How Faith in Neo-Darwinism May Be Holding Us Back

Do you believe in Neo-Darwinist evolution? New-Darwinism is often used as something of a shibboleth to separate the scientific cognoscenti from the flat-earthers and creationists. But is such a "test of scientific rationality" justified? Only if there are no alternatives to Neo-Darwinism which better fit the observed facts. But what if there were better alternatives? Who would be the flat-earthers then?

Lynn Margulis is a prominent thorn in the side of institutional neo-darwinism, and one of the foremost promoters of the theory of Symbiogenesis. On occasion, Margulis can seem like something of a flake, but it is just that quality which allows her to stand up to the pressures of conventional thinking and make her own way against the crowd and its political consensus.

Faith in any conventional form or ideology will hold humans back from discoveries that may seem to contradict those forms and ideologies. We live in an unfortunate age when academic and intellectual thought has been largely taken over by one general ideology -- which actively suppresses debate and open epistemological inquiry into topics which may be too near and dear to the hearts of the thought leaders within the uber-dominant ideology.

Even the so-called "skeptics" today are often nothing better than papered-over consensualists. "Skeptic" Michael Shermer has written a book called The Believing Brain, in which he attempts to explain human belief using game theory, neuroscience, and evolutionary psychology. But as skeptics go, Shermer tends to be something of a credulous skeptic, as he tends to accede to "consensus" a bit too easily. Like many writers and historians of science who are not actually scientists, Shermer relies on second- and third-hand anecdotes and clever phrasing a bit more than he perhaps should. One can learn nothing about the next level from "skeptics" like Shermer, who is a fashionable and consensual kind of skeptic, always safe and well far behind the cannon fodder.

Fortunately, Neo-Darwinism is only peripheral to the central political issues that drive the dictators, critics, and pseudo-skeptics of modern academia, media, and politics, so it is still permissible to question some aspects of neo-darwinian theory as long as one is not too threatening to the status quo. For example, scientists are learning that some "acquired characteristics" of parents and grand-parents can be inherited by children and grandchildren, via epigenetic means. We are likely to discover many more contradictions to conventional genetic and evolutionary theory as we go along.

But none of these piecemeal discoveries are likely to be as liberating as the potential explosion of knowledge which might arise from a real-world demonstration of controlled symbiogenesis in action.

Neo-Darwinian evolution may be the best theory we've got to explain evolution -- or there may be something better. There are still many profound discoveries waiting to be made, using the mental framework of neo-darwinian theory. It will always be useful in the sense that Newtonian physics will always be useful -- within specific limited domains.

Who is going to come closer to the global optimum, the path to rapid expansion of knowledge in evolution and biology? The rational gadfly who is unafraid to question popular convention, or the uber-conventionalist who hides behind a faith in crowd consensus?

Things can change very rapidly when radical theories and tools are discovered. Modern hierarchies of ideas and power can be overturned almost instantly in the face of the type of discoveries which are possible. Which societies are capable of withstanding radical change, which is bound to occur sooner or later? A society whose women are increasingly choosing not to have children because children cramp their style? Or a society of people who welcome change, even as they continue the eternal cycles of love, family, child-raising, birth, death, and continuation in the face of all odds and challenges?

It can be frightening to step outside the mainstream -- particularly if you do so by yourself without the support of a group. But if you take a look at the state of the modern world, it should not take you long to see that the mainstream has very little to offer a conscientious seeker or a driven pathfinder. In fact, the mainstream appears to be taking an express train to the Idiocracy.

In basic rescue and resuscitation, we first look at the ABC: airway, breathing, and circulation. Then we proceed to the finer points of diagnosis and intervention. In your lives, you need to take a similar prioritised approach. But try not to get so caught up in basic survival issues that you do not keep one eye on the sky, for falling sacred cows and orthodoxies.

Just one, small and seemingly insignificant scientific or technological discovery could overturn almost all the conventional wisdom and hierarchical power structure of your society. And there are a lot of discoveries in the pipeline at this time. Not all of them will be developed to their potential -- particularly in our modern age of faux environmentalist energy starvation and a general aversion to disruptive technologies by the ruling classes and thought leaders.

But in reality, it is not up to them any longer. They just do not realise it yet.

Poor, Bare, Forked Animals Begin to Decipher Epigenome

NIH
The epigenome is the system of genome modifiers that guide gene expression. Epigenetics determines whether a cell will be a brain cell or a liver cell, even though both cells possess the same genome. Some preliminary results are beginning to come in from the US NIH's modENCODE program.

Sarah C.R. Elgin, PhD, the Viktor Hamburger Distinguished Professor in Arts & Sciences, who led the Washington University lab that is part of one of the modENCODE teams offers an explanation.

“We learned many things from the Human Genome Project,” Elgin says, “but of course it didn’t answer every question we had!

“Including one of the oldest: We all start life as a single cell. That cell divides into many cells, each of which carries the same DNA. So why are we poor, bare, forked creatures, as Shakespeare [Al Fin: Lear ActIII SceneIV] put it, instead of ever-expanding balls of identical cells?

“This work,” says Elgin, “will help us learn the answer to this question and to many others. It will help us to put meat on the bones of the DNA sequences.” _WUNewsroom

Wikipedia

The epigenetic code that determines whether genes are silenced or expressed consists of chemical modifications to the DNA, to “tails” that hang off the histones, or other packaging proteins.

“ENCODE and modENCODE are much more complicated projects than the Human Genome Project,” Elgin says, “because the DNA sequence is pretty much the same in every cell type, whereas the chromatin structure is different in every cell type. In fact we believe it is the chromatin structure that differentiates one cell type from another.

“That means we can’t just do one genome for the organism. We have to do every different cell type to get a complete picture of the organism, and that’s a daunting prospect.” _WU

The research relies upon the most advanced bio-research and computing technologies. The amount of data generated is staggering, and far beyond what an unaided human could organise and comprehend.

But this is the beginning of the true meat of genetics. Sure, they are looking at worms and fruit flies now. But humans and all human symbionts and parasites are on the list to be comprehensively studied. The knowledge to be gained will provide unimaginable benefits.

A Fine Meth (ylome) You've Gotten Us Into This Time

Source
The methylome is the pattern of DNA methylation in cells as they become relatively differentiated. Methylomics is a branch of epigenetics -- non-coding control of gene expression. Even identical twins will have different gene expression, in part due to differing methylomes. Methylomes of cancer cells are of particular interest to medical scientists.

Chinese scientists have decoded the methylome of mature peripheral blood mononuclear cells. The tools they used may prove useful for decoding the methylomes of other types of mature and cancerous cells.

. Understanding the mechanisms and functions of DNA methylation and how it varies from tissue to tissue and between individuals will have profound implications for human health and disease.

A team of Chinese researchers decoded the essentially complete methylome (an inventory of all the bases that are methylated) of the human genome using peripheral blood mononuclear cells (PBMCs). The results are published in the online, open access journal PLoS Biology.

The research is part of YanHuang (YH) Project, which has been launched by BGI (previous known as Beijing Genomics Institute) at Shenzhen, which aims to sequence 100 Chinese individuals in 3 years to accelerate the discovery of disease genes and mutations in an Asian population.

...The research not only provides a comprehensive resource for future epigenomic research but also demonstrates a paradigm for epigenetic studies through new sequencing technology. The PBMC methylome data has been deposited to NCBI (http://www.ncbi.nlm.nih.gov/Traces/sra/, accession number: SRA008544). It is expected to form a lasting resource as part of the International Human Epigenome Project. _SD

The methylome is a unique signature of the development of a particular cell or cell type. This development was affected by both the individual's genome and his environment. A person's methylome -- in its unbelievable complexity -- is but one more way in which persons are different from each other.

We have only begun to comprehend how much we have yet to learn.

Update 10Nov10: U of Chicago researchers have made an important discovery into the nature of "demethylation" of DNA

Greater Human Genetic Diversity Than Previously Believed

ImgSource

As humans look more deeply into their genetic and epigenetic complement, they are discovering far greater genomic differences between humans than previously believed possible. The 1000 Genomes Project is reporting on results from its pilot phase:

Evan E. Eichler and coworkers of the University of Washington, Seattle, used data from the 1000 Genomes Project to analyze copy-number variations, which are differences in the number of times a particular gene sequence appears in the genome (Science 2010, 330, 641). About 1,000 genes "have been largely inaccessible to traditional genetic study as a result of their repetitive nature," Eichler said at the press briefing. Using newly developed sequence analysis algorithms and sequence tags, his team investigated copy-number variations in these genes, he said.

Eichler's team found that copy-number variations occur in fewer than 10% of human genes. Many of these genes map to regions that had been previously identified as highly repetitive and have been implicated in diseases such as schizophrenia and autism, the authors note.

Even at the pilot stage, the 1000 Genomes Project has already provided "a more complete catalog" of human genetic variation than was available previously, Durbin said. The project is already moving forward with its main phase, with the goal of sequencing 2,500 genomes. _ACSPubs

Whether 1000 genomes or 2500 genomes, the study is still quite preliminary, in terms of understanding the astounding magnitude of variation within the broad human genome and epigenome. As we begin to comprehend the vast numbers of differences in gene expression between even the closest of relatives, we may get a glimmer of understanding of how our molecular makeup generates the diverse worlds we inhabit.

Abstract of paper:

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.

A Hint of Epigenetics

The term “epigenetics” most commonly refers to heritable changes in gene activity not accounted for by alterations or mutations in the DNA sequence. But in order to understand the important developments now underway in biology, it’s more useful to take “epigenetics” in its broadest sense as “putting the gene in its living context.” _NewAtlantis

Source

Epigenetics -- non-coding control over gene expression -- is one of the most exciting areas of science at this time. We are learning that the genetic code is only the short, first chapter in a very long book. The non-genetic "code" -- the non-coding DNA and RNA -- has a logic all its own. We are just beginning to decrypt the obscure cipher. The possibilities for the transformation of life as we know it seem just as grandiose as were the hopes of the early promoters of the human genome enterprise. Only this time, we are working at a deeper level of sophistication. How many more levels will we need to descend before we reach the promised land of genetic medicine?

... some 95 or 98 percent of human DNA was useless for making proteins. Most of this “noncoding DNA” was at first dismissed as “junk” — meaningless evolutionary detritus accumulated over the ages. At best, it was viewed as a kind of bag of spare parts, borne by cells from one generation to another for possible employment in future genomic innovations. But that’s an awful lot of junk for a cell to have to lug around, duplicate at every cell division, and otherwise manage on a continuing basis.

...As organisms rise on the evolutionary scale, they tend to have more “junk DNA.” Noncoding DNA accounts for some 10 percent of the genome in many one-celled organisms, 75 percent in roundworms, and 98 percent in humans. The ironic suspicion became too obvious to ignore: maybe it’s precisely our “junk” that differentiates us from water fleas. Maybe what counts most is not so much the genes themselves as the way they are regulated and expressed. Noncoding DNA could provide the complex regulatory functions that direct genes toward service of the organism’s needs, including its developmental needs.

...Over successive generations, cells destined to become a particular type lose their ability to be transformed into any other tissue type. And so the path of differentiation leads from totipotency (the single-celled zygote is capable of developing into every cell of the body), to pluripotency (embryonic stem cells can transform themselves into many, but not all, tissue types during fetal development), to multipotency (blood stem cells can yield red cells, white cells, and platelets), to the final, fully differentiated cell of a particular tissue....Cells of the mature heart and brain, then, have inherited entirely different destinies, but the difference in those destinies was not written in their DNA sequences, which remain identical in both organs.

... _NewAtlantis

The author goes on to describe several ways in which gene expression can be drastically altered by other means than the coding of genes -- specifically by non-coding DNA and by protein :: DNA interactions. Non-coding DNA appears to play a huge role in gene expression -- as does non-coding RNA.
The ongoing discoveries of a previously-hidden epigenetic oversight of gene expression, is exciting. Yet, it is the epigenetics (and epi-epigenetics) that remain undiscovered which hold the keys to the mysteries that confound us.

The ability to reach into the subtle mechanisms of gene expression -- without mucking everything up -- will mark the beginning of a new phase of human existence.