Friday, May 29, 2015

On the Origin of Cultural Epigenetics

The Uncertain Gene - 11
I. Background

Once upon a time in the Dredd Blog System of 2009, I set a course to find out about why there is so much environmental dementia.

And how it was being passed around so promiscuously (e.g. Some Dementia Is Contagious, and links therein).

During that search, it became necessary to deepen the scope of the subject matter, because I felt that it was necessary to find out how the corruption of an individual mind takes place (About Toxins Of Power).

To increase the intensity of the focus of the search, I felt compelled to look at some of the cognitive centers in our brain structure, but especially those which have substantial degrees of cognitive autonomy.

As I look back, it is not surprising that I eventually settled on an entity called the amygdala  (The Toxic Bridge To Everywhere).

In terms of the person-to-person spread of that corruption, it was interesting to notice that various of those types of behaviors can be contagious (ibid, "Some Dementia Is Contagious" link above).

II. Expanding The Search

I then wondered how corruption spreads, in one degree or another, throughout a culture.

I hypothesized that since the amygdala was suspect in individuals, I had to also wonder if there was a cultural dynamic which was analogous to what was also in individuals (Hypothesis: The Cultural Amygdala, 2, 3, 4).

III. Individual Epigenetics

Epigenetics is a main-stream scientific concept now (One Man's Junk Gene Is Another Man's Treasure Gene?, On The Origin of Genieology).

Historical epigenetic evidence is being sought and found in ancient specimens now:
Epigenetic marks comprise a variety of stable, chemical modifications to DNA and its associated proteins that influence chromatin structure and regulate gene expression. These marks designate which genomic segments are available for transcription, providing a means for regulating gene activity without changing the underlying nucleotide sequence. Functionally, epigenetic gene regulation plays a crucial role in development, mediates gene-by-environment interactions, and underlies some complex diseases.

One widely studied type of epigenetic mark is cytosine methylation. In humans and other mammals, cytosines in CpG dinucleotide contexts are targets for epigenetic regulation via cytosine methylation. Methylated cytosines (most commonly 5-methylcytosine, or 5mC) in CpG dinucleotide contexts are vastly underrepresented in the human genome compared to other nucleotide bases and dinucleotide combinations, and are often concentrated in regions of high density, such as CpG islands. Other relatively CpG-rich regions of the genome include retrotransposable elements like Long Interspersed Elements (LINEs) and Short Interspersed Elements (SINEs), which are usually epigenetically inactivated through cytosine methylation to prevent aberrant transposition.

While cytosine methylation has been widely studied in extant species, relatively few studies have attempted to analyze epigenetic marks in the DNA of ancient or extinct organisms. Recently, however, several studies have indicated that cytosine methylation can be reconstructed in ancient specimens.
(Detection of Ancient Epigenetic Marks, emphasis added). I recently posted about a new book written by two evolutionists who see epigenetics as a tool for rescuing the theory from some of its flaws.

Yikes! Flaws in current evolutionary science (A New History of Life)?

IV. The Notion of Cultural Epigenetics

I have previously considered metaphors for the amygdala, as applied to cultural dynamics  (see Hypothesis: The Cultural Amygdala above).

But, I did not look at the work of a certain scientist, quoted in that post, closely enough to catch the application of it to epigenetic dynamics.

So, now let's expand that metaphor to the culture one lives in, but first let's revisit the work of that scientist:
Michael Skinner has just uttered an astounding sentence, but by now he is so used to slaying scientific dogma that his listener has to interrupt and ask if he realizes what he just said. Which was this: “We just published a paper last month confirming epigenetic changes in sperm which are carried forward transgenerationally. This confirms that these changes can become permanently programmed.”

... the life experiences of grandparents and even great-grandparents alter their eggs and sperm so indelibly that the change is passed on to their children, grandchildren, and beyond. It’s called transgenerational epigenetic inheritance: the phenomenon in which something in the environment alters the health not only of the individual exposed to it, but also of that individual’s descendants.
(Hypothesis: The Cultural Amygdala). My focus was narrowed too much by the notion of an organ of society working on individuals.

But, clearly "something in the environment" which alters or guides genetic dynamics is the very essence of epigenetics.

The graphic at the top of this post depicts a dynamic where genes are impacted in some way by outside influence, power, energy, and the like, epigenetically.

The culture we are born into is exactly that: an outside influence, power, energy, and the like working to shape our behavior, and "who we are" (see eg. Choose Your Trances CarefullyIt Takes A Culture To Raise A Compulsive Liar).

V. Ok, What About The Origin Part?

Today, I can only hint at where this is going by alluding to Dredd Blog posts which consider the dynamics of the genes of viruses (On the Origin of the Genes of Viruses 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12).

The hypothesis involved is that viruses were the first to traverse the gap between the abiotic and biotic realms (from abiotic molecular machine to biotic organism) (see e.g. The Abiology Rebellion).

The gist of it is that viruses were central to the dynamics involved in the first epigenetic dynamos.

Those dynamics changed a lot of genes and genomes:
If not for a virus, none of us would ever be born.

In 2000, a team of Boston scientists discovered a peculiar gene in the human genome. It encoded a protein made only by cells in the placenta. They called it syncytin.
What made syncytin peculiar was that it was not a human gene. It bore all the hallmarks of a gene from a virus.

Viruses have insinuated themselves into the genome of our ancestors for hundreds of millions of years.
It turned out that syncytin was not unique to humans. Chimpanzees had the same virus gene at the same spot in their genome. So did gorillas. So did monkeys. What’s more, the gene was strikingly similar from one species to the next.
(Are Toxins of Power Machines or Organisms?, quoting Discover Magazine). Dr. Peter Ward mentioned, in the video here, that viruses are the most likely candidates as gene traders which facilitated inexplicable evolutionary events such as the Cambrian Explosion.

One candidate dynamic of epigenetics that could have been working on the genes of viruses, when they were entirely abiotic, is most likely to have been proton tunnelling.

Proton tunnelling is still a recognized dynamic of quantum mechanics (The Uncertain Gene).

Thus, proton tunnelling has nothing exclusive to do with biology, which developed much, much later (compare Did Abiotic Intelligence Precede Biotic Intelligence? with The Uncertain Gene).

Note also that Dr. Peter Ward also hypothesizes that "microbial and/or viral intelligence" was sufficient to spur early biotic entities on to pull CO2 out of the early Earth's greenhouse atmosphere.

That type of, and degree of, intelligence is yet to be described in full.

It is a type of epigenetic dynamic that paved the way for the composition of our current atmospheric environment (again, that video is here).

VI. Conclusion

This first post in this new Dredd Blog series is getting a bit long, so I will expand upon these concepts in future posts.

Thanks to regular reader Tom for the link to the genetic research on ancient organisms.

Research that found epigenetic markers in ancient life forms, including humans.

Thursday, May 28, 2015

Will This Float Your Boat - 11

John Englander
Today I offer for your perusal the video below.

It is a presentation given in Florida this year.

"Oceanographer and consultant John Englander is a leading expert on sea level rise and its societal and financial impacts. He assists businesses and communities in understanding the risks as rising seas challenge us to adapt to a changing shoreline. His book, High Tide on Main Street, clearly explains what this coming coastal crisis means to you."

The following index is in minutes:seconds format.

It is my paraphrase of what he said at given points during the video, so as to give you an ideo of the type of information in the video:

00:59 In the last six years I have become a specialist in sea level rise [SLR]
02:30 some of the things you learn [in the video] will be new
02:50 in Florida we tend to think we are ground zero ... but lots of places are vulnerable
03:30 about 90% of people think SLR is because the polar sea ice cap is melting, but that is not the reason
04:00 this is a really scary story ... to let you see the real world ... it is diffcult
04:45 the important issue with polar sea ice melt (excluding Greenland, Antarctica) is albedo
06:00 people poo poo this issue as a "natural thing" because it has happened before but the polar ice cap has been there for 3 million years
07:00 this [SLR] is not a natural event
08:55 think of ... tides ... they come and go ... but SLR only keeps coming ... over a long period of time ... sea levl can't go down for a thousand years
11:25 we don't know "when" SLR will become catastrophic, but we do know that SLR is here and will continue to be here
13:23 our SLR models change ...
14:30 SLR estimations of "how high when" have a consistent trend of significant SLR happening sooner and SLR being higher
16:00 flooding is not the same as SLR
17:15 we can exactly predict tides, but not storms and SLR
18:20 storms do let us see the impact of SLR ... but SLR will not go away like storm flood water will ... SLR flooding stays ...
20:15 tides around the world are flooding areas every 28 days due to SLR, which they did not flood 50 years ago
22:53 any inland cities on tidal rivers, bays, and estuaries will also flood because they are impacted by SLR too
23:40 for example, Sacramento, CA levees are more vulnerable than New Orleans, LA ...
24:55 you can bet on the trend because it is clear where it is going ...
25:40 SLR impacts some areas more than others at the same time for various reasons ...

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

Wednesday, May 27, 2015

The Question Is: How Much Acceleration Is Involved In SLR - 5?

Fig. 1 Northeast Ice Stream @ Greenland
I. Background

In the series I have noted that there are dynamics involved in sea level rise (SLR) besides CO2 emissions, the resulting warming, and the subsequent ice sheet melting and/or calving.

Today, we will take a close look at one of those dynamics, an ice dynamic on the Greenland Ice Sheet (Fig. 1: Northeast Ice Stream).

Since an ice stream is a quick way that glaciers can move through ice sheets, today we look specifically at a critical ice stream on the Greenland Ice Sheet.

That is because it could determine to a significant degree when SLR acceleration takes place, and significantly affects ports of the Northeast United States (Why Sea Level Rise May Be The Greatest Threat To Civilization, 2).

First, let's take a look at a definition of an ice stream:
A fast-moving ice or ice stream is a region of an ice sheet that moves significantly faster than the surrounding ice. Ice streams are a type of glacier. They are significant features of the Antarctic where they account for 10% of the volume of the ice. They are up to 50 km wide, 2 km thick, can stretch for hundreds of kilometres, and account for most of the ice leaving the ice sheet.

The speed of an ice stream can be over 1,000 metres per year, an order of magnitude faster than the surrounding ice. The shear forces at the edge of the ice stream cause deformation and recrystallization of the ice, making it softer, and concentrating the deformation in narrow bands or shear margins. Crevasses form, particularly around the shear margins.

Most ice streams have some water at their base, which lubricates the flow. The type of bedrock also is significant. Soft, deformable sediments result in faster flow than hard rock.
(Wikipedia, Ice Stream). We must consider these ice streams in the projection of SLR, because until the ice in a flowing glacier melts or calves into the sea, there is no SLR merely because the ice is moving.

II. Zones

Another concept discussed in the context of SLR is the notion of "zones."

This applies to Greenland and Antarctica, both of which are areas where acceleration of melt and/or calving depends on the physical characteristics of the four zones:
The basic approach I took was to first establish four melt zones for the three melt locations, which locations are "non-polar", "Greenland", and "Antarctica."

The latter two are the major future sources of water from melting ice.

Those four melt zones were described in earlier posts as "Coastal", "Inland 1", "Inland 2", and "No Melt" (Will This Float Your Boat - 7).

In the evolving model, each melt zone has its own beginning phase, rate of delay, rate of melt, rate of acceleration of melt, volume of ice, and total possible contribution to SLR.
(The Question Is: How Much Acceleration Is Involved In SLR?). The concept is that sequential melt in zones is the rule, enhanced by the notion of some concurrent melt and/or calving.

That is, zones can lose ice concurrently, but generally not at the same rate:
That the zones are geographically distinct (height above sea level, distance from ocean, etc.) does not mean that there will be no overlapping melt, it just means that, by and large, the melt will proceed like dominoes sequentially falling as the ocean and air warm up.
(The Evolution of Models - 5). It so happens that on the Greenland Ice Sheet there is an ice stream that flows through more than one zone.

III. The Ice Stream Flowing Into The Greenland Sea

The south Wandel Sea and the north Greenland Sea is where the Storestrommen, Zachariae, and Nioghalvfjerdsbræ glaciers empty (Fig. 1).

Those three glaciers are branches of the larger ice stream we are discussing today:
Ice flow in the interior of the NE quadrant the Greenland sheet is focused on the large ice stream draining the north side of the summit dome. The rapid ice flow in the stream is apparent in the surface features in the stream and at the margins, in the broad scale topography that drives ice flow, and in satellite-derived motion information. The patterns of ice flow in the upper half of the stream are remarkable for their level of organization, simple geometry, and effects on local surface topography. The stream begins less than 100 km from the ice divide as a current 15 km wide and then broadens symmetrically downstream by the addition of ice from the sides to a width of more than 60 km. Elevation data and visible-band imagery show that the stream has marginal troughs tens of meters deep in its upper reach which are coincident with regions of high shear strain rate. The topography of the margins and undulating surface of the stream is generated by the ice flow; the surface undulations in the stream are fixed in location and shape over the 5 year period from 1994 to 1999. The enhanced flow presents a challenge for researchers trying to understand the history of ice discharge from a significant area in the interior of the ice sheet.
(Journal of Geophysical Research, 2001, PDF). I am focusing on this ice stream because it has become more active in the decade or so since 2001.

IV. Acceleration of Ice Streams Can Mean Acceleration of SLR

A paper in the journal Nature indicates that acceleration is in the cards:
Here, we show that the northeast Greenland ice stream, which extends more than 600 km into the interior of the ice sheet, is now undergoing sustained dynamic thinning, linked to regional warming, after more than a quarter of a century of stability. This sector of the Greenland ice sheet is of particular interest, because the drainage basin area covers 16% of the ice sheet (twice that of Jakobshavn Isbræ) and numerical model predictions suggest no significant mass loss for this sector, leading to an under-estimation of future global sea-level rise. The geometry of the bedrock and monotonic trend in glacier speed-up and mass loss suggests that dynamic drawdown of ice in this region will continue in the near future.
(Nature, Climate Change, March 2014, emphasis added). For this reason, I have generated an additional "doubling" graph and updated the data base of the Dredd Blog SLR calculation software (The Evolution of Models, 2, 3, 4, 5, 6, 7, 8, 9, 10).

V. The New Acceleration Graph

The acceleration in SLR added by the Northeast Ice Stream melt / calving acceleration is modeled by the graph in Fig. 2.

Fig. 2 Two-year Doubling Projection (updated)
The typical result is that the 3ft. / 1 m point is reached earlier than with higher doubling rates.

Dr. Hansen's expectations were 5yr doubling = 2045, 7yr doubling = 2055, and 10yr doubling = 2067.

I added a 3yr doubling which resulted in the year 2035 being the 3ft. / 1 m point (The Evolution of Models - 10).

 The .csv file on the 2yr doubling data shows the 3ft. / 1 m year as 2031, with an additional 4ft. of SLR (over the 3yr doubling) by 2100 (Fig. 2).

VI. Conclusion

The part of destiny we do not really want, the port authorities really do not want, and only insane people want, is moving closer and closer to us.

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

Tuesday, May 26, 2015

The Evolution of Models - 10

Fig. 1
In this series, I have been discussing sea level rise (SLR) as analyzed by "computer models."

I call them software models.

Those models have an impact on your life, an impact that they should not have, not because SLR software is bad, but because these models that are being used for policy have not been prepared, or at least adjusted, properly.

An example is:
"sea level rise could be 4 ft. by 2100"
(President Obama). Most experts agree that "4 ft. by 2100" is a known low ball figure produced by models that consistently underestimate SLR.

It is associated with another phrase that causes people to wonder why such a phrase ("worse than previously thought") is spoken and written so often (The Phrase is Back: "Worse Than Previously Thought").

Fig. 2
The use of the phrase is still with us, even though it shouldn;t be (Sleeping Giant in the Arctic, Climate Change Could Overwhelm California).

So, today I want to explain, using the words of a scientist "on the ground," why that is so.

The video at the bottom of the page is a clip from the recent Economist Arctic Summit 2015 (I can't imagine a more horrible place for a scientist to have to go).

Fig. 3
The well meaning scientist has to talk to an audience of blood sucking neoCapitalists, as they sharpen their teeth in preparation for the "negotiations to come."

The hapless scientist hints that he wants funding for research projects, while all the blood sucker investors want is clearly some more and more of that "blood from the Earth" (The Fleets & Terrorism Follow The Oil).

The only question asked at the end of the scientist's presentation was "can we capture the methane venting from the sea floor and sell it?" (paraphrased).

But I digress.

What caught my ear during his tortured presentation in front of those vultures was his explanation of "primitive models" (meaning old original SLR software).

He intimated that those "primitives" began to be developed in the late 1960's (~half a century ago).

Fig. 4
I have noted some of his statements in that regard (concerning SLR models) and the point in the video when he made them, so that you can take note if you watch the short video (if, on the other hand, you don't want to watch the video, the notes will give you the gist of the current folly).

Regular readers know that during this "The Evolution of Models" series, I have developed an SLR program that is data driven, and it can project the statements made by Dr. James Hansen, who predicted then what is happening now, quite a while ago:
The increasing Greenland mass loss ... can be fit just as well by exponentially increasing annual mass loss, a behavior that Hansen (2005, 2007) argues could occur because of multiple amplifying feedbacks as an ice sheet begins to disintegrate. A 10-year doubling time would lead to 1 meter sea level rise by 2067 ... 2045 ... for 5-year doubling time and 2055 ... for a 7-year doubling time.
(The Evolution of Models - 7). I added the calculations for a 3 year (Fig. 1) doubling, which Dr. Hansen had not mentioned (3yr doubling = 2035).

Since he had been exposed to the software that consistently underestimates SLR, I added the 3 year doubling graph (Fig. 1).

Dr. Hansen had given the years it would take for a 1m / 3ft. SLR with doubling in 5 year (Fig. 2). 7 year (Fig. 3), and 10 year (Fig. 4) increments ("when" is determined by rate of acceleration).

The Dredd Blog software log files and .csv file printout match Dr. Hansen's expectations: 5yr doubling = 2045, 7yr doubling = 2055, and 10yr doubling = 2067.

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

01:30 Warming is concentrated in the Arctic ... this pattern has been evident for decades
02:45 These same models that began development in the late 60's always had an Arctic amplified warming because the physics of that reflectivity is simple.
02:55 Removal of reflective cover absorb more sunlight. The primitive models got that and its of course validated by observation.
04:32 Within our lifetimes we will bear witness to this story unfolding rather rapidly.
04:40 The red line shows observations of sea ice area. It depicts how sea ice is retreating at twice the rate [doubling] that our best model projections show.
05:05 The models still don't get the true fidelity of climate, the rapidity of sea ice loss ...
05:30 ... retreating at a rate four times [doubling * 2] what model projections currently get ... the models are if anything underestimating ...
07:53 Just in the past ten years science reveals more sensitive response than was previously encoded in models.

Researcher sweating it out at an Economic Summit:

Monday, May 25, 2015

Weekend Rebel Science Excursion - 42

Amazon book cover
It is a long weekend, so let's get some rebel science done, today, while the warmongers peddle war by calling it the mother of peace (MOMCOM: A Mean Welfare Queen, War is Peace).

A new book by Dr. Peter Ward and Joe Kirschvink is the subject of today's rebel post (A New History of Life: The Radical New Discoveries about the Origins and Evolution of Life on Earth).

But to be perfectly honest, today's post is a traverse of the video (Dr. Ward @ a bookstore) at the bottom of the post.

I traverse the video, listing the times when Dr. Ward mentions selected ideas from the book, but to be more specific, I focus on some of the ideas in the book which have been talked about in Dredd Blog System "rebel science" posts over the years.

But first let me grab your attention, or inspire your prejudicial scorn, with this quote about the book from Amazon:
Charles Darwin's theories, first published more than 150 years ago, still set the paradigm of how we understand the evolution of life-but scientific advances of recent decades have radically altered that understanding. In fact the currently accepted history of life on Earth is flawed and out of date. Now two pioneering scientists, one already an award-winning popular author, deliver an eye-opening narrative that synthesizes a generation's worth of insights from new research.

Writing with zest, humor, and clarity, Ward and Kirschvink show that many of our long-held beliefs about the history of life are wrong.
(Amazon, "A New History of Life", emphasis added). For those who want to delve into it, below is a table with a time in bold, which refers to the minutes:seconds into the video, with a tag "[DBS 1, 2 ...]" containing links to various Dredd Blog posts with at least some discussion of that issue.

FWIW, Dr. Ward is keen on epigenetics, which is a direction most evolutionary scientists are taking:
"In 2010, a group of researchers at the Stanford University School of Medicine in California uncovered a set of three mutations in the microscopic roundworm Caenorhabditis elegans, each capable of extending the life span of the worms by up to 30%. This exciting discovery prompted the research team to ask whether descendants of these worms could live longer, even if they didn't inherit the original mutation from their parents. Much to the researchers' surprise, the descendants lacking the original mutation continued to exhibit longer life spans for up to three generations. How could this happen? The longevity characteristic was no longer carried in the gene sequence, yet it was somehow lingering in descendants of mutated ancestors. Where does this type of genetic memory come from? The answer lies in a phenomenon called epigenetics, which describes molecular events that occur on DNA but not within the DNA sequence. Remarkably, epigenetic changes to DNA are branded into the genome in a manner that can sometimes be inherited by future generations." (Nature, Scitable)

"Geneticists study the gene; however, for epigeneticists, there is no obvious 'epigene'. Nevertheless, during the past year, more than 2,500 articles, numerous scientific meetings and a new journal were devoted to the subject of epigenetics — an antidote to the idea that we are hard-wired by our genes. So what is epigenetics?" (Nature, Perceptions of Epigenetics)

04:00 How old is life on Earth (not as old as stated in the textbooks) [DBS 1]
06:30 Life formed from many separate environments [DBS 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]
07:30 Ideas about how life starts impinges on people's religious and political beliefs (science foundations shy away from funding it) [DBS 1, 2]
08:40 Meteorites from Mars have bacteria in them [DBS 1]
09:50 Ribos, simple sugar can be made from desert mineral borax
11:35 Darwinian ideology contemplated a huge amount of time for natural selection to work
12:50 Unitarianism has been oversold, Darwin overused it
13:12 Lamarck had some valid epigenetic ideas which he was persecuted for by his peers [DBS 1]
13:30 Lamarck's epigenetic notions were anathema to Darwin
13:47 Epigenetics has amazing impact on genetics
14:20 No one is applying epigenetics to the fossil record, which is amazing, because this is a way for quick evolutionary changes [DBS 1, 2, 3]
15:15 All animal life does not have a common ancestor
16:00 Viruses are factors in genetic based diversity in evolution [DBS 1, 2]
18:10 Epigenetics is neoLamarkian ideology; Lamarck was persecuted by Darwin; died pennyless [DBS 1]
19:00 Lamarck had some epigenetic ideas that are still valid, and will see more influence in the future [DBS 1]
19:10 Catastrophism is being revised too [DBS 1]
21:00 Snowball Earth ice ages
28:00 Life shows up in a very short amount of time, 5 mil.yrs. (my)
28:20 Major argument of "Intelligent Design" proponents is correct, Darwinian long-term evolution can't explain the proliferation of species in only 5 my
28:45 With epigenetics it takes less time & matches the record better
30:00 An early intelligence evolved to remove CO2 [DBS 1]
30:43 Catastrophe as an evolutionary extinction player was not conceived of prior to 1800
31:24 Extinction by meteorite impact
32:20 Extinction by global warming
39:50 Living fossils becoming extinct
40:46 Short term global heating
questions from audience
42:30 Hypothesis about how the Earth cooled rapidly is yet unproven
44:45 Anthropocene
50:23 Most of Earth history=no ice, sea level 240 ft. higher than now ... unless we stop (CO2) all the ice is going away & Seattle will be under water
51:20 Civilization can only exist with the climate of recent time, if the ice goes civilization goes

Dr. Peter Ward @ Seattle bookstore: [UPDATE: the video has been censored] (if you find a copy provide a link)