P.falciparum – No Black Swan Observed

_{Dave S.
November 6, 2007

Intelligent Design

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Intelligent Design}

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The tired old “ID is not scientific” has reared its ugly head again in another thread. This is simply not true.

Karl Popper famously stated that a hypothesis is scientific if it can be falsified. He used swans as an example. He stated a hypothesis:

All swans are white.

Popper said that it can never be proven that all swans are white because there is always the possibility that a black swan exists somewhere but has not yet been observed. He stated that the hypothesis is still scientific because it can be falsified – the observation of a single black swan will falsify it.

The biological ID hypothesis can be stated as:

All complex biological systems are generated by intelligent agents.

We already know, or may reasonably presume, that complex biological systems can be generated by intelligent agents. There’s a whole discipline called “Genetic Engineering” devoted to it. What we don’t know is whether any non-intelligent means can generate complex biological systems. A single observation of a complex biological system generated by a non-intelligent cause will falsify the biological ID hypothesis.

P.falciparum replicating billions of trillions of times in the past few decades represents the largest search to date for a “black swan”. This is orders of magnitude more replications than took place in the evolution of reptiles to mammals wherein there are many exceedingly complex biological systems that separate them. If P.falciparum had been seen generating any complex biological systems such as those that distinguish mammals from reptiles then it would have falsified the ID hypothesis. None were observed. This doesn’t prove ID but it certainly lends strong support to it. All perfectly scientific.

P.S. I understand that an actual black swan has been observed and Popper’s hypothetical example was indeed falsified. That is exactly how science is supposed to work. Now it’s up to the time & chance worshippers to falsify the ID hypothesis. Good luck.

Comments

bornagain77 Hi, you seem to imply that the Darwinian elephant only produced "a few measly point mutations in pfcrt", but their existance doesn't exclude bigger changes having occurred in the species. The mapping experiments to pinpoint chloroquine resistance did not survey the falcipaurm genome to catalogue all changes, just the changes responsible for one phenotype. My point is that to detect a "black swan" (e.g. a new gene) we would need to know what genes a P. falciparum strain had in the past, and compare the complement it presently has. Given that the reference sequence has only just been published - we can't tell if any new genes have turned up since, say 1990. We need two or more measurements spaced out in time. That could take a while, so in the interim two obvious alternatives exist: 1) Sequence different strains separated by geography (hence time). 2) Sequence different Plasmodium species separated by speciation (hence lots of time). Obviously (2) requires an assumption about common descent among Plasmodium species (which maybe unpopular locally) - but if accepted yields clear evidence of dozens (actually hundreds) of new genes in comparison with vivax, malariae, ovale, etc. (1) is less contentious, and is also being undertaken as we type. Early results indicate there are indeed differences in gene complement between strains.Pantrog_{November 6, 2007
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Falsificationism doesn't work. In practice, a theory can always be rescued from an anomalous observation. The question 'Is ID science or non science?' is philosophically obtuse and useful really only for propaganda or for the madness that is the American approach to separation of church and state. (For a nation to claim to be the 'land of the free' while their state dictates curriculum to their children is absurd; they can't take your guns but they can take your kids.)BenK_{November 6, 2007
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"Gradualism sucks" - Borne Hahahaha. Although Borne sounds a bit exasperated, I can understand his frustration. There's so much faith in swallowing naturalistic evolution. I can't imagine thousands of ancient fish washing up on land and choking to death until a lung develops. I take the same issue with the development of wings. Dawkin's speculation on the subject is pretty ludicrous. On another note, I think we need to wary about our word choice when, given the Darwinian hypothesis of common ancestry, we say "mammals came from reptiles." Maybe "modern mammals descended from ancient reptiles"? Just a suggestion...Berceuse_{November 6, 2007
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Pantrog, I've read your post and can't really make heads or tails out of the point you are trying to make,,,Are you saying we will find proof of evolution if we look harder and allow more broader assumptions for common decent?,,,If this is what you are saying you are totally missing the whole point. This is/was the best chance for evolution to strut its almighty stuff,,,and what did we see evolution accomplish? Well here are Dr. Behe's own words: Perhaps even more remarkable than the rarity of malaria resistance to chloroquine — and even more of an indication of the weakness of Darwinian forces — is the puny final result. Truly in this instance the Darwinian elephant labored mightily and brought forth a gnat. After a hundred billion billion chances, we end up with a few measly point mutations in pfcrt. These results from malaria are our best evidence by far of what Darwinian processes can accomplish when given a huge number of chances and strong selective pressure. Behold the result. The TREE reviewer goes on to complain about my noting that no protein-protein binding sites evolved in malaria in an astronomical number of opportunities: “He apparently thinks that evolutionary theory says anything should evolve a new binding site in response to any arbitrary situation.” (1) The reviewer’s complaint begs a large question, however: when does evolutionary theory say that a protein-protein binding site should evolve? What non-arbitrary situation would cause that? In fact, evolutionary theory says nothing about specifics of what should or shouldn’t evolve. Therefore, we need to get our ideas about what should or shouldn’t evolve not from evolutionary theory, but from evolutionary data. And what we see in our best set of data from malaria is that no such protein sites evolved by Darwinian means in an astronomical number of opportunities. Furthermore, mutations in only one protein, pfcrt, were really able to do much in the face of chloroquine, showing that the number of proteins that it may be helpful to evolve in any given situation might be extremely small: one, maybe none. Ditto for pyrimethamine resistance. If only one protein could evolve to help malaria avoid chloroquine poisoning, why should we think that a cell will luckily have a dozen or score of proteins that happen to be able to evolve to make a molecular machine? http://www.amazon.com/gp/blog/post/PLNK17G2SQARF948Lbornagain77_{November 6, 2007
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Getawitness, My point is the designer of living organisms on Earth need not be the same designer who designed the universe. It very well could be but it is not any requirement Also, with all due respect to Wm Dembski, we do not know if a designer, who was at least at one time beyond this universe, is unembodied or not. BTW- thanks for reading my blog!Joseph_{November 6, 2007
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First, I think DaveScot's example black swan example makes a lot of sense, and I second the idea of DaveScot writing a book, because unlike some people, he writes very clearly about complex subjects. Borne - I have to take issue with your post about mammels not descending from reptiles and fishes. I am sure that DaveScot has written about this many times before, and front loading is clearly an ID topic. I also think that you are discounting the Designers's abilities to a great extent, and whether or not you call the creator God or the Designer, it doesn't matter. Let there be light, and there was light! If He wants to say Let reptiles turn into Mammelss, reptiles are going to turn into mammels.Glarson24_{November 6, 2007
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"This assume Darwinism and positive upward evolution via Darwinian mechanisms. How do we know the “precursor forms” are even precursors? Why couldn’t they be separate lines that suffered genetic entropy and lost functionality? Perhaps P.falciparum simply suffered less deleterious mutations." We don't know anything with 100% certainty. That's not how science works. It might have been caused by an unembodied intelligence. There's simply no way to exclude that possibility, since we cannot know how or why such an intelligence would act. Leaving that aside, there is evidence that p. Falciparum DID change, and in a sense you are correct in suggesting the changes were less deleterious. I posted a couple of references to the publications that detail these changes.MacT_{November 6, 2007
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Together, the data point to the recent origin of p.falciparum. Precursor forms are in fact different on these measures.
This assume Darwinism and positive upward evolution via Darwinian mechanisms. How do we know the "precursor forms" are even precursors? Why couldn't they be separate lines that suffered genetic entropy and lost functionality? Perhaps P.falciparum simply suffered less deleterious mutations.Patrick_{November 6, 2007
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If biological life on Earth is designed by material beings from elsewhere, those material beings would presumably be “complex biological systems,” right? Well, then they need a designer that is ultimately not a complex biological system.
We are limited to what we can observe. Right now we can observe living organisms on this planet, so we ask "how did they (we) get here?" What are the options? No need for regress games. Take things one step at a time, figure it out and then move on.Joseph_{November 6, 2007
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Ahoy, Dave! I commend you for having put forth a fundamental ID hypothesis. A problem with the potential falsification of your hypothesis, however, is that some (many?) in the pro-ID camp advocate an actively interventionist creator whose tinkering could be manifest anytime, anywhere. So, an observable, confirmable evolutionary innovation can always be ascribed to the Big Tinkerer and need not falsify the ID hypothesis. MichaelMichael Tuite_{November 6, 2007
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If evolution is a science, and any hypothesis (speculation) on evolution is science, shouldn't then the critique of the limits of evolution also be considered science?Peter_{November 6, 2007
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Dave Scot - I agree with your definition of Intelligent Agent: "Any entity which can form an abstract model of a potential arrangement of matter and which can then manipulate matter to actualize the arrangement." It's a good one. In the light of your "monkey reaching a banana by moving a box" example, however, it appears to make the difference between monkeys and men merely one of degree and not kind. It would be helpful to me if you would elaborate a bit on that side of the issue. Thanks.Gerry Rzeppa_{November 6, 2007
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DaveScot said: "The changes moreover actually make the organism less fit in the absence of the drugs. " On a side note, in the case of organisms in certain ecological niches, less fitness is not necessarily an evolutionary disadvantage. A less vigorous parasite is less likely to kill its host, and therefore more likely to reproduce.MacT_{November 6, 2007
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DavesScot, "Intelligent agent - Any entity which can form an abstract model of a potential arrangement of matter and which can then manipulate matter to actualize the arrangement." Ok, good. That is a good description of an intelligent agent that can shift a box over to better reach a banana. We have clear, independent observations of such creatures doing exactly that. Your definition allows us to develop an elaborated theory of monkeys as intelligent agents, and to generate hypotheses that can be tested to explore more fully the extent (and limitations) of monkey intelligence. Further, we can confidently extend the concept of intelligent agency to other examples that demonstrate similar qualities to monkeys that we can define (opposable thumbs, crossmodal regions of cortex capable of supporting symbolic representation, etc). Piaget's daughter, Jacqueline, showed very similar abilities of abstract representational thinking, translated to motor action, when she solved the problem of retrieving a box outside her playpen that had to be turned in exactly the right way in order to pass through the vertical bars of the playpen. But notice that while both of these examples meet the definition of intelligent agent, any hypothesis we might formulate to further investigate their nature must take into account the definitional premises of the agents in question. It would be silly to suppose that either the monkey or Jacqueline, despite their status as intelligent agents, would be capable of designing a simple machine. For that, we would have to posit additional competence, and state a priori what that competence entails (e.g., knowledge of engineering principles, handy with metalworking tools, etc). So: What are the definitional premises of an intelligent agent that is capable of designing a complex biological system? It seems to me that by avoiding a definition that includes necessary competence, your account is leaning toward assuming omnipotence. I'm not sure that's what you actually have in mind, but once in, it is a difficult corner to get out of.MacT_{November 6, 2007
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Hi, isn't this discussion dependant on having knowledge of what P. falciparum used to be long ago, to know whether it has changed substantially - we don't have any reeaaly old samples. The Plasmodium genome sequencing project has just started - they'll be comparing strains from different sides of the planet which should be informative on this issue. But we could get an idea about the proto-falciparum IF we assume P. falciparum shares common descent with the other 4 human Plasmodium species and the 200 others found in birds, monkeys and reptiles. From recollection P. falciparum has at least one extra gene family (of 50 genes), not present in the other species which infect humans. The var gene products bind a range of human proteins, modulate T cell function, cloak the organism from the immune system and prevent splenic passage. Interestingly there are also a range of human genetic counter-adaptations (common in African/Asian populations) combating the products of var genes.Pantrog_{November 6, 2007
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My 2 cents: Intelligent Design: The Design Hypothesis and Explaing the "I" in IDJoseph_{November 6, 2007
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Let us assume there was a recent origin of P.falciparum. How does this hypothetical scenario provide positive evidence for Darwinism in itself? What Darwinian process or mechanism was involved?Patrick_{November 6, 2007
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Black swans were discovered in the 1700's in Australia and the use of the black swan in philosophy of science has been as an example to show the shortcomings of induction. Popper used the example of the black swan to show induction cannot mean certainty.jerry_{November 6, 2007
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MacT Carried over from a previous thread you, incredibly enough, want to quibble about the definition of "intelligent agent". Here's how I define it for this context: Intelligent agent - Any entity which can form an abstract model of a potential arrangement of matter and which can then manipulate matter to actualize the arrangement. For instance a monkey qualifies when it sees a banana out of reach and a box that can be repositioned so that the banana can be reached. The monkey forms an abstract model of him first repositioning the box under the banana then stepping onto the box to reach the banana. After forming the abstract model he manipulates the box and himself to realize the model. Of course that's a far shot from Genetic Engineering but that is essentially how engineering is accomplished - abstract models of potential arrangements of matter/energy are made and then the plans are actualized. This seems like a simple enough definition for any moderately intelligent person to construct. You seem to be moderately intelligent so it appears you are just being argumentative.DaveScot_{November 6, 2007
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MacT, Forgive me for jumping in on your discussion with Dave Scot, but I wanted to point out that you site evidence that comes from a entrenched preconceived philosophical bias that says, of course, evolution has occurred, just look at these genetic similarities!!! ,,,whereas DaveScot, as well as all other ID proponents, start out with the philosophical bias that intelligence may very well be required to generate fantastically Complex molecular structures we are finding in biology....Thus we put evolution to the test and see what it can actually accomplish as far as generating complexity! What happened when evolution was put to a real world test...NOTHING OF SIGNIFICANCE THAT WOULD VERIFY EVOLUTION! You cite resistance as proof of evolution, yet it is clearly explained in Dr. Behe's book that all resistance was wrought in malaria by degrading a preexisting function in the malaria...On top of that once the is removed from the malaria population the "mutated" malaria is quickly out competed by the original malaria... You said reading is hard work (I would say it depends on if you enjoy it or not?),,,But if you could do a little more hard work and actually read Dr. Behe's book before criticizing it on this site, then I think it would save us a lot of trouble correcting your mistakes on exactly what the ID theory is. I can tell that you are sincere and hope I do not offend you,,but I can guarantee you that all the hard "observed" evidence falls in IDs favor,,,Indeed if you do a little investigation you will be pleasantly surprised.bornagain77_{November 6, 2007
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MacT P.falciparum is a eukaryote with both asexual and sexual reproduction. No doubt there is variability in its genome that is expressed or repressed in recombination during sexual reproduction. The fact of the matter remains that it is essentially the same organism after billions of trillions replications in past few decades aside from a few trivial (but medically important) nucleotide changes in its genome that serve to defeat a few human produced anti-malarial drugs. The changes moreover actually make the organism less fit in the absence of the drugs. Compare this to all the large scale changes in both genotype and phenotype that made mammals out of reptiles. Just so stories of P.falciparum evolving from another plasmodium are conjecture and while it is probably true, just as it's probably true the mammals descended from reptiles, it does not change by one iota the observation of P.falciparum replicating billions of trillions of times over the past few decades and essentially not evolving at all to say nothing of evolution on the scale of reptiles to mammals.DaveScot_{November 6, 2007
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DaveScot, You accused me on another thread of avoiding the question about p. falciparum. I'm not a biologist, and I'm in a very different time zone from you, so you'll have to bear with me a little. There is ample evidence that the genetic variability of p. falciparum plays a large role in its transmission success, and tends to stymie efforts to control disease in humans. Recent work has shown that the lack of DNA variation in coding sequences is far from the whole story. In particular, introns have been shown to be deficient in single-nucleotide polymorphisms, and that extends to synonymous sites in coding regions. Together, the data point to the recent origin of p.falciparum. Precursor forms are in fact different on these measures. Don't take my word for it. Here are two (of many) sources: Neafsey DE, Hartl DL and Berriman M (2005). Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes. Mol Bio Evol 22(7): 1621-1626. Volkman et al (2001). Recent origin of Plasmodium falciparum from a single progenitor. Science 20 July, vol 293, no 5529, 482-484. Time and chance worshippers? Well, that sure advances our understanding of the issues. Read up, people. It's hard work, but it's more effective than gratuitous name-calling.MacT_{November 6, 2007
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Dave, I think you've got a book in you. I can see it starting to develop like one of those old Polaroid pictures...Lutepisc_{November 6, 2007
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DaveScot, If ancient bacterium spores are apparently being revived (Lazarus like), from such places as amber and/or salt crystals, and IDists can further this line of evidence by successfully tracing a particular (or even many different) bacteria through many points of time (many data points) through many millions of years, would not this give IDist another very hard piece of evidence that, while not directly observed as in malaria, would be in convergence with Behe's observations? I was reading yesterday where one scientist commented, that while working with amber fossils, he has revived and sequenced hundreds of ancient bacteria...with relative ease.bornagain77_{November 6, 2007
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