söndag 26 december 2010

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."

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...


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

fredag 24 december 2010

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,LinkProto.
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 . 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 ."

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.

torsdag 23 december 2010

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-kappa 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.

måndag 20 december 2010

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.

söndag 12 december 2010

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?