Friday, March 28, 2014

The Uncertain Gene - 10

DNA: molecular machines
This is probably the final post in this series, a series about how abiotic evolution might take place, but it is not the end of this subject matter [there is a new post here].

Their will be additional new series on these type subjects as long as Dredd Blog is still a blog.

The list of posts in this series, and associated posts from other series, can be accessed from links on the Series Posts Tab, at "EVOLUTION (Abiotic Machine Epoch - the first ~10.21 billion years)" and "SCIENCE (of the rebellion - *subject" where the subject is listed as "Abiology" or "abiotic evolution."

To end or suspend this series on a good note, today I am focusing on a post from the Small Things Considered blog (STCB), which focuses on a particular molecular machine mentioned in the journal NATURE VOL. 386, page 299, "Letters To Nature" (March 1997), and in other places.

STCB and other blogs call the ancient dynamo, which existed billions of years before human evolution began, a "molecular dynamo."

They then go on to point out that we humans made our very first and much more primitive dynamo billions of years later:
The dynamo was invented in the early 19th century as a device to convert the mechanical movement of magnets—preferably by turning a crank—into electric current. Using the same machine some 25 years later people found that electric current can drive mechanical movement, and the electric motor was born.
(Small Things Considered - "The Dynamo at Work"). In "The Tiniest Scientists Are Very Old" it was noted that ancient microbes used quantum mechanical principles to do work with molecular machines.

What is interesting, comparing the way the rotor on the dynamo works, with proton tunneling (The Uncertain Gene), is that a less random and seemingly more stable technique of proton translocation is used in this molecular dynamo:
Rotation of the c ring is driven by the proton gradient across the membrane. The existence of such a gradient was first postulated as the 'chemiosmotic hypothesis' by Peter Mitchell in 1961 and was highly controversial at that time. Protons pass through a narrow canal formed by two neighboring c subunits and the α subunit of the Fo particle (see figure 3). This proton transport is known to involve the D61 residues of the juxtaposed c subunits and R210 of the α subunit (in E. coli). The 'handover' of a proton between two c subunits leads to small incremental movements of the c ring with respect to the a subunit, i.e. rotation of the c ring within the membrane, with the a subunit representing the stator. When during (aerobic) respiration the cytoplasm of the cell is depleted of protons, a proton gradient is established that allows protons to flow 'downhill' back into the cytoplasm through the Fo canal. This flow sets the c ring in motion, which in turn lets the F1 γ subunit rotate. The rotating F1 γ subunit then induces the conformational alterations in the β subunits of the α3β3, that are necessary to synthesize ATP from ADP and Pi. We can calculate that it takes—depending on the c subunit stoichiometry in the c ring—between 4 and 6 protons to synthesize 1 ATP.
(ibid, "The Dynamo at Work", emphasis added). This particular use of protons in this particular case of a molecular dynamo is "planned" or "controlled" rather than being the result of unplanned, uncontrolled, random action.

It is unlike the proton tunneling mentioned in the first post of this series (ibid, "The Uncertain Gene").

Both uses of protons also took place during ancient abiotic evolution, specifically during abiotic genetic evolution / mutation in the case of RNA / DNA replication (ibid, "The Uncertain Gene").

These examples of sophisticated proton-energy based molecular machinery add support to the notion that the viral realm is a viable place to look for the original transition from pre-carbon (abiotic) entities into carbon based (biotic) "life" forms:
The virus realm may be the bridge from the molecular machine realm into the biological realm, the bridge from the abiotic evolutionary realm into the biotic evolutionary realm.
(The Uncertain Gene - 9). In fact, the viral realm has been described as a realm of molecular machines:
One of the principal goals in biology is to be able to fully understand the mechanisms of an organism in atomic detail. Viruses offer the best opportunities to achieve this goal. Written by leaders in the respective fields, this book examines a variety of viral molecular machines, using the best examples from bacteriophages and animal viruses, many causing infectious diseases of public health importance. Beginning with the viral entry into a host cell, the book takes the reader through replication of the genome, assembly of structural components, genome packaging and maturation into an infectious virion. The book conveys the state of the art knowledge of the topic generated by combining X-ray crystallography, high resolution electron microscopy, molecular genetics, biochemistry, and single molecule biophysics. Viral Molecular Machines is not only a “must-have” book for virologists but it will also be broadly useful for molecular biologists in academia and industry as well as an educational tool for teaching graduate and upper level undergraduate students.
(Viral Molecular Machines, emphasis added). While I do not dispute or criticize that observation at the macro level, I do criticize the study of viruses and microbes when it is done as if they evolved in a vacuum devoid of any experience of catastrophe on this planet or in the Cosmos (e.g. The Evolution of Anthropogenic Extinction by Catastrophe, On The Origin of Catastrophe).

And, I do criticize the cop-out that utilizes "natural selection" devoid of the larger picture of abiotic evolution, which took place without any "natural selection."

That is because "natural selection" applies only to biotic evolution of carbon based life forms which showed up billions of years after "abiotic selection" was underway  (see e.g. On the Origin of the Genes of Viruses - 6, Did Abiotic Intelligence Precede Biotic Intelligence?).

We cannot remain in a Washington, DC type of bubble (Economists - Aliens From Cygnus?) while expecting to understand either the Earth or the Cosmos around us without understanding that the five mass-extinction events must have had an important impact on evolution (see e.g. Are Microbes The Origin of PTSD?, Weekend Rebel Science Excursion - 16, On The Origin of Propaganda - 2).

And we have to take a look at the larger map to get the larger picture (see e.g. On the Origin of the Genes of Viruses - 5Putting A Face On Machine Mutation - 4).

Have a wonderful weekend.

The next post in this series is here, the previous post in this series is here.

Wind of Change, by The Scorpions

Thursday, March 27, 2014

New Continent Found - Garbage Gyre II - 7

Five Ocean Garbage Gyres
Satellites orbiting the Earth have observed hundreds of pieces of flotsam and jetsam (floating garbage) on the ocean surface in the search area where missing Malaysian Airlines Flight 370 supposedly crashed into the ocean off Australia.

But searchers cannot tell if the debris is aircraft parts or worldwide floating debris dumped there by "civilization" unless they can get close enough to the debris so as to "put eyes on the debris" and identify it.

Complicating that, Cyclone Gillian ("hurricane" in our parlance) threatened to spread the garbage around as it prevented searchers from putting eyes on the debris for a while.

In this series about ocean garbage, which first began March 25, 2009, the anniversary of the ExxonValdez dumping of civilization's Ecstasy drug (oil) into the pristine natural gulf environment of Alaska, thereby destroying it (Exxon Spill, 25 Years of Tears, Spill Baby Spill - 3), Dredd Blog began to point out that, like the atmosphere of the Earth, the oceans also are being filled with garbage and oil pollution (Garbage Garbage Garbage).
X marks Flight 370 Garbage Gyre

Have you noticed that there is so much junk out there that they can now spot oil slicks and floating garbage from space?

And that some of those oil slicks are miles and miles long, together with large chunks of garbage up to about 80 feet in length and/or width?

The reports daily say that one "satellite spots 122 pieces" here, another "satellite spots 300 pieces" there, from 100 or more miles in space (Debris field littered with 122 objects, Satellite Detects At Least 300 Objects) in a very remote area of the ocean (shown in the graphic with the caption "X marks Flight 370 Garbage Gyre").
Albatross stomach contents: Garbage Plastic

These garbage gyres are and have been killing the aquatic life in the oceans as well as killing the sea birds that also live on the ocean surface much of the time.

Whales wash up with their stomachs full of plastic garbage, as do birds (Whale dies from ingesting plastic waste).

We continued the posts about what civilization was doing to the oceans under the current post name, in August of 2009, continuing on until January of this year (New Continent Found - Garbage Gyre II, New Continent Found - Garbage Gyre II - 2, New Continent Found - Garbage Gyre II - 3, New Continent Found - Garbage Gyre II - 4, New Continent Found - Garbage Gyre II - 5, and New Continent Found - Garbage Gyre II - 6).

The missing Malaysian Flight 370 lost in a garbage gyre seems to be a fitting metaphor to describe current industrial oil-addicted civilization (Something Does Not Add Up, Titanic Mistakes Using The W Compass - 3) because we can't seem to find ourselves because of all the garbage.

The next post in this series is here, the previous post in this series is here.

What kind of being would destroy itself by destroying what it must have to sustain its life (What Kind of Intelligence Is A Lethal Mutation?, On The Origin of Catastrophe)?

Wednesday, March 26, 2014

Still Lazy After All These Years

War: the Pentagon Religion
The only thing that gets the government moving is war (Is War An Art or Is War A Disease?).

After corrupting the Ukraine into cold-war confrontation mode, the Epigovernment sent members of the government it runs over there (Epigovernment: The Tumor).

It is an evangelizing tour to preach a sermon about not interfering in other countries sovereignty  unless a god that wears a flag on its collar is on your side (Ukraine: Tea Potters In A Tempest).

A new export product, hypocrisy, is now as high on the list of things we do as the 1% toy, the stock market, is.

That is lazy, and that is the way it has been for years, as a little review of Dredd Blog posts linked above, and from this date in 2009 show:

The Lazy Economists Act

The economy shrunk at 6.3% last quarter, and corporate profits were down to a 55 year low last quarter.

One economist says these bad numbers are going to happen again in the first quarter. However, the numbers are probably going to be a bit worse:
Economists predict that the impact of the $787bn government stimulus package will not be felt until the second half of this year and that the economy could contract by another 6 per cent in the second quarter before flattening. The US government’s 10-year budget outline unveiled last month projected that the economy would contract by 1.2 per cent in 2009 before rebounding to 3.2 per cent growth in 2010. The Congressional Budget Office, however, found those estimates to be exceedingly hopeful.

“All the incoming data suggest that the economy will contract by a staggering 7 to 8 per cent in the first quarter, before the economy begins to stabilise,” said Nariman Behravesh, chief economist at IHS Global Insight.
(Financial Times, emphasis added). We have been into a decade of play pretend growth, or a bubble economy, some would say.

The cost of the Iraq and the Afghanistan wars which produces nothing but costs staggering amounts is surely to blame for much of this. We know that much of it has been waste and graft.

The new administration does not want to begin to think it is immune if it does exactly the same thing:
The United States risks repeating the same mistakes in Afghanistan that have led to billions of dollars being squandered in Iraq on its reconstruction, US auditors warned Wednesday.

The warnings come just days before President Barack Obama is due to unveil his new strategy for Afghanistan, which is expected to include an increase in reconstruction aid and civilian assistance.
(AFP). When did economists become too lazy to look ahead so that economic catastrophe could be avoided?

Do they think acting in catastrophe movies is really where it is at, or are they mentally cruising on a virtual SS Californian watching the Titanic go down?

The Lazy FBI Act

The FBI wants something renewed.


Like they have for the past 8 years. They like to call what they want renewed "The Patriot Act". The only thing correct about that name that it is in fact an act in a play.

The act that helped them play despots, torture people, and ruin our worldwide reputation.

It really must be called "The Lazy FBI Act" if we are to avoid a misnomer.

The FBI once upon a time liked to be known as the agency that "always got their man", without spying on all Americans.

Without forcing the telecoms to give up all records on Americans without a valid, constitutional warrant.

Now their motto has changed to "let AT&T or Verizon and our super computers do our work and get our man because it is now too hard to tell who is the enemy".


Tuesday, March 25, 2014

Something Does Not Add Up

We are still here
The equivalent of 29,289 Malaysian Air Flight 370 events (7,000,000 ÷ 239 = 29,289) happens every year (Guardian, Air pollution 'kills 7 million people a year', World Health Org).

This ongoing catastrophe occurs annually because of the air polluting industrial system based on fossil fuels which has been forced upon us by official decisions to continually and habitually embrace that catastrophic polluting system (The Peak of Sanity).

A system which is also causing global warming induced climate change (What We Know).

Seven million men, women, and children die each year, 19,178 a day (before we even start adding to that 7,000,000 figure those who die in damaged climate system caused disasters).

Nevertheless, in corporate media there is little to no coverage of the far greater cause of death (In the Fog of The Presstitutes - 3, Major Newspaper Coverage Plummets, Broadcast Media Coverage Below 2009 Rate).

Meanwhile, "239 missing" gets virtually 24/7 coverage, because it can be branded and sold like tooth-paste (Discussion with Noam Chomsky and Robert Trivers).

This evinces a group psychological problem of neurotic denial on a cultural level, that is, a failure of an entire media culture to acknowledge the big picture.

The fears of a media (that wants to be a celebrity rather than be the eyes of the citizens like they are supposed to) develops into the institutionalization of the dementia of denial (see e.g. Mocking America, Mocking America - 2, Mocking America - 3).

A group psychological problem that animates the observation of a mass murderer ("One death is a tragedy; one million is a statistic." - Joseph Stalin).

Monday, March 24, 2014

Exploding Plastic: Inevitable

You are still here.
I have nothing on my mind today, so I am making this up as I go.

Have you noticed (while watching the search for Malaysian Flight 370) that lots of floating things can be seen in our oceans from space?

And that it is difficult, even with our out of this world technology, to really tell the difference between garbage and non-garbage with our technology in space (what are aliens going to think)?

Regular readers know that Dredd Blog has pointed this out for years.

Our modern civilization cannot tell the difference between the Earth and a garbage dump (New Continent Found - Garbage Gyre II, posted August 29, 2009; New Continent Found - Garbage Gyre II - 6, posted January 28, 2014).

It is kinda like "America: lost on a garbage planet of its own making" it seems sometimes.

But, we keep looking for ourselves like the children on the garbage dumps in Mexico City.

As we deny that we are plagued within with the catastrophe gene (On The Origin of Catastrophe).

Kinda reminds me of the time we found a book, but did not realize it was only a map.

Under The Same Sun, by The Scorpions