Genetics Is Wholistic Until It Arrives At Energy

A. ENCODE's Updated Gene Definition

http://www.genome.org/cgi/content/full/17/6/669

The ENCODE consortium is engaged in characterizing the human genome by various high-throughput experimental and computational techniques designed to characterize functional elements (The ENCODE Project Consortium 2007). While the landmark human genome sequencing surprised many with the small number (relative to simpler organisms) of protein-coding genes that sequence annotators could identify (21,000, according to the latest estimate), ENCODE highlights the number and complexity of the RNA transcripts that the genome produces. ENCODE suggests that it has changed our view of "what is a gene" considerably more than the sequencing of the Haemophilus influenza and human genomes did (Fleischmann et al. 1995; Lander et al. 2001; Venter et al. 2001). The discrepancy between previous protein-centric view of the gene and one that is revealed by the extensive transcriptional activity of the genome prompts a reconsideration of what a gene is and made ENCODE propose a new tentative updated gene definition:

"The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products".


B. Genes Are Life's Base Organisms

Repeat from my opening post:

It is the "lifelihood" of genes that makes us and all other forms of life on Earth living organisms, and evolution has been the route of Life's ever more complexing progress since the first replication of the first gene.

Early independent peptides, primordial genes, have entered into symbiotic associations in which eventually each of the ever increasing host of functions/tasks vital for the evolving associations is taken up by the member most efficient at it, leading to gene speciation and to gene specialization.

The history of life begins with independent genes, cascading fractally from single independent genes to agregate of genes, then to agregate of agregate of genes. Cooperative association is an inherent feature of life throughout all its evolution and at all its levels, in pre-cell and in mono-cell life and in mono-cell communities and in poly-cell life-forms and in communities of poly-cell life forms.


C. Today's Genes Were Once Genomes

Today's genes are pre-today's-genomes'-genomes. Keep uncomplexing today's genomes and you get, fractally, sub-genomes until you reach the primordial independent genes. However, evolution complexing have rendered all the fractal base elements completely interdependent. There's no going back to independent genes.


D. Genetics Is Wholistic Until It Arrives At Energy

The farthest we go in reductionism in Life we shall still end up with wholism, until we arrive at energy. Energy is the base element of everything and of all in the universe. The universe and evrything in it are continuously evolving and all the evolutions are intertwined.


Dov

On Evolution's Genomic Driving Forces


A. On Evolution of Unique Human Traits
(non-updated concept. DH)

http://www.eurekalert.org/bysubject/index.php?kw=30

Cold Spring Harbor Laboratory
30-Jul-2007

Quote
AURORA, Colo. (Tues., July 31, 2007) – Today, researchers from the University of Colorado Health Sciences Center, along with colleagues from Stanford University, report the results of a large-scale, genome-wide study to investigate gene copy number differences among ten primate species, including humans. The study provides an overview of genes and gene families that have undergone major copy number expansions and contractions in different primate lineages spanning approximately 60 million years of evolutionary time. In the report, which appears online in Genome Research (www.genome.org), the scientists speculate how unique, lineage-specific gene copy number expansions and contractions in humans may underlie traits such as endurance running, higher cognitive function, and susceptibility genetic disease.

Primates first appeared on earth approximately 90 million years ago, and today, about 300 different species of primates exist. “One of the main genomic driving forces in primate evolution is gene duplication,” explains Dr. James Sikela, Professor at the University of Colorado. “To our knowledge, this study is the most comprehensive assessment of gene copy number variation across human and non-human primate species so far.”

To survey the differences in gene copy number among these species, Sikela and colleagues used DNA microarrays containing over 24,000 human genes to perform comparative genomic hybridization experiments. They compared DNA samples from humans to those of nine other primate species: chimpanzee, gorilla, bonobo, orangutan, gibbon, macaque, baboon, marmoset, and lemur. This allowed them to identify specific genes and gene families that, through evolutionary time, have undergone lineage-specific copy number gains and losses.

The authors of the report suggest that “many of the genes identified are likely to be important to lineage-specific traits found in humans and in the other primate lineages surveyed.” To illustrate this potential, the scientists highlighted several gene families that exhibited striking lineage-specific differences. In particular, the human lineage-specific copy number expansion of a gene called AQP7 could explain why humans have evolved the capacity for endurance running. AQP7, or aquaporin 7, plays a role in transporting water and glycerol across membranes. Therefore, it may facilitate the mobilization of glycogen (energy) stores during long periods of intense exercise; it may also play a role in dissipating excess heat through sweating.

The scientists also found dramatic gene copy number differences potentially associated with cognition, reproduction, immune function, and susceptibility to genetic disease. end quote


B. Non-updated Concept

1) "One of the main genomic driving forces in primate evolution is gene duplication".

No, no, no. Gene duplication is just a replication mechanism; definitely not a and certainly not main evolution driving force. The driving force is Darwin's old survival requirement. Plain and simple. During the replication process, when genes are at a junction with several options of nonidentical selfrepeat (definitely not duplication), they proceed with the option selected via the feedback of the surviving organism, which is the surviving genome.

2) "copy number expansion of a gene called AQP7 could explain why humans have evolved the capacity for endurance running. AQP7, or aquaporin 7, plays a role in transporting water and glycerol etc.,..."

No, no, no. This is placing the horse at the rear of the wagon. The better capacity for endurance running has brought about the evolution of AQP7, which in turn further increased the endurance capacity.

C. Get It Thru (True) Your Head: It Is Living Experiences That Drive the Evolution of Genomes

Again and again I re-explain the meaning and consequences of Darwin's observations, i.e. that the extent of the relative stability of compositions of genomes, genomes being Earth's live organisms, is proportional to their survival's dependence on physiological adaptation. The more the genome, the organism, depends on physiological adaptation for survival the more its composition changes. On the other hand the further complexed is the culture of the genome, of the organism, the smaller is the number of its genes that change for survival and simultanously the greater is the number of variations-changes in its genes involved in its culture. Its culture serves it for survival in lieu of physiological adaptation. It modifies its environment instead of adapting to its environments.

Oooof,

Dov

Natural Selection Is At Genomic Level

A. Back to where it started

- A recent find of a 400 million-year-old fossil of a coelacanth fin, the first finding of its kind, fills a shrinking evolutionary gap on fin-to-limbs evolution.

- In fish systems of multiple mating, females mate regularly and are able to store sperm for at least six months. Some of the intriguing questions are is there a role of female preference or of male-male competition in shaping the mating results in these fishes.


B. Darwinism seen in action in fish?

http://www.eurekalert.org/bysubject/biology.php

University of California - Riverside
31-Jul-2007

Quote:

RIVERSIDE, Calif. – A research team, including UC Riverside biologists, has found experimental evidence that supports a controversial theory of genetic conflict in the reproduction of those animals that support their developing offspring through a placenta.

The conflict has been likened to a “battle of the sexes” or an “arms race” at the molecular level between mothers and fathers. At stake: the fetus’s growth rate and how much that costs the nutrient-supplying mother.

The new research supports the idea of a genetic “arms race” going on between a live-bearing mother and her offspring, assisted by the growth-promoting genes of the father.

Part of the significance of the research is in providing experimental proof of a theory put forth in the 1990s that holds that in animals with a placenta, genetic material from the father and the mother promote different growth rates in the embryo, producing a conflict over nutrients.

The placenta is a complex organ of maternal and fetal tissues that nourishes the developing fetus in the uterus.

Most mammals, excluding marsupials like the kangaroo and the koala, have a placenta. Because of the placenta, a developing embryo remains longer inside the mother (in marsupials, early development of the newborn occurs in the mother’s external pouch).

Evidence to support the conflict over nutrients theory has been found in placental mammals. But the new study is the first to look for this conflict in a species other than mammals that also have evolved placental reproduction.

“We worked with the fish family Poeciliidae and other families in the order Cyprinodontiformes, which included the poeciliids,” said David Reznick, a professor of biology at UCR and a leading authority on live-bearing fishes, who provided all of the life history information for the study.

Reznick explained that most fishes are egg-layers, but some species in the family Poeciliidae have evolved a placenta-like structure and give live birth.

The new research tested the conflict theory by studying samples of the IGF2 growth hormone (insulin-like growth factor 2) collected from 50 species of minnows. The IGF2 gene is found in all vertebrates (including fish and people), and is the primary fetal development growth hormone.

Reznick and the other researchers found that the IGF2 gene sequences had changed in some species of the minnows, showing that segments of the gene had evolved.

“In earlier research, we had found that the placenta had evolved independently several times in these fish,” Reznick said. “In the current research, we found a strong correlation between the evolution of live-bearing and placentation in these fish and the acceleration of the rate of evolution of IGF2 in the fish. This shows that IGF2 plays a vital role in not just mammals, but in fish as well.”


>> The researchers found that the biggest genetic changes were in those species of the minnows that had developed placentas, supporting the Darwinian theory of natural selection.

The study also provides independent support for the theory of conflict between the male and female genetic material in producing offspring. <<


In most animals, the male provides his genetic material for the offspring and leaves. The mother has a more intimate relationship with the fetus, nurturing it through her placenta and, in some animals, nursing and caring for the baby after it is born.

But while the father may not be present, the genetic material he provided is hard-wired to provide fast fetal growth, so that his offspring will be the hardiest, best survivors and the ones who demand the most of the mother’s placental nutrients.

The mother, on the other hand, provides genetic material that promotes the same growth level for all of her offspring, so that her nutrients will be available to support her and the offspring from all her matings.

End of quote

C. The two suggested conclusions of the experiment

are marked above (>> <<). I suggest that the results DO NOT support a conjucture of “battle of the sexes”, that the natural selection has nothing to do with competition between the male and female genetic material, and that the selection of the the genomic constitution of the offspring is a result of the parents' genomic feedbacks during its first formation, whish IS where and how Darwin's natural survival is expressed.

Dov

Immunity and Multicellularity,
and Getting High on Verbiage


A. Immunity in social amoeba suggests ancient beginnings
2-Aug-2007 Baylor College of Medicine

http://www.physorg.com/news105283565.html

Quote:

Finding an immune system in the social amoeba (Dictyostelium discoideum) is not only surprising but it also may prove a clue as to what is necessary for an organism to become multicellular, said the Baylor College of Medicine researcher who led the research that appears today in the journal Science.

Dictyostelium discoideum usually exists as a single-celled organism. However, when stressed by starvation, the single cells band together to form a slug that can move. Eventually the slug changes to produce cells that perform specific functions – spores and stalks. In this new report, Dr. Adam Kuspa, chair of biochemistry and molecular biology at BCM, and his colleagues describe a new kind of cell they dubbed a “sentinel” cell.

Sentinel cells circulate within the slug, engulfing invading bacteria and sequestering poisons or toxins, eventually eliminating these from the slug. These cells often operate through a particular mechanism in the cells controlled by a Toll/Interleukin-1 Receptor domain protein (TirA), Kuspa and his team found.

This signaling pathway or a very similar one is present in plants and animals, he said. Now it has been identified in amoeba. It has not been found in fungi.

“Amoeba have, in the last 10 years, become appreciated as one of the four main forms of life in the crown group of eukaryotic (multicellular) organisms – plants, animals, fungi and amoeba,” said Kuspa. “What allowed them to become multicellular"”

One way to estimate the characteristics of the organism that went before those that were multicellular is to look for characteristics that are present in two, three or all four of these main groups, he said.

“Those were likely present in the progenitor organism,” said Kuspa. Because three of the four major groups of organisms have this pathway, “I argue that means that the progenitor of all multicellular organisms had this pathway. Since that organism was not likely multicellular, it must have used it as some kind of signaling to respond to bacteria in the environment.”

Looking at it from another point of view, “it’s possible that one of the properties of those (crown) organisms that allowed them to become multicellular was the ability to distinguish self from non-self – the hallmark of an immune system,” said Kuspa. “The speculation is that a requirement of multicellularity is that you develop systems to recognize pathogens and other non-self cells from yourself.”

Kuspa sees two paths for future research in the area. One is to look for evidence of the same immune mechanism and protein in other kinds of amoeba. The other is to look at unicellular organisms to determine if they have this same kind of immune signaling pathway.

“If none of the early diverging organisms that never became multicellular developed this kind of signaling system, it would subtly strengthen our argument,” he said.

end of Quote


B. Memory, Sentience and Consciousness
4 October 2005, Dov Henis

http://blog.360.yahoo.com/blog-P81pQcU1dLB..._Q--?cq=1&p=174

- Cultural functions and processes are actual, not analogical/metaphorical, extensions of inter- and intra-cell processes, and are for the same ends as those of biological processes, i.e. for survival of our genome.

- All organisms, also single-celled, have consciousness. It is the complexity of consciousness that varies from organism to organism. The baseline of consciousness is sensing mechanisms plus accompanying reaction processes.

- Immune system is common to ALL organisms. In its scope and features in humans and other animals it is prevalent and common also in plants. Its baseline is MEMORY, i.e. production and storage of a unique proprietary protein tag stored somewhere in the organism as a record of a sensed matter or - yes - of a thought (formulated or read or heard) negotiated by the correct neurons.

The base thing to remember by all of us small or big, plain or sophisticated, poor or rich, religious or humanists etc., is that ALL our characteristics and capabilities are accumulations passed to us (plus slight modifications by us) by and via ALL our predecessors all the way back to the start of life, to the self-duplication of the first Earthly gene... And it is our unique language communications that made possible the evolution of conscious humans.


C. Everything In All Organisms Is About Darwin

- Antigens are large molecules (usually proteins) on the surface of cells, viruses, fungi, bacteria, and some non-living substances such as toxins, chemicals, drugs, and foreign particles. The immune system recognizes antigens and produces antibodies that destroy substances containing the antigens.

- "Clue as to what is necessary for an organism to become multicellular? and what allowed them (amoeba) to become multicellular?" ( see A above...)

- These questions and answers are not elucidated in the form of 'pseudo-sophisticated academEnglish verbiage. They have been posed and answered long ago by one C.Darwin, and further clarified by genetics. They are all about selected forms of survival of genomes in changing or in adverse environments, and in microorganisms they are about selected forms of adaptation and survival mechanisms such as biofilm formation, quorum sensing and antimicrobial resistance, and in amoeba it is all about...(see A above...).

Dov

“Life is a disease; and the only difference between one man and another is the stage of the disease at which he lives.” (George Bernard Shaw)

AAAS Hinders Science Progress
by its life evolution presentation

A. Terms:

1) AAAS = American Association for the Advancement of Science.
2) Progress = a forward or onward movement towards an objective, a gradual betterment.
3) Science = knowledge as distinguished from ignorance or misunderstanding, sometimes systematized object study and knowledge of patterns of phenomena/process obtained and tested through agreed science-defined methods.

B. From AAAS Project 2061, Chapter 5,
on evolution of life:

1) In the section about Cells: "the structure and functioning of cells, the basic building blocks of all organisms". Here and throughout the book the Cells are refered to as Organisms.

2) On heredity: "New heritable characteristics can result from new combinations of parents’ genes or from mutations of them. Except for mutation of the DNA in an organism’s sex cells, the characteristics that result from occurrences during the organism’s lifetime cannot be biologically passed on to the next generation. Thus, for example, changes in an individual caused by use or disuse of a structure or function, or by changes in its environment, cannot be promulgated by natural selection."

C. The Above Two Presentations Are Scientifically Incorrect

1) Again and again, the cells of organisms are NOT the organisms. The cells are the the functional housings of "the basic building blocks of all organisms", which are the genomes of the organisms, of which we presently know circa 1.8 miliion species. It is now routine to extract a genome from its cell, replace it with another genome of a fresh suitable zygote, and proceed with life evoluton.

2) And again and again, "characteristics that result from occurrences during the organism’s lifetime" become feedback input to the genomes of the next generation(s) and affect the selection of path of genome's mutation upon replication, thus biologically passing on to future generation.
This is how we evolved differently from our ancestors. Our forefathers' new circumstances ( from forests to plains ) dictated new survival acts, i.e. new culture, which served as feedback to our genome, whose selection of possible mutations was made richer and biased with the new feedback possibilities.

Dov

AAASP's Hypocritical Science-Religion Congruousness
Hinders Science Progress


A. Terms:

1) AAASP = American Association Against Science Progress
2) Congruous = being in agreement, harmony, or correspondence or conforming to the circumstances or requirements of a situation, or marked or enhanced by harmonious agreement among constituent elements.
3) Hypocrisy = a feigning to be what one is not or to believe what one does not; especially : the false assumption of an appearance of virtue or religion.


B.AAAS book, 9 August 2006, In Praise of Hypocrisy

http://www.eurekalert.org/pub_releases/200...t-abe080906.php

- The Evolution Dialogues: Science, Christianity, and the Quest for Understanding
the rich and complex historical interaction of evolution and Christianity.

- Jack Haught, a Georgetown University theologian, said the book "will prove to be very helpful to teachers and students of biology, especially where questions might arise about the scientific status of Darwin's theory and the religious implications of evolution." Haught said the book "exhibits not only prudence and judiciousness, but also an erudite understanding of the distinct modes of understanding characteristic of science and religion. A major benefit of this project is that it demonstrates how a religious understanding of the world need not be looked upon as an alternative to evolutionary science and vice-versa."

Rodger Bybee, executive director of the nonprofit Biological Sciences Curriculum Study, said the book "will be an excellent, positive contribution to a contemporary understanding of evolution and religion."


C. Notes On Science-Religion Incongruity

http://blog.360.yahoo.com/blog-P81pQcU1dLB..._Q--?cq=1&p=177

plus additional entries in

http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q--?cq=1


Dov

Evolution's Drive

A. Evolution's Drive Is By Gene Regulation?

Evolution is driven by gene regulation
9-Aug-2007, Yale University

http://www.eurekalert.org/bysubject/biology.php

Quote:

New Haven, Conn. — It is not just what’s in your genes, it’s how you turn them on that accounts for the difference between species — at least in yeast — according to a report by Yale researchers in this week’s issue of Science.

“We’ve known for a while that the protein coding genes of humans and chimpanzees are about 99 percent the same,” said senior author Michael Snyder, the Cullman Professor of Molecular Cellular and Developmental Biology at Yale. “The challenge for biologists is accounting for what causes the substantial difference between the person and the chimp.”

Conventional wisdom has been that if the difference is not the gene content, the difference must be in the way regulation of genes produces their protein products.

Comparing gene regulation across similar organisms has been difficult because the nucleotide sequence of DNA regulatory regions, or promoters, are more variable than the sequences of their corresponding protein-coding regions, making them harder to identify by standard computer comparisons.

“While many molecules that bind DNA regulatory regions have been identified as transcription factors mediating gene regulation, we have now shown that we can functionally map these interactions and identify the specific targeted promoters,” said Snyder. “We were startled to find that even the closely related species of yeast had extensively differing patterns of regulation.”

In this study, the authors found the DNA binding sites by aiming at their function, rather than their sequence. First, they isolated transcription factors that were specifically bound to DNA at their promoter sites. Then, they analyzed the sequences that were isolated to determine the similarities and differences in regulatory regions between the different species.

“By using a group of closely and more distantly related yeast whose sequences were well documented, we were able to see functional differences that had been invisible to researchers before,” said Snyder. “We expect that this approach will get us closer to understanding the balance between gene content and gene regulation in the question of human-chimp diversity.”

end of quote


B. Oh, Feedback Loops, Organism's Culture!

Give them some more time and they will discover that what now seems to them "the way regulation of genes produces their protein products" will turn out to be, after all, "the way genes are regulated", which involves "regulators of gene regulation" and "regulators of regulators etc.," and it's a sure bet that it will finaly dawn on them that:

From "Human-Chimp Genomes Diversity", 2 June 2005, at

http://blog.360.yahoo.com/blog-P81pQcU1dLB..._Q--?cq=1&p=179

"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".

Dov

A thought I'd had a few times over the idea that conscious will is an illusion and life is driven by "external" natural forces is that, if that's the case, then when I decide to do something and act upon those desires, then such a viewpoint implies the universe, in its (unjustifiably assumed) entirely deterministic manner, has been "doing its thing" for who knows exactly how long, just to reach the current moment in which I had the ability to perform that action.

It's the flip side of the "conscious will is an illusion" claim, that the universe has instead been designed to support conscious actions. A point of view that supports both is that there remains an "external" immutable source of information that's subjectively interpreted in ways that are molded by consciousness. I believe this view is also more accurate in that it accounts for subjective variations in how "reality" is witnessed (objective reality is less tangible than the various subjective versions of it that we all live in).

The reason why there's a pressure to assume the universe is entirely deterministic and ruled by perfectly accurate and immutable natural laws is because those are the only forms of it that can be utilized socially, as it's only the recurring features that can be predicted and included as knowledge for future utilitization, though it appears obvious to me that not all of existance can be seen as entirely deterministic and predictable if knowledge is to remain something that changes, as then knowledge is dynamic and driven externally by things outside it (and a static knowledge seems to deny the existance of experience and time).

Also, if evolutionary pressures have resulted in conscious life, this implies either that consciousness is pervasive and unavoidable or that consciousness imparts an evolutionary advantage upon a species, in which case this leads to the conclusion that either consciousness predominates the universe or does indeed have physical influences that, at a minimum, influence the survivability of a species.

Maybe evolution is a conscious creation? (There are always (at least) two sides to a story.)