Friday, March 20, 2015

On the Origin of the Genes of Viruses - 13

Emergence all at once?
All my carping about the dearth of scientific papers concerning evolutionary abiology may have paid off.

A paper recently published, in a peer reviewed setting, addresses some of the issues I have wondered about.

But, as I explain below, it does not do so in a way I would have preferred.

Basically, I have considered the hypotheses and theories of evolution to contemplate a dynamic proceeding from simple to complex, as have others (From Simple To Complex, The Scientist).

But this paper I mentioned, and quote from below, urges a spontaneity whereby several steps are taken at the same time, in different places, and ostensibly in different species:
A minimal cell can be thought of as comprising informational, compartment-forming and metabolic subsystems. To imagine the abiotic assembly of such an overall system, however, places great demands on hypothetical prebiotic chemistry. The perceived differences and incompatibilities between these subsystems have led to the widely held assumption that one or other subsystem must have preceded the others. [from simple to complex] Here we experimentally investigate the validity of this assumption by examining the assembly of various biomolecular building blocks from prebiotically plausible intermediates and one-carbon feedstock molecules. We show that precursors of ribonucleotides, amino acids and lipids can all be derived by the reductive homologation of ​hydrogen cyanide and some of its derivatives, and thus that all the cellular subsystems could have arisen simultaneously through common chemistry. The key reaction steps are driven by ultraviolet light, use ​hydrogen sulfide as the reductant and can be accelerated by Cu(I)–Cu(II) photoredox cycling.
(Phys Org, cf Nature - Chemistry, emphasis added). Why these researchers avoided the discussion of viruses is another diversion from simple to complex.

Ignorance of the microbial realm, and even more so of the realm of abiotic viruses ("viruses are not alive") has previously been pointed out in this series:
Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones.
The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes ... existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes ...
(On the Origin of the Genes of Viruses - 2, quoting Koonin, et al.). In that same post I pointed out that the molecular machines, at work in the genetic realm, are so complex together, that instant karma emergence is less likely than simple to complex emergence is:
"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant ["junk"] since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
(ibid, emphasis in original). I am constantly amazed at the reluctance of some scientists, and some scientific writers, to go with the flow.

For example, let's review the Dredd Blog post about the mythical primordial soup:
For 80 years it has been accepted that early life began in a 'primordial soup' of organic molecules before evolving out of the oceans millions of
Souper Salesman
years later. Today the 'soup' theory has been over turned in a pioneering paper in BioEssays which claims it was the Earth's chemical energy, from hydrothermal vents on the ocean floor, which kick-started early life.

"Textbooks have it that life arose from organic soup and that the first cells grew by fermenting these organics to generate energy in the form of ATP. We provide a new perspective on why that old and familiar view won't work at all," said team leader Dr Nick lane from University College London.
(Soupy Sales & Evolutionary Tales, emphasis added). Yet, two papers commenting on "complex emergence" and/or abiotic evolution, from simple to complex, still use the "primordial soup" concept (GEN, cf Origins of Life "@ Clermont College").

Search for "primordial" in that text.

Here are some additional posts that touch upon the subject matter of today's post: (Weekend Rebel Science Excursion - 27, On the Origin of the Genes of Viruses - 11, The Uncertain Gene - 9, On the Origin of the Genes of Viruses - 8).

Have a good weekend.

The previous post in this series is here.

Thursday, March 19, 2015

The Innocence Project2

Miss Piggy Is "Using"
It is just one damn quandary after another here in the exceptional Western Civilization.

Eat your heart out, exceptional Eastern Civilization!

From time to time our science becomes "rebellious."

Indicating its rebellion by saying: "Houston, we have a problem."

One could wonder why we never went back to the moon with younger Navy Seals, hovering over the moon dust while exclaiming "we have no stinking problems!"

We civilized people do not entertain the notion of "problems" on certain exceptional levels, especially those problems in the recipe that fate "manifest destiny" cooked up for us.

"Cooked up," then put on the final exam (The Tenets of Ecocosmology).

For your plebs and mine, in our world "final" means the one just before the next one.

Like da man said:
With doublespeak, banks don't have "bad loans" or "bad debts"; they have "nonperforming assets" or "nonperforming credits" which are "rolled over" or "rescheduled." Corporations never lose money; they just experience "negative cash flow," "deficit enhancement," "net profit revenue deficiencies," or "negative contributions to profits."
(Propaganda Is A "Toxic Asset", quoting professor Lutz). Which brings me to "The Innocence Project" ... as I understand it ... or as I don't understand it:
The Innocence Project is a non-profit legal organization that is committed to exonerating wrongly convicted people through the use of DNA testing, and to reforming the criminal justice system to prevent future injustice. The Innocence Project was founded in 1992 by Barry Scheck and Peter Neufeld. To date, the work of the Innocence Project has led to the freeing of 325 wrongfully convicted people, including 18 who spent time on death row.
(Boston Wikerpedier, emphasis added). The innocence, or lack thereof, of both individuals and groups, is a concept that floats atop a massive ocean of cognition.

That is the ocean in which we, using our cognition, decided to name "the evolution of justice."

An ocean traversed by the ship of state, a ship guided by the Department of Justice always, toward a broad and wide beach, a beach with a broad and wide port.

A port where many of its sailors have concluded "any port in a storm."

But those winds still blow incessantly:
From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity. Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information — or, as 23andme, a prominent genetic testing company, says on its Web site, “The more you know about your DNA, the more you know about yourself.”

But scientists are discovering that — to a surprising degree — we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people.

Medical researchers aren’t the only scientists interested in our multitudes of personal genomes. So are forensic scientists. When they attempt to identify criminals or murder victims by matching DNA, they want to avoid being misled by the variety of genomes inside a single person.

Last year, for example, forensic scientists at the Washington State Patrol Crime Laboratory Division described how a saliva sample and a sperm sample from the same suspect in a sexual assault case didn’t match.
(On The Origin of Genieology, emphasis added). Yikes! ... There are some other wild and crazy stories that should be told before the music plays.

Such as wondering about how many people have been wrongly convicted in our criminal justice system, because of wrongful DNA assumptions of  a single genome in each individual.

However, since I feel so innocent today, let's musicate ...

A highway is located at the journey's destination, as well as being located at the journey's beginning (our criminal justice system is on the wrong highway).

"pearls and swine bereft of me
long and weary my road has been
i was lost in the cities alone in the hills
no sorrow or pity for leaving I feel

Wednesday, March 18, 2015

Out On The False Front - 2

Downtown"What we want you to think we look like" KS
Just can't get enough of history can we?

At least when it is a filler for vision (e.g. "Everything goes on like it has since the founding of the world").

That is one reason fundies and right wing nuts have a hard time with driving while looking out the wind-shield (the rear view mirror is so captivating eh?).

So, on Dredd Blog, rather than celebrate yestermyth, we look back in disdain from time to time at "yesterday," because it is so fast ("git 'r dun yesterday").

Here is some Dredd Blog evidence from this date in 2009 that a fast one "yesterday" was pulled on us:

We who are students of Noam Chomsky are always wondering whether the news we are fed is legit or just more propaganda as usual.

In that light, several stories are worth considering and worthy of serious consideration.

One of the stories which deserves praise pins AIG woes on Joseph Cassano:
He was a political science major, Class of 1977, and he seemed to be on the way to do his borough proud when he went to work on Wall Street.

He instead gave new meaning to a saying among Brooklyn crooks who forayed into Manhattan during his father's tenure as a cop.

"Manhattan make it and Brooklyn take it."

Joseph Cassano started out at Drexel Burnham Lambert under Michael Milken, "the Junk Bond King." Drexel imploded in 1990 and Milken landed in prison.

AIG promptly hired a team of Drexel people to start a Financial Products unit, Cassano among them. Cassano became the head and began dealing in securities known as "credit default swaps" out of one office in Wilton, Conn., and another in England, dubbed "the London casino."

The cop's kid jetted between a house in Westport, Conn., and an $8 million townhouse in London that AIG provided.
(Daily News, 3/17/09, emphasis added). We have written recently about how criminality is getting into high places habitually.

And we have suggested that we rethink some of our national practices and become more unafraid to prosecute international white collar crime.

Here are more links and quotes about Joseph J. Cassano:
The insurance giant’s London unit was known as A.I.G. Financial Products, or A.I.G.F.P. It was run with almost complete autonomy, and with an iron hand, by Joseph J. Cassano, according to current and former A.I.G. employees.

A onetime executive with Drexel Burnham Lambert — the investment bank made famous in the 1980s by the junk bond king Michael R. Milken, who later pleaded guilty to six felony charges — Mr. Cassano helped start the London unit in 1987.

The unit became profitable enough that analysts considered Mr. Cassano a dark horse candidate to succeed Maurice R. Greenberg, the longtime chief executive who shaped A.I.G. in his own image until he was ousted amid an accounting scandal three years ago.
(NY Times, 9/27/08). And of all places there is talk on a Workmen's Compensation site:
One of the many fascinating sidebars in the decline and fall of the AIG empire is the saga of Joe Cassano. He was the genius behind AIG's Financial Products Unit, which insured high risk sub-prime mortgage deals. In other words, he is the man most responsible for AIG's abrupt demise.
(Workers Comp Insider, 10/8/08). The big dose of poison was taken in 2005, when AIG became unhedged and therefore unhinged:
Blame former AIG executive Joseph Cassano--and the lack of oversight by AIG's senior executives and board of directors--for blowing up the largest insurance company in the world.

How'd they do it? The answer is clearly spelled out in the footnotes to AIG's (nyse: AIG - news - people ) 2007 consolidated financial statement. "In most cases AIGFP (American International Group Financial Products) does not hedge its exposures related to credit default swaps it has written."

By the close of 2007, AIG held $562 billion risky and dangerous unhedged credit default swap (CDS) contracts on its books. That amounted to more than half of all AIG's assets. AIGFP, managed by Joseph Cassano, until he was pushed out in early 2008, was the dangerous operation singled out by The New York Times Sunday as the "small, freewheeling unit" that "brought AIG to its knees."

Croesus was informed Saturday that these complex contracts were hedged until former Chairman Hank Greenberg was ousted from his post in April 2005.
(Forbes, 9/28/08). If only we can find these pieces of information. I am sure the media can. And have.

His name is not on TV, nor has the congress mentioned the name. Everyone is bad mouthing Liddy and Geitner.

Check out Banque AIG and follow it to Switzerland.

Therefore we must ask why is it being covered up?

"Yesterday", by The Beatles

Tuesday, March 17, 2015

Will This Float Your Boat - 7

Fig. 1 Antarctica melt zones (click to enlarge)
Following some new research, I have expanded the scope of the C++ Sea Level Calculation Program.

It now includes all of Antarctica, not just W. Antarctica, as you can see from the graphic to the left.

For consistency I have also updated the dimensions of the four zones of melt for both Greenland (Fig. 3) and Antarctica (Fig. 1).

Since Greenland is the location of 75% of current ice melt that contributes to Global Sea Level Rise (SLR), and since Antarctica is only responsible for 25% currently (primarily from W. Antarctica), E. Antarctica can seem insignificant.

That will change over time, as the graphs later on in this post will show, because, among other things E. Antarctica contains enough ice that if it all melted, it would cause SLR of 212.58 feet all by itself (see Fig. 4).

Lucky for us it is not melting much now, so we focus on W. Antarctica and Greenland in terms of ongoing SLR.

The updates to the software are for not only improved accuracy, but for long term
Fig 2. Detail (click to enlarge)
projections to prove some long term points.

Furthermore, "W. Antarctica" and "E. Antarctica" are somewhat arbitrary descriptions for this context.

For example, W. Antarctica in reality includes the Antarctic Peninsula, however, SLR is often calculated separately for the two.

Add to that the fact that some ice shelfs currently melting cross the E. W. boundary, such as the Ross Ice Shelf and the Fimbulisen Ice Shelf --are technically located in both W. Antarctica and E. Antarctica (see Fig. 2).

So, I use the designations "coastal, inland 1, inland 2, and no melt" (in the software design) to describe melt zones of ice (see Fig. 1 and Fig. 2).
Fig. 3 Greenland (click to enlarge)

After all, the concern is ice melt going into the oceans over a given span of time, and the SLR results of that melt.

The zones have been unified (coastal, inland 1, inland 2, no melt) as have the colors (blue, cyan, yellow, red-orange).

Now, all ice melt on the planet is included in the SLR calculations.

The difficult issues include determining the percentages of ice in each zone of Greenland and Antarctica.

Add to that the difficulty in determining the rate of acceleration of melt in each of those zones over time.

Those difficulties are exacerbated by the fact that those values (amount of ice in each zone and percentage of acceleration of melt) are in constant upward flux.
Fig. 4 USGS Data (click to enlarge)

That is, they are naturally constantly changing from year to year.

So, some of the numeric assumptions in the software must change from time to time, to keep up with real world change.

The volume of ice, potential SLR, and percentages are (see Fig. 4) figures which change too, although the major percentages in "no melt" zones are changing very little at this time.

Fig. 5  (click graph to enlarge)
Fig. 5 is the latest graph using the ~21 cm. SLR since 1750 value, so the graph begins at about a foot of SLR already existing in 2015, which makes the subsequent values much higher, so, for that reason alone they may not match prior graphs.

But more than that, when any melt zone reaches "No Melt" the graph line stops, and that zone no longer contributes any more elevation to SLR.

At least out to 2100 (both Greenland and "Other" non-polar zones do that on this graph).

As a result of using the 1750 to 2014 SLR (~21 cm.) by adding it to the CryoSat-2 data (2014 ice melt in Greenland and Antarctica), the 3ft. SLR projection of the IPCC ("~3ft. SLR by 2100") are passed much quicker now, as noted on the graph.

Notice also that after ~2068 Greenland enters the "No Melt" zone, and therefore adds no more to SLR in this century.

The following interactive map (Fig. 6) shows substantial agreement with the graph (Fig. 5) at the year 2100:

Fig. 6 Interactive Map courtesy of Climate Central.

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

Monday, March 16, 2015

The Poet Laureate of MOMCOM - 4

Mithra the Jesus


He is affection
and the present moment
because he has thrown open the house to the snow
foam of winter
and to the noises of summer
—he who purified drinking water and food
—who is the enchantment fleeing places
and the superhuman delight of resting places.
—He is affection and future,
the strength and love which we,
erect in rage and boredom,
see pass by in the sky of storms
and the flags of ecstasy.

He is love,
perfect and reinvented measure,
miraculous, unforeseen reason,
and eternity: machine loved for its qualities of fate.
We have all known the terror of his concession
and ours: delight in our health,
power of our faculties,
selfish affection
and passion for him,
—he who loves us
because his life is infinity…

And we recall him and he sets forth …
And if Adoration moves,
rings, his Promise,
rings: "Down with these superstitions,
these other bodies,
these couples and ages.
This is the time which has gone under!"

He will not go away,
he will not come down again
from some heaven,
he will not redeem the anger of women,
the laughter of men,
or all that sin:
for it is done now,
since he is
and since he is loved.

His breathing,
his heads,
his racings;
the terrifying swiftness
of form
and action
when they are perfect.

of the mind
and vastness
of the world!

His body!
the dreamed-of liberation,
the collapse of grace
joined with new violence!

All that he sees!
all the ancient kneelings
and the penalties canceled
as he passes by.

His day!
the abolition of all noisy
and restless
within more intense music.

His step!
migrations more tremendous
than early invasions.

O He and I!
pride more benevolent
than lost charity.

O world!
—and the limpid song
of new woe!

He knew us all
and loved us,
may we, this winter night,
from cape to cape,
from the noisy pole
to the castle,
from the crowd
to the beach,
from vision to vision,
our strength and our feelings tired,
hail him
and see him
and send him away,
and under tides
and on the summit
of snow deserts
follow his eyes,
—his breathing
—his body,
—his day.

by Rimbaud

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