On The Life Sciences Scene

For Brains, Almost Counts
Foresaw Pavlov

A. For gamblers' brains, almost counts
http://www.sciencenews.org/view/generic/id/40735/title/For_gamblers_brains%2C_almost_counts_
In an experiment mimicking slot machines, people’s brains reacted similarly to almost winning as to winning, possibly explaining why gambling can be addictive.

B. From :Pavlov's Smile
http://www.the-scientist.com/community/posts/list/100/122.page#1475

So why Pavlov smiled in 2008?

Pavlov demonstrated effecting placebo phenomena in multicelled organisms by manipulation of their drives-reactions. Now placebo and imagination phenomena are demonstrated also in the smaller organisms, in the genes and genomes of multicelled organisms, in our primal first stratum and 2nd stratum base organisms. A very good reason to smile.

Look at "Life's Manifest" and at "EVOLUTION Beyond Darwin 200" and reflect about them...

Now an interesting chain is exposed to our view, the Genes-Virtual Reality Chain, a most intriguing cultural evolution chain extending from the genesis of our genes to nowadays, throughout life, which is a virtual reality existence, and by virtual reality phenomena, exploitations and manipulations.

Dov Henis
(Comments From The 22nd Century)

Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578

EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Should Science Be Evangelized
Maybe Scientists Should Propagandize As Religionists Do

A. Maybe Scientists should propagandize as religionists do
http://www.physforum.com/index.php?showtopic=25187&st=0&#entry401928

B. For the AAAS science is a companion religion to "spiritual" personal religions

For the AAAS, the organization and Establishment Guild of our "scientists" (whatever this term means), for many many years science has been a religion, too, a "universal religion" besides and in addition to the "spiritual" personal religions.

The AAAS apparently considers that thus having two religions is in accordance with one of the Merriam-Webster (1827) definitions of rationalism, i.e.: "reliance on reason as the basis for establishment of religious truth". (wondering what was "religious truth" when this definition was drawn up, before understanding that religious truth is a virtual reality affair?)

But by adopting this meaning of rationalism AAAS disregards the other meanings of rationalim:

- "a theory that reason is in itself a source of knowledge superior to and independent of sense perceptions". (an 1827 unwitting reference to virtual reality...)

- "a view that reason and experience rather than the nonrational are the fundamental criteria in assessing and solution of problems"

C. So, should science be evangelized?

So why, then, should'nt the AAAS take one step further and embark on explicit evangelizing of science as "the basis for religious truth" in accordance with its hitherto implied-only tenet?

This would be an interesting field trial project in our present virtual reality 21st century technology culture concurrent with the present struggle to survive the collapsed virtual reality basis of this culture's economic tenets.

Dov Henis
(Comments From The 22nd Century)

Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578

EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Unexpected Scientific Rationale
More On The 2009 Life Sciences March

A. "Jumping genes provide unexpected diversity"
http://www.sciencenews.org/view/generic/id/40922/title/Jumping_genes_provide_unexpected_diversity
Mobile DNA elements have stuffed and shrunk the human genome, a comparison of two genomes reveal

B. Pearls of new scientific insights

- "Mobile DNA elements help shape human genomes"
- "Mobile pieces of DNA may have given humans a jump-start on evolution, a new study reveals"
- "... genes have been actively shaping human and other primate evolution"

Unbelievable indeed! Exciting unexpected new scientific insights!

C. Common current misconception...

- "Jumping genes, pieces of DNA that replicate and insert themselves into a host’s genome..."

Whereas genes are organisms, originally independent organisms that evolution rendered capable of surviving only interdependently as functional members of cooperative gene communes, i.e. genomes.

D. The "researchers" compared TWO genomes,

one was the genome of a specific person, J.C. Venter, and the other was the genome "assembled" by Venter's Human Genome Project.

Compared with the "assembled" genome, in the genome of the specific person they found 706 places into which "transposable elements had stuffed extra DNA" while in the stuffing process recombinations between the mobile elements cut 140 chunks out.

In view of this they state: "The finding indicates that transposable elements are unexpectedly potent contributors to human genetic diversity..." and “We’re finding more and more variability than we would have predicted”...

Brilliant and exciting indeed...Life Science Marches On!

Dov Henis
(Comments From The 22nd Century)
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Pointless Experiment
More Superfluous Research

A. From "Hitting the redo button on evolution"
http://www.sciencenews.org/view/generic/id/40649/title/FOR_KIDS_Hitting_the_redo_button_on_evolution
Scientists are experimenting with bacteria to see if evolution plays out the same way every time.

Some "scientists" think that in a redo of evolution things would turn out basically a repeat, with maybe some different details. Others don’t agree. They think that in a redo a small change somewhere along the line could produce very big changes later.

The point of this "experiment" was to settle the 'debate', "to see if evolution plays out the same way every time".

B. The debate subject is futile, pointless, and so is the experiment,

since it is plainly obvious that:

- any redo of any evolution scenario, especially in bio systems, cannot ever be exact. This is plainly obvious and does not need elaboration.

- it is impossible to quantify comparative changes between bio evolution redo's , nor to guesstimate what 'later' changes may be.

C. Such pointless superfluous doings do not contribute anything to comprehension of evolution

I have been presenting evidence for years that adaptation, i.e. culture, is the driver of evolution of all life including human and that genetic evolution, the primal genes' functional modifications, expressions, are generally not random constitutional phenomena but occur in biased courses set-directed by the cultural feedback of the parent multicell organism ( or the monocells community ) to the membership of their genome.

Dov Henis
(Comments From The 22nd Century)

Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578

EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Why Life's Genesis Is Unrepeatable

QUOTE (HenisDov @ May 18 2007, PhysOrg Forum)
A. If one accepts, intuitively and logically, Pasteur's observation .... We are just beginning to comprehend the nature of the raw material called Life and that the purpose of OUR life is ours to choose and develop and follow.
Dov

I am asked, by TracerTong, two questions:

A. Shouldn't it (life's genesis) be repeatable? Wouldn't scientists have already been able to repeat it?

B. What about spiritual happenings? Is it logical to assume only natural?

My answers:

A. Today's "scientists" are unable to "repeat it" because (1) they do not know how the first "life" arose and (2) they do not and will never know and will not be able to duplicate the environments and circumstances of genesis and (3) they do not and will never know and will never be able to repeat the environments and circumstances of post genesis evolution.

B. "Spiritual happenings" are virtual reality affairs. They are feasible only for living organisms that have a culture, i.e. that have a pattern of sensings and reactions to the sensings. Genes, and therefore also genomes, are organisms and display virtual reality phenomena, therefore also multicelled organisms, like dogs and humans, display such "spiritual" phenomena.

Dov Henis
(Comments From The 22nd Century)
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Life And Culture Are Virtual Realities

A. Relevant definitions of terms:

Real: not artificial or illusory, occurring or existing in actuality as a physical entity, having objective independent existence.

reality: the quality or state of being real, a real event, entity, or state of affairs, the totality of real things and events.

Virtual: being such in essence or effect though not formally recognized or admitted, hypothetical thing whose existence is inferred from apparently indirect evidence, existing within a virtual reality.

Virtual Reality: An artifactual environment, image, process or scenario conjured and experienced through sensory or neuronal stimuli and in which one's actions partially determine what happens in the environment.

B. Relevant definitions of Earth life:

Earth Life: 1. a format of temporarily constrained energy, retained in temporary constrained genetic energy packages in forms of genes, genomes and organisms 2. a real virtual affair that pops in and out of existence in its matrix, which is the energy constrained in Earth's biosphere.

Earth organism: a temporary self-replicable constrained-energy genetic system that supports and maintains Earth's biosphere by maintenance of genes.

Gene: a primal Earth's organism. (1st, base, stratum organism)

Genome: a multigenes organism consisting of a cooperative commune of its member genes. (2nd stratum organism)

Cellular organisms: mono- or multi-celled earth organisms. (3rd stratum organism)

C. Relevant comprehensions of culture

- The integrated pattern of human knowledge, belief, and behavior that depends upon the capacity for learning and transmitting knowledge to succeeding generations.

- The customary beliefs, social forms, set of shared attitudes, values, goals, and practices
and material traits of a group, and the characteristic features of its everyday existence.

- The totality of ways of the organisms' dealing with (reaction to, manipulation of, exploitation of) its environment. A biological entity selected for survival of the genome as means of extending its exploitation capabilities of the out-of-cell circumstances, consequent to the earlier evolution and selection of the genome's organ, its outermost cell membrane, for controlling the inside-of-cell genes'-commune environmental circumstances.

- The ubiqitous biological entity that drives Earth life evolution by imprinting genetics, by continuously modifying genes' expressions.

D. Comprehension of "spiritual matters"

"Spiritual matters" are virtual reality affairs. They are feasible only for living organisms that have a culture, i.e. that have a pattern of sensings and reactions to the sensings. Genes, and therefore also genomes, are organisms and display virtual reality phenomena, therefore also multicelled organisms,including humans, display such "spiritual" phenomena.

E. Virtual reality and the 21st century world economy collapse

The 21st century world economy collapse is a collapse of a culture, of the 20th century technology culture, of its values and attitudes and ethics and morals. The world's population is still (Feb 2009) clinging desperately to the collapsed concepts and expectations and makes a huge painful effort to revive the collapsed culture instead of to steadfastly modify it. It is sadly and exasperatingly obvious that the economy collapsed due to adherance to absurd virtual reality concepts and expectations, and that the only hope to survive and overcome the collapse is to understand its nature and to plan and embark on a course to a new, science-based, more rational, virtual reality culture.

Dov Henis
(Comments From The 22nd Century)

Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578

EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

What Dev Henis writes I tend to disagree. Common human culture can not be enforced. Culture is like evolution. It happens over spans of time by selection. The process is slow. It is by nature assimilative. We tend to gloss over differences and drive roughshod. This is a mistake. Culture is popular knowledge assimilation. You try to speed up the process and the elastic snaps. Cultures wherever are to be respected and knowledge reverse engineered to appreciate the foundations of the cultures. Otherwise you go on reinventing the wheel again and again. Jetset human society will end up like the Hindu Goddess Kali standing on Shiva and putting her tongue out. Charanamrit in Hindu temples have a sound scientific basis. The capmphor is a decoagulant and the basil leaf a germicide. Let us understand cultures and reverse engineer the practices instead of doing big budget research and reaching the world to a calamitous stage in just decades. Thanks. - Sharbani Ranjan Kundu, sharbani_ranjan@yahoo.co.in

Rational Steering Of Cultural Evolution

A. Re 21st century culture-economy collapse

http://www.the-scientist.com/community/posts/list/120/122.page#1625

"What Dov Henis writes I tend to disagree. Common human culture can not be enforced. Culture is like evolution. It happens over spans of time by selection. The process is slow. It is by nature assimilative. We tend to gloss over differences and drive roughshod. This is a mistake. Culture is popular knowledge assimilation. You try to speed up the process and the elastic snaps. Cultures wherever are to be respected and knowledge reverse engineered to appreciate the foundations of the cultures." Sharbani Ranjan Kundu

B. Survival mandates rational steering of cultural evolution

What Sharbani writes I tend to disagree. Nowadays human culture can be "enforced", steered. Until few hundreds of years ago specific human cultural phenotypes used to evolve over lengths of time by "natural selection", which, BTW, is also "enforced" by circumstances and environments. But in recent human history "selection" has been more and more "enforced" by some on other human cultural phenotypes, like in post WWII Japan and Germany.

Throughout life's evolution "culture" used to evolve over spans of time in response to "enforcement" by a variety of factors including circumstances, invading genes or other organisms, or invading different cultural phenotypes. However, in recent human history humans have been playing god more and more, interfering with natural "natural selection", accelerating cultural evolutions of many organisms, including humans'.

If you do not speed up the "enforced" evolutionary process, the elastic snaps. You allow and promote evolution of destructive catastrophes. Wise and prudent cultural phenotypes would elect and promote rational self re-education re-orientation.

However, human cultural phenotypes, whatever and wherever they are, that threaten the evolution of welfaring humanity, should not be respected and "understood". They should be assessed rationally and "engineered" to evolve without a threat to other human cultural phenotypes. The interference criterion should be the extent of factual and potential threat.

Suggesting,

Dov Henis
(Comments From The 22nd Century)
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Genes Are Organisms, Earth's Primal Organisms
Recapitulation of few earlier posts

The evidence is obvious all around us, as we live and sleep,
just stop running and reflect a while...

A. Again and again, comprehension of the nature of Earth life:

Earth life: 1. a format of temporarily constrained energy, retained in temporary constrained genetic energy packages in forms of genes, genomes and organisms 2. a real virtual affair that pops in and out of existence in its matrix, which is the energy constrained in Earth's biosphere.

Earth organism: a temporary self-replicable constrained-energy genetic system that supports and maintains Earth's biosphere by maintenance of genes.

Gene: a primal Earth's organism. (1st-, base-, stratum organism)

Genome: a multigenes organism consisting of a cooperative commune of its member genes. (2nd stratum organism)

Cellular organisms: mono- or multi-celled earth organisms. (3rd stratum organism)

B. Again and again, the nature, origin, function and purpose of life

Nature of Earth life: a replicating construction temporarily constraining and maintaining energy.

Origin of Earth life: serendipitous energy-induced formation of Earth's primal organisms, individual independent genes.

Nature of Earth's organisms: temporary self-replicable constrained-energy genetic systems that support and maintain Earth's biosphere by maintenance of genes.

Function of Earth life: uphold and maintain as much constrained energy as possible by upholding and maintaining Earth's biosphere. (Probably one of several constrained energy forms, including black holes).

The purpose of OUR life and its promotion is ours to choose and set. It derives solely from our cognition, which is a biological entity.

The biggest hindrance of scientific and of technological progress in comprehension and exploitation of biology is the avoidance to accept-regard genes and genomes as organisms. Equally hindering is the avoidance to accept and to explicitly and clearly define genes as The Primal Base Cardinal Earth Life Organisms, the organisms that have been evolving into all other Earth organisms.

This avoidance, fraught with implications about human conception of the nature of life, is the biggest hindrance of human culture, of human existential and social progress.

C. Sleep, most obvious evidence of genes' life and their origin

Sleep made simple. Why do organisms sleep?

Sleep is an inherent Earthlife trait. Organisms sleep because their genes-genomes sleep. And for genes, sleep is inborn because genes were the first organisms evolved on Earth and they came into being, born, through the sun's radiation energy absorbed by RNA-type oligomers, and the newborn genes were active ONLY when exposed to sunlight, which was then - prior to bio metabolic energy production - their only usable energy. Thus sleep is an inherent Earthlife trait.

D. Chirality, most obvious evidence of genes' primal, base, status in life's evolution

Darwinian evolution started at life's day one, with the genesis of the first organisms, the replicating oligomers, pre-archaea genes. It started under yet-unknown energetic conditions, by a serendipitous accident, with oligomeric (RNA?) conformations, in a soup containing all their essential molecular progenitors. These conformations happened to absorb the amounts of energy enabling their polymerization to lengths precipitated as determined by the nature and conditions of the soup.

The sugars and the nitrogen-based compounds that, together with the phosphates, are the components of the genes organisms, are chiral. There probably is an energetic advantage in homochirality and chiral homogeneity for the self-replication of biopolymers.

This serendipitous accident set up a matrix-field of energy with a potential extended between its source, sun's radiation, and the precipitating organisms. This was the genesis of the ongoing formation and maintenance of Earth's biosphere.

And since thus the biosphere started it could only evolve in more favorable energetic directions and towards stabler components. Survival. Chiral organism survival. After all this was already into the process of life's evolution...

Dov Henis
(Comments From The 22nd Century)
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Aging Seen Without The Emperor's New Clothes
( recapitulation )

A. Aging, lifetime and age

Aging = to become old, show the effects or the characteristics of increasing age, the increasing liferime. The effects and characteristics of not only the totality of the system, but also of each and every component, and of components of the components of the system. The system is the totality of the components.

lifetime = the duration of the existence of a living being, an organism, or an inanimate thing, a material, star or subatomic particle.

age = the length of an existence extending from its beginning to any given time.

B. More and more research works related to old age are published in scientific periodicals

The lengthening list of work-accounts comprises a wide array of subjects apparently related to old age, including:

- A variety of constitutional impairments,
- a variety of impaired biological processes,
- a variety of impaired genetic materials and expressions,
- a great variety of suggested things to consume or do or avoid for alleviating the symptoms,
- and a great variety of anti-aging suggestions.

C. Some examples of statements:

- A little stress may keep cells youthful.
- Intestinal stem cells, that replenish the lining, go awry in elderly flies, similar to what
happens in certain human stem cell populations.
- Yeast, worms and people may age by similar mechanisms.
- Nearly all organisms experience aging.
- In aging muscles and neurological problems, energy greedy organs, there are mitochondria
dysfunctions.
- Age-related growing 'leakiness' in cell nucleus membrane may contribute to aging and even
to diseases such as Parkinson's and Alzheimer's.
- Age-Related Hearing Impairment, presbycusis, is a complex elderlies disease caused by
overexpression of glutamate due to interaction between environmental and genetic factors.

D. Right they are: "Nearly all organisms experience aging". But why "nearly"?

Why don't "scientists" accept the obvious fact that genes are organisms and "experience aging", too?

Not only yeast, worms and people. Also genes and the interdependent-genes-communes, genomes. Theye are both organisms. They are alive. It is their "lifehood" that makes us and all life forms "alive".

By plain common sense - my favorite scientific approach - they should also be "experiencing aging"...

E. The aging of genes contributes to organisms aging

Since a genome is a cooperative commune of interdependent genes, many of its member genes "modulate its aging" to various extents at various time-rates depending on circumstances and environment and on their individual composition and functioning history. Various things happen to them or affect them and impair their functionalities.

In my plain commonsensical mind "interaction between environmental and genetic factors" is a description of organism's "aging". And in my boy's-like view of the emperor's new clothes organism's aging comprises aging of its genes-genome, and genes and genomes age as we age, and we age also as a result of the aging of our genes and genomes...

F. Finally, re "Theories about human cellular aging supported by new research"

http://www.eurekalert.org/pub_releases/2008-12/asfc-bta111908.php

"Research presented at American Society for Cell Biology conference:
Aging yeast cells accumulate damage over time, but they do so by following a pattern laid down earlier in their life by diet as well as the genes that control metabolism and the dynamics of cell structures such as mitochondria, the power plants of cells."

Cellular Aging? What is Cellular Aging?

Complexly instrumented future spacestations accumulate damage over time, and their residents, too, age and accumulate damage over time. Yes, the functionality of the stations' residents and of their intruments and equipment is impaired with age. Wonder why?

The reason for the impairment with age of the highly active instrumented-equipped stations and of their resident crew is that they "follow a pattern laid down earlier in their life by diet as well as by the residents who control metabolism and the dynamics of the stations' structures such as mitochondria, their power plants."

G. Enough. Cells just house organisms. The resident genes-genomes are THE organisms.

About time that "scientists" refresh conceptions and comprehensions and attitudes and research plannings and peer-reviewings. Let their science evolve...

Dov Henis
(Comments From The 22nd Century)
http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q--?cq=1

EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Genome linked with culture!
Listen listen, The Wheel Is Reinvented!
Plant's Genome Found Linked With Plant's Culture!

A. listen, listen
the cat's pissin
where, where?
under the chair
hurry hurry bring the plate
never mind, it's too late...

B. New from "Ecological nitrogen-limitation shapes the DNA composition of plant genomes"
http://mbe.oxfordjournals.org/cgi/content/abstract/msp038

- "The influence of ecological limitations on the composition of eukaryotic genomes is still unclear"

- "These findings indicate a fundamental role of nitrogen limitation in the evolution of plant genomes, and they link the genomes with the ecosystem context within which biota evolve."

C. "Seed of Human-Chimp Genomes Diversity"
http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q--?cq=1&p=409
Nov 2005, Dov, in biologicalEvolution forum.

Biological Evolution's Seeds of Diversity, Human and Chimpanzee/Bonobo Genomes

Chapter One, In which some wonder what made us human.

Three recent quotations from Science, representative of many other recent similar statements in various scientific publications:

1) "Understanding the genetic basis of how genotype generates phenotype will require increasing the accuracy and completeness of the currently available chimpanzee genome sequence, as well as sequencing other primate genomes."

2)"Can we now provide a DNA-based answer to the fascinating and fundamental question, "What makes us human?" Not at all! Comparison of the human and chimpanzee genomes has not yet offered any major insights into the genetic elements that underlie bipedal locomotion, big brain, linguistic abilities, elaborated abstract thought, or any other unique aspect of the human phenome."

3)"What makes us human? This question may be answered by comparison of human and chimpanzee genomes and phenomes, and ultimately those of other primates. To this end, we need to understand how genotype generates phenotype, and how this process is influenced by the physical, biological, and cultural environment."

Chapter Two, In which is explained plainly and succinctly the obvious route by which we evolved,

i.e. that genotype has not generated phenotype, that we evolved from our genotype via a group of feedback loops. From Science, Vol 308, Issue 5728, 1563-1565 , 10 June 2005, Immunology: Opposites Attract in Differentiating T Cells, Mark Bix, Sunhwa Kim,Anjana Rao:

"During differentiation, precursor cells with progressively narrowed potential give rise to progeny cells that adopt one of two (or more) divergent cell fates. This choice is influenced by intricate regulatory networks acting at multiple levels. Early in differentiation, precursor cells show low-level activation of all progeny genetic programs. Bias toward a given lineage comes from environmental inputs that activate powerful positive- and negative- feedback loops, which work in concert to impose selective gene expression patterns".

Chapter Three, In which we explain the revolutionary evolved uniqueness of the human ape's phenotype:

The 6My-old revolutionary life evolution was initiated by our forefathers who adapted from life in semi- or tropical forest circumstances to life on plains. As changed living posture and circumstances led to modified perceptive/adaptive capabilities and eventually to language communication humans have gradually replaced adaptation to changed circumstances with self-evolving cultures/civilizations for control and modification of much of their circumstances. This is essentially similar to early life's celling evolution, but with culture functioning for humans for change/control of circumstances in lieu of RNA and protein toolings that function for the in-cell genomes for adapting their cell's physiology to changing circumstances.

Chapter Four, In which appears, may be, genetic evidence/demonstration of the workings of human cultural evolution.

(a) From Science, 2 Sept 2005: "Page's team compared human and chimp Ys to see whether either lineage has lost functional genes since they split.

The researchers found that the chimp had indeed suffered the slings and arrows of evolutionary fortune. Of the 16 functional genes in this part of the human Y, chimps had lost the function of five due to mutations. In contrast, humans had all 11 functional genes also seen on the chimp Y. "The human Y chromosome hasn't lost a gene in 6 million years," says Page. "It seems like the demise of the hypothesis of the demise of the Y," says geneticist Andrew Clark of Cornell University in Ithaca, New York."

(b) But look at this: From Science, Vol 309, 16 Sept 2005, Evolving Sequence and Expression:"An analysis of the evolution of both gene sequences and expression patterns in humans and chimpanzees...shows that...surprisingly, genes expressed in the brain have changed more on the human lineage than on the chimpanzee lineage, not only in terms of gene expression but also in terms of amino acid sequences".

Surprisingly...???

Chapter Five and conclusion, In which I suggest that detailed study of other creatures that, like humans, underwent radical change of living circumstances, for example ocean-dwelling mammals, might bring to light unique evolutionary processes and features of evolutionary implications similar to those of humans. end.DH.

D. How astonishingly wondrous is the familiarity of nowadays researchers with years-old published scientific comprehensions

From "Factors Involved In Extended Historical Darwinism"
http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q--?cq=1&p=409

- Earth Life Is A Real Virtual Affair; it pops in and out of existence in its matrix, which is the energy constrained in Earth's biosphere .

- Genes are organisms, interdependent members of genes communes, genomes, all continuously undergoing evolution directed towards survival as long as possible, for maintaining Earth's biosphere as long as possible.

- Culture is a ubiquitous biological entity and is the major effector of genetic evolution, of capabilities and attributes selected for survival.

- The major course of natural selection is NOT by random mutations followed by survival, but via interdependent, interactive and interenhencing selection of biased replication routes by genes at their alternative-splicing-steps junctions, effected by the cultural feedback of the 3rd stratum multicells organism or monocells community to their prime stratum genes via their 2nd stratum genome organisms.

- Evolution of life is but a minute component of the evolution of the universe. Cosmic evolution is the evolution of energy. Life, and all objects and processes and natural laws in the universe, are - since none in exsistence at singularity - products of evolution and are continuously further evolving. Everything in the cosmos is fractal, rehappens on many scales, and is continuously evolving. Each and every system in the universe continuously evolves within the total universal evolution and all the systems' evolutions are intertwined and within it life's evolution is the evolution of genes-genomes, continuously evolving in a losing attempt to survive, to maintain - as long as possible - pockets of constrained energy that would otherwise, and anyhow eventually, expand and dilute with the whole mass and energy of the cosmos...

Dov Henis

PS: Puzzled why even Darwinians do not comprehend that Darwinism starts all the way back with Life's day one, with the pre-archaea not-yet-genomed-celled genes...

Exasperated,

Dov Henis
(Comments From 22nd Century)

2009 Passe Mantras (I)

A. Cells do, cells get.

"Cells get two chances, not just one, to fix their mistakes"...?
http://www.physorg.com/news156087023.html

- Cells do not get any chance nor do they do anything. Cells are NOT organisms. A cell is the housing, the space ship, of its resident genome, the cooperative commune of its interdependent genes membership. Cell membranes are organs, plain and simple, organs evolved by genome to protect and maintain their living milieu. About time for the myopic 21st century science to realize this and to correct its concepts, instead of mindlessly repeating its mantras...

B. "Missing piece of plant clock found", about "the underlying biochemical mechanisms that control plant clocks".
http://www.physorg.com/news156087384.html

- A coming research report will re-affirm, in sophisticated sciencelingo, that the rooster indeed brings on sunrise, or that Gazania flowers switch the sun on and off. There is no "biochemical mechanisms that control bio clocks". Bio-clocks are products of the innate active-sleep pattern of genes and genomes, parents of all Earth's Life, since in their days of genesis and early evolution direct sunlight was the only source of energy in pre-metabolism Earth life. Melatonin and some proteins are dark-and-light que signals evolved by later monocellular communities for timing intercells processes when intracell processes are at rest.

C. "Culture skews human evolution"
http://www.physorg.com/news156100530.html

"...(there is a) cultural buffering of evolution’s harsh rule of “survival of the fittest” that may be leading to the “dysevolution” of Homo sapiens.

- This is a confused concept-comprehension of evolution. Genetic evolution does not occur in accordance with an evolution rule-law, and it is not a result of survival of the fittest. Genetic evolution, i.e. changes in expressions of genes, are mostly not random and are not the source of evolution but the consequences of cultural evolution, i.e. of evolved survival patterns. First evolves the culture of the organism, i.e. its pattern of assessing of/reaction to its circumstances, then the organism's cultural pattern impacts the genes-genome and consequently the genes change their expressions.

Dov Henis
http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q--?cq=1
(Comments From The 22nd Century)
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201

Life Is Simpler Than They Tell Us

Evolution:
Genes to Genomes to Monocellular to Multicellular Organisms,
Direct Sunlight to Metabolic Energy, Too,
Triptophan to Serotinin to Melatonin to Neural System.

A. Triptophan to Serotinin to Melatonin

Melatonin is a hormone secreted by the human pineal gland during night-time darkness. It is now marketed in the US as a nutritional supplement. The hormone is an indoleamine compound derived from the essential amino acid L-tryptophan, with serotonin as an intermediate precursor.

Tryptophan is one of eight essential amino acids, not produced by the body but coming from the diet. The additional fourteen amino acids are produced metabolically.

In the brain, tryptophan converts to serotonin, the neuro-transmitter. Tryptophan is the only source for serotonin in the brain. Insufficient L-tryptophan in the diet is a cause of many severe biological malfunctions.

Some serotonin is converted in the pineal gland to melatonin, the hormone involved in intercell processes during sleep time.

B. Sunlight to Metabolic Energy

Bio-clocks are products of the innate sun-dictated active-inactive pattern of genes and genomes, parents of Earth's life. During life genesis and its early evolution direct sunlight was the only source of their usable energy. This situation persistrd well into the evolution of the early monocellular organisms, and both genes and genomes display, therefore, innate "inactive-sleep" phenomena.

The incorporation of mitochondria with some cells innitiated the metabolic bio production of bio usable energy and furnished the evolving monocellular organisms with new, additional, flexibly available local energy. This development opened up a variety of courses of evolutions of cultures of monocells communities.

C. Individual Monocells to Cooperative Monocells-Communities

As individual independent genes aggregated to cooperative genes communes, genomes, so individual monocells aggregated cooperatively into monocellular communities.

From "Life Is A Cooperative Affair" (Sept 2005)
http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q--?cq=1&p=168

"Life has always been and still is a fractal affair, repetition of phenomena on ever more complex scale. It cannot be otherwise; it evolves. And surviving-proliferating life has always been a cooperative affair since cooperation is most successful for overall survival/proliferation."

Cooperation requires all sorts of interactions, including maintenance, protection and foraging for food-energy. Organisms' interactions are "cultures". Cultures require "cultural energy". Melatonin and some proteins are dark-and-light que signals evolved by the monocells communities for timing intercells processes when the intracell processes are at "sleep-inactive" state. Melatonin is a derivative of serotonin a derivative of triptophan, and proteins are genes' toolings, energy-dependent metabolism products.

D. Monocellular to Multicellular Organisms, Monocells Culture to Neural System

Now we can appreciate the fractal nature of life's evolution. It is ever-continuous ever-enhanced ever-complexed cooperation. Now we can understand why, and grosso modo how, all the organs and processes and signals found in the multicelled organisms have their origins in the monocells communities. And this includes the functions of serotonin and melatonin and, yes, the evolution of neural cells and the neural system with their intricate outer-membrane shapes and functionings and with their high energy consumption requirements.

Now, circa four billion years after initial genesis-evolution with direct sun's energy followed with evolution with also indirect, bio, sun's energy, some of Earth life, we humans, find ouselves short of energy and in need of exploiting again more, and more directly, our sun's energy...

Dov Henis
(Comments From The 22nd Century)
http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q--?cq=1
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

See this re origins in cells clusters:

nullTS1019153]Life Is Simpler Than They Tell Us

Evolution:
Genes to Genomes to Monocellular to Multicellular Organisms,
Direct Sunlight to Metabolic Energy, Too,
Triptophan to Serotinin to Melatonin to Neural System.

Then look at this:

Live Wires
http://www.sciencenews.org/view/feature/id/41637/title/Live_Wires
Cells reach out and touch each other with tunneling nanotubes

Urging,

Dov Henis

HGT Extended Horizon
Complete Functional Gene Transfer

A. From "Aphids support symbionts with borrowed DNA"
http://www.sciencenews.org/view/generic/id/41539/title/Aphids_support_symbionts_with__borrowed_DNA

Aphids borrowed at least two genes from bacterial buddies, and those genes now support another bacterium that lives in the insect. Those two genes are active in specialized cells called bacteriomes. The insects provide a home for the bacterium and the bacterium provides essential nutrients for the insects’ growth.

While scientists have known that bacteria can transfer DNA to their hosts, most of the transferred DNA doesn’t contain genes. The new discovery is the first evidence of the transfer of functional genes from bacteria to host.

Aphids and Buchnera have lived together for more than 100 million years. They have become so interdependent that the bacterium’s genome is stripped down to the point that it no longer contains many of the genes the bacterium needs to sustain itself. One of the genes Buchnera lacks is ldcA, which encodes a molecule that helps recycle a component of the bacterium’s cell wall. Atsushi Nakabachi and Naruo Nikoh discovered that aphids contain an ldcA gene similar to one found in another bacteria, Wolbachia. The aphids make the recycling molecule in cells where Buchnera live, suggesting that the aphids are providing the bacterium with a way to build and repair cell walls. The transfer most likely happened in an ancestor of several different aphid species, one that was colonized perhaps by both Wolbachia and Buchnera.

Pea aphids also contain another gene that came probably from bacteria called Bradyrhizobium.

Scientists have previously suspected that gene transfers happen frequently between multicellular organisms and the bacteria they live closely with, but they thought that those transfers were dead ends, says John Archibald. Unless the DNA makes its way into the germ line, the tissues that will produce eggs and sperm, the transferred DNA won’t be passed along to subsequent generations of hosts. It isn’t yet clear how Wolbachia managed to insert their genes into the aphid genome in a heritable way, Archibald says.

These [findings] indicate that organisms including animals are much more flexible than expected, and can be more easily fused with other organisms,” Nakabachi says.

B. Some notes on the interesting findings

(1) I reckon that the above "the aphids make the recycling molecule" means that "the aphid's ldcA gene is expressed in the bacteriomes".

(2) The abstract starts with "Aphids borrowed the genes". We observe, apparently, a ubiquitous transaction between organisms.

It is unreasonable that an X genome, a multigenes organism of creature X, and a gene of a Y creature, an organism that is an obligate member of Y's genome community, would "incorporate" with each other just for fun or due to curiosity or by accident. A successful horizontal gene transfer between two organisms occurs rationally due to either the interests of both organisms or to the interest of the gene donor, an invader.

(3) The above "organisms including animals" refers, I reckon, to monocelled bacteria as organism and to multicelled aphids as animals.

I'm not tired of repeating over and over again my suggested conception of Earth life as a construct of three strata of organisms, genes, multigenes genomes and celled (mono- and multi-), and I'm confident that this concept will be eventually adopted by science and by the public, with profound implications for human culture.

Dov Henis
(Comments From The 22nd Century)
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Genes, Not Cells, Were Earth's First Organisms
And Are Earth's Primal Organisms
(a recapitulation)

A. Pushing back an oxygen-rich atmosphere date
http://www.sciencenews.org/view/generic/id/41755/title/Pushing_back_an_oxygen-rich_atmosphere
Hematite crystals in Australian rocks hint that Earth’s atmosphere was oxygenated earlier than previously thought.

There’s evidence of eukaryotic life, i.e. monocellular organisms with DNA sequestered in a protective nucleus, from roughly 1.9 billion years ago. Multicellular animals appear on the scene much later.

Large quantities of oxide minerals in rocks around the world indicate that the atmosphere had at least small amounts of oxygen by 2.2 billion years ago. The presence of certain biomarkers in Australian rocks has been hailed as evidence that oxygen-making organisms had evolved by 2.7 billion years ago, but recent studies have cast some doubt on that earlier date.

Now, analyses of rocks laid down 3.46 billion years ago in what is now Australia push back the oxygen era even further, Hiroshi Ohmoto, a geochemist at Pennsylvania State University in University Park, and his colleagues contend online March 15 in Nature Geoscience.

B. Earliest single-celled organisms

(Forwarded) If the 4.6 billion Earth years are compressed into a single year: the Precambrian Era, evolution of first life forms, extends from January 1 to mid-November; the Paleozoic Era, evolution of invertebrates and primitive fishes, extends through the rest of November and part of December, and the Mesozoic, era of dinosaurs, takes up most of the remainder of December. Our time, the Quaternary, would occupy only the last four hours on New Year's Eve.

For most of Earth's history, there were only single-celled organisms. Fossilised single-celled micro-organisms have been found in rocks 3·5 billion years old.

By 2.4 Ga (gigaannum = 10^9 years) the ratio of stable isotopes of carbon, iron and sulfur shows the action of living things on inorganic minerals and sediments and molecular biomarkers indicate photosynthesis, demonstrating that life on Earth was widespread by then.

C. Revised fixations that cells were the earliest Earth-life's organisms, and that tie life's genesis with organic bio-metabolism

These fixations dictate that Earth's earliest organisms were fueled by netabolically self-generated energy.

But cells were NOT the earliest Earth-life's organisms. Genes, Not Cells, Were Earth's First Organisms, And Are Earth's Primal Organisms.
Cells are no more organisms than future manned spaceships would be organisms. The innner and outermost cell membranes are multi-functional organs evolved and produced by the organisms that reside within the outermost membrane, as would be the spaceship's inner and outermost skins-walls produced by their residents, even if the membranes are organic whereas the skins-walls are not. And undoubtedly the capabilities of multi-functional spaceship skins-walls would be far below those of cell's membranes.

The primal genes came into being, phased from polymers into replicating beings, organisms, by absorbed sun energy, and proceeded to carry on their life during daylight times, fueled solely by sun energy, and this most probably was the state of life affair until sometime earlier than 3.5 Ga, which is when fossilised single-celled micro-organisms have been found in rocks.

D. It is thus rationally possible to de-couple life's genesis and onset of bio-metabolism,

and to update the comprehension of the nature of Earth life per
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578

Dov Henis
(Comments From The 22nd Century)
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
or
http://www.the-scientist.com/community/posts/list/100/122.page#1407

Sciense-Public Cultures Gap
FW: 2 Cultures in New York City

On May 9, 2009 "visionaries, scientists, authors, and the media will join together to explore the persistence of the sciense-public cultures gap and how it may be overcome":

http://www.nyas.org/snc/twocultures/index.asp

I hope that I'm wrong.

In my sad opinion this "unique and important event" will, most probably, result only with louder racing engine noise as the gas pedal is pushed further down in the science vehicle jacked-up-from-the-ground in the 21st-century technology culture.

http://www.articlesbase.com/science-articles/economy-collapse-cure-delusion-799133.html

Dov Henis

Significance Of Hour-Timing In Medical Treatment

A. Vaccine could protect against virus that causes birth defects

http://www.sciencenews.org/view/generic/id/41874/title/Vaccine_could_protect_against_virus_that_causes_birth_defects

An experimental vaccine is shown effective half the time it's administered in stopping cytomegalovirus infection in women in their child-bearing years.

No vaccine currently exists for cytomegalovirus, which can cause birth defects when it infects a pregnant woman. Because of this risk, vaccine researchers have targeted the virus for decades — without any clear benefit until now.

This is the first vaccine that really shows prevention from infection with cytomegalovirus.

B. Efficiency rate might differ with hour-of-timing of administration

http://www.articlesbase.com/science-articles/life-is-simpler-than-they-tell-us-817144.html

I suggest that the efficiency rate of the vaccine might differ depending on the hour of day at which it is administered. This since the genome-genes are inactive mostly circa 2AM and the levels of serotonin-melatonin are highest then, signalling a call for intercell maintenance time.

Dov Henis
(Comments From The 22nd Century)
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201

Works Of The Brain's Default Network

A. "Tired brain defaults differently"
http://www.sciencenews.org/view/generic/id/42054/title/Tired_brain_defaults_differently

- "Sleep deprivation may cause the brain to switch to default mode when it should be paying attention."
- "Sleep deprivation affects the brain's network"
- "Sleep is essential for the proper functioning of the brain's network"

B. "Life Is Simpler Than They Tell Us"
http://www.the-scientist.com/community/posts/list/120/122.page#1726

And "2009 Passe Mantras"
http://www.the-scientist.com/community/posts/list/120/122.page#1722

There is no biochemical mechanisms that control bio clocks. Bio-clocks are products of the innate active-sleep pattern of genes and genomes, parents of all Earth's Life, since in their days of genesis and early evolution direct sunlight was the ONLY source of energy in pre-bio-metabolism Earth life. Melatonin and some proteins are dark-and-light que signals evolved by monocellular communities for timing communal intercells maintenance processes during the daily genes' inactive time, when intracell processes are at rest.

Even though genes and genomes are both organisms, it is not clear if sleep deprivation "tires" them and thus "tires the brain". The nature of the tiredness is not clear. However, it is most probable that sleep deprivation interferes with the brain's intercells maintenance processes, thus mal-effecting proper normal functioning of the brain's network.

Suggesting,

Dov Henis
(Comments From The 22nd Century)
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201

Ambidexterity And Contralaterallization

A. "Chimps ambidextrous when digging wells"
http://www.sciencenews.org/view/generic/id/42475/title/Chimps_ambidextrous_when_digging_wells
A survey of water-collection holes dug on the banks of an African river by wild chimpanzees indicates that, unlike people, these apes don’t have a preference for using either the right or left hand on manual tasks.

B. Human dexterity preference became genetic by compulsions of changing human culture

"Human brain contralaterallization"
http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q--?cq=1&p=153

A note I e-mailed July 18, 2005 to C Walsh, Harvard, re his "Asymmetry in Human Left/Right Cerebral Cortex", Science, Vol 308, Issue 5729, 1794-1798, 17 June 2005.

A) You write: "The human left and right cerebral hemispheres are anatomically and functionally asymmetric. To test whether human cortical asymmetry has a molecular basis, we studied gene expression levels between the left and right embryonic hemispheres using serial analysis of gene expression (SAGE). We identified and verified 27 differentially expressed genes, which suggests that human cortical asymmetry is accompanied by early, marked transcriptional asymmetries.

B) The expression "asymmetry has a molecular basis" sounds strange. The aspects of the asymmetry include, of course, ALSO genes' expressions, the total asymmetry being the product of specific evolution of the human cerebral cortex.

C) In July 1997 I wrote the following "conjectural scenario":

" Humans' uniqueness on Earth was initiated by a stimulus in a zone in the brain of some of them when challenged by needs for new manipulations, and for new capabilities of analysis and assessments of wider vistas open to them when changing posture to erect due to change of environment from forests to plains. The new demands employed existing brain cells in one half of their brain, overtaxed its capabilities and led to compensation by overworking the symmetrically located cells in the second half of the split brain and this in turn led again to compensation in the first half thus causing contralaterallization that is still evolving now".

D) I suggest that the probability of a similar asymmetry might be sought in ocean mammals, having undergone a radical intensive change of living circumstance and mode, like our ancestral primates.

Respectfully,
DH

Dov Henis
(Comments From The 22nd Century)
Life's Manifest
http://www.the-scientist.com/community/posts/list/112.page#578
EVOLUTION Beyond Darwin 200
http://www.physforum.com/index.php?showtopic=14988&st=405&#entry396201
http://www.the-scientist.com/community/posts/list/100/122.page#1407