Distributed Content Agglomeration

As content management across the Internet matures, to where, as of this writing, content gets retrieved and distributed on the fly routinely from disparate sources, each of which might hold only a small part of the requested content. The retrieval sequence proceeds according to rules of modal logic operating on content metadata. The agglomerated content gets synthesized and sequenced at the point of end-user delivery. BitTorrent manages content by this model.

The biological cell manages content the same way. Each protein molecule synthesized is content delivered according to a request. The cell is the end user. But the delivery of the proteinaceous content occurs by way of a vast content management system behind the scenes. It’s hard to find in the processes of that system anything resembling a one-to-one correspondence—between anything and anything else—as in the old one-gene, one-protein model of genetic expression. The protein delivered does not correspond to any contiguous sequence of genes in the cell’s DNA, but is a product of genetic snippets gathered from many places, and edited and re-arranged before the final sequence is fed into the ribosome. This has been going on, on Earth alone let alone elsewhere, for a few billion years.

Nature is the apotheosis of technology.  Our evolutionary and historical path already is well trod.  Nature has done it.  Events of the temporal world unfold along a metabolic pathway that leads from the organic to the inorganic and back again inside the feedback loop of the stellar life cycle. Human technology and its industry, seemingly antagonistic toward nature, constitute a phase of nature’s reproductive cycle. Taking the step to the next phase is the immediate opportunity.

Intelligent Design + Darwinian Evolution = Dead End

By casting nature in the role of machinery, the notion of Intelligent Design (ID) shows itself to be an anthropomorphizing tool. The designer-artifact lens through which IDers see nature projects onto nature the general shape of the human-artifact relationship. ID anthropomorphizes the supernatural, by making deity out to be a kind of super tinkerer, thereby, I suppose, filling theists with a feeling of familiarity with the divine, even if the tinkerer lacks eyes, hands, etc. 

And . . .

By casting physical nature in the role of de-novo miracle, science shows itself to be a religious tool. The occurred-by-fiat lens through which scientists see natural law projects onto nature the general shape of the human-deity relationship. Science sanctifies the natural, by making physical laws out to be a kind of super miracle, thereby, I suppose, filling atheists with a feeling of familiarity with the divine, even if nature lacks mind, soul, etc.

Intelligent Design: A Case Study in Cherry Picking

Intelligent Design (ID) theory proposes that her complex workings make nature look so much like an artifact that we should take her to be one, one that, according to ID discourse, was willed into being by a pre-existing creative intelligence. This is in distinction to the prevailing explanation of nature offered by science.

Problem is, the putative intelligence responsible for nature is, alas, a stunningly peculiar species of intelligence. According to the IDers, it is unlike any intelligence anyone ever has encountered anywhere outside of theology (or science fiction).  IDers propose a brainless intelligence and an omniscient one at that. 

Somehow, despite all inductive evidence to the contrary, there exists, they argue, an intelligence that requires no brain, nor even solid-state circuitry, for it to attend its business. Nature’s intelligent designer doesn’t need a body of any sort at all. The designer belongs to a unique class of intelligences, of which it is the sole member.

This odd construct, a disembodied supermind, derives from a faulty analogy. IDers observing human invention, notice that nature in suggestive ways looks and acts like a high-tech machine. They reason that since explaining machinery requires reference to an intelligent designer (or several), then so must explaining nature. This line of analogical thinking constitutes a case study in the disreputable practice known as cherry picking.

The Twin Phantoms: Genes and Information

Ongoing research in molecular biology has delivered to the world the peculiar finding that the term gene refers to no determinable thing at all. Gene is an idea. It grew from an assumption. The assumption, implied by the prevailing scientific philosophy of reductionism, is that there must be a smallest unit of biological expression. And a smallest unit of biological inheritance. And that atomic entity was called a gene.

Despite gene losing its power to denote, the science of genomics continues to advance and looks determined to keep doing so. And this is also despite reductionism’s shortcomings increasingly becoming apparent, as research reveals the seemingly intractable interwovenness of the processes and subprocesses of biological metabolism.

Reductionism fails because everything that goes on inside a living cell depends on—is caused by, directly or indirectly–everything else that goes on inside the cell. And then, adding more complication, there are exogenous influences. And above it all, no locus of control. There is a lacuna of control. The cell has no brain. The sequencing of the human genome, that recent triumph of reductionism, like the cataloging of elementary particles, provides a compendium, but it resides far from the macrostructure, far from an accounting of gross outcomes. Structures and processes that define the macro world do not map readily onto elementary bits.

Secular Totem: Natural Selection

During the past few weeks I'd been enjoying an engaging exchange about evolution theory on an online science forum. One of the threads I was posting in posed the question as to whether evolution theory adheres to scientific method. My comments in the thread focused on the veracity of the concept of natural selection. I implied that natural selection theory was lacking.

Things seemed to be going well, but then *Kablooey*, the moderator recognized, rightly, that I had diverted the conversation into a rabbit hole.  I had wandered off script.  And he threw me in the penalty box --- my posts in this thread were relegated to the Trash Can.

Given the unpopularity of my posts -- my arguments won no converts -- it's tempting to believe that their final resting place in the Trash Can had something to do with that unpopularity. Nonetheless, the moderator did recognize that I was not addressing the topic of scientific method directly and deserved some kind of rebuke. But the Trash Can? 

For the curious, you can judge for yourself whether my comments are Trash-Can worthy:
http://www.scienceforums.net/topic/86744-starlarvaes-thread-hijack-from-does-evolution-follow-the-scientific-method-if-so-how/page-1

Is Natural Teleology Naturally a Secular Deity?

This frustrating exposition, after all, yields a satisfying conclusion. Nagel frustrates with his opaque writing style, and, nearly as frustrating, he rejects the NeoDarwinian account, when it comes to the origin of consciousness, rationality and value—yet retains it in his teleological alternative. That is, he schizophrenically honors the heart of the Darwinian doctrine, natural selection, while insisting that the doctrine is almost certainly wrong. Go figure.

What Darwin Got Wrong." But Nagel dismisses the centerpiece of their attack—the incoherence of natural selection theory—cavalierly, to my mind, opining in a footnote that they misinterpret the theory. Really? How so? Now, that would be worth reading.

Which is not to say that the present book is not. When someone of Nagel's stature presents secular objections to the NeoDarwinian paradigm, feathers are bound to fly, as they do in any number of critical reviews of the book. Science seems to feel pressured to circle the wagons around the Darwinian account no matter the veracity of the counter arguments. It's time to take a break.

Conventional thinkers who keep natural selection theory at the top of their list of explanatory tools can use it to explain any aspect of organic nature. They need only contend that whatever is observed, say consciousness and rational thought, or blue feathers and big beaks, is as it is because that phenotypic trait was "more adaptive" than the alternatives expressed in the ancestral population. If in some instances that explanation seems implausible, then the explanation is “genetic drift.”

In any case, Nagel sidesteps this catch-all application of Darwinian reductionism by pointing out that nature from the outset must have had the potential to sprout living beings with minds. Nothing in conventional scientific thinking accounts for this potential inhering in nature. The prospect transcends the materialist, NeoDarwinian paradigm, or at least that's Nagel's contention.

The Official Story: Narrating Public Myth, from PsyOps to NeurOps

August 4, 2013, update to this post: Narrative Science is a company that helps businesses communicate by turning data into stories. The company's software program, Quill, "is an artificial intelligence engine that generates, evaluates and gives voice to ideas as it discovers them in data." The company's website elaborates:

"Quill imports your data and builds an appropriate narrative structure to meet the goals of your audience. Using complex Artificial Intelligence algorithms, Quill extracts and organizes key facts and insights and transforms them into stories, at scale. Quill uses data to answer important questions, provide advice and deliver powerful insight in a precise, clear narrative."

That ability could come in handy. For the CIA. 

The intelligence agency's business-investment arm, In-Q-Tel, has contributed an undisclosed amount of funding to Narrative Science. My original post, below, might explain why the CIA is pursuing the engineering of stories. The agency is out to weaponize narrative.

* * *

Once upon a time, there was a public policy think tank at the University of Virginia, called the Miller Center. In October 1998, the Center invited historians, editors and journalists to mull over “the state of the art” in political history. There was a problem to be addressed, which apparently was that historical narrative had slipped through the hands of its rightful authors. And with it went those failing authors’ control of public sentiment. Implied in the conference’s mission was the felt need to figure out not only how this situation came about, but also how history’s rightful authors could recapture the historical narrative. Controlling narratives, people in high places seem to believe, facilitates controlling mass behavior, making it a subject worth study.

The Conference on Contemporary Political History kicked off with remarks from then director of the Miller Center, Philip Zelikow. (A few years later, during a leave from his directorship, Zelikow kept on a short leash the Kean-Hamilton Commission, also known as the 911 Commission, which he steered as its staff executive director.) In his opening remarks to the history conference, Zelikow laid out his concerns regarding contemporary political history:

“’Contemporary’” is defined functionally by those critical people and events that go into forming the public’s presumptions about its immediate past. This idea of ‘public presumption’ is akin to William McNeill’s notion of ‘public myth’ but without the negative implication sometimes invoked by the word ‘myth.’ Such presumptions are beliefs (1) thought to be true (although not necessarily known to be true with certainty), and (2) shared in common within the relevant political community. The sources for such presumptions are both personal (from direct experience) and vicarious (from books, movies, and myths).”

(All quotes from Zelikow are from the Miller Center Report, Vol. 14, No. 3, Winter 1999.) We will return later to McNeill and public myth. First, we need to follow Zelikow into the sources of public presumption. He identifies four:

”First, public presumptions can be ‘generational.’ They are formed by those pivotal events that become etched in the minds of those who have lived through them [. . . ]. The current set begins in approximately 1933, although the New Deal generation is fading. The Second World War and Vietnam, however, continue to resonate powerfully.

“Second, particularly ‘searing’ or ‘molding’ events take on ‘transcendent’ importance and, therefore, retain their power even as the experiencing generation passes from the scene. In the United States, beliefs about the formation of the nation and the Constitution remain powerful today, as do beliefs about slavery and the Civil War. World War II, Vietnam, and the civil rights struggle are more recent examples.

“Third, public presumptions often concern 'dramatic stories plucked out of time,' such as the Alamo, Pickett’s Charge, or the Titanic.

“Fourth, some public presumptions gain currency because they have a particular resonance for us today, either because they invoke powerful analogies to the present [. . . .] or because they offer a causal link and seem to explain ‘why we are the way we are today.’ Taken together, we see that presumptions that remain ‘contemporary’ are—with few exceptions from the 18th and 19th centuries—events and episodes from the last 60 years.”

Depending on which conspiracy theory one subscribes to, that of the Bush administration and the Kean–Hamilton Commission or some variety suggested by the 911 Truth Movement, it takes little imagination to perceive in Zelikow’s assessment a premonition or foreshadowing of events to come, his remarks about searing events taking on transcendent importance being uttered just three years prior to the attacks of 9/11.

And nowhere in his comments will one find any concern that public presumptions should reflect history accurately.

Natural Selection is Dead. Long Live Evolution.

Lecture: Evolution in Four Dimensions
Click the image for an excellent talk by Eva Jablonka, in which she describes provocative new findings in epigenetics and animal behavior. The findings move natural selection farther toward the periphery of evolutionary theory. Phenotypes, as they differetiate during evolution, seem to self-organize, as do the differentiating cells in a developing organism. My contention is that evolution and development resemble one another because they are two appearances of the same process, which is development.

If one could lay Darwin's concept of natural selection next to the current model of evolution, one would have a hard time finding much in common between them. Outside of the vaguest generalization of the evolutionary process, captured in Darwin's phrase, "Descent with modification," nothing much of the original formulation survives to contribute to the current model, the so-called Extended Synthesis.

Epigenetics, niche construction, phenotypic plasticity and other intriguing new developments in bioscience sit at the center of that synthesis and throw into question the foundations of the Darwinian model. Despite evolution theory's provisional character, however, the fossils record descent’s modifications, and they taunt us: What during descent accounts for these modifications?

Culture as Phenotype and Evolution's Crystal Ball

The issues are in the tissues.

A massage therapist once shared with me that piece of trade wisdom.  She was making a point about the interplay between mental and physical discomforts. She was not the first to link the two.

Scottish Psychiatrist R. D. Laing in the 1960s and '70s, following onto Freud and Jung, proposed that earliest experiences in life inform not only personal psychopathologies but also the myths of the tribe. He was interested particularly in myths that share a pattern with prenatal and early postnatal developmental histories and suggested that the mythic tales might recapitulate the adventures of zygotes, embryos, and fetuses.

Uterine Endometrium Adopting
The Newly Arrived Blastocyst‏

In The Facts of Life, Laing cites the story of King Sargon. As an infant, the future king was placed by his parents in a reed basket and sent down river. He drifted until AKKI, the gardener, rescued him, and AKKI then raised the foundling to adulthood. The adult Sargon then stepped into the world to become king of Assyria. Laing, as have others, pointed out the parallels between this story and that of the biblical Moses. The infant Moses also was placed by his parents in a basket and set adrift, was adopted and raised by his rescuer and eventually left the home of the rescuer to assume a position of prominence.  Laing could have included among his examples a more contemporary hero, Superman, whose parents placed him as an infant into a "basket"—a rocket ship—and sent him downstream—through interstellar space—from the doomed planet, Krypton, to Earth, where the Earthlings Jonathan and Martha Kent discovered and adopted him. The Kents raised the infant, whom they named Clark, to adulthood. The adult Clark Kent then relocated from Smallville to Metropolis, where he assumed his superhero identity.

The stories recapitulate the journeys and development of the zygote, embryo, and fetus, suggested Laing. That is, the stories parallel the prenatal story: A zygote, encased in a membrane, called the zona pellucida, travels downstream—down the fallopian tube—until, as a blastocyst, it is adopted by the uterine endometrium. Attached to the uterus, it matures into a fetus, and at the requisite time it is born into the world.

Laing also cites correspondence between Freud and Jung in which the psychoanalysts discussed another natal motif, that of the doppelganger, the hero's atrophied and subordinate twin. Examples of hero/doppelganger pairs include Gilgamesh and Enkidu, Romulus and Remus, and Don Quixote and Sancho Panza. Cain and Abel could be cited. The psychoanalysts interpreted the weak or unfortunate twin as representing that lost, discarded companion, the placenta.

Although Jung is most associated with the notion of a collective unconscious, Freud, too, toyed with the idea of a sort of phylogenetic memory. In a manuscript he shared with colleague Sandor Ferenczi, published posthumously as A Phylogenetic Fantasy, Freud speculated that some psychopathologies developed as reactions to conditions encountered by our ancestors during the ice ages.

From DNA to Phenotypes

The arrival of the first neurons provides the embryo with a mechanism, prospectively, that can record experiences, that is, with a memory. But the developmental stages prior to the appearance of the first neurons must record experiences by other means (if at all). Some other means must come into play also if phylogenetic memory can be a realistic prospect.

Part 2: "How Do Phenotypes Get To Be How They Get To Be? (or) Is Natural Selection Biology's Phlogiston?"

I submitted the previous blog post to Bjørn Østman's Carnival of Evolution. My submission did not please Mr. Østman, and he expressed his displeasure through comments posted on this blog. His comments were similar to those that the post received on www.thescienceforum.com. Both sources of commentary accused me of mischaracterizing the theory of natural selection. But unlike those on the forum, the comments of Mr. Østman mostly were informed and thoughtful.

Mr. Østman explained that I had failed to distinguish between natural selection and genetic drift. These processes participate in distributing genes, but they are distinct mechanisms, according to the normal view. He offered some details about how researchers distinguish the two—that is, about how they decide when to attribute the distribution of a gene (or allele) or a phenotypic trait primarily to drift or to selection. Despite his clarifications, and I appreciate the time he took, the criteria apparently typically used to distinguish the two mechanisms seem not really to be able to do so. The argument:

Two mechanisms are proposed as the primary causal trendsetters in gene (allele) and trait distribution. These mechanisms are genetic drift, a random process, and  natural selection, a nonrandom process. The latter explains the advance and retreat of traits in populations in terms of adaptation and fitness. The former explains the ebb and flow of traits in terms of chance. Given shifting trait frequencies through generations (in a local population of a given species), how does one distinguish outcomes due to natural selection from outcomes due to genetic drift?

Apparently one does so by determining whether a particular genotype or phenotype is more fit than a competing genotype or phenotype (in the local population of the given species). One does this by comparing the number of fertile progeny left behind by individuals with the one genotype or phenotype with the number of fertile progeny left behind by individuals with the other genotype or phenotype. The ratio is a measure of fitness of the types relative to one another. Phenotypes with similar traits also can be grouped, and averages taken.

Genotype/phenotype variants associated with a small fitness advantage (slightly better reproductive success) will tend to spread more rapidly in a small population but more slowly in a large population, due to greater opportunity for random mixing, or drift, in the large population. So, if a spreading gene or trait is associated with even a small fitness advantage, then the spread of the gene or trait in a small population can be taken to be a case natural selection. But in a large population, the advantage must be large for selection to be given credit for the spread of a gene or trait.

In other words, when the ratio of the fitness advantage to the population size crosses a threshold, then natural selection gets credit for the spread of the gene or trait, otherwise the spread is attributed to drift, or some other mechanism.

Whatever the merits of such a threshold-crossing formula, it cannot distinguish among mechanisms. Like the difference between a sluggish economy and a recession, or between the outbreak of a disease and an epidemic, or between a planet and a Pluto, the distinction between genetic drift and natural selection rests on an arbitrary threshold. It's a taxonomic distinction based on a variance from a statistical baseline. It's just a convenient way to label distribution ranges.

The differential labeling in the case of drift vs. selection is supposed to imply that a qualitative distinction is being used to distinguish two mechanisms, but nothing about the formula or its application entails that there be a qualitative distinction between or among proposed mechanisms. A difference of mechanism is implied, but there's no there there. In short, the formulas of population genetics can distinguish statistically among outcome distributions and assign labels to various distribution ranges, but that's about it.

To claim that such a formula justifies a theory of how phenotypes get to be how they get to be due to adaptation and fitness—that the formula informs us as to when changes in phenotypes are due to selection or to drift—really does beg the question, because it assumes that, among differing genotypes and phenotypes, differences in reproductive success (when they cross a statistical threshold) are DUE TO the differences among the genotypes and phenotypes of previous generations, specifically due to their relative adaptiveness. But to draw causal inferences from statistical results is some kind of logical fallacy.

I can't even say that it's assuming causation from correlation, because there's no correlation. We can't say that certain outcomes are correlated with drift and other outcomes are correlated with selection and that therefore each proposed mechanism causes the correlated outcome. The problem is that the item in question—natural selection—is taken from the outset as being a mechanism available for explaining gene distributions. Wouldn't one have to establish first that it's actually available, before one moves on to the question of which criteria distinguish it from other mechanisms? My argument is that it's not there; it's not available, unless it's just another name for the observation that some creatures enjoy more reproductive success than others, which we know is the primary cause of gene and trait distributions.

So, if natural selection cannot be the primary mechanism of macroevolution, what might be? Unlike various mechanisms that have been proposed, such as the ongoing and contingent interplay of endogenous and environmental variables called natural history ("just one damn thing after another"—this solution is proposed by Fodor and Piattelli-Palmarini in "What Darwin Got Wrong", from which I appropriated the phrase, how phenotypes get to be how they get to be), or the deliberate intervention of alien intelligences, or one of the other proposals listed HERE, the star larvae hypothesis proposes a mechanism that not only agrees with the latest discoveries in genetics, epigenetics, and the growing sense among researchers that environmental influences should be downplayed and endogenous factors emphasized in accounting for phenotypes (this is the gist of the papers collected in "Evolution, The Extended Synthesis"), but also accounts for evolution's apparent directionality.

The star larvae hypothesis proposes that evolution comprises stages of a developmental life cycle.

The Wirehead Problem and Money as AI

Here is a potential problem facing engineers of artificial intelligence: A sufficiently intelligent agent will work to tap its reward source directly, without doing otherwise useful work.  In this video Tim Tyler invokes the heroin addict for comparison. He concludes that a superintelligent agent will calculate the long-term effects of becoming a junkie and likely will conclude, as most people do, that it's not worth it.

Tyler goes on to counter this argument by conjuring a monopolistic threat.  What if the superintelligent agent wiped out its competitors?  Then, under the dynamics of a monopoly, it would grow flabby and careless, because there would be no reward in making effort in any other direction. And this situation would become conducive to its yielding to the tempation to become a junkie.

It looks like the threat already has landed. The U.S. dollar/federal reserve note is the superintelligent agent Tyler warns against. The U.S. dollar has tapped it own pleasure center, and in an accelerating cycle of masturbations it has exhausted itself.

Each step in the deregulation of the U.S. banking system brought the dollar closer to its source. Finally, when the real-estate bubble burst, the fallout revealed that the originators of money, the private banks, had crossed a deregulatory threshold, and they had exploited the lifting of essentially all conditions on the granting of loans. Because banks originate dollars by crediting loans, unconditional lending became the U.S. dollar's unfettered tap into its own pleasure center, its source. Now the junkie is going through withdrawal. And if the U.S. dollar gets fired from its job as the world's reserve currency, losing its monopoly privileges? Cold turkey.

Money as superintelligent agent reveals a bias in AI theory, or at least in AI practice, insofar as AI focuses on circuits and programs and patterns of atoms. But money is pure abstraction. It can take any form: seashells, printed paper or electronic accounting entries. Higher intelligence doesn't get bogged down in precise material specifications. It is conceptual.

Consider that money can do many things that you cannot. Indeed, it uses you, and the rest of us, to do its bidding. It is not an enabler, as we're taught to think. We are its enablers.  Look at the wonders it has created with our help.

The terrors that it has instigated? Our myth systems teem with wrathful deities and gods of destruction. Maybe the religious sensibility knows something about the superintelligent abstraction that provokes and persuades and thereby gives form to the world. G-d is a junkie?    

What Darwin Got Wrong

Life evolves seemingly endless varieties. To account for the varieties, Charles Darwin invented natural selection. He gave his invention the task of bestowing upon organisms whatever traits they have or had or will have.

What Darwin Got Wrong argues that the mechanism of natural selection is inadequate to this task. The book’s authors, Jerry Fodor and Massimo Piattelli-Palmarini (avowed atheists we learn), argue that Darwin overstated the power of natural selection, that it cannot account for how organisms got to be how they got to be. The authors don’t cite missing fossils of transitional forms or appeal to irreducible complexity, a la intelligent design argument. They just pick away at the putative logic of natural selection until nothing remains but grandma’s common-sense intuitions. They conclude that Darwin granted a truism wings to which it was not entitled.

The book attacks selectionism on various fronts, from its inability to field counterfactuals (if the arctic environment had been green, would polar bears have green fur?) to limitations placed on creaturely form by physical mechanics. But the star larvae hypothesis is interested primarily in the accounts of internal, or endogenous, constraints on the variability of phenotypes, the observable forms of organisms. The internal constraints leave environmental, or exogenous, influences with little from which to select. As the authors put it, natural selection at most can tune the piano; it cannot compose the melody.

The book, in short, is about the conceptual rigor, or lack of, of the NeoDarwinian theory. The Neo- part is important, because the authors support their case with findings from genetic sequencing and analysis. In particular, they lean on a new discipline called evolutionary developmental biology, or evo-devo, which has evolved from the discovery that DNA is conserved during evolution. This means that the genetic makeup of organisms, their genotypes, varies little across species, relative to the great diversity of phenotypes across species. How does a relatively limited genetic toolkit translate into so many forms of creatures? That is the question.

DNA Says Evolution is Not as Contingent as Imagined

(Darwin Isn’t Dead. He Just Smells Funny.*)
*Apologies to FZ

Something funny is afoot in the biological sciences. Labs peering into DNA are seeing things that nobody expected. And because the received view of evolution failed to predict these findings, and because it has little room to incorporate them, a crisis is brewing for the theory. Something more than selecting random variants is going on in evolution.

The data coming out of DNA sequencing and analysis suggest that the something more has to do with a preferred direction in evolution. Phylogenetic descent seems now to be a developmental unfolding. Several discoveries point to this conclusion:

1. Junk DNA. This is not a particularly new discovery. It’s been known for some time that all species carry around a lot of junk, DNA that appears to lie dormant. What aspect of evolution theory predicts that long stretches of inactive DNA would coast along inside organisms, seemingly contributing nothing to their survivability? Nobody saw it coming. It was an empirical surprise.

But in the context of ontogeny, the development of organisms, it is exactly what is to be expected. Each cell in the body of a complex organism inherits the same genes from the ancestral zygote, the original fertilized ovum. Despite all possessing the same genes, brain, liver, kidney, and skin cells, for example, distinguish themselves phenotypically. Each cell type looks and acts differently from the others. But, because they all inherit the same genes, there must be a lot of junk DNA in each type of cell. Brain cells don’t need genes that function uniquely in liver cells, nor do kidney cells need genes that function uniquely in skin cells. But all the cells inherit all those genes from their common ancestor, the zygote, whether they need them or not.

When it comes to cell types in a body, an invariant genetic inheritance necessarily is the case, with lots of junk in each cell as a result. Ontogeny demonstrates that diverse morphologies, or phenotypes, need not correspond to any proportionate diversity of genotype. “Adaptive radiation” of cell types in a body proceeds just fine without genetic variation.

Evolution appears to operate similarly.

The Need to Teach Religion

A while back on this blog I recommended that the public schools include religion as a subject in the standard curriculum. I've learned since that outspoken atheist philosopher Daniel Dennett makes the same recommendation. I feel vindicated, finding myself in such eminent company. His gist, and mine, is that religion is most dangerous when people don't understand it.

Militant Atheists Stir the Pot

An interesting debate—Hitchens and D’Souza are capable and entertaining—but frustrating, because the debaters fail to tease apart several discrete issues:

Do people inspired by religion or secularism tend to behave virtuously or wickedly?

Does any answer to the above question have any bearing on the existence or non-existence of God?

What are the merits and demerits of the philosophical, logical, scientific and theological arguments for and against the existence of God?

Even if the arguments for the existence of a supreme being prevail, would those successful arguments necessarily have any bearing on the status of the Bible or any other scriptural writing?

The current atheism-religion debate launched by Hitchins, Dawkins, Harris, Dennett and other militant atheists tends to conflate these issues. Much is at stake, and I commend the new breed of atheists for their in-your-face style (lord knows the other side has been in everybody’s face for a long, long time). But clarity isn’t served by rhetoric that veers herky-jerky from morality to theology to cosmology to anthropology, etc., without ever spending enough time in one place to dig in.

Good God, Why the Ungodly Fear of God?

I got a treat a while back in my inbox. A man named John Smart invited me to join an online community, the Evo-Devo Universe (EDU). Mr. Smart had found the star larvae site and liked what he saw (or thought he did). He said he thought the ideas on the site complemented other ideas being developed in the community. I looked at Mr. Smart’s own site and the EDU site and got excited about hooking up with these brazen visionaries.

I can understand Mr. Smart’s interest in star larvae. Here’s an excerpt from EDU’s Project Page:

Problem. Recent developments in cosmology, evolutionary developmental biology, and complexity sciences are providing new but scattered ways to understand our universe in a broader, ‘meta-Darwinian’ framework in which selectionist evolutionary and replicative, hierarchical developmental processes appear to generate complexity at multiple scales.

Solution. These results and hypotheses need to be explored, criticized, analyzed and possibly integrated into an expanded conceptual framework, by an interdisciplinary scholarly research community, Evo Devo Universe (EDU).

Links to members’ sites on the EDU People page lead to lots of fascinating angles on evolution, information theory, cosmology and other topics.

I replied to Mr. Smart, maybe too provocatively. I started expounding on people who have creative insights but become overly preoccuppied with establishing scientific credentials. I wrote,

People I encounter who have an interest in speculative cosmology, or whatever we might call our endeavor, tend toward extremes of scientific rigidity or New Age wooliness. At least, that is my observation. I try to keep my thoughts on these matters somewhere in the middle. The scientific types tend to be preoccupied with establishing scientific credentials for their ideas. While I have bolstered my speculations with scientific references, where I am able, I have grown less concerned with receiving blessings from science. My project is philosophical, theological, political, psychological and has many other dimensions, including the scientific. I don't feel a compunction to position all other dimensions subordinate to the scientific. I think that humankind can be served by conceptual breakthroughs in philosophy, theology, etc., as much as by breakthroughs in science. (Of course science has a certain privileged veto power, and if any idea I propose is scientifically disproven, I will have to abandon or reformulate that idea.)

He wrote back, having looked deeper into the starlarvae site, and withdrew his offer to join the EDU community. The scope of the community’s research themes specifically excludes

Non-naturalistic orthogenesis or teleology, intelligent design, supernaturalism, and theology.

So, by weaving in theology, I disqualified www.starlarvae.org from joining the club. On the site, I refer to the supernatural only dismissively or if I need to place an idea in a historical context. But I crossed the line. Mr. Smart was put off also by my dba, Advanced Theological Systems. I explained to him,

The name Advanced Theological Systems is perhaps a misguided lark, but it makes me chuckle. I worked for a while in the high-tech sector, and "Advanced [fill in the blank] Systems" became such a cliché of organizational nomenclature, I couldn't resist dropping in "theology" for the irony vis a vis sci/tech.

If I ever exorcise the theological threads from the site I'll approach you anew. I understand your apprehension. Somewhere in the blog I write about theophobia, which you might have a mild case of. It's a common affliction among many of my friends. And it unfortunately relinquishes God, with all his sociopolitical clout, to hands that I would rather not see wielding such clout.

The “Exorcise” comment referred to his offer to reconsider, if I ever scrubbed theology from the site, his invitation to join the EDU community.

It never occurred to me that the theological angle (and I’m not sure I could formulate precisely what it is) would be a showstopper. But I was fascinated. I asked him for permission to post our email exchange here on the blog, but he demurred, saying that he would have taken more care with his words if he’d been writing for a public audience. I think that’s fair, and I’m respecting his wishes.

Maybe I should quit being surprised by big thinkers who bristle before God. Poor God, so misunderstood.

RANDOM CHANCE BOGUS

Insofar as (otherwise) scientific accounts of nature invoke chance and randomness, they admit their weakness as scientific accounts.

Chance and randomness are fudge factors. They play the same role in scientific thinking as is played by miracles in religious thinking. And they reduce scientific thought to quasi-religious thought.

The question to anyone who explains anything in terms of chance and randomness is, "What are you talking about?" Take quantum physics as an example of a discipline that leans heavily on randomness. "Random" in quantum mechanics seems only to mean that physicists can’t predict the outcome of quantum processes. But that just begs the question, Why can’t the outcome be predicted? There are only three possibilities:

1) The outcome is not predictable, because, though deterministic and in principle predictable, the process involves a causal chain too complicated to unravel.

2) The outcome is not predictable, because it "just happens," that is, it is an event that occurs without having been caused. This would seem to pose a problem for science. At least miracles have causes, albeit supernatural ones. But for an event to occur with no cause whatsoever? (In quantum physics the outcome of a quantum collapse is taken to be random, even though triggered by an environmental factor, or, in the case of Roger Penrose’s Objective Reduction, the collapse is caused by gravity. But in any case, the collapse can in principle produce any of a number of outcomes, only one of which actually occurs. Which one occurs from among the possibilities is not predictable, and so the spectre random is invoked as a gloss that lets the scientists elude the responsibility of causal elucidation.)

3) The process is not predictable, because a subjective agent decides, or at least influences, the outcome.

Scientific thinking leans on chance and randomness in some cases when scientists observe seemingly teleological effects, as in the seeming directedness of evolution from simple to complex organisms, but scientists are professionally prohibited, and probably temperamentally inhibited, from invoking teleological explanations. Hence, the usefulness of the gap-fillers, chance and random.

To see in more detail why chance and randomness are conceptual fuzz and need to be expunged from scientific thinking, exposed as spectres, consider the classic example of a deck of cards, shuffled in the normal way or arranged according to a rule.

Shuffling is taken to be a randomizing of the deck, so that if you were to pick a card from position thirty in a thoroughly shuffled deck, the identity of that particular card would be a matter of chance. You can’t predict it. But the card at position thirty in a nonrandom deck, one that is set up deliberately in a contrived pattern according to a rule, should be predictable. This is how these things typically are understood.

But the opposite seems actually to be the case.

The position of any card in a shuffled deck is usually figured to be given by chance, but what’s occurred during the shuffling of the deck is that the indeterminism has been removed, and the process has become deterministic, with a determined outcome. The positions of the cards in the deck are determined by deterministic physical determinants: the stiffness of the cards, how much they’re bent back, how quickly and with how much force you roll your thumbs over the edges and so forth, starting with the original ordering of the cards in the deck. So if you knew all the physical variables, you could, in theory, predict which card would end up at position thirty. Because there’s no indeterminism involved, an algorithm will solve the problem. It’s just a matter of the physical characteristics of the cards, and how much force is imparted to them,how much they bend, and so forth.

So actually you could predict the so-called chance or random result. The “chance” or “random” aspect of the shuffling—the absence of deliberate ordering—is precisely what allows card positions to be predicted. The exclusion of indeterminate causes makes the outcome predictable.

Now, if you’re given a deck of cards, and you’re told that someone has arranged them in a particular pattern and then suddenly died or been abducted by aliens, then you have no way to determine—to predict—which card is at position thirty. Given no additional information, there’s no calculation you can do based on the physics of the cards and the initial arrangement that will tell you where any particular card is or which card is at any particular position. Additional information is needed to figure it out: the rule by which the cards were arranged.

The "random" arrangement is the predictable arrangement. The nonrandom arrangement is the unpredictable one.

The dead or abducted person’s choice in arranging the cards, the rule they select, is presumably not deterministic. That person had a range of choices and decided on one. They might have chosen a convoluted rule or a simple one. To someone who doesn’t know the rule, if it’s a convoluted one, say like find the first ace and double the value of its ordinal position in the deck and square that number and divide by five and take the second digit of the remainder for the next card . . . something like that, the result might well look like a random arrangement to someone who doesn’t know the code. Once the code and the initial arrangement are known, one can use an algorithm to determine card thirty. This is cryptography.

This example underscores a problem with the naïve view of information and information theory. There’s no way to determine whether a seemingly random set of signals actually is random—"does not encode information"—or whether the set of signals is highly ordered and contains a great deal of information, unless one knows that a code or rule was used to arrive at the order. And one knows what the rule was. Or if one knows the initial physical conditions and all of the physical variables involved. In other words, it is impossible to determine a priori the signal-to-noise ratio of any set of pulses.

Take, as another illustration, solar radiation, or sunshine, a seemingly "random" mixture of wavelengths of electromagnetic radiation. What is the information content of sunshine? It tells us about the nuclear reactions occurring inside the sun, so it has some information content. But it also tells the plants it strikes in which direction to face their leaves. Does that imply additional content? In the case of conscious minds deliberating over wavelengths so as to discern something about solar physics, sunshine is taken to contain information, and solar researchers are involved in information decoding. But the response of the plants is "automatic," not deliberate, and few people would interpret it as an instance of information processing, only energy processing. But what is the meaningful difference?

The notion that information is somehow inherent in physical nature makes sense only if we assume that there is a natural code. I suppose we WANT to believe that information inheres in nature. And so we’re led necessarily to some kind of crypto-theology. In other words, if there’s information in nature, then there’s a code (design), and then there’s a coder (designer). Any philosophy that takes information to be an inherent aspect of physical nature is necessarily a theological philosophy. One way around this, for congenital theophobes, is to deny that information inheres in nature and to admit that it inheres only in conscious minds. Same thing with computer memory. The strings of 0's and 1's are geometrical configurations of electrons in spacetime in the physical circuitry, but only a mind can determine whether any information is present.

I’m not sure many scientifically minded people would sign onto that necessity.

Anticipatory (Intelligent) Design Science

Buckminster Fuller riffs on the apparent design of Universe. Human beings access the design principles of Universe through their capacity to generalize. We have plenty of resources to feed, clothe, house everyone on Earth. Scarcity is a myth. But neither messiah nor political reform will make it happen. Only anticipatory design science delivers the goods.

Quantum Philosophy

Just posted this to Stuart Hameroff's Blog, at http://stuarthameroffblog.com/

The quantum shockwave that hit physics in the 20th Century is hitting biology in the 21st.

Can you say, “Paradigm shift”?

If Stuart is right, and biological processes as diverse as vision and photosynthesis, let alone consciousness per se, are driven by (or receive organizing information from) the funda-mental level of the universe, then we have to wonder what other processes rely on, or actualize, the Planck scale’s Platonic forms. While Stuart and other professional researchers nail down the technical evidence and arguments, I am more interested in the speculative philosophy that will complement quantum biology.

For example, it seems that if some behaviors of unicellular organisms are influenced by quantum information processing—that is, if Stuart is right—then we’re justified in asking what the range of such influence might be. If we accept the premise that biological metabolisms access quantum information, then we may as well admit that we’re in a whole new ballgame. For example, Stuart’s presentation on cilia got me thinking . . . .

The light-processing (quantum-information-extracting) cilia in the rods and cones of a human eye function like the light-sensitive flagella of protozoa, as Stuart explains in his presentation. What he does not mention, though I assume he is aware of it, is that the eukaryotic protozoa that possess cilia and flagella likely received those organelles from bacteria—spirochaetes—during endosymbiosis. This is Lynn Margulis’ revision of evolution theory’s model of the emergence of eukaryotic cells. Margulis proposed years ago that the first complex cells developed from symbiotic communities of bacteria. Initially rebuked by the scientific community, she persevered, and, with new techniques of genetic analysis supporting her ideas, she prevailed. The Margulis model of bacterial endosymbiosis is generally accepted as the most plausible account of the evolution of eukaryotic cells.

Is a prokaryotic endosymbiosis that produces the more complex eukaryotic cells best explained by purely chemical operations or by formative inputs from other souces, such as Platonic information at the Planck scale? Here’s where we hit a very sensitive scientific nerve, because we—Hameroff, et al.—propose that organisms receive information from sources other than those mediated by the senses. A conventional scientist would dismiss the very idea as being an invocation of supernaturalism, of extrasensory perception—a violation of the scientific doctrine of empiricism.

Any attempt to link the behaviors of organisms to information input from a nonlocal source (presumably Platonic information is not limited by the speed of light, because it does not propagate, but simply exists fully accessible at/from every location in spacetime) inevitably will start to resemble a doctrine of intelligent design, with the Platonic forms playing the role of the intelligent designer. This would seem to deliver to scientists a trump card that corresponds to the God card of religionists.

If any natural process eludes a precise accounting in terms of all its causal events and mechanisms, religionists have always been able to point to God’s influence, divine intervention, “Intelligent Design.” As quantum biology develops, scientists increasingly will be able to invoke their own God of the gaps: Platonic information from the Planck scale. This revision to the philosophy of science not only opens the door to the spiritual dimension, as Stuart points out, but also to teleological models of evolution and human history, such as the one developed at

www.starlarvae.org.

Let's Be Reasonable

I’m watching Bill Moyers (sitting in for Charlie Rose) interviewing the Bright philosopher Daniel Dennett. The controversy they commit themselves to, the seemingly interminable science-religion debate, seems beside the point, even obsolete, philosophically. Politically, the debate demands attention, but to commit oneself to one partisan end or the other is to function as a useful idiot for people who might not share your interests. After all, careers and fortunes are at stake. Not everyone with an argument to make is honest and altruistic, whether he brandishes a cross or an equation.

The debate implodes philosophically because it rests on a false dichotomy: science or religion. Like other polarized debates, the truth in this one likely lies somewhere in the middle. The task is to synthesize a syncretism—to jettison the superstitions and think creatively.

First, let’s unpack the two extremes and see what's inside. Cracking open religion, we sift through doctrines and dogmas, ritual practices, canonical writings, secured sanctums, reverence toward founders and exemplars, and tools for neutralizing heretics. Inside science we also find doctrines and dogmas, ritual practices, canonical writings, and so on. You get the picture. So let's figure out what to keep and what to toss.

First off, let’s dump the doctrines and dogmas. The rituals serve a purpose—cultural in the case of religious faith and, in the case of laboratory methodologies, as processes that generate empirical data. The canonical writings we can’t take exactly literally. Even the received history of science is interpreted variously by historians.

But the writings have literary and other cultural and academic value. The scriptural and apocryphal stories, the grand narratives, of a religious or secular culture help the tribe cohere, even if its citizens don’t take the stories literally. The myths and mythologies of the tribe serve as a map its collective psyche; they narrate the broad themes of experience—perhaps only within the culture, perhaps more broadly. The stories, we keep, for the depth they add to experience.

(Hardboiled rationalists might object, finding depth psychology too airy-fairy. In that case, we can scientize myth by supposing that the myth-making propensity travels with the genes, not an unnatural supposition given the role of genes in guiding brain formation. So the myths function in the realm of psychobiology concomitantly as the genes in the realm of sociobiology. Religion minus doctrine and superstition becomes ethics and mythology, with the legitimacy of the guiding myths limited to the allegorical. And in a slightly different but corresponding way the same is true for the grand narratives of science.)

Back to the unpacking. The sanctums serve to mystify, and we might want to demystify what goes on there through education, but the priestly chambers and the laboratories and technical meetings do no overt harm. Reverence toward founders and exemplars can deteriorate into cults of personality, so that’s something to watch. And the notion of heretic would seem to vanish if we eliminate doctrines and dogmas.

So, let’s drop the baggage of doctrine and dogma and stop literalizing the written canons. That much would open the debate to creative resolution (and redeem the heretics).

And let’s be clear that superstition and doctrine are not exclusive to religion and that rejecting religious doctrines doesn’t necessarily lead to atheism and fealty to the proclamations of scientists. The plotless history and future promised by the philosophy of science doesn’t seem any more inviting than do the rigid doctrines and superstitions of religion. Science says we need to reject meaning per se, because it is nothing more than a byproduct of brain metabolism. Our experiences, as epiphenomena of neural metabolism, have no intrinsic value, in the philosophy of science. Nothing can matter, scientifically speaking, because nothing actually exists but spacetime, physical particles, and physical energies. Value, meaning, and purpose exist only derivatively, as subjective noise.

We have to reject the weird nihilism of science as being as doctrinal as religious doctrine. Despite the insistences of scientists, we don’t know whether conscious experience is epiphenomenal or phenomenal. The felt free will of our experience has always been a monkey wrench in the deterministic machinery of science. Descartes tried to meet the challenge by positing two kinds of matter: physical and mental. This dualism continues to unsettle science, because the laws of physics as formulated by scientists do not allow nonphysical causes, such as mind, to affect physical objects. But I can make my arm move by willing that it happen. The path back from the moving arm through the muscular contractions and the nerve impulses to the origin of the signal in my brain leads back to my original intent to raise my arm, and not to anything else.

I make decisions that are not predetermined by the laws of science, and this fly in the ointment of science maps neatly onto the indeterminacy of quantum mechanics. Scientists generally are not keen to connect these dots—free will and quantum indeterminacy—and wooly New Age philosophers have rushed in to fill the void, but the dots, through it all, remain, waiting to be connected. Roger Penrose and Stuart Hameroff present a model of consciousness based on a specific neural process that leverages quantum indeterminacies in the brain. Their work, even if incomplete in its details, points the way toward a nondeterministic scientific phenomenology—an empirical ontology of consciousness.

Can God be far behind?