More Love...

I will continue on the same topic, love.

What is Love, asks Alva Noë, a perception expert and philosopher.

"Children do not love their parents. They are connected to them. And they need them."
OOOPS!

Then I realize he might be right. Children learn to love their parents, and they love also bad parents. Parents that never should have been parents. Because parents need not to be perfect. Later the child learn also this. Trust and wellbeing is the clue to develope a free Self, that doesn't need perfect parents. Unconditioned Love, acceptance, with no terms.

"Love is an achievement, it doesn't come for free." About that I could have different opinion. Maybe love as an accommodation is. There are many kinds of love.

Scientists like to ask: How do we perceive so much, given the impoverished data actually available to the nervous system? But the better question would be: Why do we see so little, given all there is that shows itself to us? To bring the world into focus for consciousness, we need to do a lot of work. Think of the work a child needs to do to learn to read. But once the child reads, texts have powerful, inescapable meanings.

Well, here is several errors in the thinking. The first part is ok, but the consciousness, what is it? Can we actually bring the world into consciousness? Of course not. Instead we make a mirrorimage of the world, and that mirror are we aware of. Consciousness is a lot more, very much more. The unconsciousness world in the humans are about 90 % more. In the brain the working memory that make our awareness is only a few percent of the brain capacity. I cannot think he really believes himself in what he is saying.

To be capable of reading the brain must have a certain structure and age. The abstract thinking must be developed and this doesn't happen before the age of three. What really happens to the brain at three years age? A widening of consciousness? What do that mean?

TGD says a new level of hierarchy of Plancks constants (hbar) is happening, a phase transition. Biologists say the frontal lobe is becoming active. The same thing, only said in different ways. As is - "Learning to read is, in this way, achieving an openness to the world, or at least to a world of ideas and possibilities."

Love is like this kind of phase transition, a gate (heart) in the chakra world - an achieved openness to another person. We can percieve that person. Earlier I wrote about superpositions as love. A gate is a transformation of everything old. Drunvalo draw it as a perpendicular strength of fields, changing the further direction of developement.

Perpendicular magnetism adding the strength of both fields.

There are also other gates, in infinity.

"The purpose of education is to teach us how to see (take on some glasses). It is very hard to be able to see another person. To see someone you must know him or her." We call it interference, and in order to get a reaction there must be something similiar. In everyday language we call this communication. In the end, these are the topography you must traverse, to be able to perceive, and so maybe to find, love.

Without communication, no love, without perception, no love. "Love is an emotional condition. (So is seeing.)" Emotions can be blocked, perception can be blocked and communication may not work.

"Openness over time, adjustments, adapt, shift, accommodate. Mature love is an achievement of dedication." There is always a prise to pay. But you get joy, satisfaction, peace, a feeling of being at home.

From the comments: God is love. In my world God is more real than any material thing or human feeling. If you want to know love, know God. We choose our reality.

That is the quantum world. So we must accept the quantum world in us to get love, not to be too dependent on this world of perceptions and thought, eating and pleasure. In short - not to be too decoherenced, but allow some coherence :)

Is the Creator lonely? No, he is everywhere, part of everything. That's why he is said to be Love itself. We only need to percieve... Make measurements into decoherence. Weave God into the 'grid' of Life. Living matter is only temorarily decoherenced. As matter in general, but with a different time scale.

When I look at Drunvalo's site I become astonished. He writes:

Then there are the true stories of how one particular grid, often called THE UNITY CONSCONSCIOUSNESS GRID, and how it has finally come to birth since February 2008. The birth of this new living consciousness grid is for certain, I believe, the most important story since Atlantis, and yet hardly anyone on Earth is aware that it has happened or what it means for humanity.

One thing is clear; the outcome of this global consciousness transition is going to affect every single last person on this planet. If you know what has now become history, your heart can rest knowing that what is to follow in our lives is one of the greatest gifts that Source has given to mankind.

What happened in febr. 2008? I know. The magical new time was coming. I was there and saw it. But I won't tell you. This grid works now, faster and faster...

Diamonds.

Drunvalo is remarkable! He talks to Toth. The ancient egyptian god of Life and Death, spirit and truth.

Love Can Alleviate Pain.

Love Can Alleviate Pain is a blogpost by BrainBlogger, Dario Dieguez, Jr. The early stages of a new, romantic relationship are associated with feelings of euphoria, which likely arise from brain mechanisms responsible for sensations of pleasure or reward.

I have earlier written about these things. Screaming cells, are also about the same topic.

This is not only about love. It is about patterns of brain activation; specific patterns of brain activity may mediate reward or relief of pain. Increased activation of brain regions such as the caudate and nucleus accumbens was associated with pain relief. Some brain regions activated by the “love task” described are also associated with activation of brain areas responsible for memory, attention, and sexual arousal. In addition, the researchers had no way to determine how much attention a given participant was paying to the pictures during the experiment. Surprisingly, there was no specific brain region that increased in activity during viewing pictures of a romantic partner to a degree similar to the extent of the pain relief experienced.

Specific behavioral experiences can reduce pain without drugs, they suggest.

This from a blog,Proto.
Worth reading.

The fact that placebos may work even when individuals are fully knowledgeable that they are not taking an active drug may bypass the ethical dilemma of deceiving patients. According to Ted Kaptchuk at Harvard Medical School and his colleagues at least one condition can be calmed by placebo, even when everyone knows it's just an inert pill. This raises a thorny question: should we start offering sugar pills for ailments without a treatment? The power of Nothing?

Every fibromyalgia patient know that two days are not equal, one day pain, the other not, and the main difference is in the self-reward. Feelings of pleasure. A warm hand.

Or take a re-organization at job. Never have so many been so sick.

Or, why are women more sick than men, on the general spoken. Is it the hormones or their social positions? Their ability to get rewardness for what they are doing?

Take the placebo-effect. "For most of us, the "placebo effect" is synonymous with the power of positive thinking; it works because you believe you're taking a real drug - used in clinical trials as controls for potential new medications. In fact, data on placebos is so compelling that many American physicians (one study estimates 50 percent) secretly give placebos to unsuspecting patients."

50% is a high number. And it can be strengthen actively to a lot more.
Ted Kaptchuk with colleagues explored whether or not the power of placebos can be harnessed honestly and respectfully. And got surprised.

To do this, 80 patients suffering from irritable bowel syndrome (IBS) were divided into two groups: one group, the controls, received no treatment, while the other group received a regimen of placebos—honestly described as "like sugar pills"—which they were instructed to take twice daily.

"Not only did we make it absolutely clear that these pills had no active ingredient and were made from inert substances, but we actually had 'placebo' printed on the bottle," says Kaptchuk. "We told the patients that they didn't have to even believe in the placebo effect. Just take the pills."

For a three-week period, the patients were monitored. By the end of the trial, nearly twice as many patients treated with the placebo reported adequate symptom relief as compared to the control group (59 percent vs. 35 percent). Also, on other outcome measures, patients taking the placebo doubled their rates of improvement to a degree roughly equivalent to the effects of the most powerful IBS medications.

Placebo worked better than medicine! Why?
Kaptchuk: "these findings suggest that rather than mere positive thinking, there may be significant benefit to the very performance of medical ritual. I'm excited about studying this further. Placebo may work even if patients knows it is a placebo."

I also remember a report telling about a comparision between a very good doctor, with high degree of knowledge, but a rude manner, and a gentle doctor, not so good. Guess who got better results? The gentle one of course. Why?

Could it be about rewardness, dignity and respect? To be seen as humans?

What about homeopathy? It sometimes contain absolutely no effective molecule. Only sugar pills. Is it placebo?

Even animals and small children that don't know they eat it get better. Can it be placebo, or information as they say? What is information?

Jaques Benveniste (at former digibio) and others showed that homeopathy works, but he was a victim for a cruel game and died before his time. James Randi is a Magi and knew maybe very well what he was doing? Should we rather believe such a man?

Pitkänen has done much to explain the memory.

Everyone can see how love works its miracles, but the same remedy works also elsewhere, maybe less dramatically. And rejection from a loved one feels like pain, and is in reality nocebo, the precise opposite.

Merry Christmas to everyone. Take care of each other. Show love, dignity and compassion (about compassion - it can be done in bad ways, and in good ways).

This post was maybe inspired of self-pity, sitting alone sick at home at Christmas Eve. No Santa Claus showed up. I have not been so kind, I know. Sorry.

I thought to write about how he could do it, 'scientifically' :) - maybe next Christmas.

The informational problem - cell membrane and promoter.

There are common structures and functions in genes (promoters, telomers) and cellmembranes. Promoter-genes that produce mainly RNAs are regulated much in the same way as telomers. The G-codons contra T-codons are important, as is the protonic shield around the codons. See also the first part of this informational problem.

Promoter regions are highly acetylated in humans, and many promoters contain CpG islands, which are important transcription-controlling elements and are unmethylated under normal circumstances. CpG islands have been shown to be highly acetylated. The locations of the 46,813 acetylation islands identified are significantly correlated with conserved noncoding sequences and many of them are colocalized with known regulatory elements in T cells (immune cells). The human genome project has identified 27,058 CpG islands, highly concentrated in a 1-kb region surrounding the transcription initiation site.

Telomers are very little acetylated.

Acetylation - methylation.
Histone modifications (post-translational modifications) play an important role in gene regulation. Histones are the most abundant proteins in chromatin and play key roles in modulating chromatin folding to regulate the accessibility of DNA for transcription, replication, recombination and repair. Chromatin structure change. Histone acetylation is required for gene activation and cell growth and many enzymes that regulate histone acetylation and deacetylation are transcriptional cofactors = correlated acetylation patterns with the transcriptional activity usually. The acetylated histones may recruit and/or stabilize transcription factors and/or chromatin remodeling enzymes to their target sites in chromatin. The levels and genomic distributions of specific modifications are regulated to provide chromatin responses to physiological stimuli like hormones and growth factors. Also important are the mechanisms by which aberrant histone modifications act as epigenetic factors in the pathogenesis of diseases including cancer.


The folding is the important signal. What does this mean? - That the importance of the genome is to distribute active, regulating sites, that is EM-, magnetism and affection-repellation - not the DNA-code per se. The 'letters' are meaningless alone, only the context gives a meaning. It is important if the amino acid is lysine or cysteine because the amino acids have different 'metabolic pathways' in terms of EM-effects.


A histone-code.
Acetylation (of lysine) loci may mediate the global chromatin remodeling and gene activation, and are epigenetic marks that allow prediction of functional regulatory elements. Methylation (of cytosine) is the 'lock-function' on the chromatin. A diverse array of posttranslational modifications largely impinge on histone N termini, thereby regulating access to the underlying DNA. Modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins. The combinatorial nature of histone N-terminal modifications thus reveals a "histone code" that considerably extends the information potential of the genetic code. This epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes. Histones provides complex recognition surfaces or a code for factors that regulate chromatin structure and gene activity.

The methylation pattern is heritable after cell division. DNA methylation plays an important role in cell differentiation during development and for the immunity etc. Epigenetics is the study of heritable changes in chromatin (e.g., DNA acethylation/methylation) without involving the change in DNA sequences. Imprinting involves the inheritance of a silenced allele of a gene through either a paternal or maternal germline.

The fifth base of human DNA, 5-methylcytosine (5-mC), recognized 1948, involves addition of a methyl group to the carbon 5 position of the cytosine ring, catalyzed by DNA methyltransferase in the context of the sequence 5'-CG-3', which is also referred to as a CpG dinucleotide.

Schematic representation of the biochemical pathways for cytosine methylation, demethylation, and mutagenesis of cytosine and 5-mC.
This inverse relationship between cytosine methylation and transcription has been observed in a large number of genes, although not universally. Numerous reports have shown the ability of promoter DNA methylation to inhibit transcription of a wide variety of genes in in vitro transfection assays, and in some cases, such methylation corresponds to the inactive state of the gene under study in vivo. Three possible mechanisms have been proposed.

• direct interference withthe binding of specific transcription factors to their recognitionsites in their respective promoters. Several transcription factors,including AP-2, c-Myc/Myn, the cyclic AMP-dependent activatorCREB, E2F, and NF-B, recognize sequences that contain CpG residues, others are indifferent and manyfactors have no CpG dinucleotide residues in their binding sites.

• direct binding of specific transcriptional repressorsto methylated DNA. Two such factors, MeCP-1 and MeCP-2 (methylcytosine binding) bind to methylated CpG residues in any sequence context. MeCP-1 binds to DNA containing multiple symmetrically methylated CpG sites, as opposed to hemimethylated CpGs, and manifestsas a large complex on electrophoretic mobility shift assay. The complex stability varies, and a weak or a strong promoter can make the shift. A complex with electrophoretic mobility similar to MeCP-1 forms efficiently with the methylatedbut not with unmethylated embryonic rho-globin gene promoter sequences, suggest a role for MeCP-1 or asimilar complex in developmental silencing of embryonic globingenes.

• methylation may mediate transcriptional repression is by altering chromatin structure.

Singal & Ginders, 1999:

Eukaryotic genomes are not methylated uniformly but contain methylated regions interspersed with unmethylated domains. During evolution, the dinucleotide CpG has been progressively eliminated from the genome of higher eukaryotes and is present at only 5% to 10% of its predicted frequency. Cytosine methylation appears to have played a major role in this process, because most CpG sites lost represent the conversion through deamination of methylcytosines to thymines. Approximately 70% to 80% of the remaining CpG sites contain methylated cytosines in most vertebrates, including humans. These methylated regions are typical of the bulk chromatin that represents the late replicating DNA with its attendant histone composition and nucleosomal configuration and is relatively inaccessible to transcription factors. In contrast to the rest of the genome, smaller regions of DNA, called CpG islands, ranging from 0.5 to 5 kb and occurring on average every 100 kb, have distinctive properties. These regions are unmethylated, GC rich (60% to 70%), have a ratio of CpG to GpC of at least 0.6, and thus do not show any suppression of the frequency of the dinucleotide CpG. Chromatin containing CpG islands is generally heavily acetylated, lacks histone H1, and includes a nucleosome-free region. This so called open chromatin configuration may allow, or be a consequence of, the interaction of transcription factors with gene promoters.

Two regulatory ways:
1. Approximately half of all genes in mouse and humans (ie, 40,000 to 50,000 genes) contain CpG islands (housekeeping genes that have a broad tissue pattern of expression).
2. Tissue-specific genes (40%) without CpG islands are variably methylated, often in a tissue-specific pattern, and usually methylation is inversely correlated with the transcriptional status of the genes.
The target site for DNA-MTase in DNA is the dinucleotide palindrome CG (commonly referred to as CpG, with p denoting the phosphate group)

MTase protein has inherent de novo methylating activity that may be altered by protein-protein interactions and enhanced by aberrant structures or 5-mC residues in the substrate DNA. Several studies in the last few years have demonstrated an increase in DNA-MTase activity in neoplastic cells. The intrinsic mutagenicity of 5-mC, activation of proto-oncogenes through hypomethylation, transcriptional inactivation of tumor-suppressor genes through hypermethylation, and defects in chromosomal segregation due to failure of de novo methylation may all contribute to neoplasia. Studies have linked two global mechanisms of gene regulation, DNA methylation, and histone deacetylation. Further investigations are necessary to understand the complex links between the methyltransferases, demethylases, methyl cytosine binding proteins, histone acetylation, and the transcriptional activity of genes.

Although the protein complexes (holoenzymes) that form during transcription initiation, elongation, and RNA processing are being extensively characterized in vitro, our understanding of the long-range interactions that determine the overall efficiency of transcription are less well understood in vivo. Key determinants of transcriptional initiation and reinitiation include promoters, enhancers, locus control regions (LCRs), and those involved in the organization of chromosomal and nuclear context. Position effect variegation is perhaps the best-known phenomena, where the chromosomal position of a gene and promoter element can influence its overall expression. One reason why chromosomal context can have such a dominant effect relates to the position of the element in relation to the competing effects of ‘open’, transcriptionally active chromatin with ‘condensed’ transcriptional silent chromatin. Within the context of the nucleus of the living cell, the degree of condensation of chromatin can be thought of as different ‘cloud’-like densities of chromatin loops depending on the degree of compaction. Even though the mechanisms and interactions that govern the processes of gene expression now appear more complex, the theme emerging from experimental investigation is that of a dynamic regulated system. There are multiple superfamilies of chromatin proteins that modify gene expression and chromatin condensation.

Within the spatial confines of the nucleus, chromatin is organized into loops attached to the core structure of the chromosome, which can then unravel into 30 nm fibers during interphase. The loops are attached at their base to a protein substructure termed either the nucleoskeleton, nuclear scaffold, or nuclear matrix. Interactions are generally of functional importance. Such regions have been termed matrix attachment regions, scaffold attachment regions, or base of loops. We will refer to these collectively as loop attachment regions (LARs). The current evidence from investigation of base of loop libraries and transient episomal reporter gene expression is that the LAR sequences map mainly to transcription units. Transcription and RNA processing are performed by very large protein complexes that are likely to be immobile structures within the gel-like nucleoplasm. If the RNA polymerase tracks along the template DNA dragging its RNA behind, as depicted in most models of transcription, then the RNA molecule will be wound around DNA every 10 bp. If RNA secondary structures form cotranscriptionally, then the complex is likely to result in a knot of protein and nucleic acid. For genes several kilobases long, the energy required to untangle RNA from DNA would appear to be a costly topological puzzle. The entwining problem for the cell can be sidestepped if the polymerase is made immobile and topoisomerases remove supercoils generated in the template DNA. The experimental evidence for immobile polymerases comes from a variety of observations. Perhaps the most compelling is the observation that active RNA polymerases appear to concentrate in sites, termed factories, the largest factory being the nucleolus. Labeling of nascent RNA in nuclei produces multiple foci when visualized with light microscopy. However, foci represent collections of nascent RNA around multiple polymerases (Fig. 1).

DNA is packed within the nucleus around histone octamers, a protein complex consisting of two copies each of four different histone proteins. Eight types of histone modifications are known (acetylation, methylation, phosphorylation, ubiquitylation, sumoylation, ADP ribosylation, deimination, and proline isomerisation). Each type of modification is specific to certain residues and has a different mechanism of function, and accordingly different functional consequences. There is no simple one-to-one correspondence between the type of modification and the functional consequence, but rather the combination of modification type, enzymatic activity, affected residue and the DNA sequence in the immediate vicinity of the affected histone determine the functionality of the modification in a very complex manner. The same type of modification can be enhancing or repressing transcriptional activity, depending on which histone and residue it occurs. The transactivation potential of a given transcription factor depends on the degree of differentiation of the recipient cells, on the promoter structure, and on the affinity of the binding site.

The chromatin accessibility and gene expression of a genetic domain is correlated with hyperacetylation of promoters and other regulatory elements but not with generally elevated acetylation of the entire domain. Islands of acetylation are identified in the intergenic and transcribed regions.

An estimate is that about 2% (1%) of the unique sequences in the genome are associated with the acetylated histone. Also higher repetitive sequences (as telomers) are associated with lower levels of the histone acetylation.

Higher eukaryotic genomes differ from yeast in having much lower acetylation levels and more heterochromatic regions. (Linked to the intron-sequencies?)

What about sequence-association for features of the clustered promoters?
The clustering revealed three groups with major histone signal upstream, centered and downstream of the promoter. Narrow single peak promoters tend to have a concentrated activity of histone in the upstream region, while broad promoters tend to have a concentrated activity of histone and RNA polymerase II binding in the centered and downstream regions. A subset of promoters with high gene expression level, compared to subsets with low and medium gene expression, shows dramatic increase in histone activity in the upstream cluster only; this may indicate that promoters in the centered and downstream clusters are predominantly regulated at post-initiation steps. Furthermore, the upstream cluster is depleted in CpG islands and more likely to regulate un-annotated genes.

Clustering core promoters according to their surrounding acetylation signal is a promising approach for the study of histone modifications. When examining promoters clustered into groups according to their surrounding histone acetylation signal, we find that the relative localization and intensity of histone is very specific depending on characteristic sequence features of the promoter.

The association between the clusters and the three tested genomic features promoter architecture (single peak vs. broad), CpG islands and gene annotation is highly significant.

Promoter-gene anatomy.
Promoters of genes that transcribe relatively large amounts of mRNA have similar structures. They have a TATA sequence (sometimes called the TATA box or Goldberg-Hogness box) about 30 base pairs upstream from the site where transcription begins, as well as one or more promoter elements further upstream (CAAT and CACCC sequencies). The TATA box is present in only about 10 to 15% of human genes. Two new core promoter motifs-the DPE and the MTE, is discovered. Both the DPE and MTE are conserved from Drosophila to humans, and are located downstream of the transcription start site. There are sharp differences in the properties of TATA-dependent versus DPE-dependent core promoters. For example, Caudal, which is a sequence-specific DNA-binding protein that is a master regulator of the homeotic (Hox) genes, is a DPE-specific activator. Thus, enhancer-core promoter specificity can be used to create gene regulatory networks.

The "functional anatomy" of a promoter region showed that the first 109 base pairs preceding the cap site were sufficient for the correct initiation of gene transcription by RNA polymerase. The enzyme responsible for the transcription of messenger RNAs is RNA polymerase II, that is bound to the promoter.

Fig. Typical promoter region for a protein-coding eukaryotic gene. The gene diagrammed here contains a TATA box and three upstream promoter elements.

The CAAT and TATA sequence-boxes have been found to be critical elements in numerous eukaryotic promoters, but the CACCC sequence is seldom seen except in the β-globin gene promoters in several species. In humans, this sequence appears to be critical (usually no synthesis).

Promoter Function
Promoters can function not only to bind RNA polymerase, but also to specify the places and times that transcription can occur from that gene. Histone modifications are one of the major mechanisms regulating gene expression, acting in combination with other mechanisms such as alternative promoter usage, alternative splicing, and microRNAs ( a kind of 'language'). Acetylation occurs on the N-termini of the protein octamers and neutralizes the basic charge of the affected lysine, the association between the DNA and the octamer becomes weaker, unravelling the DNA and making the genomic DNA more accessible for RNA polymerases and transcription factors. Like all histone modifications, acetylation can work on two different scales. Globally, the acetylation state of large genomic regions helps to define euchromatin and heterochromatin within the nucleus. Acetylation can also function locally, being restricted to short sequences of the genome, where it is associated with upregulated transcription of individual genes.

A promoter can be classified into different shape classes , the two most prominent classes being single peak (SP) and broad promoters (BR) (>97% of total). Single peak promoters have the majority of their CAGE tags concentrated in a narrow region, while broad promoters have a more even, widespread distribution of start sites within the promoter. SP promoters are associated with the TATA Box binding motif and tissue-specific expression, while BR promoters are associated with CpG islands and ubiquitously transcribed genes including housekeeping genes. A more direct link (higher acetylation) between histones and gene expression level in the upstream cluster, than in the centered and downstream clusters. Also as weak and strong promoters. Broad promoters tend to regulate genes with a higher gene expression level than peak promoters,

Around half of these un-annotated promoters are evolutionary conserved across mammals and are therefore likely to be promoters of yet undetected genes, including functional non-coding RNA genes. Large intergenic noncoding RNAs (lincRNAs) are a group of multi-exonic, functional RNAs that show strong conservation across mammals and are thought to be involved in various cellular processes, including embryonic stem cell pluripotency and differentiation, but they represent only a subset of the entire functional noncoding transcriptome. It is reasonable to assume that many of the un-annotated core promoters belong to ncRNA genes, yet undetected protein-coding genes, or may be alternative promoters of already annotated genes.

This association link can be interpreted within the model of three main epigenetic modes of transcription initiation: genes experiencing initiation and elongation, genes experiencing transcription initiation but not elongation, and genes experiencing neither. The mechanisms of gene-regulation in these three groups may belong to the initiation or elongation phase of transcription, respectively. This model in combination with our observations suggests that genes having the histone concentration in the centered and downstream region could predominantly be regulated at post-initiation steps. Such post-initiation regulation could be based on two general classes of regulation mechanisms : in one class, transcriptional pausing of RNA polymerase II, poor processivity, or abortive initiation prevents elongation. In the second class, transcription does take place but is immediately degraded by gene silencing.

With increasing promoter expression level, an increase in the number of promoters overlapping with repeat elements. Only ~5.8% of all lowly expressed promoters overlap with any of the repeat elements. For medium gene expression, ~7.8% of the promoters overlap with a repeat element, and for the promoters regulating highly expressed genes the result was ~11.8%.

Regulation of transcription of eukaryotic class-II genes with developmental, tissue and hormone-sensitive specificities requires as-yet not understood organization and genome-wide co-ordination of signaling by many regulators. The genome-wide co-ordinated assembly of these regulators into higher-order complexes with target genes, to effect precisely timed changes in transcriptional activity, is one of the great remaining 'black boxes' in developmental biology. Recent findings on the very tightly controlled genes have generated the notion of 'composite promoters' that have and are necessarily dependent on both a TATA box and an initiator. Thus far most examples of composite promoters have been from viruses that are dependent on usurpation of host transcriptional machinery at precisely the right moment in its life cycle and in just the right host-cell biological context. However, our studies have identified that a cellular gene, juvenile hormone esterase, behaves as a possessing a composite core promoter.

Transcription from the core promoter of the juvenile hormone esterase gene (-61 to +28) requires the presence of both an AT-rich motif (TATA box) and an initiator motif for any transcription to occur, when assayed by either transcription in vitro or by transient-transfection assay. Additional gel-shift experiments in which both the TATA box and initiator motifs are transversion mutated indicated that at least one additional binding site is utilized. The juvenile hormone esterase gene thus appears to be a model of a cellular composite core promoter with a multipartite, indispensible requirement for not just both the TATA box and initiator, but also for at least a third core element as well.

The sequence of the modelled region is shown at the upper portion of the Figure. The transcription factor binding sites are shown within the boxed regions, with the bend angle and direction of the protein-induced bend shown above. The underlined bases indicate the bases on which the protein-induced bends were centred. The lower portion of the Figure shows a model of the promoter generated using Berkeley Enhanced Rasmol. The FMR1 model is superimposed, for scale, on the structure of DNA from the nucleosome core particle of Xenopus laevi. The boxed regions correspond to the boxed regions in the upper panel. Numbers indicate the first and last base of the modelled sequence.

To be continued.

Over 8000 views.

I am astonished, perplexed. Today the 8000 visitor to this blog. When I began I did not really know what to write about, only about my fascination for the surprising things science can give you. Today I have no time to write every tread down. So much is happening. And we all keep the breath and wait for results from Cern. There will be no SuSy? Instead TGD will get support?

One of the reasons for this blog was also to discuss TGD. I believe Matti is on the right track, because he really has theories for how the biology works, and those theories are coherent. I think the new physics has to seriously consider the Life as a physical phenomen, and today common physicists are very far from that. My admiration for Matti is big. I thought to say tremendous, but remembered his aversion against that kind of words :)

Of course he cannot be right in every aspect, but that doesn't hinder me. Nobody is perfect, and none is always right. Kea once pointed this out.

But Matti refuse to discuss here. For some reason he only consider physic blogs, so the small discussion is on his blog. You must ask him for the reasons, perhaps I am a stupid and ridiculous woman that think I can say or do something to push him forward. To my great sorrow I am no physicist, but he is no biologist, so we should be even? At least I hope so.

I am very ignorant, some say even naive, in many things, and this blog is a way to get some grasp on many complex questions. Behind the CHI or QI is 'life forces' and quantum biology. I wish I can get a coherent glimpse of what that mean. Already I have a coarse picture, but it take so much time to write it down, which I regret. In the meantime I have to earn my living, take care of the household etc. I should have been younger, but this is how it is now. I am pleased that you, visitors, read my posts. Thank you.

Could antimatter be the missing darkmatter?

Kea has some really interesting thoughts on her blog.

Given the bound beta decay n→H+ν¯ and its presumably similar looking antimatter reaction, we can conclude that anti-hydrogen will not look exactly like hydrogen. That is, (i) the Particle Data Group informs us of mass differences between neutrons and anti-neutrons and (ii) we know about the mass differences between neutrinos and antineutrinos.

The fission of mercury-180 was expected to be a symmetric reaction that would result in two equal fragments, but instead produced two nuclei with quite different masses, two distinct peaks centred around the nuclei ruthenium-100 and krypton-80, an asymmetric reaction.

Some fission reactions are asymmetric, including many of those of uranium and its neighbouring actinide elements. These instead can be understood by also using the shell model, in which unequal fragments can be preferentially created if one or both of these fragments contains a "magic" number of protons and/or neutrons. For example, one of the fragments produced in many of the fission reactions involving actinides is tin-132, which is a "doubly-magic" nucleus, containing 50 protons and 82 neutrons.

Neutrons? What are their messages? Magic numbers? - The observed fragments do not contain any magic or semi-magic shells, but 80:100 (4:5). Fission isn't magic, but stability is?

CERN's ISOLDE radioactive beam facility, investigated the interplay between the macroscopic and microscopic components of nuclear fission. It used what is known as beta-delayed fission, a two-step process in which a parent nucleus beta decays and then the daughter nucleus undergoes fission if it is created in a highly excited state. This kind of reaction allows scientists to study fission reactions in relatively exotic nuclei. Firing a proton beam at a uranium target and then using laser beams and a magnetic field to filter out ions of thallium-180 from among the wide variety of nuclei produced in the proton collisions. These ions then became implanted in a carbon foil, where they underwent beta decay and some of the resulting atoms of mercury-180 then fissioned. The analysis: Search for Stopped Gluinos in pp collisions at sqrt s = 7 TeV. Analysis of a gluino, which is the gluon’s supersymmetric cousin.


The gluino force. A gluino that decays inside the CMS calorimeter will leave a single blob of energy (big blue spike) with very little in the rest of the detector. Interaction of the strong force, QCD, on weak perturbation theory, QED? Strong force force to asymmetry? Antimatter and matter have differencies in the strong force, hence wavelength too.

As if this weren’t exotic enough, this analysis looked for very long-lived gluinos, potentially existing for more than 15 minutes. In a field in which a lifetime of a millionth of a second is a long time, 15 minutes might as well be forever. A frosen force? Time is making the asymmetry? Usually antimatter is said to go to the past. This is how it could happen? This antimatter is then also turned dark? A necessary feature of supersymmetric theories is that they predict that for all known subatomic particles, each particle should have a supersymmetric cousin, which differs in the details of how the particles spin. Is time a spin feature? Is antimatter about spin?

The concept of "magic numbers" in nuclei.
The nuclear shell model, which was first proposed in 1949, explains that nuclei with certain magic numbers of neutrons and/or protons are especially stable because the neutrons and/or protons form closed shells. Nuclei that contain magic numbers of both protons and neutrons are even more stable and are said to be "doubly magic". Silicon-42 is very close to the limit of (hierarchial) nuclear existence. The silicon-42 nucleus remains stable despite containing a large excess of neutrons. The data also suggest that the proton number 14 is semi-magic because it corresponds to a closed subshell, which means large s-wave probability and the nucleus is also spherical. Whether the major shell closures and magic numbers change in very neutron-rich nuclei (potentially causing shape deformations) is a fundamental, and at present open, question.


The stable nuclides are shaded. The nuclei studied here—⁴²Si, ⁴³P and ⁴⁴S—are circled. N, number of neutrons; Z, number of protons. Table of nuclides. Also the recent As instead of P can be seen as an hierarchial form of Life?

This brings into mind the islands of stability, protons:neutrons, and the hierarchial problem. Energy loss : time? Islands of Life, what axes do it use? Varying, says Quantitative Habitability Theory. The C:O axis? Life as islands of rational/algebraic numbers in TGD. The mass gap, shell gap? Mass is not fundamental, but derived. There is currently no understanding of the way space-time could be reduced. Living matter has taken another path than ordinary matter?(a.k.a. Mysteries of Life). There are two entirely different mass scales, Planck scale and electroweak scale, how can these particles be so light? Some models are here.

The nuclei with Z=120, 124, 126 and N=184 are predicted to form spherical doubly-magic nuclei and be stable with respect to fission.

Neutron-rich and doubly magic,The existence of a new ‘doubly magic’ nucleus found with an unconventional configuration of neutrons. The oxygen–24 nucleus is also the first doubly-magic nucleus that is very unstable against radioactive decay. Could shed light on neutron-rich environments such as neutron stars and supernovae.

...protons and neutrons in nuclei occupy discrete orbitals — in much the same way as electrons do in atoms. Magic nuclei are those having the precise number of protons or neutrons required to fill a spherical set of related orbitals called a ‘shell’. Nuclei with magic neutron or proton numbers are characterized by a stronger binding, greater stability, and, therefore, are more abundant in nature. In doubly magic nuclei, both proton and neutron shells are filled, making the binding even stronger.

“It’s thanks to the doubly magic numbers that nuclei such as oxygen and calcium are abundant making it possible for us to exist on earth.” They form benchmark points for the nuclear shell model. The magic numbers in stable nuclei — which have similar numbers of protons and neutrons and don’t undergo radioactive decay — are known to be 2, 8, 20, 28, 50, 82 and 126. However, less is known about magic numbers in unstable nuclei in which the ratio of neutrons to protons is significantly greater.
Showed how the orbitals are arranged within the nucleus. The results confirmed that the arrangement was spherically symmetric — a hallmark of doubly magic nuclei- one conventional magic number (8 protons) and an unconventional magic number (16 neutrons).
“Our world-wide collective effort to understand the physics behind the extremes of our universe is bringing many pieces of the puzzle together slowly.” Twice as many neutrons as protons.
Oliver K. Manuel: All n-p interactions are strongly attractive inside the nucleus. These are accompanied by repulsive and symmetric n-n and p-p interactions that are made even more repulsive by interactions between the + charges on protons for the p-p interactions. In 2000 it was first discovered that repulsive forces between neutrons are dominant in all neutron-rich nuclei.

Can the new Neutrino Telescopes reveal the gravitational properties of antimatter? Hajdukovic 2010:

The Ice Cube, a neutrino telescope under construction at the South Pole, may test the [hypothetical] hypothesis of the gravitational repulsion between matter and antimatter. If there is such a gravitational repulsion, the gravitational field, deep inside the horizon of a black hole, might create neutrino-antineutrino pairs from the quantum vacuum. While neutrinos must stay confined inside the horizon, the antineutrinos should be violently ejected. Hence, a black hole (made from matter) should behave as a point-like source of antineutrinos. Our simplified calculations suggest, that the antineutrinos emitted by supermassive black holes in the centre of the Milky Way and Andromeda Galaxy, could be detected at the Ice Cube.

A hypothetical gravitational repulsion between matter and antimatter (“antigravity”) which dramatically differs from the mainstream conviction of equal gravity for the two. Matter and antimatter are mutually repulsive but self-attractive? (How, I want to ask? What is 'self'? it is not gravitational at all, but still attracting? Some immaterial dark force? The combination of zero energy ontology with the cosmic evolution inspires to concrete ideas about what the localization of contents of consciousness experience around narrow time interval identi ed as moment of subjective time. Can similar times be attractive? Or similar consciousnesses? Time and consciousness?)

In our Universe dominated by matter, the miniscule quantities of antimatter could not have any significant impact on gravity. However this naïf point of view neglects the physical vacuum, in which virtual matter and antimatter “appear” in equal quantities according to Quantum Field Theory (QFT),. Hence, the gravitational mass of the quantum vacuum (and thus the fate of the Universe) depends on the gravitational properties of antimatter. A gravitational field, sufficiently strong to create particle-antiparticle pairs, could exist only deep inside the horizon of a black hole. An immediate consequence is that if (for instance) a black hole is made from ordinary matter, produced particles must stay confined inside the horizon, while antiparticles should be violently ejected because of the gravitational repulsion.

Non-thermal radiation of black holes may exist even if there is no antigravity. Imagine that there is a still undiscovered interaction, repulsion between matter and antimatter, with the following features: (a) The new force acts, between particles having an appropriate “charge”, which (just as the electric charge) can be positive or negative. In order to be definite, a positive “charge” is attributed to matter and a negative one to antimatter. (b) There is an attractive force between “charges” of the same sign, and a repulsive force between “charges” of different sign. This is just opposite to the familiar case of electric charges. (c) The assumed repulsion between particles and antiparticles is stronger than the gravitational attraction between them. (d) It may be a force with much shorter range of interaction than gravitation. Such a new force is less elegant possibility than antigravity but it is evident that it can produce particle-antiparticle pairs according to equation.

Pauli has done great things even when it comes to antimatter - such as a proof of the CPT-theorem that links the properties of antimatter in the mirror to the properties of matter that moves backward in time.

Magnetic monopoles comes into mind. When a charged particle is brought close to the surface of a topological insulator, a magnetic monopole charge is induced as a mirror image of the electric charge. Quasiparticles as axions, anyons etc. which goes through zero. The electro-magnetic polarization θ(x)/2π oscillate = ±1/2 determined by the direction of the surface magnetization.
Consider the geometry, a complete boundary value problem. (q = (θ/2π)g derived by Witten, 1979). A 2D electron gas in the neighborhood of the surface will becomes a “dyon” gas with fractional statistics. Exotic particles such as the magnetic monopole, dyon, anyon, and the axion have played fundamental roles in our theoretical understanding of quantum physics.

Let us assume in the lower half space the electric field is given by an effective point charge q/ǫ1 and an image charge q1 at (0, 0, d), whereas the magnetic field is given by an image magnetic monopole g1 at (0, 0, d). In the upper half space the electric field is given by an electric charge q/ǫ1 at (0, 0, d) and an image charge q2 at (0, 0,−d), the magnetic field is given by an image magnetic monopole g2 at (0, 0,−d). It is easily seen that the above ansatz satisfies the Maxwell’s equation on each side of the boundary. At the boundary z = 0 shows that for an electric charge near the surface of a topological insulator, both an image magnetic monopole and an image electric charge will be induced.

Kaon-pion oscillations?

Grandma

I must send some wonderful pictures of me and my grandchildren, Cina and Mathias, 2 year resp. 5 months. Also the little boy understand important things, like what he would wish for christmas from Father Christmas :) The knee full of warm children, wonderful. I remember my own motherhood with four children. I also remembered it when I was babywatch on saturday evening and the little one said I did not cook his soup as his mother did, nor the milk as mom. He was really angry at me :) Puh, at last he slept, and so mom and dad came home, and Cina and I had just sat down on the floor with LEGO constructioning of fantastic castles. NO, no, she said, go away....

It is not so easy to be a mom or dad. Or big sister. They came home so fast... They thought that little Mathias was not so pleased...

He is a very intelligent boy for 5 months. He smiles as he wants to say some comment when we talk, and his eyes look so intelligent.


And he laughs at his sisters troublesome behaviour, then he tries the same, but his body doesn't do like he wants it to do. He is so frustrated. And the speech don't succeed either, aich.

Evolution is a process.

On Physics arXive Blog they talked about biology and evolution, the possibility that life as it has evolved on Earth is but a local minima in a vast landscape of evolutionary possibilities. If that's the case, biologists are studying a pitifully small fraction of something bigger. Much bigger. Then the charachter of Life could also look very much differently from what we see on Earth? Already here we have such a diversity of life forms. Take nanobacterias for instance. And yet many are undiscovered, also in the human body.

Usually biological evolution stops at the emergence of Life and the cosmical evolution starts, but there is no essential difference between the two concepts. There was a wast evolution also before Life was created on Earth. The RNA World is much about that pre-biological evolution.

As I see it Life is a phase of intermediate matter, where the quantum world is very much ruling. The Schrödinger cat is both dead and alive. It is not about chemistry, because also chemistry is ruled by the same quantum world. Merely you can see ordinary matter and living matter as two different paths of realisation. For living matter the governing rule is the capacity to react on surroundings and change the surroundings in own favor. Ordinary matter is bad at that. Essentially Life is about consciousness and qualias, which requires self-awareness and memory.

Today, we get an important insight into this state of affairs thanks to a fascinating paper by Nigel Goldenfeld and Carl Woese at the University of Illinois. Life Is Physics: Evolution As A Collective Phenomenon Far From Equilibrium. Goldenfeld is a physicist by training while Woese, also a physicist, is one of the great revolutionary figures in biology. In the 1970s, he defined a new kingdom of life, the Archae, and developed a theory of the origin of life called the RNA world hypothesis, which has gained much fame or notoriety depending on your viewpoint.

They suggest that biologists need to think about their field in a radical new way: as a branch of condensed matter physics. Their basic conjecture is that life is an emergent phenomena that occurs in systems that are far out of equilibrium. Goldenfeld and Woese say that biologists' closed way of thinking on this topic is embodied by the phrase: all life is chemistry. Nothing could be further from the truth.

And they take the example of superconductivity. No wonder.

The real explanation is much more interesting and profound. It turns out that many of the problems of superconductivity are explained by a theory which describes the relationship between electromagnetic fields and long range order. When the symmetry in this relationship breaks down, the result is superconductivity. And it doesn't just happen in materials on Earth. This kind of symmetry breaking emerges in other exotic places such as the cores of quark stars. Superconductivity is an emergent phenomenon and has little to do with the behaviour of atoms.

Life is like superconductivity. It is an emergent phenomenon and we need to understand the fundamental laws of physics that govern its behaviour. Consequently, only a discipline akin to physics can reveal such laws and biology as it is practised today does not fall into this category.

In the paper they point to some crucial facts:
- we have too little genes to encode for all that is needed, brain only would need them all. The collapse of the doctrine of one gene for one protein, with one direction of causal flow from basic codes. The key to complexity is not more genes, but more combinations and interactions generated by fewer units of code and many of these interactions (as emergent properties) must be explained at the level of their appearance, for they cannot be predicted from the separate underlying parts alone. Genes need to be treated collectively.
- majority of signaling is microbial also in the body, with coordinated division of labor, cellular differentiation and cooperative defense
- evolution was equal to 'natural selection', and relegated to a peripheral role during the development of molecular biology and high-tech biophysic. Collective phenomena are important also in microbiology etc.
- biology may extend the frontier of non-equilibrium physics, revealing principles of self-organization that seem absent in purely physical processes such as pattern formation
- sexual reproduction, fitness, growth rates

I could add to that list a lot.

What about death then? What brings the flow to cease?

The main problem with Life is its coherence and synchrony and that is not "far from equilibrium" - on the contrary, it is very much about equilibrium, but as a "bubble in bubbles", a phase transition. Energetically life is an open system, though, and requires an energy flow going through the ecosystem. Maybe, if you take entropy as the leading star but Life is about negentropy. A maximation of negentropy, (or a minimal decoherence) that is collected from environment by the superconductive nerves, perception organs, and at the far end the carbon networks. It is no random chance Life is based on carbon. This year the Nobel prize in physics went to graphene, a very interesting material in the science of what Life is, although arbitrary.

To the biologist interested in practical issues, we ask that you do not dismiss the seemingly useless and na¨ıve issues that we necessarily raise. On the one hand, a fundamental understanding of evolution may not seem to offer immediate benefits in terms of finding the next wonder drug; on the other hand, the lack of appreciation for the rapidity and pervasiveness of evolution has, within a lifetime, destroyed the effectiveness of numerous antibiotics, and probably is responsible for the limited success of the treatment of cancer. The biomedical-industrial complex cannot afford to ignore the need to create a fundamental science of biology.

That is true. Physical texts about biology often seems so naive, but they are looking for the similarities, the first principles.

The lack of structure in the way that biology is traditionally presented reflects the field’s unavoidable focus on a single sample path; however, the underlying evolutionary process itself is surely one with deep mathematical structure, capable of expression and elucidation in unifying terms based on emergent physical laws. This is a true frontier of physics, but one that will require a great deal of what has been termed (in another context of non-equilibrium physics) “open-minded spadework” to unearth.

Superconductivity is best understood as arising from the breaking of the global U(1) gauge symmetry in the effective field theory that describes the interaction between offdiagonal long-range order and the electromagnetic field. It is not about chemistry. There is nothing fundamental about the atoms or molecules. Examples are topological insulators, other examples of major significance include the Aharonov-Bohm effect, the quantum spin Hall effect, localization, and the renaissance in atomic, molecular and optical physics provided by the experimental realization of atomic Bose-Einstein condensates.

It certainly is not a microscopic theory, because it lacks a biochemical level of description, and it is certainly an effective theory, valid only when there is a separation of scales between ecosystem dynamics and gene mutation dynamics.

First, the very existence of the phenomenon of life needs to be understood.
Second, the realization or instantiation of it, on Earth, for example, needs to be understood. For the most part, it is fair to say that the discipline of biology has neglected the first condition, and in pursuit of the second, has confused understanding of the realization with understanding of the phenomenon. This has had a number of unfortunate consequences, which arguably have hindered both the conceptual development of biology and the proper application of foundational understanding to societal applications.

Perhaps the primary shortcoming of the biological enterprise is the manifest failure to account for the phenomenon of the existence of life. Without doubt, this failure reflects not only on biologists, but also on physicists. Biology is a big anomaly, echoes in my brain. Said by Matti Pitkänen.

At last something begins to happen.

Not from dark matter?

The Galactic centre is one of the most dynamic places in our Galaxy. It is thought to be home to a gigantic black hole, called Sagittarius A.
January 12th 2008: Antimatter Cloud Traced To Binary Stars. Four years of observations from the European Space Agency’s Integral (INTErnational Gamma-Ray Astrophysics Laboratory) satellite may have cleared up one of the most vexing mysteries in our Milky Way: the origin of a giant cloud of antimatter surrounding the galactic center. What? I look at NASA 01.09.08 .


Integral mapped the glow of 511 keV gamma rays from electron-positron annihilation. The map shows the whole sky, with the galactic center in the middle. The emission extends to the right.
Look at the picture of M87 in the earlier post. They show the same kind of nucleus. The cloud shows up because of the gamma rays it emits when individual particles of antimatter, in this case positrons, encounter electrons, their normal matter counterpart, and annihilate one another.

Integral found that the cloud extends farther on the western side of the galactic center than it does on the eastern side. This imbalance matches the distribution of a population of binary star systems that contain black holes or neutron stars, strongly suggesting that these binaries are churning out at least half of the antimatter, and perhaps all of it. The detection of an asymmetry. It is lopsided with twice as much on one side of the galactic centre as the other. Such a distribution is highly unusual because gas in the inner region of the galaxy is relatively evenly distributed.

The cloud itself is roughly 10,000 light-years across, and generates the energy of about 10,000 Suns. The cloud shines brightly in gamma rays due to a reaction governed by Einstein’s famous equation E=mc^2. Negatively charged subatomic particles known as electrons collide with their antimatter counterparts, positively charged positrons. When electrons and positrons meet, they can annihilate one another and convert all of their mass into gamma rays with energies of 511,000 electron-volts (511 keV). Scientists don’t understand how low-mass X-ray binaries could produce enough positrons to explain the cloud, and they also don’t know how they escape from these systems. "We expected something unexpected, but we did not expect this," says Skinner. The antimatter is probably produced in a region near the neutron stars and black holes, where powerful magnetic fields launch jets of particles that rip through space at near-light speed.

The antimatter cloud was discovered in the 1970s. What? Why do they then not talk about it, but say there is no dark matter? Incredible.

Scientists have proposed a wide range of explanations for the origin of the antimatter, which is exceedingly rare in the cosmos. For years, many theories centered around radioactive elements produced in supernovae, prodigious stellar explosions. Others suggested that the positrons come from neutron stars, novae, or colliding stellar winds. Particles of dark matter were annihilating one another, or with atomic matter, producing electrons and positrons that annihilate into 511-keV gamma rays. But other scientists remained skeptical, noting that the dark matter particles had to be significantly lighter than most theories predicted.

Well, we have just seen that the 'Higg is probably much lighter than expected. If it even exist at all?

Integral found certain types of binary systems near the galactic center are also skewed to the west. These systems are known as hard low-mass X-ray binaries, since they light up in high-energy (hard) X-rays as gas from a low-mass star spirals into a companion black hole or neutron star. Because the two "pictures" of antimatter and hard low-mass X-ray binaries line up strongly suggests the binaries are producing significant amounts of positrons. NASA’s Gamma-ray Large Area Space Telescope (GLAST), scheduled to launch in 2008, may help clarify how objects such as black holes launch particle jets. That paper we had just seen.

The unexpectedly lopsided shape is a new clue to the origin of the antimatter. The observations have significantly decreased the chances that the antimatter is coming from the annihilation or decay of astronomical dark matter. Some astronomers have suggested that exploding stars could produce the positrons. This is because radioactive nuclear elements are formed in the giant outbursts of energy, and some of these decay by releasing positrons. However, it is unclear whether these positrons can escape from the stellar debris in sufficient quantity to explain the size of the observed cloud.

Not from dark matter?
Dark matter is thought to exist throughout the Universe – undetectable matter that differs from the normal material that makes up stars, planets and us. It is also believed to be present within and around the Milky Way, in the form of a halo.

The recent study has found that the ‘positrons’ fuelling the radiation are not produced from dark matter but from an entirely different, and much less mysterious, source: massive stars explode and leave behind radioactive elements that decay into lighter particles, including positrons.

The reasoning behind the original hypothesis was that positrons, being electrically charged, would be affected by magnetic fields and thus would not be able to travel far. As the radiation was observed in places that did not match the known distribution of stars, dark matter was invoked as an alternative for the origin of the positrons.

But the recent finding by a team of astronomers led by Richard Lingenfelter at the University of California at San Diego, proves otherwise. The astronomers show that the positrons formed by radioactive decay of elements left behind after explosions of massive stars are, in fact, able to travel great distances, with many leaving the thin Galactic disc.

We can convert pure energy into equal amounts of matter and antimatter. Matter and antimatter can also convert back to energy. In a universe with equal amounts of matter and antimatter, we’d expect most of it to annihilate. We know that particles called neutral B mesons can fluctuate from matter to antimatter and back again, like a seesaw going up and down.

New physics?
SkiDaily aug 2010: The Tevatron experiments DZero found that colliding protons in their experiment produced short-lived B meson particles that almost immediately broke down into debris that included slightly more matter than antimatter. The two types of matter annihilate each other, so most of the material coming from these sorts of decays would disappear, leaving an excess of regular matter behind. But the truly exciting implication is that the experiment implies that there is new physics, beyond the widely accepted Standard Model, that must be at work. If that's the case, major scientific developments lie ahead.

The explanation for the dominance of matter in the present day universe is that the CP violation treated matter and antimatter differently. New result provides evidence of deviations from the present theory in the decays of B mesons, in agreement with earlier hints,so the measurement is consistent with any known effect is below 0.1 percent (3.2 standard deviations). When matter and anti-matter particles collide in high-energy collisions, they turn into energy and produce new particles and antiparticles. At the Fermilab proton-antiproton collider, scientists observe hundreds of millions every day.
Both CDF (top quark) and DZero (bottom quark) therefore continue to collect data.

DZero physicist wins prestigious UK prize.

Borissov, from Lancaster University in England, was recognized by the UK society for his work on B physics. He was also part of a team whose work received media attention, including a front page article in the New York Times, in May of 2010 when DZero found evidence of a bias toward matter over antimatter. This observation, called dimuon charge asymmetry, could help to explain why the universe as we know it is composed of matter. “The Standard Model is not able to explain why we have the world around us.”

But there is also a parity asymmetry?

Dark matter and antimatter relations.
Here I will explain the difference between matter, anti matter, dark matter, and negative matter in a concise and understandable way, say Hontas Farmer. Dark matter only interacts by way of gravity and the weak atomic force. Dark matter does not interact via the strong atomic force hence dark matter cannot be seen. It only interacts via the weak force which is what keeps neutrons and protons inside the nucleus of atoms together. Such is why experiments to detect dark matter directly rely on a particle of dark matter bumping into a particle of matter.

But that is difficult without some strong force in the surroundings, or that all the forces vanish?

Antimatter as dark matter?
It is conceivable that the dark matter (or at least part of it) could be antimatter, but there are very strong experimental reasons to doubt this. For example, if the dark matter out there were antimatter, we would expect it to annihilate with matter whenever it meets up with it, releasing bursts of energy primarily in the form of light. We see no evidence in careful observations for that, which leads most scientists to believe that whatever the dark matter is, it is not antimatter.
"It would take longer than the age of the universe to make one gram of antimatter."

Dark matter is not necessarily anti-matter. Dark matter is matter that for some reason doesn't emit or reflect light. It could be purely transparent, never interacting with light. Invisibility is a change of Planck constant? Antimatter goes to the past is also said. What would that mean? We cannot see the past? The largest part of dark matter which does not interact with electromagnetic radiation is not only "dark" but also by definition utterly transparent; in recognition of this, it has been referred to as transparent matter by some astronomers".
Water is also transparent.

Antimatter could be anyons? That is seen in superconduction and condensed matter physics. "Some exotic particle-like structures known as anyons appear to entwine in ways that could lead to robust quantum computing schemes", according to Kirill Shtengel. The anyons the researchers believe they have created are not true particles that can exist on their own, like electrons or protons. Instead anyons are quasiparticles that exist only inside a material, but move in ways that resemble free particles. Although braids in three dimensions unravel easily, braids trapped in two dimensions can't pull apart, which means they're able to withstand disturbances that would scramble the data and calculations in other quantum computers.

Wilczek. Quantum Computers and Anyons, in Edge Bio page.

I am very fond of anyons because I worked at the beginning on the fundamental physics involved. It was thought, until the late 70s and early 80s, that all fundamental particles, or all quantum mechanical objects that you could regard as discrete entities fell into two classes: so-called bosons after the Indian physicist Bose, and fermions, after Enrico Fermi. Bosons are particles such that if you take one around another, the quantum mechanical wave function doesn't change. Fermions are particles such that if you take one around another the quantum mechanical wave function is multiplied by a minus sign. It was thought for a long time that those were the only consistent possibilities for behavior of quantum mechanical entities. In the late 70s and early 80s, we realized that in two plus one dimensions, not in our everyday three dimensional space (plus one dimension for time), but in planar systems, there are other possibilities. In such systems, if you take one particle around another, you might get not a factor of one or minus one, but multiplication by a complex number—there are more general possibilities.

More recently, the idea that when you move one particle around another, it's possible not only that the wave function gets multiplied by a number, but that it actually gets distorted and moves around in bigger space, has generated a lot of excitement. Then you have this fantastic mapping from motion in real space as you wind things around each other, to motion of the wave function in Hibert space—in quantum mechanical space. It's that ability navigate your way through Hilbert space—that connects to quantum computing and gives you access to a gigantic space with potentially huge bandwidth that you can play around with in highly parallel ways, if you're clever about the things you do in real space.

But in anyons we're really at the primitive stage. There's very little doubt that the theory is correct, but the experiments are at a fairly primitive stage—they're just breaking now.

Back to the blackboard?

Reference: ‘An asymmetric distribution of positrons in the galactic disk revealed by gamma rays’ by Georg Weidenspointner et al. 10 January, in Nature.

Lingenfelter, R.E., Higdon, J.C. Rothschild, R.E. Is There a Dark Matter Signal in the Galactic Positron Annihilation Radiation? Physical Review Letters, 2009; 103 (3): 031301 DOI: 10.1103/PhysRevLett.103.031301

The D0 Collaboration: V.M. Abazov, et al. Evidence for an anomalous like-sign dimuon charge asymmetry. Physical Review D, 2010. http://arxiv.org/abs/1005.2757
R. L. Willett, L. N. Pfeiffer, K. W. West. Alternation and interchange of e/4 and e/2 period interference oscillations consistent with filling factor 5/2 non-Abelian quasiparticles. Physical Review B, 2010; 82: 205301 DOI: 10.1103/PhysRevB.82.205301

Kirill Shtengel. Non-Abelian anyons: New particles for less than a billion? APS Physics, 2010; 3 (93) DOI: 10.1103/Physics.3.93

The Fermilab Tevatron experiments: the APS journals Physical Review Letters and Physical Review D. Aug. 17, 2010 , and 14 may 2010.

The DZero result is based on data collected over the last eight years by the DZero experiment at Fermilab. Besides Ellison, the UC Riverside co-authors of the paper, submitted for publication in Physical Review D, are Ann Heinson, Liang Li, Mark Padilla, and Stephen Wimpenny.

http://www-d0.fnal.gov/Run2Physics/WWW/results/final/B/B10A/

Cern, antimatter, Mirror of the universe, links.