The Reasonableness of Atheism and Black Swans

As an ID proponent and creationist, the irony is that at the time in my life where I have the greatest level of faith in ID and creation, it is also the time in my life at some level I wish it were not true. I have concluded if the Christian God is the Intelligent Designer then he also makes the world a miserable place by design, that He has cursed this world because of Adam’s sin. See Malicious Intelligent Design.

Jesus prophesied of the intelligently designed outcome of humanity: “wars and rumors of wars..famines…pestilence…earthquakes.” If there is nuclear and biological weapons proliferation, overpopulation, destruction of natural resources in the next 500 years or less, things could get ugly. If such awful things are Intelligently Designed for the trajectory of planet Earth, on some level, I think it would almost be merciful if the atheists are right….

The reason I feel so much kinship with the atheists and agnostics at TSZ and elsewhere is that I share and value the skeptical mindset. Gullibility is not a virtue, skepticism is. A personal friend of Richard Dawkins was my professor and mentor who lifted me out of despair when I was about to flunk out of school. Another professor, James Trefil, who has spent some time fighting ID has been a mentor and friend. All to say, atheists and people of little religious affiliation (like Trefil) have been kind and highly positive influences on my life, and I thank God for them! Thus, though I disagree with atheists and agnostics, I find the wholesale demonization of their character highly repugnant — it’s like trash talking of my mentors, friends and family.

I have often found more wonder and solace in my science classes than I have on many Sunday mornings being screamed at by not-so-nice preachers. So despite my many disagreements with the regulars here, because I’ve enjoyed the academic climate in the sciences, I feel somewhat at home at TSZ….

Now, on to the main point of this essay! Like IDist Mike Gene, I find the atheist/agnostic viewpoint reasonable for the simple reason that most people don’t see miracles or God appearing in their every day lives if not their entire lives. It is as simple as that.

Naturalism would seem to me, given most everyone’s personal sample of events in the universe, to be a most reasonable position. The line of reasoning would be, “I don’t see miracles, I don’t see God, by way of extrapolation, I don’t think miracles and God exists. People who claim God exists must be mistaken or deluded or something else.”

The logic of such a viewpoint seems almost unassailable, and I nearly left the Christian faith 15 years ago when such simple logic was not really dealt with by my pastors and fellow parishioners. I had to re-examine such issues on my own, and the one way I found to frame the ID/Creation/Evolution issue is by arguing for the reasonableness of Black Swan events.

I will use the notion of Black Swans very loosely. The notion is stated here, and is identified with a financeer and academic by the name of Nasim Taleb. I have Taleb’s books on investing entitled Dynamic Hedging which is considered a classic monograph in mathematical finance. His math is almost impenetrable! He is something of a Super Quant. Any way:

https://en.wikipedia.org/wiki/Black_swan_theory

The black swan theory or theory of black swan events is a metaphor that describes an event that comes as a surprise, has a major effect, and is often inappropriately rationalized after the fact with the benefit of hindsight.

The theory was developed by Nassim Nicholas Taleb to explain:

1.The disproportionate role of high-profile, hard-to-predict, and rare events that are beyond the realm of normal expectations in history, science, finance, and technology.
2.The non-computability of the probability of the consequential rare events using scientific methods (owing to the very nature of small probabilities).
3.The psychological biases that blind people, both individually and collectively, to uncertainty and to a rare event’s massive role in historical affairs.

Unlike the earlier and broader “black swan problem” in philosophy (i.e. the problem of induction), Taleb’s “black swan theory” refers only to unexpected events of large magnitude and consequence and their dominant role in history. Such events, considered extreme outliers, collectively play vastly larger roles than regular occurrences.[1] More technically, in the scientific monograph Silent Risk , Taleb mathematically defines the black swan problem as “stemming from the use of degenerate metaprobability”.[2]
….
The phrase “black swan” derives from a Latin expression; its oldest known occurrence is the poet Juvenal’s characterization of something being “rara avis in terris nigroque simillima cygno” (“a rare bird in the lands and very much like a black swan”; 6.165).[3] When the phrase was coined, the black swan was presumed not to exist. The importance of the metaphor lies in its analogy to the fragility of any system of thought. A set of conclusions is potentially undone once any of its fundamental postulates is disproved. In this case, the observation of a single black swan would be the undoing of the logic of any system of thought, as well as any reasoning that followed from that underlying logic.

Juvenal’s phrase was a common expression in 16th century London as a statement of impossibility. The London expression derives from the Old World presumption that all swans must be white because all historical records of swans reported that they had white feathers.[4] In that context, a black swan was impossible or at least nonexistent. After Dutch explorer Willem de Vlamingh discovered black swans in Western Australia in 1697,[5] the term metamorphosed to connote that a perceived impossibility might later be disproven. Taleb notes that in the 19th century John Stuart Mill used the black swan logical fallacy as a new term to identify falsification.[6]

The very first question I looked at when I was having bouts of agnosticism was the question of origin of life. Now looking back, the real question being asked is “was OOL a long sequence of typical events or a black swan sequence of events.” Beyond OOL, one could go on to the question of biological evolution. If we assume Common Descent or Universal Common Ancestry (UCA), would evolution, as a matter of principle, proceed by typical or black swan events or a mix of such events (the stock market follows patterns of typical events punctuated by black swan events).

If natural selection is the mechanism of much of evolution, does the evolution of the major forms (like prokaryote vs. eukaryote, unicellular vs. multicellular, etc.) proceed by typical or black swan events?

[As a side note, when there is a Black Swan stock market crash, it isn’t a POOF, but a sequence of small steps adding up to an atypical set of events. Black Swan doesn’t necessarily imply POOF, but it can still be viewed as a highly exceptional phenomenon.]

Without getting into the naturalism vs. supernaturalism debate, one could at least make statements whether OOL, eukaryotic evolution (eukaryogenesis), multicellular evolution, evolution of Taxonomically Restricted Features (TRFs), Taxonomically Restricted Genes (TRGs), proceeded via many many typical events happening in sequence or a few (if not one) Black Swan event.

I personally believe, outside of the naturalism supernaturalism debate, that as a matter of principle, OOL, eukaryogenesis, emergence of multicellularity (especially animal multicellularity), must have transpired via Black Swan events. Why? The proverbial Chicken and Egg paradox which has been reframed in various incarnations and supplemented with notions such as Irreducible Complexity or Integrated Complexity or whatever. Behe is not alone in his notions of this sort of complexity, Andreas Wagner and Joe Thornton use similar language even though they thing such complexity is bridgeable by typical rather than Black Swan events.

When I do a sequence lookup at the National Institutes of Health (NIH) National Center of Biotechnology Information (NCBI), it is very easy to see the hierarchical patterns that would, at first glance, confirm UCA! For example look at this diagram of Bone Morphogenetic Proteins (BMP) to see the hierarchical patterns:

BMP

From such studies, one could even construct Molecular Clock Hypotheses and state hypothesized rates of molecular evolution.

The problem however is that even if some organisms share so many genes, and even if these genes can be hierarchically laid out, there are genes that are restricted only to certain groups. We might refer to them as Taxonomically Restricted Genes (TRG). I much prefer the term TRG over “orphan gene” especially since some orphan genes seem to emerge without the necessity of Black Swan events and orphan genes are not well defined and orphan genes are only a subset of TRGs. I also coin the notion of Taxonomically Restricted Feature (TRF) since I believe many heritable features of biology are not solely genetic but have heritable cytoplasmic bases (like Post Translation modifications of proteins).

TRGs and TRFs sort of just poof onto the biological scene. How would we calibrate the molecular clock for such features? It goes “from zero to sixty” in a poof.

Finally, on the question of directly observed evolution, it seems to me, that evolution in the present is mostly of the reductive and exterminating variety. Rather than Dawkins Blind Watchmaker, I see a Blind Watch Destroyer. Rather than natural selection acting in cumulative modes, I natural selection acting in reductive and exterminating modes in the present day, in the lab and field.

For those reasons, even outside the naturalism vs. supernaturalism debate, I would think a reasonable inference is that many of the most important features of biology did not emerge via large collections of small typical events but rather via some Black Swan process in the past, not by any mechanisms we see in the present. It is not an argument from incredulity so much as a proof by contradiction.

If one accepts the reasonableness of Black Swan events as the cause of the major features of biology, it becomes possible to accept that these were miracles, and if Miracles there must be a Miracle Maker (aka God). But questions of God are outside science. However, I think the inference to Black Swan events for biology may well be science.

In sum, I think atheism is a reasonable position. I also think the viewpoint that biological emergence via Black Swan events is also a highly reasonable hypothesis even though we don’t see such Black Swans in every day life. The absence of such Black Swans is not necessarily evidence against Black Swans, especially if the Black Swan will bring coherence to the trajectory of biological evolution in the present day. That is to say, it seems to me things are evolving toward simplicity and death in the present day, ergo some other mechanism than what we see with our very own eyes was the cause of OOL and bridging of major gaps in the taxonomic groupings.

Of course such a Black Swan interpretation of biology may have theological implications, but formally speaking, I think inferring Black Swan hypotheses for biology is fair game in the realm of science to the extent it brings coherence to real-time observations in the present day.

775 thoughts on “The Reasonableness of Atheism and Black Swans

  1. sez the OP: “The problem however is that even if some organisms share so many genes, and even if these genes can be hierarchically laid out, there are genes that are restricted only to certain groups. We might refer to them as Taxonomically Restricted Genes (TRG).”
    Why is this a problem? When a new gene arises in some Organism X by whatever method, that gene will be passed along to Organism X’s descendants—and only to Organism X’s descendants. If Organism X’s descendants happen to only make up a limited number of species, that new gene of Organism X will be restricted to that limited number of species; if Organism X’s descendants make up a large fraction of all species, that new gene of Organism X will be found in a large fraction of all species.

    Thus, it seems to me that the term “Taxonomically Restricted Genes” really ought to apply to all genes. Why, then would TRGs be a problem for naturalistic evolution/abiogenesis/biology, and not yet another piece of evidence which supports the hypothesis of naturalistic evolution/abiogenesis/biology?

  2. cubist:Thus, it seems to me that the term “Taxonomically Restricted Genes” really ought to apply to all genes. Why, then would TRGs be a problem for naturalistic evolution/abiogenesis/biology, and not yet another piece of evidence which supports the hypothesis of naturalistic evolution/abiogenesis/biology?

    Consider the reverse – genes found across the spectrum, pretty much at random. These would be Taxonomically Unrestricted Genes, and might suggest rampant horizontal gene transfer. But I don’t understand how this would be LESS an indication of Sal’s god in action.

  3. I’m not surprised that someone looking to rescue creationism would look in the direction of events for which the history has been erased.

    It reminds me of Bill Murray in Ghostbusters II. You can’t make much money hocking theories that are likely to be soon disproved.

  4. The problem however is that even if some organisms share so many genes, and even if these genes can be hierarchically laid out, there are genes that are restricted only to certain groups. We might refer to them as Taxonomically Restricted Genes (TRG).

    Why, was some principle of science discovered that means that new proteins cannot arise?

    If that were so, evolution would be impossible.

    It’s a baffling argument, apparently starting from the baseless assumption that evolution (including some new proteins) simply cannot occur, thus conclude that it didn’t, despite the fact that the TRGs are evolutionarily-predicted evidence that the TRG-owners actually did non-magically evolve.

    It’s not a matter of following the evidence. Not properly, anyhow.

    Glen Davidson

  5. Thank you gentleman for the skepticism and criticism.

    Regarding TRGs and TRFs this is what I had in mind. There are a group of organisms which have insulin regulated metabolisms — the animals. Insulin is a TRG (maybe some remote convergent homology outside, but not very good) to animals as far as I can tell.

    An insulin-regulated metabolism is a TRF, meaning not only does it have insulin, but all the machinery that uses it. Insulin is the signaling molecule, but there has to be senders and receivers inside the organism and things that control the insulin levels.

    1. receivers — tyrosen kinase receptors like:
    https://en.wikipedia.org/wiki/Insulin_receptor

    2. senders — pancreas

    3. control — https://en.wikipedia.org/wiki/Pancreatic_islets

    using Beta cells
    https://en.wikipedia.org/wiki/Beta_cell

    Beta cells (β cells) are a type of cell found in the pancreatic islets of the pancreas. They make up 65-80% of the cells in the islets.

    The primary function of a beta cell is to store and release insulin. Insulin is a hormone that brings about effects which reduce blood glucose concentration. Beta cells can respond quickly to spikes in blood glucose concentrations by secreting some of their stored insulin while simultaneously producing more.

    Control of insulin secretion[edit]

    Voltage-gated calcium channels and ATP-sensitive potassium ion channels are embedded in the cell surface membrane of beta cells. These ATP-sensitive potassium ion channels are normally open and the calcium ion channels are normally closed. Potassium ions diffuse out of the cell, down their concentration gradient, making the inside of the cell more negative with respect to the outside (as potassium ions carry a positive charge). At rest, this creates a potential difference across the cell surface membrane of -70mV.

    When the glucose concentration outside the cell is high, glucose molecules move into the cell by facilitated diffusion, down its concentration gradient through the GLUT2 transporter.[1] Since beta cells use glucokinase to catalyze the first step of glycolysis, metabolism only occurs around physiological blood glucose levels and above. Metabolism of the glucose produces ATP, which increases the ATP to ADP ratio.

    The ATP-sensitive potassium ion channels close when this ratio rises. This means that potassium ions can no longer diffuse out of the cell.[2] As a result, the potential difference across the membrane becomes more positive (as potassium ions accumulate inside the cell). This change in potential difference opens the voltage-gated calcium channels, which allows calcium ions from outside the cell to diffuse in down their concentration gradient. When the calcium ions enter the cell, they cause vesicles containing insulin to move to, and fuse with, the cell surface membrane, releasing insulin by exocytosis.[3]

    Ah yes, a whole nother cell type needed to make sense of the insulin molecule.

    We have transgenic yeast and bacteria with human insulin genes in them inserted by researchers trying to find cures for diabetes. Do these yeast and bacteria ever adopt insulin regulation merely because they now express insulin? Of course not. So it is more than just getting a novel gene, it is getting the novel machinery that makes sense of the gene.

    Now what does this mean? Without insulin, the machinery to regulate insulin, an insulin-regulated creature dies. This creates a chicken and egg paradox. For an organism to give birth to offspring with insulin regulated metabolism, it needs an insulin-regulated metabolism to begin with, otherwise it dies.

    Gradualism would seem to fail on principle. And even if gradual, the evolutionary trajectory is not demonstrable, just speculated, and therefore not science.

    One alternative is Hopeful Monster type evolution. Some sort of Punctuation, but this would be problematic in sexually reproducing species. But wouldn’t such a Hopeful Monster scenario qualify as a Black Swan event?

    Finally, what is the evidence that this has to be a black swan event?

    Consider all the creatures that don’t have insulin-regulated metabolisms, like plants and yeast. Do we ever expect to see these creatures with working metabolisms suddenly rework their metabolic regimen to something as complex as an insulin regulated metabolism?

    It doesn’t have to be specifically insulin, but consider that tinkering with the metabolism is lethal if not all the parts are in place.

    How can transitions happen from one metabolic regiment to another except by jumps and black swan events?

    We have insulin genes that have no homology really outside the animal group. We likely have beta cells that have no homology outside the animal group.

    I googled “Beta cell evolution” — no meaningful hits. Does any actually think the unicellular ancestor of animals had a beta cell? Of course not.

    The TRF of the Beta cell just sort of black swanned onto the scene, just like the animal form itself.

  6. Why, was some principle of science discovered that means that new proteins cannot arise?

    Ok, this is how we settle the question empirically or theoretically. How often do we expect a new protein class to emerge? If one says “infrequently” then that means it is a black swan event by definition.

    Same for cell types like the Beta Cell type required for creatures with insulin-regulated metabolisms. How often do we expect a brand new cell type to emerge in a species line. If one says “infrequently”, that’s grounds for calling it a black swan event.

  7. stcordova: Ok, this is how we settle the question empirically or theoretically.How often do we expect a new protein class to emerge?If one says “infrequently” then that means it is a black swan event by definition.

    Same for cell types like the Beta Cell type required for creatures with insulin-regulated metabolisms.How often do we expect a brand new cell type to emerge in a species line.If one says “infrequently”, that’s grounds for calling it a black swan event.

    So let me see if I’ve got this right. EVERY mutation is a black swan event, since all of them, considered separately, are extremely rare, perhaps nearly all of them are one-time events. Conserved mutations are even more unusual, and conserved beneficial mutations are vanishingly rare. All black swans, meaning that one of the foundational processes of evolution qualifies as magic.

  8. Can Cordova identify any examples of genes which are *not* TRGs—and, at least as important, explain why they aren’t TRGs?

  9. Can Cordova identify any examples of genes which are *not* TRGs—and, at least as important, explain why they aren’t TRGs?

    Aminoacyl tRNA synthetases are not TRGs. They appear in all the 3 major domains (Eukaryotes, Bacteria, Archaea). They are necessary for implementing the universal genetic code, maybe even non-standard codes.

    Here is a video:
    https://www.youtube.com/watch?v=W1eQNmtCCkw&feature=player_embedded

    They aren’t TRGs because they exist in all life forms.

    Superficially this could be used as an argument for common descent, but there are problems with the phylogeny. 🙂

    https://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetase

    Most of the aaRSs of a given specificity are evolutionarily closer to one another than to aaRSs of another specificity. However, AsnRS and GlnRS group within AspRS and GluRS, respectively. Most of the aaRSs of a given specificity also belong to a single class. However, there are two distinct versions of the LysRS – one belonging to the class I family and the other belonging to the class II family.

    In addition, the molecular phylogenies of aaRSs are often not consistent with accepted organismal phylogenies. That is, they violate the so-called canonical phylogenetic pattern shown by most other enzymes for the three domains of life – Archaea, Bacteria, and Eukarya. Furthermore, the phylogenies inferred for aaRSs of different amino acids often do not agree with one another. These are two clear indications that horizontal transfer has occurred several times during the evolutionary history of aaRSs.[4]

  10. So are you saying that some genes are horizontally transferred? I still don’t understand whether you consider vertical transmission or horizontal transmission to be the better indicator of your god. Which is it, and why is the other NOT an indicator of your god?

  11. Justice, kindness, intergrity is not profiled by identity. Yes non christians etc can be as kind as christians etc.
    Yet there is a curve. People of the true faith should be morally better then others and are. In a curve. Thats why the anglo american civilization is better morally in history and today. a reflection of more/greater percentage of the pop being of the true faith.

    yes god etc is invisible. No excuses to the human intellect because of invisible things.
    Gravity is invisible. Germs, almost, are invisible. yet human intellect must submit to these invisable truths because of the evidence.
    The evidence for god is creation. We always said that.
    Someone saying there is no god because he is invisible is not being in any way intelligent.
    They must say creation does not need a God to explain itself.
    In fact saying, so easily, that creation was from itself by chance is just boring dumb.
    I don’t care about atheists stuff and evolution stuff because its boring and has no future.

    ID/YEC is about creation equals a creator. YEC is also about a witness called the bible.
    its also about a high standard of intellectual analysis of evidence.

  12. Robert Byers:ID/YEC is about creation equals a creator. YEC is also about a witness called the bible.
    its also about a high standard of intellectual analysis of evidence.

    I think this speaks for itself.

  13. Ok, this is how we settle the question empirically or theoretically. How often do we expect a new protein class to emerge? If one says “infrequently” then that means it is a black swan event by definition.

    Same for cell types like the Beta Cell type required for creatures with insulin-regulated metabolisms. How often do we expect a brand new cell type to emerge in a species line. If one says “infrequently”, that’s grounds for calling it a black swan event.

    Okay, fine, we can call it a “black swan” event if you wish. But then we have to acknowledge that we actually expect some black swan events in life history, given the billions of years we know we’ve had. “Infrequently” is not a synonym for “improbable” or “unnatural” much less for “impossible”.

    Black swan events would only be a problem if you think that a) the earth is some few millennia old; and/or b) that life has been pre-programmed by some designer and anything “unexpected” is a violation of the designer’s program.

    But given that the earth is factually billions of years old with cellular life also billions of years old, and given that a designer’s front loaded programming (if that indeed was part of OoL) would have been undone by mutation in those years, we have zero reason to be surprised that a few rare and otherwise-unpredictable things have occurred in the history of life.

    Undirected chemical OoL might itself be a “black swan” event in the universe. But given the trillions of habitable planets, it’s stupid to claim without further evidence that the odds against OoL were prohibitive.

    Three separate people won the powerball Saturday after two months of no winners. The odds are known to be 1/292,000,000. Is an undirected chemical OoL less probable than that? How would you know? What factors have you used in calculating those odds? What biochemists agree that you’ve put the correct weight on those factors?

    You mention the stock market as an illustration of a process of “typical events punctuated by black swan events” (although without defining either “typical” or “black swan”, in modern world capitalism). So there’s your answer: Undirected evolution on our planet is a process of “typical” events punctuated by “black swan” events (but to be honest the only black swan event I fully agree with is the lucky symbiotic basis of mitochondria). Multicellularity clearly evolved more than once, so it should not be included as a black swan event.

    It’s certainly NOT a proof by contradiction to say it was too improbable to have happened, when it clearly did happen. It is exactly an argument from incredulity to say it must have been a miracle.

  14. An interesting question is how many genes are conserved across all domains of life. The aminoacyl tRNA synthetases (aaRS) genes are an example off the top of my head, but there aren’t really many more.

    How do I know that? What is the most minimal bacteria? I don’t know, but lets take M. Genitalium with 381 essential genes.

    As a matter of principle then, the at most, the most number of genes that all life forms share is 381, maybe far less.

    I’ve mentioned the 16S Ribosomal RNA gene several times at TSZ. It is highly conserved. There is also the 23S rRNA gene. The next would be the aaRS genes mentioned (46 I think), just a few more.

    This paper did a survey, and it didn’t come up with many genes at all, as far as non-RNA genes, maybe 6? It wasn’t exactly an easy read:

    http://arep.med.harvard.edu/pdf/Isenbarger08.pdf

    So, if I’m reading this correctly the range of most conserved would be around 60 at the bottom and 381 at the very outer most. Bottom line, there aren’t many conserved across all life, there must be many TRGs as a matter of principle.

    Considering the human has 20,000 genes, one can see there will be many TRGs to the human and whatever family the humans nests within. The number of TRGs in humans is not known, and is hotly disputed.

    The standard number of TRGs per organism? Some use the term Orphan, but I don’t like it. That said:

    https://en.wikipedia.org/wiki/Orphan_gene

    Orphan genes accounted for an estimated 26% of the yeast genome, but it was believed that these genes could be classified when more genomes were sequenced.[3] Since there are between an estimated 1 and 20 million animal species in the world, the discovery was ignored for some time.[10] However, the cumulative number of orphan genes in sequenced genomes did not level off as time passed.[11] In the sequencing of Schizosaccharomyces pombe and Schizosaccharomyces cerevisiae in 2002, researchers found that 14 percent and 19 percent, respectively, of the protein encoding genes were totally unique to that specific species.[3] Unfortunately for the study of orphan genes, researchers were more interested in studying the similar gene sequences and not the unknown regions.[3]

    The TRGs with no known homologs then I would consider Black Swans as a matter of principle.

    I have no problem with point mutations on an existing gene creating alleles with new function. However a whole new gene, particularly in Eukaryotic domains with exons and introns and the complexity of such genes without homology seems like it must be a Black Swan as a matter of principle.

    For someone to assert it is not a Black Swan event, they would have to assert emergence of new genes with no homology to any other gen is a common place event — but such an assertion appears clearly false.

    Take the insulin gene for example. How badly do we expect the proto-insulin genes to litter a genome before insulin became viable? That is to say, what is the necessary population of non-functioning “genes” in the genome to make a single functioning TRG like insulin?

    If every gene had some homology to every other gene, then it would be believable that no Black Swan event was needed to make TRGs, but such a universal homology is non-existent, hence, how can we in principle build a universal phylogeny with all these TRGs?

    Instead of Tree of Life, it would look like the best phylogeny would be an Orchard of Life.

  15. I wonder if Sal honestly thinks he’s swaying anyone with his bog standard Creationist “God of the Gaps” argument rebranded as “black swan”? I suppose this is another one of the lies he plans on teaching unsuspecting children.

  16. In Sal’s posts here, I detect a subtle odor of “THIS target” rather than “ANY target”. He’s boggled at the odds of exactly insulin (or whatever) occurring, and attributing this to Divine Guidance. And in the process, conveniently forgetting that any of a countless number of other possible things didn’t happen but COULD have happened — all of which he’d probably regard as a predetermined “target”.

  17. In Sal’s posts here, I detect a subtle odor of “THIS target” rather than “ANY target”.

    That is most certainly not the case. With regard to insulin, metabolism can be regulated in hypothetically in an infinite number of ways just as there are an infinite number of ways to build a matching pair of keys and locks.

    The fact that there are an infinite number of ways to implement locks and keys just as there could be hypothetically an infinite number of ways to implement metabolic regulation, doesn’t make such schemes 100% probable.

    There are an infinite number of ways to make complex Rube Goldberg machines. However the fact there is an infinite number of ways to do this doesn’t make complex Rube Goldberg machines inevitable.

    The issue with insulin is that if this is a signaling molecule, as a matter of principle, it must be different enough from other molecules to work, much like a key must be sufficiently different enough from other keys to work.

    So we have in evidence an insulin molecules that are highly different than any other molecule (non-homologous). We can then say, what is the probability the machinery ( like insulin receptors) will emerge that will match the insulin molecule? Or vice versa — given signaling insulin receptors, what is the probability of a matching insulin molecule?

    Of course one could argue there are simpler ways to make metabolic regulation, but one could also argue there are simpler ways to make Rube Goldberg machines. So why did life take the more complex route? It would seem a Black Swan process is indicated as a matter of principle.

  18. stcordova

    So we have in evidence an insulin molecules that are highly different than any other molecule (non-homologous).We can then say, what is the probability the machinery (like insulin receptors) will emerge that will match the insulin molecule?Or vice versa — given signaling insulin receptors, what is the probability of a matching insulin molecule?

    LOL! go ahead Sal, calculate the probability for us. Show your work and be sure to support any assumptions you make with the relevant scientific literature.

    Looks like just another boring episode of Personal Incredulity Theater.

  19. stcordova:Of course one could argue there are simpler ways to make metabolic regulation, but one could also argue there are simpler ways to make Rube Goldberg machines.So why did life take the more complex route?It would seem a Black Swan process is indicated as a matter of principle.

    So you are arguing that, because evolution did not find the simplest solution to a specific problem, it must be magic? But nature is chock full of wildly suboptimal solutions, and the laryngeal nerve in the giraffe’s neck is canonical. Would you say that this is a “gray swan”?

  20. stcordova

    Of course one could argue there are simpler ways to make metabolic regulation, but one could also argue there are simpler ways to make Rube Goldberg machines.So why did life take the more complex route?It would seem a Black Swan process is indicated as a matter of principle.

    Maybe we should call Sal’s “Black Swan” the Black Reptiles. New paper just out:

    Molecular characterization of insulin from squamate reptiles reveals sequence diversity and possible adaptive evolution
    Yamagishi et al
    General and Comparative Endocrinology. Vol 225, 1 Jan 2016, Pages 197–211

    Abstract: The Squamata are the most adaptive and prosperous group among ectothermic amniotes, reptiles, due to their species-richness and geographically wide habitat. Although the molecular mechanisms underlying their prosperity remain largely unknown, unique features have been reported from hormones that regulate energy metabolism. Insulin, a central anabolic hormone, is one such hormone, as its roles and effectiveness in regulation of blood glucose levels remain to be examined in squamates. In the present study, cDNAs coding for insulin were isolated from multiple species that represent various groups of squamates. The deduced amino acid sequences showed a high degree of divergence, with four lineages showing obviously higher number of amino acid substitutions than most of vertebrates, from teleosts to mammals. Among 18 sites presented to comprise the two receptor binding surfaces (one with 12 sites and the other with 6 sites), substitutions were observed in 13 sites. Among them was the substitution of HisB10, which results in the loss of the ability to hexamerize. Furthermore, three of these substitutions were reported to increase mitogenicity in human analogues. These substitutions were also reported from insulin of hystricomorph rodents and agnathan fishes, whose mitogenic potency have been shown to be increased.

    The estimated value of the non-synonymous-to-synonymous substitution ratio (ω) for the Squamata clade was larger than those of the other reptiles and aves. Even higher values were estimated for several lineages among squamates. These results, together with the regulatory mechanisms of digestion and nutrient assimilation in squamates, suggested a possible adaptive process through the molecular evolution of squamate INS. Further studies on the roles of insulin, in relation to the physiological and ecological traits of squamate species, will provide an insight into the molecular mechanisms that have led to the adaptivity and prosperity of squamates.

  21. But nature is chock full of wildly suboptimal solutions, and the laryngeal nerve in the giraffe’s neck is canonical.

    You forgot to make the peacock’s tail. 🙂

    The sight of a feather in a peacock’s tail, whenever I gaze at it, makes me sick!

    Charles Darwin

    Features that natural selection should select against are problematic for natural selection.

    But nature is chock full of wildly suboptimal solutions, and the laryngeal nerve in the giraffe’s neck is canonical.

    As with Rube Gold machines, the issue isn’t good, bad or sub optimal.

    In fact “good” Rube Gold machines are on the edge of being even functional! The purpose by designers of Rube Goldberg machines is to go to the edge of functionality and push the envelope as far as fragility. That’s what makes them an exceptional phenomenon.

    If one assumes a no-God scenario, a Black Swan process would be necessary for emergence of exceptional TRF phenomenon.

    The insulin-regulated metabolism required a new cell type. How frequently as a matter of principle do new cell types emerge? Do we have cell types emerge with no function that is later recruited?

  22. stcordova

    Features that natural selection should select against are problematic for natural selection.

    Go ahead and list them Sal. Then provide your evidence they should be selected against.

    The only problem I see here is Creationist ignorance.

  23. You guys wanted him, you got him.

    Barry owes this side a huge debt of thanks for you guys taking him.

  24. phoodoo:
    You guys wanted him, you got him.

    We got Joe G, Mung, and you too. The best and brightest ID-Creationism has to offer. 😀

  25. To a first approximation, evolution is a random walk with a selection process to pick out the paths most likely to have useful long term value. So it’s actually reasonable to expect black swan events.

  26. All I want to know is, even if all that seems like a good reason to believe in a god (despite being an obvious argument from ignorance), it’s at best an argument for some sort of vague deism. It’s mind boggling that obviously intelligent people can’t see that’s not an argument for god’s existence, but a rationalization of preexisting beliefs in specific religious myths.

    This Taleb guy is a pathetic charlatan BTW. Use some fancy terminology to simply rebrand the good old god of the gaps crap and sell tons of books to the gullible masses.

    It’s such a silly way to approach things, I mean seriously. So “improbable” events must be miracles but every day stuff aren’t, right? What’s wrong with that god that can’t do the easy stuff like poor some rain in the Scottish highlands?

  27. I’d like to thank again all who are participating in this discussion as it helps me extend and understand my own intuitions on these topics.

    1. The main point is that I think I have a grasp on why many atheists and agnostics hold the views they do regarding miracles, and I empathize with the viewpoint moreso than people realize. Imho, the atheistic and agnostic viewpoint is driven simply by the absence of seeing the Designer or real-time miracles. There are probably other dimensions to it, but that absence of seeing miracles and the Designer almost pushed me permanently into the agnostic/atheist camp 15 years ago. For the atheists and agnostics reading, does that seem like a fair and accurate characterization of some of the reasons you hold the views you do regarding God? I hope I’m representing what’s on your mind accurately.

    2. Even on the assumption of there being no God, it would seem to me, some of the major features of life emerged via processes unlike any we have seen — Black Swans. The Black Swan could be a godless process, at least in principle, but it is a Black Swan nonetheless.

    If that is the case, then I’m simply trying to argue that as a matter of principle, the best explanation for emergence of some features of life (OOL, Eukaryogenesis, Multicellularity, major TRFs etc.) cannot be reduced to mechanisms we actually have access to or are anything like what we have seen in the lab and field. As Mark Frank pointed out, there could be a variety of mechanisms in play. He argued one can’t be sure it is ID. I agree, I accept ID on some level of faith.

    But on the other hand, it may be fair to say the emergence of some of the features of life are totally incompatible with any process we’ve seen in the lab or field or what we view as a plausible theory. I introduced the Black Swan notion to try to erase the theological and metaphysical angle of the origins issue to at least argue the mechanisms proposed (like Blind Watchmakers, Neutral Evolution, common descent) are not adequate explanations. A Black Swan process (whether it involves God or not) is indicated.

    In sum, I accept the atheistic/agnostic viewpoint as reasonable, but I also find it highly unreasonable to say we really understand how the major features of life emerged. To say, “it happened by UCA”, and even if UCA were true, would still entail Black Swan processes.

  28. phoodoo: Barry owes this side a huge debt of thanks for you guys taking him.

    Side? Side of what? You make it sound like there are two sides to this when in fact there is only one side. There is the reality based community and there is everyone else and whatever idea they might have that is usually mutually exclusive to everyone else’s ideas who are not also in the RBC.

    For instance, one the one “side” we have an age for the earth. On the other “side” there are dozens of sticking plaster theories for why the other side’s age of the earth is wrong. Slow starlight, accelerated decay and so on. None of it with any actual support, but it does not need support, it just needs to sound like science to people who know nothing about science.

    It’s more like when you lift up a log and see lots of lice all running in random directions. That’s your side. All you know is that the other side is wrong, and it does not matter what your friends in the big tent think, as long as you know who the common enemy is.

    How’s that all working out for you by the way?

  29. stcordova: In sum, I accept the atheistic/agnostic viewpoint as reasonable, but I also find it highly unreasonable to say we really understand how the major features of life emerged.

    Why don’t you go back to university and study biology as you seem so interested?

  30. stcordova: I’d like to thank again all who are participating in this discussion as it helps me extend and understand my own intuitions on these topics.

    What you really mean to say is that thanks for pointing out the obvious flaws so I can patch them up so when I go back to lying to children so they won’t be able to spot those flaws themselves and it’ll seem like I know what I’m talking about…

  31. Why don’t you go back to university and study biology as you seem so interested?

    What makes you think I’m not now studying biology? I am in an interdisciplinary graduate school at an institution partnered with my alma mater where I received my MS. The evening school grad program that I’m in is tailored for people without an undergrad in biology but who wish to learn biology (i.e. like compter scientists who work in bioinformatics).

    I only responded this once, but such comments by you are reasons I leave you on my ignore list most of the time.

  32. I’m still puzzled about the kind of virtuoso believing required of young Earth Creationists. Jesus, according to the New Testament, doesn’t seem to have spent much time talking about Old Testament myths. The teachings about love for your fellow humans, charity and pacifism seem much more important. Why spend time and effort trying to force-fit observed reality into some collection of children’s stories?

    The Dalai Lama has a much more pragmatic approach.

    If scientific analysis were conclusively to demonstrate certain claims in Buddhism to be false, then we must accept the findings of science and abandon those claims.

    Dalai Lama XIV, The Universe in a Single Atom: The Convergence of Science and Spirituality

  33. stcordova: For the atheists and agnostics reading, does that seem like a fair and accurate characterization of some of the reasons you hold the views you do regarding God? I hope I’m representing what’s on your mind accurately

    Not really. Science has successfully explained events that took place long long ago and used to be attributed to miracles. God has failed to explain anything at all of what we know about pretty much anything back from the Big Bang all the way to why my team won today.

  34. dazz: …and that’s coming from the guy who admitted he doesn’t care about what’s true… go figure

    WJM is still pouting because his defense of Creationist dishonest quote-mining got smoked so badly. He needs something to ease the pain, therefore we get another one of his famous “atheists can’t have morals” lectures.

  35. William J. Murray:
    There is no form of atheism that is rationally justifiable.

    BTW, your list of purported evidence for God is a huge pile of bullshit. The cosmological, ontological and moral arguments count as “evidence”?
    “Look! design!” counts as evidence?
    “I have a book written by a guy who pretends he’s this other guy who claimed he knew this guy who said he’s the son of god… and talking snakes and dragons and….” counts as testimony slash evidence?

    ROTLMFAO!

  36. Adapa: WJM is still pouting because his defense of Creationist dishonest quote-mining got smoked so badly.He needs something to ease the pain, therefore we get another one of his famous “atheists can’t have morals” lectures.

    Wonder if he’s ever heard of the Euthyphro dilemma

  37. dazz: Wonder if he’s ever heard of the Euthyphro dilemma

    Yes, I have, and I’ve posted on this site the form of Atheism which solves that dilemma: “Good” being an innate, unchangeable, fundamental aspect of God.

  38. Adapa: WJM is still pouting because his defense of Creationist dishonest quote-mining got smoked so badly.He needs something to ease the pain, therefore we get another one of his famous “atheists can’t have morals” lectures.

    Getting a couple of guys here to admit that Petrushka was wrong about what constitutes “quote-mining” was, as far as I’m considered, an overwhelming success, considering I thought no one here would ever actually straight-out admit it.

  39. William J. Murray: Yes, I have, and I’ve posted on this site the form of Atheism which solves that dilemma: “Good” being an innate, unchangeable, fundamental aspect of God.

    “Good” relative to who or what? Flesh eating bacteria sucks for humans but it’s pretty good for the bacteria to thrive.

  40. William J. Murray: Yes, I have, and I’ve posted on this site the form of Atheism which solves that dilemma: “Good” being an innate, unchangeable, fundamental aspect of God.

    That’s ridiculous. A bald assertion of truth that turns the moral argument into a tautology. It’s not an answer to the dilemma, just a tacit admission of defeat

  41. dazz: That’s ridiculous. A bald assertion of truth that turns the moral argument into a tautology. It’s not an answer to the dilemma, just a tacit admission of defeat

    Bald assertion is WJM’s favorite debate technique. In fact it’s his only debate technique. WJM is right because WJM says he is right.

  42. William J. Murray: Getting a couple of guys here to admit that Petrushka was wrong about what constitutes “quote-mining” was, as far as I’m considered, an overwhelming success, considering I thought no one here would ever actually straight-out admit it.

    Admit what?

    Petrushka: creationist quotes of scientists are always quote mines.
    WJM: In principle, it’s possible to quote a scientist honestly.
    Others: Yes, it’s possible, but it never happens.
    WJM: See, I was right all along!

  43. Flint: Admit what?

    Petrushka: creationist quotes of scientists are always quote mines.
    WJM: In principle, it’s possible to quote a scientist honestly.
    Others: Yes, it’s possible, but it never happens.
    WJM: See, I was right all along!

    Actually Petrushka said creationist quotes of scientists in support of pro-creation arguments are always quote mines, which they are.

    That’s the key phrase WJM keeps dancing around. Of course Creationists can cite a scientist over some basic scientific fact. It’s them using the quote as evidence for Creationism that’s the problem.

    WJM just can’t find the intellectual honesty to admit he was wrong.

  44. Alan Fox:
    I’m still puzzled about the kind of virtuoso believing required of young Earth Creationists. Jesus, according to the New Testament, doesn’t seem to have spent much time talking about Old Testament myths. The teachings about love for your fellow humans, charity and pacifism seem much more important. Why spend time and effort trying to force-fit observed reality into some collection of children’s stories?

    The Dalai Lama has a much more pragmatic approach.

    My understanding is that Buddhism doesn’t make scientific claims, whereas Abrahamic religions make them by the oodle. Alas, such claims have been scientifically refuted beyond any conceivable reasonable doubt. So what can you do, except fall back on virtuoso belief?

    As soon as you admit ANY such biblical claim is false, you’ve let the camel’s nose into the tent, and now EVERY claim can be subjected to scientific testing. So it’s all or nothing, and you must swallow the camel.

  45. Adapa: Actually Petrushka said creationist quotes of scientists in support of pro-creation arguments are always quote mines, which they are.

    And what everyone has been trying to point out is that creationists have no other reason for quoting a scientist at all!!! They certainly aren’t going to try to build an anti-creationist argument, and the scientist is never going to agree with creationism.

    So my paraphrase of petrushke is the same as yours, because the phrase you added in bold is superfluous. Also correct, of course.

  46. Actually Petrushka said creationist quotes of scientists in support of pro-creation arguments are always quote mines, which they are.

    No, that’s not what he said. In response to my saying:

    It seems that anti-ID/creationists think that if one quotes a Darwinist to make an anti-Darwinism point, it must be quote-mining simply because the Darwinist rejects creationism/ID.

    petrushka said:

    Well, yes, it’s true that quoting a mainstream biologist to support a creationist argument is quote mining.

    He’s not making a claim that all creationists quote-mine; he’s claiming that the act of a creationist quoting a mainstream evolutionary biologist to make a creationist argument is quote-mining.

    By the way, if you or Petrushka were to claim that all such quotes used by creationists were factually quote-mines, I’d have simply asked you to support your assertion, which is unsupportable. You’d have to present every quote ever used and then show the context and make the quote-mining case. So, that kind of a claim is pure, unsupportable rhetoric.

  47. dazz: That’s ridiculous. A bald assertion of truth that turns the moral argument into a tautology. It’s not an answer to the dilemma, just a tacit admission of defeat

    No, it’s not a bald assertion, it’s a theological premise. The Euthypro Dilemma presents the quandary that results from two different theological premises; that (1) god chooses what is good, or (2) god is subject to an external good. Either of these two theological premises result in a moral problem.

    I have merely offered a different theological premise which solves the dilemma and presents no such moral dilemma.

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