Tuesday, November 30, 2021

As The Race To Grasp Omicron's Threat Proceeds, Honing In On The Specific Mutations Sheds Light


Image of spike protein of SARS-Cov-2 virus is shown with three small antibodies (pink)attached to its receptor binding domains. (From Physics Today, Vol. 73, No. 9, p. 22)
                  Locations of omicron mutations (blue) and base insertions/deletions (red)


If the omicron Covid variant turns out to be vaccine resistant, let us admit right now it is "game over".  Vaccine resistance means also immunity resistance, so that every human on Earth will now be a potential target for this microbe predator. The takeaway, as the reader of this post will see, means every human on the planet is liable to become a potential casualty - but especially those who have totally avoided getting any vaccinations.   

These and other insights are possible when one examines the specific mutations at work (e.g. Weekend Financial Times) and their properties as they affect the R nought value (transmission) and capacity to neutralize antibodies.  But first it is incumbent on me to call attention to the latest insane and degenerate  ploy of the Right in claiming that omicron is a "Democratic trick"  to help them win in the midterm elections next year.  

Don't take my word for it, check for yourself by doing some targeted Googling, including Dr. Ronnie Jackson omicron tweet, e.g.

The Hill
Trump's White House doctor calls omicron a midterm elections trick | TheHill

Even before this baloney from a low I.Q. quack, the resident clowns on Fox and Friends were yapping about "Every October, look for another variant". 

 I.e. The Democrats pull them out of assorted hats for political leverage. 

 Only a dumb red state goober could possibly  believe that codswallop especially given that even the most low information voter ought to grasp by now that the Repuke cult doesn't have his best interests at heart.  

That Trumpist cult is only interested in bamboozling the base to embrace vaccine rejection, by getting it to believe more garbage about vaccines and virus "hoaxes".  The latest twist: to regard Dr. Fauci as another Dr. Mengele. 

Don't know who he is?  

He was the Nazi doctor at Auschwitz who experimented on twins - mainly Jews and Gypsies- taking the parts of one (after amputation) and sewing them on to others to note the effects.  

That's today's Repuke traitor "party" for you!

In other words, pile up more dead bodies for the sacrifice to Trump!  This omicron, contrary to rightist fantasies, looks like it will be more infectious than even Delta.

Why am  I worried about this?  What communications or actual  evidence supports it?  For one, the detailed site map for omicron's mutations vs. base insertions-deletions appearing in the weekend Financial Times.  

For another, the remark of a Rockefeller Institute virologist (Theodora Hatziioannou ) appearing on page A6 of yesterday's WSJ.  She stated: 

"What is extremely worrisome is the accumulation of so many mutations. The other worrying thing is that [its] mutations overlap with the mutations we identified in our system…I don’t know how this thing is going to be anything but resistant."

 This ought to worry every sane and sentient citizen especially those who out of foolish sense of "freedom" have yet to be vaccinated.  As is well-documented by now (WSJ, Nov. 27-28, 'Vaccine Disparity Paves Way For Strains'), vaccine disparity, i.e. between vaccinated and unvaccinated populations, is what sets the stage for new virus mutations.  In particular (ibid.): 

"Just 7 percent of  people in Africa are fully vaccinated compared to 42 percent in the global population....That disparity, public officials say, helped open the door to the latest variant."

It is also a cautionary tale regarding the less pronounced vaccine disparity in the U.S., i.e. between red and blue states.   In other words, just as a new variant emerged in Africa, one could emerge in the U.S. given its own disparity - thanks to freaks and propagandists like Tucker Carlson at FOX News - who  keeps vaccine hesitancy going.  Another reason the vaccines have risen in import is based on the new finding that Merck's Covid 19 pill  Molnupiravir (presumed by some to be an alternative to the vaccines) has now been found to be 30 percent less effective  in the final study - than originally thought.  (WSJ, op. cit., p. A6, 'Merck's Covid 19 Pill Was 30% Less Effective In Final Study')  This means that vaccines, including boosters, remain the only way out of this pandemic if we ever get there .

What about the so-called multi-valent vaccines, i.e which can tackle multiple strains of the Covid virus? Well some companies are doing testing, but it will be months before a final product appears and months more before the public can get an additional shot. But that assumes no further mutations at the spike protein because millions allow it to keep churning because they are infected by the FOX News virus!

It is important, in the meantime, to get as many people vaccinated as possible and reduce the vaccine disparity that exists in the world.  As Barbados Prime Minister Mia Mottley recently put it in her UN speech: "Until all are safe, none are safe." 

As it is we may well be on the cusp of a variant (the "Omega"?)  that is vaccine resistant, which would be our worst nightmare.  Let's look at what is happening with regard to these 50 mutations found in the omicron variant thus far, 30 of which are concentrated on the spike protein where the virus capability to infect the respiratory system resides.

Focus on (1) in the lower graphic, which shows a combination of mutations at virus locations: K417N, S477N,  Q498R  and N501Y, all of which are thought to be cooperative in an antibody invasion strategy.  In this sense, this combo reflects what author Laurie Garrett warned us about in her book, 'The Coming Plague' that these viruses will keep adapting - trying ever new mutations - until they defeat our immune systems, vaccines or both.   

Look now at position (3) which features four additional new mutations at Q339D, S371L, S373P and S375F - all of which are geared to creating added obstacles for antibodies. Then there are the three mutations near the furin cleavage site at H655Y, N679K and P681H which may be associated with increased transmissibility  - putting the R nought value Omicron now near 2.0.  This is close to the value peculiar to the Spanish Flu virus in 1918 which decimated 5% of the global population.  

Lastly, there are 15 mutations in the receptor binding domain  - the part of the spike that mediates how easily the virus attaches itself to respiratory epithelial cells.  These 15  mutations represent more than have ever before been detected in this domain.

The bottom line takeaway from all this?  Omicron's genomic profile is unique from all other circulating variants, and far more a threat to our protective arsenals.  We now have the actual data that show there are more specific mutations that translate to more opportunities to disable antibodies and current vaccine protections. See, e.g.

Moderna chief predicts existing vaccines will struggle with Omicron

A few more mutations targeting the same spike protein may mean the neutralizing of all vaccines- present and future.  We also know it is distinct from earlier variants in another crucial way: it causes one part of some multi-part viral tests - called PCR tests- not to work. That means depending on such tests may mean 'flying blind' in terms of where omicron is, who has it - and how many.  

 It may stretch people to the point of despair that we may have to deal with Covid and its variants for the rest of our lives.  But that  may well be the least of our worries going forward.  Dozens of ancient viruses are emerging from melting permafrost as I write, and any one may have the infectious ability of Covid-19.  If a 30,000 year old virus (like Pithovirus sibericum)  can maintain its infectious ability then many others may well be capable of revisiting us in catastrophic fashion.  

The point?  Emerging viruses - as well as Covid -  are bloody serious stuff and not to be made the fodder for politicization or deranged conspiracy ideations as the Right has  done.  As Janice exclaimed when she saw Jackson's tweet on ALL In last night, and then the Fox and Friends clowns:  "They just want to destroy the country!"  I replied:  "What do you expect of goddam traitors in a traitor cult?"    She then asked: "If this was really a Democratic trick why is it all around the word in 19 countries now?" And I added: "Think low I.Q.  Very low!"  Further, if this doesn't show once and for all that these twits are unqualified, unelectable cockroaches then I don't know what does.  

Jackson and his putrid cohort bark that omicron is a Democratic trick to keep control of congress in next year's mid terms -  but the truth is a GOP resounding defeat ought to be the reality in ANY case, minus any other considerations! Do serious citizens, voters really want asswits like Jackson and Bimbo Lauren Bobert, nutcase Marjorie Taylor Greene and other other Reep conspiracy mongers and losers running the country? 

REALLY?  If that is true then I'm afraid Janice's persistent claim that the average IQ of the nation really is "subnormal" is proven.  Like in moron to imbecile range.   And we as a nation will certainly go very much the same way as the good Germans in 1933.

  See Also:

by Thom Hartmann | December 4, 2021 - 8:24am | permalink

by P.M. Carpenter | November 30, 2021 - 7:24am | permalink


by Amanda Marcotte | November 30, 2021 - 8:50am | permalink

— from Salon


by Thom Hartmann | December 2, 2021 - 8:38am | permalink

— from The Hartmann Report


Over 800,000 Americans are now dead from Covid, as we track daily at TrumpDeathToll.org.

Multiple studies suggest as many as a third of the roughly 50 million Americans who’ve contracted Covid are now disabled by having had the disease, many for life. These mostly unvaccinated people are now crippled with “long Covid” conditions ranging from chronic exhaustion to dementia to life-shortening heart and kidney disease, which can’t be helping the labor shortages across key sectors of our economy.

Dr. Fauci has been working for two years to try to reduce that death toll, and on Fox they’re calling him Dr. Mengele? As the Auschwitz Memorial museum tweeted after Logan’s comments:

“Exploiting the tragedy of people who became victims of criminal pseudo-medical experiments in Auschwitz in a debate about vaccines, pandemic and people who fight for saving human lives is shameful. It is disrespectful to victims & a sad symptom of moral and intellectual decline.”

Monday, November 29, 2021

'Meta' or "Metaverse" - A New Opportunity, Passing Fad Or Virtual Malignancy?

"While the metaverse could revolutionize work and play, it is essential to remain wary of the dangers that will emerge if it subsumes daily life. Virtual environments will supercharge disinformation campaigns, espionage and surveillance. Struggles for control of the metaverse’s physical infrastructure could very well aggravate global conflicts... A failure to anticipate these possibilities may put the global world order at risk of being replaced by a virtual, and perhaps less virtuous, one" . - Zoe Weinberg, NY Times, 'The Metaverse Is Coming and the World Is Not Ready For It'.

Amidst the turbulent real world wherein all our political futures may well be at stake it is incomprehensible that anyone - any citizen - would take refuge in a virtual world as an avatar.  This is not the mark of a conscious participant in the world-  or the nation  - but of a loser or psychopath.  I am specifically referring here to anyone who'd deign to live 24/7 in a virtual world - or even 12/7.   Hence, it was appalling to read in one NY Times piece on Saturday about a kid declaring he wanted a "VR headset" for Xmas.  Why?  Is he tired of regular video games and now seeks pure escape as an avatar in a fantasy world? 

 Where is there such a misbegotten world? Well, in the much hyped "metaverse" - already spawned into a quasi reality -   as Facebook guru Mark Zuckerberg renamed his creation "Meta".  He plans to make 'Meta' as indispensable to billions as he has Facebook, if not more. Is this good?  It can't be if it divorces pandemic-stressed humans even further from reality. As columnist JoAnna Novak  (We’re Longing for the One Thing the Metaverse Can’t Give Us ) from the NY Times warned:

"Through virtual and augmented reality (also Ray-Ban Stories smart glasses), Meta’s technology aims to change how we live, how we connect with friends and family. (Imagine teleporting hologram-you to concerts or Thanksgiving dinners.) Except for all its patter about bringing people together, Meta advances a fundamental human disconnection: It removes our bodies from the equation.


"I, for one, will not go gentle into the metaverse. Not because I’m anti-technology (I’m not) or unreasonably attached to the pleasures of gel ink pens and hard-bound books (I may be). It’s because after I’ve struggled with anorexia and bulimia for more than 20 years, the last thing I want is technology that further estranges me from my body. “If we lose touch with ourselves,” the philosopher Richard Kearney writes, “we lose touch with the world. No tactile connection, no resonance between self and other.”

Is this hyperbolic? No!  Losing touch with oneself and others means becoming more unreal, and therein lies the danger of full blown psychosis. Articles about touch hunger and touch starvation since Covid began already reveal just how vital real tactile connection is. It is also conceivable that the increasingly unhinged behavior we are seeing is tied to this 'touch famine' -   everything from fights with attendants on planes, to the increased crime rates now in urban areas.

There is also a dopey, naive assumption that entering this "metaverse" will just be hunky dory -- no problems!  As one mom in a related NY Times piece expressed her own fears of kids merely stuck inside  -  glued to screens during the pandemic:

"My children do not know how to read a room, observe the set of a jaw or assess the determination of a glare. They wave at strangers and are apt to start up conversations, assuming that the other person bears them good will. "

Imagine how much less able these kids would be in a virtual world,  trying to assess the "set of jaws" of avatars-(or their "staring  glares") in a metaverse. It would be as if such kids were left to fend for themselves amidst a virtual jungle of totally disguised  threats rivaling those in the outside, real world.  

These threats posed as malignant or innocuous- looking avatars are not to be scoffed at. Prof. Julia Shaw ('Evil: The Science Behind Humanity's Dark Side')   has shown this clearly (pp. 112- 114) in terms of how bots -as well as avatars, presumably - can "change their algorithms" and learn to manipulate their environments in destructive ways.  AI might enable a less benign person to devise an avatar resembling a demon, marauding across a virtual landscape, e.g. 

And preying on innocents, for example. Acknowledging this, Prof. Shaw insists we need "new rules in place - even laws- that decide who is accountable".  Even asking:  "Can we hold technology legally accountable?"  Well, in truth, I don't believe we are there yet.   But details like this ought to be nailed down and the sooner the better! For example, as Prof. Shaw asks: "Is it really a crime if that which is doing the crime is not a human?"   Say if the avatar is actually a bot-driven entity in the guise of Satan, e.g.

And it attacks an innocent avatar,  albeit also bot -driven, named "Kendra" (from the "Messiah Game"), e.g. 

Can it be held accountable? Can the technology be held accountable? What if your kid's avatar in 'Meta'  encounters a welcoming "Kendra"   - innocent as she is -  but an algorithm trigger suddenly shape-shifts "Kendra"  into the "Satan" form -which grabs your kid's avatar?  Prof. Shaw rightly argues such actions put evil into a novel and more frightening context we need to urgently address. Again, how do we regard any kind of virtual act especially one involving an attack of one avatar on another? Is it real, or merely imaginary? 

For now-  and on a more tranquil, less horrific note-   let me reference 'Second Life' -actually a version of the metaverse that has existed before - and failed. Anyone recall it?  Some, in fact a lot, of what's been circulating in the hype-prone media about the metaverse, could be ripped straight from the tech headlines in the late 2000s. Indeed, much of what's been currently claimed as "new" - by the likes of Zuckerberg and others- was already in use for 2nd Life.  That included: working in virtual offices, investing in virtual real estate, playing virtual games and -  wait for it!  - participating in digital currency transactions and buying digital art (think NFTs or non-fungible tokens in today's parlance.)  

Everyone at the time, as I recall, declared it "isn't a passing fad"  like Pong, even as it became one.  There simply was too much real world stuff going on to get lost in some unreal virtual world.  Today things are radically different because too many brains (psyches?) are already enmeshed in an inner reality thanks to the pandemic - which has discouraged outside interactions.  At the same time the rise of AI (artificial intelligence) has made giant leaps with 'smart' machines and devices everywhere-  even your smart TV watching you, and "Alexa" ready to deliver answers in the wink of an eye.   But these same AI systems that add convenience to daily life can add mounds of malevolence to an insulated virtual world. 

 Thus, on the one hand a kid might behold a virtual Ariane Grande staging a concert on his Fortnite app. 

But on the other, a demonic entity - avatar such as previously described and which assaults the Ariane avatar.   If you are a virtual witness to said attack, how would you describe it?   Will there even be a virtual cop to whom you can report the "crime"? How about an instant administrator of the virtual world site? If you are asked for evidence what do you say?  

The potential for such avatar mischief has a growing cadre of techies looking at ways to impose standards - including for use of avatars- on the construction of any future metaverse.  The idea would be to reflect standards such as now applicable on the web, and the internet itself.  There is also the potential to undercut the external use of algorithms to jack up conflict such as we beheld with Facebook, e.g.

In this case, we have the concept underlying "Web3", i.e. the new metaverse can be built with open source code and a similar kind of blockchain--based system undergirding cryptocurrencies like bitcoin. With such technologies it may well be feasible to use a global system of computers that can operate both a metaverse and all the applications people may wish to build atop them.   The very openness- and use of open source code-  would be attractive to legions of users - precisely because it would enable them to route around the gatekeepers who might dictate what they put in the metaverse.  Or leave out! Especially  the algorithms that feed advert $$$ and generate never-ending conflict in the current iteration of the net.  Hell, even Zuckerberg, in a Zoom conference four weeks ago, praised the virtues of a metaverse built with open standards, interoperability,  and with new "democratic" forms of governance, i.e. not created by one gargantuan company.

Another aspect that could prevent a totally insular, more dangerous virtual reality to dominate is the potential for a shared, mixed reality, i.e. blending a virtual world accessed through VR headsets with an augmented reality  (AR)accessed via phones and future AR headsets. The shared (AR/VR) mixed reality would be made possible using something like Facebook's Oculus 2 headsets.  Those devices feature "front facing" cameras so enable a view of the outside world to "pass through" allowing players in a game, for example, to be outside - and inside VR. 

Of course, once the pandemic ends  - and with it the lockdowns and social distancing etc.  -  it is possible that people will be so desperate to return to real world, outdoor living that VR or VR/AR mixed realities will cease to hold them in thrall. This applies especially to young teens already captive to Instagram.  Instagram, in particular, is a hub of youth anxiety and mental health problems. The company’s own research indicates that the app exacerbates body image issues for nearly a third of teenage girls experiencing them, according to a recent Wall Street Journal report. Equally troubling is that Facebook appears to have been proceeding with 'Meta'  apps without fully and properly consulting child safety experts.

 On the other hand,  if an AR/VR mixed reality emerges to dilute virtual addiction levels, who knows the extent of benefits that may accrue?  If that materializes then this new metaverse may turn out to be largely a world of hype like Second Life turned out to be.   Merely another palsied effort to suck everyone out of the real world and into the addictive virtual one.  If that indeed turns out to be the case then it means the latest incarnation (in 'Meta')  can't win against the stiff competition from the 3-dimensional domain of recreation, socialization known as real life. People will then be back to confronting the known prosaic evils and outside  threats - as opposed to internal VR manifestations powered by AI and leading to more unhealthy fixation and addiction.

See Also:

by Tom Valovic | November 16, 2021 - 6:59am | permalink


by Lynn Stuart Parramore | December 2, 2021 - 7:35am | permalink

The Basic Principles of Radio Astronomy - Part 2

 The next important feature when considering the basic principles of radio astronomy is the polarization of the radio source. This is given that the information is considerable and every non-thermal process emits some random polarization which can be described by two components, and electric (E) vector and a magnetic (H) vector:

1) E(y, t) = E 0 sin 2 p u (t – y/c )

2) H(x, t) = H 0 sin 2 p (t –x/c )

Electromagnetic waves with the above vectors are often represented as in the diagram below:

Where S denotes the Poynting vector: S = E X H.  The EM- waves are  polarized when their E- field  components are preferentially oriented in a particular directionBasically, the up and down motion of the EM radio waves is converted to the up and down motion of electrons in the antenna wire which gives rise to the current detected at the telescope.

Other forms of polarization include:

Linearly or horizontally polarized: I.e. the E- vector is confined to one  (horizontal) plane

---------à E

Vertically polarized: I.e. the E- vector is confined to one  (vertical) plane


Circular: The E-vector rotates through 360 degrees

Elliptic: Any polarization not circular or plane, but note in most texts circular is regarded as a limiting case of elliptic polarization.

The equivalent circuit for a basic radio telescope system may be represented as shown below:

This contains a motor producing an oscillating potential difference (V)  and two resistors:

A  (Antenna resistance)   and

B       (transmission line and receiver resistance)

Further:  A   =  r    +   R ℓ
Where R ℓ  is the radiation loss resistance, and r   is the fictitious resistance due to oscillating electrons which radiate. Since there is an oscillating voltage there is an oscillating current, i.e.

I   =  V /  (  R r    +  R     +  R B )
The Power is then:  P   =   I 2  R B 

The maximum power is obtained under the condition:

dP/ dRB  =  0   (N.B.  In general, R     0,  and  R  << R r 

dP/ dB  =   d/ dR B R B V2  /  (R r B) 2 

=  V2 { [(R r R B) 2  -   R B   2(R r R B)] /(R r R B)4   

dP/ dR B  =  R 2  R B 2 /(R r B) 4

Then the available power is: 

PA   = V2 /4R B   =  V2 /4R r 

The diffuse power is:  P r  =  I R 2

Let the total area of an antenna be A T  then the total power:

P T  =  A T  F

Where F is the energy flux of the incoming wave . 

The Gain of an antenna:

 For an isotropic lossless antenna the flux emitted is:

F  =  (1/4p )   1/ d 2

(Where P is the applied Power )

For an anisotropic antenna:

F  =  g (1/4p )   1/ d 2

 Where the gain  g is subject to the constraint:

  ò 4p  g  dw   =    4p


r  =   ò   g  dw /4p    

For all secondary lobes then the beam efficiency of the antenna is:  1 -  r

The relation between the gain of the antenna and its effective aperture (A') such that:

g( (q ,  φ )  =   4p  A' (q ,  φ)/ l2 

Now, every radio telescope receives waves that come from fairly restricted areas of  the sky and this is defined by what's called the beam.  Every antenna - and by extension radio telescope- has a main lobe called the "main beam" and also side lobes off to the side.  The side lobes have different causes but most result from diffraction (Consult the astronomy archives for past answers pertaining to diffraction in optical telescopes).   The pattern of a radio telescope beam and typical side lobes are shown below:

                              Main lobe and directions for side lobes

Note the side lobes are weak but can still represent a significant fraction of the power a radio telescope receives. Generally 80-90 percent of the signal entering a receiver from a typical dish comes through the main beam, the other 10-20 percent through the side lobes.  In the case of the initial radio telescope diagram, try to imagine the wave fronts coming in at an oblique angle instead of directly., e.g.

Here, the arrival of the left side of the wave is later than the right, because it happens to travel an extra distance.  If one finds this distance d is such that:

 d sin  q     =     l/  2

Then we have the left -radio wave fully cancelling the right and no signal gets through. Obviously one wants to avoid this condition.  Ideally then, we need: 

 d sin  q     =  0.

Again, every radio telescope has maximum reception in location and this falls off according to the beam pattern.  A convenient way to specify this pattern is by using the beam width and one half the peak (power) height.   

From this one can deduce the optimum beam width in terms of the resolution. Thus, if two objects are closer than the beam width then they will blur into one, and the astronomer will be unable to distinguish the sources.  This conveys the importance of a narrow beam width, which just means the signal falls off rapidly as one shifts from one side of the source to the other.The narrower the beam width the better the resolution of the radio telescope. In general:

Beam width =  Resolution =   Wavelength /   diameter    =     l/  

Hence, if the wavelength is 21 cm (say for the hydrogen line) and the diameter  of the telescope is 10 m (1000 cm) we have:   21cm /  1000 cm  = 0.021 arcseconds

Again, these basic principles only cover the  most superficial details of the components of radio telescopes and how they work. To get more details it is good to consult basic texts such as this excellent introduction:

Next:  The plasma physics of radio astronomy