söndagen den 18:e november 2012

Nature, nurture and natural selection. Epigenetic memory.

Nowhere has the debate about nature and nurture been so controversial as in the study of mental ability in humans. IQ is a phenotypic measurement of relative performance on a series of mental ability tests. Our immune system is a sort of loose brain, in that most immune cells float free in our body, while our brain's neurons function within a highly interconnected web. Both systems are functionally similar.

As Jean Piaget used to say, intelligence is what you use when you don’t know what to do, when all the standard answers are inadequate.  To be smart is another thing. It is about making the right choises. We can subconsciously try out variations, using many brain regions. Eventually, as quality improves, we become conscious of our new invention. 

This is when we become aware of our intentions and thoughts? As examle mathematics? The Libet readiness potential?

 

Brain developement and nature - nurture effect.
Heritability patterns of IQ for young, preschool individuals are generally more to the nurture factors than for elder humans. How is this tested when we know that the developement of the nerves and theit net formations in the brain is very much depending on the nurture effects? Twins have been used in the majority of studies to estimate the heritability of IQ, both monozygote and dizygote twins.  MZ twins are substantially more similar in IQ than DZ twins, whether they are raised together or apart. Reported estimates of heritability for IQ from twin studies are remarkably consistent in the range of 0.5–0.8, across many age groups. Studies with adults show that they have a higher heritability of IQ than children do and that heritability could be as high as 0.8. Here can you also test your IQ.

Gerald Edelman won the Nobel Prize in 1972 for his discovery that the immune system doesn't operate through an instruction/memory model, as had been thought, but rather through evolutionary natural selection procedures. He found, rather, that through natural selection processes occurring over eons of time, we are born with a vast number of specific antibodies that each recognize and respond to a specific type of harmful invader that shares our environment. If we lack such a natural immunity to a specific invader (such as the AIDS virus), we may die if infected. Our immune system can't learn how to destroy the invader; it simply has or hasn't the capacity at birth. Edelman then studied our functionally similar brain to see whether it also operates principally on natural selection, rather than on instruction and learning. His controversial theory, Neural Darwinism, (here a review) argues that our brain does operate on the basis of natural selection—or at least that natural selection is the process that explains instruction and learning. Neuronal selection is another term with good results.

The powerful role that emotion plays in regulating brain activity, and the preponderance of parallel (rather than linear) processing in our brain, points to a biological model, not technological.

Edelmann proposes that the electrochemical dynamics of our brain's development and operation resemble the rich, layered ecology of a jungle environment. A jungle has no external developer, no predetermined goals. Indeed, it's a messy place characterized more by organic excess than by goal-directed economy and efficiency. No one organism or group runs the jungle. All plants and animals participate in the process, each carrying out a variety of ecological functions. The jungle environment doesn't instruct organisms how to behave, for example, by teaching trees how to position their limbs and roots to get sunlight and soil nutrients. Evolution works by selection, not instruction. The environment selects from among the built-in options available—it doesn't modify (instruct) the competing organisms. (No homunculus is there?) An infant brain doesn't have to learn how to recognize specific sounds and line segments; such basic neural networks are operational at birth. We don't teach a child to walk or talk; we simply provide opportunities for adaptations to an already operational process. Gazzaniga (1992) argues that all we do in life is discover what's already built into our brain. What we see as learning is actually a search through our brain's existing library of operating networks for the combinations of those that best allow us to respond to the immediate challenge; our DNA couldn't possibly encode our brain's networks for every possible combination of sights/sounds/smells/textures/tastes/movements that our brain can process. Instead, it encodes a basic developmental program that regulates how neurons will differentiate and interconnect.

The homunculus-theory has been a big obstacle in biology.He has unconscious thoughts, here discussed by Fracis Crich and Christof Koch, 2000.

Many has thought of the nurture side as being dominant, but these new theories argue that nature plays a  more important role than previously believed. They also suggest that many current beliefs about instruction, learning, and memory are wrong. The theories will become culturally controversial because they will require reconceptualizations of such concepts as parenting, teaching, learning, identity, free will, and human potential. Further, some people may misuse the theories to support racist, sexist, and elitist beliefs. Certainly those who reject Darwinian evolution will be disturbed by the evolutionary base of the new theories.

Fernando et al. suggests a neuronal basis for causal inference, function copying, and natural selection within the human brain. To date, no model of neuronal topology copying exists. We present three increasingly sophisticated mechanisms to demonstrate how topographic map formation coupled with Spike-Time Dependent Plasticity (STDP) can copy neuronal topology motifs.  A unit of selection is an entity that can replicate, and have hereditary variation. If these units have differential fitness they can evolve by natural selection.
Both Edelman and Changeux's groups have produced an impressive range of detailed models of hill-climbing type (exploration and exploitation) algorithms that can explain a wide range of behavioural and cognitive phenomena at various levels of abstraction [16]; such as category formation [12], reinforcement learning using spike-time dependent plasticity modulated by dopamine reward [17], visual-motor control in a robotic brain-based device [18], temporal sequence learning [19], effortful cognition in the Stroop task [20], and planning [21]. Importantly, both these research programs avoid the need for replication of neuronal groups, i.e. none of their algorithms require units of selection. The algorithms of Edelman and Changeux fundamentally consist of a population of stochastic hill-climbers [25]. Each neuronal group is randomly initialized, and those groups that are closest to a good solution obtain a greater quantity of synaptic resources allowing them to ‘grow’ and/or ‘change’. 

The heritability of IQ , (here wikipedia), investigates the relative importance of genetics and environment for phenotypic variation in intelligence quotient (IQ) in a population. If there is biological inheritance, heredity, of IQ, then the relatives of a person with a high IQ should exhibit a comparably high IQ with a much higher probability than the general population.

In biology, and specifically genetics, epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence.
This is why the differentiated cells in a multi-cellular organism express only the genes that are necessary for their own activity. Epigenetic changes are preserved when cells divide, but usually (?) not into the germline, which is conserved, sheltered, and divide very slowly (in off-state).

Several neurophysiological factors have been correlated with intelligence in humans, including the ratio of brain weight to body weight and the size, shape and activity level of different parts of the brain. Specific features that may affect IQ include the size and shape of the frontal lobes, the amount of blood and chemical activity in the frontal lobes, the total amount of gray matter in the brain, the overall thickness of the cortex and the glucose metabolic rate.

IQ is a polygenic trait (50 genes?) under normal circumstances according to recent research. However, certain single gene genetic disorders can severely affect intelligence, with phenylketonuria as an example. The example of phenylketonuria (PKU) is informative. Untreated, this is a completely penetrant genetic disorder causing brain damage and progressive mental retardation. PKU can be treated by the elimination of phenylalanine from the diet. Hence, a character (PKU) that used to have a virtually perfect heritability is not heritable any more if modern medicine is available (the actual allele causing PKU would still be inherited, but the phenotype PKU would not be expressed anymore).

Various studies have as instance found the heritability of IQ to be between 0.7 and 0.8 in adults and 0.45 in childhood in US.

Governments have implemented several health policies regarding nutrients and toxins known to influence cognitive function, as laws requiring fortification of certain food products and laws establishing safe levels of pollutants (e.g. lead, mercury, and organochlorides). Improvements in nutrition, and in public policy in general, have been implicated in worldwide IQ increases.

This new field of epigenetics means that a lot of the traditional assumptions in the field of genetic engineering are dangerously wrong. For example, the assumption that it is only the sequence of codons that create certain behaviours or attributes. It is not only the sequence but how that sequence interacts with other sequences which determines it's function - that means that a lot of the richness of expression is being completely stultified when they simply worry about the basic sequence, as they do in genetic modification.

Matt Ridley blog: In other words, hygienic, well-fed life enables people to maximize their genetic potential so that the only variation left is innate. Intelligence becomes significantly more heritable when environmental hurdles to a child's development have been dismantled. 
An objection to this is that in the well-fed conditions there are lots of diseases, so stress is obviously also a shelter for us. This is seen as instance in the cancer research on chaperones, or stress-proteins, also on kinases and regulation.

The American Psychological Association's report "Intelligence: Knowns and Unknowns" (1995) states that "there is no doubt that normal child development requires a certain minimum level of responsible care. Here, environment is playing a role in what is believed to be fully genetic (intelligence) but it was found that severely deprived, neglectful, or abusive environments have highly negative effects on many aspects of children's intellect development.  Regarding sex differences so have most standard tests of intelligence been constructed to show equal results, but some studies show small differences. Males do better on visual-spatial tasks, with a particularly large difference on mental rotation (nearly 1 SD), which is significant for their generally better performance in tasks that involve aiming and throwing. Males also do relatively better on on tests of proportional and mechanical reasoning as well as on mathematics. Females do better on verbal tests and some memory tests. They do relatively better in tests of literature, English composition, Spanish, reading, and spelling. More males have dyslexia and stuttering. Possible causes include gender roles and differences in brain structure which in turn may be due genetics and/or environment. Differences in sex hormones may be another explanation. Female exposure to high levels of male hormones in utero is associated with higher spatial abilities as well as more spatial ability as well as more play with "boys' toys" and less with 'girls' toys". Males with higher testosterone levels do better on visuo-spatial abilities and worse on verbal abilities. Older males given testosterone score better on visuo-spatial tests."

I almost never played with dolls nor 'girl toys'. More about gender differencies here.
  • HEREDITY refers to traits passing on from parent to offspring.
  • HERITABILITY refers to the proportion/percentage of VARIABILITY that can be attributed to genetic differences. Please note that this does not mean that that same proportion of the trait is attributed to Genetics. 
Note: Cognition, thinking, will, intention, consciousness are still open fundamental questions. Correlation studies are also just that, correlations. This maybe also shed some light also on the question what exactly is natural selection? Natural selection acts on the phenotypePhenotype is determined by an organism's genetic make-up (genotype) and the environment in which the organism lives.
A prerequisite for natural selection to result in adaptive evolution, novel traits and speciation, is the presence of heritable genetic variation that results in fitness differences. In the past, most changes in the genetic material were considered neutral or close to neutral because they occurred in noncoding DNA or resulted in a synonymous substitution. However, recent research suggests that many mutations in non-coding DNA do have slight deleterious effects.
But they can also give advantages! An example is intelligence and learning abilities?
 
Epigenetics is underlying the nurture effect. An example is how plants "remember" the length of the cold winter period in order to exquisitely time flowering so that pollination, development, seed dispersal and germination can all happen at the appropriate time. This requires an epigenetic longlasting 'memory', which explains how an organism can create a biological memory of some variable condition, such as quality of nutrition or temperature.They found that a key gene called 'Flowering Locus C' is either completely off or completely on in any one cell and also later in its progeny. They found that the longer the cold period, the higher the proportion of cells that have FLC stably flipped to the off position. This delays flowering and is down to a phenomenon known as epigenetic memory.
To provide experimental evidence to back up the model, the group used a technique where any cell that had the FLC gene switched on, showed up blue under a microscope. From  observations, it was clear that cells were either completely switched or not switched at all, in agreement with the theory.
They also showed that the histone proteins near the FLC gene were modified during the cold period, in such a way that would account for the switching off of the gene.
  • Andrew Angel, Jie Song, Caroline Dean, Martin Howard. A Polycomb-based switch underlying quantitative epigenetic memory. Nature, 2011; DOI: 10.1038/nature10241
The FTL gene was found in Arabidopsis research, one of the most extensively studied herbs. As instance here, Regulation of flowering in A. by an FTL homologue.
Reward sensory value-labelling, sleep connected to future expectations, etc. also requires some memory modulation.
 
Also stochastic resonance of different non-chemical forms? Stochastic resonance is a phenomenon that occurs in a threshold measurement system. This requires signals, and for plants light and carbon are signalling systems, also for animals the carbon signalling systems are real energetic entities, underlying the choise for the different molecular motors. See also the Negentropy Maximation Principle NMP in TGD.
The energy problem with too little available energy in biological ATP is maybe also partly solved?
See the short intro in earlier post.

söndagen den 11:e november 2012

Methyldynamics behind virtually all pathologies?

A remarkable growth in the understanding of epigenetics and the impact of epigenetics on contemporary biology has occurred in recent years. This growth in the field of epigenetics has transformed our conceptualization of the impact of the environment upon our genes and upon our health. The nature and nurture relation is essential for function. Epigenetic modifications shape behavior, modulate stress responsivity, and alter immune function. This facet of epigenetics seeks to understand the interactive linkages that connect the psychological and social environment with the epigenetic processes that modulate gene expression and influence behavior. In a similar manner, the integrative field of psychoneuroimmunology continues to advance the understanding of the complex networks that connect brain, behavior and immunity. Stressors and/or adverse psychosocial environments can affect gene expression by altering the epigenetic patterns. The emphasis on genome itself is no longer particularly important. The dynamic modulations behind gene function are more interesting.

The Human Epigenome Project:  Methylation is the only flexible genomic parameter that can change genome function under exogenous influence. Hence it constitutes the main and so far missing link between genetics, disease and the environment that is widely thought to play a decisive role in the aetiology of virtually all human pathologies.

DNA expression is regulated by acetylation and deacetylation as a compression - expansion of the DNA chromatine. Also epigenetic factors are important for both  1) histone modulation and 2) arginine-lysine changes of DNA expansion (activation) /compression (inhibition), 3) and/or ncRNA expression. Both NO (from arginine) and histone deacetylase activity (HDAC; see next post) regulate gene expressions and the direction of other cellular processes. The biological influences achieved by various histone and DNA modifying enzymes eventually require that histone and DNA be modified in a highly dynamic way. Epigenetic modifications can be modulated by directly inhibiting modifying enzymes or blocking co-factor recruiting pathways, as instance. The best characterized 'erasers' are the histone deacetylases (HDACs). For a review of HDACs see (De Ruijter et al., 2003), but they are found for all categorizations of modulations.


DNA associates with histone proteins to form chromatin. From Wikipedia, epigenetics. A better figure is here.  A ribbon diagram of a nucleosome with central histones, their amino terminal tails, with DNA wrapped about the exterior surface. + short video of the DNA compression.

Epigenetics and Psychoneuroimmunology: Mechanisms and Models Mathews and Janusek 2010

In vertebrates, approximately 2 meters of DNA are contained within each cell and this DNA is packaged into chromatin in a manner that permits transcription of some loci and suppression of other loci. The basic unit of chromatin is the nucleosome, which is comprised of four core histones (H2A, H2B, H3, H4, two of each) around which 146 base pairs of DNA are wrapped.  The core histones are predominantly globular except for their amino terminal “tails,” which are unstructured. A striking feature of histones, and particularly of their tails, is the large number and types of amino acid residues that can be modified. These distinct types of modification include; acetylation, methylation, phosphorylation, ubiquitylation, sumoylation, deimination and proline isomerization (Kouzarides, 2007). Histones modification has been detected at over sixty different amino acid residues, but with extra complexity resulting from methylation at lysine or arginine residues that may be of three forms: mono-, di-, or trimethyl for lysines and mono- or di- (asymmetric or symmetric) for arginine. This vast array of modifications provide for enormous modification of functional responsivity.

The "epigenome" refers to the overall epigenetic state of a cell.  Epigenetic changes are preserved when cells divide, but mostly within one individual organism's lifetime, but, if gene disactivation occurs in a sperm or egg cell that results in fertilization, then some epigenetic changes can be transferred to the next generation. This raises the question of whether or not epigenetic changes in an organism can alter the basic structure of its DNA, a form of Lamarckism. This was in fact how the inherited epigenetic mechanism was detected by swedish scientists not so long ago. Diabetics and starvation as instance had herited effects, see the Överkalix study with Marcus Pembrey and colleagues.

The "epigenetic code"
could represent the total state of the cell; relevant forms of epigenetic information such as the histone code or direct DNA methylation patterns, or RNA modifications. The way that the cells stay differentiated in the case of DNA methylation is clearer to us than it is in the case of histone shape.

One  thinking is that this tendency of acetylation is associated with "active" transcription as biophysical nature. Because it normally has a positively charged nitrogen at its end, lysine can bind the negatively charged phosphates of the DNA backbone. The acetylation event converts the positively charged amine group on the side chain into a neutral amide linkage. This removes the positive charge, thus loosening the DNA from the histone. This is the "cis" model of epigenetic function. There is also a 'trans' function.
 
Although histone modifications occur throughout the entire sequence, the unstructured N-termini of histones (called histone tails) are particularly highly modified. These modifications include acetylation, methylation, ubiquitylation, phosphorylation and sumoylation. Acetylation is the most highly studied of these modifications.

Differing histone modifications are likely to function in differing ways; acetylation at one position is likely to function differently than acetylation at another position. Also, multiple modifications may occur at the same time, and these modifications may work together to change the behavior of the nucleosome. The idea that multiple dynamic modifications regulate gene transcription in a systematic and reproducible way is called the histone code

There are several layers of regulation of gene expression. One way that genes are regulated is through the remodeling of chromatin. If the way that DNA is wrapped around the histones changes, gene expression can change as well. Chromatin remodeling is accomplished through two main mechanisms:
  1. The first way is post translational modification of the amino acids that make up histone proteins, long chains of amino acids, and if they are changed, the shape of the histone sphere might be modified. DNA is not completely unwound during replication. It is possible, then, that the modified histones may be carried into each new copy of the DNA. Once there, these histones may act as templates, initiating the surrounding new histones to be shaped in the new manner. By altering the shape of the histones around it, these modified histones would ensure that a differentiated cell would stay differentiated, and not convert back into being a stem cell.
  2. The second way is the addition of methyl groups to the DNA, mostly at CpG sites, to convert cytosine to 5-methylcytosine. 5-Methylcytosine performs much like a regular cytosine, pairing up with a guanine. However, some areas of the genome are methylated more heavily than others, and highly methylated areas tend to be less transcriptionally active, through a mechanism not fully understood. Methylation of cytosines can also persist from the germ line of one of the parents into the zygote, marking the chromosome as being inherited from this parent (genetic imprinting). Certain enzymes  have a higher affinity for the methylated cytosine, and induce then more methylation. Hypermethylation typically occurs at CpG islands in the promoter region and is associated with gene inactivation. Global hypomethylation has also been implicated
The RNA World, = before gene regulation.
There is an RNA component, possibly involved in epigenetic gene regulation. Small interfering RNAs can modulate transcriptional gene expression via epigenetic modulation of targeted promoters.
Other epigenetic changes are mediated by the production of different splice forms of RNA, alternative splicing, see below,  or by formation of double-stranded RNA (RNAi). Descendants of the cell in which the gene was turned on will inherit this activity, even if the original stimulus for gene-activation is no longer present. These genes are most often turned on or off by signal transduction, although in some systems where syncytia or gap junctions are important, RNA may spread directly to other cells or nuclei by diffusion.

Alternative splicing modulation of the pyruvate kinase M gene involves a choice between mutually exclusive exons 9 and 10, writes Wang et al in Manipulation of PK-M mutually exclusive alternative splicing by antisense oligonucleotides, 2012. One alternative is crucial for aerobic glycolysis (the Warburg effect) and tumour growth. Splicing enhancer elements that activate exon 10 are mainly found in exon 10 itself, and deleting or mutating these elements increases the inclusion of exon 9 in cancer cells. The 'antisensing of oligonucleotides'-mediated switch in alternative splicing leads to apoptosis in glioblastoma cell lines, and this is caused by the downregulation of PK-M2,not from another kinase. Note that this are changes in RNA:s only, not genes, so there are a very rich RNA regulating world that we are mostly unaware of yet.

Emotions are strong modulators.
This excerpt links the exon modulations and signalling events in cells induced by motherly care first week after birth.
The exact mechanism whereby maternal LG behavior (L=low) influences methylation of the GR promoter is currently unknown. Yet a series of studies implicate the involvement of the transcription factor, nerve growth factor-inducible protein A (NGFI-A), which functions to transcribe the gene that encodes for GR in the hippocampus. It is proposed that NGFI-A, couples with other transcription factors, cyclic-AMP response element binding protein (CREB) and specific protein 1 (SP-1), to bind to the GR 5’ untranslated promoter exon 17. The binding of this complex of proteins has been theorized to contribute to the reconfiguring of the methylation pattern of GR promoter exon 17. The timing is critical in that this re-configuration of methylation is dependent upon levels of maternal LG during the first postnatal week (Weaver et al., 2004; Weaver et al., 2007). Following birth there is rapid de novo methylation of GR exon 17, which is then demethylated over the course of the first postnatal week. It is this postnatal demethylation that is regulated by maternal LG behavior.
  • Other chapters in this remarcable study: 
  • Epigenetic Perpetuation of Behavior Across Generations 
  • Child Abuse, Suicide, and Epigenetic Modification 
  • Prenatal Depression, Epigenetics and Infant Stress Response 
  • Maternal Separation Stress, AVP, and Epigenetics 
  • Early Life Adversity and Epigenetic Modification of BDNF Expression = Brain derived neurotrophic factor 
  • Stress-Induced Depression Models and Epigenetic Modification of BDNF 
  • Epigenetic Mechanisms in Aging-Associated Memory Impairment 
  • Resilience to Stress-Induced Depression and Epigenetics 
  • Stressor Duration and Epigenetic Modification 
  • Post Traumatic Stress Disorder and Epigenetics 

From the study: It is clear that epigenetic modifications (e.g. those described above) serve as the molecular basis for environmental signals that influence behavioral outcomes and, as such, provide a bridge between the psychosocial world and the biological. This is congruent with psychoneuroimmunology, which seeks to understand the impact of environmental stimuli, especially psychosocial stimuli, on behavior, emotions, neuroendocrine stress responsivity, and immune function. There is no doubt that the genome of an individual provides the blueprint for biological responsivity. However, the epigenome adds another layer ‘on top of the genome’ and serves to modulate gene expression in response to environmental cues. It is likely that the interconnectivity among brain, behavior, and immunity may in fact be directed epigenetically. How, when and where the genetic blueprint will be used in response to a particular stimulus will be a summation of biological networks within the individual. This will include not just DNA recognition events or transcriptional circuits but also the instruction for the use of the blueprint, by epigenetic responsivity that regulates ordered or disordered gene expression patterns. Given the focus of psychoneuroimmunology, epigenetic approaches are particularly appealing and, most importantly, consistent with the concept that brain, behavior and immunity are intimately linked and responsive to environmental context. Intriguing and emerging evidence implicates epigenetic modifications as mediators of psychosocial-biological effects and makes analysis of epigenetics/epigenomics essential to understanding the interconnections among those systems that represent the core of pyschoneuroimmunology. These epigenetic effects have been demonstrated to be related to forms of histone modification, DNA methylation and/or ncRNA expression for a variety of immune based diseases including; systemic lupus erythematosus and rheumatoid arthritis (Martino and Prescott, 2010; Trenkmann et al., 2010) type 1 diabetes, celiac disease and idiopathic thrombocytopenia (Brooks et al., 2010), multiple sclerosis (Lincoln and Cook, 2009), as well as asthma and allergy (Martino and Prescott, 2010; Handel et al., 2010). There have been suggestions that psychosocial distress may contribute to either the exacerbation or development of these diseases. It is therefore plausible that psychosocial distress may impact the immune system by epigenetic processes. Evolving evidence suggests that epigenetic modification may contribute to major psychoses and depression (Feinberg, 2010; Janssen et al., 2010) or obesity (Handel et al., 2010). Not all genes may be responsive or susceptible to epigenetic modification. Much of DNA is inaccessible within a cell and may not be responsive to environmentally induced chromatin remodeling signals (Fraser and Bickmore, 2007). For example, Weaver et al. found that infusion of an HDAC inhibitor into the adult rat hippocampus altered expression of only about 2% of all genes normally expressed (Weaver et al., 2006). It is possible that a relatively restricted pool of adult genes may be dynamically responsive to environmental cues. Certainly, it is unlikely that all genes can be modified through environmentally induced epigenetic processes. Future investigations will be challenged to link epigenetic modifications to functional changes in the expression of specific genes and moreover, to relate these changes to physiological and/or psychological outcomes. It is such linkages that are essential to draw meaningful conclusions as to the biological and health-relevant significance of epigenetic modification. It is unclear whether the evaluations of surrogate epigenetic marks in blood, saliva, and/or buccal swabs reflect such marks in other disease associated tissues. Epigenetic marks are tissue and cell specific, as well as dependent on stage of life and gender. In conclusion, it is likely that epigenetic patterns translate or at least contribute to the relationship between the environment and human health. This possibility opens wide a vista of potential interventions, including behavioral or dietary interventions that can take advantage of the plasticity of the epigenome (Handel et al., 2010).

Drug development has focused mainly on histone acetyltransferase (HAT) and histone deacetylase (HDAC). This is the reason for this short introduction. There are news about memory formation and synaptic plasticity. I wanted to put them in a context.

"Epigenetics, Brain, Behavior, and Immunity" gives a good overview of epigenetics  provided with a consideration of the nature of epigenetic regulation including DNA methylation, histone modification and chromatin re-modeling. Illustrative examples of recent scientific developments are highlighted to demonstrate the influence of epigenetics in areas of research relevant to those who investigate phenomena within the scientific discipline of psychoneuroimmunology. These examples are presented in order to provide a perspective on how epigenetic analysis will add insight into the molecular processes that connect the brain with behavior, neuroendocrine responsivity and immune outcome.

This is something pointed out also by Radoslav Bozov in his paper 'Theory of Carbon Signaling. Negentropy vs Entropy. Emergence of Self Propagated Biological Systems', with whom I have discussed much. See also my earlier posts Life is part of the environment, the molecular mechanisms of innate immunity, cancer not a result of mutations the informational problem - cell membrane and promoter - telomeres and loops. Also thanks to TGD.

torsdagen den 1:e november 2012

First snow.

Can you make a snowball today, the kids wondered when the first snow fell? Oh, I'll try, surely mom can make a snowman, though nobody else can... and here he is. He lived in three days til the head dropped off. We tried to shelter it with a scarf and a cap.


And don't look at the background...
When I woke up this morning
from my slumber
I saw it clearly

My heart is like a cave
with the peculiar ability
to open wide up at occasions
and filled with diamonds, so bristling and shining
like Aladdins cave in the story.


Once a woman said to me
Oh, nice to meet you
such a beautiful soul
filled with light and angels around

I had to laugh at her
Me? Beautiful?
She must be kidding
I am just ordinary, common, clumpsy...
Another said, look at the cat!
She sees many light balls around
I just smiled

You must be something special, you said
but not necessarily in a positive tone

Nice, smooth aura, filled with yellow light, said an old woman
You said, there is a light around you
Oh, I wish I could see those things...

You should be writing, said one
so nice words
I know, I am so splitted
thousand things to do
thousand stories to tell
thousand humans to heal
thousand duties

Where do I start?
How would I find the inner peace to do it?
Listen to the heart, it is calling
and has called a long time already.

Some said, you have to follow your heart
or you will be seriously ill
I believe so.
Where your soul wander
there you have to follow.

This is my favourite, you said
look, a heart, from me
Oh, so beautiful
a cave opened up
filled with thousand bristling diamonds
the Aladdin cave?

fredagen den 8:e juni 2012

Artificial atoms, mechanized molecules and synthetic chrystals.

Artificial atoms or Quantum dots.
Artificial atom is an object that has bound, discrete electronic states, as is the case with naturally occurring atoms. Semiconductor quantum dots are the most common example of artificial atoms, and are analogies for real atoms. Artificial atoms are made up of more than one atom, but are like single atoms in one important way: when you provide the right amount (or quanta) of energy, they will give off coloured light.

Programmable matter refers to matter which has the ability to change its physical properties (shape, density, moduli, optical properties, etc.) in a programmable fashion, based upon user input or autonomous sensing. Programmable matter is thus linked to the concept of a material which inherently has the ability to perform information processing. .
Programmable matter is a term originally coined in 1991 by Toffoli and Margolus to refer to an ensemble of fine-grained computing elements arranged in space. Their paper describes a computing substrate that is composed of fine-grained compute nodes distributed throughout space which communicate using only nearest neighbor interactions. In this context, programmable matter refers to compute models similar to cellular automata and Lattice Gas Automata. The CAM-8 architecture is an example hardware realization of this model. This function is also known as "digital referenced areas" (DRA) in some forms of self-replicating machine science.
1. The programming could be external to the material and might be achieved by the "application of light, voltage, electric or magnetic fields, etc.". For example, in this school of thought, a liquid crystal display is a form of programmable matter.
2. The individual units of the ensemble can compute and the result of their computation is a change in the ensemble's physical properties.
3.  Scale is one key differentiator between different forms of programmable matter. Nano - cm, and even bigger. At the nanoscale end of the spectrum there are a tremendous number of different bases for programmable matter, ranging from shape changing molecules to quantum dots or artificial atoms. In the micrometer to sub-millimeter range examples include claytronics, MEMS-based units, cells created using synthetic biology, and the utility fog concept.
  
"Simple" programmable matter see also Smart material.
 Materials that can change their properties based on some input, but do not have the ability to do complex computation by themselves.
1. The physical properties of several complex fluids can be modified by applying a current or voltage, as is the case with liquid crystals.
2.  Metamaterials are artificial composites that can be controlled to react in ways that do not occur in nature. One example developed by David Smith and then by John Pendry and David Schuri is of a material that can have its index of refraction tuned so that it can have a different index of refraction at different points in the material.
3.  Molecules that can change (mechanostereochemistry) their shape, as well as other properties, in response to external stimuli. Can be used individually or en masse, ex, molecules that can change their electrical properties as mechanized molecules,  mechanically-interlocked molecular architectures such as molecular Borromean rings, catenanes and rotaxanes utilizing molecular recognition and molecular self-assembly processes. These topologies can be employed as molecular switches and as motor-molecules, and even applied these structures in the fabrication of nanoelectronic devices and nanoelectromechanical systems (NEMS).
π–stack charachters have been applied to the DNA structure  too, as reductive  electron-transport system, and its oxidative hairpins for hole transfer through DNA. These interactions are important in base stacking of DNA nucleotides, protein folding and protein chrystal formation, template-directed synthesis, materials science, and molecular recognition, Despite intense experimental and theoretical interest, there is no unified description of the factors that contribute to pi stacking interactions. There are compelling computational evidence for the importance of direct interaction in pi stacking. It  seems that the relative contributions of electrostatics, dispersion, and direct interactions to the substituent effects seen in pi stacking interactions are highly dependent on geometry and experimental design. The chromophore has also a special role, and it has been linked to quantum biology. see Mechanisms for DNA charge transport..


Self-Reconfiguring Modular Robotics is a field of robotics in which a group of basic robot modules work together to dynamically form shapes and create behaviours suitable for many tasks. Like Programmable matter SRCMR aims to offer significant improvement to any kind of objects or system by introducing many new possibilities for example:
1. Most important is the incredible flexibility that comes from the ability to change the physical structure and behavior of a solution by changing the software that controls modules.
2. The ability to self-repair by automatically replacing a broken module will make SRCMR solution incredibly resilient.
3. Reducing the environmental foot print by reusing the same modules in many different solutions.

Claytronics,  nanoscale robots ('claytronic atoms', or catoms) designed to form much larger scale machines or mechanisms. The catoms will be sub-millimeter computers that will eventually have the ability to move around, communicate with other computers, change color, and electrostatically connect to other catoms to form different shapes.

Quantum wells, a potential well with only discrete energy values, can hold one or more electrons. Those electrons behave like artificial atoms which, like real atoms, can form covalent bonds, but these are extremely weak. Because of their larger sizes, other properties are also widely different. One way to create quantization is to confine particles, which were originally free to move in three dimensions, to two dimensions, forcing them to occupy a planar region. The effects of quantum confinement take place when the quantum well thickness becomes comparable to the de Broglie wavelength of the carriers (generally electrons and holes), leading to energy levels called "energy subbands", i.e., the carriers can only have discrete energy values. Quantum wells are formed in semiconductors by having a material, like gallium arsenide sandwiched between two layers of a material with a wider bandgap, like aluminium arsenide. These structures can be grown by molecular beam epitaxy or chemical vapor deposition with control of the layer thickness down to monolayers. Thin metal films can also support quantum well states, in particular, metallic thin overlayers grown in metal and semiconductor surfaces. The electron (or hole) is confined by the vacuum-metal interface in one side, and in general, by an absolute gap with semiconductor substrates, or by a projected band gap with metal substrates.

Synthetic biology aims to engineer cells with "novel biological functions." Such cells are usually used to create larger systems (e.g., biofilms) which can be "programmed" utilizing synthetic gene networks such as genetic toggle switches, to change their color, shape, etc. Protocells and other minimal solutions.
Construction of a chemical system capable of replication and evolution, fed only by small molecule nutrients, is now conceivable. This could be achieved by stepwise integration of decades of work on the reconstitution of DNA, RNA and protein syntheses from pure components. Such a minimal cell project would initially define the components sufficient for each subsystem, allow detailed kinetic analyses and lead to improved in vitro methods for synthesis of biopolymers, therapeutics and biosensors. Completion would yield a functionally and structurally understood self-replicating biosystem. Safety concerns for synthetic life will be alleviated by extreme dependence on elaborate laboratory reagents and conditions for viability. Our proposed minimal genome is 113 kbp long and contains 151 genes. We detail building blocks already in place and major hurdles to overcome for completion.
 An external file that holds a picture, illustration, etc.
Object name is msb4100090-f1.jpg Object name is msb4100090-f1.jpg A minimal cell containing biological macromolecules and pathways proposed to be necessary and sufficient for replication from small molecule nutrients. 

See also



Quantum dots are like man-made, detected 1980,  artificial atoms that are described by discrete states.
It is a portion of matter (e.g., semiconductor) whose excitons are confined in all three spatial dimensions. Consequently, such materials have electronic properties intermediate between those of bulk semiconductors and those of discrete molecules. They could only be used in low temperature settings earlie, but this new technology described in Science Daily does not. Quantum dots have previously ranged in size from 2-10 nanometers in diameter.  While typically composed of several thousand atoms, all the atoms pool their electrons to “sing with one voice”, that is, the electrons are shared and coordinated as if there is only one atomic nucleus at the centre.

As with any crystalline semiconductor, a quantum dot's electronic wave functions extend over the crystal lattice. Similar to a molecule, a quantum dot has both a quantized energy spectrum and a quantized density of electronic states near the edge of the band gap. The quantum dot absorption features correspond to transitions between discrete,three-dimensional particle in a box states of the electron and the hole, both confined to the same nanometer-size box.These discrete transitions are reminiscent of atomic spectra and have resulted in quantum dots also being called artificial atoms.
Its electronic characteristics are closely related to the size and shape of the individual crystal. Generally, the smaller the size of the crystal, the larger the band gap, the greater the difference in energy between the highest valence band and the lowest conduction band becomes, therefore more energy is needed to excite the dot, and concurrently, more energy is released when the crystal returns to its resting state. A main advantage with quantum dots is that, because of the high level of control possible over the size of the crystals produced, it is possible to have very precise control over the conductive properties of the material. Quantum dots of different sizes can be assembled into a gradient multi-layer nanofilm.

 Quantum Dots
The National Institute of Nanotechnology at the University of Alberta announced that they created the smallest quantum dot, 2009. From What's the spin on quantum dots.

In a semiconductor crystal lattice, the electrons are squeezed together, since no two nearby electrons can share exactly the same energy level according to Pauli exclusion principle, leading to quantum confinement. The energy level can then be modeled using particle in a box, which leads to the conclusion that the energy levels of the quantum dot is dependent on its size. When the size of the quantum dot is smaller than the critical characteristic length called the Exciton Bohr radius, the electrons crowding lead to the splitting of the original energy levels into smaller ones with smaller gaps between each successive level. The Exciton Bohr radius is larger than the Bohr radius due to the effect of dielectric screening and the influence of periodic lattice structure of the crystal. The quantum dots that have radii larger than the Exciton Bohr radius are said to be in the 'weak confinement regime' and the ones that have radii smaller than the Exciton Bohr radius are said to be in the 'strong confinement regime'. Thus, if the size of the quantum dot is small enough that the quantum confinement effects dominate(typically less than 10 nm), the electronic and optical properties change, and the fluorescent wavelength is determined by the size.

 
3D confined electron wave functions in a quantum dot. Here, rectangular and triangular-shaped quantum dots are shown. Energy states in rectangular dots are more s-type and p-type. However, in a triangular dot the wave functions are mixed due to confinement symmetry.

Besides confinement in all three dimensions (i.e., a quantum dot), other quantum confined semiconductors include:
  • Quantum wires, which confine electrons or holes in two spatial dimensions and allow free propagation in the third.
  • Quantum wells, which confine electrons or holes in one dimension and allow free propagation in two dimensions. Wells can be of many kinds.
Different sized quantum dots emit different color light due to quantum confinement.

The images in this series represent the electron densities in a quantum dot artificial atom.
Quantum Dot Wave Function  (Image 1)

Part of a series of images depicting electron densities in a quantum dot artificial atom

The visuals were generated by the nanoelectronic modeling tool called NENO 3-D, and were visualized on the nanoVIS rendering service at www.nanoHUB.org, a rich, Web-based resource for research, education and collaboration in nanotechnology.

NanoHUB.org was created by the National Science Foundation (NSF)-funded Network for Computational Nanotechnology (NCN), a network of universities with a vision to pioneer the development of nanotechnology, from science to manufacturing, through innovative theory, exploratory simulation and novel cyberinfrastructure. NCN students, staff and faculty are developing the NanoHUB science gateway, while making use of it in their own research and education. Collaborators and partners across the world have joined NCN in this effort.

NanoHUB hosts over 790 resources to help users learn about nanotechnology, including online presentations, courses, learning modules, podcasts, animations, teaching materials and more. Most importantly, NanoHUB offers simulation tools that can be accessed from your Web browser, so you can not only learn about, but also simulate nanotechnology devices. NanoHUB also provides collaboration environment via Workspaces, online meetings and user groups.

 (Date of Image: May 2006)  Image 2.
 Part of a series of images depicting electron densities in a quantum dot artificial atom
Part of a series of images depicting electron densities in a quantum dot artificial atom
Image 3
Credit: Wei Qiao, David Ebert, Marek Korkusinski, Gerhard Klimeck; Network for Computational Nanotechnology, Purdue University

Download the high-resolution JPG version of the image. (399 KB
Use your mouse to right-click (Mac users may need to Ctrl-click) the link above and choose the option that will save the file or target to your computer.



Synthetic chrystals.
Element Six, the world leader in synthetic diamond supermaterials, working in partnership with academics in Harvard University, California Institute of Technology and Max-Planck-Institut für Quantenoptik, has used its Element Six single crystal synthetic diamond grown by chemical vapour deposition (CVD) to demonstrate the capability of quantum bit memory to exceed one second at room temperature.

 
Using synthetic diamond, Element Six and Harvard University have set a new room temperature quantum information storage record of more than one second – a thousand times longer than previously recorded.

It proved the ability of synthetic diamond to provide the read-out of a quantum bit which had preserved its spin polarisation for several minutes and its memory coherence for over a second. This is the first time that such long memory times have been reported for a material at room temperature, giving synthetic diamond a significant advantage over rival materials and technologies that require complex infrastructure which necessitates, for example, cryogenic cooling.

The versatility, robustness, and potential scalability of this synthetic diamond system may allow for new applications in quantum information science and quantum based sensors used, for example, in nano-scale imaging of chemical/biological processes.


Steve Coe, Element Six Group Innovation Director, explained the success of the collaboration:

"The field of synthetic diamond science is moving very quickly and is requiring Element Six to develop synthesis processes with impurity control at the level of parts per trillion – real nano-engineering control of CVD diamond synthesis. We have been working closely with Professor Lukin's team in Harvard for three years - this result published in Science is an example of how successful this collaboration has been."

Professor Mikhail Lukin of Harvard University's Department of Physics described the significance of the research findings:

"Element Six's unique and engineered synthetic diamond material has been at the heart of these important developments. The demonstration of a single qubit quantum memory with seconds of storage time at room temperature is a very exciting development, which combines the four key requirements of initialisation, memory, control and measurement. These findings might one day lead to novel quantum communication and computation technologies, but in the nearer term may enable a range of novel and disruptive quantum sensor technologies, such as those being targeted to image magnetic fields on the nano-scale for use in imaging chemical and biological processes."
 

The findings represent the latest developments in quantum information processing, which involves manipulating individual atomic sized impurities in synthetic diamond and exploiting the quantum property spin of an individual electron, with superposition so this quantum spin (qubit) can be both 0 and 1 simultaneously. It is this property that provides a framework for quantum computing, but also for more immediate applications such as novel magnetic sensing technologies.

See also  About protons and atoms.

onsdagen den 6:e juni 2012

Quantum Biology.


Photosynthetic quantum mechanism.

DNA.

Morphogenetic fields. Short.


Tubulins/qubits.


Dendritic cytoskeleton.



Electronics of benzoediazepins.

Quantum Biology and the Hidden Nature of Nature
John Hockenberry, Paul Davies, Seth Lloyd, Thorsten Ritz 

The Kaye Playhouse at Hunter College

Chromatophores etc.  World Science Festival 2012. Can the spooky world of quantum physics explain bird navigation, photosynthesis and even our delicate sense of smell? Clues are mounting that the rules governing the subatomic realm may play an unexpectedly pivotal role in the visible world. Leading thinkers in the emerging field of quantum biology explored the hidden hand of quantum physics on the scales of everyday life.
 
Thorsten Ritz is a biophysicist interested in the role of quantum mechanics in biological systems, ranging from photosynthetic light harvesting systems to sensory cells. He has championed the idea that a quantum mechanical reaction may lie at the heart of the magnetic compass of birds and other animals. Straddling and often breaking the barriers between theory and experiment and physics and biology, he has worked with biologists to provide the first experimental evidence supporting a quantum-based compass in birds.
He is currently an associate professor of physics and astronomy at the University of California, Irvine. His work has received national and international recognition, including awards from the Royal Institute of Navigation (UK), Institute of Physics (UK), American Physical Society, Alfred P. Sloan Foundation, and the Research Cooperation.

Working with a variety of groups to construct and operate quantum computers and quantum communication systems, Seth Lloyd is the first person to develop a realizable model for quantum computation. His research focuses on the role of information in complex systems and the quantum mechanics of living systems (known as `quantum life’), economics, and cosmology.
Lloyd is the author of over a hundred scientific papers, including the publication Programming the Universe. He is currently the professor of quantum-mechanical engineering at MIT and the director of the W.M. Keck Center for Extreme Quantum Information Theory.

Paul Davies is a theoretical physicist, cosmologist, astrobiologist and best-selling author. He is Regents’ Professor at Arizona State University, where he directs the Beyond Center for Fundamental Concepts in Science—a cosmic think tank that tackles the big questions of existence, from the origin of the universe to the origin of life and the nature of time. Davies also directs a National Cancer Institute research program that studies cancer from a physics perspective. Among his research accomplishments, he has helped explain how black holes radiate energy, what caused the ripples in the cosmic afterglow of the big bang, and why life on Earth may have come from Mars.
Davies has written about 30 books, most recently The Eerie Silence: Are We Alone in the Universe? His preoccupation with deep conceptual problems and his fearless championing of bold new ideas earned Davies the epithet of “The Disruptor” in a recent profile in Nature magazine. His many media projects include presenting two six-part series on “The Big Questions” for Australian television. He has received awards from The Royal Society and the UK Institute of Physics, and also received the 1995 Templeton Prize. In 2007 he was named a Member of the Order of Australia in the Queen’s birthday honors list.

tisdagen den 5:e juni 2012

Invisible hats and bent spacetime.

Mathematicians can conjure matter waves inside an invisible hat May 29, 2012




This graphic shows a matter wave hitting a 'Schrodinger's hat'. The intensity of the wave inside the device is magnified (red peak). Outside, the incident plane waves wrap around the device and re-join on the other side as if the device is not there. (Credit: Gunther Uhlmann, U. of Washington.)

Invisibility, the subject of magic, myth or imagination, is becoming reality. Mathematicians and others have been working on invisibility cloaks – perhaps not yet concealing Harry Potter's invisible sleeve, or Star Trek, the mythical Hermes/Perseus' helmet' but at least shielding small objects from detection by microwaves or sound waves. It started 'by mistake' in 2003 with inverse problems and breast cancer problems. The work is a type of inverse problem that uses measurements from the surface of a body — say a human body, or the Earth — to deduce what's inside.  "This was the opposite of what we were looking for," Uhlmann recalled. "We were trying to make invisible things visible, and not the opposite." The group published its findings, including the mysterious case, in the journal Mathematics Research Letters. See story on the unexpected discovery.

The very first prototype of a cloaking device  has been made by David Smith's group at Duke University.

The first invisible cloaks were microstates. Carpet cloaks were proposed  by John Pendry, as a way of extending the operating range. Here an prototype article from 2006. And Ulf Leonhardt, also from 2006, in Science. Today there are many kinds of cloaks.

To make an object literally vanish before a person's eyes, a cloak would have to simultaneously interact with all of the wavelengths, or colors, that make up light. The visual appearance of objects is determined by the extent to which they modify light due to geometric scattering and material absorption. Thus, in order to hide the object from being detected, the invisibility cloak must conceal the changes to the light in both geometry and spectrum. Conventional optical components rely on gradual phase shifts accumulated during light propagation to shape light beams.

Leonhardt on invisibility: He gives more examples than these.
Why is light bent? Light rays obey Fermat's Principle of the least optical path. The refractive index n determines the optical length; distances in media with high n appear longer to light than distances in media with low n. When n varies, light rays try to stay as long as possible in regions of relatively low refractive index. In the mirage, light rays bend their paths to stay longer in the hot thin air above the desert where n is low.
Fermat's Principle also explains Snell's law of refraction (discovered by the Arabian scientist Ibn Sahl more than a millennium ago). Refraction is familiar to everyone who has tried to gauge directions underwater. Imagine an angler sees a fish. Is the fish where it appears to be? No, because the water surface refracts the light coming from the fish (the sunlight reflected off the fish). The image of the fish reaches the eye of the angler at a different direction than the "line of sight". The angler is misled, unless he has learned from experience. Light is refracted at the water surface, because the refractive index n of air is smaller than the refractive index of water and, according to Fermat's Principle, light tries to stay as long as possible in a region of low n. In media where n gradually varies, like in the desert air above the hot sand, light is not refracted, but bent.
Another example is the green flash. When the Sun is setting the Sun's rays are bent in the atmosphere, because the air is thinner at higher altitudes and so the refractive index is lower there. The light rays are bent in the opposite way to a mirage (but for the same reason). So, when the Sun appears to be setting, she has already set, because of the light bending in the atmosphere. The refractive index n of air is larger for higher frequencies of light; blue or green light is refracted stronger than orange or red light, so blue or green light is more strongly bent. The blue light, however, is scattered in the atmosphere, coloring the sky blue, due to Rayleigh scattering (conjectured by Alhazen of Basra during the early eleventh century and by Leonardo da Vinci ca. 1500). Therefore, the last light from the setting Sun is green and appears as a green flash when the atmospheric conditions are right. 
A new solution to the problem of invisibility based on the use of dielectric (nonconducting) anisotropic metamaterials. Our optical cloak not only suggests that true invisibility materials are within reach, it also represents a major step towards transformation optics.

One system employs the natural birefringence of the calcite. In such materials the refraction of light depends on the polarization. Today also graphene has been used for achieving spatial patterns, which by manipulating the graphene also can be changed. "by designing and manipulating spatially inhomogeneous, nonuniform conductivity patterns across a flake of graphene, one can have this material as a one-atom-thick platform for infrared metamaterials and transformation optical devices. Varying the graphene chemical potential by using static electric field yields a way to tune the graphene conductivity in the terahertz and infrared frequencies. Such degree of freedom provides the prospect of having different “patches” with different conductivities on a single flake of graphene."

Leonhardt, cont.


Imagine the material appears to move the points of space to different locations: it performs a coordinate transformation from a virtual space (A) to physical space (B). It creates the illusion that light flows through the empty virtual space (A), whereas in reality it propagates in (B). In physical space, one point of virtual space has been expanded to finite size. As light would not notice a single point it flows around the expanded region without any distortion. So the interior of the expanded point is hidden and the act of hiding is concealed. In short, the material makes a cloaking device. An optical medium changes the measure of distance perceived by light. Suppose that the medium preserves the right angles between light rays and wavefronts like the Mercator Projection preserves the angles between longitude and latitude. In this case, the medium could smoothly guide light without reflection. In mathematics, maps that preserve angles are known as conformal maps and their optical implementation with an appropriate refractive-index profile is an Optical Conformal Mapping. Most conformal maps require more then one sheet to represent them, but rather several or even infinitely many, sewn together at branch cuts between branch points. Some generate mind-boggling Riemann surfaces like the one that represents the tiling on the title page of the book on complex analysis shown below. The picture beside the book shows the tiling behind the scenes of the figure on light propagation. Riemann surfaces have inspired some of M.C. Escher's intriguing paintings. Their many branches can be used to hide regions of space, provided an optical medium facilitates the mapping. If one has something to hide, one should hide it on Riemann sheets. Light that has passed the branch cut to another sheet of the optical Riemann surface will get stuck there and never return.

 
From Leonhardts page. Remarcable! Go to his page for more ref.
  1. U. Leonhardt, Optical Conformal Mapping, Science Express, May 25 (2006).
  2. U. Leonhardt, Notes on Conformal Invisibility Devices, New Journal of Physics 8, 118 (2006).
  3. A. Hendi, J. Henn, and U. Leonhardt, Ambiguities in the Scattering Tomography for Central Potentials, Physical Review Letters 97, 073902 (2006).
  4. U. Leonhardt and T. G. Philbin, General Relativity in Electrical Engineering, New Journal of Physics 8, 247 (2006).
  5. T. Ochiai, U. Leonhardt, and J. C. Nacher, A novel design of dielectric perfect invisibility devices, J. Math. Phys. 49, 032903 (2008).
  6. U. Leonhardt and T. Tyc, Broadband Invisibility by Non-Euclidean Cloaking, Science Express, November 20 (2008). For downloading a free copy click here.


Macrostates hidden.
Now they electromagnetically hide objects that can be seen with the naked eye and do so at visible wavelengths, so called optical transformations. To build such a cloak you need a material that will bend the incoming and outgoing light rays by different amounts — determined by the dimensions of the object underneath.  The cloaks are also relatively cheap and easy to make, being constructed from the natural material as calcite, the refractive index of which depends on the relative orientation of an incoming light wave’s polarization axis and the calcite’s optical axis. Calcite is perfect for the job because the speed at which polarized light passes through it depends on the crystal's orientation. So by sticking together two pieces of crystal, it is possible to create a cloak that bends incoming and outgoing light by the desired amount. See Fooling an observer.
All the invisibility cloaks demonstrated thus far, however, have relied on nano- or micro-fabricated artificial composite materials with spatially varying electromagnetic properties, which limit the size of the cloaked region to a few wavelengths. Here we report realisation of a macroscopic volumetric invisibility cloak constructed from natural birefringent crystals. The cloak operates at visible frequencies and is capable of hiding three-dimensional objects of the scale of centimetres and millimetres.
From the work of Yu Luo et al. carpet cloaks can be built from homogeneous – rather than more complex inhomogeneous – materials, as long as those materials are anisotropic.

These orientations were fixed such that lightwaves with a given polarization that bounce off a wedge-shaped object placed underneath the cloak emerge travelling in the same direction and at the same height that they would have done had they bounced straight off the mirror beneath the object. The wedge, having a base length, width and height of 38 mm, 10 mm and 2 mm respectively, can easily be seen with the naked eye. 
Whirlpools and invisibilities. A hole carved out of space–time, a pocket in reality, or a chicken crossing the road. Carpet cloaks render covered objects invisible by bending light rays as they enter the cloak and then when they exit it — after they have bounced off the hidden object. The light is deviated in such a way that the rays seem to have been reflected directly from the ground underneath the object — as though the object was not there. Invisibility of macroscopic objects is a reality at last, says a Nature article.

Today they can also make cloaks  that flexes with temperature. See Design of an optical reference cavity with low thermal noise and flexible thermal expansion properties. And topological transitions by manipulating the photonic environment and photonic density. They describe a transition in the topology of the iso-frequency surface from a closed ellipsoid to an open hyperboloid by increased rates of spontaneous emission of emitters positioned near the metamaterial.

New degrees of freedom are attained by introducing abrupt phase changes over the scale of the wavelength. A two-dimensional array of optical resonators with spatially varying phase response and subwavelength separation can imprint such phase discontinuities on propagating light as it traverses the interface between two media. Anomalous reflection and refraction phenomena are observed in this regime in optically thin arrays of metallic antennas on silicon with a linear phase variation along the interface, which are in excellent agreement with generalized laws derived from Fermat’s principle


Another sytem is  anomalous localised resonance. Stealth technology is designed to make objects of military interest as black as possible to radar. Here the first line of defence is to reflect incoming radar waves off at odd angles. The waves that reach the object are then absorbed without reflection using impedance matching. They disappear without any echo detectable by radar.   Perfect invisibility devices with isotropic media are proven to be impossible due to the wave nature of light. No illusion is perfect, or, expressed in mathematical terms, the inverse scattering problem for linear waves in isotropic media has unique solutions. But the imperfections of invisibility might be invisibly small. Maybe the device would create a slight haze, instead of a perfect image

A group has built a cylindrical “invisibility cloak” that shields objects from water waves by directing those waves around the object as if it weren’t there. Wikipedia: 
Janos Perczel, 22, an undergraduate student at St Andrews University in Fife, has developed an optical sphere which could be used to create an "invisibility cloak". He said that by slowing down light by way of an optical illusion, the light can then be bent around an object to "conceal" it. Attempts have already been made to create invisibility cloaks but research shows that efforts are limited because any cloak would only work within certain backgrounds. But by slowing down the rays of light, Mr Perczel says the cloak wearer can move around ever-changing backgrounds.
Mr Perczel, from Hungary, came up with the idea under the guidance of "invisibility expert" Professor Ulf Leonhardt at the university's school of physics and astronomy. The student recognised the potential of the invisible sphere and spent eight months fine tuning his project. The key development lies in the ability of the sphere, an optical device, to not only remain invisible itself but to slow light.
According to Prof Leonhardt, all optical illusions can slow down rays of light and the sphere can be used to bend this illusion around an object, reflecting off it and making it appear to be invisible. Mr Perczel added: "When the light is bent it engulfs the object, much like water covering a rock sitting in a river bed, and carries on its path, making it seem as if nothing is there. Light however can only be sped up to a speed faster than it would travel in space, under certain conditions, and this restricts invisibility cloaks to work in a limited part of the spectrum, essentially just one colour. This would be ideal if somebody was planning to stand still in camouflage. However, the moment they start to move, the scenery would begin to distort, revealing the person under the cloak. By slowing all of the light down with an invisible sphere, it does not need to be accelerated to such high speeds and can therefore work in all parts of the spectrum." See "Student makes 'invisibility cloak'". Belfast Telegraph. 9 August 2011. Leonhardt, Ulf; Smith, David R (2008). "Focus on Cloaking and Transformation Optics". New Journal of Physics 10 (11): 115019.
So, bending light can be illusory? That we have known for some time. Gravitational lenses use the same technique? They can even reveal hypothetical dark matter stars? See also wikipedia articles:

Invisibility in 3D.
Hiding a realistic object using a broadband terahertz invisibility cloak by Fan Zhou, Yongjun Bao, Wei Cao, Colin Stuart, Jianqiang Gu, Weili Zhang, and Cheng Sun. Scientific Reports 1 2011. Here Tolga Ergin, Karlsruhe Institute of Technology in Germany popular in BBC, based on the concept that you can "transform space" with a material. The carpet cloak was originally designed to work in two dimensions. There has been difficulties in fabricating cloaking devices that are optically large in all three dimensions.   The Karlsruhe team used a technique called laser writing to create their 3-D cloak. This uses a very finely focused laser, to "write" into a light-sensitive material.
"Wherever you put the focus spot into the material, it will harden," explained Dr Ergin. "It's a similar process to photography - when you develop it, whatever hasn't been exposed to the laser will be washed away." Fan Zhou et al. in Nature offers a technical feasible solution for designing and fabricating 3D THz transformation optics :
The first experimental demonstration of a 3D THz cloaking device fabricated using a scalable Projection Microstereolithography process, is presented. The cloak operates at a broad frequency range between 0.3 and 0.6 THz, and is placed over an α-lactose monohydrate absorber with rectangular shape. Characterized using angular-resolved reflection THz time-domain spectroscopy (THz-TDS), the results indicate that the THz invisibility cloak has successfully concealed both the geometrical and spectroscopic signatures of the absorber, making it undetectable to the observer.
Spectra maps of four experimental cases. From the Nature paper.
In this case, the researchers use the device to cloak a bump one micrometre (one thousandth of a millimetre) high. "But in theory there are no limits [to the size of the object you could hide]", said Dr Ergin. "You could blow this up and hide a house."  (I guess that is adressed to the fond money keepers?)
"Photonic crystals usually work because the constitutive elements are not visible to the wavelength by which one observes them," Professor Hess explained.
"So if you look at the desk in front of you, you don't see the individual atoms because they are so small. You just see whole structure - the wood or the plastic."
This means that cloaking devices for visible light would have to be made up of much smaller rods. So for this technique, the laser beam would have to be made even smaller.
Currently, the rods can be made as small as 200 nanometres. To hide a bump from visible light would require rods as small as 10 nanometres.
  • J. Fischer, T. Ergin, and M. Wegener, “Three-dimensional polarization-independent visible-frequency carpet invisibility cloak”, Optics Letters, in press.
In 2010, Wegener and his team from KIT, Karlsruhe, presented their first 3D invisibility cloak. In 2011, the effects of the Karlsruhe invisibility cloak are also visible to the bare eye.  Pressrelease here.

Plasmonic invisibility effects
Plasmon is waves of electrons in metals. " ... may induce a dramatic drop in the scattering cross-section, making the object nearly invisible to an observer," Achieving transparency with plasmonic coatings, by Andrea Alu, Nader Engheta 2005. You've seen cloaking technology at work on television, when blue backgrounds are used to make a person invisible. A human could be made impossible to detect in longer-wavelength radiation such as microwaves, but not from visible light. A spaceship might be made transparent to radio waves or some other long-wavelength detector. Here we see how a proper design of these lossless metamaterial covers near their plasma resonance may induce a dramatic drop in the scattering cross section, making the object nearly invisible to an observer.

The earlier article: Extremely Low Frequency Plasmons in Metallic Microstructures, JB Pendry, I Youngs, AJ Holden and WJ Stewart, Phys. Rev. Lett. 76 4773-6 (1996).

Ultra-compact On-Chip Plasmonic Light Concentrator, by Ye Luo, Maysamreza Chamanzar, Ali Adibi,  18 Apr 2012 present
a novel approach for achieving tightly concentrated optical field by a hybrid photonic-plasmonic device in an integrated platform, which is a triangle-shaped metal taper mounted on top of a dielectric waveguide. This device, which we call a plasmomic light concentrator (PLC), can achieve side-coupling of light energy from the dielectric waveguide to the plasmonic region and light focusing into the apex of the metal taper (at the scale ~10nm) at the same time. For demonstration, we numerically investigate a PLC, which is a metal (Au) taper on a dielectric (Si3N4) waveguide at working wavelengths around 800nm. We show that three major effects (mode beat, nanofocusing, and weak resonance) interplay to generate this light concentration phenomenon and govern the performance of the device. By coordinating these effects, the PLC can be designed to be super compact while maintaining high efficiency over a wide band. In particular, we demonstrate that under optimized size parameters and wavelength a field concentration factor (FCF), which is the ratio of the norm of the electric field at the apex over the average norm of the electric field in the inputting waveguide, of about 13 can be achieved with the length of the device less than 1um for a moderate tip radius 20nm. Moreover, we show that a FCF of 5-10 is achievable over a wavelength range 700-1100nm when the length of the device is further reduced to about 400nm.

Cloak allows objects to move undetected, in hidden ways.
The latest development, by Martin McCall et.al. might see cloaks add yet another dimension to their capability: time, in ‘Space-time cloak’ to conceal events, 2010  He has mathematically extended the idea of a cloak that conceals objects to one that conceals events.

Scientists have developed a recipe for manipulating the speed of light as it passes over an object. WAU.  Can that be true?
McCall:
The idea is to create a tunnel through which an object could perform an action – move or change shape, f. ex. – while appearing as doing nothing at all. The cloak could also find uses in signal processing: a detector placed inside the cloak would be able to "pause" a signal travelling through the wall while it first deals with a signal passing through the tunnel. When the leading edge of a light wave hits the cloak, the material is manipulated to speed up the light, but when the trailing edge hits, the light is slowed down and delayed. "Between these two parts of the light, there will be a temporal void — a space in which there will be no illuminating light for a brief period of time," 
The mathematics behind the invisibility cloak involves a geometric transform – which takes a point, inflates it and renders anything that lies inside the resulting bubble unreachable by the waves —  true for water waves just as  for electromagnetic waves. The object functions just like a whirlpool, and indeed generates the same solutions to the Navier-Stokes equations of fluid dynamics as a whirlpool does. Tornadoes also move things in unexpected manners.
  • McCall MW, Favaro A, Kinsler P, et al, A spacetime cloak, or a history editor, JOURNAL OF OPTICS, 2011, Vol:13, ISSN:2040-8978 (publication doi) The cloak works by locally manipulating the speed of light of an initially uniform light distribution, whilst the light rays themselves always follow straight paths. Any 'perfect' spacetime cloak would necessarily rely upon the technology of electromagnetic metamaterials, which has already been shown to be capable of deforming light in ways hitherto unforeseen—to produce, for example, an electromagnetic object cloak. Nevertheless, we show how it is possible to use intensity-dependent refractive indices to construct an approximate STC, an implementation that would enable the distinct signature of successful event cloaking to be observed. Potential demonstrations include systems that apparently violate quantum statistics, 'interrupt-without-interrupt' computation on convergent data channels and the illusion of a Star Trek transporter.
  • McCall MW, Favaro A, Kinsler P, et al, A spacetime cloak, or a history editor, J OPT-UK, 2011, Vol:13, ISSN:2040-8978 (doi)
He also studies materials with a negative  refractive indexes.
  • McCall MW, What is negative refraction?, JOURNAL OF MODERN OPTICS, 2009, Vol:56, Pages:1727-1740, ISSN:0950-0340 (publication doi) We review various published definitions associated with the phenomenon of negative phase velocity propagation of electromagnetic waves in meta-media, as observed through negative refraction.
  • Kinsler P, Favaro A, McCall MW, Four Poynting theorems, EUROPEAN JOURNAL OF PHYSICS, 2009, Vol:30, Pages:983-993, ISSN:0143-0807(publication doi) The Poynting vector is an invaluable tool for analysing electromagnetic problems. However, even a rigorous stress–energy tensor approach can still leave us with the question: is it best defined as E × H or as D × B? Typical electromagnetic treatments provide yet another perspective: they regard E × B as the appropriate definition, because E and B are taken to be the fundamental electromagnetic fields. The astute reader will even notice the fourth possible combination of fields, i.e. D × H. Faced with this diverse selection, we have decided to treat each possible flux vector on its merits, deriving its associated energy continuity equation but applying minimal restrictions to the allowed host media. We then discuss each form, and how it represents the response of the medium. Finally, we derive a propagation equation for each flux vector using a directional fields approach, a useful result which enables further interpretation of each flux and its interaction with the medium. 
  • (About Poynting's theorem. the general question of the physical interpretation of Poynting's theorem and compare two typical derivations of it. One of these uses the work done on a charge by an external electromagnet field, while the other considers the work done by the total field, external plus self-field).

Wormholes and magnetic monopoles?
Magnetic monopoles has not yet been found (only one record), but Joseph Polchinski (2002) described the existence of monopoles as "one of the safest bets that one can make". Monopoles are hypothetical particles that display an odd form of magnetism. Can one end be hidden? As for the hidden Higgs, dark matter, tachyons, gravitons etc.?

Monopoles first received theoretical support when the brilliant theoretical physicist Paul Dirac showed mathematically that one possible reason for the quantization of the electric charge (in other words, why electric charge only occurs in integer amounts) is the existence of a complementary magnetic particle with a quantized magnetic charge. This put monopoles on fairly firm footing as far as quantum electrodynamics was concerned. When magnetic monopoles began popping up in grand unification theories as a consequence of the dissociation of electromagnetism, the strong force and the weak force, they gained even more adherents among theorists.
  • A. Greenleaf, Y. Kurylev, M. Lassas, G. Uhlmann: Electromagnetic wormholes and virtual magnetic monopoles from metamaterials. Physical Review Letters 99, 183901 (2007) preprint.
  • Claus Montonen and D. Olive, 1977. Magnetic monopoles as gauge particles? Cern.

Negative compressibility: Metamaterial would stretch when compressed, and vice versa, under any circumstances. New materials with 'negative compressibility': compress when they are pulled and expand when they are pushed. Metamaterials that do this have been built before. For example, vibrating aluminium bars with tiny cavities inside them create waves that oppose the push or pull applied. But the designs must be vibrated at just the right frequency to see the effect. Zachary Nicolaou and Adilson Motter of Northwestern University in Evanston, Illinois, have now designed a metamaterial that stretches when compressed, and vice versa, under any circumstances. 'What is interesting is that they study systems that are not responding to a vibration but to a steady applied force,' says John Pendry of Imperial College London.  NewScientist article.

 A metamaterial that stretches when compressed and contracts when pulled could one day lead to materials that offer protection against blasts. From Next Big Future where more can be read about this.


Based on a Nature article; Mechanical metamaterials with negative compressibility transitions. These destabilizations give rise to a stress-induced solid–solid phase transition associated with a twisted hysteresis curve for the stress–strain relationship. The strain-driven counterpart of negative compressibility transitions is a force amplification phenomenon, where an increase in deformation induces a discontinuous increase in response force.

Positively Negative, JB Pendry, Nature ‘News and Views’ 423 22-23 (2003)

   
Negative refraction = light would refract the other way, through a negative angle. a) Light incident on a normal material refracts at a positive angle (blue), but in a negative-index material the refraction angle is negative (red). Negative refraction occurs only in specially engineered materials. The response of a material to electric and magnetic fields is characterized by its permittivity, e, and its permeability, m, respectively.

It is easy to fabricate an artificial material with negative e using a lattice of thin metal wires. We then showed how to do the same thing for m: the required magnetic response was obtained from a lattice of metal ‘split rings’ that resonate with magnetic fields of a given frequency; the induced currents give a negative magnetic response. The third paper, by Smith and colleagues made the key advance. This team made a structure that combined these elements in a microwave experiment, the first demonstration of negative e and negative m in the same material. They went on to demonstrate negative refraction in their material.

The search for monopoles continues through experiments like the Monopole and Exotics Detector, or MoEDAL experiment, at CERN. This monopole is a singularity (a closed string?), but monopole could also be a duality with one pole shielded?   

The solid-solid phase transition link contain headings like Challenges of Paradigm Building for Solid-State Transformations  and Diffusional Transformations with Order-Disorder Transformations, phase separations and decomposition, magnetoresistence, time-resolvation, effect of pressure or strain on magnetic transitions etc.


A whirlpool or a wormhole? See

The team devised in 2007 wormholes in which waves disappear in one place and pop up somewhere else. Rays travel through the wormhole and emerge on the other end. "Invisibility research has led to discovery of 'wormholes'" ,

 

Their wormhole, named after the concept in general relativity, is a tunnel that would make light waves seem to disappear in one place and reappear somewhere else.  "The idea is to create a tunnel of invisibility, a secret connection between two different points in space,"  Gunther Uhlmann said. It takes the invisibility concept from one dimension to two dimensions. "The wormhole comes from blowing up a line."
The wormhole discovery was covered in Nature, Scientific American and National Geographic.


Back to the Schrödinger hat!
"Schrödinger's hat," refer to the  Schrödinger's cat in quantum mechanics. The name is also a nod to the ability to create something from what appears to be nothing, with L. Krauss words. 

 
Gunther Uhlmann, (also doing inverse problems)  Allan Greenleaf, Yaroslav Kurylev, and Matti Lassas at the University of Helsinki in Finland, all of whom are co-authors on the new paper. 
  • A. Greenleaf, Y. Kurylev, M. Lassas, G. Uhlmann: Schrodinger's Hat: Electromagnetic, acoustic and quantum amplifiers via transformation optics. Submitted PNAS, preprint
As a first application, the researchers propose manipulating matter waves, which are the mathematical description (also in reality?) of particles in quantum mechanics. The researchers envision building a quantum microscope that could capture quantum waves. A quantum microscope could, for example, be used to monitor electronic processes on computer chips.
 
The team calls their modified invisibility cloak a Schrödinger's hat because tiny "parts" of waves or wavefunctions can be secretly stored, rather like a magician's hat, and detected. And the trick is that the rest of the wave would be scarcely changed. Outside the Schrödinger's hat the wavefunction would be "the old wavefunction multiplied by a constant, [which] may be very small". iInvisibility cloaks can be understood through an analogy with Einstein's general theory of relativity. This theory shows how very massive objects distort the underlying fabric of the universe, space–time. In the same way, certain man-made structures known as metamaterials distort an equivalent fabric, a virtual "optical space".

"You can isolate and magnify what you want to see, and make the rest invisible," said  Uhlmann. "You can amplify the waves tremendously. And although the wave has been magnified a lot, you still cannot see what is happening inside the container."
"In some sense you are doing something magical, because it looks like a particle is being created. It's like pulling something out of your hat," he said. Matter waves inside the hat can also be shrunk, but concealing very small objects "is not so interesting."

The hat acting as invisible concentrators of waves.  Compression! And expansion!


Sounds like mind-matter? Is mind a wormhole?


An artificial wormhole would work only for electromagnetic waves with a specified frequency. The wormhole device is just an optical device similar to a lens;  not similar to space-time wormholes studied in general relativity, they point out.

The invisibility cloaking means coating of an object with a special metamaterial so that light goes around the object. The existing invisibility cloak uses tiny copper wires embedded in fiberglass panels to manipulate incoming waves.; from  Invisibility cloaking and electromagnetic wormholes.


The team helped develop the original mathematics to formulate cloaks.
Maxwell's equations have transformation laws that allow for design of electromagnetic parameters that would steer light around a hidden region, returning it to its original path on the far side. As waves hit the left side of the cloak they start to bend, so that waves leaving the cloak on the right appear as if they had never encountered an obstacle. In a  paper, they solve equations showing how to make a cloak invisible to all incoming frequencies, including visible light. They also calculate how to shield living, glowing or electrically active objects.

 

  •  "Full wave invisibility of active devices at all frequencies" to the journal Communications in Mathematical Physics. Coauthors are Allan Greenleaf at the University of Rochester, a longtime collaborator; Matti Lassas at the Helsinki University of Technology, a former post-doctoral researcher at UW; and Yaroslav Kurylev at Loughborough University in the UK.  prove invisibility with respect to solutions of the Helmholtz and Maxwell’s equations, a singular transformation that pushes isotropic electromagnetic parameters forward into singular, anisotropic ones. We define the notion of finite energy solutions of the Helmholtz and Maxwell’s equations for such singular electromagnetic parameters, and study the behavior of the solutions on the entire domain, including the cloaked region and its boundary. Due to the singularity of the metric, one needs to work with weak solutions. Analyzing the behavior of such solutions inside the cloaked region, we show that, depending on the chosen construction, there appear new “hidden” boundary conditions at the surface separating the cloaked and uncloaked regions. We also consider the effect on invisibility of active devices inside the cloaked region, interpreted as collections of sources and sinks or internal currents. When these conditions are overdetermined, as happens for Maxwell’s equations, generic internal currents prevent the existence of finite energy solutions and invisibility is compromised...
The materials must be built at the nanoscale because they are constructed to match the incoming waves. The longer the wavelength the easier it is to build. That explains why the first working cloak, immortalized in a YouTube video, hid a copper cylinder from microwaves with wavelengths more than a thousand times longer than those of visible light.

A postdoctoral researcher working with Uhlmann, Hongyu Liu, published a paper showing that a wall could be made to appear when there is actually nothing there. Look for references on his page.

"It all comes from the same idea, making things expand and contract, making things look different things than what they really are."

Acoustic Cloaks.

"From the experimental point of view, I think the most exciting thing is how easy it seems to be to build materials for acoustic cloaking," Uhlmann said. Wavelengths for microwave, sound and quantum matter waves are longer than light or electromagnetic waves, making it easier to build the materials to cloak objects from observation using these phenomena.
  • Acoustic cloaking theory, by A. Norris, Proc. R. Soc. A vol. 464 no. 2097 2411-2434, doi: 10.1098/rspa.2008.0076

Newly Developed Cloak Hides Underwater Objects from Sonar, 2011 demonstrated an acoustic cloak, a technology that renders underwater objects invisible to sonar and other ultrasound waves,  a working prototype developed of metamaterial. "We are talking about controlling sound waves by bending and twisting them in a designer space," said Nicholas Fang. Fang's team designed a two-dimensional cylindrical cloak made of 16 concentric rings of acoustic circuits structured to guide sound waves. Each ring has a different index of refraction, meaning that sound waves vary their speed from the outer rings to the inner ones.
"Basically what you are looking at is an array of cavities that are connected by channels. The sound is going to propagate inside those channels, and the cavities are designed to slow the waves down," Fang said. "As you go further inside the rings, sound waves gain faster and faster speed." Since speeding up requires energy, the sound waves instead propagate around the cloak's outer rings, guided by the channels in the circuits. The specially structured acoustic circuits actually bend the sound waves to wrap them around the outer layers of the cloak.




The cloak offers acoustic invisibility to ultrasound waves from 40 to 80 KHz, although with modification could theoretically be tuned to cover tens of megahertz. "The geometry is not theoretically scaled with wavelengths. The nice thing about the circuit element approach is that you can scale the channels down while maintaining the same wave propagation technology."
  • Shu Zhang, Chunguang Xia, Nicholas Fang. Broadband Acoustic Cloak for Ultrasound Waves. Physical Review Letters, 2011; 
Acoustic Cloak: Closer to Achieving the Acoustic Undetectability of Objects, later 2011. achieving what is known as "acoustic undetectability." It is a new prototype two-dimensional acoustic cloak that can make sound waves with a specific frequency reaching an object avoid it as if it was not there. The position of each cylinder in the cloak has been obtained by using optimization techniques based on genetic algorithms (numerical algorithms which mimic Darwinian evolution). "This research complements the contributions made by our group to the problem of acoustic undetectability. Its novelty lies in the use of genetic algorithms," says José Sánchez-Dehesa.  Sound waves of a specific frequency ­- 3061 Hz, with a 100 Hz bandwidth - maintain their original pattern, both as they go around the object and past it.
  • V. M. García-Chocano, L. Sanchis, A. Díaz-Rubio, J. Martínez-Pastor, F. Cervera, R. Llopis-Pontiveros, J. Sánchez-Dehesa. Acoustic cloak for airborne sound by inverse design. Applied Physics Letters, 2011; 99 (7): 074102 DOI: 10.1063/1.3623761

Diffusional transformations.
'Thermal cloak' hides objects from heat', Sebastien Guenneau, et al.  has proposed isolating or cloaking objects from sources of heat - essentially "thermal cloaking." An  open-access journal Optics Express, taps into some of the same principles as optical cloaking and may lead to novel ways to control heat in electronics and, on an even larger scale, might someday prove useful for spacecraft and solar technologies.
Until now, he explains, cloaking research has revolved around manipulating trajectories of waves. These include electromagnetic (light), pressure (sound), elastodynamic (seismic), and hydrodynamic (ocean) waves. The biggest difference in their study of heat, he points out, is that the physical phenomenon involved is diffusion, not wave propagation.

Colour diagram showing thermally cloaked region (Optics Express) The thermally cloaked region is shown in the centre of this heat map.

"Heat isn't a wave - it simply diffuses from hot to cold regions," Guenneau, Institut Fresnel in France, says. "The mathematics and physics at play are much different. For instance, a wave can travel long distances with little attenuation, whereas temperature usually diffuses over smaller distances."
To create their thermal invisibility cloak, Guenneau &co applied the mathematics of transformation optics to equations for thermal diffusion and discovered that their idea could work. The researchers propose a cloak made of 20 rings of material, each with its own "diffusivity" - the degree to which it can transmit and dissipate heat. "We can design a cloak so that heat diffuses around an invisibility region, which is then protected from heat, or we can force heat to concentrate in a small volume, which will then heat up very rapidly."

This diffusion = wave was also found by  Masao Nagasawa in the Schrödinger Equations and Diffusion Theory, 1993. Schrödingers wave equation can be used for diffusion.

The approach is fundamentally different from temperature-changing cloaks that heat and cool actively to mimic objects of different temperatures and have proven to "hide" a tank.

Quantum measurements.
In order to avoid perturbation and the decoherence from the observation of position, indirect methods of measurement have been developed.

Avshalom Elitzur and Lev Vaidman at Tel Aviv University in Israel pointed 1993 out that it is not always necessary to observe particles directly to learn something of their nature. The Elitzur-Vaidman bomb-tester paradox says: A BOMB triggered by a single photon of light is a scary thought. If such a thing existed in the classical world, you would never even be aware of it. Any photon entering your eye to tell you about it would already have set off the bomb, but you can also use quantum matter waves to detect a light-triggered bomb with light (interferometer, where a photon will take both paths at once and produce an interference pattern), In Elitzur and Vaidman's thought experiment, half the time there is a photon-triggered bomb blocking one path (see diagram). Only the real photon can trigger the bomb, so if it is the ghostly copy that gets blocked by the bomb, there is no explosion.
In 1995 Paul Kwiat, Anton Zeilinger et al.  demonstrated in a real experiment that such "interaction-free" measurements are indeed possible by repeatedly, but weakly, tests for the presence of the object, by bouncing photons off mirrors.   See Paul G. Kwiat, The Tao of Quantum Interrogation, (2001).

In 2000, Shuichiro Inoue, Gunnar Bjork and Jonas Söderholm of the Royal Institute of Technology in Stockholm, Sweden, used a technique involving two weakly interacting Bose-Einstein condensates,  to show that you could get an image of a piece of an object without shining light on it. The concept of interference visibility can, and should, be generalized to describe weakly interacting multiply occupied coherent bosonic systems. There were no radiation damage to the tissue because no X-rays actually hit it. Visibility is not a good measure of a well-defined relative phase.

The 'hat' may be an easier way to perform such measurements, see the Schrödinger hat could spy on quantum particles. In the 'wormhole' not all the light passes around  – often, a small amount will leak in. If the inside of the cloak had almost the same resonant frequency as that of the incoming light, say Uhlmann and colleagues, that wave's energy would build up, forming a localized excitation. This excitation behaves much like a particle, which the group has dubbed a "quasmon". This quasmon could then be released by making a slight alteration to the cloak's resonant frequency, perhaps through the application of a weak magnetic field. A little like 'tasting' the environment, to eavesdrop , like computer viruses do?
The potential of a Schrödinger's hat can be seen in the example of an electron in a box. Although the electron's wavefunction is spread throughout the box, a scientist may be able to guess the location of areas where it drops to zero. That scientist could then position a Schrödinger's hat at such a location, with no fear of the electron "noticing" the sensor's presence and collapsing into a definite state. If the experiment were to be repeated several times, the scientist might be able to map out where the electron definitely is not – and in doing so, learn something about where it actually is. 
Ulf Leonhardt, at St Andrews Univ. in the UK, a member of Uhlmann's group, says that a device that works for microwaves could be made using circuit-board materials. A device for plasmons  could be made from metal and plastic rings. He thinks a Schrödinger hat could even be developed for sound – allowing its users to eavesdrop on sound without disturbing it. 
Leonhardt has shown us how to make artificial black holes, a video about Invisibility, levitate objects and even make things disappear. See also Perfect imaging, Fibre-optical black holes, Quantum levitation, Invisibility, Quantum catastrophes and Light in moving media