"All the World's a Stage We Pass Through" R. Ayana

Showing posts with label darwin. Show all posts
Showing posts with label darwin. Show all posts

Monday, 7 November 2016

Programmed Evolution: Ontogeny, Phylogeny, Teleology and Evolution’s Empirical Conundrum


Programmed Evolution:
Ontogeny, Phylogeny, Teleology and Evolution’s Empirical Conundrum

 Burning Bush Instructs the Primates by R. Ayana

 

 

 

 


Scientists and philosophers of science have proposed various metrics by which to assess the merits of scientific theories. An often cited one is Karl Popper’s requirement that a theory be in principle empirically falsifiable. For example, the discovery of rabbit fossils in Precambrian geological strata would demolish Darwinian theory. Another often cited measure of merit is a theory’s ability to make accurate predictions. This has always been a difficult hurdle for Darwinian evolution. What predictions can the theory make?

Unfortunately for Darwinian theory, the difficulties are several. They include the time scale required, the need to rely on necessarily incomplete fossil remains, and the small sample (one planet). But something new has changed the situation. Darwinian theory now is in a position to belly up to the bar and, like other respectable scientific theories, make some bold predictions.

What has changed is our ability to analyze DNA. Genomic sequencing and analysis projects are in full swing around the world. Researchers are using new technologies to, not only sequence DNA, but also statistically analyze those sequences across species. So, Darwinians, what’s going to come of it? If you understand how changes in DNA propagate through generations within a species and into new species, if you understand the sources of genetic novelty, if you understand why some genes are preserved in a species and others selected out, then let’s have some predictions.

What will ongoing genetic sequencing and analysis turn up that will corroborate Darwinian evolution and falsify rivals?

But before we try to pin Darwinists to the mat, let’s entertain a relevant thought experiment, as an intermission:

Let’s suppose that we observe a complex process, one that involves discernibly discrete entities. We might call these entities organisms. We notice that over time, as the process progresses, the organisms give rise to new organisms. And we notice that older organisms perish.

We notice that the descendants differ from their ancestors. As more generations turnover, the forms of the descendants vary more dramatically. Morphological forms, and their attendant functions and behaviors, proliferate through the population of descendant organisms. And, having been fortunate enough to observe the process from its outset, we know that the multiplicity of forms descended, ultimately, from a single ancestral form.

An intriguing process. How to account for it? Let’s consider two competing theories.

(1) We might conjure an explanation that invokes a more or less deterministic influence, one that bridges the generations and guides the process as it works its way from the ancestral form to the many descendant forms. Such an influence would be teleological. We might call this formative influence a genetic program. Its action across the generations would constitute development, an unfolding of pre-programmed potential into a multiplicity of forms.

(2) Alternatively, we might conjure an explanation that invokes nondeterministic, nonteleological factors. We might say that the process is the result of two interacting subprocesses, one being unpredictable changes that exaggerate variation among the members of a generation, and the second being the varying numbers of progeny that members of each generation leave behind. We might call the first subprocess random mutation and the second process natural selection, and we might posit a relationship between the two that causes descendant populations to display a diversity of morphologies (and functions and behaviors) based on pure chance and environmental selection. There is no preprogrammed potential unfolding, just selection among various traits among individuals and a disproportionate retention in descendant generations of the selected traits.

Now comes the hard part: determining which explanation best accounts for the observed process of descent. Being conscientious scientists, we want empirical corroboration. What observations might we make, in principle, that could determine which explanation has the greater merit? How would one distinguish, empirically, a teleological process from a Darwinian one? What would one look for to detect the presence or absence of a program?




Phylogeny: Polymorphous descent from a common ancestor. In principle, what sort of observation would establish the presence or absence of a program?






 

Ontogeny: Polymorphous descent from a c
ommon ancestor. In principle, what sort of observation would establish the presence or absence of a program? 


One observation that would help clear the air is the discovery of an information code in the organisms that expresses itself as the organisms’ various morphological traits. The codes for the traits we might call genes. If we were to find genes in ancestors that lay waiting, unexpressed, but are preserved and jump to life in descendant species, this would bolster the case for a programmatic process. 



A Darwinian process would not predict such a discovery. Darwinism includes no anticipatory mechanism whereby genes needed in the future would be present, though dormant, in ancestors. Only a teleological theory would predict an anticipatory genome. Anticipatory evidence would suggest a pre-coded program underlying the process of multi-generational morphological diversification.

And this is precisely what we observe in ontogeny. We observe that genes dormant in the fertilized ovum do not express themselves until the time comes for them to produce muscle cells, liver cells, brain cells, etc. Then these dormant genes spring to life. Their expression unfolds sequentially to create descendant species of cells of multifarious types.

Or at least this is the prevailing account. Alternatively, maybe it’s just a coincidence that genes dormant in the fertilized ovum are useful in descendant cell types. Maybe nature is resourceful and discovers uses for the inherited supply of genes. It might be the case that the differentiation of cell types during embryonic development has nothing to do with any precoded program. Maybe it’s happenstance, the result of random mutations and natural selection.

This line of thinking probably is not worth pursuing. But is phylogenetic descent really that different? Would the discovery of descendant genes in ancestors argue for a programmed phylogeny, or would it argue only for the happenstance of random mutations and natural selection?

These are no longer rhetorical questions, because genomic sequencing and analysis is finding unexpected, unpredicted instances of descendant genes in ancestors. Does Darwinian evolution predict that the genomes of primitive species should contain genetic programs for newer, more complex species—?The discovery challenges the logic of normal evolution theory, because it suggests that evolution, as ontogeny is thought to do, unfolds from a pre-programmed genetic potential. These findings are ongoing:

A news release (11/24/2005) issued by the journal Trends in Genetics announces that

"Corals and sea anemones (the flowers of the sea), long regarded as merely simple sea-dwelling animals, turn out to be more genetically complex than first realised. They have just as many genes as most mammals, including humans, and many of the genes that were thought to have been "invented" in vertebrates are actually very old and are present in these "simple" animals."

The full text of the release is available at http://www.sars.no/research/technau_Science.pdf

Newer (2007) sequencing and analysis results corroborate the anemone anomalies. Another example comes from research at the European Molecular Biology Laboratory, which found human genes in a marine worm. The news release (11/24/2005) announcing the finding is at http://www.embl-heidelberg.de/aboutus/news/press/press05/press25nov05/index.html

Additional research discovered that genes essential for human nerve cells to communicate with one another are present already in bacteria. This research is described in a NIH news release (6/1/2004) at http://www.nichd.nih.gov/new/releases/genes.cfm These and other anomalous (in the Darwinian context) results of genome analysis are collected at http://www.panspermia.org/oldgenes.htm.

This page of Brig Klyce’s "Cosmic Ancestry" web site includes commentary on the relevance of these findings to panspermia. The discovery of advanced genes in primitive organisms suggests that the evolution of life on Earth constitutes an ontogeny—the ontogeny of Gaia.


If a process of descent is programmatic, then it would seem to be dependent on some kind of timing mechanism. What triggers the production of new descendant types? How does the developing embryo know when to kick out a new cell/tissue type? In the case of ontogeny, researchers posit various chemical signals from within the organism and/or from its gestating parent as potential triggers. In the case of phylogeny the timing triggers are harder to determine.

Nonetheless, various candidates present themselves. Phylogeny might also be paced by chemical signals. Organisms exchange chemical signals all the time, through eating one another, through exchanges of pheromones. Terence McKenna argues that ingestion of plant drugs among our primate ancestors played a role in human speciation. Other environmental triggers might include the terraforming of Earth’s atmosphere by the release of oxygen from photosynthesis. Glaciations might act as triggers. Industrial pollution is another candidate.

Maybe the prevailing accounts of ontogeny and phylogeny are artifacts of the time scales involved. If we could observe a sped-up movie of evolution might we perceive a programmatic development from the first to the most recent species—the gestation of a pregnant planet from impregation to delivery? If the embryonic development of a long-lived organism required a few billion years, might it not look like a Darwinian process?

So how do approaches to evolution stack up as scientific theories based on their abilities to predict? A teleological, programmed model, predicts that genes active in descendant species can be found already in distant ancestors. What does the Darwinian model predict? Genomic sequencing and analysis is in the early stages. There’s time to render predictions. The star larvae hypothesis predicts an accumulating pile of anomalous data that will stretch the Darwinian model to the breaking point. Those data, however, will find themselves well integrated in a new paradigm, one that proposes an overarching ontogeny that envelops evolution and repositions biology into the role of larvae to the stars.



Starman Vortex by R. Ayana

For more information about new evolutionary paradigms see http://nexusilluminati.blogspot.com/search/label/evolution  
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Tuesday, 20 January 2015

God is on the ropes: The brilliant new science that has creationists and the Christian right terrified


God is on the ropes: The brilliant new science that has creationists and the Christian right terrified

God is on the ropes: The brilliant new science that has creationists and the Christian right terrified 
Charles Darwin (Credit: Wikimedia/WDG Photo via Shutterstock/Salon)



A young MIT professor is finishing Darwin's task — and threatening to undo everything the wacky right holds dear



The Christian right’s obsessive hatred of Darwin is a wonder to behold, but it could someday be rivaled by the hatred of someone you’ve probably never even heard of. Darwin earned their hatred because he explained the evolution of life in a way that doesn’t require the hand of God. Darwin didn’t exclude God, of course, though many creationists seem incapable of grasping this point. But he didn’t require God, either, and that was enough to drive some people mad.

Darwin also didn’t have anything to say about how life got started in the first place — which still leaves a mighty big role for God to play, for those who are so inclined. But that could be about to change, and things could get a whole lot worse for creationists because of Jeremy England, a young MIT professor who’s proposed a theory, based in thermodynamics, showing that the emergence of life was not accidental, but necessary. “[U]nder certain conditions, matter inexorably acquires the key physical attribute associated with life,” he was quoted as saying in an article in Quanta magazine early in 2014, that’s since been republished by Scientific American and, more recently, by Business Insider. In essence, he’s saying, life itself evolved out of simpler non-living systems.

The notion of an evolutionary process broader than life itself is not entirely new. Indeed, there’s evidence, recounted by Eric Havelock in “The Liberal Temper in Greek Politics,” that it was held by the pre-Socratic natural philosophers, who also first gave us the concept of the atom, among many other things. But unlike them or other earlier precursors, England has a specific, unifying, testable evolutionary mechanism in mind.

Quanta fleshed things out a bit more like this:

From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. Jeremy England, a 31-year-old assistant professor at the Massachusetts Institute of Technology, has derived a mathematical formula that he believes explains this capacity. The formula, based on established physics, indicates that when a group of atoms is driven by an external source of energy (like the sun or chemical fuel) and surrounded by a heat bath (like the ocean or atmosphere), it will often gradually restructure itself in order to dissipate increasingly more energy. This could mean that under certain conditions, matter inexorably acquires the key physical attribute associated with life.

It doesn’t mean we should expect life everywhere in the universe — lack of a decent atmosphere or being too far from the sun still makes most of our solar system inhospitable for life with or without England’s perspective. But it does mean that “under certain conditions” where life is possible — as it is here on Earth, obviously — it is also quite probable, if not, ultimately, inevitable. Indeed, life on Earth could well have developed multiple times independently of each other, or all at once, or both. The first truly living organism could have had hundreds, perhaps thousands of siblings, all born not from a single physical parent, but from a physical system, literally pregnant with the possibility of producing life. And similar multiple births of life could have happened repeatedly at different points in time.

That also means that Earth-like planets circling other suns would have a much higher likelihood of carrying life as well. We’re fortunate to have substantial oceans as well as an atmosphere — the heat baths referred to above — but England’s theory suggests we could get life with just one of them — and even with much smaller versions, given enough time. Giordano Bruno, who was burnt at the stake for heresy in 1600, was perhaps the first to take Copernicanism to its logical extension, speculating that stars were other suns, circled by other worlds, populated by beings like ourselves. His extreme minority view in his own time now looks better than ever, thanks to England.

If England’s theory works out, it will obviously be an epochal scientific advance. But on a lighter note, it will also be a fitting rebuke to pseudo-scientific creationists, who have long mistakenly claimed that thermodynamics disproves evolution (here, for example), the exact opposite of what England’s work is designed to show — that thermodynamics drives evolution, starting even before life itself first appears, with a physics-based logic that applies equally to living and non-living matter.

Most important in this regard is the Second Law of Thermodynamics, which states that in any closed process, there is an increase in the total entropy (roughly speaking, a measure of disorder). The increase in disorder is the opposite of increasing order due to evolution, the creationists reason, ergo — a contradiction! Overlooking the crucial word “closed,” of course. There are various equivalent ways of stating the law, one of which is that energy cannot pass from a cooler to a warmer body without extra work being done.

Ginsberg’s theorem (as in poet Allen Ginsberg) puts it like this: “You can’t win. You can’t break even. You can’t even get out of the game.” Although creationists have long mistakenly believed that evolution is a violation of the Second Law, actual scientists have not. For example, physicist Stephen G. Brush, writing for the American Physical Society in 2000, in “Creationism Versus Physical Science,” noted: “As Ludwig Boltzmann noted more than a century ago, thermodynamics correctly interpreted does not just allow Darwinian evolution, it favors it.”

A simple explanation of this comes from a document in the thermodynamics FAQ subsection of TalkOrigins Archive (the  first and foremost online repository of reliable information on the creation/evolution controversy), which in part explains:

https://farm4.staticflickr.com/3682/10459129914_619de13b05_b.jpgCreationists thus misinterpret the 2nd law to say that things invariably progress from order to disorder.

However, they neglect the fact that life is not a closed system. The sun provides more than enough energy to drive things. If a mature tomato plant can have more usable energy than the seed it grew from, why should anyone expect that the next generation of tomatoes can’t have more usable energy still?

That passage goes right to the heart of the matter. Evolution is no more a violation of the Second Law than life itself is. A more extensive, lighthearted, non-technical treatment of the creationist’s misunderstanding and what’s really going on can be found here.

The driving flow of energy — whether from the sun or some other source — can give rise to what are known as dissipative structures, which are self-organized by the process of dissipating the energy that flows through them. Russian-born Belgian physical chemist Ilya Prigogine won the 1977 Nobel Prize in Chemistry for his work developing the concept. All living things are dissipative structures, as are many non-living things as well — cyclones, hurricanes and tornados, for example. Without explicitly using the term “dissipative structures,” the passage above went on to invoke them thus:

Snowflakes, sand dunes, tornadoes, stalactites, graded river beds, and lightning are just a few examples of order coming from disorder in nature; none require an intelligent program to achieve that order. In any nontrivial system with lots of energy flowing through it, you are almost certain to find order arising somewhere in the system. If order from disorder is supposed to violate the 2nd law of thermodynamics, why is it ubiquitous in nature?

In a very real sense, Prigogine’s work laid the foundations for what England is doing today, which is why it might be overstated to credit England with originating this theory, as several commentators at Quanta pointed out, noting other progenitors as well (here, here and here, among others). But already England appears to have assembled a collection of analytical tools, along with a sophisticated multidisciplinary theoretical approach, which promises to do much more than simply propound a theory, but to generate a whole new research agenda giving detailed meaning to that theoretical conjecture. And that research agenda is already starting to produce results. (See his research group home page for more.) It’s the development of this sort of detailed body of specific mutually interrelated results that will distinguish England’s articulation of his theory from other earlier formulations that have not yet been translated into successful theory-testing research agendas.

Above all, as described on the home page mentioned above, England is involved in knitting together the understanding of life and various stages of life-like processes combining the perspectives of biology and physics:

Living things are good at collecting information about their surroundings, and at putting that information to use through the ways they interact with their environment so as to survive and replicate themselves. Thus, talking about biology inevitably leads to talking about decision, purpose, and function.

At the same time, living things are also made of atoms that, in and of themselves, have no particular function. Rather, molecules and the atoms from which they are built exhibit well-defined physical properties having to do with how they bounce off of, stick to, and combine with each other across space and over time.

Making sense of life at the molecular level is all about building a bridge between these two different ways of looking at the world.

If that sounds intriguing, you might enjoy this hour-long presentation of his work (with splashes of local Swedish color) — especially (but not only) if you’re a science nerd:




Whether or not England’s theory proves out in the end, he’s already doing quite a lot to build that bridge between worldviews and inspire others to make similar efforts. Science is not just about making new discoveries, but about seeing the world in new ways — which then makes new discoveries almost inevitable. And England has already succeeded in that.  As the Quanta article explained:

England’s theoretical results are generally considered valid. It is his interpretation — that his formula represents the driving force behind a class of phenomena in nature that includes life — that remains unproven. But already, there are ideas about how to test that interpretation in the lab.

“He’s trying something radically different,” said Mara Prentiss, a professor of physics at Harvard who is contemplating such an experiment after learning about England’s work. “As an organizing lens, I think he has a fabulous idea. Right or wrong, it’s going to be very much worth the investigation.”

Creationists often cast themselves as humble servants of God, and paint scientists as arrogant, know-it-all rebels against him. But, unsurprisingly, they’ve got it all backwards, once again. England’s work reminds us that it’s scientists’ willingness to admit our own ignorance and confront it head on — rather than papering over it — that unlocks the great storehouse of wonders we live in and gives us our most challenging, satisfying quests.

Paul Rosenberg is a California-based writer/activist, senior editor for Random Lengths News, and a columnist for Al Jazeera English. Follow him on Twitter at @PaulHRosenberg.


From Salon @ http://www.salon.com/2015/01/03/god_is_on_the_ropes_the_brilliant_new_science_that_has_creationists_and_the_christian_right_terrified/


For more information about extraterrestrial life see http://nexusilluminati.blogspot.com/search/label/extraterrestrial%20life   
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