their X chromosomes, researchers developed a way to make X chromosomes from different parents light up as green or red in mice. A mouse’s left and right retinas. Hao Wu and Jeremy Nathans/Cell Press

“It’s incredibly important,” said Dr. Willard, the Duke geneticist. “This is the most stunning display of what Mary Lyon said 50 years ago.”

 

Dr. Nathans hopes his colored maps can serve as an atlas for the effects of X-chromosome inactivation on women’s bodies. Because each X chromosome carries different variants of the same genes, father-dominated tissues may behave differently from mother-dominated ones.

How one cell ends up silencing its mother’s or father’s X chromosome is still not entirely clear. Scientists are just starting to decipher some of the key steps in the process. “The knowledge of this is exploding,” said Dr. Jeannie T. Lee, a Howard Hughes Medical Institute investigator at Harvard Medical School.

 

Scientists don’t know how a cell chooses one chromosome or another to silence. But they’ve identified a number of the molecules that do the silencing. The leader of this molecular team is known as Xist.

 

Ever since it was discovered in the 1990s, scientists have debated how Xist managed to shut down an entire chromosome. Some researchers suggested that one Xist molecule landed on one spot on the X chromosome and then others attached to it, spreading along its length. But recent studies by Dr. Lee and colleagues show that Xist molecules envelop the X chromosome like a swarm of bees. “It’s going to all the genes all at once,” she said.

 

Once Xist latches on, it lures other types of molecules. Together they enshroud the X chromosome. When a cell divides, new copies of the molecules silence the same chromosome in its descendants.

 

Why women’s cells should bother with such an elaborate dance has also intrigued scientists. While scientists have proposed a number of explanations ever since X-chromosome inactivation was discovered, Gabriel A.B. Marais, an evolutionary biologist at the University of Lyons in France, said that none fit the current evidence very well. “The situation is very confusing,” he confessed.

 

It’s possible, for example, that males have to increase the production of proteins from their X chromosome because they have only one copy of its genes. But this creates a quandary for females, because they may overdose themselves. They shut down one of the hyperactive X chromosomes to regain a balance of their own.

 

Females might have evolved to choose randomly between their parents’ chromosomes because it gave them more genetic versatility. Sometimes a gene on one X chromosome is defective. Cells that use the healthy copy of the X chromosome can compensate. Males, by contrast, are far more prone to genetic disorders linked to the X chromosome, such as color blindness. With only one X chromosome in their cells, they have no backup.

 

Dr. Nathans speculates that using chromosomes from both parents is especially useful in the nervous system. It could create more ways to process information. “Diversity in the brain is the name of the game,” he said.

 

But the X chromosome may also pose a risk to women. Dr. Lee and her colleagues have found that when they shut down Xist in female mice, the animals were more likely to develop cancer. She suspects that when a cell stops making Xist, its inactivated X chromosome wakes up. The extra proteins it makes can drive a cell to grow uncontrollably.

 

“That has bearing on stem cell therapy,” she added. When stem cells are reared in the lab, they sometimes stop making Xist as well. Dr. Lee is concerned that female stem cells may rouse sleeping X chromosomes, with devastating consequences.

 

Before stem cells can be safely used in medical treatments, we may finally need to solve the mystery that Henking originally labeled with an X.

Discovery of Quantum Vibrations in 'Microtubules' Inside Brain Neurons Supports Controversial Theory of Consciousness

Science News

... from universities, journals, and other research organizations
http://www.sciencedaily.com/releases/2014/01/140116085105.htm#.UtlgfyUV_6M.twitter

Jan. 16, 2014 — A review and update of a controversial 20-year-old theory of consciousness published in Physics of Life Reviews claims that consciousness derives from deeper level, finer scale activities inside brain neurons. The recent discovery of quantum vibrations in "microtubules" inside brain neurons corroborates this theory, according to review authors Stuart Hameroff and Sir Roger Penrose. They suggest that EEG rhythms (brain waves) also derive from deeper level microtubule vibrations, and that from a practical standpoint, treating brain microtubule vibrations could benefit a host of mental, neurological, and cognitive conditions.

---

The theory, called "orchestrated objective reduction" ('Orch OR'), was first put forward in the mid-1990s by eminent mathematical physicist Sir Roger Penrose, FRS, Mathematical Institute and Wadham College, University of Oxford, and prominent anesthesiologist Stuart Hameroff, MD, Anesthesiology, Psychology and Center for Consciousness Studies, The University of Arizona, Tucson. They suggested that quantum vibrational computations in microtubules were "orchestrated" ("Orch") by synaptic inputs and memory stored in microtubules, and terminated by Penrose "objective reduction" ('OR'), hence "Orch OR." Microtubules are major components of the cell structural skeleton.

Orch OR was harshly criticized from its inception, as the brain was considered too "warm, wet, and noisy" for seemingly delicate quantum processes.. However, evidence has now shown warm quantum coherence in plant photosynthesis, bird brain navigation, our sense of smell, and brain microtubules. The recent discovery of warm temperature quantum vibrations in microtubules inside brain neurons by the research group led by Anirban Bandyopadhyay, PhD, at the National Institute of Material Sciences in Tsukuba, Japan (and now at MIT), corroborates the pair's theory and suggests that EEG rhythms also derive from deeper level microtubule vibrations. In addition, work from the laboratory of Roderick G. Eckenhoff, MD, at the University of Pennsylvania, suggests that anesthesia, which selectively erases consciousness while sparing non-conscious brain activities, acts via microtubules in brain neurons.

"The origin of consciousness reflects our place in the universe, the nature of our existence. Did consciousness evolve from complex computations among brain neurons, as most scientists assert? Or has consciousness, in some sense, been here all along, as spiritual approaches maintain?" ask Hameroff and Penrose in the current review. "This opens a potential Pandora's Box, but our theory accommodates both these views, suggesting consciousness derives from quantum vibrations in microtubules, protein polymers inside brain neurons, which both govern neuronal and synaptic function, and connect brain processes to self-organizing processes in the fine scale, 'proto-conscious' quantum structure of reality."

After 20 years of skeptical criticism, "the evidence now clearly supports Orch OR," continue Hameroff and Penrose. "Our new paper updates the evidence, clarifies Orch OR quantum bits, or "qubits," as helical pathways in microtubule lattices, rebuts critics, and reviews 20 testable predictions of Orch OR published in 1998 -- of these, six are confirmed and none refuted."

An important new facet of the theory is introduced. Microtubule quantum vibrations (e.g. in megahertz) appear to interfere and produce much slower EEG "beat frequencies." Despite a century of clinical use, the underlying origins of EEG rhythms have remained a mystery. Clinical trials of brief brain stimulation aimed at microtubule resonances with megahertz mechanical vibrations using transcranial ultrasound have shown reported improvements in mood, and may prove useful against Alzheimer's disease and brain injury in the future.

Lead author Stuart Hameroff concludes, "Orch OR is the most rigorous, comprehensive and successfully-tested theory of consciousness ever put forth. From a practical standpoint, treating brain microtubule vibrations could benefit a host of mental, neurological, and cognitive conditions."

The review is accompanied by eight commentaries from outside authorities, including an Australian group of Orch OR arch-skeptics. To all, Hameroff and Penrose respond robustly.

Penrose, Hameroff and Bandyopadhyay will explore their theories during a session on "Microtubules and the Big Consciousness Debate" at the Brainstorm Sessions, a public three-day event at the Brakke Grond in Amsterdam, the Netherlands, January 16-18, 2014. They will engage skeptics in a debate on the nature of consciousness, and Bandyopadhyay and his team will couple microtubule vibrations from active neurons to play Indian musical instruments. "Consciousness depends on anharmonic vibrations of microtubules inside neurons, similar to certain kinds of Indian music, but unlike Western music which is harmonic," Hameroff explains.

The Perverted Science of Global Warming Gets Dirty(er)

John Ransom | Jan 20, 2014        

 

Because one would suppose that in policies promoted by properly-thinking, modern progressives-- who worship all things science— and have no time for mumbo jumbo about faith and religion, that at the very least they’d have data to support that their policies will cool the earth, solve world hunger, bring people out of poverty, improve education, create income equality, or pay female White House staffers commensurate with men.

OK, the last one was outrageous. Never gonna happen under Obama.

What was I thinking?

At the very least, I was thinking that people like Ericynot, BoatBoy, DoctorRoy or Hillinger would enjoy me being bald and eating dog food.

Heck, I’d even make a video of it.

But the problem remains: Sea levels aren’t rising, storms aren’t nastier and more brutish. The only science that’s being done is the type where estimates are used where data is called for and predictions are being used instead of conclusions.

Stumped by the fact that temperatures are not accurately reflecting current climate “models”- in fact temperatures have remained stable for 17 years- scientists on the government gravy train are trying to tie any weather event to so-called climate change.

Or income inequality. Which really?Aren’t they the same things?
Hurricanes? Global warming.
Tornadoes? Global warming?
Drought? Global warming?
Blizzards, dropping temperatures, meteorites, Big Gulps? Global warming.

Last year I documented how researchers made up a map showing how vegetation could change in the arctic because of global warming.

The map, no lie, was called the “most accurate map” ever produced of its type.

A long last, scientists have revealed the single most important document ever, I wrote.It’s a crayon-colored map showing how “trees” could grow in the arctic.

If finally, mercifully, any one of the so-called “climate models” that so far have failed to “model” climate accurately, suddenly and then accurately begin to “model” climate in real time, then, well, WOW!

“Experts say the wooded areas in the region could increase by 50% over the coming decades,” writes the UK’s Daily Mail, “and accelerate global warming in the process. Researchers have unveiled the most accurate map ever (!) of how vegetation could change in the region.”

In the meantime,ThinkProgresshas published a remarkable paper calledArctic Sea Ice Death Spiral And Cold Weatherthat proves, or at least,says- same thing if you are a liberal - that globalwarmingis to blame for …coldweather in Germany.

Stumped by the fact that temperatures are not accurately reflecting current climate “models”- in fact temperatures have remained stable for 17 years- scientists on the government gravy train are trying to tie any weather event to so-called climate change.

Even homosexuality has been tied to global warming via population control.

“With the natural world on the brink of demise largely because of overpopulation,” G. Roger Denson, a self-appointed social theoretician wrote on the Huffington Post,“unrestrained homosexuality, as one of a variety of ethical and democratic measures available to us today, offers perhaps the most natural option to be enjoined.”

Unrestrained gayness? Seriously?

Going in through the out door with another man doesn’t seem “the most natural option to be enjoined” in trying to cool down the earth’s atmosphere.  But in the interest of fairness if G. Roger Denson wants to produce an actual scientific paper proving me wrong, I got a can of dog food and clipping shears here waiting.

Because one would suppose that in policies promoted by properly-thinking, modern progressives-- who worship all things science— and have no time for mumbo jumbo about faith and religion, that at the very least they’d have data to support that their policies will cool the earth, solve world hunger, bring people out of poverty, improve education, create income equality, or pay female White House staffers commensurate with men.

OK, the last one was outrageous. Never gonna happen under Obama.

What was I thinking? At the very least, I was thinking that people like Ericynot, BoatBoy, DoctorRoy or Hillinger would enjoy me being bald and eating dog food.  Heck, I’d even make a video of it.

But the problem remains: Sea levels aren’t rising, storms aren’t nastier and more brutish. The only science that’s being done is the type where estimates are used where data is called for and predictions are being used instead of conclusions.

Stumped by the fact that temperatures are not accurately reflecting current climate “models”- in fact temperatures have remained stable for 17 years- scientists on the government gravy train are trying to tie any weather event to so-called climate change.

Or income inequality. Which really?Aren’t they the same things?
Hurricanes? Global warming.
Tornadoes? Global warming?
Drought? Global warming?
Blizzards, dropping temperatures, meteorites, Big Gulps? Global warming.

Last year I documented how researchers made up a map showing how vegetation could change in the arctic because of global warming.

The map, no lie, was called the “most accurate map” ever produced of its type.
A long last, scientists have revealed the single most important document ever, I wrote.It’s a crayon-colored map showing how “trees” could grow in the arctic.

If finally, mercifully, any one of the so-called “climate models” that so far have failed to “model” climate accurately, suddenly and then accurately begin to “model” climate in real time, then, well, WOW!

“Experts say the wooded areas in the region could increase by 50% over the coming decades,” writes the UK’s Daily Mail, “and accelerate global warming in the process. Researchers have unveiled the most accurate map ever (!) of how vegetation could change in the region.”

In the meantime,ThinkProgresshas published a remarkable paper calledArctic Sea Ice Death Spiral And Cold Weatherthat proves, or at least,says- same thing if you are a liberal - that globalwarmingis to blame for …coldweather in Germany.

Stumped by the fact that temperatures are not accurately reflecting current climate “models”- in fact temperatures have remained stable for 17 years- scientists on the government gravy train are trying to tie any weather event to so-called climate change.

Even homosexuality has been tied to global warming via population control.

“With the natural world on the brink of demise largely because of overpopulation,” G. Roger Denson, a self-appointed social theoretician wrote on the Huffington Post,“unrestrained homosexuality, as one of a variety of ethical and democratic measures available to us today, offers perhaps the most natural option to be enjoined.”

Unrestrained gayness? Seriously?

Going in through the out door with another man doesn’t seem “the most natural option to be enjoined” in trying to cool down the earth’s atmosphere. But in the interest of fairness if G. Roger Denson wants to produce an actual scientific paper proving me wrong, I got a can of dog food and clipping shears here waiting.

Reasonable Gun Control That Follows 2n'd Amendment Possible

I wrote this piece during an exhaustingly long argument with gun owners, attempting to show I am not against gun ownership, but it is possible to have it while protecting 2n'd Amendment rights.  As they declared the issue "black and white" and admitted to refuse to listen to anything from the other side (and man, did they ever prove it), I thought I'd post it and see what people who do listen and reason think about it.

Any gun control measures should be on the states, not the federal government (except where needed, like border defense and the flow of guns between states.  Perhaps gun owners in a state should be made to be part of a well-regulated militia, provided of course they pass all background checks.  Imports of guns should be strictly regulated.  No more than one gun per citizen (unless you are a collector, a shooting range, or can prove a need otherwise), and the owners should be licensed (with periodic renewals), their weapon registered and regularly inspected by the state, and they should pay insurance just like car owners(given that only one out of thousands of guns is involved in personal injury, the premium shouldn't be very high).  Furthermore, if someone's gun is used in a crime, accidental wounding, or suicide attempt) the owner too should be prosecuted, fined, and have their license suspended for a period of time.  You own a gun, you are responsible for what happens with it.

Another roles the feds could play is to provides incentives and disincentives for states to provide for such regulation.

Does this sound reasonable or not?  It's certainly is consistent with the 2n'd Amendment, all of it, matches the Founding Fathers' ideas, allows for self-defense by firearm, and if that "last resort" should come, make private gun owners a much more effective fighting force.  And firearms deaths would have to drop more, I believe.

Atheists Face Discrimination in the U.S.

November 16, 2009

Atheists are one of the most despised minorities in the U.S., and anti-atheist bigotry is both widespread and socially acceptable in many areas. When we consider the fact that many religious believers have convinced themselves that our refusal to share their beliefs makes us inherently immoral, it is not surprising that they condemn us. Some go so far as to claim that we are less than fully human, reducing the prohibitions against inflicting harm on us that might normally be in place.

One response I have routinely encountered from Christians, and even a few atheists, is that negative attitudes aside, atheists are not actually discriminated against. Ah denial, is there nothing you can't do?

What is Discrimination?

Discrimination is not the same thing as being treated unfairly. In the legal context in which discrimination is most relevant, it can be defined broadly as unequal treatment for a reason other than ability or legal rights. More precise definitions and tests of discrimination are dependent on the context. Thus, employment discrimination may work a bit differently than discrimination involving educational opportunity. Still, we can abstract some general principles from U.S. law. Federal (and state) laws prohibit discrimination in areas such as employment, housing, voting rights, educational opportunity, and civil rights on the basis of race, age, sex, nationality, disability, and religion.

Both Title VII of the Civil Rights Act of 1964 and the Fair Housing Act of 1968 explicitly prohibit discrimination on the basis of religion and the other factors noted above. That is, it is unlawful to discriminate against someone (i.e., to treat them unequally in certain specified matters) on the basis of their religious beliefs (or lack thereof).

Examples of Discrimination Against Atheists

What follows is by no means intended to be an exhaustive list. I intend only to provide a handful of notable examples which can be used to educate those arguing that there atheists in the U.S. do not face any sort of discrimination on the basis of their atheism.

• Some judges consider atheism to be a sufficient reason for denying custody to a parent during custody hearings.
• Many private organizations, such as the Boy Scouts of America, deny membership solely on the basis of lack of god-belief. Some of these organizations also manage to receive public funding.
• Atheists face many forms of employment discrimination, ranging from differential hiring practices to wrongful termination. A school district in Texas went so far as to refuse to do business with an atheist.
• In addition to widespread anti-atheist bigotry in the U.S. military, there are reports of institutionalized discrimination designed to quash complaints made by atheists who dare to speak out.
• A handful of states retain laws to prevent atheists from being permitted to hold public office in clear violation of the U.S. Constitution.
• The mainstream media in the U.S. regularly excludes atheists, even from stories about atheism, while giving voice to religious believers.

A survey of atheist and other freethought groups completed by Margaret Downey in 2000 reveled that the overwhelming majority of instances of discrimination against atheists are never reported. Why? According to Downey,

...the fear of suffering further discrimination as a “whistleblower” was widespread. Some victims told me that they did not want to go public lest still more hatred come their way. This is the trauma of discrimination, just the sort of intimidation that discourages discrimination reports and makes it difficult to find plaintiffs for needed litigation.

We can all find examples of discrimination against atheists on their basis of their lack of god-belief. We should also be able to understand why there are not many more examples in the public record.

Read more: http://www.atheistrev.com/2009/11/atheists-face-discrimination-in-us.html#ixzz2qy6sVnkT

A New Method to Measure Consciousness Proposed: Scientific American

A New Method to Measure Consciousness Proposed: Scientific American

A New Method to Measure Consciousness Proposed

It's an important new tool for doctors, but what is it actually measuring?

By Partha Mitra

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Can consciousness be measured? Image: iStock/akarelias

 

Leonardo Da Vinci, in his Treatise on Painting (Trattato della Pittura), advises painters to pay particular attention to the motions of the mind, moti mentali. “The movement which is depicted must be appropriate to the mental state of the figure,” he advises; otherwise the figure will be considered twice dead: “dead because it is a depiction, and dead yet again in not exhibiting motion either of the mind or of the body.” Francesco Melzi, student and friend to Da Vinci, compiled the Treatise posthumously from fragmented notes left to him. The vivid portrayal of emotions in the paintings from Leonardo’s school shows that his students learned to read the moti mentali of their subjects in exquisite detail.

Associating an emotional expression of the face with a “motion of the mind” was an astonishing insight by Da Vinci and a surprisingly modern metaphor. Today we correlate specific patterns of electrochemical dynamics (i.e. “motions”) of the central nervous system, with emotional feelings.
Consciousness, the substrate for any emotional feeling, is itself a “motion of the mind,” an ephemeral state characterized by certain dynamical patterns of electrical activity. Even if all the neurons, their constituent parts and neuronal circuitry remained structurally the same, a change in the dynamics can mean the difference between consciousness and unconsciousness. 

But what kind of motion is it? What are the patterns of electrical activity that correspond to our subjective state of being conscious, and why?  Can they be measured and quantified? This is not only a theoretical or philosophical question but also one that is of vital interest to the anesthesiologist trying to regulate the level of consciousness during surgery, or for the neurologist trying to differentiate between different states of consciousness following brain trauma.

Recently, Casali et al have presented a quantitative metric. It provides, according to the authors, a numerical measure of consciousness, separating vegetative states from minimally conscious states. The study provides hints of being able to identify the enigmatic locked-in state, in which the subject is conscious but is unable to communicate with the external world due to motor deficits. What is most interesting is the claim that the measures provide scientific insight into consciousness, by providing an objective measure.

Their metric, like other existing clinical measures of consciousness, is based on Electroencephalography (EEG), where voltages recorded from electrodes placed on the scalp provide a coarse picture of neural activity in the brain. EEG can be used to measure either ongoing brain activity, or that evoked by an external stimulus. In Casali’s case, the activity in question is evoked directly in the brain using a transient magnetic field (Transcranial Magnetic Stimulation). This involves applying a transient magnetic field, which generates an electric field in a particular region of the brain due to Faraday’s law, a bit like attaching a battery to the neural circuitry. This causes currents to flow in the brain, not just in the stimulated region, but in other regions connected to it as well. The spatial and temporal patterns of these currents in the brain are then inferred from the EEG measurements and quantified to produce the metric.

The novelty in the study lies in the method used to quantify the spatiotemporal distribution of current, which is also the basis of the theoretical claims. The idea is that when the brain is unconscious, the evoked activity is either localized (the authors call this “lack of integration”), or widespread and uniform, as might be expected during slow wave sleep or epileptic seizures (“lack of differentiation”). The conscious state on the other hand is supposed to correspond to a distributed, but non-uniform spatiotemporal pattern of current sources. The authors apply a standard data compression scheme (the Lempel-Ziv algorithm, which is used for example in the GIF image format) to distinguish between the two scenarios. The degree of compressibility of the current distribution as inferred from EEG is the consciousness metric they propose.

The scientists report that their measure performs impressively in distinguishing states of consciousness within subjects, as well as across subjects in different clinically identified consciousness stages.  These promising results will no doubt attract further study. However, the claim that the measure is theoretically grounded in a conceptual understanding of consciousness deserves a closer look. It is tempting to think that a concretely grounded clinical study of consciousness naturally advances our scientific understanding of the phenomenon, but is this necessarily the case?

It is common in medicine to see engineering-style associative measurements, measurements which aid pragmatic actions but do not originate from a fundamental understanding. Physicians in antiquity were able to diagnose diabetes mellitus (etymologically “sweet urine”, a reference to this original diagnostic method), without any particular insights into the underlying pathology. Clinical utility is not automatically a guarantee of scientific understanding.

There is reason to be cautious even in clinical terms. Some previous attempts to numerically quantify consciousness have proven problematic, a serious matter since awareness during surgery could lead to real suffering. An anesthesiologist cautions in a commentary not to “trust the BIS or any other monitor over common sense and experience.”  A human expert still remains the ultimate arbiter of the state of consciousness of another human.  This is unlikely to change soon.

There are both practical and conceptual hurdles to developing a “consciousness metric.”  In practical terms, we have very little access to the details of the neuronal dynamics in the human brain. DARPA, not shy of ambitious technical challenges, has limited itself to 200 electrodes in a recent call for proposals to directly record from and stimulate the human brain for deep brain stimulation therapy. That is about one billionth of the estimated number of neurons in the brain. The EEG provides a very low capacity, indirect measurement channel into the brain. If we can’t measure the dynamics of the brain neurons in any detail, this could limit any attempt to quantify consciousness.

However, it is theoretically possible that even a limited measurement channel could carry the necessary information. We are looking for a categorical judgment between conscious and unconscious states, a single bit of information that can be solicited from a conscious and communicative subject in an eye-blink or a nod of the head. The conceptual hurdle is the more significant one. The defining characteristic of the conscious state is that of subjective, first person awareness, which fundamentally militates against objective measurements by an independent observer, who can have no access to the primary phenomena except through the subjective report of the conscious individual. It may be possible (and useful) to obtain better and better correlative measurements of this subjective report; but do the measurements themselves shed any light into the phenomenon of consciousness?

To clarify the underlying issues, consider a Turing-like test for consciousness metrics. If a measure of consciousness is to have scientific status, it should not ascribe a high degree of consciousness to a passive, inanimate system at thermodynamic equilibrium. Otherwise we are left with some kind of pan-psychic notion of consciousness. Nevertheless, a simple thought experiment shows that it would be easy to construct such a system for the metric under discussion.

The measure in question relies on the spatiotemporal patterns of currents invoked by a transient magnetic field. However, Maxwell’s equations dictate that a transient magnetic field will generate a pattern of currents in any chunk of matter – matching up some distribution of those evoked currents is simply a matter of the material properties. Consider for example a network of resistor, capacitors and inductors with circuit time-constants tuned to be in the hundred-millisecond range (to match EEG timescales). A radio antenna could be used to detect the changing magnetic field and absorb its energy. It should not be difficult to produce a circuit arrangement that produces a transient, spatiotemporally non-uniform current distribution that is adequately incompressible, and therefore fools the device into producing a high consciousness score.

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One could also ask if the metric helps us answer a basic evolutionary question: can it differentiate organisms into “conscious” and “non-conscious” categories? While most neuroscientists would not hesitate to ascribe consciousness to vertebrate animals or to invertebrates with complex brains (think Octopus or Honeybee), they would hesitate when it comes to the invertebrates with simpler nervous systems (Are Jellyfish conscious? How about the Sponges?) Since the methodology under discussion has been prepared with humans in mind, and ultimately depends on correlating with subjective reporting, it is difficult to see how it could be extended across the phylogenetic tree in a way that would help resolve these basic science questions about consciousness.

Where to look for measures of consciousness that advance our scientific understanding? Most neuroscientists would agree that consciousness is associated specifically with animal nervous systems (not trees or rocks). Rather than look generically for abstract mathematical descriptions of consciousness, we may need to specifically study the detailed architecture of brain systems involved in arousal, attention, and so on. Complex animal nervous systems have presumably evolved consciousness because it has some important utility. If the architecture of brain systems involved in arousal shows convergent evolution between invertebrates and vertebrates, this could give us important scientific insights into consciousness as a biological phenomenon. Better neurobiological insights into consciousness could in turn generate advances in clinical measures.

We have come a long way since Da Vinci, but human observers, in the form of teams of expert physicians, remain essential to judging the subtleties of the “motions of the mind” that we call consciousness. No matter how sophisticated our tools, consciousness is still a core mystery with ample scope for conceptual breakthroughs and creative thinking.

Are you a scientist who specializes in neuroscience, cognitive science, or psychology? And have you read a recent peer-reviewed paper that you would like to write about? Please send suggestions to Mind Matters editor Gareth Cook, a Pulitzer prize-winning journalist and regular contributor to NewYorker.com. Gareth is also the series editor of Best American Infographics, and can be reached at garethideas AT gmail.com or Twitter @garethideas.

ABOUT THE AUTHOR(S)

Partha Mitra is Crick-Clay Professor at Cold Spring Harbor Laboratory. He obtained a PhD in Theoretical Physics at Harvard and was a member of the Theory Group at Bell Laboratories. He has written a book on analyzing brain dynamics and is currently engaged in mapping mouse brain circuits. You can follow him @partha_mitra

String Theory: A Cosmic Concerto

Posted on January 19, 2014 at 5:00 pm

By Joshua Carter

             

Image Credit: Vlad Studios

Imagine you are sitting in a big symphony hall, listening to an orchestra play, for the first time. You’ve never been to see a live orchestra, but you decided to go anyway. There’s a first time for everything, right? The orchestra is performing a Violin Concerto by Beethoven. As the soloist runs her hands and fingers along the neck of the violin, she produces different notes or pitches. Every note the violin produces has a different sound, pitch, and vibration. With each note comes a different possible direction for the music being created. This concept can be applied to quantum physics as well, within string theory.

QUANTUM BASICS:

As you may know, everything is made up of small particles. Matter is made from atoms, which are in turn made of three basic components: electrons, neutrons, and protons. The electron is fundamental, but neutrons and protons are made of even smaller particles, known as quarks. Quarks are, as far as we know, truly elementary.

What we know about the subatomic composition of the universe is known as the Standard Model of Particle Physics. It describes the fundamental building blocks out of which the world is made, and the forces through which these blocks interact. There are twelve basic building blocks. Six of these building blacks are quarks. They go by the names: up, down, charm, strange, bottom and top. (A proton, for instance, is made of two up quarks and one down quark.) The other six are leptons. These include the electron and its two heavier siblings, the muon and the tauon, as well as three neutrinos.

Within the universe there are four fundamental forces: gravity, electromagnetism, and weak and strong nuclear forces. Each of these four forces is produced by particles that act as carries of the force. The behavior of all of these particles and forces is described by the Standard Model, with one notable exception: gravity.

STRING THEORY:

In the past ten years, string theory has emerged as the most promising candidate for a quantum explanation for gravity. But there is more to string theory than just explaining gravity on a molecular level; string theory is, essentially, the theory of everything.

Image Credit: Ench Gallery

The idea behind string theory is that each fundamental particle in the Standard Model is made up of tiny strings. These strings manifest in different ways to produce the different particles that we observe. For example, if a string ‘loops’ up a certain way, it will produce a photon. If it loops up another way it will form a neutrino. Another way, a quark… so on and so on. So, if string theory is correct, the entire universe is made up of strings. And to make it even more complicated and mind boggling, string theory works in ten dimensions!

MULTIPLE DIMENSIONS:

In one theory called M-theory, there are eleven dimensions rather than the three space-time dimensions we are used to and can perceive. The original version of string theories from the 1980s stated that the eleventh dimension would be a very small circle or a line. If these formulations are fundamental, then string theory requires ten dimensions. The idea of space-time dimension is not fixed in string theory; it is best thought of as different in different circumstances (Polchinski 1998).

Image Credit: Jean-Francis Colonna

MULTIPLE UNIVERSES:

Now, this is where things get really interesting. Like I said, each string can oscillate in different ways to form different particles. If you relate what I’ve already said to the violinist, you can get a simplified version of string theory that is easy to explain and comprehend. Just like the different notes on a violin, each different vibration of the string is a different fundamental particle. You play one note and you get a quark. A different note and you get a photon. So, every different note is a different possible particle. And every different chord and harmony within the music, is a different outcome. By different outcomes, I am talking about different universes. If string theory is correct and every different vibration of the string produces a different ‘something,’ then there should be hundreds of billions of different universes. Maybe even more universes than there are stars in the known universe.

A COSMIC CONCERTO:

Now, let’s return to the idea that the strings of string theory are like the notes played by our violinist. Each vibration of the strings creates the fundamental particles and to the forces of nature, which make up everything in the universe. Just as the orchestra and violinist are playing Beethoven, they could just as well be playing a different piece of music, with different notes and different vibrations.
Mathematically, that different piece of music, would produce different notes or vibrations, which would, in turn, create different particles and different forces of nature… meaning, a different universe. So, just as there are an endless number of possible pieces of music the orchestra could play, so our universe must be one of billions of other universes.

Image Credit: Stephen Hawking’s Grand Design/Discovery Channel

We can’t see these different strings because they are outside of our own universe. They have a different history and background than the strings in our universe. Some universes are unstable and collapse back to where they came from, a big crunch. Others, may not produce gravity, and would never be able to produce stars and would be dark and cold. Others will go on to produce stars, galaxies and planets, just like our universe.

According to Stephen Hawking, “we should not be surprised to find ourselves in a universe that is perfect for us. Our very presence means our universe must be just right” (Stephen Hawking’s Grand Design 2010).   If string theory is correct, there may be a universe in which someone, exactly like you, decided not to go see the orchestra play. So, they would never be able to relate string theory to the beautiful music that you heard.

So, the next time you listen to a piece of music, regardless of the genre, try to think outside the box, or in this case, outside the universal box.